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About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 4938N

Calculation Name: 3HSM-A-Xray372

Preferred Name: Ryanodine receptor 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3HSM

Chain ID: A

ChEMBL ID: CHEMBL3288

UniProt ID: P11716

Base Structure: X-ray

Registration Date: 2023-06-21

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1876684.662108
FMO2-HF: Nuclear repulsion 1805259.870159
FMO2-HF: Total energy -71424.791948
FMO2-MP2: Total energy -71625.429743


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:11:VAL)


Summations of interaction energy for fragment #1(A:11: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.
-1.4932.1931.275-1.412-3.5470.002
Interaction energy analysis for fragmet #1(A:11:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.010
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].
3A13PHE0-0.064-0.0413.187-2.2250.5480.127-1.109-1.7910.001
4A14LEU00.0650.0365.3170.0870.126-0.001-0.001-0.0350.000
5A15ARG10.8670.9277.2150.5760.5760.0000.0000.0000.000
6A16THR0-0.012-0.01911.8820.0270.0270.0000.0000.0000.000
7A17ASP-1-0.909-0.97715.396-0.074-0.0740.0000.0000.0000.000
8A18ASP-1-0.870-0.90711.446-0.117-0.1170.0000.0000.0000.000
9A19GLU-1-0.911-0.96714.8700.0510.0510.0000.0000.0000.000
10A20VAL0-0.064-0.04812.5930.0370.0370.0000.0000.0000.000
11A21VAL00.0250.03314.535-0.019-0.0190.0000.0000.0000.000
12A22LEU00.016-0.01114.7980.0100.0100.0000.0000.0000.000
13A23GLN00.0310.01014.0560.0210.0210.0000.0000.0000.000
14A24CYS00.0150.02015.992-0.007-0.0070.0000.0000.0000.000
15A25SER0-0.003-0.01417.1260.0240.0240.0000.0000.0000.000
16A26ALA00.0340.02219.633-0.013-0.0130.0000.0000.0000.000
17A27THR0-0.070-0.05223.390-0.006-0.0060.0000.0000.0000.000
18A28VAL00.0350.00222.553-0.004-0.0040.0000.0000.0000.000
19A29LEU00.0070.03318.9910.0060.0060.0000.0000.0000.000
20A30LYS10.8880.94011.110-0.209-0.2090.0000.0000.0000.000
21A31GLU-1-0.910-0.96213.1710.3970.3970.0000.0000.0000.000
22A32GLN0-0.067-0.02716.2820.0040.0040.0000.0000.0000.000
23A33LEU0-0.0050.00719.978-0.002-0.0020.0000.0000.0000.000
24A34LYS10.8230.93213.671-0.280-0.2800.0000.0000.0000.000
25A35LEU0-0.0020.00119.621-0.005-0.0050.0000.0000.0000.000
26A36CYS0-0.013-0.00318.9380.0150.0150.0000.0000.0000.000
27A37LEU00.0130.00020.057-0.012-0.0120.0000.0000.0000.000
28A38ALA00.0130.00921.9070.0060.0060.0000.0000.0000.000
29A39ALA00.0300.00624.643-0.009-0.0090.0000.0000.0000.000
30A40GLU-1-0.931-0.96127.6540.0570.0570.0000.0000.0000.000
31A41GLY00.026-0.00530.4000.0000.0000.0000.0000.0000.000
32A42PHE0-0.043-0.01731.171-0.004-0.0040.0000.0000.0000.000
33A43GLY00.0180.01235.2830.0000.0000.0000.0000.0000.000
34A44ASN0-0.023-0.01233.369-0.005-0.0050.0000.0000.0000.000
35A45ARG10.9360.96032.072-0.016-0.0160.0000.0000.0000.000
36A46LEU00.0280.03430.676-0.001-0.0010.0000.0000.0000.000
37A47CYS0-0.0320.00025.1220.0020.0020.0000.0000.0000.000
38A48PHE0-0.040-0.01027.196-0.004-0.0040.0000.0000.0000.000
39A49LEU0-0.050-0.03523.3680.0040.0040.0000.0000.0000.000
40A50GLU-1-0.867-0.93423.2690.1070.1070.0000.0000.0000.000
41A51PRO0-0.026-0.01122.4400.0130.0130.0000.0000.0000.000
42A52THR00.0250.00619.0680.0140.0140.0000.0000.0000.000
43A61ASP-1-0.871-0.94721.4700.1750.1750.0000.0000.0000.000
44A62LEU00.0660.01418.706-0.009-0.0090.0000.0000.0000.000
45A63ALA0-0.063-0.01822.462-0.009-0.0090.0000.0000.0000.000
