* \\\\ CHARMM36 All-Hydrogen Nucleic Acid Topology File ////
* Alexander D. MacKerell Jr. and coworkers
* April 2011
* All comments to the CHARMM web site: www.charmm.org
* parameter set discussion forum
*
36 1
AUTOGENERATE ANGLE DIHE
!updated 2016/8. see toppar_all.history.
!2010/2011 additions
! ejd, 2010 RNA update
! adm, 2011 DNA update
! For DNA update, new atom type required for P of DNA. This required
! replication of a number of parameters and the creation of new
! patches, DEOX and DEO5, to convert RNA to DNA, such that previous
! CHARMM scripts to generate DNA will no longer work. Note that the
! atom type change to P3 ONLY applies to the phosphodester linkage in
! DNA and NOT to terminal phosphates, DMP etc.
!
!example of new generate/patch combination to generate DNA
!
!read sequence card
!* 1bna, strand 1
!*
!3
!cyt gua cyt
!
!generate a first 5ter last 3ter setup warn
!
!patch deo5 a 1 setup warn !special patch for 5-terminal deoxy residue
!patch deox a 2 setup warn !new patch to convert RNA to DNA
!patch deox a 3 setup warn !no special patch required for 3-terminal deoxy residue
!
!autogenerate angles dihedrals !Use of AUTOGENERATE is essential
!
!references
!
!NUCLEIC ACIDS
!
!Denning, E.J., Priyakumar, U.D., Nilsson, L., and MacKerell Jr., A.D.,
!"Impact of 2'-hydroxyl sampling on the conformational properties of
!RNA: Update of the CHARMM all-atom additive force field for RNA,"
!JCC, 32: 1929-1943, 2011, PMC3082605
!
!Hart, K., Foloppe, N., Baker, C.M., Denning, E.J., Nilsson, L.
!and MacKerell Jr., A.D. "Optimization of the CHARMM additive force
!field for DNA: Improved treatment of the BI/BII conformational
!equilibrium," JCTC, 8:348–362, 2012, PMC3285246
!
!Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for
!Nucleic Acids: 1) Parameter Optimization Based on Small Molecule and
!Condensed Phase Macromolecular Target Data. JCC, 2000, 21: 86-104.
!
!MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for
!Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA
!and RNA in Solution. JCC, 2000, 21: 105-120.
!
MASS -1 HN1 1.00800 H ! Nucleic acid amine proton
MASS -1 HN2 1.00800 H ! Nucleic acid ring nitrogen proton
MASS -1 HN3 1.00800 H ! Nucleic acid aromatic carbon proton
MASS -1 HN4 1.00800 H ! Nucleic acid phosphate hydroxyl proton
MASS -1 HN5 1.00800 H ! Nucleic acid ribose hydroxyl proton
MASS -1 HN6 1.00800 H ! Nucleic acid ribose aliphatic proton
MASS -1 HN7 1.00800 H ! Nucleic acid proton (equivalent to protein HA)
MASS -1 HN8 1.00800 H ! Bound to CN8 in nucleic acids/model compounds
MASS -1 HN9 1.00800 H ! Bound to CN9 in nucleic acids/model compounds
MASS -1 CN1 12.01100 C ! Nucleic acid carbonyl carbon
MASS -1 CN1T 12.01100 C ! Nucleic acid carbonyl carbon (T/U C2)
MASS -1 CN2 12.01100 C ! Nucleic acid aromatic carbon to amide
MASS -1 CN3 12.01100 C ! Nucleic acid aromatic carbon
MASS -1 CN3T 12.01100 C ! Nucleic acid aromatic carbon, Thy C5
MASS -1 CN4 12.01100 C ! Nucleic acid purine C8 and ADE C2
MASS -1 CN5 12.01100 C ! Nucleic acid purine C4 and C5
MASS -1 CN5G 12.01100 C ! Nucleic acid guanine C5
MASS -1 CN7 12.01100 C ! Nucleic acid carbon (equivalent to protein CT1)
MASS -1 CN7B 12.01100 C ! Nucleic acid aliphatic carbon for C1'
MASS -1 CN8 12.01100 C ! Nucleic acid carbon (equivalent to protein CT2)
MASS -1 CN8B 12.01100 C ! Nucleic acid carbon (equivalent to protein CT2)
MASS -1 CN9 12.01100 C ! Nucleic acid carbon (equivalent to protein CT3)
