892 lines
37 KiB
Plaintext
892 lines
37 KiB
Plaintext
* \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File ////
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* Alexander D. MacKerell Jr. and coworkers
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* April 2011
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* All comments to the CHARMM web site: www.charmm.org
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* parameter set discussion forum
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*
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36 1
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AUTOGENERATE ANGLE DIHE
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!updated 2016/8. see toppar_all.history.
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!2010/2011 additions
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! ejd, 2010 RNA update
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! adm, 2011 DNA update
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! For DNA update, new atom type required for P of DNA. This required
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! replication of a number of parameters and the creation of new
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! patches, DEOX and DEO5, to convert RNA to DNA, such that previous
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! CHARMM scripts to generate DNA will no longer work. Note that the
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! atom type change to P3 ONLY applies to the phosphodester linkage in
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! DNA and NOT to terminal phosphates, DMP etc.
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!
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!example of new generate/patch combination to generate DNA
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!
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!read sequence card
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!* 1bna, strand 1
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!*
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!3
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!cyt gua cyt
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!
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!generate a first 5ter last 3ter setup warn
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!
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!patch deo5 a 1 setup warn !special patch for 5-terminal deoxy residue
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!patch deox a 2 setup warn !new patch to convert RNA to DNA
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!patch deox a 3 setup warn !no special patch required for 3-terminal deoxy residue
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!
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!autogenerate angles dihedrals !Use of AUTOGENERATE is essential
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!
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!references
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!
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!NUCLEIC ACIDS
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!
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!Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D.,
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!"Impact of 2'-hydroxyl sampling on the conformational properties of
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!RNA: Update of the CHARMM all-atom additive force field for RNA,"
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!JCC, 32: 1929-1943, 2011, PMC3082605
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!
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!Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L.
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!and MacKerell Jr., A.D. "Optimization of the CHARMM additive force
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!field for DNA: Improved treatment of the BI/BII conformational
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!equilibrium," JCTC, 8:348–362, 2012, PMC3285246
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!
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!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
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!Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and
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!Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104.
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!
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!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
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!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
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!and RNA in Solution. JCC, 2000, 21: 105-120.
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!
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MASS -1 HN1 1.00800 H ! Nucleic acid amine proton
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MASS -1 HN2 1.00800 H ! Nucleic acid ring nitrogen proton
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MASS -1 HN3 1.00800 H ! Nucleic acid aromatic carbon proton
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MASS -1 HN4 1.00800 H ! Nucleic acid phosphate hydroxyl proton
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MASS -1 HN5 1.00800 H ! Nucleic acid ribose hydroxyl proton
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MASS -1 HN6 1.00800 H ! Nucleic acid ribose aliphatic proton
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MASS -1 HN7 1.00800 H ! Nucleic acid proton (equivalent to protein HA)
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MASS -1 HN8 1.00800 H ! Bound to CN8 in nucleic acids/model compounds
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MASS -1 HN9 1.00800 H ! Bound to CN9 in nucleic acids/model compounds
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MASS -1 CN1 12.01100 C ! Nucleic acid carbonyl carbon
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MASS -1 CN1T 12.01100 C ! Nucleic acid carbonyl carbon (T/U C2)
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MASS -1 CN2 12.01100 C ! Nucleic acid aromatic carbon to amide
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MASS -1 CN3 12.01100 C ! Nucleic acid aromatic carbon
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MASS -1 CN3T 12.01100 C ! Nucleic acid aromatic carbon, Thy C5
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MASS -1 CN4 12.01100 C ! Nucleic acid purine C8 and ADE C2
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MASS -1 CN5 12.01100 C ! Nucleic acid purine C4 and C5
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MASS -1 CN5G 12.01100 C ! Nucleic acid guanine C5
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MASS -1 CN7 12.01100 C ! Nucleic acid carbon (equivalent to protein CT1)
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MASS -1 CN7B 12.01100 C ! Nucleic acid aliphatic carbon for C1'
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MASS -1 CN8 12.01100 C ! Nucleic acid carbon (equivalent to protein CT2)
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MASS -1 CN8B 12.01100 C ! Nucleic acid carbon (equivalent to protein CT2)
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MASS -1 CN9 12.01100 C ! Nucleic acid carbon (equivalent to protein CT3)
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MASS -1 NN1 14.00700 N ! Nucleic acid amide nitrogen
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MASS -1 NN2 14.00700 N ! Nucleic acid protonated ring nitrogen
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MASS -1 NN2B 14.00700 N ! From NN2, for N9 in GUA different from ADE
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MASS -1 NN2U 14.00700 N ! Nucleic acid protonated ring nitrogen, ura N3
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MASS -1 NN2G 14.00700 N ! Nucleic acid protonated ring nitrogen, gua N1
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MASS -1 NN3 14.00700 N ! Nucleic acid unprotonated ring nitrogen
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MASS -1 NN3A 14.00700 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
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MASS -1 NN3G 14.00700 N ! Nucleic acid unprotonated ring nitrogen, gua N3
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MASS -1 NN4 14.00700 N ! Nucleic acid purine N7
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MASS -1 NN6 14.00700 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3)
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MASS -1 ON1 15.99940 O ! Nucleic acid carbonyl oxygen
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MASS -1 ON1C 15.99940 O ! Nucleic acid carbonyl oxygen, cyt O2
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MASS -1 ON2 15.99940 O ! Nucleic acid phosphate ester oxygen
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MASS -1 ON3 15.99940 O ! Nucleic acid =O in phosphate
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MASS -1 ON4 15.99940 O ! Nucleic acid phosphate hydroxyl oxygen
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MASS -1 ON5 15.99940 O ! Nucleic acid ribose hydroxyl oxygen
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MASS -1 ON6 15.99940 O ! Nucleic acid deoxyribose ring oxygen
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MASS -1 ON6B 15.99940 O ! Nucleic acid ribose ring oxygen
