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: LJLZ9

Calculation Name: 4GML-A-Xray321

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: 2021-09-07

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. 1.20200129
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. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -3071133.913626
FMO2-HF: Nuclear repulsion 2975840.853569
FMO2-HF: Total energy -95293.060056
FMO2-MP2: Total energy -95571.263924


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.
-7.627-2.77518.019-4.681-18.184-0.042
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 : 0.016 / q_NPA : -0.007
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-7PHE 0-0.027-0.0223.414-1.827-0.3140.017-0.582-0.9470.001
4A-6GLN 00.007-0.0022.765-0.8840.0730.282-0.326-0.9130.000
5A-5GLY 00.0560.0314.2890.4250.5290.002-0.029-0.0760.000
6A-4PRO 00.020-0.0077.5190.0120.0120.0000.0000.0000.000
7A-3HIS 00.0140.0118.0340.0590.0590.0000.0000.0000.000
8A-2MET 0-0.076-0.0353.720-0.258-0.0240.004-0.043-0.1940.000
9A-1LEU 00.0140.0187.110-0.015-0.0150.0000.0000.0000.000
10A0GLU -1-0.927-0.9579.524-0.171-0.1710.0000.0000.0000.000
11A1093GLU -1-0.964-0.9859.051-0.182-0.1820.0000.0000.0000.000
12A1094ASN 00.0130.0046.962-0.053-0.0530.0000.0000.0000.000
13A1095ILE 00.0410.0272.753-0.654-0.0070.157-0.167-0.638-0.001
14A1096GLN 0-0.005-0.0242.257-3.619-1.5814.762-2.571-4.229-0.016
15A1097GLU -1-0.951-0.9703.0300.973-0.2460.1461.256-0.1830.000
16A1098LYS 10.9751.0076.1300.1550.1550.0000.0000.0000.000
17A1099ILE 0-0.019-0.0252.350-0.202-0.4051.873-0.343-1.326-0.003
18A1100ALA 0-0.036-0.0305.3410.0290.0290.0000.0000.0000.000
19A1101PHE 0-0.039-0.0036.701-0.007-0.0070.0000.0000.0000.000
20A1102ILE 0-0.0110.0098.670-0.004-0.0040.0000.0000.0000.000
21A1103PHE 0-0.012-0.0266.8520.0030.0030.0000.0000.0000.000
22A1104ASN 00.0260.01810.2560.0170.0170.0000.0000.0000.000
23A1105ASN 0-0.014-0.01012.283-0.007-0.0070.0000.0000.0000.000
24A1106LEU 00.0220.04313.590-0.006-0.0060.0000.0000.0000.000
25A1107SER 0-0.023-0.03215.796-0.008-0.0080.0000.0000.0000.000
26A1108GLN 00.050-0.00419.3470.0050.0050.0000.0000.0000.000
27A1109SER 0-0.036-0.00421.938-0.001-0.0010.0000.0000.0000.000
28A1110ASN 00.0050.00117.6960.0060.0060.0000.0000.0000.000
29A1111MET 00.0250.03416.8390.0050.0050.0000.0000.0000.000
30A1112THR 00.019-0.01217.6440.0090.0090.0000.0000.0000.000
31A1113GLN 0-0.030-0.01916.9450.0050.0050.0000.0000.0000.000
32A1114LYS 10.9300.96913.439-0.071-0.0710.0000.0000.0000.000
33A1115VAL 0-0.053-0.02413.8550.0150.0150.0000.0000.0000.000
34A1116GLU -1-0.918-0.98215.1360.0870.0870.0000.0000.0000.000
35A1117GLU -1-0.798-0.88413.7870.0450.0450.0000.0000.0000.000
