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toppar_drude_nucleic_acid_2020b.str
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toppar_drude_nucleic_acid_2020b.str
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* DRUDE topology and parameter stream file
* Nucleic acids
*
!requires toppar_drude_master*.str
!nucleic acids
!references
!
!Lemkul, J.A. and MacKerell, A.D., Jr., "Polarizable Force Field for
!DNA Based on the Classical Drude Oscillator: I. Refinement using
!Quantum Mechanical Base Stacking and Conformational Energetics,"
!J. Chem. Theory Comput., 13; 2053-2071, 2017, DOI: 10.1021/acs.jctc.7b00067
!
!Lemkul, J.A. and MacKerell, A.D., Jr., "Polarizable Force Field for
!DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular
!Dynamics Simulations of Duplex DNA," J. Chem. Theory Comput.,
!13; 2072-2085, 2017, DOI: 10.1021/acs.jctc.7b00068
!
!Savelyev, A. and MacKerell, A.D., Jr., "All-Atom Polarizable Force
!Field for DNA Based on the Classical Drude Oscillator Model," Journal
!of Computational Chemistry, 35; 1219-1239, 2014, DOI: 10.1002/jcc.23611,
!NIHMSID #585697
!
!RNA
!Lemkul, J.A. and MacKerell, A.D., Jr., "Polarizable Force Field for
!RNA Based on the Classical Drude Oscillator," J. Comput. Chem.,
!39, 2624–2646, 2018, DOI: 10.1002/jcc.25709, NIHMSID #990779
!
!Nucleic Acid Bases
!Baker, C.M., Anisimov, V.M., and MacKerell, A.D., Jr., "Development of
!CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the
!Classical Drude Oscillator Model," Journal of Physical Chemistry B,
!115; 580-596, 2011, PMC3166616
!
read rtf card append
* Topology for Drude nucleic acids
*
38
!
DECL +P
DECL +O1P
DECL +O2P
DECL +O5'
DECL -O3'
DEFA FIRS 5TER LAST 3TER
AUTOGENERATE ANGLES DIHEDRALS DRUDE PATCH
RESI CYT -1.000 ! Cytosine, jal update 06/15
!
! H42 H41
! \ /
! N4
! |
! C4
! / \\
! H5-C5 N3
! || |
! H6-C6 C2
! \ / \\
! N1 O2
! /
! O1P H5' H4' O4' /
! | | \ / \ /
! -P-O5'-C5'----C4' C1'-H1'
! | | \ /
! O2P H5'' C3'-C2'-H2''
! / \ \
! O3' H3' O2'-H2'
!GROUP
ATOM P PD1A 1.192 ALPHA -0.974 THOLE 2.098 !
ATOM O1P OD2C2B -0.856 ALPHA -0.931 THOLE 1.083 !
ATOM O2P OD2C2B -0.856 ALPHA -0.931 THOLE 1.083 !
ATOM O5' OD30B -0.520 ALPHA -0.901 THOLE 0.181 !
ATOM C5' CD32C 0.228 ALPHA -1.642 THOLE 0.862 !
ATOM H5' HDA2A 0.026
ATOM H5'' HDA2A 0.026
GROUP !!NA base
ATOM N1 ND2R6C -0.016 ALPHA -1.220 THOLE 0.450 !
ATOM C6 CD2R6H -0.139 ALPHA -1.354 THOLE 1.804 !
ATOM H6 HDR6B 0.251
ATOM C2 CD2O4A 0.369 ALPHA -1.580 THOLE 1.200 !
ATOM O2 OD2C1B 0.000 ALPHA -0.679 THOLE 0.675
ATOM LP2A LPDNA1 -0.243
ATOM LP2B LPDNA1 -0.203
ATOM N3 ND2R6B 0.000 ALPHA -0.509 THOLE 0.737
ATOM LP3 LPDNA1 -0.491
ATOM C4 CD2R6B 0.575 ALPHA -1.583 THOLE 1.200 !
ATOM N4 ND2B1 -0.644 ALPHA -1.330 THOLE 1.000 !
ATOM H41 HDP1A 0.346
ATOM H42 HDP1A 0.346
ATOM C5 CD2R6J -0.279 ALPHA -1.538 THOLE 1.100 !
ATOM H5 HDR6A 0.128
GROUP !! THF
ATOM C4' CD315B 0.100 ALPHA -1.562 THOLE 1.103 !
