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: 39Q6L

Calculation Name: 3SWH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SWH

Chain ID: A

ChEMBL ID:

UniProt ID: Q62768

Base Structure: X-ray

Registration Date: 2023-06-21

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 295
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4100781.907635
FMO2-HF: Nuclear repulsion 3981020.776127
FMO2-HF: Total energy -119761.131509
FMO2-MP2: Total energy -120106.688129


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:1156:ALA)


Summations of interaction energy for fragment #1(A:1156:ALA)
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.
-9.579-6.3776.38-3.654-5.9260.004
Interaction energy analysis for fragmet #1(A:1156:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.003
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].
3A1158PHE00.021-0.0252.576-6.002-1.8331.551-2.193-3.5270.012
4A1159GLU-1-0.851-0.9243.326-3.717-3.0750.009-0.161-0.4900.000
5A1160PRO00.009-0.0024.9260.0720.221-0.001-0.017-0.1300.000
6A1161PHE0-0.0190.0116.3470.0650.0650.0000.0000.0000.000
7A1162VAL00.0300.0237.400-0.084-0.0840.0000.0000.0000.000
8A1163ILE00.008-0.0178.658-0.051-0.0510.0000.0000.0000.000
9A1164GLN0-0.0160.00811.0420.0220.0220.0000.0000.0000.000
10A1165TRP00.0150.00711.1260.0470.0470.0000.0000.0000.000
11A1166LEU0-0.059-0.03111.199-0.017-0.0170.0000.0000.0000.000
12A1167ASP-1-0.855-0.93014.965-0.152-0.1520.0000.0000.0000.000
13A1168GLU-1-0.907-0.92917.2400.0580.0580.0000.0000.0000.000
14A1169ASN0-0.046-0.03517.682-0.017-0.0170.0000.0000.0000.000
15A1170GLU-1-0.781-0.82119.147-0.091-0.0910.0000.0000.0000.000
16A1171GLU-1-0.892-0.94921.127-0.007-0.0070.0000.0000.0000.000
17A1172VAL00.0420.00222.0720.0040.0040.0000.0000.0000.000
18A1173SER0-0.094-0.08821.8200.0010.0010.0000.0000.0000.000
19A1174ARG10.7910.87223.9390.0420.0420.0000.0000.0000.000
20A1175ASP-1-0.881-0.92226.6580.0070.0070.0000.0000.0000.000
21A1176PHE0-0.086-0.05127.5110.0030.0030.0000.0000.0000.000
22A1177LEU0-0.016-0.01228.8180.0000.0000.0000.0000.0000.000
23A1178HIS0-0.009-0.01630.625-0.003-0.0030.0000.0000.0000.000
24A1179GLY00.0230.02032.6340.0000.0000.0000.0000.0000.000
25A1180ALA0-0.051-0.02232.3800.0020.0020.0000.0000.0000.000
26A1181LEU00.018-0.01034.3240.0000.0000.0000.0000.0000.000
27A1182GLU-1-0.919-0.94036.5210.0000.0000.0000.0000.0000.000
28A1183ARG10.8350.90733.345-0.022-0.0220.0000.0000.0000.000
29A1184ASP-1-0.687-0.78238.4580.0030.0030.0000.0000.0000.000
30A1185LYS10.9290.97340.2530.0020.0020.0000.0000.0000.000
31A1186LYS10.7700.88342.291-0.004-0.0040.0000.0000.0000.000
32A1187ASP-1-0.901-0.94543.3330.0110.0110.0000.0000.0000.000
33A1188GLY0-0.052-0.01145.0080.0000.0000.0000.0000.0000.000