36A1118LEU 0-0.041-0.0148.720-0.001-0.0010.0000.0000.0000.000
37A1119LYS 10.8940.93911.725-0.107-0.1070.0000.0000.0000.000
38A1120GLU -1-0.956-0.94814.3580.0210.0210.0000.0000.0000.000
39A1121THR 0-0.083-0.05311.435-0.018-0.0180.0000.0000.0000.000
40A1122VAL 0-0.052-0.0297.445-0.039-0.0390.0000.0000.0000.000
41A1123LYS 10.9600.98910.2230.0400.0400.0000.0000.0000.000
42A1124GLU -1-0.809-0.92410.0040.2520.2520.0000.0000.0000.000
43A1125GLU -1-0.914-0.96111.0790.1440.1440.0000.0000.0000.000
44A1126PHE 0-0.050-0.0346.0310.0210.0210.0000.0000.0000.000
45A1127MET 00.0210.0225.8390.2790.2790.0000.0000.0000.000
46A1128PRO 00.032-0.0047.1170.1580.1580.0000.0000.0000.000
47A1129TRP 00.0030.0022.163-1.4420.0521.592-0.761-2.3260.000
48A1130VAL 00.0250.0172.488-1.573-0.3941.795-1.146-1.828-0.016
49A1131SER 00.008-0.0034.979-0.151-0.0830.000-0.003-0.0640.000
50A1132GLN 0-0.026-0.0142.4411.0771.7980.645-0.305-1.0600.000
51A1133TYR 0-0.010-0.0071.938-1.758-1.9876.403-2.354-3.819-0.007
52A1134LEU 00.0120.0122.7042.129-0.6590.3382.746-0.2960.000
53A1135VAL 00.0100.0036.477-0.160-0.1600.0000.0000.0000.000
54A1136MET 00.0220.0095.104-0.150-0.1500.0000.0000.0000.000
55A1137LYS 10.9250.9723.6790.0100.3460.003-0.053-0.2850.000
56A1138ARG 10.8520.9436.645-0.283-0.2830.0000.0000.0000.000
57A1139VAL 00.0640.0339.168-0.062-0.0620.0000.0000.0000.000
58A1140SER 0-0.037-0.0099.747-0.068-0.0680.0000.0000.0000.000
59A1141ILE 0-0.018-0.00911.307-0.041-0.0410.0000.0000.0000.000
60A1142GLU -1-0.818-0.86412.4850.1240.1240.0000.0000.0000.000
61A1143PRO 00.0500.00614.9260.0120.0120.0000.0000.0000.000
62A1144ASN 0-0.041-0.01917.432-0.001-0.0010.0000.0000.0000.000
63A1145PHE 00.0280.01415.084-0.006-0.0060.0000.0000.0000.000
64A1146HIS 0-0.0230.00314.3400.0060.0060.0000.0000.0000.000
65A1147SER 00.0620.01016.7340.0090.0090.0000.0000.0000.000
66A1148LEU 0-0.0170.02716.570-0.001-0.0010.0000.0000.0000.000
67A1149TYR 0-0.012-0.04912.1420.0130.0130.0000.0000.0000.000
68A1150SER 0-0.010-0.00714.7690.0190.0190.0000.0000.0000.000
69A1151ASN 00.001-0.03017.128-0.007-0.0070.0000.0000.0000.000
70A1152PHE 00.0320.02411.916-0.003-0.0030.0000.0000.0000.000
71A1153LEU 0-0.026-0.01612.4790.0010.0010.0000.0000.0000.000
72A1154ASP -1-0.891-0.93616.1300.1370.1370.0000.0000.0000.000
73A1155THR 0-0.079-0.05518.542-0.015-0.0150.0000.0000.0000.000
74A1156LEU 0-0.044-0.01313.278-0.010-0.0100.0000.0000.0000.000
75A1157LYS 10.8930.95517.412-0.108-0.1080.0000.0000.0000.000
76A1158ASN 00.0750.04314.386-0.010-0.0100.0000.0000.0000.000
77A1159PRO 00.018-0.00516.1190.0300.0300.0000.0000.0000.000
78A1160GLU -1-0.878-0.93915.7450.2190.2190.0000.0000.0000.000
