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: 7G92K

Calculation Name: 4GML-A-Xray372

Preferred Name: CCR4-NOT transcription complex subunit 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4GML

Chain ID: A

ChEMBL ID: CHEMBL4105919

UniProt ID: A5YKK6

Base Structure: X-ray

Registration Date: 2023-06-20

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 235
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3074241.706997
FMO2-HF: Nuclear repulsion 2978946.550334
FMO2-HF: Total energy -95295.156663
FMO2-MP2: Total energy -95573.431878


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:-9:VAL)


Summations of interaction energy for fragment #1(A:-9:VAL)
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.
-10.908-2.1114.72-5.277-18.242-0.039
Interaction energy analysis for fragmet #1(A:-9:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / 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].
3A-7PHE0-0.016-0.0193.479-1.915-0.3280.009-0.634-0.9610.002
4A-6GLN0-0.0010.0052.566-1.405-0.1930.388-0.525-1.074-0.001
5A-5GLY00.0640.0334.3260.4280.5250.001-0.031-0.0670.000
6A-4PRO00.027-0.0097.480-0.029-0.0290.0000.0000.0000.000
7A-3HIS00.0160.0127.8410.0350.0350.0000.0000.0000.000
8A-2MET0-0.063-0.0273.711-0.200-0.0260.000-0.022-0.1520.000
9A-1LEU0-0.013-0.0017.103-0.064-0.0640.0000.0000.0000.000
10A0GLU-1-0.922-0.9549.523-0.228-0.2280.0000.0000.0000.000
11A1093GLU-1-0.834-0.9068.595-0.320-0.3200.0000.0000.0000.000
12A1094ASN00.0110.0036.999-0.106-0.1060.0000.0000.0000.000
13A1095ILE00.0480.0292.920-0.603-0.0080.085-0.148-0.5330.000
14A1096GLN00.0370.0042.274-3.370-0.8323.840-2.431-3.947-0.017
15A1097GLU-1-0.953-0.9722.9871.056-0.2760.1371.369-0.174-0.001
16A1098LYS10.8500.9236.0750.3770.3770.0000.0000.0000.000
17A1099ILE0-0.007-0.0192.708-0.678-0.0810.693-0.236-1.056-0.002
18A1100ALA0-0.041-0.0285.3330.0800.0800.0000.0000.0000.000
19A1101PHE0-0.007-0.0056.6440.0470.0470.0000.0000.0000.000
20A1102ILE0-0.0320.0058.6320.0250.0250.0000.0000.0000.000
21A1103PHE0-0.002-0.0206.7230.0340.0340.0000.0000.0000.000
22A1104ASN00.0150.0089.7830.0390.0390.0000.0000.0000.000
23A1105ASN0-0.012-0.00812.190-0.003-0.0030.0000.0000.0000.000
24A1106LEU00.0230.04113.250-0.001-0.0010.0000.0000.0000.000
25A1107SER0-0.019-0.03215.7030.0040.0040.0000.0000.0000.000
26A1108GLN00.051-0.00619.2500.0030.0030.0000.0000.0000.000
27A1109SER0-0.035-0.00721.8440.0010.0010.0000.0000.0000.000
28A1110ASN00.0190.01517.5750.0060.0060.0000.0000.0000.000
29A1111MET00.0250.03817.066-0.001-0.0010.0000.0000.0000.000
30A1112THR00.020-0.01017.5890.0010.0010.0000.0000.0000.000
31A1113GLN0-0.026-0.01816.5900.0030.0030.0000.0000.0000.000
