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: 4N72N

Calculation Name: 1D3U-B-Xray307

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 201
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2220806.895695
FMO2-HF: Nuclear repulsion 2142381.608341
FMO2-HF: Total energy -78425.287354
FMO2-MP2: Total energy -78657.641711


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.
-4.2270.6440.718-2.202-3.3850.008
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 : -0.026 / q_NPA : -0.036
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].
3B1102SER 00.0470.0362.974-0.8111.8610.299-1.279-1.6920.012
4B1103ASP -1-0.829-0.9283.1443.3214.6960.323-0.680-1.018-0.004
5B1104ALA 00.011-0.0124.8450.7790.8450.000-0.002-0.0630.000
6B1105ALA 0-0.051-0.0206.969-0.118-0.1180.0000.0000.0000.000
7B1106GLU -1-0.888-0.9557.3661.0321.0320.0000.0000.0000.000
8B1107ARG 10.9260.9733.140-6.300-5.5420.096-0.241-0.6120.000
9B1108ASN 0-0.001-0.0038.802-0.236-0.2360.0000.0000.0000.000
10B1109LEU 0-0.043-0.01411.820-0.156-0.1560.0000.0000.0000.000
11B1110ALA 00.0270.01311.564-0.105-0.1050.0000.0000.0000.000
12B1111PHE 00.0230.01712.843-0.105-0.1050.0000.0000.0000.000
13B1112ALA 0-0.007-0.01314.622-0.090-0.0900.0000.0000.0000.000
14B1113LEU 0-0.037-0.02816.251-0.071-0.0710.0000.0000.0000.000
15B1114SER 00.0270.02616.350-0.042-0.0420.0000.0000.0000.000
16B1115GLU -1-0.826-0.87618.8700.2760.2760.0000.0000.0000.000
17B1116LEU 0-0.082-0.05920.854-0.037-0.0370.0000.0000.0000.000
18B1117ASP -1-0.891-0.94721.7370.2300.2300.0000.0000.0000.000
19B1118ARG 10.7770.85722.914-0.294-0.2940.0000.0000.0000.000
20B1119ILE 0-0.050-0.04024.769-0.027-0.0270.0000.0000.0000.000
21B1120THR 0-0.007-0.01026.615-0.017-0.0170.0000.0000.0000.000
22B1121ALA 00.0760.05527.571-0.018-0.0180.0000.0000.0000.000
23B1122GLN 0-0.054-0.02728.944-0.024-0.0240.0000.0000.0000.000
24B1123LEU 0-0.025-0.01830.851-0.013-0.0130.0000.0000.0000.000
25B1124LYS 10.9430.97832.297-0.128-0.1280.0000.0000.0000.000
26B1125LEU 0-0.064-0.03030.311-0.011-0.0110.0000.0000.0000.000
27B1126PRO 00.0170.00231.6020.0040.0040.0000.0000.0000.000
28B1127ARG 11.0381.02327.617-0.121-0.1210.0000.0000.0000.000
29B1128HIS 00.0620.02629.3200.0090.0090.0000.0000.0000.000
30B1129VAL 0-0.011-0.00830.6020.0000.0000.0000.0000.0000.000
31B1130GLU -1-0.900-0.95024.7250.1980.1980.0000.0000.0000.000
32B1131GLU -1-0.901-0.97025.6490.1260.1260.0000.0000.0000.000
33B1132GLU -1-0.815-0.88125.8350.1050.1050.0000.0000.0000.000
34B1133ALA 0-0.021-0.01226.0200.0030.0030.0000.0000.0000.000
35B1134ALA 00.0460.01321.6860.0160.0160.0000.0000.0000.000
