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

tag_button

FMODB ID: JQ5V9

Calculation Name: 1D3U-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1D3U

Chain ID: B

ChEMBL ID:

UniProt ID: P62001

Base Structure: X-ray

Registration Date: 2023-09-24

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2221105.533622
FMO2-HF: Nuclear repulsion 2142679.93176
FMO2-HF: Total energy -78425.601862
FMO2-MP2: Total energy -78657.975633


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(B:1100:MET)


Summations of interaction energy for fragment #1(B:1100: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.
-6.809-1.5470.74-2.402-3.5990.012
Interaction energy analysis for fragmet #1(B:1100:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.035
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].
3B1102SER00.0210.0212.984-3.860-0.7780.323-1.508-1.8970.015
4B1103ASP-1-0.819-0.9233.1484.7876.1150.329-0.640-1.017-0.004
5B1104ALA00.007-0.0144.8480.8020.880-0.001-0.001-0.0750.000
6B1105ALA0-0.052-0.0226.971-0.174-0.1740.0000.0000.0000.000
7B1106GLU-1-0.880-0.9527.3711.1041.1040.0000.0000.0000.000
8B1107ARG10.9320.9793.223-6.954-6.1800.089-0.253-0.6100.001
9B1108ASN0-0.006-0.0048.888-0.275-0.2750.0000.0000.0000.000
10B1109LEU0-0.038-0.01111.906-0.177-0.1770.0000.0000.0000.000
11B1110ALA00.0260.01211.598-0.129-0.1290.0000.0000.0000.000
12B1111PHE00.0130.01012.922-0.121-0.1210.0000.0000.0000.000
13B1112ALA0-0.004-0.01414.697-0.096-0.0960.0000.0000.0000.000
14B1113LEU0-0.020-0.02216.250-0.079-0.0790.0000.0000.0000.000
15B1114SER00.0200.02516.410-0.049-0.0490.0000.0000.0000.000
16B1115GLU-1-0.837-0.88018.9410.3030.3030.0000.0000.0000.000
17B1116LEU0-0.077-0.05520.934-0.039-0.0390.0000.0000.0000.000
18B1117ASP-1-0.888-0.94721.7380.2470.2470.0000.0000.0000.000
19B1118ARG10.7720.85622.984-0.322-0.3220.0000.0000.0000.000
20B1119ILE0-0.047-0.03824.836-0.029-0.0290.0000.0000.0000.000
21B1120THR00.003-0.00826.677-0.018-0.0180.0000.0000.0000.000
22B1121ALA00.0760.05427.589-0.020-0.0200.0000.0000.0000.000
23B1122GLN0-0.060-0.03129.013-0.026-0.0260.0000.0000.0000.000
24B1123LEU0-0.026-0.01830.925-0.013-0.0130.0000.0000.0000.000
25B1124LYS10.9400.97532.338-0.139-0.1390.0000.0000.0000.000
26B1125LEU0-0.060-0.02730.380-0.012-0.0120.0000.0000.0000.000
27B1126PRO00.0160.00131.6030.0040.0040.0000.0000.0000.000
28B1127ARG11.0391.02327.616-0.134-0.1340.0000.0000.0000.000
29B1128HIS00.0600.02529.3200.0100.0100.0000.0000.0000.000
30B1129VAL0-0.012-0.00630.6010.0010.0010.0000.0000.0000.000
31B1130GLU-1-0.895-0.94724.7250.2190.2190.0000.0000.0000.000