MASS -1 NN1 14.00700 N ! Nucleic acid amide nitrogen
MASS -1 NN2 14.00700 N ! Nucleic acid protonated ring nitrogen
MASS -1 NN2B 14.00700 N ! From NN2, for N9 in GUA different from ADE
MASS -1 NN2U 14.00700 N ! Nucleic acid protonated ring nitrogen, ura N3
MASS -1 NN2G 14.00700 N ! Nucleic acid protonated ring nitrogen, gua N1
MASS -1 NN3 14.00700 N ! Nucleic acid unprotonated ring nitrogen
MASS -1 NN3A 14.00700 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
MASS -1 NN3G 14.00700 N ! Nucleic acid unprotonated ring nitrogen, gua N3
MASS -1 NN4 14.00700 N ! Nucleic acid purine N7
MASS -1 NN6 14.00700 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3)
MASS -1 ON1 15.99940 O ! Nucleic acid carbonyl oxygen
MASS -1 ON1C 15.99940 O ! Nucleic acid carbonyl oxygen, cyt O2
MASS -1 ON2 15.99940 O ! Nucleic acid phosphate ester oxygen
MASS -1 ON3 15.99940 O ! Nucleic acid =O in phosphate
MASS -1 ON4 15.99940 O ! Nucleic acid phosphate hydroxyl oxygen
MASS -1 ON5 15.99940 O ! Nucleic acid ribose hydroxyl oxygen
MASS -1 ON6 15.99940 O ! Nucleic acid deoxyribose ring oxygen
MASS -1 ON6B 15.99940 O ! Nucleic acid ribose ring oxygen
MASS -1 P 30.97400 P ! phosphorus
MASS -1 P2 30.97400 P ! phosphorus, adm, 2011 DNA update
MASS -1 P3 30.97400 P ! pyrophosphate phosphorus
MASS -1 P4 30.97400 P ! protonated pyrophosphate phosphorus
DECL +P
DECL +O1P
DECL +O2P
DECL +O5'
DECL -O3'
DEFA FIRS none LAST none
AUTOGENERATE ANGLES DIHEDRALS PATCH
RESI GUA -1.00 ! O6
ATOM P P 1.50 ! ||
ATOM O1P ON3 -0.78 ! C6
ATOM O2P ON3 -0.78 ! / \
ATOM O5' ON2 -0.57 ! H1-N1 C5--N7\\
ATOM C5' CN8B -0.08 ! | || C8-H8
ATOM H5' HN8 0.09 ! C2 C4--N9/
ATOM H5'' HN8 0.09 ! / \\ / \
GROUP ! H21-N2 N3 \
ATOM C4' CN7 0.16 ! | \
ATOM H4' HN7 0.09 ! H22 \
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 N9 NN2B -0.02 ! | | \ / \
ATOM C4 CN5 0.26 ! O2P H5'' C3'--C2' H1'
ATOM N2 NN1 -0.68 ! / \ / \
ATOM H21 HN1 0.32 ! O3' H3' O2' H2''
ATOM H22 HN1 0.35 ! | |
ATOM N3 NN3G -0.74 ! H2'
ATOM C2 CN2 0.75
ATOM N1 NN2G -0.34
ATOM H1 HN2 0.26
ATOM C6 CN1 0.54
ATOM O6 ON1 -0.51
ATOM C5 CN5G 0.00
ATOM N7 NN4 -0.60
ATOM C8 CN4 0.25
ATOM H8 HN3 0.16
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' N9 C1' C2' N9 C4 N9 C8 C4 N3
BOND C2 N2 C2 N1 N2 H21
BOND N2 H22 N1 H1 N1 C6 C6 C5
BOND C5 N7 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'' C8 H8
DOUBLE C2 N3 C4 C5 N7 C8 C6 O6
IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22
DONO H21 N2
DONO H22 N2
DONO H1 N1
DONO H2' O2'
ACCE O6 C6
ACCE N3
ACCE N7
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
! Chi and sugar-phosphate backbone in B-DNA like conformation
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 !puck
BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374
BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304
BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377
BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355
BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327
BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375
BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341
BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01
BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01
BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393
BILD C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03
BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239
BILD N9 N7 *C8 H8 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 ADE -1.00 ! H61 H62!
