FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: 89K7Y

Calculation Name: 4P9J-C-Xray372

Preferred Name: Ryanodine receptor 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4P9J

Chain ID: C

ChEMBL ID: CHEMBL3288

UniProt ID: P11716

Base Structure: X-ray

Registration Date: 2023-09-23

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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1877024.092369
FMO2-HF: Nuclear repulsion 1805720.979347
FMO2-HF: Total energy -71303.113022
FMO2-MP2: Total energy -71510.010863


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(C:-2:SER)


Summations of interaction energy for fragment #1(C:-2:SER)
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.
-3.367-1.784-0.006-0.744-0.8320.003
Interaction energy analysis for fragmet #1(C:-2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.020 / q_NPA : -0.018
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].
3C0ALA00.0510.0343.784-2.184-0.601-0.006-0.744-0.8320.003
4C1070ASP-1-0.884-0.9435.724-0.983-0.9830.0000.0000.0000.000
5C1071ARG10.9180.9508.2380.9990.9990.0000.0000.0000.000
6C1072VAL00.0160.00911.3890.1050.1050.0000.0000.0000.000
7C1073ARG10.7690.88914.4310.4650.4650.0000.0000.0000.000
8C1074ILE00.0650.01817.3900.0140.0140.0000.0000.0000.000
9C1075PHE0-0.054-0.02820.6070.0150.0150.0000.0000.0000.000
10C1076ARG10.9110.95023.4620.2730.2730.0000.0000.0000.000
11C1077ALA00.0610.04526.2990.0080.0080.0000.0000.0000.000
12C1078GLU-1-0.878-0.93029.946-0.137-0.1370.0000.0000.0000.000
13C1079LYS10.8430.89228.4340.1860.1860.0000.0000.0000.000
14C1080SER0-0.0460.00132.7580.0030.0030.0000.0000.0000.000
15C1081TYR0-0.042-0.05734.0980.0090.0090.0000.0000.0000.000
16C1082THR0-0.015-0.03033.897-0.004-0.0040.0000.0000.0000.000
17C1083VAL0-0.0300.01035.5030.0080.0080.0000.0000.0000.000
18C1084GLN0-0.012-0.03136.692-0.002-0.0020.0000.0000.0000.000
19C1085SER0-0.018-0.00439.1050.0030.0030.0000.0000.0000.000
20C1086GLY00.0660.03840.940-0.003-0.0030.0000.0000.0000.000
21C1087ARG10.8830.94040.4040.0800.0800.0000.0000.0000.000
22C1088TRP00.0170.00837.1670.0010.0010.0000.0000.0000.000
23C1089TYR0-0.004-0.04636.769-0.004-0.0040.0000.0000.0000.000
24C1090PHE0-0.047-0.02029.3100.0020.0020.0000.0000.0000.000
25C1091GLU-1-0.701-0.82132.769-0.117-0.1170.0000.0000.0000.000
26C1092PHE00.021-0.01323.473-0.009-0.0090.0000.0000.0000.000
27C1093GLU-1-0.895-0.92029.210-0.142-0.1420.0000.0000.0000.000
28C1094ALA00.0070.01325.228-0.016-0.0160.0000.0000.0000.000
29C1095VAL00.0380.02625.1730.0150.0150.0000.0000.0000.000
30C1096THR0-0.023-0.01520.2380.0140.0140.0000.0000.0000.000
31C1097THR00.023-0.00821.6580.0000.0000.0000.0000.0000.000
32C1098GLY00.0250.01318.0930.0070.0070.0000.0000.0000.000
33C1099GLU-1-0.834-0.90414.199-0.408-0.4080.0000.0000.0000.000
34C1100MET0-0.0300.00517.238-0.044-0.0440.0000.0000.0000.000
35C1101ARG10.8020.89215.7450.5060.5060.0000.0000.0000.000
36C1102VAL00.0320.01221.895-0.004-0.0040.0000.0000.0000.000