ATOM H4' HDA1R5 0.055
ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LPRA LPD -0.152
ATOM LPRB LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1' CD315A 0.094 ALPHA -1.562 THOLE 1.103 !
ATOM H1' HDA1R5 0.055
GROUP !! PRO2, changed from EtOH - jal 7/18/2014
!! jal 7/18/2014
ATOM C2' CD315B 0.000 ALPHA -1.242 THOLE 1.103 !
ATOM H2'' HDA1R5 0.100
ATOM O2' OD31A 0.000 ALPHA -0.628 THOLE 0.181
ATOM H2' HDP1A 0.260
ATOM LPHA LPD -0.180
ATOM LPHB LPD -0.180
GROUP
ATOM C3' CD315B 0.254 ALPHA -1.642 THOLE 0.862 !
ATOM H3' HDA1R5 0.026
ATOM O3' OD30BR -0.520 ALPHA -0.901 THOLE 0.181 !
BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6 C6 N1
BOND C2 O2 C4 N4 N4 H41 N4 H42 C5 H5 C6 H6
BOND LP2A O2 LP2B O2
BOND LP3 N3
BOND N1 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2'
BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1'
BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P
BOND P O2P O3' +P
BOND O4' LPRA O4' LPRB
BOND O4' LPX
BOND O2' LPHA O2' LPHB
IMPR C2 N1 N3 O2 C4 N3 C5 N4
IMPR N4 C4 H41 H42
! Base lone pairs
LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99
! O4' Lone pairs
LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0
! O2' Lone pairs
LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0
!Anisotropies
! Base anisotropies
ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM
!O4' Anisotropy
ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222
!O2' anisotropy
ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162
!Phosphate Anisotropy
ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000
ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000
ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000
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'
IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251
IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896
IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364
IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337
IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356
IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237
IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334
IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337
IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01
IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01
IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
RESI THY -1.000 ! Thymine, jal update 06/15
!
! H51 O4
! | ||
! H52-C5M C4 H3
! | \ / \ /
! H53 C5 N3
! || |
! H6-C6 C2
! \ / \\
! N1 O2
! /
! O1P H5' H4' O4' /
! | | \ / \ /
! -P-O5'-C5'----C4' C1'-H1'
! | | \ /
! O2P H5'' C3'-C2'-H2''
! / \ \
! O3' H3' O2'-H2'
!
GROUP
ATOM P PD1A 1.192 ALPHA -0.974 THOLE 2.098 !
ATOM O1P OD2C2B -0.856 ALPHA -0.931 THOLE 1.083 !
ATOM O2P OD2C2B -0.856 ALPHA -0.931 THOLE 1.083 !
ATOM O5' OD30B -0.520 ALPHA -0.901 THOLE 0.181 !
ATOM C5' CD32C 0.228 ALPHA -1.642 THOLE 0.862 !
ATOM H5' HDA2A 0.026
ATOM H5'' HDA2A 0.026
GROUP
ATOM N1 ND2R6D -0.192 ALPHA -0.979 THOLE 1.257 !
ATOM C6 CD2R6H 0.138 ALPHA -1.545 THOLE 0.934 !
ATOM H6 HDR6B 0.282
ATOM C2 CD2O4A 0.524 ALPHA -1.025 THOLE 1.528 !
ATOM O2 OD2C1B 0.000 ALPHA -0.987 THOLE 1.545 !
ATOM LP2A LPDNA1 -0.131
ATOM LP2B LPDNA1 -0.229
ATOM N3 ND2R6C -0.506 ALPHA -0.766 THOLE 1.447
ATOM H3 HDP1A 0.297
ATOM C4 CD2O4A 0.493 ALPHA -1.013 THOLE 0.866 !
ATOM O4 OD2C1B 0.000 ALPHA -0.791 THOLE 1.000 !
ATOM LP4A LPDNA1 -0.236
ATOM LP4B LPDNA1 -0.234
ATOM C5 CD2R6J -0.174 ALPHA -1.209 THOLE 1.448 !
ATOM C5M CD33A -0.173 ALPHA -1.545 THOLE 0.826 !
ATOM H51 HDA3A 0.047
ATOM H52 HDA3A 0.047
ATOM H53 HDA3A 0.047
GROUP !! THF
ATOM C4' CD315B 0.100 ALPHA -1.562 THOLE 1.103 !
