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: VQL11

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 OptH
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 -2193441.241921
FMO2-HF: Nuclear repulsion 2120090.889274
FMO2-HF: Total energy -73350.352647
FMO2-MP2: Total energy -73568.889729


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.
33.0347.4568.598-9.663-13.3580.02
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 : -0.937 / q_NPA : -0.972
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-1-0.717-0.8203.80438.07739.933-0.027-0.809-1.0200.004
4A1027VAL0-0.006-0.0036.619-1.564-1.5640.0000.0000.0000.000
5A1028VAL00.003-0.0029.512-0.674-0.6740.0000.0000.0000.000
6A1029PHE00.0170.00913.019-0.545-0.5450.0000.0000.0000.000
7A1030LEU0-0.013-0.00816.122-0.222-0.2220.0000.0000.0000.000
8A1031ILE0-0.012-0.01819.314-0.308-0.3080.0000.0000.0000.000
9A1032ASH0-0.039-0.06422.179-0.266-0.2660.0000.0000.0000.000
10A1033GLY00.033-0.00225.892-0.011-0.0110.0000.0000.0000.000
11A1034SER00.0260.00027.753-0.356-0.3560.0000.0000.0000.000
12A1035GLU-1-0.786-0.89231.1558.5848.5840.0000.0000.0000.000
13A1036GLY0-0.0200.00633.486-0.135-0.1350.0000.0000.0000.000
14A1037VAL00.0090.00927.2900.0000.0000.0000.0000.0000.000
15A1038ARG10.8290.88830.566-8.593-8.5930.0000.0000.0000.000
16A1039SER0-0.048-0.03432.2690.1200.1200.0000.0000.0000.000
17A1040GLY00.0480.02930.302-0.031-0.0310.0000.0000.0000.000
18A1041PHE00.0180.01124.8990.3130.3130.0000.0000.0000.000
19A1042PRO0-0.013-0.01826.4900.3930.3930.0000.0000.0000.000
20A1043LEU00.0200.00626.4100.2420.2420.0000.0000.0000.000
21A1044LEU00.0220.01922.7070.3430.3430.0000.0000.0000.000
22A1045LYS10.8180.90522.172-10.460-10.4600.0000.0000.0000.000
23A1046ASP-1-0.889-0.91221.48211.99211.9920.0000.0000.0000.000
24A1047PHE00.0410.01318.9470.4580.4580.0000.0000.0000.000
25A1048VAL00.0080.00016.5420.5590.5590.0000.0000.0000.000
26A1049GLN0-0.022-0.02116.5960.7500.7500.0000.0000.0000.000
27A1050ARG10.8740.93217.129-11.321-11.3210.0000.0000.0000.000
28A1051VAL00.0020.01013.2420.4680.4680.0000.0000.0000.000
29A1052VAL0-0.025-0.02812.3371.1111.1110.0000.0000.0000.000
30A1053GLU-1-0.934-0.97612.54415.07815.0780.0000.0000.0000.000
31A1054SER0-0.058-0.01113.509-0.064-0.0640.0000.0000.0000.000
32A1055LEU0-0.091-0.0348.3631.4861.4860.0000.0000.0000.000
33A1056ASP-1-0.844-0.9276.65028.34628.3460.0000.0000.0000.000
34A1057VAL0-0.015-0.0136.3943.2593.2590.0000.0000.0000.000
35A1058GLY00.000-0.0286.945-2.085-2.0850.0000.0000.0000.000
36A1059PRO0-0.042-0.0066.1063.2173.2170.0000.0000.0000.000
37A1060ASP-1-0.859-0.9233.98645.36245.6980.000-0.055-0.2800.000
38A1061ARG10.8370.9462.607-26.157-24.2581.201-1.120-1.980-0.013
39A1062VAL0-0.0040.0152.3513.0713.9773.216-2.200-1.921-0.022
40A1063ARG10.8200.9094.526-42.406-42.245-0.001-0.012-0.1480.000
41A1064VAL00.0340.0077.148-0.444-0.4440.0000.0000.0000.000
42A1065ALA0-0.032-0.01210.393-0.573-0.5730.0000.0000.0000.000
43A1066LEU0-0.006-0.00213.520-0.230-0.2300.0000.0000.0000.000
44A1067VAL00.0130.00916.922-0.400-0.4000.0000.0000.0000.000
45A1068GLN0-0.022-0.02219.950-0.394-0.3940.0000.0000.0000.000