79A1161PHE 00.005-0.0048.3780.0350.0350.0000.0000.0000.000
80A1162ASN 00.015-0.00712.2310.0670.0670.0000.0000.0000.000
81A1163LYS 10.9730.99314.532-0.223-0.2230.0000.0000.0000.000
82A1164MET 0-0.045-0.0049.7590.0550.0550.0000.0000.0000.000
83A1165VAL 00.0810.0449.7490.0550.0550.0000.0000.0000.000
84A1166LEU 0-0.0060.02611.047-0.003-0.0030.0000.0000.0000.000
85A1167ASN 0-0.010-0.02512.780-0.047-0.0470.0000.0000.0000.000
86A1168GLU -1-0.870-0.9367.0720.9780.9780.0000.0000.0000.000
87A1169THR 0-0.029-0.03110.423-0.023-0.0230.0000.0000.0000.000
88A1170TYR 00.019-0.00512.554-0.043-0.0430.0000.0000.0000.000
89A1171ARG 10.8970.94910.081-0.585-0.5850.0000.0000.0000.000
90A1172ASN 0-0.032-0.0307.960-0.095-0.0950.0000.0000.0000.000
91A1173ILE 00.0010.00711.902-0.046-0.0460.0000.0000.0000.000
92A1174LYS 10.9420.96515.446-0.206-0.2060.0000.0000.0000.000
93A1175VAL 00.0040.04211.875-0.023-0.0230.0000.0000.0000.000
94A1176LEU 00.0050.00414.425-0.024-0.0240.0000.0000.0000.000
95A1177LEU 0-0.048-0.00717.109-0.016-0.0160.0000.0000.0000.000
96A1178THR 0-0.031-0.04318.211-0.012-0.0120.0000.0000.0000.000
97A1179SER 0-0.043-0.01118.066-0.013-0.0130.0000.0000.0000.000
98A1180ASP -1-0.836-0.91220.0520.0200.0200.0000.0000.0000.000
99A1181LYS 10.7950.90522.103-0.053-0.0530.0000.0000.0000.000
100A1182ALA 0-0.014-0.01924.641-0.006-0.0060.0000.0000.0000.000
101A1183ALA 00.024-0.00125.7400.0040.0040.0000.0000.0000.000
102A1184ALA 0-0.014-0.01426.9690.0010.0010.0000.0000.0000.000
103A1185ASN 00.0770.03721.3820.0000.0000.0000.0000.0000.000
104A1186PHE 00.0040.00322.8440.0080.0080.0000.0000.0000.000
105A1187SER 00.028-0.00617.6180.0100.0100.0000.0000.0000.000
106A1188ASP -1-0.800-0.89417.1710.0400.0400.0000.0000.0000.000
107A1189ARG 10.8960.96418.255-0.018-0.0180.0000.0000.0000.000
108A1190SER 0-0.086-0.05418.9340.0080.0080.0000.0000.0000.000
109A1191LEU 00.0210.02512.8420.0120.0120.0000.0000.0000.000
110A1192LEU 00.0160.02015.7480.0240.0240.0000.0000.0000.000
111A1193LYS 10.9330.96317.794-0.055-0.0550.0000.0000.0000.000
112A1194ASN 0-0.032-0.01815.653-0.001-0.0010.0000.0000.0000.000
113A1195LEU 00.0340.01211.4490.0180.0180.0000.0000.0000.000
114A1196GLY 00.0420.02315.4140.0110.0110.0000.0000.0000.000
115A1197HIS 0-0.063-0.05118.714-0.008-0.0080.0000.0000.0000.000
116A1198TRP 0-0.007-0.00812.665-0.011-0.0110.0000.0000.0000.000
117A1199LEU 00.0190.00816.7280.0080.0080.0000.0000.0000.000
118A1200GLY 0-0.0010.03717.803-0.003-0.0030.0000.0000.0000.000
119A1201MET 0-0.025-0.02218.739-0.011-0.0110.0000.0000.0000.000
120A1202ILE 0-0.026-0.01314.747-0.005-0.0050.0000.0000.0000.000
121A1203THR 0-0.040-0.03818.733-0.005-0.0050.0000.0000.0000.000