32B1131GLU-1-0.905-0.97325.6480.1440.1440.0000.0000.0000.000
33B1132GLU-1-0.824-0.88525.8390.1250.1250.0000.0000.0000.000
34B1133ALA0-0.021-0.01526.0480.0040.0040.0000.0000.0000.000
35B1134ALA00.0570.02121.6910.0190.0190.0000.0000.0000.000
36B1135ARG10.7930.87821.909-0.104-0.1040.0000.0000.0000.000
37B1136LEU0-0.034-0.01723.570-0.003-0.0030.0000.0000.0000.000
38B1137TYR00.0740.01716.761-0.007-0.0070.0000.0000.0000.000
39B1138ARG10.9660.97416.919-0.273-0.2730.0000.0000.0000.000
40B1139GLU-1-0.826-0.89619.8540.1020.1020.0000.0000.0000.000
41B1140ALA00.003-0.00721.942-0.011-0.0110.0000.0000.0000.000
42B1141VAL0-0.020-0.00115.3530.0000.0000.0000.0000.0000.000
43B1142ARG10.8600.92618.276-0.097-0.0970.0000.0000.0000.000
44B1143LYS10.8800.95219.399-0.124-0.1240.0000.0000.0000.000
45B1144GLY0-0.017-0.00819.251-0.009-0.0090.0000.0000.0000.000
46B1145LEU0-0.060-0.04420.2770.0010.0010.0000.0000.0000.000
47B1146ILE00.0610.02318.052-0.008-0.0080.0000.0000.0000.000
48B1147ARG10.9560.98317.620-0.206-0.2060.0000.0000.0000.000
49B1148GLY00.0190.01620.538-0.032-0.0320.0000.0000.0000.000
50B1149ARG10.8290.92322.232-0.248-0.2480.0000.0000.0000.000
51B1150SER00.0570.04020.6100.0200.0200.0000.0000.0000.000
52B1151ILE00.0610.02115.231-0.037-0.0370.0000.0000.0000.000
53B1152GLU-1-0.840-0.92919.6950.4270.4270.0000.0000.0000.000
54B1153SER0-0.051-0.02922.232-0.036-0.0360.0000.0000.0000.000
55B1154VAL0-0.021-0.02721.976-0.027-0.0270.0000.0000.0000.000
56B1155MET00.0060.03020.320-0.041-0.0410.0000.0000.0000.000
57B1156ALA00.0660.03923.515-0.024-0.0240.0000.0000.0000.000
58B1157ALA0-0.041-0.01526.734-0.023-0.0230.0000.0000.0000.000
59B1158CYS0-0.068-0.03224.849-0.020-0.0200.0000.0000.0000.000
60B1159VAL00.0830.05726.398-0.017-0.0170.0000.0000.0000.000
61B1160TYR00.0220.01528.824-0.020-0.0200.0000.0000.0000.000
62B1161ALA0-0.045-0.03929.925-0.014-0.0140.0000.0000.0000.000
63B1162ALA00.0270.02329.404-0.013-0.0130.0000.0000.0000.000
64B1163CYS0-0.030-0.01131.462-0.011-0.0110.0000.0000.0000.000
65B1164ARG10.8740.93334.582-0.114-0.1140.0000.0000.0000.000
66B1165LEU0-0.064-0.04631.621-0.011-0.0110.0000.0000.0000.000
67B1166LEU0-0.021-0.01532.470-0.008-0.0080.0000.0000.0000.000
68B1167LYS10.7680.90736.561-0.086-0.0860.0000.0000.0000.000
69B1168VAL00.0400.03436.003-0.003-0.0030.0000.0000.0000.000
70B1169PRO00.0070.00037.9440.0070.0070.0000.0000.0000.000
71B1170ARG10.8940.95935.322-0.125-0.1250.0000.0000.0000.000
72B1171THR0-0.013-0.01538.0520.0000.0000.0000.0000.0000.000
73B1172LEU0-0.026-0.02532.9670.0050.0050.0000.0000.0000.000
74B1173ASP-1-0.847-0.94034.6030.1350.1350.0000.0000.0000.000