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MASS -1 P 30.97400 P ! phosphorus
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MASS -1 P2 30.97400 P ! phosphorus, adm, 2011 DNA update
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MASS -1 P3 30.97400 P ! pyrophosphate phosphorus
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MASS -1 P4 30.97400 P ! protonated pyrophosphate phosphorus
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DECL +P
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DECL +O1P
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DECL +O2P
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DECL +O5'
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DECL -O3'
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DEFA FIRS none LAST none
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AUTOGENERATE ANGLES DIHEDRALS PATCH
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RESI GUA -1.00 ! O6
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ATOM P P 1.50 ! ||
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ATOM O1P ON3 -0.78 ! C6
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ATOM O2P ON3 -0.78 ! / \
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ATOM O5' ON2 -0.57 ! H1-N1 C5--N7\\
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ATOM C5' CN8B -0.08 ! | || C8-H8
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ATOM H5' HN8 0.09 ! C2 C4--N9/
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ATOM H5'' HN8 0.09 ! / \\ / \
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GROUP ! H21-N2 N3 \
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ATOM C4' CN7 0.16 ! | \
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ATOM H4' HN7 0.09 ! H22 \
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ATOM O4' ON6B -0.50 ! \
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ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \
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ATOM H1' HN7 0.09 ! | | \ / \ \
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GROUP ! -P-O5'-C5'---C4' C1'
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ATOM N9 NN2B -0.02 ! | | \ / \
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ATOM C4 CN5 0.26 ! O2P H5'' C3'--C2' H1'
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ATOM N2 NN1 -0.68 ! / \ / \
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ATOM H21 HN1 0.32 ! O3' H3' O2' H2''
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ATOM H22 HN1 0.35 ! | |
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ATOM N3 NN3G -0.74 ! H2'
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ATOM C2 CN2 0.75
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ATOM N1 NN2G -0.34
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ATOM H1 HN2 0.26
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ATOM C6 CN1 0.54
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ATOM O6 ON1 -0.51
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ATOM C5 CN5G 0.00
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ATOM N7 NN4 -0.60
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ATOM C8 CN4 0.25
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ATOM H8 HN3 0.16
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GROUP
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ATOM C2' CN7B 0.14
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ATOM H2'' HN7 0.09
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ATOM O2' ON5 -0.66
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ATOM H2' HN5 0.43
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GROUP
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ATOM C3' CN7 0.01
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ATOM H3' HN7 0.09
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ATOM O3' ON2 -0.57
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BOND P O1P P O2P P O5'
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BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
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BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3
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BOND C2 N2 C2 N1 N2 H21
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BOND N2 H22 N1 H1 N1 C6 C6 C5
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BOND C5 N7 C2' C3' C3' O3' O3' +P
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BOND C2' O2' O2' H2'
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BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
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BOND C5' H5'' C8 H8
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DOUBLE C2 N3 C4 C5 N7 C8 C6 O6
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IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22
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DONO H21 N2
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DONO H22 N2
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DONO H1 N1
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DONO H2' O2'
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ACCE O6 C6
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ACCE N3
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ACCE N7
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ACCE O1P P
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ACCE O2P P
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ACCE O2'
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ACCE O3'
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ACCE O4'
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ACCE O5'
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! Chi and sugar-phosphate backbone in B-DNA like conformation
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BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
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BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
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BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
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BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
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BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
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BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
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BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
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BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
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BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
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BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
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BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck
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BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
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BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
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BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374
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BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304
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BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377
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BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355
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BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327
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BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375
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BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341
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BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01
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BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01
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BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393
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BILD C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03
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BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239
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BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
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BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
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BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
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BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
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BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
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BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
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BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
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BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
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BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
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RESI ADE -1.00 ! H61 H62!