ATOM H4' HDA1R5 0.055
ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LPRA LPD -0.152
ATOM LPRB LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1' CD315A 0.094 ALPHA -1.562 THOLE 1.103 !
ATOM H1' HDA1R5 0.055
GROUP !! PRO2, changed from EtOH - jal 7/18/2014
!! jal 7/18/2014
ATOM C2' CD315B 0.000 ALPHA -1.242 THOLE 1.103 !
ATOM H2'' HDA1R5 0.100
ATOM O2' OD31A 0.000 ALPHA -0.628 THOLE 0.181
ATOM H2' HDP1A 0.260
ATOM LPHA LPD -0.180
ATOM LPHB LPD -0.180
GROUP
ATOM C3' CD315B 0.254 ALPHA -1.642 THOLE 0.862 !
ATOM H3' HDA1R5 0.026
ATOM O3' OD30BR -0.520 ALPHA -0.901 THOLE 0.181 !
BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6
BOND C6 N1 C2 O2 N3 H3 C4 O4 C5 C5M
BOND C5M H51 C5M H52 C5M H53 C6 H6
BOND LP2A O2 LP2B O2
BOND LP4A O4 LP4B O4
BOND N1 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2'
BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1'
BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P
BOND P O2P O3' +P
BOND O4' LPRA O4' LPRB
BOND O4' LPX
BOND O2' LPHA O2' LPHB
IMPR C2 N1 N3 O2 C4 N3 C5 O4 C5 C4 C6 C5M
! Base lone pairs
LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4A O4 C4 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4B O4 C4 C5 distance 0.35 angle 110.0 dihe 180.0
! O4' Lone pairs
LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0
! O2' Lone pairs
LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0
!Anisotropies
! Base anisotropies
ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY O4 C4 N3 C5 A11 0.6968 A22 1.2194 !based on NMA
!O4' Anisotropy
ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222
!O2' anisotropy
ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162
!Phosphate Anisotropy
ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000
ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000
ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000
DONO H3 N3
ACCE O2 C2
ACCE O4 C4
ACCE O1P P
ACCE O2P P
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284
IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212
IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001
IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251
IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896
IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704
IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432
IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813
IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191
IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795
IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327
IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900
IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0
IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0
IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0
RESI URA -1.000 ! Uracil
!
! O4
! ||
! C4 H3
! / \ /
! H5-C5 N3
! || |
! H6-C6 C2
! \ / \\
! N1 O2
! /
! O1P H5' H4' O4' /
! | | \ / \ /
! -P-O5'-C5'----C4' C1'-H1'
! | | \ /
! O2P H5'' C3'-C2'-H2''
! / \ \
! O3' H3' O2'-H2'
!
GROUP
ATOM P PD1A 1.192 ALPHA -0.974 THOLE 2.098 !
ATOM O1P OD2C2B -0.856 ALPHA -0.931 THOLE 1.083 !
ATOM O2P OD2C2B -0.856 ALPHA -0.931 THOLE 1.083 !
ATOM O5' OD30B -0.520 ALPHA -0.901 THOLE 0.181 !
ATOM C5' CD32C 0.228 ALPHA -1.642 THOLE 0.862 !
ATOM H5' HDA2A 0.026
ATOM H5'' HDA2A 0.026
GROUP
ATOM N1 ND2R6D -0.240 ALPHA -1.192 THOLE 1.639 ! ND2R6C --> ND2R6D
ATOM C6 CD2R6H 0.095 ALPHA -0.500 THOLE 0.544
ATOM H6 HDR6B 0.341
ATOM C2 CD2O4A 0.636 ALPHA -1.072 THOLE 1.120
ATOM O2 OD2C1B 0.000 ALPHA -0.799 THOLE 1.076
ATOM LP2A LPDNA1 -0.126
ATOM LP2B LPDNA1 -0.229
ATOM N3 ND2R6C -0.593 ALPHA -1.631 THOLE 1.574
ATOM H3 HDP1A 0.317
ATOM C4 CD2O4A 0.557 ALPHA -1.072 THOLE 1.079
ATOM O4 OD2C1B 0.000 ALPHA -0.657 THOLE 1.156
ATOM LP4A LPDNA1 -0.254
ATOM LP4B LPDNA1 -0.192
ATOM C5 CD2R6J -0.321 ALPHA -1.949 THOLE 1.307
ATOM H5 HDR6A 0.009
GROUP !! THF
ATOM C4' CD315B 0.100 ALPHA -1.562 THOLE 1.103 !