34A1189PHE0-0.064-0.02439.552-0.001-0.0010.0000.0000.0000.000
35A1190GLN00.0190.00743.842-0.002-0.0020.0000.0000.0000.000
36A1191GLN0-0.010-0.02743.208-0.001-0.0010.0000.0000.0000.000
37A1192THR0-0.028-0.01440.0330.0020.0020.0000.0000.0000.000
38A1193SER0-0.026-0.00842.6060.0010.0010.0000.0000.0000.000
39A1194GLU-1-0.939-0.96445.3100.0010.0010.0000.0000.0000.000
40A1195HIS0-0.002-0.02544.747-0.002-0.0020.0000.0000.0000.000
41A1196ALA0-0.078-0.02540.367-0.001-0.0010.0000.0000.0000.000
42A1197LEU00.0200.01241.9350.0010.0010.0000.0000.0000.000
43A1198PHE00.0300.01937.250-0.001-0.0010.0000.0000.0000.000
44A1199SER00.0620.02839.6230.0010.0010.0000.0000.0000.000
45A1200CYS00.0320.00337.079-0.001-0.0010.0000.0000.0000.000
46A1201SER0-0.085-0.09735.4410.0010.0010.0000.0000.0000.000
47A1202VAL0-0.049-0.02333.189-0.001-0.0010.0000.0000.0000.000
48A1203VAL0-0.055-0.03232.4940.0000.0000.0000.0000.0000.000
49A1204ASP-1-0.857-0.93231.1720.0240.0240.0000.0000.0000.000
50A1205VAL00.0290.01128.0240.0040.0040.0000.0000.0000.000
51A1206PHE00.0550.01626.677-0.001-0.0010.0000.0000.0000.000
52A1207SER0-0.0160.00026.3030.0050.0050.0000.0000.0000.000
53A1208GLN00.0080.01423.2620.0030.0030.0000.0000.0000.000
54A1209LEU00.0530.02322.7030.0080.0080.0000.0000.0000.000
55A1210ASN00.002-0.01121.732-0.008-0.0080.0000.0000.0000.000
56A1211GLN0-0.0140.00521.7380.0200.0200.0000.0000.0000.000
57A1212SER0-0.0160.00218.9200.0190.0190.0000.0000.0000.000
58A1213PHE00.027-0.00416.8630.0240.0240.0000.0000.0000.000
59A1214GLU-1-0.894-0.95417.0270.1040.1040.0000.0000.0000.000
60A1215ILE0-0.045-0.03715.5050.0260.0260.0000.0000.0000.000
61A1216ILE00.0180.02012.1620.0540.0540.0000.0000.0000.000
62A1217LYS10.8670.94612.418-0.042-0.0420.0000.0000.0000.000
63A1218LYS10.8690.93413.544-0.131-0.1310.0000.0000.0000.000
64A1219LEU0-0.0640.0128.7220.0910.0910.0000.0000.0000.000
65A1220GLU-1-0.945-0.98010.1310.2860.2860.0000.0000.0000.000
66A1221CYS0-0.041-0.0295.7400.3020.341-0.001-0.002-0.0360.000
67A1222PRO0-0.045-0.0065.351-0.206-0.2060.0000.0000.0000.000
68A1223ASP-1-0.795-0.9234.762-2.156-2.079-0.001-0.005-0.0700.000
69A1224PRO00.0200.0076.556-0.022-0.0220.0000.0000.0000.000
70A1225GLN0-0.028-0.0257.6650.1710.1710.0000.0000.0000.000
71A1226ILE00.0160.0191.8940.436-1.4384.823-1.276-1.673-0.008
72A1227VAL0-0.034-0.0145.9990.3370.3370.0000.0000.0000.000
73A1228GLY00.0160.0039.0560.0980.0980.0000.0000.0000.000
74A1229HIS00.0090.0108.3190.1720.1720.0000.0000.0000.000
75A1230TYR00.0330.0095.587-0.013-0.0130.0000.0000.0000.000
76A1231MET00.0040.01010.8030.0710.0710.0000.0000.0000.000
77A1232ARG10.9070.96511.5870.6040.6040.0000.0000.0000.000
78A1233ARG10.7830.89113.2160.1740.1740.0000.0000.0000.000
