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: NN68Q

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 OptAll
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 -1875825.565246
FMO2-HF: Nuclear repulsion 1804522.210078
FMO2-HF: Total energy -71303.355168
FMO2-MP2: Total energy -71510.265446


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.
-3.247-1.864-0.008-0.587-0.7880.003
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 : -0.021
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].
3C0ALA00.0520.0303.856-1.952-0.569-0.008-0.587-0.7880.003
4C1070ASP-1-0.887-0.9475.762-1.020-1.0200.0000.0000.0000.000
5C1071ARG10.9310.9598.4310.9790.9790.0000.0000.0000.000
6C1072VAL0-0.003-0.00111.5420.1670.1670.0000.0000.0000.000
7C1073ARG10.7750.89514.0980.4760.4760.0000.0000.0000.000
8C1074ILE00.0520.00617.0140.0080.0080.0000.0000.0000.000
9C1075PHE0-0.054-0.03120.2450.0210.0210.0000.0000.0000.000
10C1076ARG10.8660.93323.2770.2740.2740.0000.0000.0000.000
11C1077ALA00.0570.03926.1560.0090.0090.0000.0000.0000.000
12C1078GLU-1-0.852-0.90729.621-0.133-0.1330.0000.0000.0000.000
13C1079LYS10.8280.89028.1310.1860.1860.0000.0000.0000.000
14C1080SER0-0.055-0.01432.8510.0030.0030.0000.0000.0000.000
15C1081TYR0-0.023-0.03834.3730.0090.0090.0000.0000.0000.000
16C1082THR0-0.018-0.02733.721-0.006-0.0060.0000.0000.0000.000
17C1083VAL0-0.0110.01235.5120.0080.0080.0000.0000.0000.000
18C1084GLN0-0.027-0.03536.678-0.002-0.0020.0000.0000.0000.000
19C1085SER0-0.004-0.00139.1170.0030.0030.0000.0000.0000.000
20C1086GLY00.0560.03340.958-0.003-0.0030.0000.0000.0000.000
21C1087ARG10.8760.94140.6770.0860.0860.0000.0000.0000.000
22C1088TRP00.0130.00837.3010.0010.0010.0000.0000.0000.000
23C1089TYR00.005-0.04236.720-0.006-0.0060.0000.0000.0000.000
24C1090PHE0-0.060-0.03229.1450.0030.0030.0000.0000.0000.000
25C1091GLU-1-0.706-0.83732.778-0.122-0.1220.0000.0000.0000.000
26C1092PHE00.007-0.02023.517-0.009-0.0090.0000.0000.0000.000
27C1093GLU-1-0.887-0.91329.175-0.150-0.1500.0000.0000.0000.000
28C1094ALA00.0050.00925.241-0.018-0.0180.0000.0000.0000.000
29C1095VAL00.0340.02225.4070.0120.0120.0000.0000.0000.000
30C1096THR0-0.032-0.01920.2040.0140.0140.0000.0000.0000.000
31C1097THR00.022-0.00221.769-0.003-0.0030.0000.0000.0000.000
32C1098GLY00.0330.01717.7330.0010.0010.0000.0000.0000.000
33C1099GLU-1-0.822-0.90413.835-0.462-0.4620.0000.0000.0000.000
34C1100MET0-0.030-0.00316.774-0.040-0.0400.0000.0000.0000.000
35C1101ARG10.7550.85915.8800.5450.5450.0000.0000.0000.000
36C1102VAL00.0310.00421.4870.0010.0010.0000.0000.0000.000
37C1103GLY00.0090.00725.1380.0060.0060.0000.0000.0000.000
38C1104TRP00.0140.00927.9090.0040.0040.0000.0000.0000.000
39C1105ALA00.002-0.00825.657-0.017-0.0170.0000.0000.0000.000
40C1106ARG10.8560.93927.3400.1830.1830.0000.0000.0000.000
41C1107PRO00.0280.02027.991-0.013-0.0130.0000.0000.0000.000
