mirror of
https://github.com/openmm/openmmforcefields.git
synced 2026-06-06 18:39:48 +09:00
2784 lines
169 KiB
XML
2784 lines
169 KiB
XML
<ForceField>
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<Info>
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<DateGenerated>2021-01-26</DateGenerated>
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<Source Source="leaprc.RNA.ROC" md5hash="1fe3856d015119bcc053605d6c4b5b1c" sourcePackage="AmberTools" sourcePackageVersion="20.15">leaprc.RNA.ROC</Source>
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<Reference>Zgarbova, M.; Otyepka, M.; Sponer, J.; Mladek, A.; Banas, P.; Cheatham, T.E.; Jurecka, P. Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J. Chem. Theory Comput., 2011, 7, 2886-2902.</Reference>
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</Info>
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<AtomTypes>
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<Type element="C" name="RNA-C" class="C" mass="12.01"/>
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<Type element="C" name="RNA-CA" class="CA" mass="12.01"/>
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<Type element="C" name="RNA-CB" class="CB" mass="12.01"/>
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<Type element="C" name="RNA-CI" class="CI" mass="12.01"/>
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<Type element="C" name="RNA-CK" class="CK" mass="12.01"/>
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<Type element="C" name="RNA-CP" class="CP" mass="12.01"/>
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<Type element="C" name="RNA-CM" class="CM" mass="12.01"/>
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<Type element="C" name="RNA-CS" class="CS" mass="12.01"/>
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<Type element="C" name="RNA-CQ" class="CQ" mass="12.01"/>
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<Type element="C" name="RNA-CT" class="CT" mass="12.01"/>
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<Type element="C" name="RNA-C5" class="C5" mass="12.01"/>
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<Type element="C" name="RNA-C4" class="C4" mass="12.01"/>
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<Type element="H" name="RNA-H" class="H" mass="1.008"/>
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<Type element="H" name="RNA-HC" class="HC" mass="1.008"/>
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<Type element="H" name="RNA-H1" class="H1" mass="1.008"/>
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<Type element="H" name="RNA-H2" class="H2" mass="1.008"/>
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<Type element="H" name="RNA-HA" class="HA" mass="1.008"/>
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<Type element="H" name="RNA-H4" class="H4" mass="1.008"/>
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<Type element="H" name="RNA-H5" class="H5" mass="1.008"/>
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<Type element="H" name="RNA-HO" class="HO" mass="1.008"/>
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<Type element="N" name="RNA-NA" class="NA" mass="14.01"/>
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<Type element="N" name="RNA-NB" class="NB" mass="14.01"/>
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<Type element="N" name="RNA-NC" class="NC" mass="14.01"/>
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<Type element="N" name="RNA-N2" class="N2" mass="14.01"/>
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<Type element="N" name="RNA-N*" class="N*" mass="14.01"/>
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<Type element="O" name="RNA-O" class="O" mass="16.0"/>
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<Type element="O" name="RNA-O2" class="O2" mass="16.0"/>
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<Type element="O" name="RNA-OH" class="OH" mass="16.0"/>
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<Type element="O" name="RNA-OS" class="OS" mass="16.0"/>
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<Type element="P" name="RNA-P" class="P" mass="30.97"/>
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<Type element="C" name="RNA-CF" class="CF" mass="12.01"/>
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</AtomTypes>
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<Residues>
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<Residue name="A">
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<Atom name="P" type="RNA-P" charge="1.1662"/>
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<Atom name="OP1" type="RNA-O2" charge="-0.776"/>
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<Atom name="OP2" type="RNA-O2" charge="-0.776"/>
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<Atom name="O5'" type="RNA-OS" charge="-0.4989"/>
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<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
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<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
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<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
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<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
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<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
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<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
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<Atom name="C1'" type="RNA-CT" charge="0.0394"/>
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<Atom name="H1'" type="RNA-H2" charge="0.2007"/>
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<Atom name="N9" type="RNA-N*" charge="-0.0251"/>
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<Atom name="C8" type="RNA-C5" charge="0.2006"/>
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<Atom name="H8" type="RNA-H5" charge="0.1553"/>
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<Atom name="N7" type="RNA-NB" charge="-0.6073"/>
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<Atom name="C5" type="RNA-CB" charge="0.0515"/>
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<Atom name="C6" type="RNA-CA" charge="0.7009"/>
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<Atom name="N6" type="RNA-N2" charge="-0.9019"/>
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<Atom name="H61" type="RNA-H" charge="0.4115"/>
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<Atom name="H62" type="RNA-H" charge="0.4115"/>
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<Atom name="N1" type="RNA-NC" charge="-0.7615"/>
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<Atom name="C2" type="RNA-CQ" charge="0.5875"/>
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<Atom name="H2" type="RNA-H5" charge="0.0473"/>
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<Atom name="N3" type="RNA-NC" charge="-0.6997"/>
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<Atom name="C4" type="RNA-CB" charge="0.3053"/>
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<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
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<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
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<Atom name="C2'" type="RNA-CT" charge="0.067"/>
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<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
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<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
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<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
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<Atom name="O3'" type="RNA-OS" charge="-0.5246"/>
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<Bond atomName1="P" atomName2="OP1"/>
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<Bond atomName1="P" atomName2="OP2"/>
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<Bond atomName1="P" atomName2="O5'"/>
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<Bond atomName1="O5'" atomName2="C5'"/>
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<Bond atomName1="C5'" atomName2="H5'"/>
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<Bond atomName1="C5'" atomName2="H5''"/>
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<Bond atomName1="C5'" atomName2="C4'"/>
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<Bond atomName1="C4'" atomName2="H4'"/>
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<Bond atomName1="C4'" atomName2="O4'"/>
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<Bond atomName1="C4'" atomName2="C3'"/>
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<Bond atomName1="O4'" atomName2="C1'"/>
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<Bond atomName1="C1'" atomName2="H1'"/>
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<Bond atomName1="C1'" atomName2="N9"/>
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<Bond atomName1="C1'" atomName2="C2'"/>
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<Bond atomName1="N9" atomName2="C8"/>
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<Bond atomName1="N9" atomName2="C4"/>
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<Bond atomName1="C8" atomName2="H8"/>
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<Bond atomName1="C8" atomName2="N7"/>
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<Bond atomName1="N7" atomName2="C5"/>
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<Bond atomName1="C5" atomName2="C6"/>