37C1103GLY00.0290.01525.3330.0070.0070.0000.0000.0000.000
38C1104TRP0-0.0040.00027.7970.0010.0010.0000.0000.0000.000
39C1105ALA00.014-0.00325.606-0.010-0.0100.0000.0000.0000.000
40C1106ARG10.8710.94027.0650.1770.1770.0000.0000.0000.000
41C1107PRO00.0560.02427.589-0.015-0.0150.0000.0000.0000.000
42C1108GLU-1-0.819-0.89026.321-0.198-0.1980.0000.0000.0000.000
43C1109LEU00.004-0.00321.651-0.009-0.0090.0000.0000.0000.000
44C1110ARG10.7530.82419.2440.2900.2900.0000.0000.0000.000
45C1111PRO0-0.013-0.01216.477-0.018-0.0180.0000.0000.0000.000
46C1112ASP-1-0.942-0.97812.025-0.845-0.8450.0000.0000.0000.000
47C1113VAL0-0.0230.00313.156-0.073-0.0730.0000.0000.0000.000
48C1114GLU-1-0.895-0.94013.404-0.663-0.6630.0000.0000.0000.000
49C1115LEU00.021-0.00516.1310.0510.0510.0000.0000.0000.000
50C1116GLY00.0420.02719.907-0.001-0.0010.0000.0000.0000.000
51C1117ALA0-0.022-0.01317.1980.0180.0180.0000.0000.0000.000
52C1118ASP-1-0.798-0.88819.155-0.318-0.3180.0000.0000.0000.000
53C1119GLU-1-0.743-0.84821.594-0.229-0.2290.0000.0000.0000.000
54C1120LEU0-0.078-0.02922.5420.0190.0190.0000.0000.0000.000
55C1121ALA0-0.032-0.02723.2660.0010.0010.0000.0000.0000.000
56C1122TYR00.0140.03025.145-0.003-0.0030.0000.0000.0000.000
57C1123VAL0-0.066-0.03322.0200.0050.0050.0000.0000.0000.000
58C1124PHE00.0400.03125.1020.0000.0000.0000.0000.0000.000
59C1125ASN0-0.045-0.03918.2500.0080.0080.0000.0000.0000.000
60C1126GLY00.0950.02622.6550.0150.0150.0000.0000.0000.000
61C1127HIS0-0.110-0.04716.4100.0440.0440.0000.0000.0000.000
62C1128ARG10.9110.92916.0700.2800.2800.0000.0000.0000.000
63C1129GLY00.0070.03122.9100.0190.0190.0000.0000.0000.000
64C1130GLN00.0190.00319.232-0.019-0.0190.0000.0000.0000.000
65C1131ARG10.7770.89024.1250.1380.1380.0000.0000.0000.000
66C1132TRP0-0.037-0.03716.399-0.021-0.0210.0000.0000.0000.000
67C1133HIS0-0.005-0.01623.3520.0150.0150.0000.0000.0000.000
68C1134LEU0-0.058-0.00122.6640.0140.0140.0000.0000.0000.000
69C1135GLY00.0250.02320.1230.0060.0060.0000.0000.0000.000
70C1136SER0-0.044-0.02319.8740.0030.0030.0000.0000.0000.000
71C1137GLU-1-0.827-0.90021.854-0.131-0.1310.0000.0000.0000.000
72C1138PRO0-0.055-0.02224.873-0.012-0.0120.0000.0000.0000.000
73C1139PHE00.0640.02026.1950.0070.0070.0000.0000.0000.000
74C1140GLY00.0110.02427.729-0.011-0.0110.0000.0000.0000.000
75C1141ARG10.8230.89128.6530.1160.1160.0000.0000.0000.000
76C1142PRO0-0.027-0.01024.830-0.008-0.0080.0000.0000.0000.000
77C1143TRP0-0.018-0.01021.6760.0080.0080.0000.0000.0000.000
78C1144GLN0-0.086-0.03926.0260.0000.0000.0000.0000.0000.000
79C1145SER0-0.088-0.06226.8810.0000.0000.0000.0000.0000.000
80C1146GLY00.006-0.00127.9530.0120.0120.0000.0000.0000.000
81C1147ASP-1-0.811-0.88329.152-0.128-0.1280.0000.0000.0000.000
82C1148VAL0-0.032-0.02729.958-0.010-0.0100.0000.0000.0000.000
83C1149VAL0-0.024-0.00727.7510.0060.0060.0000.0000.0000.000
84C1150GLY00.0250.01231.085-0.001-0.0010.0000.0000.0000.000