46A1069TYR0-0.028-0.04023.3650.1400.1400.0000.0000.0000.000
47A1070SER0-0.039-0.01525.867-0.133-0.1330.0000.0000.0000.000
48A1071ASP-1-0.826-0.90829.4379.1769.1760.0000.0000.0000.000
49A1072ARG10.9010.95529.101-9.528-9.5280.0000.0000.0000.000
50A1073THR00.0310.00623.544-0.038-0.0380.0000.0000.0000.000
51A1074ARG10.8560.92624.290-11.377-11.3770.0000.0000.0000.000
52A1075PRO0-0.006-0.00519.4410.2010.2010.0000.0000.0000.000
53A1076GLU-1-0.840-0.90419.90211.67611.6760.0000.0000.0000.000
54A1077PHE0-0.050-0.03213.996-0.279-0.2790.0000.0000.0000.000
55A1078TYR00.0360.00814.652-0.091-0.0910.0000.0000.0000.000
56A1079LEU00.0280.0288.5470.1700.1700.0000.0000.0000.000
57A1080ASN0-0.004-0.00310.3311.0321.0320.0000.0000.0000.000
58A1081SER0-0.064-0.01512.270-1.045-1.0450.0000.0000.0000.000
59A1082HIS00.0150.00813.257-0.959-0.9590.0000.0000.0000.000
60A1083MET00.0040.00411.1831.3521.3520.0000.0000.0000.000
61A1084ASP-1-0.819-0.93011.51418.42918.4290.0000.0000.0000.000
62A1085GLN00.0680.02512.354-1.264-1.2640.0000.0000.0000.000
63A1086GLN00.0030.00813.913-1.362-1.3620.0000.0000.0000.000
64A1087GLY00.0320.01816.215-0.820-0.8200.0000.0000.0000.000
65A1088VAL00.0110.00212.024-0.661-0.6610.0000.0000.0000.000
66A1089ILE00.0370.02415.478-0.832-0.8320.0000.0000.0000.000
67A1090SER0-0.057-0.04318.005-1.044-1.0440.0000.0000.0000.000
68A1091ALA0-0.055-0.02818.196-0.717-0.7170.0000.0000.0000.000
69A1092ILE00.0290.02516.109-0.548-0.5480.0000.0000.0000.000
70A1093ARG10.9230.95620.317-12.928-12.9280.0000.0000.0000.000
71A1094ARG10.9170.96321.637-13.163-13.1630.0000.0000.0000.000
72A1095LEU0-0.0130.02520.749-0.364-0.3640.0000.0000.0000.000
73A1096THR00.003-0.00324.958-0.382-0.3820.0000.0000.0000.000
74A1097LEU0-0.0250.00227.4820.2220.2220.0000.0000.0000.000
75A1098LEU0-0.066-0.01526.836-0.230-0.2300.0000.0000.0000.000
76A1099GLY00.0030.00729.194-0.307-0.3070.0000.0000.0000.000
77A1100GLY0-0.040-0.02831.6150.2240.2240.0000.0000.0000.000
78A1101PRO0-0.0180.00133.9250.0130.0130.0000.0000.0000.000
79A1102THR00.0400.00332.876-0.139-0.1390.0000.0000.0000.000
80A1103PRO0-0.0170.01328.6640.1410.1410.0000.0000.0000.000
81A1104ASN00.0060.01129.582-0.181-0.1810.0000.0000.0000.000
82A1105THR00.0520.01524.4920.4380.4380.0000.0000.0000.000
83A1106GLY00.0300.00724.7660.5580.5580.0000.0000.0000.000
84A1107ALA0-0.001-0.00924.9860.4490.4490.0000.0000.0000.000
85A1108ALA0-0.014-0.00523.2830.4170.4170.0000.0000.0000.000
86A1109LEU0-0.003-0.00520.2640.7270.7270.0000.0000.0000.000
87A1110GLU-1-0.879-0.95120.03712.69412.6940.0000.0000.0000.000
88A1111PHE0-0.038-0.01120.6040.4860.4860.0000.0000.0000.000
89A1112VAL00.0430.00115.8840.5490.5490.0000.0000.0000.000
90A1113LEU0-0.006-0.00115.8740.8750.8750.0000.0000.0000.000
91A1114ARG10.9180.95316.806-13.080-13.0800.0000.0000.0000.000
92A1115ASN0-0.042-0.02518.596-0.061-0.0610.0000.0000.0000.000
93A1116ILE0-0.048-0.01413.9480.1350.1350.0000.0000.0000.000
94A1117LEU0-0.0170.00811.3541.2191.2190.0000.0000.0000.000
95A1118THR00.0310.02113.0460.2810.2810.0000.0000.0000.000
96A1119SER00.0420.01211.6230.6210.6210.0000.0000.0000.000
