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: LNKV9

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2229120.381423
FMO2-HF: Nuclear repulsion 2150692.775168
FMO2-HF: Total energy -78427.606255
FMO2-MP2: Total energy -78659.814328


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.
-12.894-10.2046.515-4.451-4.755-0.032
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 : -0.018 / q_NPA : -0.025
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].
3B1102SER00.0270.0292.561-0.0812.6830.165-1.395-1.5340.003
4B1103ASP-1-0.760-0.9051.964-6.295-7.4026.148-2.623-2.419-0.038
5B1104ALA0-0.037-0.0294.5280.6440.742-0.001-0.003-0.0930.000
6B1105ALA0-0.022-0.0116.346-0.089-0.0890.0000.0000.0000.000
7B1106GLU-1-0.849-0.9206.518-2.105-2.1050.0000.0000.0000.000
8B1107ARG10.9500.9812.594-4.611-3.6760.203-0.430-0.7090.003
9B1108ASN0-0.045-0.0298.1910.0050.0050.0000.0000.0000.000
10B1109LEU0-0.022-0.00711.198-0.012-0.0120.0000.0000.0000.000
11B1110ALA00.0390.01810.7960.0040.0040.0000.0000.0000.000
12B1111PHE0-0.0110.01112.3440.0230.0230.0000.0000.0000.000
13B1112ALA00.002-0.01414.253-0.013-0.0130.0000.0000.0000.000
14B1113LEU0-0.019-0.02715.142-0.011-0.0110.0000.0000.0000.000
15B1114SER00.0180.01315.639-0.010-0.0100.0000.0000.0000.000
16B1115GLU-1-0.820-0.88918.2070.1400.1400.0000.0000.0000.000
17B1116LEU0-0.057-0.03620.290-0.006-0.0060.0000.0000.0000.000
18B1117ASP-1-0.905-0.92321.150-0.025-0.0250.0000.0000.0000.000
19B1118ARG10.8090.87022.427-0.110-0.1100.0000.0000.0000.000
20B1119ILE0-0.038-0.02624.3430.0010.0010.0000.0000.0000.000
21B1120THR0-0.032-0.05225.135-0.007-0.0070.0000.0000.0000.000
22B1121ALA00.0650.03926.802-0.003-0.0030.0000.0000.0000.000
23B1122GLN0-0.037-0.01028.457-0.005-0.0050.0000.0000.0000.000
24B1123LEU0-0.009-0.01030.194-0.002-0.0020.0000.0000.0000.000
25B1124LYS10.9000.96131.581-0.015-0.0150.0000.0000.0000.000
26B1125LEU0-0.035-0.01629.682-0.002-0.0020.0000.0000.0000.000
27B1126PRO00.0120.00330.884-0.005-0.0050.0000.0000.0000.000
28B1127ARG10.8980.93725.0560.1180.1180.0000.0000.0000.000
29B1128HIS00.1050.04528.133-0.006-0.0060.0000.0000.0000.000
30B1129VAL0-0.040-0.03329.4750.0000.0000.0000.0000.0000.000
31B1130GLU-1-0.818-0.87224.106-0.087-0.0870.0000.0000.0000.000
32B1131GLU-1-0.859-0.95224.409-0.132-0.1320.0000.0000.0000.000
33B1132GLU-1-0.772-0.84824.697-0.084-0.0840.0000.0000.0000.000
34B1133ALA0-0.021-0.00924.9710.0020.0020.0000.0000.0000.000
35B1134ALA00.0390.01420.6970.0050.0050.0000.0000.0000.000
36B1135ARG10.7820.86720.7080.0750.0750.0000.0000.0000.000
37B1136LEU0-0.053-0.03222.739-0.001-0.0010.0000.0000.0000.000
38B1137TYR00.0910.02115.8380.0150.0150.0000.0000.0000.000
39B1138ARG10.9340.96316.7140.2520.2520.0000.0000.0000.000
40B1139GLU-1-0.809-0.87919.301-0.131-0.1310.0000.0000.0000.000
41B1140ALA0-0.015-0.01021.1320.0090.0090.0000.0000.0000.000
42B1141VAL0-0.011-0.00314.6230.0300.0300.0000.0000.0000.000
43B1142ARG10.8510.90517.8360.1640.1640.0000.0000.0000.000
44B1143LYS10.8430.91719.0390.0560.0560.0000.0000.0000.000
45B1144GLY00.0000.00418.7890.0180.0180.0000.0000.0000.000
46B1145LEU0-0.053-0.03419.8250.0350.0350.0000.0000.0000.000