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ATOM P P 1.50 ! \ /
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ATOM O1P ON3 -0.78 ! N6
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ATOM O2P ON3 -0.78 ! |
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ATOM O5' ON2 -0.57 ! C6
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ATOM C5' CN8B -0.08 ! // \
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ATOM H5' HN8 0.09 ! N1 C5--N7\\
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ATOM H5'' HN8 0.09 ! | || C8-H8
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GROUP ! C2 C4--N9/
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ATOM C4' CN7 0.16 ! / \\ / \
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ATOM H4' HN7 0.09 ! H2 N3 \
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ATOM O4' ON6B -0.50 ! \
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ATOM C1' CN7B 0.16 ! \
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ATOM H1' HN7 0.09 ! \
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GROUP ! O1P H5' H4' O4' \
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ATOM N9 NN2 -0.05 ! | | \ / \ \
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ATOM C5 CN5 0.28 ! -P-O5'-C5'---C4' C1'
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ATOM N7 NN4 -0.71 ! | | \ / \
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ATOM C8 CN4 0.34 ! O2P H5'' C3'--C2' H1'
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ATOM H8 HN3 0.12 ! / \ / \
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ATOM N1 NN3A -0.74 ! O3' H3' O2' H2''
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ATOM C2 CN4 0.50 ! | |
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ATOM H2 HN3 0.13 ! H2'
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ATOM N3 NN3A -0.75
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ATOM C4 CN5 0.43
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ATOM C6 CN2 0.46
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ATOM N6 NN1 -0.77
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ATOM H61 HN1 0.38
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ATOM H62 HN1 0.38
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GROUP
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ATOM C2' CN7B 0.14
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ATOM H2'' HN7 0.09
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ATOM O2' ON5 -0.66
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ATOM H2' HN5 0.43
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GROUP
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ATOM C3' CN7 0.01
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ATOM H3' HN7 0.09
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ATOM O3' ON2 -0.57
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BOND P O1P P O2P P O5'
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BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
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BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3
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BOND C2 N1 C6 N6
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BOND N6 H61 N6 H62 C6 C5 C5 N7
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BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P
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BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
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BOND C5' H5'' C8 H8 C2 H2
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DOUBLE N1 C6 C2 N3 C4 C5 N7 C8
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IMPR N6 C6 H61 H62 C6 N1 C5 N6
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DONO H61 N6
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DONO H62 N6
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DONO H2' O2'
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ACCE N3
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ACCE N7
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ACCE N1
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ACCE O1P P
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ACCE O2P P
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ACCE O2'
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ACCE O3'
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ACCE O4'
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ACCE O5'
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BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
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BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
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BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
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BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
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BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
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BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
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BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
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BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
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BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
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BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
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BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck
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BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
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BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
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BILD C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367
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BILD C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312
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BILD C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382
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BILD C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0
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BILD N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0
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BILD C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0
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BILD N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342
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BILD C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337