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<Bond atomName1="C5" atomName2="C4"/>
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<Bond atomName1="C6" atomName2="N6"/>
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<Bond atomName1="C6" atomName2="N1"/>
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<Bond atomName1="N6" atomName2="H61"/>
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<Bond atomName1="N6" atomName2="H62"/>
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<Bond atomName1="N1" atomName2="C2"/>
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<Bond atomName1="C2" atomName2="H2"/>
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<Bond atomName1="C2" atomName2="N3"/>
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<Bond atomName1="N3" atomName2="C4"/>
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<Bond atomName1="C3'" atomName2="H3'"/>
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<Bond atomName1="C3'" atomName2="C2'"/>
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<Bond atomName1="C3'" atomName2="O3'"/>
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<Bond atomName1="C2'" atomName2="H2'"/>
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<Bond atomName1="C2'" atomName2="O2'"/>
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<Bond atomName1="O2'" atomName2="HO2'"/>
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<ExternalBond atomName="P"/>
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<ExternalBond atomName="O3'"/>
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</Residue>
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<Residue name="A3">
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<Atom name="P" type="RNA-P" charge="1.1662"/>
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<Atom name="OP1" type="RNA-O2" charge="-0.776"/>
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<Atom name="OP2" type="RNA-O2" charge="-0.776"/>
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<Atom name="O5'" type="RNA-OS" charge="-0.4989"/>
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<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
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<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
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<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
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<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
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<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
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<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
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<Atom name="C1'" type="RNA-CT" charge="0.0394"/>
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<Atom name="H1'" type="RNA-H2" charge="0.2007"/>
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<Atom name="N9" type="RNA-N*" charge="-0.0251"/>
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<Atom name="C8" type="RNA-C5" charge="0.2006"/>
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<Atom name="H8" type="RNA-H5" charge="0.1553"/>
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<Atom name="N7" type="RNA-NB" charge="-0.6073"/>
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<Atom name="C5" type="RNA-CB" charge="0.0515"/>
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<Atom name="C6" type="RNA-CA" charge="0.7009"/>
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<Atom name="N6" type="RNA-N2" charge="-0.9019"/>
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<Atom name="H61" type="RNA-H" charge="0.4115"/>
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<Atom name="H62" type="RNA-H" charge="0.4115"/>
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<Atom name="N1" type="RNA-NC" charge="-0.7615"/>
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<Atom name="C2" type="RNA-CQ" charge="0.5875"/>
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<Atom name="H2" type="RNA-H5" charge="0.0473"/>
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<Atom name="N3" type="RNA-NC" charge="-0.6997"/>
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<Atom name="C4" type="RNA-CB" charge="0.3053"/>
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<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
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<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
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<Atom name="C2'" type="RNA-CT" charge="0.067"/>
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<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
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<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
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<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
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<Atom name="O3'" type="RNA-OH" charge="-0.6541"/>
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<Atom name="HO3'" type="RNA-HO" charge="0.4376"/>
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<Bond atomName1="P" atomName2="OP1"/>
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<Bond atomName1="P" atomName2="OP2"/>
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<Bond atomName1="P" atomName2="O5'"/>
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<Bond atomName1="O5'" atomName2="C5'"/>
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<Bond atomName1="C5'" atomName2="H5'"/>
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<Bond atomName1="C5'" atomName2="H5''"/>
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<Bond atomName1="C5'" atomName2="C4'"/>
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<Bond atomName1="C4'" atomName2="H4'"/>
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<Bond atomName1="C4'" atomName2="O4'"/>
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<Bond atomName1="C4'" atomName2="C3'"/>
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<Bond atomName1="O4'" atomName2="C1'"/>
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<Bond atomName1="C1'" atomName2="H1'"/>
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<Bond atomName1="C1'" atomName2="N9"/>
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<Bond atomName1="C1'" atomName2="C2'"/>
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<Bond atomName1="N9" atomName2="C8"/>
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<Bond atomName1="N9" atomName2="C4"/>
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<Bond atomName1="C8" atomName2="H8"/>
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<Bond atomName1="C8" atomName2="N7"/>
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<Bond atomName1="N7" atomName2="C5"/>
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<Bond atomName1="C5" atomName2="C6"/>
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<Bond atomName1="C5" atomName2="C4"/>
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<Bond atomName1="C6" atomName2="N6"/>
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<Bond atomName1="C6" atomName2="N1"/>
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<Bond atomName1="N6" atomName2="H61"/>
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<Bond atomName1="N6" atomName2="H62"/>
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<Bond atomName1="N1" atomName2="C2"/>
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<Bond atomName1="C2" atomName2="H2"/>
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<Bond atomName1="C2" atomName2="N3"/>
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<Bond atomName1="N3" atomName2="C4"/>
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<Bond atomName1="C3'" atomName2="H3'"/>
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<Bond atomName1="C3'" atomName2="C2'"/>
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<Bond atomName1="C3'" atomName2="O3'"/>
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<Bond atomName1="C2'" atomName2="H2'"/>
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<Bond atomName1="C2'" atomName2="O2'"/>
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<Bond atomName1="O2'" atomName2="HO2'"/>
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<Bond atomName1="O3'" atomName2="HO3'"/>
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<ExternalBond atomName="P"/>
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</Residue>
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<Residue name="A5">
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<Atom name="HO5'" type="RNA-HO" charge="0.4295"/>
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<Atom name="O5'" type="RNA-OH" charge="-0.6223"/>
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<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
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<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
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<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
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<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
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<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
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<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
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<Atom name="C1'" type="RNA-CT" charge="0.0394"/>
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<Atom name="H1'" type="RNA-H2" charge="0.2007"/>
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<Atom name="N9" type="RNA-N*" charge="-0.0251"/>
