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: 3J1ML

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2222576.19566
FMO2-HF: Nuclear repulsion 2144149.319564
FMO2-HF: Total energy -78426.876096
FMO2-MP2: Total energy -78659.146248


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.
-8.257-2.3131.217-3.159-4.002-0.005
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 : -0.007 / q_NPA : -0.016
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].
3B1102SER00.0120.0232.295-0.5662.6030.640-1.723-2.0850.011
4B1103ASP-1-0.792-0.9092.671-2.2410.0050.562-1.322-1.487-0.016
5B1104ALA0-0.003-0.0164.8530.3360.408-0.001-0.002-0.0680.000
6B1105ALA0-0.044-0.0246.930-0.093-0.0930.0000.0000.0000.000
7B1106GLU-1-0.856-0.9416.582-1.799-1.7990.0000.0000.0000.000
8B1107ARG10.9510.9893.523-3.480-3.0230.016-0.112-0.3620.000
9B1108ASN0-0.038-0.0248.0620.0200.0200.0000.0000.0000.000
10B1109LEU0-0.029-0.00811.122-0.026-0.0260.0000.0000.0000.000
11B1110ALA00.0250.01210.5850.0030.0030.0000.0000.0000.000
12B1111PHE00.0170.01612.1310.0150.0150.0000.0000.0000.000
13B1112ALA0-0.005-0.01213.987-0.012-0.0120.0000.0000.0000.000
14B1113LEU0-0.023-0.02514.925-0.016-0.0160.0000.0000.0000.000
15B1114SER00.0160.01815.407-0.011-0.0110.0000.0000.0000.000
16B1115GLU-1-0.824-0.87918.0260.1350.1350.0000.0000.0000.000
17B1116LEU0-0.079-0.04920.041-0.005-0.0050.0000.0000.0000.000
18B1117ASP-1-0.927-0.96220.742-0.036-0.0360.0000.0000.0000.000
19B1118ARG10.7930.85922.101-0.106-0.1060.0000.0000.0000.000
20B1119ILE0-0.041-0.03323.996-0.001-0.0010.0000.0000.0000.000
21B1120THR00.007-0.00425.6180.0010.0010.0000.0000.0000.000
22B1121ALA00.0720.05026.653-0.002-0.0020.0000.0000.0000.000
23B1122GLN0-0.058-0.02928.131-0.002-0.0020.0000.0000.0000.000
24B1123LEU0-0.023-0.01630.0340.0000.0000.0000.0000.0000.000
25B1124LYS10.9450.98231.398-0.008-0.0080.0000.0000.0000.000
26B1125LEU0-0.052-0.02429.584-0.003-0.0030.0000.0000.0000.000
27B1126PRO00.012-0.00230.613-0.005-0.0050.0000.0000.0000.000
28B1127ARG10.9120.94825.3760.1150.1150.0000.0000.0000.000
29B1128HIS00.0910.03728.309-0.006-0.0060.0000.0000.0000.000
30B1129VAL0-0.020-0.01429.7410.0000.0000.0000.0000.0000.000
31B1130GLU-1-0.818-0.88524.218-0.086-0.0860.0000.0000.0000.000
32B1131GLU-1-0.884-0.96424.642-0.133-0.1330.0000.0000.0000.000
33B1132GLU-1-0.771-0.84324.993-0.078-0.0780.0000.0000.0000.000
34B1133ALA0-0.031-0.02125.1990.0040.0040.0000.0000.0000.000
35B1134ALA00.0560.01920.7480.0070.0070.0000.0000.0000.000
36B1135ARG10.7600.84921.2630.0770.0770.0000.0000.0000.000
37B1136LEU0-0.037-0.01823.2270.0010.0010.0000.0000.0000.000
38B1137TYR00.0660.01516.1050.0160.0160.0000.0000.0000.000
39B1138ARG10.9670.97616.5850.2490.2490.0000.0000.0000.000
40B1139GLU-1-0.816-0.88519.620-0.111-0.1110.0000.0000.0000.000
41B1140ALA0-0.002-0.00721.7450.0080.0080.0000.0000.0000.000
42B1141VAL0-0.024-0.00515.3840.0250.0250.0000.0000.0000.000
43B1142ARG10.8600.91718.2760.1410.1410.0000.0000.0000.000
44B1143LYS10.8440.92919.4050.0410.0410.0000.0000.0000.000
45B1144GLY0-0.017-0.00919.2460.0180.0180.0000.0000.0000.000
46B1145LEU0-0.070-0.04620.2730.0280.0280.0000.0000.0000.000