36B1135ARG 10.7950.87921.905-0.089-0.0890.0000.0000.0000.000
37B1136LEU 0-0.033-0.01723.567-0.005-0.0050.0000.0000.0000.000
38B1137TYR 00.0800.01916.702-0.005-0.0050.0000.0000.0000.000
39B1138ARG 10.9670.97616.915-0.236-0.2360.0000.0000.0000.000
40B1139GLU -1-0.825-0.89719.8510.0710.0710.0000.0000.0000.000
41B1140ALA 0-0.002-0.00921.939-0.011-0.0110.0000.0000.0000.000
42B1141VAL 0-0.034-0.00915.349-0.002-0.0020.0000.0000.0000.000
43B1142ARG 10.8680.92918.274-0.072-0.0720.0000.0000.0000.000
44B1143LYS 10.8870.95619.397-0.101-0.1010.0000.0000.0000.000
45B1144GLY 0-0.020-0.00519.250-0.007-0.0070.0000.0000.0000.000
46B1145LEU 0-0.059-0.04320.2750.0030.0030.0000.0000.0000.000
47B1146ILE 00.0510.01818.020-0.004-0.0040.0000.0000.0000.000
48B1147ARG 10.9620.98717.618-0.159-0.1590.0000.0000.0000.000
49B1148GLY 00.0180.01720.536-0.029-0.0290.0000.0000.0000.000
50B1149ARG 10.8230.92022.182-0.213-0.2130.0000.0000.0000.000
51B1150SER 00.0610.04120.5360.0180.0180.0000.0000.0000.000
52B1151ILE 00.0720.02415.148-0.033-0.0330.0000.0000.0000.000
53B1152GLU -1-0.842-0.92919.6130.3840.3840.0000.0000.0000.000
54B1153SER 0-0.060-0.03222.154-0.032-0.0320.0000.0000.0000.000
55B1154VAL 0-0.019-0.02821.889-0.024-0.0240.0000.0000.0000.000
56B1155MET 00.0090.03120.231-0.038-0.0380.0000.0000.0000.000
57B1156ALA 00.0590.03823.428-0.022-0.0220.0000.0000.0000.000
58B1157ALA 0-0.041-0.01326.650-0.021-0.0210.0000.0000.0000.000
59B1158CYS 0-0.069-0.03124.846-0.019-0.0190.0000.0000.0000.000
60B1159VAL 00.0810.05626.311-0.016-0.0160.0000.0000.0000.000
61B1160TYR 00.0140.01328.736-0.018-0.0180.0000.0000.0000.000
62B1161ALA 0-0.044-0.04129.920-0.013-0.0130.0000.0000.0000.000
63B1162ALA 00.0340.02629.401-0.012-0.0120.0000.0000.0000.000
64B1163CYS 0-0.035-0.01531.458-0.010-0.0100.0000.0000.0000.000
65B1164ARG 10.8620.93034.518-0.100-0.1000.0000.0000.0000.000
66B1165LEU 0-0.051-0.04131.617-0.009-0.0090.0000.0000.0000.000
67B1166LEU 0-0.024-0.01432.466-0.008-0.0080.0000.0000.0000.000
68B1167LYS 10.7680.90636.557-0.074-0.0740.0000.0000.0000.000
69B1168VAL 00.0450.03335.997-0.002-0.0020.0000.0000.0000.000
70B1169PRO 00.0100.00337.8640.0060.0060.0000.0000.0000.000
71B1170ARG 10.8850.95535.240-0.112-0.1120.0000.0000.0000.000
72B1171THR 0-0.007-0.01437.9670.0000.0000.0000.0000.0000.000
73B1172LEU 0-0.035-0.03032.8830.0040.0040.0000.0000.0000.000
74B1173ASP -1-0.842-0.94034.5230.1220.1220.0000.0000.0000.000
75B1174GLU -1-0.761-0.86935.3950.1170.1170.0000.0000.0000.000
76B1175ILE 0-0.008-0.00129.7300.0070.0070.0000.0000.0000.000
77B1176ALA 0-0.074-0.04730.9530.0120.0120.0000.0000.0000.000