79A1234PHE00.030-0.01114.7190.0390.0390.0000.0000.0000.000
80A1235ALA00.0080.00716.6250.0220.0220.0000.0000.0000.000
81A1236LYS10.9390.96518.0490.1990.1990.0000.0000.0000.000
82A1237THR00.0320.02318.7260.0190.0190.0000.0000.0000.000
83A1238ILE00.009-0.00120.1720.0100.0100.0000.0000.0000.000
84A1239SER00.003-0.03222.9570.0110.0110.0000.0000.0000.000
85A1240ASN00.0080.00223.2270.0070.0070.0000.0000.0000.000
86A1241VAL00.0090.02524.1400.0070.0070.0000.0000.0000.000
87A1242LEU00.0210.00526.7700.0040.0040.0000.0000.0000.000
88A1243LEU0-0.0070.00428.2390.0030.0030.0000.0000.0000.000
89A1244GLN00.0490.02729.5000.0000.0000.0000.0000.0000.000
90A1245TYR00.004-0.01631.0480.0040.0040.0000.0000.0000.000
91A1246ALA0-0.033-0.02832.6580.0020.0020.0000.0000.0000.000
92A1247ASP-1-0.900-0.92534.065-0.033-0.0330.0000.0000.0000.000
93A1248ILE0-0.005-0.00633.8180.0020.0020.0000.0000.0000.000
94A1249VAL00.000-0.00237.1130.0020.0020.0000.0000.0000.000
95A1250SER0-0.020-0.05538.0170.0010.0010.0000.0000.0000.000
96A1251LYS10.8360.94438.6120.0310.0310.0000.0000.0000.000
97A1252ASP-1-0.886-0.94541.914-0.011-0.0110.0000.0000.0000.000
98A1253PHE00.0240.03943.1840.0020.0020.0000.0000.0000.000
99A1254ALA00.0240.00044.9830.0010.0010.0000.0000.0000.000
100A1255SER0-0.102-0.06247.0060.0010.0010.0000.0000.0000.000
101A1256TYR00.0510.00144.0610.0020.0020.0000.0000.0000.000
102A1257CYS0-0.055-0.00148.5710.0010.0010.0000.0000.0000.000
103A1258SER00.0570.03451.1580.0000.0000.0000.0000.0000.000
104A1259LYS10.9040.96754.1230.0120.0120.0000.0000.0000.000
105A1260GLU-1-0.986-1.00355.727-0.003-0.0030.0000.0000.0000.000
106A1261LYS10.8880.91752.0310.0010.0010.0000.0000.0000.000
107A1262GLU-1-0.787-0.91051.503-0.009-0.0090.0000.0000.0000.000
108A1263LYN0-0.0210.03946.860-0.001-0.0010.0000.0000.0000.000
109A1264VAL00.0470.02245.279-0.001-0.0010.0000.0000.0000.000
110A1265PRO00.0450.02345.293-0.001-0.0010.0000.0000.0000.000
111A1266CYS00.0030.00644.946-0.002-0.0020.0000.0000.0000.000
112A1267ILE00.0500.03041.952-0.001-0.0010.0000.0000.0000.000
113A1268LEU00.0050.00940.577-0.001-0.0010.0000.0000.0000.000
114A1269MET0-0.057-0.01740.057-0.002-0.0020.0000.0000.0000.000
115A1270ASN0-0.022-0.03739.957-0.004-0.0040.0000.0000.0000.000
116A1271ASN00.026-0.00236.9560.0000.0000.0000.0000.0000.000
117A1272THR0-0.0170.00235.680-0.002-0.0020.0000.0000.0000.000
118A1273GLN00.0250.02935.145-0.006-0.0060.0000.0000.0000.000
119A1274GLN00.0250.00433.972-0.004-0.0040.0000.0000.0000.000
120A1275LEU0-0.027-0.02831.0040.0000.0000.0000.0000.0000.000
121A1276ARG10.8820.92630.8450.0390.0390.0000.0000.0000.000
122A1277VAL0-0.0290.00831.274-0.004-0.0040.0000.0000.0000.000
123A1278GLN00.0250.00128.981-0.003-0.0030.0000.0000.0000.000