47B1146ILE00.0590.01717.7520.0070.0070.0000.0000.0000.000
48B1147ARG10.9660.99317.801-0.103-0.1030.0000.0000.0000.000
49B1148GLY00.0220.01720.365-0.030-0.0300.0000.0000.0000.000
50B1149ARG10.8240.92222.219-0.149-0.1490.0000.0000.0000.000
51B1150SER00.0570.03220.5300.0080.0080.0000.0000.0000.000
52B1151ILE00.0570.02314.956-0.037-0.0370.0000.0000.0000.000
53B1152GLU-1-0.803-0.89719.3260.2590.2590.0000.0000.0000.000
54B1153SER0-0.070-0.05521.839-0.037-0.0370.0000.0000.0000.000
55B1154VAL0-0.011-0.01921.488-0.025-0.0250.0000.0000.0000.000
56B1155MET00.0110.03019.589-0.030-0.0300.0000.0000.0000.000
57B1156ALA00.0600.03622.808-0.019-0.0190.0000.0000.0000.000
58B1157ALA0-0.036-0.01726.086-0.014-0.0140.0000.0000.0000.000
59B1158CYS0-0.069-0.03424.374-0.015-0.0150.0000.0000.0000.000
60B1159VAL00.0750.04825.477-0.014-0.0140.0000.0000.0000.000
61B1160TYR00.0310.02327.929-0.007-0.0070.0000.0000.0000.000
62B1161ALA0-0.044-0.03829.264-0.006-0.0060.0000.0000.0000.000
63B1162ALA00.0310.02028.546-0.006-0.0060.0000.0000.0000.000
64B1163CYS0-0.027-0.00730.637-0.005-0.0050.0000.0000.0000.000
65B1164ARG10.8650.93033.614-0.013-0.0130.0000.0000.0000.000
66B1165LEU0-0.058-0.03831.154-0.002-0.0020.0000.0000.0000.000
67B1166LEU0-0.021-0.00931.471-0.004-0.0040.0000.0000.0000.000
68B1167LYS10.7470.88535.7370.0200.0200.0000.0000.0000.000
69B1168VAL00.0320.02835.0270.0000.0000.0000.0000.0000.000
70B1169PRO0-0.006-0.00936.9760.0040.0040.0000.0000.0000.000
71B1170ARG10.9000.95434.3270.0030.0030.0000.0000.0000.000
72B1171THR0-0.058-0.05837.1820.0020.0020.0000.0000.0000.000
73B1172LEU0-0.028-0.02532.2860.0010.0010.0000.0000.0000.000
74B1173ASP-1-0.793-0.89034.0110.0620.0620.0000.0000.0000.000
75B1174GLU-1-0.750-0.84634.9520.0260.0260.0000.0000.0000.000
76B1175ILE0-0.003-0.00529.0860.0020.0020.0000.0000.0000.000
77B1176ALA0-0.049-0.04030.4650.0090.0090.0000.0000.0000.000
78B1177ASP-1-0.781-0.85231.5010.0700.0700.0000.0000.0000.000
79B1178ILE0-0.0080.01328.5540.0050.0050.0000.0000.0000.000
80B1179ALA0-0.0060.01626.7070.0090.0090.0000.0000.0000.000
81B1180ARG10.9240.95519.818-0.304-0.3040.0000.0000.0000.000
82B1181VAL0-0.035-0.02125.2570.0160.0160.0000.0000.0000.000
83B1182ASP-1-0.723-0.87227.9650.1120.1120.0000.0000.0000.000
84B1183LYS10.8640.91631.103-0.062-0.0620.0000.0000.0000.000
85B1184LYS10.8950.95333.320-0.122-0.1220.0000.0000.0000.000
86B1185GLU-1-0.840-0.90727.1320.1450.1450.0000.0000.0000.000
87B1186ILE00.0760.04928.115-0.005-0.0050.0000.0000.0000.000
88B1187GLY0-0.005-0.00929.750-0.012-0.0120.0000.0000.0000.000
89B1188ARG10.8760.92730.606-0.134-0.1340.0000.0000.0000.000
90B1189SER00.0290.01726.377-0.006-0.0060.0000.0000.0000.000
91B1190TYR00.0460.01728.255-0.010-0.0100.0000.0000.0000.000
92B1191ARG10.9030.95030.178-0.078-0.0780.0000.0000.0000.000
93B1192PHE0-0.029-0.00825.504-0.008-0.0080.0000.0000.0000.000
94B1193ILE00.0670.02725.026-0.008-0.0080.0000.0000.0000.000
95B1194ALA00.0200.01128.191-0.014-0.0140.0000.0000.0000.000
96B1195ARG10.9320.95931.430-0.055-0.0550.0000.0000.0000.000
97B1196ASN0-0.023-0.01327.917-0.011-0.0110.0000.0000.0000.000
98B1197LEU0-0.0180.02225.325-0.010-0.0100.0000.0000.0000.000