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BILD N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01
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BILD H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01
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BILD C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337
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BILD N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01
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BILD H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01
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BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
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BILD N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0
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BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
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BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
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BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
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BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
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BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
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BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
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BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
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BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
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RESI CYT -1.00
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ATOM P P 1.50 !
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ATOM O1P ON3 -0.78 ! H42 H41
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ATOM O2P ON3 -0.78 ! \ /
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ATOM O5' ON2 -0.57 ! N4
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ATOM C5' CN8B -0.08 ! |
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ATOM H5' HN8 0.09 ! C4
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ATOM H5'' HN8 0.09 ! / \\
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GROUP ! H5-C5 N3
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ATOM C4' CN7 0.16 ! || |
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ATOM H4' HN7 0.09 ! H6-C6 C2
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ATOM O4' ON6B -0.50 ! \ / \\
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ATOM C1' CN7B 0.16 ! N1 O2
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ATOM H1' HN7 0.09 ! \
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GROUP ! \
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ATOM N1 NN2 -0.13 ! \
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ATOM C6 CN3 0.05 ! O1P H5' H4' O4' \
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ATOM H6 HN3 0.17 ! | | \ / \ \
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ATOM C5 CN3 -0.13 ! -P-O5'-C5'---C4' C1'
|
||
ATOM H5 HN3 0.07 ! | | \ / \
|
||
ATOM C2 CN1 0.52 ! O2P H5'' C3'--C2' H1'
|
||
ATOM O2 ON1C -0.49 ! / \ / \
|
||
ATOM N3 NN3 -0.66 ! O3' H3' O2' H2''
|
||
ATOM C4 CN2 0.65 ! | |
|
||
ATOM N4 NN1 -0.75 ! H2'
|
||
ATOM H41 HN1 0.37
|
||
ATOM H42 HN1 0.33
|
||
GROUP
|
||
ATOM C2' CN7B 0.14
|
||
ATOM H2'' HN7 0.09
|
||
ATOM O2' ON5 -0.66
|
||
ATOM H2' HN5 0.43
|
||
GROUP
|
||
ATOM C3' CN7 0.01
|
||
ATOM H3' HN7 0.09
|
||
ATOM O3' ON2 -0.57
|
||
BOND P O1P P O2P P O5'
|
||
BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
|
||
BOND C1' N1 C1' C2' N1 C2 N1 C6
|
||
BOND C2 N3 C4 N4 N4 H41 N4 H42
|
||
BOND C4 C5 C2' C3' C3' O3' O3' +P
|
||
BOND C2' O2' O2' H2'
|
||
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
|
||
BOND C5' H5'' C5 H5 C6 H6
|
||
DOUBLE C2 O2 C5 C6 N3 C4
|
||
IMPR C2 N1 N3 O2 C4 N3 C5 N4
|
||
IMPR N4 C4 H41 H42
|
||
DONO H42 N4
|
||
DONO H2' O2'
|
||
DONO H41 N4
|
||
ACCE O2 C2
|
||
ACCE N3
|
||
ACCE O1P P
|
||
ACCE O2P P
|
||
ACCE O2'
|
||
ACCE O3'
|
||
ACCE O4'
|
||
ACCE O5'
|
||
|
||
BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
|
||
BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
|
||
BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
|
||
BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
|
||
BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
|
||
BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
|
||
BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
|
||
BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
|
||
BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
|
||
BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
|
||
BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251
|
||
BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896
|
||
BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi
|
||
BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364
|
||
BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337
|
||
BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356
|
||
BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237
|
||
BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334
|
||
BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337
|
||
BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01
|
||
BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01
|
||
BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
|
||
BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
|
||
BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
|
||
BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
|
||
BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
|
||
BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
|
||
BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
|
||
BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
|
||
BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
|
||
BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
|
||
|
||
RESI THY -1.00 ! H51 O4
|
||
ATOM P P 1.50 ! | ||
|
||
ATOM O1P ON3 -0.78 ! H52-C5M C4 H3
|
||
ATOM O2P ON3 -0.78 ! | \ / \ /
|
||
ATOM O5' ON2 -0.57 ! H53 C5 N3
|
||
ATOM C5' CN8B -0.08 ! || |
|
||
ATOM H5' HN8 0.09 ! H6-C6 C2
|
||
ATOM H5'' HN8 0.09 ! \ / \\
|
||
GROUP ! N1 O2
|
||
ATOM C4' CN7 0.16 ! \
|
||
ATOM H4' HN7 0.09 ! \
|
||
ATOM O4' ON6B -0.50 ! \
|
||
ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \
|
||
ATOM H1' HN7 0.09 ! | | \ / \ \
|
||
GROUP ! -P-O5'-C5'---C4' C1'
|
||
ATOM N1 NN2B -0.34 ! | | \ / \
|
||
ATOM C6 CN3 0.17 ! O2P H5'' C3'--C2' H1'
|
||
ATOM H6 HN3 0.17 ! / \ / \
|
||
ATOM C2 CN1T 0.51 ! O3' H3' O2' H2''
|
||
ATOM O2 ON1 -0.41 ! | |
|
||
ATOM N3 NN2U -0.46 ! H2'
|
||
ATOM H3 HN2 0.36 !
|
||
ATOM C4 CN1 0.50 !
|
||
ATOM O4 ON1 -0.45 !
