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: M35VZ

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 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 235
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3071476.639339
FMO2-HF: Nuclear repulsion 2976182.820436
FMO2-HF: Total energy -95293.818903
FMO2-MP2: Total energy -95572.039975


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.
-7.795-2.88717.753-4.419-18.244-0.041
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 : 0.021 / q_NPA : -0.005
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-7PHE0-0.029-0.0233.414-1.823-0.2780.014-0.579-0.9800.002
4A-6GLN00.012-0.0012.765-0.8830.0860.283-0.336-0.9160.000
5A-5GLY00.0530.0324.2890.4110.5110.001-0.030-0.0710.000
6A-4PRO00.021-0.0077.5190.0010.0010.0000.0000.0000.000
7A-3HIS00.0150.0118.0340.0580.0580.0000.0000.0000.000
8A-2MET0-0.076-0.0353.723-0.264-0.0270.003-0.042-0.1970.000
9A-1LEU00.0140.0187.110-0.026-0.0260.0000.0000.0000.000
10A0GLU-1-0.927-0.9579.524-0.185-0.1850.0000.0000.0000.000
11A1093GLU-1-0.965-0.9859.052-0.198-0.1980.0000.0000.0000.000
12A1094ASN00.0150.0056.963-0.061-0.0610.0000.0000.0000.000
13A1095ILE00.0430.0282.753-0.658-0.0110.155-0.165-0.637-0.001
14A1096GLN0-0.006-0.0242.257-3.635-1.5844.702-2.519-4.235-0.016
15A1097GLU-1-0.956-0.9723.0301.002-0.2230.1401.261-0.1760.000
16A1098LYS10.9751.0076.1300.1760.1760.0000.0000.0000.000
17A1099ILE0-0.017-0.0242.350-0.195-0.3981.871-0.338-1.330-0.003
18A1100ALA0-0.039-0.0315.3420.0390.0390.0000.0000.0000.000
19A1101PHE0-0.038-0.0036.702-0.004-0.0040.0000.0000.0000.000
20A1102ILE0-0.0100.0098.670-0.004-0.0040.0000.0000.0000.000
21A1103PHE0-0.009-0.0256.8510.0040.0040.0000.0000.0000.000
22A1104ASN00.0240.01710.2570.0210.0210.0000.0000.0000.000
23A1105ASN0-0.013-0.00912.283-0.007-0.0070.0000.0000.0000.000
24A1106LEU00.0230.04213.590-0.007-0.0070.0000.0000.0000.000
25A1107SER0-0.028-0.03215.796-0.008-0.0080.0000.0000.0000.000
26A1108GLN00.050-0.00519.3470.0050.0050.0000.0000.0000.000
27A1109SER0-0.034-0.00421.938-0.001-0.0010.0000.0000.0000.000
28A1110ASN00.0070.00317.6960.0060.0060.0000.0000.0000.000
29A1111MET00.0250.03316.8390.0050.0050.0000.0000.0000.000
30A1112THR00.018-0.01217.6430.0090.0090.0000.0000.0000.000
31A1113GLN0-0.029-0.01916.9530.0050.0050.0000.0000.0000.000
32A1114LYS10.9290.96913.439-0.074-0.0740.0000.0000.0000.000
33A1115VAL0-0.050-0.02313.8550.0150.0150.0000.0000.0000.000
34A1116GLU-1-0.918-0.98215.1350.0890.0890.0000.0000.0000.000
35A1117GLU-1-0.800-0.88413.7870.0440.0440.0000.0000.0000.000
36A1118LEU0-0.038-0.0148.720-0.002-0.0020.0000.0000.0000.000