42C1108GLU-1-0.817-0.90326.074-0.203-0.2030.0000.0000.0000.000
43C1109LEU00.0310.00521.531-0.006-0.0060.0000.0000.0000.000
44C1110ARG10.7430.82618.7360.3120.3120.0000.0000.0000.000
45C1111PRO0-0.015-0.00716.427-0.015-0.0150.0000.0000.0000.000
46C1112ASP-1-0.947-0.98311.790-0.865-0.8650.0000.0000.0000.000
47C1113VAL0-0.026-0.00212.966-0.091-0.0910.0000.0000.0000.000
48C1114GLU-1-0.850-0.90313.715-0.698-0.6980.0000.0000.0000.000
49C1115LEU00.004-0.00616.4480.0500.0500.0000.0000.0000.000
50C1116GLY00.0610.03220.244-0.003-0.0030.0000.0000.0000.000
51C1117ALA0-0.020-0.01216.9740.0140.0140.0000.0000.0000.000
52C1118ASP-1-0.815-0.89618.942-0.340-0.3400.0000.0000.0000.000
53C1119GLU-1-0.736-0.84621.444-0.244-0.2440.0000.0000.0000.000
54C1120LEU0-0.067-0.01822.5810.0180.0180.0000.0000.0000.000
55C1121ALA0-0.038-0.02623.2000.0050.0050.0000.0000.0000.000
56C1122TYR00.0240.02325.215-0.001-0.0010.0000.0000.0000.000
57C1123VAL0-0.066-0.02822.1970.0080.0080.0000.0000.0000.000
58C1124PHE00.0380.02925.204-0.002-0.0020.0000.0000.0000.000
59C1125ASN0-0.016-0.02718.0050.0030.0030.0000.0000.0000.000
60C1126GLY00.0920.03122.4620.0150.0150.0000.0000.0000.000
61C1127HIS0-0.099-0.04416.0290.0420.0420.0000.0000.0000.000
62C1128ARG10.8450.90215.4190.3730.3730.0000.0000.0000.000
63C1129GLY00.0170.03622.4890.0210.0210.0000.0000.0000.000
64C1130GLN00.0150.00719.622-0.020-0.0200.0000.0000.0000.000
65C1131ARG10.7700.86624.3000.1630.1630.0000.0000.0000.000
66C1132TRP0-0.021-0.02816.408-0.029-0.0290.0000.0000.0000.000
67C1133HIS0-0.002-0.01023.4130.0180.0180.0000.0000.0000.000
68C1134LEU0-0.073-0.01522.5430.0130.0130.0000.0000.0000.000
69C1135GLY00.0190.02020.3860.0060.0060.0000.0000.0000.000
70C1136SER0-0.041-0.02419.943-0.014-0.0140.0000.0000.0000.000
71C1137GLU-1-0.828-0.88022.013-0.155-0.1550.0000.0000.0000.000
72C1138PRO0-0.024-0.01624.920-0.016-0.0160.0000.0000.0000.000
73C1139PHE00.0500.01326.3120.0060.0060.0000.0000.0000.000
74C1140GLY00.0140.02027.756-0.011-0.0110.0000.0000.0000.000
75C1141ARG10.7840.86528.5730.1330.1330.0000.0000.0000.000
76C1142PRO0-0.014-0.00824.629-0.008-0.0080.0000.0000.0000.000
77C1143TRP0-0.010-0.00221.2440.0090.0090.0000.0000.0000.000
78C1144GLN0-0.084-0.04025.8780.0010.0010.0000.0000.0000.000
79C1145SER0-0.075-0.05626.7310.0000.0000.0000.0000.0000.000
80C1146GLY00.000-0.00627.9220.0130.0130.0000.0000.0000.000
81C1147ASP-1-0.802-0.87828.862-0.146-0.1460.0000.0000.0000.000
82C1148VAL0-0.038-0.02729.982-0.009-0.0090.0000.0000.0000.000
83C1149VAL0-0.026-0.00627.5410.0050.0050.0000.0000.0000.000
84C1150GLY00.0400.02930.9680.0010.0010.0000.0000.0000.000
85C1151CYS0-0.064-0.03030.289-0.010-0.0100.0000.0000.0000.000
86C1152MET00.0180.00832.8910.0080.0080.0000.0000.0000.000
87C1153ILE0-0.0080.00533.203-0.007-0.0070.0000.0000.0000.000
88C1154ASP-1-0.716-0.84036.265-0.090-0.0900.0000.0000.0000.000