|
||
ATOM C5 CN3T -0.15
|
||
ATOM C5M CN9 -0.11
|
||
ATOM H51 HN9 0.07
|
||
ATOM H52 HN9 0.07
|
||
ATOM H53 HN9 0.07
|
||
GROUP
|
||
ATOM C2' CN7B 0.14
|
||
ATOM H2'' HN7 0.09
|
||
ATOM O2' ON5 -0.66
|
||
ATOM H2' HN5 0.43
|
||
GROUP
|
||
ATOM C3' CN7 0.01
|
||
ATOM H3' HN7 0.09
|
||
ATOM O3' ON2 -0.57
|
||
BOND P O1P P O2P P O5'
|
||
BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
|
||
BOND C1' N1 C1' C2' N1 C2 N1 C6
|
||
BOND C2 N3 N3 H3 N3 C4 C4 C5
|
||
BOND C5 C5M C2' C3' C3' O3' O3' +P
|
||
BOND C2' O2' O2' H2'
|
||
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
|
||
BOND C5' H5'' C6 H6 C5M H51 C5M H52 C5M H53
|
||
DOUBLE C2 O2 C4 O4 C5 C6
|
||
IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M
|
||
DONO H3 N3
|
||
DONO H2' O2'
|
||
ACCE O2 C2
|
||
ACCE O4 C4
|
||
ACCE O1P P
|
||
ACCE O2P P
|
||
ACCE O2'
|
||
ACCE O3'
|
||
ACCE O4'
|
||
ACCE O5'
|
||
|
||
BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
|
||
BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
|
||
BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
|
||
BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
|
||
BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284
|
||
BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212
|
||
BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001
|
||
BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996
|
||
BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
|
||
BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
|
||
BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251
|
||
BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896
|
||
BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi
|
||
BILD C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704
|
||
BILD C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432
|
||
BILD C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813
|
||
BILD N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191
|
||
BILD N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795
|
||
BILD C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327
|
||
BILD C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900
|
||
BILD C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000
|
||
BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
|
||
BILD C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0
|
||
BILD C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0
|
||
BILD H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0
|
||
BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
|
||
BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
|
||
BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
|
||
BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
|
||
BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
|
||
BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
|
||
BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
|
||
BILD C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0
|
||
|
||
RESI URA -1.00 ! O4
|
||
ATOM P P 1.50 ! ||
|
||
ATOM O1P ON3 -0.78 ! C4 H3
|
||
ATOM O2P ON3 -0.78 ! / \ /
|
||
ATOM O5' ON2 -0.57 ! H5-C5 N3
|
||
ATOM C5' CN8B -0.08 ! || |
|
||
ATOM H5' HN8 0.09 ! H6-C6 C2
|
||
ATOM H5'' HN8 0.09 ! \ / \\
|
||
GROUP ! N1 O2
|
||
ATOM C4' CN7 0.16 ! \
|
||
ATOM H4' HN7 0.09 ! \
|
||
ATOM O4' ON6B -0.50 ! \
|
||
ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \
|
||
ATOM H1' HN7 0.09 ! | | \ / \ \
|
||
GROUP ! -P-O5'-C5'---C4' C1'
|
||
ATOM N1 NN2B -0.34 ! | | \ / \
|
||
ATOM C6 CN3 0.20 ! O2P H5'' C3'--C2' H1'
|
||
ATOM H6 HN3 0.14 ! / \ / \
|
||
ATOM C2 CN1T 0.55 ! O3' H3' O2' H2''
|
||
ATOM O2 ON1 -0.45 ! | |
|
||
ATOM N3 NN2U -0.46 ! H2'
|
||
ATOM H3 HN2 0.36 !
|
||
ATOM C4 CN1 0.53 !
|
||
ATOM O4 ON1 -0.48 !
|
||
ATOM C5 CN3 -0.15 !
|
||
ATOM H5 HN3 0.10 !
|
||
GROUP
|
||
ATOM C2' CN7B 0.14
|
||
ATOM H2'' HN7 0.09
|
||
ATOM O2' ON5 -0.66
|
||
ATOM H2' HN5 0.43
|
||
GROUP
|
||
ATOM C3' CN7 0.01
|
||
ATOM H3' HN7 0.09
|
||
ATOM O3' ON2 -0.57
|
||
BOND P O1P P O2P P O5'
|
||
BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1'
|
||
BOND C1' N1 C1' C2' N1 C2 N1 C6
|
||
BOND C2 N3 N3 H3 N3 C4 C4 C5
|
||
BOND C2' C3' C3' O3' O3' +P
|
||
BOND C2' O2' O2' H2'
|
||
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
|
||
BOND C5' H5'' C5 H5 C6 H6
|
||
DOUBLE C2 O2 C4 O4 C5 C6
|
||
IMPR C2 N1 N3 O2 C4 N3 C5 O4
|
||
DONO H3 N3
|
||
DONO H2' O2'
|
||
ACCE O2 C2
|
||
ACCE O4 C4
|
||
ACCE O1P P
|
||
ACCE O2P P
|
||
ACCE O2'
|
||
ACCE O3'
|
||
ACCE O4'
|
||
ACCE O5'
|
||
BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401
|
||
BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
|
||
BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
|
||
BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160
|
||
BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284
|
||
BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212
|
||
BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001
|
||
BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996
|
||
BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
|
||
BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
|
||
BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251
|
||
BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896
|
||
BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746
|
||
BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379
|
||
BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338
|
||
BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373
|
||
BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218
|
||
BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383
|
||
BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227
|
||
BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03
|
||
BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
|
||
BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
|
||
BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
|
||
BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
|
||
BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
|
||
BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
|
||
BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
|
||
BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
|
||
BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
|
||
BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
|
||
|
||
! NOTE the option to regenerate all angles and dihedrals allows
|
||
! the explicit inclusion of the THET and DIHE terms to be omitted
|
||
! even if the PRES is used in a PATCH statement. It is important to
|
||
! inspect the patches prior to use to determine if they should be used
|
||
! in a GENErate or PATCh statement and/or if the AUTOgeneration of
|
||
! angles and dihedrals is required.