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<Atom name="C8" type="RNA-C5" charge="0.2006"/>
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<Atom name="H8" type="RNA-H5" charge="0.1553"/>
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<Atom name="N7" type="RNA-NB" charge="-0.6073"/>
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<Atom name="C5" type="RNA-CB" charge="0.0515"/>
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<Atom name="C6" type="RNA-CA" charge="0.7009"/>
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<Atom name="N6" type="RNA-N2" charge="-0.9019"/>
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<Atom name="H61" type="RNA-H" charge="0.4115"/>
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<Atom name="H62" type="RNA-H" charge="0.4115"/>
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<Atom name="N1" type="RNA-NC" charge="-0.7615"/>
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<Atom name="C2" type="RNA-CQ" charge="0.5875"/>
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<Atom name="H2" type="RNA-H5" charge="0.0473"/>
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<Atom name="N3" type="RNA-NC" charge="-0.6997"/>
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<Atom name="C4" type="RNA-CB" charge="0.3053"/>
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<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
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<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
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<Atom name="C2'" type="RNA-CT" charge="0.067"/>
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<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
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<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
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<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
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<Atom name="O3'" type="RNA-OS" charge="-0.5246"/>
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<Bond atomName1="HO5'" atomName2="O5'"/>
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<Bond atomName1="O5'" atomName2="C5'"/>
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<Bond atomName1="C5'" atomName2="H5'"/>
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<Bond atomName1="C5'" atomName2="H5''"/>
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<Bond atomName1="C5'" atomName2="C4'"/>
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<Bond atomName1="C4'" atomName2="H4'"/>
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<Bond atomName1="C4'" atomName2="O4'"/>
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<Bond atomName1="C4'" atomName2="C3'"/>
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<Bond atomName1="O4'" atomName2="C1'"/>
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<Bond atomName1="C1'" atomName2="H1'"/>
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<Bond atomName1="C1'" atomName2="N9"/>
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<Bond atomName1="C1'" atomName2="C2'"/>
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<Bond atomName1="N9" atomName2="C8"/>
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<Bond atomName1="N9" atomName2="C4"/>
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<Bond atomName1="C8" atomName2="H8"/>
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<Bond atomName1="C8" atomName2="N7"/>
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<Bond atomName1="N7" atomName2="C5"/>
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<Bond atomName1="C5" atomName2="C6"/>
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<Bond atomName1="C5" atomName2="C4"/>
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<Bond atomName1="C6" atomName2="N6"/>
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<Bond atomName1="C6" atomName2="N1"/>
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<Bond atomName1="N6" atomName2="H61"/>
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|
<Bond atomName1="N6" atomName2="H62"/>
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|
<Bond atomName1="N1" atomName2="C2"/>
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|
<Bond atomName1="C2" atomName2="H2"/>
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|
<Bond atomName1="C2" atomName2="N3"/>
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|
<Bond atomName1="N3" atomName2="C4"/>
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|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
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|
<ExternalBond atomName="O3'"/>
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|
</Residue>
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|
<Residue name="AN">
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|
<Atom name="HO5'" type="RNA-HO" charge="0.4295"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6223"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0394"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.2007"/>
|
|
<Atom name="N9" type="RNA-N*" charge="-0.0251"/>
|
|
<Atom name="C8" type="RNA-C5" charge="0.2006"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.1553"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.6073"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.0515"/>
|
|
<Atom name="C6" type="RNA-CA" charge="0.7009"/>
|
|
<Atom name="N6" type="RNA-N2" charge="-0.9019"/>
|
|
<Atom name="H61" type="RNA-H" charge="0.4115"/>
|
|
<Atom name="H62" type="RNA-H" charge="0.4115"/>
|
|
<Atom name="N1" type="RNA-NC" charge="-0.7615"/>
|
|
<Atom name="C2" type="RNA-CQ" charge="0.5875"/>
|
|
<Atom name="H2" type="RNA-H5" charge="0.0473"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.6997"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.3053"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6541"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4376"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="N6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N6" atomName2="H61"/>
|
|
<Bond atomName1="N6" atomName2="H62"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="H2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
</Residue>
|
|
<Residue name="C">
|
|
<Atom name="P" type="RNA-P" charge="1.1662"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.776"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.776"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4989"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0066"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.2029"/>
|
|
<Atom name="N1" type="RNA-N*" charge="-0.0484"/>
|
|
<Atom name="C6" type="RNA-C4" charge="0.0053"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.1958"/>
|
|
<Atom name="C5" type="RNA-C4" charge="-0.5215"/>
|
|
<Atom name="H5" type="RNA-HA" charge="0.1928"/>
|
|
<Atom name="C4" type="RNA-CA" charge="0.8185"/>
|
|
<Atom name="N4" type="RNA-N2" charge="-0.953"/>
|
|
<Atom name="H41" type="RNA-H" charge="0.4234"/>
|
|
<Atom name="H42" type="RNA-H" charge="0.4234"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.7584"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.7538"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.6252"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5246"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="H5"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C4" atomName2="N4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N4" atomName2="H41"/>
|
|
<Bond atomName1="N4" atomName2="H42"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<ExternalBond atomName="P"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="C3">
|
|
<Atom name="P" type="RNA-P" charge="1.1662"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.776"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.776"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4989"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0066"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.2029"/>
|
|
<Atom name="N1" type="RNA-N*" charge="-0.0484"/>
|
|
<Atom name="C6" type="RNA-C4" charge="0.0053"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.1958"/>
|
|
<Atom name="C5" type="RNA-C4" charge="-0.5215"/>
|
|
<Atom name="H5" type="RNA-HA" charge="0.1928"/>
|
|
<Atom name="C4" type="RNA-CA" charge="0.8185"/>
|
|
<Atom name="N4" type="RNA-N2" charge="-0.953"/>
|
|
<Atom name="H41" type="RNA-H" charge="0.4234"/>
|
|
<Atom name="H42" type="RNA-H" charge="0.4234"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.7584"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.7538"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.6252"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6541"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4376"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="H5"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C4" atomName2="N4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N4" atomName2="H41"/>
|
|
<Bond atomName1="N4" atomName2="H42"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
<ExternalBond atomName="P"/>
|
|
</Residue>
|
|
<Residue name="C5">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4295"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6223"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0066"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.2029"/>
|
|
<Atom name="N1" type="RNA-N*" charge="-0.0484"/>
|
|
<Atom name="C6" type="RNA-C4" charge="0.0053"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.1958"/>
|
|
<Atom name="C5" type="RNA-C4" charge="-0.5215"/>
|
|
<Atom name="H5" type="RNA-HA" charge="0.1928"/>
|
|
<Atom name="C4" type="RNA-CA" charge="0.8185"/>