89C1155LEU0-0.061-0.01636.086-0.002-0.0020.0000.0000.0000.000
90C1156THR0-0.071-0.05940.0150.0060.0060.0000.0000.0000.000
91C1157GLU-1-0.962-0.98041.341-0.084-0.0840.0000.0000.0000.000
92C1158ASN0-0.066-0.01538.335-0.003-0.0030.0000.0000.0000.000
93C1159THR0-0.016-0.01436.304-0.005-0.0050.0000.0000.0000.000
94C1160ILE00.0030.00230.794-0.003-0.0030.0000.0000.0000.000
95C1161ILE00.0010.00234.3890.0020.0020.0000.0000.0000.000
96C1162PHE00.0120.00328.579-0.008-0.0080.0000.0000.0000.000
97C1163THR00.0130.01032.9620.0060.0060.0000.0000.0000.000
98C1164LEU0-0.008-0.00629.405-0.011-0.0110.0000.0000.0000.000
99C1165ASN0-0.010-0.03332.9050.0040.0040.0000.0000.0000.000
100C1166GLY00.0110.00835.4060.0080.0080.0000.0000.0000.000
101C1167GLU-1-0.857-0.89936.619-0.099-0.0990.0000.0000.0000.000
102C1168VAL00.0280.00335.792-0.008-0.0080.0000.0000.0000.000
103C1169LEU0-0.071-0.02629.6510.0020.0020.0000.0000.0000.000
104C1170MET0-0.0160.00833.678-0.002-0.0020.0000.0000.0000.000
105C1171SER00.018-0.01032.061-0.006-0.0060.0000.0000.0000.000
106C1172ASP-1-0.869-0.94430.362-0.135-0.1350.0000.0000.0000.000
107C1173SER0-0.090-0.05233.3040.0050.0050.0000.0000.0000.000
108C1174GLY0-0.027-0.00136.1250.0060.0060.0000.0000.0000.000
109C1175SER0-0.031-0.01936.3760.0060.0060.0000.0000.0000.000
110C1176GLU-1-0.817-0.92135.945-0.104-0.1040.0000.0000.0000.000
111C1177THR0-0.059-0.01436.030-0.003-0.0030.0000.0000.0000.000
112C1178ALA00.0120.01830.668-0.001-0.0010.0000.0000.0000.000
113C1179PHE00.007-0.00626.706-0.007-0.0070.0000.0000.0000.000
114C1180ARG10.9150.93632.8930.1120.1120.0000.0000.0000.000
115C1181GLU-1-0.917-0.94934.974-0.104-0.1040.0000.0000.0000.000
116C1182ILE0-0.052-0.00732.606-0.003-0.0030.0000.0000.0000.000
117C1183GLU-1-0.873-0.93632.842-0.134-0.1340.0000.0000.0000.000
118C1184ILE00.0280.00234.784-0.009-0.0090.0000.0000.0000.000
119C1185GLY00.0460.02734.401-0.007-0.0070.0000.0000.0000.000
120C1186ASP-1-0.931-0.97632.450-0.140-0.1400.0000.0000.0000.000
121C1187GLY0-0.001-0.00134.7670.0030.0030.0000.0000.0000.000
122C1188PHE0-0.053-0.03030.971-0.012-0.0120.0000.0000.0000.000
123C1189LEU0-0.0250.00329.8550.0100.0100.0000.0000.0000.000
124C1190PRO00.0090.02730.062-0.011-0.0110.0000.0000.0000.000
125C1191VAL0-0.042-0.02423.942-0.008-0.0080.0000.0000.0000.000
126C1192CYS00.0040.01223.8200.0040.0040.0000.0000.0000.000
127C1193SER00.0380.00518.316-0.008-0.0080.0000.0000.0000.000
128C1194LEU0-0.0080.00218.3700.0100.0100.0000.0000.0000.000
129C1195GLY00.0810.04814.127-0.048-0.0480.0000.0000.0000.000
130C1196PRO00.0080.00110.3140.1280.1280.0000.0000.0000.000
131C1197GLY0-0.019-0.01713.5940.0330.0330.0000.0000.0000.000
132C1198GLN0-0.0280.02015.7400.1000.1000.0000.0000.0000.000
133C1199VAL00.010-0.00118.772-0.001-0.0010.0000.0000.0000.000
134C1200GLY00.0560.03122.4590.0050.0050.0000.0000.0000.000
