Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 1NKGZ

Calculation Name: 4IGI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4IGI

Chain ID: A

ChEMBL ID:

UniProt ID: E9PWQ3

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2194375.315828
FMO2-HF: Nuclear repulsion 2121024.232374
FMO2-HF: Total energy -73351.083455
FMO2-MP2: Total energy -73569.627674


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1024:GLU)


Summations of interaction energy for fragment #1(A:1024:GLU)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-20-16.90238.068-19.402-21.7640.142
Interaction energy analysis for fragmet #1(A:1024:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.837 / q_NPA : -0.901
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A1026ASP-1-0.716-0.8193.80443.07744.832-0.026-0.740-0.9890.003
4A1027VAL00.000-0.0026.620-1.862-1.8620.0000.0000.0000.000
5A1028VAL0-0.002-0.0049.552-0.667-0.6670.0000.0000.0000.000
6A1029PHE00.0230.01012.968-0.643-0.6430.0000.0000.0000.000
7A1030LEU0-0.015-0.00716.162-0.215-0.2150.0000.0000.0000.000
8A1031ILE0-0.011-0.01919.351-0.348-0.3480.0000.0000.0000.000
9A1032ASH0-0.005-0.03122.219-0.253-0.2530.0000.0000.0000.000
10A1033GLY00.030-0.00325.932-0.022-0.0220.0000.0000.0000.000
11A1034SER00.010-0.00927.791-0.380-0.3800.0000.0000.0000.000
12A1035GLU-1-0.780-0.88331.1938.7308.7300.0000.0000.0000.000
13A1036GLY0-0.0290.00333.530-0.143-0.1430.0000.0000.0000.000
14A1037VAL0-0.004-0.00227.3040.0020.0020.0000.0000.0000.000
15A1038ARG10.8530.89730.611-8.648-8.6480.0000.0000.0000.000
16A1039SER0-0.046-0.03132.3130.1230.1230.0000.0000.0000.000
17A1040GLY00.0470.02730.352-0.035-0.0350.0000.0000.0000.000
18A1041PHE00.0120.00925.0490.3160.3160.0000.0000.0000.000
19A1042PRO0-0.009-0.01526.5350.3960.3960.0000.0000.0000.000
20A1043LEU00.0150.00426.4570.2420.2420.0000.0000.0000.000
21A1044LEU00.0240.02022.5810.3460.3460.0000.0000.0000.000
22A1045LYS10.8170.89622.221-10.587-10.5870.0000.0000.0000.000
23A1046ASP-1-0.857-0.88021.52811.95211.9520.0000.0000.0000.000
24A1047PHE00.0600.02318.8390.4630.4630.0000.0000.0000.000
25A1048VAL00.0080.00016.5930.5530.5530.0000.0000.0000.000
26A1049GLN0-0.026-0.02316.6450.6680.6680.0000.0000.0000.000
27A1050ARG10.8370.89717.176-11.231-11.2310.0000.0000.0000.000
28A1051VAL00.0130.01313.2830.4580.4580.0000.0000.0000.000
29A1052VAL0-0.027-0.02812.1021.0951.0950.0000.0000.0000.000
30A1053GLU-1-0.944-0.96912.59014.99914.9990.0000.0000.0000.000
31A1054SER0-0.054-0.01213.559-0.164-0.1640.0000.0000.0000.000
32A1055LEU0-0.077-0.0288.3941.3981.3980.0000.0000.0000.000
33A1056ASP-1-0.796-0.8716.85428.21928.2190.0000.0000.0000.000
34A1057VAL0-0.018-0.0116.4243.3093.3090.0000.0000.0000.000
35A1058GLY00.007-0.0136.942-2.286-2.2860.0000.0000.0000.000
36A1059PRO0-0.0210.0046.1023.2283.2280.0000.0000.0000.000
37A1060ASP-1-0.884-0.9354.22644.46044.723-0.001-0.040-0.2220.000
38A1061ARG10.7830.8672.639-27.115-24.8660.800-1.212-1.836-0.013
39A1062VAL0-0.0020.0182.3623.3254.5213.009-2.218-1.987-0.023
40A1063ARG10.8260.9154.561-46.995-46.833-0.001-0.012-0.1490.000
41A1064VAL00.0270.0017.166-0.594-0.5940.0000.0000.0000.000
42A1065ALA0-0.032-0.01210.423-0.579-0.5790.0000.0000.0000.000