32A1114LYS10.8470.91612.8400.0430.0430.0000.0000.0000.000
33A1115VAL0-0.034-0.01813.829-0.001-0.0010.0000.0000.0000.000
34A1116GLU-1-0.835-0.91315.1250.0250.0250.0000.0000.0000.000
35A1117GLU-1-0.759-0.84413.021-0.068-0.0680.0000.0000.0000.000
36A1118LEU0-0.023-0.0048.652-0.017-0.0170.0000.0000.0000.000
37A1119LYS10.8050.87411.683-0.043-0.0430.0000.0000.0000.000
38A1120GLU-1-0.974-0.95714.270-0.050-0.0500.0000.0000.0000.000
39A1121THR0-0.074-0.05911.564-0.023-0.0230.0000.0000.0000.000
40A1122VAL0-0.056-0.0287.148-0.065-0.0650.0000.0000.0000.000
41A1123LYS10.9590.99310.1600.1420.1420.0000.0000.0000.000
42A1124GLU-1-0.796-0.9249.9730.1400.1400.0000.0000.0000.000
43A1125GLU-1-0.913-0.95811.2240.0710.0710.0000.0000.0000.000
44A1126PHE0-0.046-0.0356.0430.0270.0270.0000.0000.0000.000
45A1127MET00.0020.0175.8230.1850.1850.0000.0000.0000.000
46A1128PRO00.0390.0017.0580.1110.1110.0000.0000.0000.000
47A1129TRP00.0010.0022.205-1.857-0.2461.641-0.828-2.4250.000
48A1130VAL00.0170.0142.571-1.483-0.5702.012-1.035-1.890-0.014
49A1131SER00.003-0.0044.890-0.229-0.146-0.001-0.004-0.0780.000
50A1132GLN0-0.036-0.0262.5550.7191.4510.628-0.294-1.065-0.001
51A1133TYR0-0.024-0.0042.018-1.920-1.1624.962-1.768-3.952-0.007
52A1134LEU00.0040.0072.8511.246-0.1950.2631.487-0.3090.001
53A1135VAL00.0040.0026.489-0.084-0.0840.0000.0000.0000.000
54A1136MET00.0010.0034.941-0.071-0.0710.0000.0000.0000.000
55A1137LYS10.8990.9582.907-0.800-0.1260.062-0.177-0.5590.001
56A1138ARG10.7960.9017.136-0.201-0.2010.0000.0000.0000.000
57A1139VAL00.0430.0239.536-0.040-0.0400.0000.0000.0000.000
58A1140SER0-0.020-0.0079.945-0.063-0.0630.0000.0000.0000.000
59A1141ILE0-0.011-0.00411.551-0.033-0.0330.0000.0000.0000.000
60A1142GLU-1-0.788-0.85013.0450.0590.0590.0000.0000.0000.000
61A1143PRO00.0520.01215.3340.0050.0050.0000.0000.0000.000
62A1144ASN0-0.057-0.02417.747-0.003-0.0030.0000.0000.0000.000
63A1145PHE00.0300.00915.362-0.008-0.0080.0000.0000.0000.000
64A1146HIS0-0.0050.01914.621-0.006-0.0060.0000.0000.0000.000
65A1147SER00.0320.00016.8560.0090.0090.0000.0000.0000.000
66A1148LEU0-0.0050.02216.0790.0000.0000.0000.0000.0000.000
67A1149TYR00.002-0.03012.2970.0010.0010.0000.0000.0000.000
68A1150SER0-0.007-0.00514.7340.0120.0120.0000.0000.0000.000
69A1151ASN0-0.004-0.01616.999-0.007-0.0070.0000.0000.0000.000
70A1152PHE00.0430.02412.006-0.002-0.0020.0000.0000.0000.000
71A1153LEU0-0.013-0.00812.111-0.002-0.0020.0000.0000.0000.000
72A1154ASP-1-0.854-0.91115.8030.1050.1050.0000.0000.0000.000
73A1155THR0-0.069-0.04918.514-0.010-0.0100.0000.0000.0000.000
74A1156LEU0-0.020-0.00413.206-0.007-0.0070.0000.0000.0000.000
75A1157LYS10.8830.95517.367-0.066-0.0660.0000.0000.0000.000
76A1158ASN00.0810.04814.6230.0070.0070.0000.0000.0000.000