37A1119LYS10.8940.93911.724-0.110-0.1100.0000.0000.0000.000
38A1120GLU-1-0.960-0.94914.3580.0200.0200.0000.0000.0000.000
39A1121THR0-0.078-0.05111.434-0.019-0.0190.0000.0000.0000.000
40A1122VAL0-0.052-0.0297.444-0.042-0.0420.0000.0000.0000.000
41A1123LYS10.9590.99010.2230.0480.0480.0000.0000.0000.000
42A1124GLU-1-0.810-0.92410.0040.2510.2510.0000.0000.0000.000
43A1125GLU-1-0.913-0.96111.0800.1420.1420.0000.0000.0000.000
44A1126PHE0-0.048-0.0336.0310.0180.0180.0000.0000.0000.000
45A1127MET00.0210.0225.8390.2760.2760.0000.0000.0000.000
46A1128PRO00.029-0.0047.1170.1570.1570.0000.0000.0000.000
47A1129TRP00.0010.0012.163-1.4570.0421.588-0.756-2.3300.000
48A1130VAL00.0250.0182.487-1.472-0.3231.794-1.118-1.825-0.016
49A1131SER00.002-0.0054.979-0.140-0.070-0.001-0.002-0.0660.000
50A1132GLN0-0.022-0.0132.4411.0541.7770.642-0.301-1.0650.000
51A1133TYR0-0.012-0.0061.939-1.784-1.9756.254-2.239-3.825-0.007
52A1134LEU00.0150.0132.7042.113-0.6870.3052.799-0.3050.000
53A1135VAL00.0160.0056.477-0.167-0.1670.0000.0000.0000.000
54A1136MET00.0150.0055.105-0.156-0.1560.0000.0000.0000.000
55A1137LYS10.9240.9723.679-0.0450.2920.002-0.054-0.2860.000
56A1138ARG10.8610.9476.645-0.314-0.3140.0000.0000.0000.000
57A1139VAL00.0570.0319.168-0.067-0.0670.0000.0000.0000.000
58A1140SER0-0.032-0.0099.747-0.072-0.0720.0000.0000.0000.000
59A1141ILE0-0.028-0.01411.307-0.043-0.0430.0000.0000.0000.000
60A1142GLU-1-0.815-0.86212.4850.1380.1380.0000.0000.0000.000
61A1143PRO00.0530.00714.9260.0130.0130.0000.0000.0000.000
62A1144ASN0-0.042-0.02017.432-0.001-0.0010.0000.0000.0000.000
63A1145PHE00.0280.01515.084-0.007-0.0070.0000.0000.0000.000
64A1146HIS0-0.0250.00214.3400.0050.0050.0000.0000.0000.000
65A1147SER00.0580.00916.7340.0100.0100.0000.0000.0000.000
66A1148LEU0-0.0140.02716.570-0.002-0.0020.0000.0000.0000.000
67A1149TYR0-0.011-0.04912.1420.0120.0120.0000.0000.0000.000
68A1150SER0-0.014-0.00914.7690.0200.0200.0000.0000.0000.000
69A1151ASN00.005-0.02917.128-0.008-0.0080.0000.0000.0000.000
70A1152PHE00.0320.02511.915-0.004-0.0040.0000.0000.0000.000
71A1153LEU0-0.028-0.01712.4790.0000.0000.0000.0000.0000.000
72A1154ASP-1-0.893-0.93716.1300.1430.1430.0000.0000.0000.000
73A1155THR0-0.075-0.05318.541-0.016-0.0160.0000.0000.0000.000
74A1156LEU0-0.037-0.01013.278-0.011-0.0110.0000.0000.0000.000
75A1157LYS10.8870.95217.411-0.112-0.1120.0000.0000.0000.000
76A1158ASN00.0790.04614.388-0.011-0.0110.0000.0000.0000.000
77A1159PRO00.018-0.00416.1190.0310.0310.0000.0000.0000.000
78A1160GLU-1-0.878-0.94015.7460.2240.2240.0000.0000.0000.000
79A1161PHE00.005-0.0048.3780.0350.0350.0000.0000.0000.000