ATOM H4' HDA1R5 0.055
ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LPRA LPD -0.152
ATOM LPRB LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1' CD315A 0.094 ALPHA -1.562 THOLE 1.103 !
ATOM H1' HDA1R5 0.055
GROUP !! PRO2, changed from EtOH - jal 7/18/2014
!! jal 7/18/2014
ATOM C2' CD315B 0.000 ALPHA -1.242 THOLE 1.103 !
ATOM H2'' HDA1R5 0.100
ATOM O2' OD31A 0.000 ALPHA -0.628 THOLE 0.181
ATOM H2' HDP1A 0.260
ATOM LPHA LPD -0.180
ATOM LPHB LPD -0.180
GROUP
ATOM C3' CD315B 0.254 ALPHA -1.642 THOLE 0.862 !
ATOM H3' HDA1R5 0.026
ATOM O3' OD30BR -0.520 ALPHA -0.901 THOLE 0.181 !
BOND N1 C2 C2 N3 N3 C4 C4 C5 C5 C6
BOND C6 N1 C2 O2 N3 H3 C4 O4 C5 H5
BOND C6 H6
BOND LP2A O2 LP2B O2
BOND LP4A O4 LP4B O4
BOND N1 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2'
BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1'
BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P
BOND P O2P O3' +P
BOND O4' LPRA O4' LPRB
BOND O4' LPX
BOND O2' LPHA O2' LPHB
IMPR C2 N1 N3 O2 C4 N3 C5 O4
! Base lone pairs
LONEPAIR relative LP2A O2 C2 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP2B O2 C2 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4A O4 C4 N3 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP4B O4 C4 C5 distance 0.35 angle 110.0 dihe 180.0
! O4' Lone pairs
LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0
! O2' Lone pairs
LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0
!Anisotropies
! Base anisotropies
ANISOTROPY O2 C2 N1 N3 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY O4 C4 N3 C5 A11 0.6968 A22 1.2194 !based on NMA
!O4' Anisotropy
ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222
!O2' anisotropy
ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162
!Phosphate Anisotropy
ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000
ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000
ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000
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'
IC -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160
IC O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284
IC C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212
IC C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001
IC C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251
IC C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896
IC O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746
IC C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379
IC C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338
IC C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373
IC N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218
IC N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383
IC C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227
IC C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03
IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0
IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
RESI ADE -1.000 ! Adenine, jal update 06/15
!
! H61 H62
! \ /
! N6
! |
! C6
! // \
! N1 C5--N7\\
! | || C8-H8
! C2 C4--N9/
! / \\ / \
! H2 N3 \
! \
! /
! O1P H5' H4' O4' /
! | | \ / \ /
! -P-O5'-C5'----C4' C1'-H1'
! | | \ /
! O2P H5'' C3'-C2'-H2''
! / \ \
! O3' H3' O2'-H2'
!
GROUP
ATOM P PD1A 1.192 ALPHA -0.974 THOLE 2.098 !
ATOM O1P OD2C2B -0.856 ALPHA -0.931 THOLE 1.083 !
ATOM O2P OD2C2B -0.856 ALPHA -0.931 THOLE 1.083 !
ATOM O5' OD30B -0.520 ALPHA -0.901 THOLE 0.181 !
ATOM C5' CD32C 0.228 ALPHA -1.642 THOLE 0.862
ATOM H5' HDA2A 0.026
ATOM H5'' HDA2A 0.026
GROUP
ATOM N9 ND2R5D 0.066 ALPHA -0.676 THOLE 0.935
ATOM C4 CD2R6F 0.227 ALPHA -1.045 THOLE 1.100
ATOM N3 ND2R6B 0.000 ALPHA -1.602 THOLE 0.006
ATOM LP3 LPDNA1 -0.507
ATOM C2 CD2R6C 0.208 ALPHA -1.120 THOLE 1.469
ATOM H2 HDR6C 0.176
ATOM N1 ND2R6B 0.000 ALPHA -1.507 THOLE 0.967
ATOM LP1 LPDNA1 -0.472
ATOM C6 CD2R6C 0.402 ALPHA -1.454 THOLE 0.557
ATOM N6 ND2B1 -0.742 ALPHA -1.230 THOLE 1.000 !
