FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: G57R1

Calculation Name: 4P9J-C-Xray372

Preferred Name: Ryanodine receptor 1

Target Type: SINGLE PROTEIN

Ligand Name:
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ligand 3-letter code:
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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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1875962.341482
FMO2-HF: Nuclear repulsion 1804659.823947
FMO2-HF: Total energy -71302.517534
FMO2-MP2: Total energy -71509.35629


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.
-3.373-1.878-0.008-0.68-0.8070.002
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 : -0.022
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].
3C0ALA00.0480.0343.813-1.969-0.474-0.008-0.680-0.8070.002
4C1070ASP-1-0.889-0.9415.788-0.995-0.9950.0000.0000.0000.000
5C1071ARG10.9070.9418.2691.0461.0460.0000.0000.0000.000
6C1072VAL00.0210.01511.4210.1150.1150.0000.0000.0000.000
7C1073ARG10.7880.91014.4620.4890.4890.0000.0000.0000.000
8C1074ILE00.0720.02117.7620.0160.0160.0000.0000.0000.000
9C1075PHE0-0.058-0.02920.6380.0140.0140.0000.0000.0000.000
10C1076ARG10.9210.95923.7650.2980.2980.0000.0000.0000.000
11C1077ALA00.0510.04426.3670.0090.0090.0000.0000.0000.000
12C1078GLU-1-0.940-0.98230.010-0.157-0.1570.0000.0000.0000.000
13C1079LYS10.9820.98127.7530.2120.2120.0000.0000.0000.000
14C1080SER0-0.0530.01632.8180.0040.0040.0000.0000.0000.000
15C1081TYR00.016-0.00134.1530.0090.0090.0000.0000.0000.000
16C1082THR0-0.013-0.04734.046-0.004-0.0040.0000.0000.0000.000
17C1083VAL0-0.0270.01335.5690.0080.0080.0000.0000.0000.000
18C1084GLN0-0.012-0.03636.762-0.002-0.0020.0000.0000.0000.000
19C1085SER0-0.0060.00239.1740.0030.0030.0000.0000.0000.000
20C1086GLY00.0530.03441.014-0.003-0.0030.0000.0000.0000.000
21C1087ARG10.9220.96740.4590.0840.0840.0000.0000.0000.000
22C1088TRP00.0110.00737.2210.0020.0020.0000.0000.0000.000
23C1089TYR00.000-0.05336.839-0.005-0.0050.0000.0000.0000.000
24C1090PHE0-0.052-0.02229.4360.0020.0020.0000.0000.0000.000
25C1091GLU-1-0.710-0.81332.784-0.125-0.1250.0000.0000.0000.000
26C1092PHE00.012-0.01823.557-0.010-0.0100.0000.0000.0000.000
27C1093GLU-1-0.911-0.94229.157-0.146-0.1460.0000.0000.0000.000
28C1094ALA0-0.0040.00925.153-0.017-0.0170.0000.0000.0000.000
29C1095VAL00.0280.02525.1110.0160.0160.0000.0000.0000.000
30C1096THR0-0.018-0.02520.4910.0130.0130.0000.0000.0000.000
31C1097THR00.021-0.00621.718-0.002-0.0020.0000.0000.0000.000
32C1098GLY0-0.0010.00018.1170.0070.0070.0000.0000.0000.000
33C1099GLU-1-0.840-0.92114.271-0.451-0.4510.0000.0000.0000.000
34C1100MET0-0.0250.00917.265-0.044-0.0440.0000.0000.0000.000
35C1101ARG10.8830.94816.0080.5250.5250.0000.0000.0000.000
36C1102VAL00.0260.01121.921-0.005-0.0050.0000.0000.0000.000
37C1103GLY00.0310.01425.3910.0070.0070.0000.0000.0000.000
38C1104TRP00.0080.01127.8810.0010.0010.0000.0000.0000.000