80A1162ASN00.013-0.00812.2300.0700.0700.0000.0000.0000.000
81A1163LYS10.9740.99314.531-0.229-0.2290.0000.0000.0000.000
82A1164MET0-0.042-0.0039.7590.0540.0540.0000.0000.0000.000
83A1165VAL00.0800.0459.7490.0560.0560.0000.0000.0000.000
84A1166LEU0-0.0060.02511.0470.0000.0000.0000.0000.0000.000
85A1167ASN0-0.012-0.02512.780-0.048-0.0480.0000.0000.0000.000
86A1168GLU-1-0.869-0.9367.0721.0041.0040.0000.0000.0000.000
87A1169THR0-0.023-0.02910.423-0.020-0.0200.0000.0000.0000.000
88A1170TYR00.016-0.00512.554-0.043-0.0430.0000.0000.0000.000
89A1171ARG10.8940.94810.081-0.603-0.6030.0000.0000.0000.000
90A1172ASN0-0.027-0.0277.961-0.097-0.0970.0000.0000.0000.000
91A1173ILE00.0040.01011.902-0.046-0.0460.0000.0000.0000.000
92A1174LYS10.9400.96415.447-0.215-0.2150.0000.0000.0000.000
93A1175VAL00.0100.04311.875-0.025-0.0250.0000.0000.0000.000
94A1176LEU00.0100.00814.426-0.025-0.0250.0000.0000.0000.000
95A1177LEU0-0.0380.00017.110-0.018-0.0180.0000.0000.0000.000
96A1178THR0-0.043-0.05218.209-0.014-0.0140.0000.0000.0000.000
97A1179SER0-0.017-0.00118.067-0.014-0.0140.0000.0000.0000.000
98A1180ASP-1-0.857-0.92920.0520.0230.0230.0000.0000.0000.000
99A1181LYS10.7900.90922.103-0.057-0.0570.0000.0000.0000.000
100A1182ALA0-0.009-0.01424.641-0.006-0.0060.0000.0000.0000.000
101A1183ALA00.0300.00225.7400.0040.0040.0000.0000.0000.000
102A1184ALA0-0.009-0.01226.9690.0010.0010.0000.0000.0000.000
103A1185ASN00.0750.03721.3820.0000.0000.0000.0000.0000.000
104A1186PHE00.0050.00422.8450.0080.0080.0000.0000.0000.000
105A1187SER00.034-0.00217.6190.0100.0100.0000.0000.0000.000
106A1188ASP-1-0.805-0.89717.1720.0470.0470.0000.0000.0000.000
107A1189ARG10.8930.96218.256-0.022-0.0220.0000.0000.0000.000
108A1190SER0-0.082-0.05218.9350.0080.0080.0000.0000.0000.000
109A1191LEU00.0240.02712.8420.0120.0120.0000.0000.0000.000
110A1192LEU00.0100.01715.7480.0250.0250.0000.0000.0000.000
111A1193LYS10.9320.96217.795-0.060-0.0600.0000.0000.0000.000
112A1194ASN0-0.026-0.01515.653-0.002-0.0020.0000.0000.0000.000
113A1195LEU00.0330.01211.4490.0170.0170.0000.0000.0000.000
114A1196GLY00.0380.02215.4140.0120.0120.0000.0000.0000.000
115A1197HIS0-0.059-0.04918.714-0.009-0.0090.0000.0000.0000.000
116A1198TRP0-0.006-0.00712.665-0.014-0.0140.0000.0000.0000.000
117A1199LEU00.0150.00716.7280.0070.0070.0000.0000.0000.000
118A1200GLY0-0.0020.03817.803-0.003-0.0030.0000.0000.0000.000
119A1201MET0-0.020-0.02118.739-0.012-0.0120.0000.0000.0000.000
120A1202ILE0-0.025-0.01214.747-0.006-0.0060.0000.0000.0000.000
121A1203THR0-0.042-0.03918.733-0.005-0.0050.0000.0000.0000.000
122A1204LEU00.0330.01521.426-0.011-0.0110.0000.0000.0000.000