43A1066LEU0-0.008-0.00113.545-0.296-0.2960.0000.0000.0000.000
44A1067VAL00.0120.00816.952-0.400-0.4000.0000.0000.0000.000
45A1068GLN0-0.008-0.01519.978-0.448-0.4480.0000.0000.0000.000
46A1069TYR0-0.023-0.03923.3970.1420.1420.0000.0000.0000.000
47A1070SER0-0.039-0.04125.878-0.135-0.1350.0000.0000.0000.000
48A1071ASP-1-0.813-0.87529.4419.3749.3740.0000.0000.0000.000
49A1072ARG10.8250.90129.102-9.732-9.7320.0000.0000.0000.000
50A1073THR00.0260.00623.534-0.046-0.0460.0000.0000.0000.000
51A1074ARG10.7920.86024.321-11.669-11.6690.0000.0000.0000.000
52A1075PRO0-0.0010.00019.4500.1890.1890.0000.0000.0000.000
53A1076GLU-1-0.791-0.84019.86711.78011.7800.0000.0000.0000.000
54A1077PHE0-0.040-0.03314.041-0.333-0.3330.0000.0000.0000.000
55A1078TYR00.0350.00814.7650.0360.0360.0000.0000.0000.000
56A1079LEU00.0290.0318.6880.1430.1430.0000.0000.0000.000
57A1080ASN00.0060.00110.4121.1131.1130.0000.0000.0000.000
58A1081SER0-0.068-0.01912.408-1.309-1.3090.0000.0000.0000.000
59A1082HIS00.0080.00613.270-1.129-1.1290.0000.0000.0000.000
60A1083MET00.0080.00211.1781.3161.3160.0000.0000.0000.000
61A1084ASP-1-0.762-0.90011.51418.28918.2890.0000.0000.0000.000
62A1085GLN00.0510.01812.696-1.082-1.0820.0000.0000.0000.000
63A1086GLN0-0.0120.00113.938-1.306-1.3060.0000.0000.0000.000
64A1087GLY00.0120.01016.245-0.822-0.8220.0000.0000.0000.000
65A1088VAL00.0080.00212.028-0.635-0.6350.0000.0000.0000.000
66A1089ILE00.0280.02015.504-0.887-0.8870.0000.0000.0000.000
67A1090SER0-0.062-0.05118.038-1.052-1.0520.0000.0000.0000.000
68A1091ALA0-0.064-0.03118.193-0.726-0.7260.0000.0000.0000.000
69A1092ILE00.0340.02516.108-0.555-0.5550.0000.0000.0000.000
70A1093ARG10.9210.95020.351-13.138-13.1380.0000.0000.0000.000
71A1094ARG10.9250.97321.603-13.283-13.2830.0000.0000.0000.000
72A1095LEU0-0.0240.02020.691-0.360-0.3600.0000.0000.0000.000
73A1096THR00.0140.00624.990-0.381-0.3810.0000.0000.0000.000
74A1097LEU0-0.0240.00727.5140.2430.2430.0000.0000.0000.000
75A1098LEU0-0.067-0.02026.757-0.235-0.2350.0000.0000.0000.000
76A1099GLY00.0400.02529.225-0.307-0.3070.0000.0000.0000.000
77A1100GLY0-0.022-0.00531.6470.2620.2620.0000.0000.0000.000
78A1101PRO0-0.034-0.00333.9580.0000.0000.0000.0000.0000.000
79A1102THR00.0410.00633.454-0.184-0.1840.0000.0000.0000.000
80A1103PRO0-0.0140.01528.5960.1610.1610.0000.0000.0000.000
81A1104ASN0-0.0050.00229.551-0.212-0.2120.0000.0000.0000.000
82A1105THR00.0670.01824.4590.4380.4380.0000.0000.0000.000
83A1106GLY00.0210.00124.7180.5670.5670.0000.0000.0000.000
84A1107ALA0-0.023-0.02424.9320.4630.4630.0000.0000.0000.000
85A1108ALA0-0.0010.00023.3440.4270.4270.0000.0000.0000.000
86A1109LEU00.004-0.00120.0950.7400.7400.0000.0000.0000.000
87A1110GLU-1-0.772-0.88619.99013.46813.4680.0000.0000.0000.000
88A1111PHE0-0.030-0.00620.7720.5180.5180.0000.0000.0000.000
89A1112VAL00.0550.01315.8300.5680.5680.0000.0000.0000.000
90A1113LEU0-0.007-0.00115.7230.9560.9560.0000.0000.0000.000
91A1114ARG10.8200.89216.770-12.969-12.9690.0000.0000.0000.000
92A1115ASN0-0.072-0.04318.607-0.219-0.2190.0000.0000.0000.000
93A1116ILE0-0.042-0.01513.9920.1550.1550.0000.0000.0000.000
94A1117LEU0-0.0150.01011.2691.3551.3550.0000.0000.0000.000