47B1146ILE00.0390.00517.1480.0100.0100.0000.0000.0000.000
48B1147ARG10.9360.97418.367-0.076-0.0760.0000.0000.0000.000
49B1148GLY00.0440.03020.497-0.024-0.0240.0000.0000.0000.000
50B1149ARG10.8180.92021.547-0.163-0.1630.0000.0000.0000.000
51B1150SER00.0490.03520.3000.0110.0110.0000.0000.0000.000
52B1151ILE00.0300.01814.719-0.036-0.0360.0000.0000.0000.000
53B1152GLU-1-0.767-0.89419.1310.2480.2480.0000.0000.0000.000
54B1153SER0-0.048-0.03321.844-0.034-0.0340.0000.0000.0000.000
55B1154VAL0-0.009-0.01321.126-0.025-0.0250.0000.0000.0000.000
56B1155MET00.0180.03119.639-0.030-0.0300.0000.0000.0000.000
57B1156ALA00.0490.02722.713-0.019-0.0190.0000.0000.0000.000
58B1157ALA0-0.031-0.01626.167-0.014-0.0140.0000.0000.0000.000
59B1158CYS0-0.075-0.03424.018-0.015-0.0150.0000.0000.0000.000
60B1159VAL00.0660.03225.375-0.014-0.0140.0000.0000.0000.000
61B1160TYR00.0370.02727.802-0.006-0.0060.0000.0000.0000.000
62B1161ALA0-0.039-0.02628.938-0.005-0.0050.0000.0000.0000.000
63B1162ALA00.0280.01828.257-0.006-0.0060.0000.0000.0000.000
64B1163CYS0-0.027-0.00830.365-0.005-0.0050.0000.0000.0000.000
65B1164ARG10.8580.92033.384-0.011-0.0110.0000.0000.0000.000
66B1165LEU0-0.056-0.02830.794-0.001-0.0010.0000.0000.0000.000
67B1166LEU0-0.023-0.01431.092-0.002-0.0020.0000.0000.0000.000
68B1167LYS10.7510.87535.3270.0240.0240.0000.0000.0000.000
69B1168VAL00.0450.03835.0900.0010.0010.0000.0000.0000.000
70B1169PRO0-0.0180.00336.8980.0040.0040.0000.0000.0000.000
71B1170ARG10.9230.95234.0240.0040.0040.0000.0000.0000.000
72B1171THR0-0.030-0.04537.0140.0010.0010.0000.0000.0000.000
73B1172LEU0-0.035-0.02532.0280.0000.0000.0000.0000.0000.000
74B1173ASP-1-0.805-0.89633.6760.0590.0590.0000.0000.0000.000
75B1174GLU-1-0.740-0.84235.0060.0250.0250.0000.0000.0000.000
76B1175ILE0-0.0080.00428.8790.0010.0010.0000.0000.0000.000
77B1176ALA0-0.036-0.03730.3620.0090.0090.0000.0000.0000.000
78B1177ASP-1-0.780-0.84032.0340.0680.0680.0000.0000.0000.000
79B1178ILE0-0.0260.00128.9830.0040.0040.0000.0000.0000.000
80B1179ALA00.0090.02126.4440.0090.0090.0000.0000.0000.000
81B1180ARG10.9000.94719.592-0.314-0.3140.0000.0000.0000.000
82B1181VAL0-0.035-0.02225.0690.0180.0180.0000.0000.0000.000
83B1182ASP-1-0.716-0.85927.7820.1060.1060.0000.0000.0000.000
84B1183LYS10.8630.91430.977-0.059-0.0590.0000.0000.0000.000
85B1184LYS10.8900.94733.530-0.120-0.1200.0000.0000.0000.000
86B1185GLU-1-0.845-0.91126.9790.1360.1360.0000.0000.0000.000
87B1186ILE00.0710.05127.789-0.006-0.0060.0000.0000.0000.000
88B1187GLY00.0190.00229.442-0.012-0.0120.0000.0000.0000.000
89B1188ARG10.8660.93230.272-0.135-0.1350.0000.0000.0000.000
90B1189SER00.0420.00526.039-0.007-0.0070.0000.0000.0000.000
91B1190TYR00.0120.00427.905-0.010-0.0100.0000.0000.0000.000
92B1191ARG10.9290.96130.056-0.074-0.0740.0000.0000.0000.000
93B1192PHE0-0.042-0.00624.943-0.006-0.0060.0000.0000.0000.000
94B1193ILE00.0470.01724.691-0.009-0.0090.0000.0000.0000.000
95B1194ALA00.0260.01427.761-0.013-0.0130.0000.0000.0000.000
96B1195ARG10.9230.95831.163-0.048-0.0480.0000.0000.0000.000
97B1196ASN0-0.0020.00427.224-0.012-0.0120.0000.0000.0000.000
98B1197LEU0-0.0020.01724.647-0.013-0.0130.0000.0000.0000.000