77A1159PRO00.0320.00716.0010.0260.0260.0000.0000.0000.000
78A1160GLU-1-0.796-0.89915.7820.2210.2210.0000.0000.0000.000
79A1161PHE00.0250.0018.1580.0400.0400.0000.0000.0000.000
80A1162ASN00.002-0.01412.1330.0580.0580.0000.0000.0000.000
81A1163LYS10.8550.93314.354-0.212-0.2120.0000.0000.0000.000
82A1164MET0-0.0050.0219.7380.0510.0510.0000.0000.0000.000
83A1165VAL00.0630.0359.1890.0720.0720.0000.0000.0000.000
84A1166LEU00.0040.02010.8280.0180.0180.0000.0000.0000.000
85A1167ASN0-0.054-0.04812.896-0.020-0.0200.0000.0000.0000.000
86A1168GLU-1-0.788-0.8626.9411.1271.1270.0000.0000.0000.000
87A1169THR0-0.019-0.02010.382-0.005-0.0050.0000.0000.0000.000
88A1170TYR0-0.055-0.04912.441-0.031-0.0310.0000.0000.0000.000
89A1171ARG10.8410.8929.257-0.736-0.7360.0000.0000.0000.000
90A1172ASN0-0.031-0.0307.764-0.076-0.0760.0000.0000.0000.000
91A1173ILE00.0070.00911.793-0.048-0.0480.0000.0000.0000.000
92A1174LYS10.9260.94515.333-0.246-0.2460.0000.0000.0000.000
93A1175VAL0-0.0010.03411.975-0.027-0.0270.0000.0000.0000.000
94A1176LEU00.0020.00314.116-0.030-0.0300.0000.0000.0000.000
95A1177LEU0-0.034-0.00217.022-0.022-0.0220.0000.0000.0000.000
96A1178THR0-0.027-0.03618.244-0.015-0.0150.0000.0000.0000.000
97A1179SER0-0.040-0.00718.059-0.015-0.0150.0000.0000.0000.000
98A1180ASP-1-0.858-0.93320.0080.0590.0590.0000.0000.0000.000
99A1181LYS10.7470.88121.968-0.093-0.0930.0000.0000.0000.000
100A1182ALA0-0.004-0.01524.572-0.008-0.0080.0000.0000.0000.000
101A1183ALA00.0160.00825.6480.0040.0040.0000.0000.0000.000
102A1184ALA0-0.024-0.01326.8730.0000.0000.0000.0000.0000.000
103A1185ASN00.0300.00920.724-0.007-0.0070.0000.0000.0000.000
104A1186PHE00.0250.00122.7260.0080.0080.0000.0000.0000.000
105A1187SER00.0320.00317.4020.0070.0070.0000.0000.0000.000
106A1188ASP-1-0.780-0.88016.9520.0970.0970.0000.0000.0000.000
107A1189ARG10.9060.96718.144-0.044-0.0440.0000.0000.0000.000
108A1190SER0-0.065-0.04919.1770.0040.0040.0000.0000.0000.000
109A1191LEU00.0260.03412.5210.0060.0060.0000.0000.0000.000
110A1192LEU00.0150.01515.6840.0210.0210.0000.0000.0000.000
111A1193LYS10.8940.94717.641-0.079-0.0790.0000.0000.0000.000
112A1194ASN0-0.040-0.02615.886-0.008-0.0080.0000.0000.0000.000
113A1195LEU00.0370.01411.4210.0090.0090.0000.0000.0000.000
114A1196GLY00.0430.01915.5220.0070.0070.0000.0000.0000.000
115A1197HIS0-0.021-0.03118.991-0.012-0.0120.0000.0000.0000.000
116A1198TRP0-0.023-0.01412.346-0.022-0.0220.0000.0000.0000.000
117A1199LEU00.0250.00916.7910.0020.0020.0000.0000.0000.000
118A1200GLY00.0050.03317.766-0.005-0.0050.0000.0000.0000.000
119A1201MET0-0.038-0.02518.601-0.012-0.0120.0000.0000.0000.000
120A1202ILE0-0.006-0.00514.421-0.010-0.0100.0000.0000.0000.000