97A1120SER0-0.074-0.02412.7090.2030.2030.0000.0000.0000.000
98A1121THR0-0.020-0.01814.163-0.355-0.3550.0000.0000.0000.000
99A1122GLY00.024-0.00510.756-0.119-0.1190.0000.0000.0000.000
100A1123SER0-0.034-0.0098.3523.5653.5650.0000.0000.0000.000
101A1124ARG10.8400.8832.781-65.467-61.9401.160-1.885-2.8010.008
102A1125ILE00.0110.0086.7062.9972.9970.0000.0000.0000.000
103A1126ALA0-0.051-0.0268.964-0.283-0.2830.0000.0000.0000.000
104A1127GLU-1-0.949-0.9694.56854.16254.363-0.001-0.002-0.1980.000
105A1128GLY0-0.010-0.0086.2384.7334.7330.0000.0000.0000.000
106A1129VAL0-0.051-0.0152.565-1.1550.5051.223-0.862-2.0200.004
107A1130PRO0-0.0020.0023.934-6.153-5.8540.000-0.058-0.2410.000
108A1131GLN00.0110.0006.600-1.448-1.4480.0000.0000.0000.000
109A1132LEU0-0.0020.0048.314-2.217-2.2170.0000.0000.0000.000
110A1133LEU00.0050.00810.9740.0090.0090.0000.0000.0000.000
111A1134ILE00.0160.00513.258-0.838-0.8380.0000.0000.0000.000
112A1135VAL00.0020.00216.344-0.208-0.2080.0000.0000.0000.000
113A1136LEU0-0.0020.00519.499-0.282-0.2820.0000.0000.0000.000
114A1137THR0-0.023-0.05022.618-0.236-0.2360.0000.0000.0000.000
115A1138ALA00.0110.00026.2700.0320.0320.0000.0000.0000.000
116A1139GLU-1-0.773-0.81629.6909.3399.3390.0000.0000.0000.000
117A1140PRO0-0.012-0.00530.6160.2820.2820.0000.0000.0000.000
118A1141SER0-0.036-0.02129.3220.0240.0240.0000.0000.0000.000
119A1142GLY0-0.020-0.00731.116-0.289-0.2890.0000.0000.0000.000
120A1143ASP-1-0.829-0.91229.55210.20410.2040.0000.0000.0000.000
121A1144ASP-1-0.799-0.90530.69310.07410.0740.0000.0000.0000.000
122A1145VAL00.0610.01326.2890.3110.3110.0000.0000.0000.000
123A1146ARG10.9460.99326.483-9.599-9.5990.0000.0000.0000.000
124A1147GLY0-0.065-0.02826.9960.3350.3350.0000.0000.0000.000
125A1148PRO00.0720.03824.3650.4100.4100.0000.0000.0000.000
126A1149SER0-0.059-0.03022.5490.6210.6210.0000.0000.0000.000
127A1150VAL0-0.048-0.02321.9720.5380.5380.0000.0000.0000.000
128A1151VAL00.0070.00821.4490.5590.5590.0000.0000.0000.000
129A1152LEU0-0.011-0.01718.0210.7170.7170.0000.0000.0000.000
130A1153LYS10.8250.93417.479-12.302-12.3020.0000.0000.0000.000
131A1154GLN0-0.073-0.04817.8560.5410.5410.0000.0000.0000.000
132A1155GLY0-0.0180.00217.5140.2810.2810.0000.0000.0000.000
133A1156GLY0-0.0020.00613.6220.9620.9620.0000.0000.0000.000
134A1157ALA0-0.023-0.00712.4791.5391.5390.0000.0000.0000.000
135A1158VAL0-0.008-0.01211.668-1.002-1.0020.0000.0000.0000.000
136A1159PRO0-0.040-0.02213.9720.4500.4500.0000.0000.0000.000
137A1160ILE00.0040.00614.054-0.302-0.3020.0000.0000.0000.000
138A1161GLY00.0060.00817.8350.0410.0410.0000.0000.0000.000
139A1162ILE0-0.018-0.01818.999-0.311-0.3110.0000.0000.0000.000
140A1163GLY00.0440.00522.869-0.088-0.0880.0000.0000.0000.000
141A1164ILE0-0.036-0.03225.019-0.116-0.1160.0000.0000.0000.000
142A1165GLY00.0060.00428.627-0.133-0.1330.0000.0000.0000.000
143A1166ASN0-0.050-0.03232.423-0.087-0.0870.0000.0000.0000.000
144A1167ALA0-0.0200.01528.682-0.041-0.0410.0000.0000.0000.000
145A1168ASP-1-0.794-0.89730.6789.1269.1260.0000.0000.0000.000
146A1169ILE00.030-0.00229.2520.3580.3580.0000.0000.0000.000