78B1177ASP -1-0.799-0.87731.8410.1390.1390.0000.0000.0000.000
79B1178ILE 0-0.0020.02128.8620.0050.0050.0000.0000.0000.000
80B1179ALA 0-0.0210.00427.1340.0210.0210.0000.0000.0000.000
81B1180ARG 10.9770.99120.006-0.369-0.3690.0000.0000.0000.000
82B1181VAL 0-0.037-0.01425.4190.0020.0020.0000.0000.0000.000
83B1182ASP -1-0.750-0.89128.0900.1620.1620.0000.0000.0000.000
84B1183LYS 10.9450.96231.280-0.110-0.1100.0000.0000.0000.000
85B1184LYS 10.9000.95933.550-0.134-0.1340.0000.0000.0000.000
86B1185GLU -1-0.841-0.91627.4690.1920.1920.0000.0000.0000.000
87B1186ILE 00.0900.04728.3600.0000.0000.0000.0000.0000.000
88B1187GLY 0-0.003-0.00430.040-0.006-0.0060.0000.0000.0000.000
89B1188ARG 10.8570.91130.620-0.149-0.1490.0000.0000.0000.000
90B1189SER 00.0440.03126.664-0.003-0.0030.0000.0000.0000.000
91B1190TYR 00.0450.01528.539-0.008-0.0080.0000.0000.0000.000
92B1191ARG 10.9120.95830.627-0.124-0.1240.0000.0000.0000.000
93B1192PHE 0-0.040-0.01325.757-0.010-0.0100.0000.0000.0000.000
94B1193ILE 00.0630.02625.376-0.009-0.0090.0000.0000.0000.000
95B1194ALA 00.0290.01628.331-0.009-0.0090.0000.0000.0000.000
96B1195ARG 10.9290.95431.617-0.103-0.1030.0000.0000.0000.000
97B1196ASN 0-0.051-0.03527.903-0.016-0.0160.0000.0000.0000.000
98B1197LEU 0-0.0220.01625.406-0.006-0.0060.0000.0000.0000.000
99B1198ASN 0-0.050-0.02029.427-0.007-0.0070.0000.0000.0000.000
100B1199LEU 00.0170.01230.360-0.006-0.0060.0000.0000.0000.000
101B1200THR 00.019-0.00634.1530.0020.0020.0000.0000.0000.000
102B1201PRO 00.0700.01137.7810.0020.0020.0000.0000.0000.000
103B1202LYS 10.9850.99640.505-0.038-0.0380.0000.0000.0000.000
104B1203LYS 10.9160.96734.390-0.058-0.0580.0000.0000.0000.000
105B1204LEU 00.0270.01334.0870.0030.0030.0000.0000.0000.000
106B1205PHE 0-0.0270.00738.1340.0040.0040.0000.0000.0000.000
107B1206VAL 00.0380.03539.893-0.001-0.0010.0000.0000.0000.000
108B1207LYS 11.0110.99342.834-0.048-0.0480.0000.0000.0000.000
109B1208PRO 00.0470.02046.1940.0020.0020.0000.0000.0000.000
110B1209THR 00.0640.02948.1770.0020.0020.0000.0000.0000.000
111B1210ASP -1-0.882-0.93644.3020.0610.0610.0000.0000.0000.000
112B1211TYR 0-0.067-0.03741.0520.0040.0040.0000.0000.0000.000
113B1212VAL 0-0.039-0.00445.8840.0010.0010.0000.0000.0000.000
114B1213ASN 00.0420.01047.812-0.001-0.0010.0000.0000.0000.000
115B1214LYS 10.8580.94540.409-0.092-0.0920.0000.0000.0000.000
116B1215PHE 0-0.003-0.01843.1690.0010.0010.0000.0000.0000.000
117B1216ALA 00.0150.00047.1630.0000.0000.0000.0000.0000.000
118B1217ASP -1-0.852-0.90046.6730.0620.0620.0000.0000.0000.000