95A1118THR00.0290.02113.0330.3340.3340.0000.0000.0000.000
96A1119SER00.0470.01811.2180.0400.0400.0000.0000.0000.000
97A1120SER0-0.051-0.02112.2810.8530.8530.0000.0000.0000.000
98A1121THR0-0.037-0.02614.177-0.423-0.4230.0000.0000.0000.000
99A1122GLY00.031-0.00310.499-0.188-0.1880.0000.0000.0000.000
100A1123SER0-0.045-0.0138.3903.9133.9130.0000.0000.0000.000
101A1124ARG10.8020.8621.825-88.963-90.56714.029-5.650-6.7760.058
102A1125ILE00.000-0.0026.6103.1223.1220.0000.0000.0000.000
103A1126ALA0-0.048-0.0228.897-0.523-0.5230.0000.0000.0000.000
104A1127GLU-1-0.925-0.9664.89752.16552.329-0.001-0.001-0.1620.000
105A1128GLY0-0.012-0.0075.8424.9374.9370.0000.0000.0000.000
106A1129VAL0-0.062-0.0162.567-1.8090.3512.139-1.448-2.8510.011
107A1130PRO0-0.0040.0033.849-6.522-6.2090.001-0.064-0.2500.000
108A1131GLN00.003-0.0086.498-1.404-1.4040.0000.0000.0000.000
109A1132LEU0-0.011-0.0028.162-2.410-2.4100.0000.0000.0000.000
110A1133LEU00.0060.00810.9740.0260.0260.0000.0000.0000.000
111A1134ILE00.0240.01113.315-0.904-0.9040.0000.0000.0000.000
112A1135VAL0-0.001-0.00116.363-0.196-0.1960.0000.0000.0000.000
113A1136LEU0-0.0090.00219.439-0.304-0.3040.0000.0000.0000.000
114A1137THR0-0.004-0.03622.665-0.211-0.2110.0000.0000.0000.000
115A1138ALA0-0.003-0.00526.3160.0200.0200.0000.0000.0000.000
116A1139GLU-1-0.791-0.85029.7379.3859.3850.0000.0000.0000.000
117A1140PRO0-0.0040.00430.6170.2730.2730.0000.0000.0000.000
118A1141SER0-0.026-0.01329.3800.0480.0480.0000.0000.0000.000
119A1142GLY0-0.021-0.00931.062-0.300-0.3000.0000.0000.0000.000
120A1143ASP-1-0.843-0.91229.35310.38410.3840.0000.0000.0000.000
121A1144ASP-1-0.774-0.89031.21310.08910.0890.0000.0000.0000.000
122A1145VAL00.0640.01326.2880.3290.3290.0000.0000.0000.000
123A1146ARG10.8800.95426.390-9.524-9.5240.0000.0000.0000.000
124A1147GLY0-0.042-0.01226.8870.3170.3170.0000.0000.0000.000
125A1148PRO00.0670.03124.2660.3730.3730.0000.0000.0000.000
126A1149SER0-0.054-0.02322.4460.6220.6220.0000.0000.0000.000
127A1150VAL0-0.027-0.01421.8920.5550.5550.0000.0000.0000.000
128A1151VAL0-0.0050.00321.4020.5670.5670.0000.0000.0000.000
129A1152LEU0-0.014-0.01617.9070.7260.7260.0000.0000.0000.000
130A1153LYS10.7860.92117.364-12.480-12.4800.0000.0000.0000.000
131A1154GLN0-0.067-0.04417.7760.5320.5320.0000.0000.0000.000
132A1155GLY0-0.0150.00417.4030.2830.2830.0000.0000.0000.000
133A1156GLY0-0.0040.00513.5741.0491.0490.0000.0000.0000.000
134A1157ALA0-0.026-0.00712.4161.6041.6040.0000.0000.0000.000
135A1158VAL0-0.003-0.01411.540-1.074-1.0740.0000.0000.0000.000
136A1159PRO0-0.038-0.01813.9720.4270.4270.0000.0000.0000.000
137A1160ILE00.0020.00313.953-0.368-0.3680.0000.0000.0000.000
138A1161GLY00.0090.01217.8350.0480.0480.0000.0000.0000.000
139A1162ILE0-0.012-0.01518.994-0.335-0.3350.0000.0000.0000.000
140A1163GLY00.0460.00522.869-0.080-0.0800.0000.0000.0000.000
141A1164ILE0-0.039-0.03425.123-0.134-0.1340.0000.0000.0000.000
142A1165GLY00.0120.00728.678-0.135-0.1350.0000.0000.0000.000
143A1166ASN0-0.060-0.03832.474-0.144-0.1440.0000.0000.0000.000
144A1167ALA0-0.0220.01828.637-0.041-0.0410.0000.0000.0000.000
145A1168ASP-1-0.789-0.89730.6669.1939.1930.0000.0000.0000.000