122A1204LEU 00.0310.01521.426-0.011-0.0110.0000.0000.0000.000
123A1205ALA 00.0000.00022.885-0.008-0.0080.0000.0000.0000.000
124A1206LYS 10.8160.94018.858-0.170-0.1700.0000.0000.0000.000
125A1207ASN 0-0.034-0.02024.098-0.004-0.0040.0000.0000.0000.000
126A1208LYS 10.9160.95621.540-0.142-0.1420.0000.0000.0000.000
127A1209PRO 00.0320.00924.2740.0030.0030.0000.0000.0000.000
128A1210ILE 00.0090.00021.9380.0100.0100.0000.0000.0000.000
129A1211LEU 0-0.015-0.00423.244-0.013-0.0130.0000.0000.0000.000
130A1212HIS 00.0390.01224.0830.0060.0060.0000.0000.0000.000
131A1213THR 0-0.002-0.00123.071-0.002-0.0020.0000.0000.0000.000
132A1214ASP -1-0.990-0.96919.9030.1820.1820.0000.0000.0000.000
133A1215LEU 0-0.012-0.03720.5650.0060.0060.0000.0000.0000.000
134A1216ASP -1-0.855-0.92122.8800.0730.0730.0000.0000.0000.000
135A1217VAL 00.0320.00424.692-0.005-0.0050.0000.0000.0000.000
136A1218LYS 10.9530.97126.892-0.060-0.0600.0000.0000.0000.000
137A1219SER 00.0140.00729.176-0.007-0.0070.0000.0000.0000.000
138A1220LEU 00.0340.02823.625-0.003-0.0030.0000.0000.0000.000
139A1221LEU 0-0.037-0.02327.683-0.004-0.0040.0000.0000.0000.000
140A1222LEU 0-0.033-0.01830.232-0.004-0.0040.0000.0000.0000.000
141A1223GLU -1-0.686-0.83327.6940.0580.0580.0000.0000.0000.000
142A1224ALA 0-0.004-0.02128.351-0.003-0.0030.0000.0000.0000.000
143A1225TYR 0-0.099-0.05330.078-0.004-0.0040.0000.0000.0000.000
144A1226VAL 0-0.033-0.01632.983-0.003-0.0030.0000.0000.0000.000
145A1227LYS 10.8650.96427.543-0.048-0.0480.0000.0000.0000.000
146A1228GLY 00.0720.05432.504-0.003-0.0030.0000.0000.0000.000
147A1229GLN 00.053-0.01831.7490.0050.0050.0000.0000.0000.000
148A1230GLN 0-0.0180.00027.5780.0030.0030.0000.0000.0000.000
149A1231GLU -1-0.780-0.89726.8070.0380.0380.0000.0000.0000.000
150A1232LEU 00.0050.00927.1240.0060.0060.0000.0000.0000.000
151A1233LEU 0-0.101-0.05927.0450.0020.0020.0000.0000.0000.000
152A1234TYR 0-0.031-0.01420.7320.0030.0030.0000.0000.0000.000
153A1235VAL 00.0320.02023.7340.0080.0080.0000.0000.0000.000
154A1236VAL 00.0070.01525.5510.0060.0060.0000.0000.0000.000
155A1237PRO 00.0190.00024.8560.0030.0030.0000.0000.0000.000
156A1238PHE 0-0.050-0.01018.9010.0060.0060.0000.0000.0000.000
157A1239VAL 00.021-0.01123.1110.0080.0080.0000.0000.0000.000
158A1240ALA 00.009-0.00125.5290.0020.0020.0000.0000.0000.000
159A1241LYS 10.8740.93721.753-0.073-0.0730.0000.0000.0000.000
160A1242VAL 0-0.0040.01921.8090.0050.0050.0000.0000.0000.000
161A1243LEU 00.0440.00223.1570.0010.0010.0000.0000.0000.000
162A1244GLU -1-0.872-0.91025.1250.0730.0730.0000.0000.0000.000
163A1245SER 0-0.074-0.03423.153-0.001-0.0010.0000.0000.0000.000
164A1246SER 0-0.056-0.04825.546-0.001-0.0010.0000.0000.0000.000