|
|
<Atom name="N4" type="RNA-N2" charge="-0.953"/>
|
|
<Atom name="H41" type="RNA-H" charge="0.4234"/>
|
|
<Atom name="H42" type="RNA-H" charge="0.4234"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.7584"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.7538"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.6252"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5246"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="H5"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C4" atomName2="N4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N4" atomName2="H41"/>
|
|
<Bond atomName1="N4" atomName2="H42"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="CN">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4295"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6223"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0066"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.2029"/>
|
|
<Atom name="N1" type="RNA-N*" charge="-0.0484"/>
|
|
<Atom name="C6" type="RNA-C4" charge="0.0053"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.1958"/>
|
|
<Atom name="C5" type="RNA-C4" charge="-0.5215"/>
|
|
<Atom name="H5" type="RNA-HA" charge="0.1928"/>
|
|
<Atom name="C4" type="RNA-CA" charge="0.8185"/>
|
|
<Atom name="N4" type="RNA-N2" charge="-0.953"/>
|
|
<Atom name="H41" type="RNA-H" charge="0.4234"/>
|
|
<Atom name="H42" type="RNA-H" charge="0.4234"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.7584"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.7538"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.6252"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6541"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4376"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="H5"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C4" atomName2="N4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N4" atomName2="H41"/>
|
|
<Bond atomName1="N4" atomName2="H42"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
</Residue>
|
|
<Residue name="DA">
|
|
<Atom name="P" type="RNA-P" charge="1.1659"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4954"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0431"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1838"/>
|
|
<Atom name="N9" type="RNA-N*" charge="-0.0268"/>
|
|
<Atom name="C8" type="RNA-CK" charge="0.1607"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.1877"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.6175"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.0725"/>
|
|
<Atom name="C6" type="RNA-CA" charge="0.6897"/>
|
|
<Atom name="N6" type="RNA-N2" charge="-0.9123"/>
|
|
<Atom name="H61" type="RNA-H" charge="0.4167"/>
|
|
<Atom name="H62" type="RNA-H" charge="0.4167"/>
|
|
<Atom name="N1" type="RNA-NC" charge="-0.7624"/>
|
|
<Atom name="C2" type="RNA-CQ" charge="0.5716"/>
|
|
<Atom name="H2" type="RNA-H5" charge="0.0598"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.7417"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.38"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5232"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="N6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N6" atomName2="H61"/>
|
|
<Bond atomName1="N6" atomName2="H62"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="H2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<ExternalBond atomName="P"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="DA3">
|
|
<Atom name="P" type="RNA-P" charge="1.1659"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4954"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0431"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1838"/>
|
|
<Atom name="N9" type="RNA-N*" charge="-0.0268"/>
|
|
<Atom name="C8" type="RNA-CK" charge="0.1607"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.1877"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.6175"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.0725"/>
|
|
<Atom name="C6" type="RNA-CA" charge="0.6897"/>
|
|
<Atom name="N6" type="RNA-N2" charge="-0.9123"/>
|
|
<Atom name="H61" type="RNA-H" charge="0.4167"/>
|
|
<Atom name="H62" type="RNA-H" charge="0.4167"/>
|
|
<Atom name="N1" type="RNA-NC" charge="-0.7624"/>
|
|
<Atom name="C2" type="RNA-CQ" charge="0.5716"/>
|
|
<Atom name="H2" type="RNA-H5" charge="0.0598"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.7417"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.38"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6549"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4396"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="N6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N6" atomName2="H61"/>
|
|
<Bond atomName1="N6" atomName2="H62"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="H2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
<ExternalBond atomName="P"/>
|
|
</Residue>
|
|
<Residue name="DA5">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4422"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6318"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0431"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1838"/>
|
|
<Atom name="N9" type="RNA-N*" charge="-0.0268"/>
|
|
<Atom name="C8" type="RNA-CK" charge="0.1607"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.1877"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.6175"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.0725"/>
|
|
<Atom name="C6" type="RNA-CA" charge="0.6897"/>
|
|
<Atom name="N6" type="RNA-N2" charge="-0.9123"/>
|
|
<Atom name="H61" type="RNA-H" charge="0.4167"/>
|
|
<Atom name="H62" type="RNA-H" charge="0.4167"/>
|
|
<Atom name="N1" type="RNA-NC" charge="-0.7624"/>
|
|
<Atom name="C2" type="RNA-CQ" charge="0.5716"/>
|
|
<Atom name="H2" type="RNA-H5" charge="0.0598"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.7417"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.38"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5232"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="N6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N6" atomName2="H61"/>
|
|
<Bond atomName1="N6" atomName2="H62"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="H2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="DAN">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4422"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6318"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0431"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1838"/>
|
|
<Atom name="N9" type="RNA-N*" charge="-0.0268"/>
|
|
<Atom name="C8" type="RNA-CK" charge="0.1607"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.1877"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.6175"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.0725"/>
|
|
<Atom name="C6" type="RNA-CA" charge="0.6897"/>
|
|
<Atom name="N6" type="RNA-N2" charge="-0.9123"/>
|
|
<Atom name="H61" type="RNA-H" charge="0.4167"/>
|
|
<Atom name="H62" type="RNA-H" charge="0.4167"/>
|
|
<Atom name="N1" type="RNA-NC" charge="-0.7624"/>
|
|
<Atom name="C2" type="RNA-CQ" charge="0.5716"/>
|
|
<Atom name="H2" type="RNA-H5" charge="0.0598"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.7417"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.38"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6549"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4396"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="N6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N6" atomName2="H61"/>
|
|
<Bond atomName1="N6" atomName2="H62"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="H2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
</Residue>
|
|
<Residue name="DC">
|
|
<Atom name="P" type="RNA-P" charge="1.1659"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4954"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="-0.0116"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1963"/>
|
|
<Atom name="N1" type="RNA-N*" charge="-0.0339"/>
|
|
<Atom name="C6" type="RNA-CM" charge="-0.0183"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.2293"/>
|
|
<Atom name="C5" type="RNA-CM" charge="-0.5222"/>
|
|
<Atom name="H5" type="RNA-HA" charge="0.1863"/>
|
|
<Atom name="C4" type="RNA-CA" charge="0.8439"/>
|
|
<Atom name="N4" type="RNA-N2" charge="-0.9773"/>
|
|
<Atom name="H41" type="RNA-H" charge="0.4314"/>
|
|
<Atom name="H42" type="RNA-H" charge="0.4314"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.7748"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.7959"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.6548"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5232"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="H5"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C4" atomName2="N4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N4" atomName2="H41"/>
|
|
<Bond atomName1="N4" atomName2="H42"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<ExternalBond atomName="P"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="DC3">
|
|
<Atom name="P" type="RNA-P" charge="1.1659"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4954"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="-0.0116"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1963"/>
|
|
<Atom name="N1" type="RNA-N*" charge="-0.0339"/>
|
|
<Atom name="C6" type="RNA-CM" charge="-0.0183"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.2293"/>
|
|
<Atom name="C5" type="RNA-CM" charge="-0.5222"/>
|
|
<Atom name="H5" type="RNA-HA" charge="0.1863"/>
|
|
<Atom name="C4" type="RNA-CA" charge="0.8439"/>
|
|
<Atom name="N4" type="RNA-N2" charge="-0.9773"/>
|
|
<Atom name="H41" type="RNA-H" charge="0.4314"/>
|
|