85C1151CYS0-0.061-0.02130.398-0.007-0.0070.0000.0000.0000.000
86C1152MET00.0140.00533.0090.0070.0070.0000.0000.0000.000
87C1153ILE0-0.0150.00333.118-0.005-0.0050.0000.0000.0000.000
88C1154ASP-1-0.735-0.86336.227-0.085-0.0850.0000.0000.0000.000
89C1155LEU0-0.051-0.01936.135-0.001-0.0010.0000.0000.0000.000
90C1156THR0-0.082-0.04139.9690.0050.0050.0000.0000.0000.000
91C1157GLU-1-0.938-0.97641.546-0.078-0.0780.0000.0000.0000.000
92C1158ASN0-0.068-0.02038.232-0.003-0.0030.0000.0000.0000.000
93C1159THR0-0.013-0.01536.404-0.004-0.0040.0000.0000.0000.000
94C1160ILE00.0000.00530.913-0.003-0.0030.0000.0000.0000.000
95C1161ILE00.0210.01334.4680.0020.0020.0000.0000.0000.000
96C1162PHE00.009-0.00328.516-0.006-0.0060.0000.0000.0000.000
97C1163THR00.0090.00633.1320.0050.0050.0000.0000.0000.000
98C1164LEU00.0090.01129.839-0.010-0.0100.0000.0000.0000.000
99C1165ASN0-0.024-0.04433.2940.0030.0030.0000.0000.0000.000
100C1166GLY00.002-0.00235.7360.0070.0070.0000.0000.0000.000
101C1167GLU-1-0.867-0.90036.910-0.086-0.0860.0000.0000.0000.000
102C1168VAL00.006-0.00936.156-0.007-0.0070.0000.0000.0000.000
103C1169LEU0-0.064-0.02530.2020.0020.0020.0000.0000.0000.000
104C1170MET0-0.0160.00434.201-0.002-0.0020.0000.0000.0000.000
105C1171SER00.007-0.01132.291-0.003-0.0030.0000.0000.0000.000
106C1172ASP-1-0.828-0.92730.304-0.113-0.1130.0000.0000.0000.000
107C1173SER0-0.124-0.06633.1480.0050.0050.0000.0000.0000.000
108C1174GLY0-0.018-0.01036.1150.0060.0060.0000.0000.0000.000
109C1175SER0-0.052-0.01836.5210.0040.0040.0000.0000.0000.000
110C1176GLU-1-0.806-0.92036.338-0.089-0.0890.0000.0000.0000.000
111C1177THR0-0.067-0.01436.378-0.004-0.0040.0000.0000.0000.000
112C1178ALA0-0.0020.00130.7650.0010.0010.0000.0000.0000.000
113C1179PHE00.014-0.00726.631-0.005-0.0050.0000.0000.0000.000
114C1180ARG10.9150.94032.7940.0990.0990.0000.0000.0000.000
115C1181GLU-1-0.926-0.95035.034-0.093-0.0930.0000.0000.0000.000
116C1182ILE0-0.0420.00032.894-0.004-0.0040.0000.0000.0000.000
117C1183GLU-1-0.901-0.95133.438-0.120-0.1200.0000.0000.0000.000
118C1184ILE00.0210.00834.623-0.009-0.0090.0000.0000.0000.000
119C1185GLY00.0240.01734.698-0.007-0.0070.0000.0000.0000.000
120C1186ASP-1-0.919-0.97032.596-0.132-0.1320.0000.0000.0000.000
121C1187GLY0-0.0040.00334.5530.0020.0020.0000.0000.0000.000
122C1188PHE0-0.055-0.04130.798-0.011-0.0110.0000.0000.0000.000
123C1189LEU0-0.0170.00529.5720.0090.0090.0000.0000.0000.000
124C1190PRO0-0.0050.02529.703-0.011-0.0110.0000.0000.0000.000
125C1191VAL0-0.040-0.01523.723-0.010-0.0100.0000.0000.0000.000
126C1192CYS00.0080.00823.9110.0070.0070.0000.0000.0000.000
127C1193SER00.0300.00218.318-0.011-0.0110.0000.0000.0000.000
128C1194LEU0-0.021-0.00518.6370.0170.0170.0000.0000.0000.000
129C1195GLY00.0780.04314.552-0.054-0.0540.0000.0000.0000.000
130C1196PRO00.0150.00910.3930.1160.1160.0000.0000.0000.000
131C1197GLY0-0.016-0.02113.5680.0370.0370.0000.0000.0000.000
132C1198GLN0-0.0490.01215.9070.0970.0970.0000.0000.0000.000