99B1198ASN0-0.015-0.00529.431-0.014-0.0140.0000.0000.0000.000
100B1199LEU00.0280.02729.924-0.006-0.0060.0000.0000.0000.000
101B1200THR00.029-0.00234.0100.0070.0070.0000.0000.0000.000
102B1201PRO00.0710.01037.680-0.001-0.0010.0000.0000.0000.000
103B1202LYS10.9780.99140.2540.0260.0260.0000.0000.0000.000
104B1203LYS10.8900.95034.1530.0380.0380.0000.0000.0000.000
105B1204LEU00.0300.01833.609-0.002-0.0020.0000.0000.0000.000
106B1205PHE0-0.0290.00637.6440.0040.0040.0000.0000.0000.000
107B1206VAL00.0380.03339.054-0.005-0.0050.0000.0000.0000.000
108B1207LYS10.9840.99842.0760.0220.0220.0000.0000.0000.000
109B1208PRO00.0600.02245.3430.0010.0010.0000.0000.0000.000
110B1209THR00.0460.01647.3490.0020.0020.0000.0000.0000.000
111B1210ASP-1-0.864-0.93243.477-0.012-0.0120.0000.0000.0000.000
112B1211TYR0-0.035-0.01839.0840.0000.0000.0000.0000.0000.000
113B1212VAL0-0.054-0.01545.0610.0020.0020.0000.0000.0000.000
114B1213ASN0-0.011-0.01246.9180.0010.0010.0000.0000.0000.000
115B1214LYS10.8350.92439.899-0.014-0.0140.0000.0000.0000.000
116B1215PHE00.019-0.00642.3660.0020.0020.0000.0000.0000.000
117B1216ALA0-0.003-0.00646.3790.0010.0010.0000.0000.0000.000
118B1217ASP-1-0.838-0.89245.841-0.005-0.0050.0000.0000.0000.000
119B1218GLU-1-0.839-0.90841.9380.0160.0160.0000.0000.0000.000
120B1219LEU0-0.051-0.01546.5260.0020.0020.0000.0000.0000.000
121B1220GLY00.0480.02849.8840.0000.0000.0000.0000.0000.000
122B1221LEU0-0.090-0.03151.8090.0000.0000.0000.0000.0000.000
123B1222SER00.024-0.04253.463-0.002-0.0020.0000.0000.0000.000
124B1223GLU-1-0.857-0.93254.263-0.009-0.0090.0000.0000.0000.000
125B1224LYS10.8690.93456.042-0.001-0.0010.0000.0000.0000.000
126B1225VAL00.0260.01355.3040.0000.0000.0000.0000.0000.000
127B1226ARG10.7990.88449.0440.0030.0030.0000.0000.0000.000
128B1227ARG10.8920.93354.4380.0070.0070.0000.0000.0000.000
129B1228ARG10.8310.90956.995-0.002-0.0020.0000.0000.0000.000
130B1229ALA00.0270.00253.9890.0010.0010.0000.0000.0000.000
131B1230ILE0-0.043-0.03552.0860.0010.0010.0000.0000.0000.000
132B1231GLU-1-0.815-0.88354.5610.0000.0000.0000.0000.0000.000
133B1232ILE0-0.006-0.00556.9150.0010.0010.0000.0000.0000.000
134B1233LEU0-0.058-0.04150.9970.0010.0010.0000.0000.0000.000
135B1234ASP-1-0.843-0.90754.707-0.003-0.0030.0000.0000.0000.000
136B1235GLU-1-0.822-0.89356.1040.0030.0030.0000.0000.0000.000
137B1236ALA0-0.001-0.01055.5010.0010.0010.0000.0000.0000.000
138B1237TYR0-0.068-0.03850.5980.0010.0010.0000.0000.0000.000
139B1238LYS10.8320.90555.2780.0010.0010.0000.0000.0000.000
140B1239ARG10.8360.91058.522-0.006-0.0060.0000.0000.0000.000
141B1240GLY00.0040.02856.3730.0010.0010.0000.0000.0000.000
142B1241LEU0-0.039-0.02656.2090.0020.0020.0000.0000.0000.000
143B1242THR0-0.018-0.01151.1390.0020.0020.0000.0000.0000.000
144B1243SER00.0520.01349.8390.0010.0010.0000.0000.0000.000
145B1244GLY00.0020.00648.0170.0010.0010.0000.0000.0000.000
146B1245LYS10.8160.91047.947-0.018-0.0180.0000.0000.0000.000
147B1246SER00.0140.00644.624-0.002-0.0020.0000.0000.0000.000
148B1247PRO00.0520.00943.770-0.001-0.0010.0000.0000.0000.000
149B1248ALA00.0610.03643.472-0.002-0.0020.0000.0000.0000.000
150B1249GLY00.0170.01045.6150.0000.0000.0000.0000.0000.000