<Atom name="H42" type="RNA-H" charge="0.4314"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.7748"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.7959"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.6548"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6549"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4396"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="H5"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C4" atomName2="N4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N4" atomName2="H41"/>
|
|
<Bond atomName1="N4" atomName2="H42"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
<ExternalBond atomName="P"/>
|
|
</Residue>
|
|
<Residue name="DC5">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4422"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6318"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="-0.0116"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1963"/>
|
|
<Atom name="N1" type="RNA-N*" charge="-0.0339"/>
|
|
<Atom name="C6" type="RNA-CM" charge="-0.0183"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.2293"/>
|
|
<Atom name="C5" type="RNA-CM" charge="-0.5222"/>
|
|
<Atom name="H5" type="RNA-HA" charge="0.1863"/>
|
|
<Atom name="C4" type="RNA-CA" charge="0.8439"/>
|
|
<Atom name="N4" type="RNA-N2" charge="-0.9773"/>
|
|
<Atom name="H41" type="RNA-H" charge="0.4314"/>
|
|
<Atom name="H42" type="RNA-H" charge="0.4314"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.7748"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.7959"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.6548"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5232"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="H5"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C4" atomName2="N4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N4" atomName2="H41"/>
|
|
<Bond atomName1="N4" atomName2="H42"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="DCN">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4422"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6318"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="-0.0116"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1963"/>
|
|
<Atom name="N1" type="RNA-N*" charge="-0.0339"/>
|
|
<Atom name="C6" type="RNA-CM" charge="-0.0183"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.2293"/>
|
|
<Atom name="C5" type="RNA-CM" charge="-0.5222"/>
|
|
<Atom name="H5" type="RNA-HA" charge="0.1863"/>
|
|
<Atom name="C4" type="RNA-CA" charge="0.8439"/>
|
|
<Atom name="N4" type="RNA-N2" charge="-0.9773"/>
|
|
<Atom name="H41" type="RNA-H" charge="0.4314"/>
|
|
<Atom name="H42" type="RNA-H" charge="0.4314"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.7748"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.7959"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.6548"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6549"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4396"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="H5"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C4" atomName2="N4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N4" atomName2="H41"/>
|
|
<Bond atomName1="N4" atomName2="H42"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
</Residue>
|
|
<Residue name="DG">
|
|
<Atom name="P" type="RNA-P" charge="1.1659"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4954"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0358"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1746"/>
|
|
<Atom name="N9" type="RNA-N*" charge="0.0577"/>
|
|
<Atom name="C8" type="RNA-CK" charge="0.0736"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.1997"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.5725"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.1991"/>
|
|
<Atom name="C6" type="RNA-C" charge="0.4918"/>
|
|
<Atom name="O6" type="RNA-O" charge="-0.5699"/>
|
|
<Atom name="N1" type="RNA-NA" charge="-0.5053"/>
|
|
<Atom name="H1" type="RNA-H" charge="0.352"/>
|
|
<Atom name="C2" type="RNA-CA" charge="0.7432"/>
|
|
<Atom name="N2" type="RNA-N2" charge="-0.923"/>
|
|
<Atom name="H21" type="RNA-H" charge="0.4235"/>
|
|
<Atom name="H22" type="RNA-H" charge="0.4235"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.6636"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.1814"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5232"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="O6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N1" atomName2="H1"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="N2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N2" atomName2="H21"/>
|
|
<Bond atomName1="N2" atomName2="H22"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<ExternalBond atomName="P"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="DG3">
|
|
<Atom name="P" type="RNA-P" charge="1.1659"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4954"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0358"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1746"/>
|
|
<Atom name="N9" type="RNA-N*" charge="0.0577"/>
|
|
<Atom name="C8" type="RNA-CK" charge="0.0736"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.1997"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.5725"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.1991"/>
|
|
<Atom name="C6" type="RNA-C" charge="0.4918"/>
|
|
<Atom name="O6" type="RNA-O" charge="-0.5699"/>
|
|
<Atom name="N1" type="RNA-NA" charge="-0.5053"/>
|
|
<Atom name="H1" type="RNA-H" charge="0.352"/>
|
|
<Atom name="C2" type="RNA-CA" charge="0.7432"/>
|
|
<Atom name="N2" type="RNA-N2" charge="-0.923"/>
|
|
<Atom name="H21" type="RNA-H" charge="0.4235"/>
|
|
<Atom name="H22" type="RNA-H" charge="0.4235"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.6636"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.1814"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6549"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4396"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="O6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N1" atomName2="H1"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="N2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N2" atomName2="H21"/>
|
|
<Bond atomName1="N2" atomName2="H22"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
<ExternalBond atomName="P"/>
|
|
</Residue>
|
|
<Residue name="DG5">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4422"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6318"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0358"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1746"/>
|
|
<Atom name="N9" type="RNA-N*" charge="0.0577"/>
|
|
<Atom name="C8" type="RNA-CK" charge="0.0736"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.1997"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.5725"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.1991"/>
|
|
<Atom name="C6" type="RNA-C" charge="0.4918"/>
|
|
<Atom name="O6" type="RNA-O" charge="-0.5699"/>
|
|
<Atom name="N1" type="RNA-NA" charge="-0.5053"/>
|
|
<Atom name="H1" type="RNA-H" charge="0.352"/>
|
|
<Atom name="C2" type="RNA-CA" charge="0.7432"/>
|
|
<Atom name="N2" type="RNA-N2" charge="-0.923"/>
|
|
<Atom name="H21" type="RNA-H" charge="0.4235"/>
|
|
<Atom name="H22" type="RNA-H" charge="0.4235"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.6636"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.1814"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5232"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="O6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N1" atomName2="H1"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="N2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N2" atomName2="H21"/>
|
|
<Bond atomName1="N2" atomName2="H22"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="DGN">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4422"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6318"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0358"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1746"/>
|
|
<Atom name="N9" type="RNA-N*" charge="0.0577"/>
|
|
<Atom name="C8" type="RNA-CK" charge="0.0736"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.1997"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.5725"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.1991"/>
|
|
<Atom name="C6" type="RNA-C" charge="0.4918"/>
|
|
<Atom name="O6" type="RNA-O" charge="-0.5699"/>
|
|
<Atom name="N1" type="RNA-NA" charge="-0.5053"/>
|
|
<Atom name="H1" type="RNA-H" charge="0.352"/>
|
|
<Atom name="C2" type="RNA-CA" charge="0.7432"/>
|
|
<Atom name="N2" type="RNA-N2" charge="-0.923"/>
|
|
<Atom name="H21" type="RNA-H" charge="0.4235"/>
|
|
<Atom name="H22" type="RNA-H" charge="0.4235"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.6636"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.1814"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6549"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4396"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="O6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N1" atomName2="H1"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="N2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N2" atomName2="H21"/>
|
|
<Bond atomName1="N2" atomName2="H22"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
</Residue>
|
|
<Residue name="DT">
|
|
<Atom name="P" type="RNA-P" charge="1.1659"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4954"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.068"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1804"/>
|
|
<Atom name="N1" type="RNA-N*" charge="-0.0239"/>
|
|
<Atom name="C6" type="RNA-CM" charge="-0.2209"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.2607"/>
|
|
<Atom name="C5" type="RNA-CM" charge="0.0025"/>
|
|
<Atom name="C7" type="RNA-CT" charge="-0.2269"/>
|
|
<Atom name="H71" type="RNA-HC" charge="0.077"/>
|
|
<Atom name="H72" type="RNA-HC" charge="0.077"/>
|
|