99B1198ASN0-0.009-0.00728.713-0.014-0.0140.0000.0000.0000.000
100B1199LEU00.0100.01629.542-0.005-0.0050.0000.0000.0000.000
101B1200THR00.0340.00533.5150.0070.0070.0000.0000.0000.000
102B1201PRO00.0560.00637.191-0.002-0.0020.0000.0000.0000.000
103B1202LYS10.9931.00039.5740.0280.0280.0000.0000.0000.000
104B1203LYS10.8860.94833.7280.0430.0430.0000.0000.0000.000
105B1204LEU00.0160.01633.177-0.002-0.0020.0000.0000.0000.000
106B1205PHE00.0020.02037.2470.0050.0050.0000.0000.0000.000
107B1206VAL00.0340.02138.856-0.004-0.0040.0000.0000.0000.000
108B1207LYS10.8470.92341.9350.0210.0210.0000.0000.0000.000
109B1208PRO00.0520.01145.3410.0010.0010.0000.0000.0000.000
110B1209THR00.0560.01947.5270.0020.0020.0000.0000.0000.000
111B1210ASP-1-0.779-0.86643.285-0.015-0.0150.0000.0000.0000.000
112B1211TYR0-0.036-0.04038.5200.0000.0000.0000.0000.0000.000
113B1212VAL0-0.037-0.01344.7930.0020.0020.0000.0000.0000.000
114B1213ASN0-0.018-0.00946.5910.0010.0010.0000.0000.0000.000
115B1214LYS10.7930.89439.508-0.015-0.0150.0000.0000.0000.000
116B1215PHE00.0330.00742.3300.0010.0010.0000.0000.0000.000
117B1216ALA00.0020.00246.4080.0020.0020.0000.0000.0000.000
118B1217ASP-1-0.823-0.88145.986-0.004-0.0040.0000.0000.0000.000
119B1218GLU-1-0.828-0.90741.7410.0170.0170.0000.0000.0000.000
120B1219LEU0-0.043-0.00846.3380.0020.0020.0000.0000.0000.000
121B1220GLY00.0480.03349.7350.0000.0000.0000.0000.0000.000
122B1221LEU0-0.078-0.03151.6620.0000.0000.0000.0000.0000.000
123B1222SER00.003-0.05553.100-0.003-0.0030.0000.0000.0000.000
124B1223GLU-1-0.815-0.90254.359-0.008-0.0080.0000.0000.0000.000
125B1224LYS10.8780.94355.5710.0000.0000.0000.0000.0000.000
126B1225VAL00.0280.01655.0990.0000.0000.0000.0000.0000.000
127B1226ARG10.7640.85048.7270.0030.0030.0000.0000.0000.000
128B1227ARG10.8590.90554.2440.0080.0080.0000.0000.0000.000
129B1228ARG10.8120.89856.774-0.001-0.0010.0000.0000.0000.000
130B1229ALA00.0300.00253.6080.0010.0010.0000.0000.0000.000
131B1230ILE0-0.029-0.02852.0030.0010.0010.0000.0000.0000.000
132B1231GLU-1-0.819-0.87954.462-0.001-0.0010.0000.0000.0000.000
133B1232ILE0-0.024-0.01456.5560.0010.0010.0000.0000.0000.000
134B1233LEU0-0.036-0.02650.8640.0010.0010.0000.0000.0000.000
135B1234ASP-1-0.830-0.90254.511-0.003-0.0030.0000.0000.0000.000
136B1235GLU-1-0.806-0.87655.8350.0010.0010.0000.0000.0000.000
137B1236ALA0-0.010-0.01655.2100.0010.0010.0000.0000.0000.000
138B1237TYR0-0.068-0.04150.0880.0010.0010.0000.0000.0000.000
139B1238LYS10.8320.89754.9180.0020.0020.0000.0000.0000.000
140B1239ARG10.8180.90958.097-0.005-0.0050.0000.0000.0000.000
141B1240GLY00.0140.01455.6690.0010.0010.0000.0000.0000.000
142B1241LEU0-0.033-0.01655.5880.0020.0020.0000.0000.0000.000
143B1242THR00.0070.01150.7440.0030.0030.0000.0000.0000.000
144B1243SER00.0450.01049.9090.0010.0010.0000.0000.0000.000
145B1244GLY00.0120.00747.6570.0010.0010.0000.0000.0000.000
146B1245LYS10.7650.88248.116-0.016-0.0160.0000.0000.0000.000
147B1246SER00.0170.00544.570-0.002-0.0020.0000.0000.0000.000
148B1247PRO00.0440.01043.673-0.001-0.0010.0000.0000.0000.000
149B1248ALA00.0640.04143.301-0.002-0.0020.0000.0000.0000.000
150B1249GLY00.0220.01045.4530.0000.0000.0000.0000.0000.000