123A1205ALA00.0030.00022.885-0.009-0.0090.0000.0000.0000.000
124A1206LYS10.8130.93918.857-0.178-0.1780.0000.0000.0000.000
125A1207ASN0-0.034-0.02024.098-0.004-0.0040.0000.0000.0000.000
126A1208LYS10.9190.95821.540-0.148-0.1480.0000.0000.0000.000
127A1209PRO00.0330.01124.2740.0030.0030.0000.0000.0000.000
128A1210ILE00.010-0.00121.9380.0100.0100.0000.0000.0000.000
129A1211LEU0-0.014-0.00223.244-0.013-0.0130.0000.0000.0000.000
130A1212HIS00.0370.01124.0840.0060.0060.0000.0000.0000.000
131A1213THR00.001-0.00123.071-0.003-0.0030.0000.0000.0000.000
132A1214ASP-1-0.986-0.96719.9030.1880.1880.0000.0000.0000.000
133A1215LEU0-0.018-0.04020.5660.0060.0060.0000.0000.0000.000
134A1216ASP-1-0.851-0.91822.8800.0770.0770.0000.0000.0000.000
135A1217VAL00.0320.00424.693-0.005-0.0050.0000.0000.0000.000
136A1218LYS10.9580.97426.892-0.062-0.0620.0000.0000.0000.000
137A1219SER00.0140.00729.177-0.007-0.0070.0000.0000.0000.000
138A1220LEU00.0270.02323.625-0.003-0.0030.0000.0000.0000.000
139A1221LEU0-0.029-0.02027.684-0.004-0.0040.0000.0000.0000.000
140A1222LEU0-0.033-0.01530.233-0.004-0.0040.0000.0000.0000.000
141A1223GLU-1-0.684-0.83327.6950.0610.0610.0000.0000.0000.000
142A1224ALA0-0.016-0.02928.352-0.004-0.0040.0000.0000.0000.000
143A1225TYR0-0.087-0.04730.078-0.004-0.0040.0000.0000.0000.000
144A1226VAL0-0.026-0.01132.984-0.003-0.0030.0000.0000.0000.000
145A1227LYS10.8590.96027.529-0.051-0.0510.0000.0000.0000.000
146A1228GLY00.0770.05732.505-0.003-0.0030.0000.0000.0000.000
147A1229GLN00.066-0.01031.7490.0050.0050.0000.0000.0000.000
148A1230GLN0-0.0180.00027.5790.0030.0030.0000.0000.0000.000
149A1231GLU-1-0.805-0.91226.8070.0410.0410.0000.0000.0000.000
150A1232LEU00.0120.01427.1250.0070.0070.0000.0000.0000.000
151A1233LEU0-0.099-0.05627.0450.0020.0020.0000.0000.0000.000
152A1234TYR0-0.030-0.01520.7320.0030.0030.0000.0000.0000.000
153A1235VAL00.0300.01923.7350.0080.0080.0000.0000.0000.000
154A1236VAL00.0090.01625.5510.0060.0060.0000.0000.0000.000
155A1237PRO00.0230.00224.8560.0030.0030.0000.0000.0000.000
156A1238PHE0-0.053-0.01318.9010.0060.0060.0000.0000.0000.000
157A1239VAL00.022-0.01023.1110.0080.0080.0000.0000.0000.000
158A1240ALA00.0100.00025.5290.0020.0020.0000.0000.0000.000
159A1241LYS10.8720.93621.753-0.079-0.0790.0000.0000.0000.000
160A1242VAL0-0.0040.01821.8090.0050.0050.0000.0000.0000.000
161A1243LEU00.0470.00323.1570.0010.0010.0000.0000.0000.000
162A1244GLU-1-0.873-0.91125.1250.0780.0780.0000.0000.0000.000
163A1245SER0-0.068-0.03123.153-0.001-0.0010.0000.0000.0000.000
164A1246SER0-0.060-0.04825.546-0.001-0.0010.0000.0000.0000.000
165A1247ILE00.0310.02928.612-0.003-0.0030.0000.0000.0000.000