75B1174GLU-1-0.766-0.87335.4750.1290.1290.0000.0000.0000.000
76B1175ILE0-0.013-0.00429.8100.0070.0070.0000.0000.0000.000
77B1176ALA0-0.069-0.04731.0280.0130.0130.0000.0000.0000.000
78B1177ASP-1-0.797-0.87731.9120.1520.1520.0000.0000.0000.000
79B1178ILE00.0000.02428.9320.0050.0050.0000.0000.0000.000
80B1179ALA0-0.0250.00227.2070.0230.0230.0000.0000.0000.000
81B1180ARG10.9730.99120.060-0.403-0.4030.0000.0000.0000.000
82B1181VAL0-0.033-0.01425.4890.0030.0030.0000.0000.0000.000
83B1182ASP-1-0.748-0.88928.1600.1800.1800.0000.0000.0000.000
84B1183LYS10.9440.96231.355-0.122-0.1220.0000.0000.0000.000
85B1184LYS10.8990.95833.629-0.148-0.1480.0000.0000.0000.000
86B1185GLU-1-0.848-0.92127.5440.2170.2170.0000.0000.0000.000
87B1186ILE00.0880.04728.4410.0000.0000.0000.0000.0000.000
88B1187GLY00.003-0.00430.121-0.006-0.0060.0000.0000.0000.000
89B1188ARG10.8610.91530.700-0.168-0.1680.0000.0000.0000.000
90B1189SER00.0380.02826.748-0.003-0.0030.0000.0000.0000.000
91B1190TYR00.0440.01428.625-0.008-0.0080.0000.0000.0000.000
92B1191ARG10.9010.95330.686-0.141-0.1410.0000.0000.0000.000
93B1192PHE0-0.036-0.01125.759-0.011-0.0110.0000.0000.0000.000
94B1193ILE00.0720.03225.379-0.010-0.0100.0000.0000.0000.000
95B1194ALA00.0280.01428.334-0.009-0.0090.0000.0000.0000.000
96B1195ARG10.9230.95231.620-0.121-0.1210.0000.0000.0000.000
97B1196ASN0-0.040-0.02927.906-0.017-0.0170.0000.0000.0000.000
98B1197LEU0-0.0280.01325.409-0.006-0.0060.0000.0000.0000.000
99B1198ASN0-0.047-0.02029.429-0.007-0.0070.0000.0000.0000.000
100B1199LEU00.0150.01430.363-0.007-0.0070.0000.0000.0000.000
101B1200THR00.020-0.00534.1560.0020.0020.0000.0000.0000.000
102B1201PRO00.0670.00837.7850.0020.0020.0000.0000.0000.000
103B1202LYS10.9810.99340.508-0.047-0.0470.0000.0000.0000.000
104B1203LYS10.9180.96734.394-0.072-0.0720.0000.0000.0000.000
105B1204LEU00.0290.01634.0890.0020.0020.0000.0000.0000.000
106B1205PHE0-0.0310.00438.1370.0040.0040.0000.0000.0000.000
107B1206VAL00.0400.03639.898-0.001-0.0010.0000.0000.0000.000
108B1207LYS11.0040.99342.837-0.055-0.0550.0000.0000.0000.000
109B1208PRO00.0520.02146.2460.0020.0020.0000.0000.0000.000
110B1209THR00.0620.02848.2650.0020.0020.0000.0000.0000.000
111B1210ASP-1-0.885-0.93644.3430.0690.0690.0000.0000.0000.000
112B1211TYR0-0.053-0.03241.1410.0050.0050.0000.0000.0000.000
113B1212VAL0-0.050-0.01045.9710.0010.0010.0000.0000.0000.000
114B1213ASN00.0390.00747.843-0.001-0.0010.0000.0000.0000.000
115B1214LYS10.8580.94540.477-0.102-0.1020.0000.0000.0000.000
116B1215PHE00.007-0.01243.2520.0010.0010.0000.0000.0000.000
117B1216ALA00.006-0.00347.2430.0000.0000.0000.0000.0000.000