121A1203THR0-0.040-0.03018.543-0.004-0.0040.0000.0000.0000.000
122A1204LEU00.0430.02321.212-0.012-0.0120.0000.0000.0000.000
123A1205ALA00.0090.00622.742-0.009-0.0090.0000.0000.0000.000
124A1206LYS10.7560.90019.086-0.130-0.1300.0000.0000.0000.000
125A1207ASN0-0.029-0.02623.847-0.002-0.0020.0000.0000.0000.000
126A1208LYS10.9000.94521.306-0.120-0.1200.0000.0000.0000.000
127A1209PRO00.0290.01124.0260.0030.0030.0000.0000.0000.000
128A1210ILE00.0020.00121.7090.0090.0090.0000.0000.0000.000
129A1211LEU0-0.0060.00623.150-0.013-0.0130.0000.0000.0000.000
130A1212HIS00.0280.00223.9850.0070.0070.0000.0000.0000.000
131A1213THR0-0.0080.00023.260-0.005-0.0050.0000.0000.0000.000
132A1214ASP-1-0.883-0.91819.7050.1930.1930.0000.0000.0000.000
133A1215LEU0-0.016-0.02020.4060.0120.0120.0000.0000.0000.000
134A1216ASP-1-0.828-0.89822.7640.0840.0840.0000.0000.0000.000
135A1217VAL00.0360.00524.516-0.004-0.0040.0000.0000.0000.000
136A1218LYS10.9610.97526.753-0.070-0.0700.0000.0000.0000.000
137A1219SER00.0210.00528.960-0.007-0.0070.0000.0000.0000.000
138A1220LEU00.0280.02523.436-0.002-0.0020.0000.0000.0000.000
139A1221LEU0-0.040-0.02127.566-0.003-0.0030.0000.0000.0000.000
140A1222LEU0-0.038-0.02030.102-0.005-0.0050.0000.0000.0000.000
141A1223GLU-1-0.672-0.82327.2990.0860.0860.0000.0000.0000.000
142A1224ALA0-0.020-0.02728.183-0.003-0.0030.0000.0000.0000.000
143A1225TYR0-0.094-0.07029.970-0.004-0.0040.0000.0000.0000.000
144A1226VAL0-0.015-0.00833.233-0.004-0.0040.0000.0000.0000.000
145A1227LYS10.7900.90327.760-0.078-0.0780.0000.0000.0000.000
146A1228GLY00.0510.04132.424-0.003-0.0030.0000.0000.0000.000
147A1229GLN00.038-0.03731.6450.0060.0060.0000.0000.0000.000
148A1230GLN0-0.0020.00327.6160.0020.0020.0000.0000.0000.000
149A1231GLU-1-0.742-0.87326.3600.0740.0740.0000.0000.0000.000
150A1232LEU0-0.0080.00527.0060.0060.0060.0000.0000.0000.000
151A1233LEU0-0.099-0.05326.9250.0010.0010.0000.0000.0000.000
152A1234TYR00.001-0.00320.530-0.001-0.0010.0000.0000.0000.000
153A1235VAL00.0250.01723.5920.0080.0080.0000.0000.0000.000
154A1236VAL00.0040.01225.4120.0040.0040.0000.0000.0000.000
155A1237PRO00.0270.00624.8070.0010.0010.0000.0000.0000.000
156A1238PHE0-0.037-0.00618.8780.0040.0040.0000.0000.0000.000
157A1239VAL00.025-0.00823.0880.0060.0060.0000.0000.0000.000
158A1240ALA00.003-0.00125.4740.0000.0000.0000.0000.0000.000
159A1241LYS10.8030.89022.131-0.078-0.0780.0000.0000.0000.000
160A1242VAL0-0.0060.01521.8410.0020.0020.0000.0000.0000.000
161A1243LEU00.0410.00223.225-0.001-0.0010.0000.0000.0000.000
162A1244GLU-1-0.819-0.88325.4050.0710.0710.0000.0000.0000.000
163A1245SER0-0.049-0.02623.018-0.004-0.0040.0000.0000.0000.000
164A1246SER0-0.062-0.04425.548-0.002-0.0020.0000.0000.0000.000