|
||
! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the
|
||
! documentation
|
||
|
||
PRES DEO5 0.00 ! Patch to make the 5-terminal nucleotide into DEOXYribose
|
||
DELETE ATOM O2' ! Follow with AUTOGENERATE ANGLES DIHEDRALS
|
||
|
||
GROUP ! To correct O4' atom type in DNA (NF)
|
||
ATOM C4' CN7 0.16 !
|
||
ATOM H4' HN7 0.09 !
|
||
ATOM O4' ON6 -0.50 !
|
||
ATOM C1' CN7B 0.16 !
|
||
ATOM H1' HN7 0.09 !
|
||
GROUP
|
||
ATOM C2' CN8 -0.18
|
||
ATOM H2' HN8 0.09
|
||
ATOM H2'' HN8 0.09
|
||
|
||
BOND C2' H2'
|
||
BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0
|
||
|
||
PRES DEOX 1.50 ! Patch to make non 5-terminal DEOXyribose nucleotides
|
||
DELETE ATOM O2' ! Follow with AUTOGENERATE ANGLES DIHEDRALS
|
||
|
||
ATOM P P2 1.50 ! switch type P to type P2 as required to apply
|
||
! 2011 DNA update to zeta in DNA only
|
||
GROUP ! To correct O4' atom type in DNA (NF)
|
||
ATOM C4' CN7 0.16 !
|
||
ATOM H4' HN7 0.09 !
|
||
ATOM O4' ON6 -0.50 !
|
||
ATOM C1' CN7B 0.16 !
|
||
ATOM H1' HN7 0.09 !
|
||
GROUP
|
||
ATOM C2' CN8 -0.18
|
||
ATOM H2' HN8 0.09
|
||
ATOM H2'' HN8 0.09
|
||
|
||
BOND C2' H2'
|
||
BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0
|
||
|
||
PRES DEOS 1.50 ! Patch to convert a single nucleotide in an RNA strand to deoxy
|
||
! for non 5-terminal DEOXyribose nucleotides
|
||
! Do NOT use with patch deox
|
||
DELETE ATOM O2' ! Follow with AUTOGENERATE ANGLES DIHEDRALS
|
||
|
||
GROUP ! To correct O4' atom type in DNA (NF)
|
||
ATOM C4' CN7 0.16 !
|
||
ATOM H4' HN7 0.09 !
|
||
ATOM O4' ON6 -0.50 !
|
||
ATOM C1' CN7B 0.16 !
|
||
ATOM H1' HN7 0.09 !
|
||
GROUP
|
||
ATOM C2' CN8 -0.18
|
||
ATOM H2' HN8 0.09
|
||
ATOM H2'' HN8 0.09
|
||
|
||
ATOM +P P2 1.50 ! convert i+1 phosphorous to P2 for DNA
|
||
|
||
BOND C2' H2'
|
||
BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0
|
||
|
||
PRES DEOR 3.00 ! Patch to maintain a single RNA nucleotide in a DNA oligonucleotide
|
||
! Note that patch should be invoked once all the DEOX patches
|
||
! for the strand have been called
|
||
!
|
||
ATOM P P2 1.50 ! switch type P to type P2 as required for DNA in i-1 nucleotide
|
||
ATOM +P P 1.50 ! revert i+1 phosphorous from P2 to P type for RNA
|
||
|
||
PRES 5TER 0.00 ! 5'-terminal HYDROXYL patch, from MeOH
|
||
! use in generate statement
|
||
GROUP
|
||
ATOM H5T HN5 0.43
|
||
ATOM O5' ON5 -0.66
|
||
ATOM C5' CN8B 0.05
|
||
ATOM H5' HN8 0.09
|
||
ATOM H5'' HN8 0.09
|
||
!
|
||
DELETE ATOM P
|
||
DELETE ATOM O1P
|
||
DELETE ATOM O2P
|
||
!
|
||
BOND H5T O5'
|
||
DONO H5T O5'
|
||
BILD H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000
|
||
|
||
PRES 5MET 0.00 ! 5'-ribose METHYL patch
|
||
! use in generate statement, doesn't work with DEOx patches
|
||
GROUP
|
||
ATOM C5' CN9 -0.27
|
||
ATOM H5' HN9 0.09
|
||
ATOM H5'' HN9 0.09
|
||
ATOM H53' HN9 0.09 ! Can't use ''' and avoid conflict with THY
|
||
!
|
||
DELETE ATOM O5'
|
||
DELETE ATOM P
|
||
DELETE ATOM O1P
|
||
DELETE ATOM O2P
|
||
!
