FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 3Q52L

Calculation Name: 5JH5-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5JH5

Chain ID: A

ChEMBL ID:

UniProt ID: Q5H9F3

Base Structure: X-ray

Registration Date: 2023-06-20

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 OptAll
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 271
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3680738.305727
FMO2-HF: Nuclear repulsion 3567601.32382
FMO2-HF: Total energy -113136.981908
FMO2-MP2: Total energy -113452.510429


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:1065:MET)


Summations of interaction energy for fragment #1(A:1065:MET)
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.
-13.182-11.06915.943-6.534-11.520.013
Interaction energy analysis for fragmet #1(A:1065:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.043
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].
3A1067ARG10.8450.9173.8810.1011.602-0.010-0.649-0.8420.004
4A1068GLU-1-0.736-0.8715.0890.6290.796-0.001-0.004-0.1610.000
5A1069VAL00.0400.0365.9140.2220.2220.0000.0000.0000.000
6A1070TRP00.0370.0122.562-1.2681.5251.203-1.095-2.900-0.012
7A1071MET0-0.092-0.0295.8670.3950.3950.0000.0000.0000.000
8A1072ALA00.0380.0248.9220.0150.0150.0000.0000.0000.000
9A1073VAL00.0040.0168.2650.0270.0270.0000.0000.0000.000
10A1074PHE00.003-0.0415.809-0.0530.022-0.001-0.005-0.0690.000
11A1075SER0-0.067-0.04511.042-0.072-0.0720.0000.0000.0000.000
12A1076TYR00.0160.02213.623-0.052-0.0520.0000.0000.0000.000
13A1077LEU0-0.040-0.00310.9940.0120.0120.0000.0000.0000.000
14A1078SER00.021-0.02015.617-0.006-0.0060.0000.0000.0000.000
15A1079HIS10.8630.89616.415-0.290-0.2900.0000.0000.0000.000
16A1080GLN00.0780.05217.1920.0320.0320.0000.0000.0000.000
17A1081ASP-1-0.766-0.85314.0960.4060.4060.0000.0000.0000.000
18A1082LEU00.0140.01211.8980.1290.1290.0000.0000.0000.000
19A1083CYS0-0.060-0.03912.1830.1260.1260.0000.0000.0000.000
20A1084VAL0-0.018-0.00411.4750.0010.0010.0000.0000.0000.000
21A1085CYS0-0.001-0.0068.3970.0210.0210.0000.0000.0000.000
22A1086MET0-0.082-0.0457.9040.2030.2030.0000.0000.0000.000
23A1087ARG10.9280.96310.130-0.468-0.4680.0000.0000.0000.000
24A1088VAL00.0090.0384.273-0.156-0.090-0.001-0.005-0.0600.000
25A1089CYS00.0220.0283.546-0.0080.4150.176-0.111-0.4880.000
26A1090ARG10.9950.9896.006-0.501-0.5010.0000.0000.0000.000
27A1091THR00.0340.0113.971-1.704-1.2080.035-0.148-0.3830.001
28A1092TRP00.065-0.0072.281-6.043-10.43912.626-3.728-4.5020.022
29A1093ASN0-0.0370.0036.562-0.712-0.7120.0000.0000.0000.000
30A1094ARG10.9240.9579.334-1.162-1.1620.0000.0000.0000.000
31A1095TRP00.0350.0052.226-0.6540.3341.916-0.789-2.115-0.002
32A1096CYS00.0350.0278.871-0.202-0.2020.0000.0000.0000.000