165A1247ILE00.0360.02728.565-0.003-0.0030.0000.0000.0000.000
166A1248ARG10.8520.93623.370-0.087-0.0870.0000.0000.0000.000
167A1249SER00.0170.02827.6260.0010.0010.0000.0000.0000.000
168A1250VAL0-0.017-0.01528.941-0.005-0.0050.0000.0000.0000.000
169A1251VAL0-0.022-0.00630.488-0.004-0.0040.0000.0000.0000.000
170A1252PHE0-0.0020.00227.046-0.002-0.0020.0000.0000.0000.000
171A1253ARG10.9401.00730.914-0.054-0.0540.0000.0000.0000.000
172A1254PRO00.0140.02332.9960.0000.0000.0000.0000.0000.000
173A1255PRO0-0.004-0.00836.000-0.001-0.0010.0000.0000.0000.000
174A1256ASN00.020-0.01833.0290.0010.0010.0000.0000.0000.000
175A1257PRO00.0590.01635.4950.0010.0010.0000.0000.0000.000
176A1258TRP00.0100.00626.153-0.002-0.0020.0000.0000.0000.000
177A1259THR00.003-0.03630.8170.0030.0030.0000.0000.0000.000
178A1260MET0-0.005-0.00232.350-0.002-0.0020.0000.0000.0000.000
179A1261ALA0-0.042-0.00734.476-0.002-0.0020.0000.0000.0000.000
180A1262ILE0-0.018-0.01028.839-0.001-0.0010.0000.0000.0000.000
181A1263MET00.0260.01632.9150.0000.0000.0000.0000.0000.000
182A1264ASN00.0420.02034.773-0.004-0.0040.0000.0000.0000.000
183A1265VAL00.0180.01433.836-0.002-0.0020.0000.0000.0000.000
184A1266LEU0-0.013-0.01130.613-0.001-0.0010.0000.0000.0000.000
185A1267ALA00.0330.01634.802-0.002-0.0020.0000.0000.0000.000
186A1268GLU-1-0.796-0.90238.2640.0420.0420.0000.0000.0000.000
187A1269LEU0-0.018-0.01733.083-0.002-0.0020.0000.0000.0000.000
188A1270HIS0-0.056-0.02737.235-0.002-0.0020.0000.0000.0000.000
189A1271GLN0-0.033-0.00438.489-0.002-0.0020.0000.0000.0000.000
190A1272GLU-1-0.737-0.84639.4030.0370.0370.0000.0000.0000.000
191A1273HIS0-0.045-0.02740.7010.0010.0010.0000.0000.0000.000
192A1274ASP-1-0.874-0.91738.1540.0360.0360.0000.0000.0000.000
193A1275LEU0-0.054-0.00333.6800.0010.0010.0000.0000.0000.000
194A1276LYS10.9040.95731.113-0.049-0.0490.0000.0000.0000.000
195A1277LEU00.0830.01836.4010.0020.0020.0000.0000.0000.000
196A1278ASN00.0200.00030.855-0.001-0.0010.0000.0000.0000.000
197A1279LEU0-0.0090.00429.6740.0020.0020.0000.0000.0000.000
198A1280LYS10.8530.91733.170-0.034-0.0340.0000.0000.0000.000
199A1281PHE00.0140.00733.9170.0000.0000.0000.0000.0000.000
200A1282GLU-1-0.885-0.95428.2120.0660.0660.0000.0000.0000.000
201A1283ILE0-0.007-0.00732.2030.0020.0020.0000.0000.0000.000
202A1284GLU-1-0.842-0.90233.8300.0360.0360.0000.0000.0000.000
203A1285VAL0-0.038-0.01831.470-0.001-0.0010.0000.0000.0000.000
204A1286LEU0-0.0170.00129.0860.0010.0010.0000.0000.0000.000
205A1287CYS0-0.043-0.02532.1900.0010.0010.0000.0000.0000.000
206A1288LYS10.9470.98135.493-0.036-0.0360.0000.0000.0000.000
207A1289ASN0-0.0270.00129.739-0.004-0.0040.0000.0000.0000.000
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