ATOM H61 HDP1A 0.373
ATOM H62 HDP1A 0.373
ATOM C5 CD2R6F -0.118 ALPHA -1.238 THOLE 1.854
ATOM N7 ND2R5E 0.000 ALPHA -1.362 THOLE 0.252 !
ATOM LP7 LPDNA1 -0.189
ATOM C8 CD2R5F 0.038 ALPHA -1.357 THOLE 1.452 !
ATOM H8 HDR5B 0.165
GROUP !! THF
ATOM C4' CD315B 0.100 ALPHA -1.562 THOLE 1.103 !
ATOM H4' HDA1R5 0.055
ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LPRA LPD -0.152
ATOM LPRB LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1' CD315A 0.094 ALPHA -1.562 THOLE 1.103 !
ATOM H1' HDA1R5 0.055
GROUP !! PRO2, changed from EtOH - jal 7/18/2014
!! jal 7/18/2014
ATOM C2' CD315B 0.000 ALPHA -1.242 THOLE 1.103 !
ATOM H2'' HDA1R5 0.100
ATOM O2' OD31A 0.000 ALPHA -0.628 THOLE 0.181
ATOM H2' HDP1A 0.260
ATOM LPHA LPD -0.180
ATOM LPHB LPD -0.180
GROUP
ATOM C3' CD315B 0.254 ALPHA -1.642 THOLE 0.862 !
ATOM H3' HDA1R5 0.026
ATOM O3' OD30BR -0.520 ALPHA -0.901 THOLE 0.181 !
BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6
BOND C6 C5 C5 C4 N9 C8 C8 N7 N7 C5
BOND C8 H8 C6 N6 N6 H61 N6 H62 C2 H2
BOND LP1 N1 !LP1 C2 LP1 C6
BOND LP3 N3 !LP3 C2 LP3 C4
BOND LP7 N7 !LP7 C5 LP7 C8
BOND N9 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2'
BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1'
BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P
BOND P O2P O3' +P
BOND O4' LPRA O4' LPRB !C1' LPRA C1' LPRB C4' LPRA C4' LPRB
BOND O4' LPX !C1' LPX C4' LPX
BOND O2' LPHA O2' LPHB !C2' LPHA C2' LPHB
! Base lone pairs
LONEPAIR bisector LP1 N1 C2 C6 distance 0.35 angle 179.99 dihe 179.99
LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99
LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99
! O4' Lone pairs
LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0
! O2' Lone pairs
LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0
!Anisotropies
! Base anisotropies
ANISOTROPY N1 LP1 C6 C2 A11 0.808 A22 1.384 !based on PYRM
ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM
ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID
!O4' Anisotropy
ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222
!O2' anisotropy
ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162
!Phosphate Anisotropy
ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000
ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000
ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000
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'
IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck
IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367
IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312
IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382
IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0
IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0
IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0
IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342
IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337
IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01
IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01
IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337
IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01
IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01
IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
RESI GUA -1.000 ! Guanine, jal update 06/15
!
! O6
! ||
! C6
! / \
! H1-N1 C5--N7\\
! | || C8-H8
! C2 C4--N9/
! / \\ / \
! H21-N2 N3 \
! | \
! H22 \
! \
! /
! O1P H5' H4' O4' /
! | | \ / \ /
! -P-O5'-C5'----C4' C1'-H1'
! | | \ /
! O2P H5'' C3'-C2'-H2''
! / \ \
! O3' H3' O2'-H2'
! |
GROUP
ATOM P PD1A 1.192 ALPHA -0.974 THOLE 2.098 !
ATOM O1P OD2C2B -0.856 ALPHA -0.931 THOLE 1.083 !
ATOM O2P OD2C2B -0.856 ALPHA -0.931 THOLE 1.083 !
ATOM O5' OD30B -0.520 ALPHA -0.901 THOLE 0.181 !
ATOM C5' CD32C 0.228 ALPHA -1.642 THOLE 0.862
ATOM H5' HDA2A 0.026
ATOM H5'' HDA2A 0.026
GROUP
ATOM N9 ND2R5F 0.197 ALPHA -0.880 THOLE 1.351
ATOM C4 CD2R6F 0.227 ALPHA -1.259 THOLE 0.797
ATOM N3 ND2R6B 0.000 ALPHA -0.771 THOLE 1.265 !