39C1105ALA00.009-0.00825.685-0.011-0.0110.0000.0000.0000.000
40C1106ARG10.8590.92327.1180.1940.1940.0000.0000.0000.000
41C1107PRO00.0510.01827.654-0.017-0.0170.0000.0000.0000.000
42C1108GLU-1-0.982-0.99326.415-0.204-0.2040.0000.0000.0000.000
43C1109LEU0-0.007-0.01421.713-0.008-0.0080.0000.0000.0000.000
44C1110ARG10.8050.87319.3780.3170.3170.0000.0000.0000.000
45C1111PRO0-0.011-0.00916.527-0.018-0.0180.0000.0000.0000.000
46C1112ASP-1-0.938-0.97312.221-0.931-0.9310.0000.0000.0000.000
47C1113VAL0-0.0290.00013.209-0.080-0.0800.0000.0000.0000.000
48C1114GLU-1-0.963-0.97713.195-0.789-0.7890.0000.0000.0000.000
49C1115LEU00.023-0.00616.2070.0540.0540.0000.0000.0000.000
50C1116GLY00.0380.01919.9850.0000.0000.0000.0000.0000.000
51C1117ALA0-0.020-0.01317.2780.0190.0190.0000.0000.0000.000
52C1118ASP-1-0.819-0.90319.226-0.355-0.3550.0000.0000.0000.000
53C1119GLU-1-0.740-0.86321.657-0.252-0.2520.0000.0000.0000.000
54C1120LEU0-0.083-0.03222.6710.0210.0210.0000.0000.0000.000
55C1121ALA0-0.033-0.03123.3650.0020.0020.0000.0000.0000.000
56C1122TYR00.0150.03325.220-0.003-0.0030.0000.0000.0000.000
57C1123VAL0-0.065-0.02822.0750.0060.0060.0000.0000.0000.000
58C1124PHE00.0300.02425.1880.0000.0000.0000.0000.0000.000
59C1125ASN0-0.037-0.02818.2590.0050.0050.0000.0000.0000.000
60C1126GLY00.0860.02822.7140.0160.0160.0000.0000.0000.000
61C1127HIS0-0.100-0.04316.4870.0470.0470.0000.0000.0000.000
62C1128ARG10.9200.92916.4930.2750.2750.0000.0000.0000.000
63C1129GLY00.0010.03022.9280.0200.0200.0000.0000.0000.000
64C1130GLN00.0200.00319.228-0.019-0.0190.0000.0000.0000.000
65C1131ARG10.8300.93724.2130.1490.1490.0000.0000.0000.000
66C1132TRP0-0.047-0.03816.790-0.022-0.0220.0000.0000.0000.000
67C1133HIS0-0.013-0.02823.4330.0150.0150.0000.0000.0000.000
68C1134LEU0-0.0580.00322.7610.0150.0150.0000.0000.0000.000
69C1135GLY00.0210.01920.1960.0060.0060.0000.0000.0000.000
70C1136SER0-0.058-0.03719.6330.0180.0180.0000.0000.0000.000
71C1137GLU-1-0.859-0.93521.932-0.139-0.1390.0000.0000.0000.000
72C1138PRO0-0.054-0.01824.953-0.013-0.0130.0000.0000.0000.000
73C1139PHE00.0570.01026.2770.0070.0070.0000.0000.0000.000
74C1140GLY00.0140.02527.817-0.011-0.0110.0000.0000.0000.000
75C1141ARG10.9420.95928.6410.1240.1240.0000.0000.0000.000
76C1142PRO0-0.043-0.01724.810-0.007-0.0070.0000.0000.0000.000
77C1143TRP0-0.024-0.01121.5900.0090.0090.0000.0000.0000.000
78C1144GLN0-0.065-0.03626.050-0.002-0.0020.0000.0000.0000.000
79C1145SER0-0.095-0.04926.9700.0000.0000.0000.0000.0000.000
80C1146GLY00.0130.00427.9810.0120.0120.0000.0000.0000.000
81C1147ASP-1-0.819-0.87529.229-0.133-0.1330.0000.0000.0000.000
82C1148VAL0-0.024-0.02129.987-0.011-0.0110.0000.0000.0000.000
83C1149VAL0-0.031-0.01527.9540.0060.0060.0000.0000.0000.000
84C1150GLY00.0320.01531.112-0.001-0.0010.0000.0000.0000.000
85C1151CYS0-0.057-0.02330.410-0.008-0.0080.0000.0000.0000.000
86C1152MET00.0090.00333.0960.0070.0070.0000.0000.0000.000