151B1250LEU0-0.036-0.01948.289-0.001-0.0010.0000.0000.0000.000
152B1251VAL00.0130.01547.295-0.001-0.0010.0000.0000.0000.000
153B1252ALA00.0290.02248.508-0.001-0.0010.0000.0000.0000.000
154B1253ALA0-0.018-0.01250.3470.0000.0000.0000.0000.0000.000
155B1254ALA0-0.010-0.00253.094-0.001-0.0010.0000.0000.0000.000
156B1255LEU00.0380.01349.678-0.001-0.0010.0000.0000.0000.000
157B1256TYR0-0.0090.00753.9180.0000.0000.0000.0000.0000.000
158B1257ILE00.0040.00855.8510.0000.0000.0000.0000.0000.000
159B1258ALA00.0160.00356.570-0.001-0.0010.0000.0000.0000.000
160B1259SER0-0.055-0.03556.5400.0000.0000.0000.0000.0000.000
161B1260LEU0-0.060-0.03358.5810.0000.0000.0000.0000.0000.000
162B1261LEU0-0.050-0.04361.7050.0000.0000.0000.0000.0000.000
163B1262GLU-1-0.797-0.87860.8310.0010.0010.0000.0000.0000.000
164B1263GLY0-0.0050.01362.868-0.001-0.0010.0000.0000.0000.000
165B1264GLU-1-0.779-0.84557.4670.0040.0040.0000.0000.0000.000
166B1265LYS10.8670.92358.080-0.018-0.0180.0000.0000.0000.000
167B1266ARG10.8710.95053.408-0.012-0.0120.0000.0000.0000.000
168B1267THR0-0.044-0.06554.3290.0010.0010.0000.0000.0000.000
169B1268GLN00.001-0.01653.9460.0010.0010.0000.0000.0000.000
170B1269ARG10.8360.88447.611-0.039-0.0390.0000.0000.0000.000
171B1270GLU-1-0.746-0.83549.6550.0230.0230.0000.0000.0000.000
172B1271VAL0-0.0050.00148.7160.0000.0000.0000.0000.0000.000
173B1272ALA0-0.042-0.02947.9180.0000.0000.0000.0000.0000.000
174B1273GLU-1-0.821-0.86844.9140.0410.0410.0000.0000.0000.000
175B1274VAL00.0220.01643.8820.0020.0020.0000.0000.0000.000
176B1275ALA0-0.044-0.02143.1080.0000.0000.0000.0000.0000.000
177B1276ARG10.7610.85437.443-0.048-0.0480.0000.0000.0000.000
178B1277VAL0-0.061-0.02142.2600.0030.0030.0000.0000.0000.000
179B1278THR00.0700.03845.064-0.001-0.0010.0000.0000.0000.000
180B1279GLU-1-0.726-0.86647.6640.0330.0330.0000.0000.0000.000
181B1280VAL0-0.0010.00550.930-0.003-0.0030.0000.0000.0000.000
182B1281THR0-0.023-0.01247.534-0.002-0.0020.0000.0000.0000.000
183B1282VAL00.0300.01449.857-0.002-0.0020.0000.0000.0000.000
184B1283ARG10.8390.89852.135-0.035-0.0350.0000.0000.0000.000
185B1284ASN0-0.046-0.03853.655-0.002-0.0020.0000.0000.0000.000
186B1285ARG10.8750.93151.557-0.028-0.0280.0000.0000.0000.000
187B1286TYR00.0460.01454.830-0.001-0.0010.0000.0000.0000.000
188B1287LYS10.8810.93457.267-0.024-0.0240.0000.0000.0000.000
189B1288GLU-1-0.788-0.87155.5650.0190.0190.0000.0000.0000.000
190B1289LEU00.007-0.00755.119-0.001-0.0010.0000.0000.0000.000
191B1290VAL00.0180.00759.418-0.001-0.0010.0000.0000.0000.000
192B1291GLU-1-0.832-0.89862.5360.0180.0180.0000.0000.0000.000
193B1292LYS10.8600.92358.766-0.019-0.0190.0000.0000.0000.000
194B1293LEU0-0.016-0.01259.129-0.001-0.0010.0000.0000.0000.000
195B1294LYS10.9280.98063.662-0.009-0.0090.0000.0000.0000.000
196B1295ILE0-0.0030.00960.986-0.001-0.0010.0000.0000.0000.000
197B1296LYS10.9010.94665.477-0.007-0.0070.0000.0000.0000.000
198B1297VAL00.016-0.00163.317-0.001-0.0010.0000.0000.0000.000
199B1298PRO00.0050.01965.5430.0010.0010.0000.0000.0000.000
200B1299ILE00.1060.04866.1620.0010.0010.0000.0000.0000.000
201B1300ALA0-0.034-0.00662.1370.0010.0010.0000.0000.0000.000