165A1247ILE 00.0300.02928.612-0.003-0.0030.0000.0000.0000.000
166A1248ARG 10.8910.94524.288-0.090-0.0900.0000.0000.0000.000
167A1249SER 00.0260.03627.6550.0020.0020.0000.0000.0000.000
168A1250VAL 0-0.013-0.01829.081-0.006-0.0060.0000.0000.0000.000
169A1251VAL 0-0.028-0.01430.563-0.005-0.0050.0000.0000.0000.000
170A1252PHE 0-0.0050.00327.246-0.003-0.0030.0000.0000.0000.000
171A1253ARG 10.9611.03831.054-0.060-0.0600.0000.0000.0000.000
172A1254PRO 00.0140.02533.079-0.001-0.0010.0000.0000.0000.000
173A1255PRO 00.010-0.00436.0530.0000.0000.0000.0000.0000.000
174A1256ASN 00.002-0.02932.9940.0000.0000.0000.0000.0000.000
175A1257PRO 00.0530.01535.5900.0000.0000.0000.0000.0000.000
176A1258TRP 00.0200.01326.372-0.002-0.0020.0000.0000.0000.000
177A1259THR 00.004-0.04131.2200.0020.0020.0000.0000.0000.000
178A1260MET 0-0.013-0.00632.409-0.002-0.0020.0000.0000.0000.000
179A1261ALA 0-0.0300.00234.525-0.003-0.0030.0000.0000.0000.000
180A1262ILE 0-0.021-0.01228.868-0.002-0.0020.0000.0000.0000.000
181A1263MET 00.0150.00732.922-0.001-0.0010.0000.0000.0000.000
182A1264ASN 00.0430.01734.747-0.003-0.0030.0000.0000.0000.000
183A1265VAL 00.0110.01133.976-0.002-0.0020.0000.0000.0000.000
184A1266LEU 0-0.014-0.01230.642-0.002-0.0020.0000.0000.0000.000
185A1267ALA 00.0270.01534.926-0.002-0.0020.0000.0000.0000.000
186A1268GLU -1-0.800-0.89638.4350.0340.0340.0000.0000.0000.000
187A1269LEU 0-0.026-0.02133.202-0.002-0.0020.0000.0000.0000.000
188A1270HIS 0-0.075-0.03237.382-0.002-0.0020.0000.0000.0000.000
189A1271GLN 0-0.065-0.02838.629-0.002-0.0020.0000.0000.0000.000
190A1272GLU -1-0.819-0.90939.5320.0270.0270.0000.0000.0000.000
191A1273HIS 0-0.101-0.07340.8430.0010.0010.0000.0000.0000.000
192A1274ASP -1-0.883-0.94039.0350.0230.0230.0000.0000.0000.000
193A1275LEU 0-0.077-0.00633.8400.0000.0000.0000.0000.0000.000
194A1276LYS 10.9050.95731.198-0.031-0.0310.0000.0000.0000.000
195A1277LEU 00.0770.01336.5510.0020.0020.0000.0000.0000.000
196A1278ASN 00.0210.00531.3620.0010.0010.0000.0000.0000.000
197A1279LEU 00.0120.01229.8990.0020.0020.0000.0000.0000.000
198A1280LYS 10.9300.98133.290-0.024-0.0240.0000.0000.0000.000
199A1281PHE 00.0150.00633.8400.0010.0010.0000.0000.0000.000
200A1282GLU -1-0.925-0.97328.0310.0560.0560.0000.0000.0000.000
201A1283ILE 00.000-0.00532.0550.0030.0030.0000.0000.0000.000
202A1284GLU -1-0.864-0.91833.7600.0320.0320.0000.0000.0000.000
203A1285VAL 0-0.055-0.02531.1930.0000.0000.0000.0000.0000.000
204A1286LEU 0-0.019-0.00328.9450.0020.0020.0000.0000.0000.000
205A1287CYS 0-0.030-0.01231.9890.0020.0020.0000.0000.0000.000
206A1288LYS 10.9951.00135.330-0.034-0.0340.0000.0000.0000.000
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