<Atom name="H73" type="RNA-HC" charge="0.077"/>
|
|
<Atom name="C4" type="RNA-C" charge="0.5194"/>
|
|
<Atom name="O4" type="RNA-O" charge="-0.5563"/>
|
|
<Atom name="N3" type="RNA-NA" charge="-0.434"/>
|
|
<Atom name="H3" type="RNA-H" charge="0.342"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.5677"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.5881"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5232"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C7"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C7" atomName2="H71"/>
|
|
<Bond atomName1="C7" atomName2="H72"/>
|
|
<Bond atomName1="C7" atomName2="H73"/>
|
|
<Bond atomName1="C4" atomName2="O4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N3" atomName2="H3"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<ExternalBond atomName="P"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="DT3">
|
|
<Atom name="P" type="RNA-P" charge="1.1659"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.7761"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4954"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.068"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1804"/>
|
|
<Atom name="N1" type="RNA-N*" charge="-0.0239"/>
|
|
<Atom name="C6" type="RNA-CM" charge="-0.2209"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.2607"/>
|
|
<Atom name="C5" type="RNA-CM" charge="0.0025"/>
|
|
<Atom name="C7" type="RNA-CT" charge="-0.2269"/>
|
|
<Atom name="H71" type="RNA-HC" charge="0.077"/>
|
|
<Atom name="H72" type="RNA-HC" charge="0.077"/>
|
|
<Atom name="H73" type="RNA-HC" charge="0.077"/>
|
|
<Atom name="C4" type="RNA-C" charge="0.5194"/>
|
|
<Atom name="O4" type="RNA-O" charge="-0.5563"/>
|
|
<Atom name="N3" type="RNA-NA" charge="-0.434"/>
|
|
<Atom name="H3" type="RNA-H" charge="0.342"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.5677"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.5881"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6549"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4396"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C7"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C7" atomName2="H71"/>
|
|
<Bond atomName1="C7" atomName2="H72"/>
|
|
<Bond atomName1="C7" atomName2="H73"/>
|
|
<Bond atomName1="C4" atomName2="O4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N3" atomName2="H3"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
<ExternalBond atomName="P"/>
|
|
</Residue>
|
|
<Residue name="DT5">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4422"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6318"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.068"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1804"/>
|
|
<Atom name="N1" type="RNA-N*" charge="-0.0239"/>
|
|
<Atom name="C6" type="RNA-CM" charge="-0.2209"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.2607"/>
|
|
<Atom name="C5" type="RNA-CM" charge="0.0025"/>
|
|
<Atom name="C7" type="RNA-CT" charge="-0.2269"/>
|
|
<Atom name="H71" type="RNA-HC" charge="0.077"/>
|
|
<Atom name="H72" type="RNA-HC" charge="0.077"/>
|
|
<Atom name="H73" type="RNA-HC" charge="0.077"/>
|
|
<Atom name="C4" type="RNA-C" charge="0.5194"/>
|
|
<Atom name="O4" type="RNA-O" charge="-0.5563"/>
|
|
<Atom name="N3" type="RNA-NA" charge="-0.434"/>
|
|
<Atom name="H3" type="RNA-H" charge="0.342"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.5677"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.5881"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5232"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C7"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C7" atomName2="H71"/>
|
|
<Bond atomName1="C7" atomName2="H72"/>
|
|
<Bond atomName1="C7" atomName2="H73"/>
|
|
<Bond atomName1="C4" atomName2="O4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N3" atomName2="H3"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="DTN">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4422"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6318"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="-0.0069"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0754"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1629"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1176"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3691"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.068"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1804"/>
|
|
<Atom name="N1" type="RNA-N*" charge="-0.0239"/>
|
|
<Atom name="C6" type="RNA-CM" charge="-0.2209"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.2607"/>
|
|
<Atom name="C5" type="RNA-CM" charge="0.0025"/>
|
|
<Atom name="C7" type="RNA-CT" charge="-0.2269"/>
|
|
<Atom name="H71" type="RNA-HC" charge="0.077"/>
|
|
<Atom name="H72" type="RNA-HC" charge="0.077"/>
|
|
<Atom name="H73" type="RNA-HC" charge="0.077"/>
|
|
<Atom name="C4" type="RNA-C" charge="0.5194"/>
|
|
<Atom name="O4" type="RNA-O" charge="-0.5563"/>
|
|
<Atom name="N3" type="RNA-NA" charge="-0.434"/>
|
|
<Atom name="H3" type="RNA-H" charge="0.342"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.5677"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.5881"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.0713"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0985"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="-0.0854"/>
|
|
<Atom name="H2'" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="H2''" type="RNA-HC" charge="0.0718"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6549"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4396"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C7"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C7" atomName2="H71"/>
|
|
<Bond atomName1="C7" atomName2="H72"/>
|
|
<Bond atomName1="C7" atomName2="H73"/>
|
|
<Bond atomName1="C4" atomName2="O4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N3" atomName2="H3"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="H2''"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
</Residue>
|
|
<Residue name="G">
|
|
<Atom name="P" type="RNA-P" charge="1.1662"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.776"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.776"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4989"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0191"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.2006"/>
|
|
<Atom name="N9" type="RNA-N*" charge="0.0492"/>
|
|
<Atom name="C8" type="RNA-CP" charge="0.1374"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.164"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.5709"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.1744"/>
|
|
<Atom name="C6" type="RNA-C" charge="0.477"/>
|
|
<Atom name="O6" type="RNA-O" charge="-0.5597"/>
|
|
<Atom name="N1" type="RNA-NA" charge="-0.4787"/>
|
|
<Atom name="H1" type="RNA-H" charge="0.3424"/>
|
|
<Atom name="C2" type="RNA-CA" charge="0.7657"/>
|
|
<Atom name="N2" type="RNA-N2" charge="-0.9672"/>
|
|
<Atom name="H21" type="RNA-H" charge="0.4364"/>
|
|
<Atom name="H22" type="RNA-H" charge="0.4364"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.6323"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.1222"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5246"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="O6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N1" atomName2="H1"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="N2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N2" atomName2="H21"/>
|
|
<Bond atomName1="N2" atomName2="H22"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<ExternalBond atomName="P"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="G3">
|
|
<Atom name="P" type="RNA-P" charge="1.1662"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.776"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.776"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4989"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0191"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.2006"/>
|
|
<Atom name="N9" type="RNA-N*" charge="0.0492"/>
|
|
<Atom name="C8" type="RNA-CP" charge="0.1374"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.164"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.5709"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.1744"/>
|
|
<Atom name="C6" type="RNA-C" charge="0.477"/>
|
|
<Atom name="O6" type="RNA-O" charge="-0.5597"/>
|
|
<Atom name="N1" type="RNA-NA" charge="-0.4787"/>
|
|
<Atom name="H1" type="RNA-H" charge="0.3424"/>
|
|
<Atom name="C2" type="RNA-CA" charge="0.7657"/>
|
|
<Atom name="N2" type="RNA-N2" charge="-0.9672"/>
|
|
<Atom name="H21" type="RNA-H" charge="0.4364"/>
|
|
<Atom name="H22" type="RNA-H" charge="0.4364"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.6323"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.1222"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6541"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4376"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="O6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N1" atomName2="H1"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="N2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N2" atomName2="H21"/>
|
|
<Bond atomName1="N2" atomName2="H22"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
<ExternalBond atomName="P"/>
|
|
</Residue>
|
|
<Residue name="G5">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4295"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6223"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0191"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.2006"/>
|
|
<Atom name="N9" type="RNA-N*" charge="0.0492"/>
|
|
<Atom name="C8" type="RNA-CP" charge="0.1374"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.164"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.5709"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.1744"/>