135C1201HIS0-0.098-0.05325.043-0.014-0.0140.0000.0000.0000.000
136C1202LEU00.0330.01327.0630.0050.0050.0000.0000.0000.000
137C1203ASN0-0.040-0.02029.6010.0080.0080.0000.0000.0000.000
138C1204LEU00.0290.00531.304-0.001-0.0010.0000.0000.0000.000
139C1205GLY00.0570.02935.0040.0050.0050.0000.0000.0000.000
140C1206GLN0-0.019-0.02734.9350.0040.0040.0000.0000.0000.000
141C1207ASP-1-0.836-0.87739.942-0.081-0.0810.0000.0000.0000.000
142C1208VAL00.0290.01240.875-0.004-0.0040.0000.0000.0000.000
143C1209SER0-0.080-0.05942.436-0.001-0.0010.0000.0000.0000.000
144C1210SER0-0.038-0.02738.800-0.003-0.0030.0000.0000.0000.000
145C1211LEU0-0.072-0.01536.706-0.006-0.0060.0000.0000.0000.000
146C1212ARG10.9080.95536.7320.1030.1030.0000.0000.0000.000
147C1213PHE0-0.004-0.02535.7860.0060.0060.0000.0000.0000.000
148C1214PHE00.0570.05439.1760.0040.0040.0000.0000.0000.000
149C1215ALA0-0.024-0.02440.5340.0030.0030.0000.0000.0000.000
150C1216ILE0-0.115-0.05241.4790.0040.0040.0000.0000.0000.000
151C1217CYS0-0.064-0.02639.6300.0000.0000.0000.0000.0000.000
152C1218GLY00.0590.01240.043-0.007-0.0070.0000.0000.0000.000
153C1219LEU0-0.051-0.01541.6370.0020.0020.0000.0000.0000.000
154C1220GLN0-0.029-0.02344.7410.0050.0050.0000.0000.0000.000
155C1221GLU-1-0.832-0.91243.102-0.088-0.0880.0000.0000.0000.000
156C1222GLY0-0.0220.00745.260-0.001-0.0010.0000.0000.0000.000
157C1223PHE0-0.026-0.02639.299-0.002-0.0020.0000.0000.0000.000
158C1224GLU-1-0.916-0.96541.981-0.083-0.0830.0000.0000.0000.000
159C1225PRO0-0.024-0.01039.452-0.007-0.0070.0000.0000.0000.000
160C1226PHE00.0650.01034.7840.0010.0010.0000.0000.0000.000
161C1227ALA0-0.010-0.01638.0120.0020.0020.0000.0000.0000.000
162C1228ILE00.0050.02238.9730.0030.0030.0000.0000.0000.000
163C1229ASN0-0.033-0.02038.5890.0070.0070.0000.0000.0000.000
164C1230MET0-0.089-0.02034.175-0.003-0.0030.0000.0000.0000.000
165C1231GLN0-0.005-0.00139.1970.0050.0050.0000.0000.0000.000
166C1232ARG10.8600.92638.2350.1000.1000.0000.0000.0000.000
167C1233PRO00.0230.02439.6600.0040.0040.0000.0000.0000.000
168C1234VAL00.006-0.00842.8210.0010.0010.0000.0000.0000.000
169C1235THR0-0.034-0.03145.8990.0010.0010.0000.0000.0000.000
170C1236THR0-0.0080.01148.3200.0010.0010.0000.0000.0000.000
171C1237TRP00.0380.02351.9640.0010.0010.0000.0000.0000.000
172C1238PHE00.011-0.00754.6780.0000.0000.0000.0000.0000.000
173C1239SER0-0.029-0.01058.1850.0020.0020.0000.0000.0000.000
174C1240LYS10.9800.97361.7860.0310.0310.0000.0000.0000.000
175C1241SER00.0060.01064.3990.0010.0010.0000.0000.0000.000
176C1242LEU00.0860.04164.903-0.001-0.0010.0000.0000.0000.000
177C1243PRO0-0.032-0.03066.3930.0000.0000.0000.0000.0000.000
178C1244GLN0-0.062-0.01560.9470.0010.0010.0000.0000.0000.000
179C1245PHE0-0.0210.00158.615-0.002-0.0020.0000.0000.0000.000
180C1246GLU-1-0.971-0.97962.920-0.034-0.0340.0000.0000.0000.000