ATOM LP3 LPDNA1 -0.459
ATOM C2 CD2R6C 0.587 ALPHA -1.109 THOLE 1.628
ATOM N1 ND2R6C -0.366 ALPHA -1.568 THOLE 0.971 !
ATOM H1 HDP1A 0.287
ATOM N2 ND2B1 -0.736 ALPHA -1.404 THOLE 0.498 !
ATOM H21 HDP1A 0.327
ATOM H22 HDP1A 0.327
ATOM C6 CD2O4A 0.272 ALPHA -0.943 THOLE 1.440 !
ATOM O6 OD2C1B 0.000 ALPHA -0.617 THOLE 1.639 !
ATOM LP6A LPDNA1 -0.259
ATOM LP6B LPDNA1 -0.138
ATOM C5 CD2R6F 0.004 ALPHA -1.788 THOLE 1.033
ATOM N7 ND2R5E 0.000 ALPHA -0.650 THOLE 1.146 !
ATOM LP7 LPDNA1 -0.322
ATOM C8 CD2R5F -0.113 ALPHA -1.427 THOLE 1.309
ATOM H8 HDR5B 0.165
GROUP !! THF
ATOM C4' CD315B 0.100 ALPHA -1.562 THOLE 1.103 !
ATOM H4' HDA1R5 0.055
ATOM O4' OD305A 0.000 ALPHA -0.618 THOLE 1.545
ATOM LPRA LPD -0.152
ATOM LPRB LPD -0.152
ATOM LPX LPD 0.000 !dummy for anisotropic polarizability
ATOM C1' CD315A 0.094 ALPHA -1.562 THOLE 1.103 !
ATOM H1' HDA1R5 0.055
GROUP !! PRO2, changed from EtOH - jal 7/18/2014
!! jal 7/18/2014
ATOM C2' CD315B 0.000 ALPHA -1.242 THOLE 1.103 !
ATOM H2'' HDA1R5 0.100
ATOM O2' OD31A 0.000 ALPHA -0.628 THOLE 0.181
ATOM H2' HDP1A 0.260
ATOM LPHA LPD -0.180
ATOM LPHB LPD -0.180
GROUP
ATOM C3' CD315B 0.254 ALPHA -1.642 THOLE 0.862 !
ATOM H3' HDA1R5 0.026
ATOM O3' OD30BR -0.520 ALPHA -0.901 THOLE 0.181 !
BOND N9 C4 C4 N3 N3 C2 C2 N1 N1 C6 C6 C5
BOND C5 C4 N9 C8 C8 N7 C5 N7 C8 H8 C6 O6
BOND N1 H1 C2 N2 N2 H21 N2 H22
BOND LP3 N3 !LP3 C2 LP3 C4
BOND LP7 N7 !LP7 C5 LP7 C8
BOND LP6A O6 LP6B O6 !LP6A C6 LP6B C6
BOND N9 C1' C1' H1' C1' C2' C2' H2'' C2' O2' O2' H2'
BOND C2' C3' C3' H3' C3' O3' C3' C4' C4' O4' O4' C1'
BOND C4' C5' C4' H4' C5' H5' C5' H5'' C5' O5' O5' P P O1P
BOND P O2P O3' +P
BOND O4' LPRA O4' LPRB !C1' LPRA C1' LPRB C4' LPRA C4' LPRB
BOND O4' LPX !C1' LPX C4' LPX
BOND O2' LPHA O2' LPHB !C2' LPHA C2' LPHB
IMPR C2 N3 N1 N2 C6 N1 C5 O6 N2 H21 C2 H22
! Base lone pairs
LONEPAIR bisector LP3 N3 C2 C4 distance 0.35 angle 179.99 dihe 179.99
LONEPAIR relative LP6A O6 C6 N1 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR relative LP6B O6 C6 C5 distance 0.35 angle 110.0 dihe 180.0
LONEPAIR bisector LP7 N7 C5 C8 distance 0.35 angle 179.99 dihe 179.99
! O4' Lone pairs
LONEPAIR bisector LPRA O4' C1' C4' distance 0.35 angle 110.0 dihe 90.0
LONEPAIR bisector LPRB O4' C1' C4' distance 0.35 angle 110.0 dihe 270.0
LONEPAIR bisector LPX O4' C1' C4' distance 0.10 angle 0.0 dihe 0.0
! O2' Lone pairs
LONEPAIR relative LPHA O2' C2' H2' distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LPHB O2' C2' H2' distance 0.35 angle 110.0 dihe 269.0
!Anisotropies
! Base anisotropies
ANISOTROPY N3 LP3 C4 C2 A11 0.808 A22 1.384 !based on PYRM
ANISOTROPY O6 C6 C5 N1 A11 0.6968 A22 1.2194 !based on NMA
ANISOTROPY N7 LP7 C8 C5 A11 0.808 A22 1.384 !based on IMID
!O4' Anisotropy
ANISOTROPY O4' LPX LPRA LPRB A11 0.8889 A22 1.2222
!O2' anisotropy
ANISOTROPY O2' C2' LPHA LPHB A11 0.8108 A22 1.2162
!Phosphate Anisotropy
ANISOTROPY O5' O1P -O3' O2P A11 1.0000 A22 0.6000
ANISOTROPY -O3' O2P O5' O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5' -O3' A11 0.6000 A22 1.0000
ANISOTROPY O2P P -O3' O5' A11 0.6000 A22 1.0000