147A1170SER0-0.0010.00928.5030.4400.4400.0000.0000.0000.000
148A1171GLU-1-0.858-0.93028.23010.20110.2010.0000.0000.0000.000
149A1172MET0-0.028-0.00824.6290.6420.6420.0000.0000.0000.000
150A1173GLN00.0000.00023.7690.5330.5330.0000.0000.0000.000
151A1174THR0-0.070-0.02524.2740.3000.3000.0000.0000.0000.000
152A1175ILE0-0.023-0.02820.9410.4160.4160.0000.0000.0000.000
153A1176SER0-0.024-0.01219.7950.8680.8680.0000.0000.0000.000
154A1177PHE0-0.001-0.00315.749-0.388-0.3880.0000.0000.0000.000
155A1178ILE00.002-0.01018.774-0.404-0.4040.0000.0000.0000.000
156A1179PRO00.022-0.01021.1830.1790.1790.0000.0000.0000.000
157A1180ASP-1-0.906-0.95021.25812.80312.8030.0000.0000.0000.000
158A1181PHE0-0.043-0.03015.3120.2150.2150.0000.0000.0000.000
159A1182ALA0-0.0200.01319.9830.2360.2360.0000.0000.0000.000
160A1183VAL0-0.010-0.00121.494-0.209-0.2090.0000.0000.0000.000
161A1184ALA0-0.0040.00224.250-0.055-0.0550.0000.0000.0000.000
162A1185ILE0-0.022-0.00525.678-0.102-0.1020.0000.0000.0000.000
163A1186PRO00.0370.01828.931-0.050-0.0500.0000.0000.0000.000
164A1187THR0-0.022-0.04931.282-0.102-0.1020.0000.0000.0000.000
165A1188PHE00.0820.02527.3420.1890.1890.0000.0000.0000.000
166A1189ARG10.8980.96228.484-8.106-8.1060.0000.0000.0000.000
167A1190GLU-1-0.792-0.87629.2039.0259.0250.0000.0000.0000.000
168A1191LEU00.0340.03222.9920.2480.2480.0000.0000.0000.000
169A1192GLY0-0.003-0.00623.8550.4280.4280.0000.0000.0000.000
170A1193THR0-0.086-0.06523.8690.2850.2850.0000.0000.0000.000
171A1194ILE00.0290.01621.9900.0680.0680.0000.0000.0000.000
172A1195GLN00.0050.00318.8950.9990.9990.0000.0000.0000.000
173A1196GLN00.0330.02116.6150.5640.5640.0000.0000.0000.000
174A1197VAL00.0570.03117.4440.6260.6260.0000.0000.0000.000
175A1198ILE0-0.022-0.00115.4770.6920.6920.0000.0000.0000.000
176A1199SER00.0170.00013.6811.4111.4110.0000.0000.0000.000
177A1200GLU-1-0.903-0.96812.68515.80715.8070.0000.0000.0000.000
178A1201ARG10.8750.93313.171-14.692-14.6920.0000.0000.0000.000
179A1202VAL00.005-0.0088.9231.3461.3460.0000.0000.0000.000
180A1203ILE0-0.060-0.0338.7152.6952.6950.0000.0000.0000.000
181A1204GLN0-0.0340.0098.8661.1511.1510.0000.0000.0000.000
182A1205LEU0-0.0060.0069.6260.5260.5260.0000.0000.0000.000
183A1206ASN0-0.010-0.0075.5311.9641.9640.0000.0000.0000.000
184A1207ARG10.9730.9712.211-87.489-83.9081.827-2.660-2.7490.039
185A1208GLU-1-0.913-0.9517.34331.04731.0470.0000.0000.0000.000
186A1209GLU-1-0.859-0.9279.76716.47816.4780.0000.0000.0000.000
187A1210LEU0-0.023-0.0308.723-1.645-1.6450.0000.0000.0000.000
188A1211SER0-0.041-0.00511.586-1.467-1.4670.0000.0000.0000.000
189A1212SER0-0.066-0.03413.541-1.642-1.6420.0000.0000.0000.000
190A1213LEU0-0.067-0.00414.574-1.307-1.3070.0000.0000.0000.000
191A1214LYS10.8990.93916.532-16.023-16.0230.0000.0000.0000.000
192A1215PRO00.0150.03017.674-0.360-0.3600.0000.0000.0000.000
193A1216ILE0-0.003-0.00219.909-0.554-0.5540.0000.0000.0000.000
194A1217LEU0-0.004-0.00621.8620.0650.0650.0000.0000.0000.000
195A1218THR0-0.001-0.02225.574-0.315-0.3150.0000.0000.0000.000
196A1219PRO0-0.031-0.00328.193-0.194-0.1940.0000.0000.0000.000
197A1220SER00.0320.03130.213-0.377-0.3770.0000.0000.0000.000