ATOM P P 1.50 ! \ /
ATOM O1P ON3 -0.78 ! N6
ATOM O2P ON3 -0.78 ! |
ATOM O5' ON2 -0.57 ! C6
ATOM C5' CN8B -0.08 ! // \
ATOM H5' HN8 0.09 ! N1 C5--N7\\
ATOM H5'' HN8 0.09 ! | || C8-H8
GROUP ! C2 C4--N9/
ATOM C4' CN7 0.16 ! / \\ / \
ATOM H4' HN7 0.09 ! H2 N3 \
ATOM O4' ON6B -0.50 ! \
ATOM C1' CN7B 0.16 ! \
ATOM H1' HN7 0.09 ! \
GROUP ! O1P H5' H4' O4' \
ATOM N9 NN2 -0.05 ! | | \ / \ \
ATOM C5 CN5 0.28 ! -P-O5'-C5'---C4' C1'
ATOM N7 NN4 -0.71 ! | | \ / \
ATOM C8 CN4 0.34 ! O2P H5'' C3'--C2' H1'
ATOM H8 HN3 0.12 ! / \ / \
ATOM N1 NN3A -0.74 ! O3' H3' O2' H2''
ATOM C2 CN4 0.50 ! | |
ATOM H2 HN3 0.13 ! H2'
ATOM N3 NN3A -0.75
ATOM C4 CN5 0.43
ATOM C6 CN2 0.46
ATOM N6 NN1 -0.77
ATOM H61 HN1 0.38
ATOM H62 HN1 0.38
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' N9 C1' C2' N9 C4 N9 C8 C4 N3
BOND C2 N1 C6 N6
BOND N6 H61 N6 H62 C6 C5 C5 N7
BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P
BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5'
BOND C5' H5'' C8 H8 C2 H2
DOUBLE N1 C6 C2 N3 C4 C5 N7 C8
IMPR N6 C6 H61 H62 C6 N1 C5 N6
DONO H61 N6
DONO H62 N6
DONO H2' O2'
ACCE N3
ACCE N7
ACCE N1
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 !puck
BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
BILD C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367
BILD C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312
BILD C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382
BILD C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0
BILD N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0
BILD C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0
BILD N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342
BILD C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337
BILD N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01
BILD H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01
BILD C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337
BILD N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01
BILD H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01
BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
BILD N1 N3 *C2 H2 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 CYT -1.00
ATOM P P 1.50 !
ATOM O1P ON3 -0.78 ! H42 H41
ATOM O2P ON3 -0.78 ! \ /
ATOM O5' ON2 -0.57 ! N4
ATOM C5' CN8B -0.08 ! |
ATOM H5' HN8 0.09 ! C4
ATOM H5'' HN8 0.09 ! / \\
GROUP ! H5-C5 N3
ATOM C4' CN7 0.16 ! || |
ATOM H4' HN7 0.09 ! H6-C6 C2
ATOM O4' ON6B -0.50 ! \ / \\
ATOM C1' CN7B 0.16 ! N1 O2
ATOM H1' HN7 0.09 ! \
GROUP ! \
ATOM N1 NN2 -0.13 ! \
ATOM C6 CN3 0.05 ! O1P H5' H4' O4' \
ATOM H6 HN3 0.17 ! | | \ / \ \
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