|
||
BOND C5' H53'
|
||
IC C3' C4' C5' H53' 0.0000 0.00 180.00 0.00 0.0000
|
||
IC H53' C4' *C5' H5' 0.0000 0.00 120.00 0.00 0.0000
|
||
IC H53' C4' *C5' H5'' 0.0000 0.00 -120.00 0.00 0.0000
|
||
|
||
PRES 5PHO -1.00 ! 5'terminal PHOSPHATE patch
|
||
! use in generate statement
|
||
GROUP
|
||
ATOM C5' CN8B -0.08
|
||
ATOM H5' HN8 0.09
|
||
ATOM H5'' HN8 0.09
|
||
ATOM P P 1.50
|
||
ATOM O1P ON3 -0.82
|
||
ATOM O2P ON3 -0.82
|
||
ATOM O5' ON2 -0.62
|
||
ATOM O5T ON4 -0.68
|
||
ATOM H5T HN4 0.34
|
||
BOND O5T P H5T O5T
|
||
DONO H5T O5T
|
||
! Built in B-DNA-like conformation (NF)
|
||
BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000
|
||
BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000
|
||
BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000
|
||
BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000
|
||
BILD H5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000
|
||
|
||
PRES 5POM -1.00 ! 5'terminal Methyl-Phosphate patch
|
||
! use in generate statement
|
||
GROUP
|
||
ATOM C5' CN8B -0.08
|
||
ATOM H5' HN8 0.09
|
||
ATOM H5'' HN8 0.09
|
||
ATOM P P 1.50
|
||
ATOM O1P ON3 -0.78
|
||
ATOM O2P ON3 -0.78
|
||
ATOM O5' ON2 -0.57
|
||
ATOM O5T ON2 -0.57
|
||
ATOM C5T CN9 -0.17
|
||
ATOM H5T1 HN9 0.09
|
||
ATOM H5T2 HN9 0.09
|
||
ATOM H5T3 HN9 0.09
|
||
|
||
BOND O5T P O5T C5T C5T H5T1 C5T H5T2
|
||
BOND C5T H5T3
|
||
!DONO H5T O5T
|
||
! Built in B-DNA-like conformation (NF)
|
||
BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000
|
||
BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000
|
||
BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000
|
||
BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000
|
||
BILD C5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000
|
||
BILD H5T1 C5T O5T P 0.0000 000.00 180.20 000.00 0.0000
|
||
BILD H5T2 C5T O5T P 0.0000 000.00 60.00 000.00 0.0000
|
||
BILD H5T3 C5T O5T P 0.0000 000.00 -60.00 000.00 0.0000
|
||
|
||
PRES 3TER 0.00 ! 3'terminal HYDROXYL patch, from MeOH
|
||
! use in generate statement
|
||
GROUP
|
||
ATOM C3' CN7 0.14
|
||
ATOM H3' HN7 0.09
|
||
ATOM O3' ON5 -0.66
|
||
ATOM H3T HN5 0.43
|
||
BOND O3' H3T
|
||
DONO H3T O3'
|
||
BILD H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284
|
||
|
||
PRES 3PHO -1.00 ! 3'terminal PHOSPHATE patch
|
||
! use in generate statement
|
||
GROUP
|
||
ATOM C3' CN7 0.01
|
||
ATOM H3' HN7 0.09
|
||
ATOM P3 P 1.50
|
||
ATOM O1P3 ON3 -0.82
|
||
ATOM O2P3 ON3 -0.82
|
||
ATOM O3' ON2 -0.62
|
||
ATOM O3T ON4 -0.68
|
||
ATOM H3T HN4 0.34
|
||
BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T H3T
|
||
DONO H3T O3T
|
||
ACCE O3T
|
||
ACCE O1P3
|
||
ACCE O2P3
|
||
! Build in B-DNA-like conformation (NF)
|
||
BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000
|
||
BILD C3' O3' P3 O3T 0.0000 000.00 -95.20 000.00 0.0000
|
||
BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000
|
||
BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000
|
||
BILD H3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000
|
||
|
||
PRES 3POM -1.00 ! 3'terminal Methyl Phosphate patch
|
||
! use in generate statement
|
||
! To build model compound with OPO3-CH3 at the 3' end (nicolas)
|
||
GROUP
|
||
ATOM C3' CN7 0.01
|
||
ATOM H3' HN7 0.09
|
||
ATOM P3 P 1.50
|
||
ATOM O1P3 ON3 -0.78
|
||
ATOM O2P3 ON3 -0.78
|
||