33A1097CYS0-0.0340.01110.750-0.274-0.2740.0000.0000.0000.000
34A1098ASP-1-0.738-0.84011.9230.3050.3050.0000.0000.0000.000
35A1099LYS11.0161.00213.908-0.228-0.2280.0000.0000.0000.000
36A1100ARG10.7770.85911.387-0.249-0.2490.0000.0000.0000.000
37A1101LEU0-0.0070.01011.414-0.030-0.0300.0000.0000.0000.000
38A1102TRP0-0.063-0.07014.909-0.057-0.0570.0000.0000.0000.000
39A1103THR00.0320.02519.308-0.027-0.0270.0000.0000.0000.000
40A1104ARG10.9560.97921.968-0.152-0.1520.0000.0000.0000.000
41A1105ILE0-0.042-0.01821.7090.0310.0310.0000.0000.0000.000
42A1106ASP-1-0.842-0.92024.8170.1520.1520.0000.0000.0000.000
43A1107LEU0-0.037-0.02824.7300.0210.0210.0000.0000.0000.000
44A1108ASN00.0360.01928.186-0.013-0.0130.0000.0000.0000.000
45A1109HIS10.8980.95331.083-0.110-0.1100.0000.0000.0000.000
46A1110CYS0-0.052-0.00427.7810.0010.0010.0000.0000.0000.000
47A1111LYS11.0081.00030.809-0.123-0.1230.0000.0000.0000.000
48A1112SER0-0.028-0.02029.914-0.007-0.0070.0000.0000.0000.000
49A1113ILE00.0630.01929.2830.0130.0130.0000.0000.0000.000
50A1114THR00.0570.03526.263-0.004-0.0040.0000.0000.0000.000
51A1115PRO00.0580.01227.8380.0090.0090.0000.0000.0000.000
52A1116LEU00.0220.01223.1700.0110.0110.0000.0000.0000.000
53A1117MET00.0190.02123.2340.0320.0320.0000.0000.0000.000
54A1118LEU0-0.006-0.00124.4300.0100.0100.0000.0000.0000.000
55A1119SER0-0.0050.00023.2870.0100.0100.0000.0000.0000.000
56A1120GLY00.0070.00220.5120.0230.0230.0000.0000.0000.000
57A1121ILE00.0330.02320.8620.0350.0350.0000.0000.0000.000
58A1122ILE0-0.0010.00023.0920.0040.0040.0000.0000.0000.000
59A1123ARG10.8000.87313.665-0.732-0.7320.0000.0000.0000.000
60A1124ARG10.8340.92117.008-0.451-0.4510.0000.0000.0000.000
61A1125GLN0-0.110-0.06119.905-0.028-0.0280.0000.0000.0000.000
62A1126PRO00.0230.02722.735-0.008-0.0080.0000.0000.0000.000
63A1127VAL0-0.030-0.01723.902-0.016-0.0160.0000.0000.0000.000
64A1128SER0-0.015-0.02126.189-0.016-0.0160.0000.0000.0000.000
65A1129LEU0-0.025-0.01826.8120.0220.0220.0000.0000.0000.000
66A1130ASP-1-0.771-0.84829.0710.1170.1170.0000.0000.0000.000
67A1131LEU0-0.007-0.01629.6080.0150.0150.0000.0000.0000.000
68A1132SER0-0.003-0.00232.396-0.006-0.0060.0000.0000.0000.000
69A1133TRP00.012-0.01234.4850.0050.0050.0000.0000.0000.000
70A1134THR0-0.060-0.03731.8130.0000.0000.0000.0000.0000.000
71A1135ASN0-0.027-0.02234.857-0.003-0.0030.0000.0000.0000.000
72A1136ILE0-0.0260.00832.3850.0000.0000.0000.0000.0000.000
73A1137SER00.025-0.01535.863-0.008-0.0080.0000.0000.0000.000
74A1138LYS10.9460.96337.147-0.076-0.0760.0000.0000.0000.000
75A1139LYS10.9741.00136.106-0.116-0.1160.0000.0000.0000.000
76A1140GLN00.0190.02732.812-0.003-0.0030.0000.0000.0000.000
77A1141LEU00.0600.03233.0760.0100.0100.0000.0000.0000.000