166A1248ARG10.8930.94624.288-0.095-0.0950.0000.0000.0000.000
167A1249SER00.0210.03327.6550.0020.0020.0000.0000.0000.000
168A1250VAL0-0.009-0.01729.081-0.006-0.0060.0000.0000.0000.000
169A1251VAL0-0.025-0.01330.562-0.005-0.0050.0000.0000.0000.000
170A1252PHE0-0.0070.00227.246-0.003-0.0030.0000.0000.0000.000
171A1253ARG10.9631.03831.054-0.063-0.0630.0000.0000.0000.000
172A1254PRO00.0130.02433.079-0.001-0.0010.0000.0000.0000.000
173A1255PRO00.011-0.00236.0530.0000.0000.0000.0000.0000.000
174A1256ASN00.004-0.02932.9940.0000.0000.0000.0000.0000.000
175A1257PRO00.0540.01635.5900.0000.0000.0000.0000.0000.000
176A1258TRP00.0180.01126.372-0.002-0.0020.0000.0000.0000.000
177A1259THR00.003-0.04131.2200.0020.0020.0000.0000.0000.000
178A1260MET0-0.004-0.00232.409-0.002-0.0020.0000.0000.0000.000
179A1261ALA0-0.0360.00034.525-0.003-0.0030.0000.0000.0000.000
180A1262ILE0-0.024-0.01428.867-0.002-0.0020.0000.0000.0000.000
181A1263MET00.0180.00832.9220.0000.0000.0000.0000.0000.000
182A1264ASN00.0450.01834.747-0.003-0.0030.0000.0000.0000.000
183A1265VAL00.0080.01033.977-0.003-0.0030.0000.0000.0000.000
184A1266LEU0-0.018-0.01530.642-0.002-0.0020.0000.0000.0000.000
185A1267ALA00.0280.01634.926-0.002-0.0020.0000.0000.0000.000
186A1268GLU-1-0.802-0.89638.4360.0360.0360.0000.0000.0000.000
187A1269LEU0-0.025-0.02133.203-0.002-0.0020.0000.0000.0000.000
188A1270HIS0-0.072-0.03037.383-0.002-0.0020.0000.0000.0000.000
189A1271GLN0-0.064-0.02838.629-0.002-0.0020.0000.0000.0000.000
190A1272GLU-1-0.821-0.90939.5330.0290.0290.0000.0000.0000.000
191A1273HIS0-0.096-0.07040.8440.0010.0010.0000.0000.0000.000
192A1274ASP-1-0.884-0.94139.0360.0240.0240.0000.0000.0000.000
193A1275LEU0-0.078-0.00733.8410.0000.0000.0000.0000.0000.000
194A1276LYS10.9050.95731.203-0.034-0.0340.0000.0000.0000.000
195A1277LEU00.0790.01436.5520.0020.0020.0000.0000.0000.000
196A1278ASN00.0220.00631.3630.0010.0010.0000.0000.0000.000
197A1279LEU00.0060.00929.9000.0030.0030.0000.0000.0000.000
198A1280LYS10.9320.98233.290-0.026-0.0260.0000.0000.0000.000
199A1281PHE00.0160.00733.8400.0010.0010.0000.0000.0000.000
200A1282GLU-1-0.921-0.97228.0310.0600.0600.0000.0000.0000.000
201A1283ILE0-0.005-0.00732.0550.0030.0030.0000.0000.0000.000
202A1284GLU-1-0.860-0.91733.7600.0340.0340.0000.0000.0000.000
203A1285VAL0-0.056-0.02531.1930.0000.0000.0000.0000.0000.000
204A1286LEU0-0.020-0.00428.9450.0020.0020.0000.0000.0000.000
205A1287CYS0-0.029-0.01131.9890.0020.0020.0000.0000.0000.000
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207A1289ASN0-0.017-0.00230.206-0.001-0.0010.0000.0000.0000.000
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