124A1279LEU00.0480.02225.3760.0000.0000.0000.0000.0000.000
125A1280GLU-1-0.954-0.97226.101-0.055-0.0550.0000.0000.0000.000
126A1281LYS10.9710.99326.990-0.002-0.0020.0000.0000.0000.000
127A1282MET0-0.081-0.04321.3050.0020.0020.0000.0000.0000.000
128A1283PHE0-0.105-0.04622.181-0.009-0.0090.0000.0000.0000.000
129A1284GLU-1-0.922-0.96922.697-0.049-0.0490.0000.0000.0000.000
130A1285ALA0-0.042-0.00821.1240.0010.0010.0000.0000.0000.000
131A1286MET0-0.060-0.03117.482-0.003-0.0030.0000.0000.0000.000
132A1287GLY00.0680.03917.556-0.027-0.0270.0000.0000.0000.000
133A1288GLY00.0280.00919.727-0.005-0.0050.0000.0000.0000.000
134A1289LYS10.8570.93322.1620.0960.0960.0000.0000.0000.000
135A1290GLU-1-0.978-0.99818.641-0.120-0.1200.0000.0000.0000.000
136A1291LEU0-0.054-0.00216.524-0.030-0.0300.0000.0000.0000.000
137A1292ASP-1-0.780-0.90414.474-0.393-0.3930.0000.0000.0000.000
138A1293ALA00.011-0.00116.5750.0340.0340.0000.0000.0000.000
139A1294GLU-1-0.920-0.95917.085-0.297-0.2970.0000.0000.0000.000
140A1295ALA00.0090.00516.3700.0300.0300.0000.0000.0000.000
141A1296SER00.0210.00518.4260.0320.0320.0000.0000.0000.000
142A1297GLY0-0.0110.01821.4950.0200.0200.0000.0000.0000.000
143A1298THR0-0.057-0.04321.0990.0180.0180.0000.0000.0000.000
144A1299LEU00.0390.01820.6440.0150.0150.0000.0000.0000.000
145A1300LYS10.9070.94324.3730.1230.1230.0000.0000.0000.000
146A1301GLU-1-0.914-0.95126.667-0.083-0.0830.0000.0000.0000.000
147A1302LEU0-0.0050.02325.5430.0070.0070.0000.0000.0000.000
148A1303GLN00.0340.00128.4720.0100.0100.0000.0000.0000.000
149A1304VAL0-0.026-0.00330.8560.0070.0070.0000.0000.0000.000
150A1305LYS10.9310.96029.0090.0900.0900.0000.0000.0000.000
151A1306LEU00.0070.01330.2260.0050.0050.0000.0000.0000.000
152A1307ASN0-0.035-0.01634.0700.0080.0080.0000.0000.0000.000
153A1308ASN00.0370.01136.5360.0040.0040.0000.0000.0000.000
154A1309VAL00.0710.05235.2710.0020.0020.0000.0000.0000.000
155A1310LEU0-0.033-0.01738.3570.0030.0030.0000.0000.0000.000
156A1311ASP-1-0.892-0.94940.165-0.034-0.0340.0000.0000.0000.000
157A1312GLU-1-0.957-0.96140.202-0.038-0.0380.0000.0000.0000.000
158A1313LEU0-0.003-0.00239.8010.0020.0020.0000.0000.0000.000
159A1314SER0-0.006-0.01944.0100.0020.0020.0000.0000.0000.000
160A1315HIS0-0.049-0.01546.1560.0020.0020.0000.0000.0000.000
161A1316VAL00.0030.00546.2930.0020.0020.0000.0000.0000.000
162A1317PHE00.0390.00947.6770.0020.0020.0000.0000.0000.000
163A1318ALA0-0.0200.04449.3720.0020.0020.0000.0000.0000.000
164A1319THR00.009-0.00351.2340.0010.0010.0000.0000.0000.000
165A1320SER0-0.118-0.09951.9510.0010.0010.0000.0000.0000.000
166A1321PHE0-0.053-0.05252.7220.0010.0010.0000.0000.0000.000
167A1322GLN0-0.0040.00156.3980.0000.0000.0000.0000.0000.000