119B1218GLU -1-0.924-0.96743.1620.0880.0880.0000.0000.0000.000
120B1219LEU 0-0.057-0.01647.3240.0000.0000.0000.0000.0000.000
121B1220GLY 00.0190.00950.708-0.003-0.0030.0000.0000.0000.000
122B1221LEU 0-0.069-0.02052.645-0.003-0.0030.0000.0000.0000.000
123B1222SER 00.021-0.03254.3580.0000.0000.0000.0000.0000.000
124B1223GLU -1-0.934-0.98655.9530.0430.0430.0000.0000.0000.000
125B1224LYS 10.9000.94857.004-0.036-0.0360.0000.0000.0000.000
126B1225VAL 00.0490.02655.872-0.001-0.0010.0000.0000.0000.000
127B1226ARG 10.8200.90050.015-0.055-0.0550.0000.0000.0000.000
128B1227ARG 10.9540.99355.318-0.038-0.0380.0000.0000.0000.000
129B1228ARG 10.9270.97057.904-0.038-0.0380.0000.0000.0000.000
130B1229ALA 00.018-0.00154.7320.0000.0000.0000.0000.0000.000
131B1230ILE 0-0.028-0.03052.8830.0010.0010.0000.0000.0000.000
132B1231GLU -1-0.894-0.93055.4030.0350.0350.0000.0000.0000.000
133B1232ILE 0-0.012-0.01057.648-0.001-0.0010.0000.0000.0000.000
134B1233LEU 0-0.067-0.04651.7970.0000.0000.0000.0000.0000.000
135B1234ASP -1-0.919-0.96255.1630.0420.0420.0000.0000.0000.000
136B1235GLU -1-0.873-0.93056.8790.0330.0330.0000.0000.0000.000
137B1236ALA 00.006-0.01056.166-0.001-0.0010.0000.0000.0000.000
138B1237TYR 0-0.078-0.03451.4430.0000.0000.0000.0000.0000.000
139B1238LYS 10.9320.96855.900-0.036-0.0360.0000.0000.0000.000
140B1239ARG 10.8660.92959.078-0.035-0.0350.0000.0000.0000.000
141B1240GLY 0-0.0050.02156.8480.0000.0000.0000.0000.0000.000
142B1241LEU 0-0.045-0.03256.7450.0010.0010.0000.0000.0000.000
143B1242THR 0-0.021-0.01451.7860.0020.0020.0000.0000.0000.000
144B1243SER 00.0520.01550.3250.0030.0030.0000.0000.0000.000
145B1244GLY 0-0.022-0.00748.426-0.001-0.0010.0000.0000.0000.000
146B1245LYS 10.8970.96448.338-0.049-0.0490.0000.0000.0000.000
147B1246SER 00.0090.00645.3840.0010.0010.0000.0000.0000.000
148B1247PRO 00.0380.00144.439-0.002-0.0020.0000.0000.0000.000
149B1248ALA 00.0750.04644.084-0.002-0.0020.0000.0000.0000.000
150B1249GLY 00.0250.01246.216-0.001-0.0010.0000.0000.0000.000
151B1250LEU 0-0.020-0.02248.865-0.003-0.0030.0000.0000.0000.000
152B1251VAL 00.0050.01747.866-0.002-0.0020.0000.0000.0000.000
153B1252ALA 00.0380.02549.108-0.002-0.0020.0000.0000.0000.000
154B1253ALA 0-0.013-0.01150.927-0.002-0.0020.0000.0000.0000.000
155B1254ALA 00.0100.00553.758-0.002-0.0020.0000.0000.0000.000
156B1255LEU 00.0270.01150.469-0.002-0.0020.0000.0000.0000.000
157B1256TYR 0-0.028-0.00354.675-0.001-0.0010.0000.0000.0000.000
158B1257ILE 00.0080.00156.438-0.002-0.0020.0000.0000.0000.000
159B1258ALA 00.003-0.00157.674-0.002-0.0020.0000.0000.0000.000
160B1259SER 0-0.031-0.01057.235-0.001-0.0010.0000.0000.0000.000