118B1217ASP-1-0.848-0.89846.7410.0680.0680.0000.0000.0000.000
119B1218GLU-1-0.919-0.96443.2370.0960.0960.0000.0000.0000.000
120B1219LEU0-0.063-0.02147.399-0.001-0.0010.0000.0000.0000.000
121B1220GLY00.0270.01350.784-0.003-0.0030.0000.0000.0000.000
122B1221LEU0-0.081-0.02652.720-0.003-0.0030.0000.0000.0000.000
123B1222SER00.030-0.02754.4250.0000.0000.0000.0000.0000.000
124B1223GLU-1-0.928-0.98355.9530.0480.0480.0000.0000.0000.000
125B1224LYS10.9020.95157.024-0.040-0.0400.0000.0000.0000.000
126B1225VAL00.0420.02255.956-0.001-0.0010.0000.0000.0000.000
127B1226ARG10.8180.89950.034-0.061-0.0610.0000.0000.0000.000
128B1227ARG10.9610.99655.403-0.042-0.0420.0000.0000.0000.000
129B1228ARG10.9280.97157.969-0.042-0.0420.0000.0000.0000.000
130B1229ALA00.022-0.00154.8180.0000.0000.0000.0000.0000.000
131B1230ILE0-0.031-0.03152.9370.0010.0010.0000.0000.0000.000
132B1231GLU-1-0.893-0.93255.4920.0400.0400.0000.0000.0000.000
133B1232ILE0-0.020-0.01357.736-0.001-0.0010.0000.0000.0000.000
134B1233LEU0-0.065-0.04251.8840.0010.0010.0000.0000.0000.000
135B1234ASP-1-0.909-0.95555.1670.0480.0480.0000.0000.0000.000
136B1235GLU-1-0.880-0.93256.8830.0380.0380.0000.0000.0000.000
137B1236ALA00.001-0.01356.255-0.001-0.0010.0000.0000.0000.000
138B1237TYR0-0.078-0.03951.4460.0000.0000.0000.0000.0000.000
139B1238LYS10.9360.96955.903-0.041-0.0410.0000.0000.0000.000
140B1239ARG10.8660.93059.081-0.039-0.0390.0000.0000.0000.000
141B1240GLY00.0010.02656.8500.0000.0000.0000.0000.0000.000
142B1241LEU0-0.051-0.03556.8200.0010.0010.0000.0000.0000.000
143B1242THR0-0.020-0.01351.8370.0020.0020.0000.0000.0000.000
144B1243SER00.0550.01650.3270.0040.0040.0000.0000.0000.000
145B1244GLY0-0.019-0.00748.482-0.001-0.0010.0000.0000.0000.000
146B1245LYS10.8940.96448.425-0.056-0.0560.0000.0000.0000.000
147B1246SER00.0150.01145.4670.0010.0010.0000.0000.0000.000
148B1247PRO00.0440.00344.526-0.002-0.0020.0000.0000.0000.000
149B1248ALA00.0740.04544.170-0.003-0.0030.0000.0000.0000.000
150B1249GLY00.0140.00546.300-0.001-0.0010.0000.0000.0000.000
151B1250LEU0-0.014-0.01948.949-0.003-0.0030.0000.0000.0000.000
152B1251VAL00.0100.02047.954-0.003-0.0030.0000.0000.0000.000
153B1252ALA00.0320.02749.189-0.002-0.0020.0000.0000.0000.000
154B1253ALA0-0.026-0.01651.009-0.002-0.0020.0000.0000.0000.000
155B1254ALA00.0120.00753.844-0.003-0.0030.0000.0000.0000.000
156B1255LEU00.0390.01650.552-0.002-0.0020.0000.0000.0000.000
157B1256TYR0-0.044-0.01254.758-0.002-0.0020.0000.0000.0000.000
158B1257ILE00.0100.00156.518-0.002-0.0020.0000.0000.0000.000
159B1258ALA00.0190.00657.758-0.002-0.0020.0000.0000.0000.000