78A1142SER00.005-0.02534.4880.0000.0000.0000.0000.0000.000
79A1143TRP0-0.025-0.01128.637-0.007-0.0070.0000.0000.0000.000
80A1144LEU00.0010.00328.3200.0090.0090.0000.0000.0000.000
81A1145ILE00.0440.02130.7520.0040.0040.0000.0000.0000.000
82A1146ASN0-0.015-0.00533.164-0.009-0.0090.0000.0000.0000.000
83A1147ARG10.8430.92128.285-0.151-0.1510.0000.0000.0000.000
84A1148LEU00.0280.02926.0090.0190.0190.0000.0000.0000.000
85A1149PRO00.0570.02527.713-0.010-0.0100.0000.0000.0000.000
86A1150GLY0-0.0030.00726.988-0.014-0.0140.0000.0000.0000.000
87A1151LEU00.0050.01428.067-0.002-0.0020.0000.0000.0000.000
88A1152ARG10.7990.88329.546-0.114-0.1140.0000.0000.0000.000
89A1153ASP-1-0.701-0.77830.3300.0980.0980.0000.0000.0000.000
90A1154LEU0-0.008-0.00631.2680.0140.0140.0000.0000.0000.000
91A1155VAL00.0360.02233.348-0.009-0.0090.0000.0000.0000.000
92A1156LEU00.018-0.01034.4690.0090.0090.0000.0000.0000.000
93A1157SER00.033-0.01537.166-0.001-0.0010.0000.0000.0000.000
94A1158GLY00.0350.01438.6260.0060.0060.0000.0000.0000.000
95A1159CYS0-0.118-0.02637.6210.0050.0050.0000.0000.0000.000
96A1160SER00.0380.01240.324-0.005-0.0050.0000.0000.0000.000
97A1161TRP00.0480.00642.4990.0050.0050.0000.0000.0000.000
98A1162ILE00.0200.01142.9680.0020.0020.0000.0000.0000.000
99A1163ALA0-0.009-0.00138.7680.0020.0020.0000.0000.0000.000
100A1164VAL00.0600.02440.3110.0030.0030.0000.0000.0000.000
101A1165SER00.0260.02641.3800.0000.0000.0000.0000.0000.000
102A1166ALA0-0.066-0.04538.361-0.002-0.0020.0000.0000.0000.000
103A1167LEU0-0.012-0.02437.1260.0020.0020.0000.0000.0000.000
104A1168CYS0-0.0280.00140.371-0.002-0.0020.0000.0000.0000.000
105A1169SER0-0.043-0.00338.676-0.004-0.0040.0000.0000.0000.000
106A1170SER00.0740.02440.903-0.001-0.0010.0000.0000.0000.000
107A1171SER0-0.052-0.02936.726-0.004-0.0040.0000.0000.0000.000
108A1172CYS0-0.0210.00836.2540.0080.0080.0000.0000.0000.000
109A1173PRO0-0.0110.00332.669-0.007-0.0070.0000.0000.0000.000
110A1174LEU0-0.015-0.00435.047-0.003-0.0030.0000.0000.0000.000
111A1175LEU0-0.060-0.02633.8640.0010.0010.0000.0000.0000.000
112A1176ARG10.8730.89228.865-0.100-0.1000.0000.0000.0000.000
113A1177THR0-0.009-0.01433.979-0.003-0.0030.0000.0000.0000.000
114A1178LEU0-0.005-0.00435.8880.0070.0070.0000.0000.0000.000
115A1179ASP-1-0.819-0.86537.4150.0790.0790.0000.0000.0000.000
116A1180VAL00.020-0.00638.8150.0060.0060.0000.0000.0000.000
117A1181GLN00.003-0.01340.212-0.006-0.0060.0000.0000.0000.000
118A1182TRP00.0270.00642.5700.0050.0050.0000.0000.0000.000
119A1183VAL0-0.101-0.01841.4830.0010.0010.0000.0000.0000.000
120A1184GLU-1-0.728-0.86044.2240.0570.0570.0000.0000.0000.000
121A1185GLY0-0.035-0.02546.5370.0030.0030.0000.0000.0000.000
122A1186LEU0-0.067-0.03245.077-0.001-0.0010.0000.0000.0000.000