ATOM O3' ON2 -0.57
|
||
ATOM O3T ON2 -0.57
|
||
ATOM C3T CN9 -0.17
|
||
ATOM H3T1 HN9 0.09
|
||
ATOM H3T2 HN9 0.09
|
||
ATOM H3T3 HN9 0.09
|
||
|
||
BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T C3T
|
||
BOND C3T H3T1 C3T H3T2 C3T H3T3
|
||
ACCE O3'
|
||
ACCE O5'
|
||
ACCE O1P3
|
||
ACCE O2P3
|
||
BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000
|
||
BILD C3' O3' P3 O3T 0.0000 000.00 -95.22 000.00 0.0000
|
||
BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000
|
||
BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000
|
||
BILD C3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000
|
||
BILD H3T1 C3T O3T P3 0.0000 000.00 180.00 000.00 0.0000
|
||
BILD H3T2 C3T O3T P3 0.0000 000.00 60.00 000.00 0.0000
|
||
BILD H3T3 C3T O3T P3 0.0000 000.00 -60.00 000.00 0.0000
|
||
|
||
PRES 3PO3 -2.00 ! 3'terminal PHOSPHATE patch
|
||
! use in generate statement
|
||
! Added by Nicolas, to be consistent with model componds
|
||
GROUP
|
||
ATOM C3' CN7 -0.09
|
||
ATOM H3' HN7 0.09
|
||
ATOM P3 P 1.10
|
||
ATOM O3' ON2 -0.40
|
||
ATOM O1P3 ON3 -0.90
|
||
ATOM O2P3 ON3 -0.90
|
||
ATOM O3P3 ON3 -0.90
|
||
BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3P3
|
||
ACCE O1P3
|
||
ACCE O2P3
|
||
ACCE O3P3
|
||
BILD C4' C3' O3' P3 0.0000 000.00 180.00 000.00 0.0000
|
||
BILD C3' O3' P3 O3P3 0.0000 000.00 -39.52 000.00 0.0000
|
||
BILD O3P3 O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000
|
||
BILD O3P3 O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000
|
||
BILD O3' P3 O3P3 O3T 0.0000 000.00 180.00 000.00 0.0000
|
||
BILD P3 O3P3 O3T H3T 0.0000 000.00 180.00 000.00 0.0000
|
||
|
||
PRES DELB 0.00 ! patch to delete all possible base atoms
|
||
! of Cyt,Gua,Ade,Thy and Ura
|
||
!
|
||
!note: error messages will be obtained due to atoms not present in
|
||
!residue being "deleted" by this patch
|
||
!cyt section
|
||
DELE ATOM N1
|
||
DELE ATOM C6
|
||
DELE ATOM H6
|
||
DELE ATOM C2
|
||
DELE ATOM O2
|
||
DELE ATOM N3
|
||
DELE ATOM C4
|
||
DELE ATOM N4
|
||
DELE ATOM H41
|
||
DELE ATOM H42
|
||
DELE ATOM C5
|
||
DELE ATOM H5
|
||
!gua section
|
||
DELE ATOM N9
|
||
DELE ATOM H1
|
||
DELE ATOM N2
|
||
DELE ATOM H21
|
||
DELE ATOM H22
|
||
DELE ATOM O6
|
||
DELE ATOM N7
|
||
DELE ATOM C8
|
||
DELE ATOM H8
|
||
!ade section
|
||
DELE ATOM H2
|
||
DELE ATOM N6
|
||
DELE ATOM H61
|
||
DELE ATOM H62
|
||
!thy/ura section
|
||
DELE ATOM H3
|
||
DELE ATOM O4
|
||
DELE ATOM C5M
|
||
DELE ATOM H51
|
||
DELE ATOM H52
|
||
DELE ATOM H53
|
||
|
||
PRES CY35 0.0 ! patch to make a cyclic 3'-5' nucleotide
|
||
! use AUTOGEN ANGLE DIHE after this patch
|
||
BOND O3' P ! but before water-generation
|
||
|
||
PRES LKNA 0.0 ! Patch to join to nucleic acid segments (eg for IMAGES)
|
||
! eg: patch sega 10 segb 1
|
||
! sega should have std 3' (gene sega ... last none)
|
||
! segb should have std 5' (gene segb ... first none)
|
||
! USE AUTOgen ANGL DIHE after this patch,
|
||
! but before water-generation
|
||
BOND 1O3' 2P
|
||
IC 1O3' 2P 2O5' 2C5' 1.6001 101.45 -39.25 119.00 1.4401
|
||
IC 1O3' 2O5' *2P 2O1P 1.6001 101.45 -115.82 109.74 1.4802
|
||
IC 1O3' 2O5' *2P 2O2P 1.6001 101.45 115.90 109.80 1.4801
|
||
IC 1C4' 1C3' 1O3' 2P 1.5284 111.92 159.13 119.05 1.6001
|
||
IC 1C3' 1O3' 2P 2O5' 1.4212 119.05 -98.86 101.45 1.5996
|
||
|
||
end
|
||
|