133C1199VAL00.0210.00418.706-0.007-0.0070.0000.0000.0000.000
134C1200GLY00.0870.03722.3570.0080.0080.0000.0000.0000.000
135C1201HIS0-0.105-0.05024.917-0.016-0.0160.0000.0000.0000.000
136C1202LEU00.0300.01327.3310.0040.0040.0000.0000.0000.000
137C1203ASN0-0.024-0.01829.7660.0070.0070.0000.0000.0000.000
138C1204LEU00.012-0.00731.4410.0010.0010.0000.0000.0000.000
139C1205GLY00.0600.02835.0370.0050.0050.0000.0000.0000.000
140C1206GLN0-0.015-0.02135.3230.0040.0040.0000.0000.0000.000
141C1207ASP-1-0.836-0.88139.952-0.079-0.0790.0000.0000.0000.000
142C1208VAL00.0460.02740.937-0.003-0.0030.0000.0000.0000.000
143C1209SER0-0.100-0.06242.2090.0000.0000.0000.0000.0000.000
144C1210SER0-0.041-0.03539.098-0.002-0.0020.0000.0000.0000.000
145C1211LEU0-0.073-0.02236.827-0.005-0.0050.0000.0000.0000.000
146C1212ARG10.8920.94136.7880.0970.0970.0000.0000.0000.000
147C1213PHE0-0.001-0.02135.7100.0070.0070.0000.0000.0000.000
148C1214PHE00.0530.05039.4370.0030.0030.0000.0000.0000.000
149C1215ALA0-0.032-0.02840.8350.0030.0030.0000.0000.0000.000
150C1216ILE0-0.106-0.04541.6320.0040.0040.0000.0000.0000.000
151C1217CYS0-0.044-0.01840.0150.0010.0010.0000.0000.0000.000
152C1218GLY00.040-0.00140.284-0.007-0.0070.0000.0000.0000.000
153C1219LEU0-0.039-0.00541.9460.0020.0020.0000.0000.0000.000
154C1220GLN0-0.029-0.02244.9800.0040.0040.0000.0000.0000.000
155C1221GLU-1-0.818-0.90343.509-0.080-0.0800.0000.0000.0000.000
156C1222GLY0-0.0250.00445.172-0.001-0.0010.0000.0000.0000.000
157C1223PHE0-0.044-0.03039.193-0.002-0.0020.0000.0000.0000.000
158C1224GLU-1-0.925-0.96941.857-0.080-0.0800.0000.0000.0000.000
159C1225PRO0-0.012-0.00939.479-0.006-0.0060.0000.0000.0000.000
160C1226PHE00.0690.00434.8130.0010.0010.0000.0000.0000.000
161C1227ALA00.0010.00438.0130.0010.0010.0000.0000.0000.000
162C1228ILE0-0.0090.01238.9850.0030.0030.0000.0000.0000.000
163C1229ASN0-0.041-0.02838.4430.0070.0070.0000.0000.0000.000
164C1230MET0-0.078-0.02534.695-0.003-0.0030.0000.0000.0000.000
165C1231GLN0-0.0230.00839.5020.0060.0060.0000.0000.0000.000
166C1232ARG10.8610.92138.2880.1020.1020.0000.0000.0000.000
167C1233PRO00.0450.03539.7640.0040.0040.0000.0000.0000.000
168C1234VAL00.003-0.01042.8780.0010.0010.0000.0000.0000.000
169C1235THR0-0.019-0.00546.0760.0010.0010.0000.0000.0000.000
170C1236THR0-0.0060.00048.2670.0000.0000.0000.0000.0000.000
171C1237TRP00.0190.00451.8810.0010.0010.0000.0000.0000.000
172C1238PHE0-0.003-0.00254.9260.0000.0000.0000.0000.0000.000
173C1239SER0-0.002-0.00558.2600.0020.0020.0000.0000.0000.000
174C1240LYS10.9790.97361.6170.0330.0330.0000.0000.0000.000
175C1241SER0-0.0050.00464.5150.0010.0010.0000.0000.0000.000
176C1242LEU00.0960.04865.095-0.001-0.0010.0000.0000.0000.000
177C1243PRO0-0.008-0.01766.132-0.001-0.0010.0000.0000.0000.000
178C1244GLN0-0.065-0.01761.0540.0000.0000.0000.0000.0000.000
179C1245PHE0-0.0320.00058.512-0.002-0.0020.0000.0000.0000.000
180C1246GLU-1-0.986-0.99062.957-0.036-0.0360.0000.0000.0000.000