123A1187LYS10.9090.94048.524-0.056-0.0560.0000.0000.0000.000
124A1188ASP-1-0.696-0.80351.8790.0440.0440.0000.0000.0000.000
125A1189ALA0-0.070-0.01654.066-0.001-0.0010.0000.0000.0000.000
126A1190GLN00.0690.03948.902-0.001-0.0010.0000.0000.0000.000
127A1191MET00.0160.00247.6520.0030.0030.0000.0000.0000.000
128A1192ARG10.8460.92149.951-0.044-0.0440.0000.0000.0000.000
129A1193ASP-1-0.857-0.92748.9530.0560.0560.0000.0000.0000.000
130A1194LEU0-0.049-0.02142.7210.0020.0020.0000.0000.0000.000
131A1195LEU0-0.0150.00445.4270.0010.0010.0000.0000.0000.000
132A1196SER0-0.043-0.01147.767-0.002-0.0020.0000.0000.0000.000
133A1197PRO0-0.016-0.01247.8050.0030.0030.0000.0000.0000.000
134A1198PRO00.0110.01045.382-0.001-0.0010.0000.0000.0000.000
135A1199THR00.0420.00748.474-0.002-0.0020.0000.0000.0000.000
136A1200ASP-1-0.751-0.84450.1990.0390.0390.0000.0000.0000.000
137A1201ASN0-0.016-0.01652.7450.0000.0000.0000.0000.0000.000
138A1202ARG10.7470.83550.121-0.036-0.0360.0000.0000.0000.000
139A1203PRO00.0390.02456.9220.0010.0010.0000.0000.0000.000
140A1204GLY00.0290.02059.607-0.001-0.0010.0000.0000.0000.000
141A1205GLN0-0.067-0.04555.4940.0020.0020.0000.0000.0000.000
142A1206MET00.0150.02552.0910.0000.0000.0000.0000.0000.000
143A1207ASP-1-0.767-0.85448.2770.0350.0350.0000.0000.0000.000
144A1208ASN00.0320.01447.0900.0030.0030.0000.0000.0000.000
145A1209ARG10.8280.89945.559-0.044-0.0440.0000.0000.0000.000
146A1210SER0-0.007-0.00544.7800.0050.0050.0000.0000.0000.000
147A1211LYS10.8200.89438.505-0.078-0.0780.0000.0000.0000.000
148A1212LEU00.0280.00640.0920.0030.0030.0000.0000.0000.000
149A1213ARG10.9070.95640.662-0.052-0.0520.0000.0000.0000.000
150A1214ASN0-0.039-0.03237.422-0.004-0.0040.0000.0000.0000.000
151A1215ILE0-0.0420.00138.8820.0020.0020.0000.0000.0000.000
152A1216VAL00.0240.02138.315-0.004-0.0040.0000.0000.0000.000
153A1217GLU-1-0.805-0.88837.9130.0640.0640.0000.0000.0000.000
154A1218LEU0-0.003-0.00939.6820.0050.0050.0000.0000.0000.000
155A1219ARG10.7990.88638.445-0.076-0.0760.0000.0000.0000.000
156A1220LEU00.023-0.00742.6820.0040.0040.0000.0000.0000.000
157A1221ALA00.0450.02045.109-0.002-0.0020.0000.0000.0000.000
158A1222GLY00.0490.01646.3960.0030.0030.0000.0000.0000.000
159A1223LEU0-0.053-0.02646.0910.0020.0020.0000.0000.0000.000
160A1224ASP-1-0.825-0.89750.0480.0470.0470.0000.0000.0000.000
161A1225ILE0-0.050-0.03849.6980.0000.0000.0000.0000.0000.000
162A1226THR00.021-0.03453.732-0.002-0.0020.0000.0000.0000.000
163A1227ASP-1-0.740-0.88755.2640.0350.0350.0000.0000.0000.000
164A1228ALA0-0.029-0.01056.7240.0000.0000.0000.0000.0000.000
165A1229SER0-0.018-0.04851.6060.0010.0010.0000.0000.0000.000
166A1230LEU00.0240.01251.9410.0010.0010.0000.0000.0000.000