146A1169ILE00.029-0.00229.2460.3680.3680.0000.0000.0000.000
147A1170SER00.0140.01628.5030.4490.4490.0000.0000.0000.000
148A1171GLU-1-0.856-0.92528.20610.36310.3630.0000.0000.0000.000
149A1172MET0-0.024-0.00424.6870.6680.6680.0000.0000.0000.000
150A1173GLN0-0.013-0.00623.7690.4760.4760.0000.0000.0000.000
151A1174THR0-0.070-0.03024.2150.2990.2990.0000.0000.0000.000
152A1175ILE0-0.015-0.02320.9190.4340.4340.0000.0000.0000.000
153A1176SER0-0.012-0.00519.7950.8890.8890.0000.0000.0000.000
154A1177PHE00.006-0.00215.375-0.445-0.4450.0000.0000.0000.000
155A1178ILE00.015-0.00618.656-0.436-0.4360.0000.0000.0000.000
156A1179PRO00.031-0.00221.1070.1680.1680.0000.0000.0000.000
157A1180ASP-1-0.814-0.89620.21013.43013.4300.0000.0000.0000.000
158A1181PHE0-0.041-0.02714.9990.1970.1970.0000.0000.0000.000
159A1182ALA0-0.0290.01119.8880.2260.2260.0000.0000.0000.000
160A1183VAL0-0.015-0.01121.407-0.232-0.2320.0000.0000.0000.000
161A1184ALA00.0000.00924.218-0.044-0.0440.0000.0000.0000.000
162A1185ILE0-0.0120.00425.629-0.122-0.1220.0000.0000.0000.000
163A1186PRO00.0400.01528.931-0.056-0.0560.0000.0000.0000.000
164A1187THR0-0.024-0.05331.267-0.165-0.1650.0000.0000.0000.000
165A1188PHE00.0970.03627.6400.2060.2060.0000.0000.0000.000
166A1189ARG10.8430.91728.537-8.202-8.2020.0000.0000.0000.000
167A1190GLU-1-0.771-0.84829.2588.9788.9780.0000.0000.0000.000
168A1191LEU00.0250.03522.6270.2330.2330.0000.0000.0000.000
169A1192GLY00.0110.00123.9100.4260.4260.0000.0000.0000.000
170A1193THR0-0.094-0.06823.9250.2670.2670.0000.0000.0000.000
171A1194ILE00.0150.00822.2270.0580.0580.0000.0000.0000.000
172A1195GLN00.0150.00118.5221.0111.0110.0000.0000.0000.000
173A1196GLN0-0.037-0.02117.2570.6570.6570.0000.0000.0000.000
174A1197VAL00.0530.02817.4250.6040.6040.0000.0000.0000.000
175A1198ILE0-0.0160.00015.6330.6770.6770.0000.0000.0000.000
176A1199SER00.0280.00713.6771.4181.4180.0000.0000.0000.000
177A1200GLU-1-0.861-0.93012.64715.65915.6590.0000.0000.0000.000
178A1201ARG10.8020.89913.065-14.253-14.2530.0000.0000.0000.000
179A1202VAL00.0170.0038.8671.2991.2990.0000.0000.0000.000
180A1203ILE0-0.039-0.0178.6082.7002.7000.0000.0000.0000.000
181A1204GLN0-0.048-0.0288.7681.0741.0740.0000.0000.0000.000
182A1205LEU00.0140.0149.5360.5880.5880.0000.0000.0000.000
183A1206ASN0-0.017-0.0135.5862.1422.1420.0000.0000.0000.000
184A1207ARG10.9300.9451.744-112.696-116.25618.119-8.017-6.5420.106
185A1208GLU-1-0.907-0.9467.25131.12031.1200.0000.0000.0000.000
186A1209GLU-1-0.865-0.9219.71916.31016.3100.0000.0000.0000.000
187A1210LEU0-0.015-0.0198.624-1.582-1.5820.0000.0000.0000.000
188A1211SER0-0.037-0.01711.155-1.148-1.1480.0000.0000.0000.000
189A1212SER0-0.033-0.01013.400-1.575-1.5750.0000.0000.0000.000
190A1213LEU0-0.055-0.00314.989-1.286-1.2860.0000.0000.0000.000
191A1214LYS10.8210.89416.388-16.597-16.5970.0000.0000.0000.000
192A1215PRO00.0250.03417.586-0.381-0.3810.0000.0000.0000.000
193A1216ILE0-0.012-0.00819.783-0.557-0.5570.0000.0000.0000.000
194A1217LEU00.001-0.00221.6210.0700.0700.0000.0000.0000.000
195A1218THR0-0.010-0.02225.465-0.323-0.3230.0000.0000.0000.000
196A1219PRO0-0.0190.00628.199-0.174-0.1740.0000.0000.0000.000
197A1220SER00.0300.02130.116-0.377-0.3770.0000.0000.0000.000