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heme.frcmod
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heme.frcmod
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BBA,1834,(2013),1722: Force field modifcations for all-atom heme /parametros Dario
MASS
N0 14.01 0.530 Sp2 N in non-pure aromatic systems (heme b558 NP)
N9 14.01 0.530 Sp2 N in non-pure aromatic systems (heme b558 NO)
NZ 14.01 0.530 Sp2 N in non-pure aromatic systems (heme b595 NP)
NY 14.01 0.530 Sp2 N in non-pure aromatic systems (heme b595 NO)
N5 14.01 0.530 Sp2 N in non-pure aromatic systems (heme d NO)
N6 14.01 0.530 Sp2 N in non-pure aromatic systems (heme d NP)
Y4 14.01 0.530 Sp2 N in non-pure aromatic systems (heme d spirolactone ring)
CY 12.0
CX 12.0
CD 12.0
BOND
N0-CC 316.000 1.38400
N9-CC 316.000 1.38400
NZ-CC 316.000 1.38400
NY-CC 316.000 1.38400
N5-CC 316.000 1.38400
N6-CC 316.000 1.38400
CC-CB 273.000 1.44400
CC-CD 391.000 1.39100
CB-CB 418.000 1.35700
CB-CT 297.000 1.50100
CB-CY 297.000 1.50100
CD-HC 338.000 1.09000
CY-HC 340.000 1.08000
CX-HC 340.000 1.08000
CY-CX 570.000 1.34000
Y4-ce 406.9 1.3942 SOURCE3_SOURCE5 69 0.0151
Y4-cf 564.4 1.2964 CORR_SOURCE5 101 0.0097
CT-c3 300.9 1.5375 SOURCE1_SOURCE5 88072 0.0058
CD-ce 460.7 1.4042 SOURCE1_SOURCES 0.0076
CD-cf 460.7 1.4042 SOURCE1_SOURCES 0.0076
ANGLE
N9-CC-CB 70.000 110.300
N0-CC-CB 70.000 110.300
N9-CC-CD 70.000 125.500
N0-CC-CD 70.000 125.500
CC-N0-CC 70.000 105.400
CC-N9-CC 70.000 105.400
NY-CC-CB 70.000 110.300
NZ-CC-CB 70.000 110.300
NY-CC-CD 70.000 125.500
NZ-CC-CD 70.000 125.500
CC-NZ-CC 70.000 105.400
CC-NY-CC 70.000 105.400
N5-CC-CB 70.000 110.300
N6-CC-CB 70.000 110.300
N5-CC-CD 70.000 125.500
N6-CC-CD 70.000 125.500
CC-N6-CC 70.000 105.400
CC-N5-CC 70.000 105.400
CC-CB-CB 70.000 107.000
CC-CD-CC 70.000 124.100
CB-CC-CD 70.000 125.400
CC-CB-CT 70.000 124.900
CB-CB-CT 70.000 128.200
CC-CD-HC 30.000 118.000
CB-CT-HC 35.000 109.500
CB-CT-H1 35.000 109.500
CB-CB-CY 70.000 128.200
CB-CY-HC 35.000 120.000
CB-CY-CX 70.000 120.000
CY-CX-HC 35.000 120.000
CC-CB-CY 70.000 124.900
CX-CY-HC 35.000 120.000
CB-CT-CT 63.000 114.000
HC-CX-HC 35.000 120.000
HO-OH-HO 60.000 134.000
OH-C-OH 80.000 120.000
Y4-ce-c3 66.4 116.23 SOURCE5 5 1.2988
Y4-ce-ce 68.600 120.790 same as ce-ce-nf, penalty score= 0.4
Y4-cf-c3 66.9 120.68 SOURCE4_SOURCE5 7 2.0560
Y4-cf-cf 68.6 120.79 SOURCE5 9 1.8014
cf-Y4-ce 66.200 121.710 same as ca-ne-cf, penalty score= 2.2