151B1250LEU0-0.019-0.01748.347-0.001-0.0010.0000.0000.0000.000
152B1251VAL00.0120.01547.301-0.001-0.0010.0000.0000.0000.000
153B1252ALA00.0380.02948.508-0.001-0.0010.0000.0000.0000.000
154B1253ALA0-0.019-0.01750.315-0.001-0.0010.0000.0000.0000.000
155B1254ALA00.0020.00453.115-0.001-0.0010.0000.0000.0000.000
156B1255LEU00.0360.01849.805-0.001-0.0010.0000.0000.0000.000
157B1256TYR0-0.038-0.00653.9680.0000.0000.0000.0000.0000.000
158B1257ILE00.0150.00755.8070.0000.0000.0000.0000.0000.000
159B1258ALA00.0200.00556.864-0.001-0.0010.0000.0000.0000.000
160B1259SER0-0.039-0.01956.501-0.001-0.0010.0000.0000.0000.000
161B1260LEU0-0.067-0.04258.5700.0000.0000.0000.0000.0000.000
162B1261LEU0-0.022-0.02961.709-0.001-0.0010.0000.0000.0000.000
163B1262GLU-1-0.841-0.89460.8530.0010.0010.0000.0000.0000.000
164B1263GLY0-0.0120.00362.938-0.001-0.0010.0000.0000.0000.000
165B1264GLU-1-0.799-0.85357.6710.0040.0040.0000.0000.0000.000
166B1265LYS10.9030.94558.215-0.018-0.0180.0000.0000.0000.000
167B1266ARG10.9120.97353.444-0.012-0.0120.0000.0000.0000.000
168B1267THR0-0.068-0.09054.5020.0010.0010.0000.0000.0000.000
169B1268GLN00.0000.00153.6210.0020.0020.0000.0000.0000.000
170B1269ARG10.8700.91247.654-0.039-0.0390.0000.0000.0000.000
171B1270GLU-1-0.763-0.84249.8010.0230.0230.0000.0000.0000.000
172B1271VAL0-0.009-0.00148.9370.0000.0000.0000.0000.0000.000
173B1272ALA0-0.053-0.02948.0210.0000.0000.0000.0000.0000.000
174B1273GLU-1-0.847-0.90344.7510.0410.0410.0000.0000.0000.000
175B1274VAL00.0350.02043.9940.0010.0010.0000.0000.0000.000
176B1275ALA0-0.055-0.02543.477-0.001-0.0010.0000.0000.0000.000
177B1276ARG10.7660.85937.514-0.049-0.0490.0000.0000.0000.000
178B1277VAL0-0.047-0.01542.3860.0030.0030.0000.0000.0000.000
179B1278THR00.0690.03245.137-0.001-0.0010.0000.0000.0000.000
180B1279GLU-1-0.729-0.87547.8010.0340.0340.0000.0000.0000.000
181B1280VAL0-0.0080.00351.200-0.003-0.0030.0000.0000.0000.000
182B1281THR0-0.033-0.01148.134-0.002-0.0020.0000.0000.0000.000
183B1282VAL00.0300.01550.143-0.002-0.0020.0000.0000.0000.000
184B1283ARG10.8520.90852.386-0.036-0.0360.0000.0000.0000.000
185B1284ASN0-0.035-0.03353.099-0.003-0.0030.0000.0000.0000.000
186B1285ARG10.8690.92351.716-0.028-0.0280.0000.0000.0000.000
187B1286TYR00.0450.02154.947-0.001-0.0010.0000.0000.0000.000
188B1287LYS10.9781.00357.458-0.027-0.0270.0000.0000.0000.000
189B1288GLU-1-0.775-0.86055.9830.0200.0200.0000.0000.0000.000
190B1289LEU0-0.014-0.01955.055-0.001-0.0010.0000.0000.0000.000
191B1290VAL00.0130.00159.439-0.001-0.0010.0000.0000.0000.000
192B1291GLU-1-0.918-0.96662.5730.0180.0180.0000.0000.0000.000
193B1292LYS10.8530.92359.128-0.019-0.0190.0000.0000.0000.000
194B1293LEU0-0.042-0.02859.348-0.001-0.0010.0000.0000.0000.000
195B1294LYS10.9130.97263.920-0.010-0.0100.0000.0000.0000.000
196B1295ILE0-0.0010.01261.241-0.001-0.0010.0000.0000.0000.000
197B1296LYS10.9460.96565.601-0.007-0.0070.0000.0000.0000.000
198B1297VAL00.006-0.01763.565-0.001-0.0010.0000.0000.0000.000
199B1298PRO00.0040.02065.5510.0010.0010.0000.0000.0000.000
200B1299ILE00.0930.04566.4490.0010.0010.0000.0000.0000.000
201B1300ALA0-0.025-0.00162.3500.0010.0010.0000.0000.0000.000