160B1259SER0-0.030-0.00957.315-0.001-0.0010.0000.0000.0000.000
161B1260LEU0-0.070-0.04459.374-0.001-0.0010.0000.0000.0000.000
162B1261LEU0-0.028-0.03462.462-0.001-0.0010.0000.0000.0000.000
163B1262GLU-1-0.873-0.92161.5290.0400.0400.0000.0000.0000.000
164B1263GLY0-0.021-0.00263.8110.0000.0000.0000.0000.0000.000
165B1264GLU-1-0.819-0.87458.7400.0500.0500.0000.0000.0000.000
166B1265LYS10.8950.94459.019-0.052-0.0520.0000.0000.0000.000
167B1266ARG10.9300.98753.975-0.059-0.0590.0000.0000.0000.000
168B1267THR0-0.061-0.06454.837-0.001-0.0010.0000.0000.0000.000
169B1268GLN00.015-0.00154.2360.0030.0030.0000.0000.0000.000
170B1269ARG10.9350.96848.571-0.080-0.0800.0000.0000.0000.000
171B1270GLU-1-0.796-0.87650.3460.0690.0690.0000.0000.0000.000
172B1271VAL0-0.0100.00249.5820.0030.0030.0000.0000.0000.000
173B1272ALA0-0.052-0.03348.6720.0030.0030.0000.0000.0000.000
174B1273GLU-1-0.904-0.95445.2150.0960.0960.0000.0000.0000.000
175B1274VAL00.0430.02844.6040.0050.0050.0000.0000.0000.000
176B1275ALA0-0.063-0.03144.1910.0030.0030.0000.0000.0000.000
177B1276ARG10.8030.89238.102-0.123-0.1230.0000.0000.0000.000
178B1277VAL0-0.051-0.01642.8980.0020.0020.0000.0000.0000.000
179B1278THR00.0510.01545.625-0.002-0.0020.0000.0000.0000.000
180B1279GLU-1-0.793-0.92548.2080.0710.0710.0000.0000.0000.000
181B1280VAL0-0.0110.00351.552-0.003-0.0030.0000.0000.0000.000
182B1281THR0-0.0250.00048.865-0.003-0.0030.0000.0000.0000.000
183B1282VAL00.0310.02150.791-0.003-0.0030.0000.0000.0000.000
184B1283ARG10.9390.96752.913-0.067-0.0670.0000.0000.0000.000
185B1284ASN0-0.042-0.03553.185-0.004-0.0040.0000.0000.0000.000
186B1285ARG10.8460.91952.342-0.065-0.0650.0000.0000.0000.000
187B1286TYR00.0390.02155.492-0.002-0.0020.0000.0000.0000.000
188B1287LYS10.9630.99558.037-0.053-0.0530.0000.0000.0000.000
189B1288GLU-1-0.845-0.93356.8560.0540.0540.0000.0000.0000.000
190B1289LEU0-0.012-0.01755.837-0.002-0.0020.0000.0000.0000.000
191B1290VAL00.0070.00460.073-0.002-0.0020.0000.0000.0000.000
192B1291GLU-1-0.901-0.96363.2070.0430.0430.0000.0000.0000.000
193B1292LYS10.9150.96559.950-0.048-0.0480.0000.0000.0000.000
194B1293LEU0-0.041-0.01760.179-0.001-0.0010.0000.0000.0000.000
195B1294LYS10.9100.97264.622-0.034-0.0340.0000.0000.0000.000
196B1295ILE00.0060.01362.194-0.001-0.0010.0000.0000.0000.000
197B1296LYS10.9280.95466.317-0.035-0.0350.0000.0000.0000.000
198B1297VAL00.028-0.00764.0170.0010.0010.0000.0000.0000.000
199B1298PRO0-0.0110.01766.1600.0000.0000.0000.0000.0000.000
200B1299ILE00.0980.04667.105-0.001-0.0010.0000.0000.0000.000
201B1300ALA0-0.032-0.01262.8460.0010.0010.0000.0000.0000.000