|
|
<Atom name="C6" type="RNA-C" charge="0.477"/>
|
|
<Atom name="O6" type="RNA-O" charge="-0.5597"/>
|
|
<Atom name="N1" type="RNA-NA" charge="-0.4787"/>
|
|
<Atom name="H1" type="RNA-H" charge="0.3424"/>
|
|
<Atom name="C2" type="RNA-CA" charge="0.7657"/>
|
|
<Atom name="N2" type="RNA-N2" charge="-0.9672"/>
|
|
<Atom name="H21" type="RNA-H" charge="0.4364"/>
|
|
<Atom name="H22" type="RNA-H" charge="0.4364"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.6323"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.1222"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5246"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="O6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N1" atomName2="H1"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="N2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N2" atomName2="H21"/>
|
|
<Bond atomName1="N2" atomName2="H22"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="GN">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4295"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6223"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0191"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.2006"/>
|
|
<Atom name="N9" type="RNA-N*" charge="0.0492"/>
|
|
<Atom name="C8" type="RNA-CP" charge="0.1374"/>
|
|
<Atom name="H8" type="RNA-H5" charge="0.164"/>
|
|
<Atom name="N7" type="RNA-NB" charge="-0.5709"/>
|
|
<Atom name="C5" type="RNA-CB" charge="0.1744"/>
|
|
<Atom name="C6" type="RNA-C" charge="0.477"/>
|
|
<Atom name="O6" type="RNA-O" charge="-0.5597"/>
|
|
<Atom name="N1" type="RNA-NA" charge="-0.4787"/>
|
|
<Atom name="H1" type="RNA-H" charge="0.3424"/>
|
|
<Atom name="C2" type="RNA-CA" charge="0.7657"/>
|
|
<Atom name="N2" type="RNA-N2" charge="-0.9672"/>
|
|
<Atom name="H21" type="RNA-H" charge="0.4364"/>
|
|
<Atom name="H22" type="RNA-H" charge="0.4364"/>
|
|
<Atom name="N3" type="RNA-NC" charge="-0.6323"/>
|
|
<Atom name="C4" type="RNA-CB" charge="0.1222"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6541"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4376"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N9"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N9" atomName2="C8"/>
|
|
<Bond atomName1="N9" atomName2="C4"/>
|
|
<Bond atomName1="C8" atomName2="H8"/>
|
|
<Bond atomName1="C8" atomName2="N7"/>
|
|
<Bond atomName1="N7" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="C6"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C6" atomName2="O6"/>
|
|
<Bond atomName1="C6" atomName2="N1"/>
|
|
<Bond atomName1="N1" atomName2="H1"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="N2"/>
|
|
<Bond atomName1="C2" atomName2="N3"/>
|
|
<Bond atomName1="N2" atomName2="H21"/>
|
|
<Bond atomName1="N2" atomName2="H22"/>
|
|
<Bond atomName1="N3" atomName2="C4"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
</Residue>
|
|
<Residue name="OHE">
|
|
<Atom name="H" type="RNA-HO" charge="0.226"/>
|
|
<Atom name="O" type="RNA-OH" charge="-0.621"/>
|
|
<Bond atomName1="H" atomName2="O"/>
|
|
<ExternalBond atomName="O"/>
|
|
</Residue>
|
|
<Residue name="U">
|
|
<Atom name="P" type="RNA-P" charge="1.1662"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.776"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.776"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4989"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0674"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1824"/>
|
|
<Atom name="N1" type="RNA-N*" charge="0.0418"/>
|
|
<Atom name="C6" type="RNA-CS" charge="-0.1126"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.2188"/>
|
|
<Atom name="C5" type="RNA-CS" charge="-0.3635"/>
|
|
<Atom name="H5" type="RNA-HA" charge="0.1811"/>
|
|
<Atom name="C4" type="RNA-C" charge="0.5952"/>
|
|
<Atom name="O4" type="RNA-O" charge="-0.5761"/>
|
|
<Atom name="N3" type="RNA-NA" charge="-0.3549"/>
|
|
<Atom name="H3" type="RNA-H" charge="0.3154"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.4687"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.5477"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5246"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="H5"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C4" atomName2="O4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N3" atomName2="H3"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<ExternalBond atomName="P"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="U3">
|
|
<Atom name="P" type="RNA-P" charge="1.1662"/>
|
|
<Atom name="OP1" type="RNA-O2" charge="-0.776"/>
|
|
<Atom name="OP2" type="RNA-O2" charge="-0.776"/>
|
|
<Atom name="O5'" type="RNA-OS" charge="-0.4989"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0674"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1824"/>
|
|
<Atom name="N1" type="RNA-N*" charge="0.0418"/>
|
|
<Atom name="C6" type="RNA-CS" charge="-0.1126"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.2188"/>
|
|
<Atom name="C5" type="RNA-CS" charge="-0.3635"/>
|
|
<Atom name="H5" type="RNA-HA" charge="0.1811"/>
|
|
<Atom name="C4" type="RNA-C" charge="0.5952"/>
|
|
<Atom name="O4" type="RNA-O" charge="-0.5761"/>
|
|
<Atom name="N3" type="RNA-NA" charge="-0.3549"/>
|
|
<Atom name="H3" type="RNA-H" charge="0.3154"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.4687"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.5477"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6541"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4376"/>
|
|
<Bond atomName1="P" atomName2="OP1"/>
|
|
<Bond atomName1="P" atomName2="OP2"/>
|
|
<Bond atomName1="P" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="H5"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C4" atomName2="O4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N3" atomName2="H3"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
|
|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
|
|
<Bond atomName1="C3'" atomName2="O3'"/>
|
|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
|
|
<ExternalBond atomName="P"/>
|
|
</Residue>
|
|
<Residue name="U5">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4295"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6223"/>
|
|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0674"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1824"/>
|
|
<Atom name="N1" type="RNA-N*" charge="0.0418"/>
|
|
<Atom name="C6" type="RNA-CS" charge="-0.1126"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.2188"/>
|
|
<Atom name="C5" type="RNA-CS" charge="-0.3635"/>
|
|
<Atom name="H5" type="RNA-HA" charge="0.1811"/>
|
|
<Atom name="C4" type="RNA-C" charge="0.5952"/>
|
|
<Atom name="O4" type="RNA-O" charge="-0.5761"/>
|
|
<Atom name="N3" type="RNA-NA" charge="-0.3549"/>
|
|
<Atom name="H3" type="RNA-H" charge="0.3154"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.4687"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.5477"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OS" charge="-0.5246"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
|
|
<Bond atomName1="O5'" atomName2="C5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5'"/>
|
|
<Bond atomName1="C5'" atomName2="H5''"/>
|
|
<Bond atomName1="C5'" atomName2="C4'"/>
|
|
<Bond atomName1="C4'" atomName2="H4'"/>
|
|
<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
|
|
<Bond atomName1="O4'" atomName2="C1'"/>
|
|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
|
|
<Bond atomName1="C1'" atomName2="C2'"/>
|
|
<Bond atomName1="N1" atomName2="C6"/>
|
|
<Bond atomName1="N1" atomName2="C2"/>
|
|
<Bond atomName1="C6" atomName2="H6"/>
|
|
<Bond atomName1="C6" atomName2="C5"/>
|
|
<Bond atomName1="C5" atomName2="H5"/>
|
|
<Bond atomName1="C5" atomName2="C4"/>
|
|
<Bond atomName1="C4" atomName2="O4"/>
|
|
<Bond atomName1="C4" atomName2="N3"/>
|
|
<Bond atomName1="N3" atomName2="H3"/>
|
|
<Bond atomName1="N3" atomName2="C2"/>
|
|
<Bond atomName1="C2" atomName2="O2"/>
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|
<Bond atomName1="C3'" atomName2="H3'"/>
|
|
<Bond atomName1="C3'" atomName2="C2'"/>
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<Bond atomName1="C3'" atomName2="O3'"/>
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|
<Bond atomName1="C2'" atomName2="H2'"/>
|
|
<Bond atomName1="C2'" atomName2="O2'"/>
|
|
<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<ExternalBond atomName="O3'"/>
|
|
</Residue>
|
|
<Residue name="UN">
|
|
<Atom name="HO5'" type="RNA-HO" charge="0.4295"/>
|
|
<Atom name="O5'" type="RNA-OH" charge="-0.6223"/>
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|
<Atom name="C5'" type="RNA-CI" charge="0.0558"/>
|
|
<Atom name="H5'" type="RNA-H1" charge="0.0679"/>
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|
<Atom name="H5''" type="RNA-H1" charge="0.0679"/>
|
|
<Atom name="C4'" type="RNA-CF" charge="0.1065"/>
|
|
<Atom name="H4'" type="RNA-H1" charge="0.1174"/>
|
|
<Atom name="O4'" type="RNA-OS" charge="-0.3548"/>
|
|
<Atom name="C1'" type="RNA-CT" charge="0.0674"/>
|
|
<Atom name="H1'" type="RNA-H2" charge="0.1824"/>
|
|
<Atom name="N1" type="RNA-N*" charge="0.0418"/>
|
|
<Atom name="C6" type="RNA-CS" charge="-0.1126"/>
|
|
<Atom name="H6" type="RNA-H4" charge="0.2188"/>
|
|
<Atom name="C5" type="RNA-CS" charge="-0.3635"/>
|
|
<Atom name="H5" type="RNA-HA" charge="0.1811"/>
|
|
<Atom name="C4" type="RNA-C" charge="0.5952"/>
|
|
<Atom name="O4" type="RNA-O" charge="-0.5761"/>
|
|
<Atom name="N3" type="RNA-NA" charge="-0.3549"/>
|
|
<Atom name="H3" type="RNA-H" charge="0.3154"/>
|
|
<Atom name="C2" type="RNA-C" charge="0.4687"/>
|
|
<Atom name="O2" type="RNA-O" charge="-0.5477"/>
|
|
<Atom name="C3'" type="RNA-CT" charge="0.2022"/>
|
|
<Atom name="H3'" type="RNA-H1" charge="0.0615"/>
|
|
<Atom name="C2'" type="RNA-CT" charge="0.067"/>
|