87C1153ILE0-0.0190.00233.177-0.006-0.0060.0000.0000.0000.000
88C1154ASP-1-0.759-0.89236.309-0.092-0.0920.0000.0000.0000.000
89C1155LEU0-0.042-0.01736.289-0.001-0.0010.0000.0000.0000.000
90C1156THR0-0.097-0.04640.0460.0050.0050.0000.0000.0000.000
91C1157GLU-1-0.938-0.97841.491-0.085-0.0850.0000.0000.0000.000
92C1158ASN0-0.065-0.01638.296-0.004-0.0040.0000.0000.0000.000
93C1159THR00.000-0.00936.517-0.005-0.0050.0000.0000.0000.000
94C1160ILE00.0040.00730.897-0.003-0.0030.0000.0000.0000.000
95C1161ILE00.0140.01034.5520.0020.0020.0000.0000.0000.000
96C1162PHE00.009-0.00628.575-0.006-0.0060.0000.0000.0000.000
97C1163THR00.0130.01033.2210.0050.0050.0000.0000.0000.000
98C1164LEU00.0160.01129.922-0.011-0.0110.0000.0000.0000.000
99C1165ASN0-0.019-0.04933.3190.0040.0040.0000.0000.0000.000
100C1166GLY0-0.006-0.00435.7630.0070.0070.0000.0000.0000.000
101C1167GLU-1-0.957-0.96537.107-0.088-0.0880.0000.0000.0000.000
102C1168VAL00.006-0.00536.180-0.008-0.0080.0000.0000.0000.000
103C1169LEU0-0.091-0.03430.3110.0030.0030.0000.0000.0000.000
104C1170MET0-0.0160.00234.283-0.002-0.0020.0000.0000.0000.000
105C1171SER0-0.004-0.01132.372-0.004-0.0040.0000.0000.0000.000
106C1172ASP-1-0.816-0.92130.321-0.120-0.1200.0000.0000.0000.000
107C1173SER0-0.131-0.06833.2300.0050.0050.0000.0000.0000.000
108C1174GLY0-0.003-0.00236.2000.0060.0060.0000.0000.0000.000
109C1175SER0-0.063-0.02336.5420.0020.0020.0000.0000.0000.000
110C1176GLU-1-0.774-0.91536.424-0.095-0.0950.0000.0000.0000.000
111C1177THR0-0.090-0.02236.516-0.004-0.0040.0000.0000.0000.000
112C1178ALA0-0.0040.00030.8060.0000.0000.0000.0000.0000.000
113C1179PHE00.016-0.00326.768-0.005-0.0050.0000.0000.0000.000
114C1180ARG10.9140.94832.8740.1080.1080.0000.0000.0000.000
115C1181GLU-1-0.937-0.95935.108-0.102-0.1020.0000.0000.0000.000
116C1182ILE0-0.044-0.00133.095-0.004-0.0040.0000.0000.0000.000
117C1183GLU-1-0.902-0.94933.801-0.129-0.1290.0000.0000.0000.000
118C1184ILE00.0240.01634.691-0.010-0.0100.0000.0000.0000.000
119C1185GLY00.0390.02634.760-0.008-0.0080.0000.0000.0000.000
120C1186ASP-1-0.907-0.95932.678-0.142-0.1420.0000.0000.0000.000
121C1187GLY0-0.0130.00134.6580.0020.0020.0000.0000.0000.000
122C1188PHE0-0.050-0.03930.727-0.013-0.0130.0000.0000.0000.000
123C1189LEU0-0.017-0.00729.7400.0100.0100.0000.0000.0000.000
124C1190PRO00.0030.02829.778-0.012-0.0120.0000.0000.0000.000
125C1191VAL0-0.053-0.01623.764-0.010-0.0100.0000.0000.0000.000
126C1192CYS00.0230.01123.8680.0070.0070.0000.0000.0000.000
127C1193SER00.0220.00018.340-0.011-0.0110.0000.0000.0000.000
128C1194LEU0-0.025-0.01118.6680.0200.0200.0000.0000.0000.000
129C1195GLY00.0760.04514.584-0.056-0.0560.0000.0000.0000.000
130C1196PRO00.0260.00810.4550.1150.1150.0000.0000.0000.000
131C1197GLY0-0.021-0.02213.6010.0400.0400.0000.0000.0000.000
132C1198GLN0-0.0300.01516.3350.0910.0910.0000.0000.0000.000
133C1199VAL00.025-0.00218.738-0.007-0.0070.0000.0000.0000.000