161B1260LEU 0-0.035-0.02259.293-0.001-0.0010.0000.0000.0000.000
162B1261LEU 0-0.036-0.03862.382-0.001-0.0010.0000.0000.0000.000
163B1262GLU -1-0.886-0.92961.4470.0360.0360.0000.0000.0000.000
164B1263GLY 0-0.018-0.00263.7300.0000.0000.0000.0000.0000.000
165B1264GLU -1-0.835-0.88258.6630.0460.0460.0000.0000.0000.000
166B1265LYS 10.8580.93258.943-0.047-0.0470.0000.0000.0000.000
167B1266ARG 10.9250.97953.902-0.054-0.0540.0000.0000.0000.000
168B1267THR 0-0.044-0.04954.768-0.001-0.0010.0000.0000.0000.000
169B1268GLN 00.014-0.00254.1600.0030.0030.0000.0000.0000.000
170B1269ARG 10.9260.96648.506-0.074-0.0740.0000.0000.0000.000
171B1270GLU -1-0.804-0.88050.2730.0630.0630.0000.0000.0000.000
172B1271VAL 0-0.0100.00049.5070.0030.0030.0000.0000.0000.000
173B1272ALA 0-0.056-0.03348.5940.0020.0020.0000.0000.0000.000
174B1273GLU -1-0.898-0.95245.1430.0880.0880.0000.0000.0000.000
175B1274VAL 00.0410.02544.5280.0040.0040.0000.0000.0000.000
176B1275ALA 0-0.062-0.03044.1120.0020.0020.0000.0000.0000.000
177B1276ARG 10.7870.88438.030-0.112-0.1120.0000.0000.0000.000
178B1277VAL 0-0.046-0.01442.8190.0020.0020.0000.0000.0000.000
179B1278THR 00.0480.01245.547-0.002-0.0020.0000.0000.0000.000
180B1279GLU -1-0.784-0.92248.1320.0650.0650.0000.0000.0000.000
181B1280VAL 0-0.0110.00351.478-0.003-0.0030.0000.0000.0000.000
182B1281THR 0-0.043-0.00848.782-0.003-0.0030.0000.0000.0000.000
183B1282VAL 00.0290.02250.713-0.002-0.0020.0000.0000.0000.000
184B1283ARG 10.9440.97052.833-0.061-0.0610.0000.0000.0000.000
185B1284ASN 0-0.036-0.03053.106-0.004-0.0040.0000.0000.0000.000
186B1285ARG 10.8390.91652.257-0.058-0.0580.0000.0000.0000.000
187B1286TYR 00.0470.02355.408-0.002-0.0020.0000.0000.0000.000
188B1287LYS 10.9590.99257.955-0.048-0.0480.0000.0000.0000.000
189B1288GLU -1-0.850-0.93656.7700.0480.0480.0000.0000.0000.000
190B1289LEU 0-0.007-0.01555.751-0.002-0.0020.0000.0000.0000.000
191B1290VAL 00.0110.00759.988-0.002-0.0020.0000.0000.0000.000
192B1291GLU -1-0.901-0.96363.1220.0380.0380.0000.0000.0000.000
193B1292LYS 10.9080.95959.863-0.043-0.0430.0000.0000.0000.000
194B1293LEU 0-0.041-0.01860.092-0.001-0.0010.0000.0000.0000.000
195B1294LYS 10.9070.97064.534-0.030-0.0300.0000.0000.0000.000
196B1295ILE 00.0030.01362.107-0.001-0.0010.0000.0000.0000.000
197B1296LYS 10.9230.94966.231-0.031-0.0310.0000.0000.0000.000
198B1297VAL 00.023-0.00663.9360.0010.0010.0000.0000.0000.000
199B1298PRO 0-0.0210.01166.0810.0000.0000.0000.0000.0000.000
200B1299ILE 00.0650.02767.023-0.001-0.0010.0000.0000.0000.000
201B1300ALA -1-0.891-0.94862.7700.0470.0470.0000.0000.0000.000