168A1323PRO00.0090.00057.7510.0000.0000.0000.0000.0000.000
169A1324HIS00.0520.03760.2380.0000.0000.0000.0000.0000.000
170A1325ILE00.010-0.01257.7000.0000.0000.0000.0000.0000.000
171A1326GLU-1-0.927-0.98261.898-0.015-0.0150.0000.0000.0000.000
172A1327GLU-1-0.950-0.96364.058-0.009-0.0090.0000.0000.0000.000
173A1328CYS0-0.013-0.00464.9510.0010.0010.0000.0000.0000.000
174A1329VAL00.031-0.01564.1070.0000.0000.0000.0000.0000.000
175A1330ARG10.9270.97267.2360.0110.0110.0000.0000.0000.000
176A1331GLN00.0130.00369.9910.0000.0000.0000.0000.0000.000
177A1332MET0-0.068-0.00967.6460.0000.0000.0000.0000.0000.000
178A1333GLY00.0080.00571.3820.0000.0000.0000.0000.0000.000
179A1334ASP-1-0.859-0.92073.124-0.009-0.0090.0000.0000.0000.000
180A1335ILE00.0210.08473.5200.0000.0000.0000.0000.0000.000
181A1336LEU0-0.049-0.02973.1650.0000.0000.0000.0000.0000.000
182A1337SER0-0.145-0.13476.3540.0000.0000.0000.0000.0000.000
183A1338GLN0-0.061-0.03978.8570.0000.0000.0000.0000.0000.000
184A1339VAL0-0.0220.01579.0720.0000.0000.0000.0000.0000.000
185A1340LYS10.8810.93981.7010.0080.0080.0000.0000.0000.000
186A1352SER00.009-0.00381.4920.0000.0000.0000.0000.0000.000
187A1353VAL00.0490.00976.5980.0000.0000.0000.0000.0000.000
188A1354ALA00.010-0.01675.6100.0000.0000.0000.0000.0000.000
189A1355GLN0-0.0150.01775.4430.0000.0000.0000.0000.0000.000
190A1356ASP-1-0.906-0.96176.435-0.008-0.0080.0000.0000.0000.000
191A1357ALA0-0.027-0.02272.1470.0000.0000.0000.0000.0000.000
192A1358ASP-1-0.852-0.93772.084-0.008-0.0080.0000.0000.0000.000
193A1359ASN0-0.042-0.03072.6260.0000.0000.0000.0000.0000.000
194A1360VAL0-0.005-0.00470.9820.0000.0000.0000.0000.0000.000
195A1361LEU0-0.019-0.00666.7860.0000.0000.0000.0000.0000.000
196A1362GLN00.0290.02468.4060.0000.0000.0000.0000.0000.000
197A1363PRO0-0.033-0.02268.8830.0000.0000.0000.0000.0000.000
198A1364ILE00.000-0.00162.7460.0000.0000.0000.0000.0000.000
199A1365MET0-0.018-0.00963.8640.0000.0000.0000.0000.0000.000
200A1366ASP-1-0.913-0.93862.032-0.007-0.0070.0000.0000.0000.000
201A1367LEU00.0410.00357.4010.0000.0000.0000.0000.0000.000
202A1368LEU0-0.098-0.07159.7790.0000.0000.0000.0000.0000.000
203A1369ASP-1-0.860-0.91760.176-0.007-0.0070.0000.0000.0000.000
204A1370SER00.0580.06859.8490.0000.0000.0000.0000.0000.000
205A1371ASN00.0270.02256.3550.0000.0000.0000.0000.0000.000
206A1372LEU0-0.034-0.00855.0900.0000.0000.0000.0000.0000.000
207A1373THR0-0.021-0.04854.7670.0000.0000.0000.0000.0000.000
208A1374LEU0-0.055-0.03453.1470.0010.0010.0000.0000.0000.000
209A1375PHE00.004-0.02650.6300.0000.0000.0000.0000.0000.000
210A1376ALA0-0.054-0.02050.078-0.001-0.0010.0000.0000.0000.000
211A1377LYS10.9000.95650.4840.0030.0030.0000.0000.0000.000
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