134C1200GLY00.0830.03422.3900.0090.0090.0000.0000.0000.000
135C1201HIS0-0.083-0.02724.949-0.015-0.0150.0000.0000.0000.000
136C1202LEU00.0240.01227.5180.0040.0040.0000.0000.0000.000
137C1203ASN0-0.014-0.01229.7980.0070.0070.0000.0000.0000.000
138C1204LEU00.012-0.00831.4740.0010.0010.0000.0000.0000.000
139C1205GLY00.0520.02635.0670.0050.0050.0000.0000.0000.000
140C1206GLN0-0.011-0.02035.3840.0050.0050.0000.0000.0000.000
141C1207ASP-1-0.847-0.88739.982-0.083-0.0830.0000.0000.0000.000
142C1208VAL00.0470.02140.969-0.003-0.0030.0000.0000.0000.000
143C1209SER0-0.099-0.05942.240-0.001-0.0010.0000.0000.0000.000
144C1210SER0-0.040-0.02839.038-0.002-0.0020.0000.0000.0000.000
145C1211LEU0-0.059-0.02036.958-0.005-0.0050.0000.0000.0000.000
146C1212ARG10.9030.95336.8560.1020.1020.0000.0000.0000.000
147C1213PHE0-0.008-0.03035.6490.0070.0070.0000.0000.0000.000
148C1214PHE00.0500.05039.4660.0030.0030.0000.0000.0000.000
149C1215ALA0-0.030-0.02740.8630.0030.0030.0000.0000.0000.000
150C1216ILE0-0.100-0.04041.7840.0040.0040.0000.0000.0000.000
151C1217CYS0-0.019-0.00440.0100.0010.0010.0000.0000.0000.000
152C1218GLY00.030-0.00340.311-0.007-0.0070.0000.0000.0000.000
153C1219LEU0-0.028-0.00541.9730.0010.0010.0000.0000.0000.000
154C1220GLN0-0.017-0.02145.0070.0030.0030.0000.0000.0000.000
155C1221GLU-1-0.864-0.92643.589-0.084-0.0840.0000.0000.0000.000
156C1222GLY0-0.0280.00445.258-0.001-0.0010.0000.0000.0000.000
157C1223PHE0-0.041-0.02839.360-0.003-0.0030.0000.0000.0000.000
158C1224GLU-1-0.921-0.97241.952-0.085-0.0850.0000.0000.0000.000
159C1225PRO0-0.004-0.00639.509-0.007-0.0070.0000.0000.0000.000
160C1226PHE00.0690.00535.0230.0010.0010.0000.0000.0000.000
161C1227ALA0-0.005-0.00938.0920.0010.0010.0000.0000.0000.000
162C1228ILE0-0.0160.01439.0150.0030.0030.0000.0000.0000.000
163C1229ASN0-0.040-0.02138.5570.0070.0070.0000.0000.0000.000
164C1230MET0-0.076-0.02235.170-0.004-0.0040.0000.0000.0000.000
165C1231GLN0-0.0070.01839.5540.0060.0060.0000.0000.0000.000
166C1232ARG10.8490.90938.5000.1070.1070.0000.0000.0000.000
167C1233PRO00.0470.03739.8040.0040.0040.0000.0000.0000.000
168C1234VAL00.004-0.00742.9080.0010.0010.0000.0000.0000.000
169C1235THR0-0.013-0.00546.1060.0010.0010.0000.0000.0000.000
170C1236THR0-0.026-0.01548.2970.0010.0010.0000.0000.0000.000
171C1237TRP00.0510.02451.9110.0010.0010.0000.0000.0000.000
172C1238PHE0-0.008-0.00254.9560.0000.0000.0000.0000.0000.000
173C1239SER00.003-0.00858.2900.0020.0020.0000.0000.0000.000
174C1240LYS10.9670.97261.6470.0350.0350.0000.0000.0000.000
175C1241SER0-0.007-0.00264.5430.0010.0010.0000.0000.0000.000
176C1242LEU00.0920.04765.126-0.001-0.0010.0000.0000.0000.000
177C1243PRO0-0.010-0.01866.164-0.001-0.0010.0000.0000.0000.000
178C1244GLN0-0.072-0.02161.1180.0000.0000.0000.0000.0000.000
179C1245PHE0-0.049-0.01158.615-0.002-0.0020.0000.0000.0000.000
180C1246GLU-1-0.957-0.97163.028-0.039-0.0390.0000.0000.0000.000