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 ike conformation
IC -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha
IC -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802
IC -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801
IC P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta
IC O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma
IC C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta
IC C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon
IC C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta
IC O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck
IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896
IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi
IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374
IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304
IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377
IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355
IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327
IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375
IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341
IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01
IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01
IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393
IC C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03
IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239
IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0
IC C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212
IC H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284
IC O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0
IC C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0
IC C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0
IC C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0
IC C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0
PRES 5TER 0.000 ! 5-terminal HYDROXYL patch, from MeOH
!
! Base
! H5T1 H4' O4' /
! | \ / \ /
! H5T-O5T-C5T----C4' C1'-H1'
! | \ /
! H5T2 C3'-C2D-H2D
! / \ \
! O3' H3' H2Da
! |
DELETE ATOM P
DELETE ATOM O1P
DELETE ATOM O2P
DELETE ATOM DP
DELETE ATOM DO1P
DELETE ATOM DO2P
DELETE ATOM DO5'
DELETE ATOM DC5'
GROUP
ATOM H5T HDP1A 0.360
ATOM O5' OD31A 0.000 ALPHA -1.028 THOLE 1.3
ATOM C5' CD32A -0.060 ALPHA -1.000 THOLE 1.3
ATOM H5' HDA2A 0.080
ATOM H5'' HDA2A 0.080
ATOM LP5A LPD -0.230
ATOM LP5B LPD -0.230
BOND O5' H5T
BOND O5' LP5A O5' LP5B
LONEPAIR relative LP5A O5' C5' H5T distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP5B O5' C5' H5T distance 0.35 angle 110.0 dihe 269.0
ANISOTROPY O5' C5' LP5A LP5B A11 0.8108 A22 1.2162
DONO H5T O5'
IC H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000
PRES 3TER -0.000 ! 3-terminal HYDROXYL patch, from PRO2 (jal 7/18/2014)
!
! \
! C3T-
! / \
! O3T H3'
! |
! H3T
GROUP
ATOM C3' CD315B 0.000 ALPHA -1.242 THOLE 1.103 ! neutralize group charge
ATOM H3' HDA1R5 0.100
ATOM O3' OD31G 0.000 ALPHA -0.628 THOLE 0.181
ATOM H3T HDP1A 0.360
ATOM LP3A LPD -0.230
ATOM LP3B LPD -0.230
BOND O3' H3T
BOND O3' LP3A O3' LP3B