167A1231ARG10.9680.98553.054-0.032-0.0320.0000.0000.0000.000
168A1232LEU0-0.037-0.02151.547-0.001-0.0010.0000.0000.0000.000
169A1233ILE00.0410.02847.4960.0010.0010.0000.0000.0000.000
170A1234ILE00.0090.00249.2340.0000.0000.0000.0000.0000.000
171A1235ARG10.8140.90851.484-0.038-0.0380.0000.0000.0000.000
172A1236HIS0-0.026-0.01447.648-0.002-0.0020.0000.0000.0000.000
173A1237MET0-0.0020.00543.1500.0020.0020.0000.0000.0000.000
174A1238PRO0-0.039-0.03145.400-0.001-0.0010.0000.0000.0000.000
175A1239LEU00.0230.02140.682-0.002-0.0020.0000.0000.0000.000
176A1240LEU0-0.0140.01143.0000.0010.0010.0000.0000.0000.000
177A1241SER0-0.0230.01041.905-0.002-0.0020.0000.0000.0000.000
178A1242LYS10.8410.90338.219-0.053-0.0530.0000.0000.0000.000
179A1243LEU00.0130.00043.1920.0040.0040.0000.0000.0000.000
180A1244HIS00.0000.00541.488-0.003-0.0030.0000.0000.0000.000
181A1245LEU00.0500.00445.7780.0030.0030.0000.0000.0000.000
182A1246SER00.0100.00047.3280.0000.0000.0000.0000.0000.000
183A1247TYR00.021-0.01748.7050.0040.0040.0000.0000.0000.000
184A1248CYS0-0.0630.02149.8690.0010.0010.0000.0000.0000.000
185A1249ASN0-0.001-0.01152.573-0.004-0.0040.0000.0000.0000.000
186A1250HIS0-0.075-0.03156.029-0.004-0.0040.0000.0000.0000.000
187A1251VAL0-0.0150.00753.206-0.001-0.0010.0000.0000.0000.000
188A1252THR0-0.012-0.01456.674-0.001-0.0010.0000.0000.0000.000
189A1253ASP-1-0.690-0.82058.3550.0280.0280.0000.0000.0000.000
190A1254GLN00.0360.02559.931-0.001-0.0010.0000.0000.0000.000
191A1255SER0-0.063-0.04455.5400.0000.0000.0000.0000.0000.000
192A1256ILE00.0600.03054.1440.0000.0000.0000.0000.0000.000
193A1257ASN0-0.0020.02256.752-0.002-0.0020.0000.0000.0000.000
194A1258LEU0-0.046-0.03257.436-0.001-0.0010.0000.0000.0000.000
195A1259LEU0-0.033-0.01651.1330.0000.0000.0000.0000.0000.000
196A1260THR00.0240.00753.862-0.001-0.0010.0000.0000.0000.000
197A1261ALA00.0080.02256.256-0.002-0.0020.0000.0000.0000.000
198A1262VAL00.019-0.00257.5730.0000.0000.0000.0000.0000.000
199A1263GLY00.0130.00757.7820.0000.0000.0000.0000.0000.000
200A1264THR0-0.069-0.02954.1900.0010.0010.0000.0000.0000.000
201A1265THR00.0170.00049.382-0.001-0.0010.0000.0000.0000.000
202A1266THR0-0.001-0.02649.0100.0000.0000.0000.0000.0000.000
203A1267ARG10.8930.97550.735-0.019-0.0190.0000.0000.0000.000
204A1268ASP-1-0.764-0.88151.4160.0200.0200.0000.0000.0000.000
205A1269SER0-0.034-0.01245.944-0.001-0.0010.0000.0000.0000.000
206A1270LEU0-0.059-0.03746.3330.0020.0020.0000.0000.0000.000
207A1271THR0-0.0140.00943.501-0.002-0.0020.0000.0000.0000.000
208A1272GLU-1-0.826-0.90641.5110.0450.0450.0000.0000.0000.000
209A1273ILE0-0.021-0.00445.8320.0020.0020.0000.0000.0000.000
210A1274ASN00.0100.00144.833-0.003-0.0030.0000.0000.0000.000
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