|
<Atom name="H2'" type="RNA-H1" charge="0.0972"/>
|
|
<Atom name="O2'" type="RNA-OH" charge="-0.6139"/>
|
|
<Atom name="HO2'" type="RNA-HO" charge="0.4186"/>
|
|
<Atom name="O3'" type="RNA-OH" charge="-0.6541"/>
|
|
<Atom name="HO3'" type="RNA-HO" charge="0.4376"/>
|
|
<Bond atomName1="HO5'" atomName2="O5'"/>
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<Bond atomName1="O5'" atomName2="C5'"/>
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<Bond atomName1="C5'" atomName2="H5'"/>
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<Bond atomName1="C5'" atomName2="H5''"/>
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<Bond atomName1="C5'" atomName2="C4'"/>
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<Bond atomName1="C4'" atomName2="H4'"/>
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<Bond atomName1="C4'" atomName2="O4'"/>
|
|
<Bond atomName1="C4'" atomName2="C3'"/>
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|
<Bond atomName1="O4'" atomName2="C1'"/>
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|
<Bond atomName1="C1'" atomName2="H1'"/>
|
|
<Bond atomName1="C1'" atomName2="N1"/>
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|
<Bond atomName1="C1'" atomName2="C2'"/>
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|
<Bond atomName1="N1" atomName2="C6"/>
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|
<Bond atomName1="N1" atomName2="C2"/>
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|
<Bond atomName1="C6" atomName2="H6"/>
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|
<Bond atomName1="C6" atomName2="C5"/>
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|
<Bond atomName1="C5" atomName2="H5"/>
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<Bond atomName1="C5" atomName2="C4"/>
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|
<Bond atomName1="C4" atomName2="O4"/>
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|
<Bond atomName1="C4" atomName2="N3"/>
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|
<Bond atomName1="N3" atomName2="H3"/>
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|
<Bond atomName1="N3" atomName2="C2"/>
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<Bond atomName1="C2" atomName2="O2"/>
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<Bond atomName1="C3'" atomName2="H3'"/>
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<Bond atomName1="C3'" atomName2="C2'"/>
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|
<Bond atomName1="C3'" atomName2="O3'"/>
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|
<Bond atomName1="C2'" atomName2="H2'"/>
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<Bond atomName1="C2'" atomName2="O2'"/>
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<Bond atomName1="O2'" atomName2="HO2'"/>
|
|
<Bond atomName1="O3'" atomName2="HO3'"/>
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</Residue>
|
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</Residues>
|
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<HarmonicBondForce>
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<Bond type1="RNA-C" type2="RNA-C" length="0.1525" k="259407.99999999994"/>
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<Bond type1="RNA-C" type2="RNA-CA" length="0.1409" k="392459.19999999995"/>
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<Bond type1="RNA-C" type2="RNA-CB" length="0.1419" k="374049.5999999999"/>
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<Bond type1="RNA-C" type2="RNA-CM" length="0.1444" k="343087.99999999994"/>
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<Bond type1="RNA-C" type2="RNA-CS" length="0.1444" k="343087.99999999994"/>
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<Bond type1="RNA-C" type2="RNA-CT" length="0.1522" k="265265.6"/>
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<Bond type1="RNA-C" type2="RNA-N*" length="0.1383" k="354803.19999999995"/>
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<Bond type1="RNA-C" type2="RNA-NA" length="0.1388" k="349782.3999999999"/>
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<Bond type1="RNA-C" type2="RNA-NC" length="0.1358" k="382417.5999999999"/>
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<Bond type1="RNA-C" type2="RNA-O" length="0.12290000000000001" k="476975.9999999999"/>
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<Bond type1="RNA-C" type2="RNA-O2" length="0.125" k="548940.7999999999"/>
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<Bond type1="RNA-C" type2="RNA-OH" length="0.13640000000000002" k="376559.99999999994"/>
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<Bond type1="RNA-C" type2="RNA-OS" length="0.1323" k="376559.99999999994"/>
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<Bond type1="RNA-C" type2="RNA-H4" length="0.10800000000000001" k="307105.5999999999"/>
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<Bond type1="RNA-C" type2="RNA-H5" length="0.10800000000000001" k="307105.5999999999"/>
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<Bond type1="RNA-CA" type2="RNA-CA" length="0.13999999999999999" k="392459.19999999995"/>
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<Bond type1="RNA-CA" type2="RNA-CB" length="0.1404" k="392459.19999999995"/>
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</HarmonicBondForce>
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<HarmonicAngleForce>
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<Improper type1="CJ" type2="RNA-CT" type3="RNA-H1" type4="RNA-OH" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
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|
<Improper type1="CJ" type2="RNA-CT" type3="RNA-H1" type4="RNA-H1" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
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<Improper type1="CJ" type2="RNA-H1" type3="RNA-H1" type4="RNA-OS" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
|
|
<Improper type1="CJ" type2="RNA-CT" type3="RNA-H1" type4="RNA-OS" periodicity1="2" phase1="3.141592653589793" k1="0.0"/>
|
|
</PeriodicTorsionForce>
|
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<NonbondedForce coulomb14scale="0.8333333333333334" lj14scale="0.5">
|
|
<UseAttributeFromResidue name="charge"/>
|
|
<Atom type="RNA-C" sigma="0.3399669508423535" epsilon="0.359824"/>
|
|
<Atom type="RNA-CA" sigma="0.3399669508423535" epsilon="0.359824"/>
|
|
<Atom type="RNA-CB" sigma="0.3399669508423535" epsilon="0.359824"/>
|
|
<Atom type="RNA-CI" sigma="0.3399669508423535" epsilon="0.4577296"/>
|
|
<Atom type="RNA-CK" sigma="0.3399669508423535" epsilon="0.359824"/>
|
|
<Atom type="RNA-CP" sigma="0.3399669508423535" epsilon="0.359824"/>
|
|
<Atom type="RNA-CM" sigma="0.3399669508423535" epsilon="0.359824"/>
|
|
<Atom type="RNA-CS" sigma="0.3399669508423535" epsilon="0.359824"/>
|
|
<Atom type="RNA-CQ" sigma="0.3399669508423535" epsilon="0.359824"/>
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|
<Atom type="RNA-CT" sigma="0.3399669508423535" epsilon="0.4577296"/>
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|
<Atom type="RNA-C5" sigma="0.3399669508423535" epsilon="0.359824"/>
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|
<Atom type="RNA-C4" sigma="0.3399669508423535" epsilon="0.359824"/>
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|
<Atom type="RNA-H" sigma="0.10690784617684071" epsilon="0.06568879999999999"/>
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|
<Atom type="RNA-HC" sigma="0.2649532787749369" epsilon="0.06568879999999999"/>
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<Atom type="RNA-H1" sigma="0.2471353044121301" epsilon="0.06568879999999999"/>
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|
<Atom type="RNA-H2" sigma="0.22931733004932334" epsilon="0.06568879999999999"/>
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|
<Atom type="RNA-HA" sigma="0.25996424595335105" epsilon="0.06276"/>
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|
<Atom type="RNA-H4" sigma="0.2510552587719476" epsilon="0.06276"/>
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|
<Atom type="RNA-H5" sigma="0.24214627159054422" epsilon="0.06276"/>
|
|
<Atom type="RNA-HO" sigma="1.0" epsilon="0.0"/>
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|
<Atom type="RNA-NA" sigma="0.3249998523775958" epsilon="0.7112800000000001"/>
|
|
<Atom type="RNA-NB" sigma="0.3249998523775958" epsilon="0.7112800000000001"/>
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|
<Atom type="RNA-NC" sigma="0.3249998523775958" epsilon="0.7112800000000001"/>
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|
<Atom type="RNA-N2" sigma="0.3249998523775958" epsilon="0.7112800000000001"/>
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|
<Atom type="RNA-N*" sigma="0.3249998523775958" epsilon="0.7112800000000001"/>
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|
<Atom type="RNA-O" sigma="0.2959921901149463" epsilon="0.87864"/>
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|
<Atom type="RNA-O2" sigma="0.2959921901149463" epsilon="0.87864"/>
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|
<Atom type="RNA-OH" sigma="0.3066473387839048" epsilon="0.8803136"/>
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|
<Atom type="RNA-OS" sigma="0.3000012343465779" epsilon="0.7112800000000001"/>
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|
<Atom type="RNA-P" sigma="0.37417746161894255" epsilon="0.8368000000000001"/>
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|
<Atom type="RNA-CF" sigma="0.3399669508423535" epsilon="0.4577296"/>
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|
</NonbondedForce>
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</ForceField>
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