LONEPAIR relative LP3A O3' C3' H3T distance 0.35 angle 110.0 dihe 91.0
LONEPAIR relative LP3B O3' C3' H3T distance 0.35 angle 110.0 dihe 269.0
ANISOTROPY O3' C3' LP3A LP3B A11 0.8108 A22 1.2162
DONO H3T O3'
IC H3T O3' C3' C4' 0.0000 0.00 -180.00 0.00 0.0000
PRES DEOX -0.520 ! Patch to make DEOXYribose from default ribose bases
! modified by jal 7/18/2014 due to RNA-specific atom type for O3'
DELETE ATOM O2'
DELETE ATOM LPHA
DELETE ATOM LPHB
DELETE ATOM DO2'
DELETE ANISOTROPY O3' +O2P +O5' +O1P A11 1.0000 A22 0.6000
GROUP
ATOM O3' OD30B -0.520 ALPHA -0.901 THOLE 0.181
GROUP
ATOM C2' CD325B -0.144 ALPHA -1.617 THOLE 1.103 !neutralize group charge
ATOM H2' HDA2R5 0.072
ATOM H2'' HDA2R5 0.072
BOND C2' H2'
BOND C3' O3'
BOND O3' +P
ANISOTROPY O3' +O2P +O5' +O1P A11 1.0000 A22 0.6000
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C1' C3' *C2' H2' 0.0000 0.0000 -115.00 0.0000 0.0000
PRES DEO3 0.000 ! for the 3'-terminal DNA nucleotides
DELETE ATOM O2'
DELETE ATOM LPHA
DELETE ATOM LPHB
DELETE ATOM DO2'
GROUP
ATOM C2' CD325B -0.144 ALPHA -1.617 THOLE 1.103 !neutralize group charge
ATOM H2' HDA2R5 0.072
ATOM H2'' HDA2R5 0.072
BOND C2' H2'
BOND C3' O3'
IC C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212
IC C1' C3' *C2' H2' 0.0000 0.0000 -115.00 0.0000 0.0000
!! jal - for making nucleotides, updated with DMP in 2020b
PRES 3POM -0.680
GROUP
ATOM P3 PD1A 1.192 ALPHA -0.974 THOLE 2.098
ATOM O3P1 OD2C2B -0.856 ALPHA -0.931 THOLE 1.083
ATOM O3P2 OD2C2B -0.856 ALPHA -0.931 THOLE 1.083
ATOM O3T OD30B -0.520 ALPHA -0.901 THOLE 0.181
ATOM C3T CD32C 0.282 ALPHA -1.642 THOLE 0.862
ATOM H3T1 HDA2A 0.026
ATOM H3T2 HDA2A 0.026
ATOM H3T3 HDA2A 0.026
BOND O3' P3
BOND P3 O3P1 P3 O3P2 P3 O3T
BOND O3T C3T
BOND C3T H3T1 C3T H3T2 C3T H3T3
ANISOTROPY O3T O3P1 O3' O3P2 A11 1.0000 A22 0.6000
ANISOTROPY O3' O3P2 O3T O3P1 A11 1.0000 A22 0.6000
ANISOTROPY O3P1 P3 O3T O3' A11 0.6000 A22 1.0000
ANISOTROPY O3P2 P3 O3' O3T A11 0.6000 A22 1.0000
IC P3 O3' C3' C4' 0.0000 000.00 180.00 000.00 0.0000
IC C3' O3' P3 O3T 0.0000 000.00 -95.22 000.00 0.0000
IC O3T O3' *P3 O3P1 0.0000 000.00 -115.82 000.00 0.0000
IC O3T O3' *P3 O3P2 0.0000 000.00 115.90 000.00 0.0000
IC C3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000
IC H3T1 C3T O3T P3 0.0000 000.00 180.00 000.00 0.0000
IC H3T2 C3T O3T P3 0.0000 000.00 60.00 000.00 0.0000
IC H3T3 C3T O3T P3 0.0000 000.00 -60.00 000.00 0.0000
PRES 5POM -0.319
GROUP
ATOM O5T OD30B -0.520 ALPHA -0.901 THOLE 0.181
ATOM C5T CD33C 0.123 ALPHA -1.642 THOLE 0.862
ATOM H5T1 HDA3A 0.026
ATOM H5T2 HDA3A 0.026
ATOM H5T3 HDA3A 0.026
BOND P O5T
BOND O5T C5T
BOND C5T H5T1 C5T H5T2 C5T H5T3
ANISOTROPY O5T O1P O5' O2P A11 1.0000 A22 0.6000
ANISOTROPY O5' O2P O5T O1P A11 1.0000 A22 0.6000
ANISOTROPY O1P P O5T O5' A11 0.6000 A22 1.0000
ANISOTROPY O2P P O5' O5T A11 0.6000 A22 1.0000
IC O5T P O5' C5' 1.5837 102.73 72.47 116.87 1.4386
IC O5' P O5T C5T 1.5843 102.73 72.47 116.85 1.4394
IC O1P P O5T C5T 1.4910 107.70 -41.57 116.85 1.4394
IC O2P P O5' C5' 1.4906 107.67 -41.56 116.87 1.4386
IC H5T1 C5T O5T P 1.1128 110.79 -42.95 116.85 1.5837