cf-CD-HC 48.5 117.44 1.1566
c3-CT-HC 46.3 109.80 SOURCE3_SOURCE5 179054 0.7972
ce-CD-HC 49.8 118.22 CORR_SOURCE5 1522 1.3445
CC-CD-ce 64.6 126.14 CORR_SOURCE5 122 1.8142
CT-c3-oh 67.5 110.19 SOURCE3_SOURCE5 10188 1.4761
CT-c3-ce 63.5 110.92 CORR_SOURCE5 1159 1.8552
CT-c3-c3 62.9 111.51 SOURCE3_SOURCE5 61999 1.8007
CD-ce-c3 63.7 119.75 CORR_SOURCES 1.7771
c3-cf-CD 63.7 119.75 CORR_SOURCES 1.7771
CC-CD-cf 64.7 125.25 CORR_SOURCE5 1.6363
Y4-ce-CD 68.600 120.790 same as ce-ce-nf, penalty score= 0.4
Y4-cf-CD 68.6 120.79 SOURCE5 9 1.8014
DIHEDRAL
X -N9-CC-X 4 5.700 180.000 2.000
X -N0-CC-X 4 5.700 180.000 2.000
X -NY-CC-X 4 5.700 180.000 2.000
X -NZ-CC-X 4 5.700 180.000 2.000
X -N5-CC-X 4 5.700 180.000 2.000
X -N6-CC-X 4 5.700 180.000 2.000
X -CC-CB-X 4 3.150 180.000 2.000
X -CB-CB-X 4 21.500 180.000 2.000
X -CD-CC-X 4 7.900 180.000 2.000
X -CB-CT-X 1 0.000 180.000 2.000
X -CB-CY-X 4 0.000 180.000 2.000
X -CY-CX-X 4 30.000 180.000 2.000
X -Y4-ce-X 2 1.6 180.0 2.0 single bond
Y4-ce-c3-c3 6 0.0 0.0 3.0 same as X -c3-cc-X , penalty score=136.0
Y4-ce-c3-oh 6 0.0 0.0 3.0 same as X -c3-cc-X , penalty score=136.0
Y4-cf-c3-os 6 0.0 0.0 3.0 same as X -c3-cd-X , penalty score=136.0
c3-c3-cf-Y4 6 0.0 0.0 3.0 same as X -c3-cd-X , penalty score=136.0
c3-cf-Y4-ce 2 1.6 180.0 2.0 same as X -cf-nf-X , penalty score=138.0
cf-cf-Y4-ce 2 1.6 180.0 2.0 same as X -cf-nf-X , penalty score=138.0
HC-CT-c3-c3 1 0.16 0.0 3. Junmei et al, 1999
X -cf-CD-X 4 4.000 180.000 2.0 c2-c2 single bond, parm99
X -ce-CD-X 4 4.000 180.000 2.0 c2-c2 single bond, parm99
X -c3-CT-X 9 1.400 0.000 3.0 JCC,7,(1986),230
CD-cf-Y4-ce 2 1.6 180.0 2.0 same as X -cf-nf-X , penalty score=138.0
X -c3-ce-X 6 0.000 0.000 3.00 same as X-c3-ca-X
X -c3-cf-X 6 0.000 0.000 3.00 same as X-c3-ca-X
IMPROPER
X -X -CC-X 0 1.000 180.000 2.000
X -X -CB-X 0 1.000 180.000 2.000
X -X -N0-X 0 1.000 180.000 2.000
X -X -N9-X 0 1.000 180.000 2.000
X -X -NZ-X 0 1.000 180.000 2.000
X -X -NY-X 0 1.000 180.000 2.000
X -X -N5-X 0 1.000 180.000 2.000
X -X -N6-X 0 1.000 180.000 2.000
X -X -OH-HO 0 1.000 180.000 2.000
CT-OH-C-OH 0 10.5 180.000 2.000
Y4-c3-ce-ce 1.1 180.000 2.000 Using the default value
Y4-c3-cf-cf 1.1 180.000 2.000 Using the default value
NONBON
N0 1.8240 0.1700 0.0
N9 1.8240 0.1700 0.0
NZ 1.8240 0.1700 0.0
NY 1.8240 0.1700 0.0
N5 1.8240 0.1700 0.0
N6 1.8240 0.1700 0.0
Y4 1.8240 0.1700 0.0
CX 1.9080 0.0860 0.0
CY 1.9080 0.0860 0.0