46A64ILE00.0180.00124.782-0.010-0.0100.0000.0000.0000.000
47A65CYS0-0.0050.00120.226-0.005-0.0050.0000.0000.0000.000
48A66CYS0-0.070-0.02019.3060.0030.0030.0000.0000.0000.000
49A67PHE00.008-0.00818.764-0.018-0.0180.0000.0000.0000.000
50A68THR00.0330.01318.0490.0130.0130.0000.0000.0000.000
51A69LEU0-0.059-0.02313.036-0.010-0.0100.0000.0000.0000.000
52A70GLU-1-0.879-0.94417.319-0.031-0.0310.0000.0000.0000.000
53A71GLN00.0260.01419.730-0.021-0.0210.0000.0000.0000.000
54A72SER00.005-0.00915.2910.0080.0080.0000.0000.0000.000
55A73LEU0-0.037-0.01018.295-0.012-0.0120.0000.0000.0000.000
56A74SER00.0600.05220.5110.0050.0050.0000.0000.0000.000
57A75VAL00.1060.03521.5410.0050.0050.0000.0000.0000.000
58A76ARG10.8860.95524.2620.0600.0600.0000.0000.0000.000
59A77ALA00.0230.01123.9130.0040.0040.0000.0000.0000.000
60A78LEU0-0.0070.00024.0030.0040.0040.0000.0000.0000.000
61A79GLN00.027-0.01426.2870.0020.0020.0000.0000.0000.000
62A80GLU-1-0.894-0.94329.169-0.058-0.0580.0000.0000.0000.000
63A81MET0-0.029-0.01026.1830.0030.0030.0000.0000.0000.000
64A82LEU0-0.019-0.01229.0480.0040.0040.0000.0000.0000.000
65A83ALA0-0.030-0.01032.0330.0030.0030.0000.0000.0000.000
66A84ASN0-0.122-0.04933.4800.0040.0040.0000.0000.0000.000
67A85THR0-0.0120.00533.4770.0000.0000.0000.0000.0000.000
68A97GLY00.025-0.00619.303-0.004-0.0040.0000.0000.0000.000
69A98HIS00.0450.06714.211-0.024-0.0240.0000.0000.0000.000
70A99ARG10.8970.94613.8480.1240.1240.0000.0000.0000.000
71A100THR0-0.028-0.0208.315-0.047-0.0470.0000.0000.0000.000
72A101LEU0-0.0040.00110.7970.0310.0310.0000.0000.0000.000
73A102LEU0-0.034-0.03110.634-0.065-0.0650.0000.0000.0000.000
74A103TYR0-0.026-0.0578.4570.0400.0400.0000.0000.0000.000
75A104GLY00.0600.03513.883-0.008-0.0080.0000.0000.0000.000
76A105HIS0-0.090-0.04215.9300.0170.0170.0000.0000.0000.000
77A106ALA00.013-0.01017.8700.0090.0090.0000.0000.0000.000
78A107ILE0-0.038-0.04115.562-0.009-0.0090.0000.0000.0000.000
79A108LEU0-0.0010.01618.9910.0100.0100.0000.0000.0000.000
80A109LEU00.001-0.01317.142-0.001-0.0010.0000.0000.0000.000
81A110ARG10.9540.99120.958-0.002-0.0020.0000.0000.0000.000
82A111HIS00.0030.02522.2540.0010.0010.0000.0000.0000.000
83A112ALA00.0080.00722.313-0.005-0.0050.0000.0000.0000.000
84A113HIS0-0.032-0.00724.367-0.005-0.0050.0000.0000.0000.000
85A114SER00.020-0.00527.267-0.007-0.0070.0000.0000.0000.000
86A115ARG10.8700.93527.163-0.032-0.0320.0000.0000.0000.000
87A116MET0-0.0240.00728.408-0.005-0.0050.0000.0000.0000.000
88A117TYR00.0280.00424.6220.0030.0030.0000.0000.0000.000
89A118LEU00.0260.02021.3270.0020.0020.0000.0000.0000.000
90A119SER0-0.035-0.02125.047-0.007-0.0070.0000.0000.0000.000
91A120CYS0-0.0140.00527.1990.0060.0060.0000.0000.0000.000
92A121LEU0-0.039-0.01228.736-0.003-0.0030.0000.0000.0000.000
93A122THR00.004-0.01432.3000.0000.0000.0000.0000.0000.000
94A123THR0-0.059-0.03635.4200.0000.0000.0000.0000.0000.000
95A124SER00.017-0.01135.4450.0000.0000.0000.0000.0000.000
96A125ARG10.8990.96036.508-0.024-0.0240.0000.0000.0000.000
97A126SER00.0610.03336.4810.0030.0030.0000.0000.0000.000
98A127MET0-0.063-0.01338.2070.0000.0000.0000.0000.0000.000
99A128THR0-0.041-0.02940.392-0.001-0.0010.0000.0000.0000.000
100A129ASP-1-0.858-0.92939.5350.0160.0160.0000.0000.0000.000
101A130LYS10.9920.98632.048-0.022-0.0220.0000.0000.0000.000
102A131LEU0-0.038-0.02234.981-0.001-0.0010.0000.0000.0000.000
103A132ALA0-0.060-0.02630.957-0.001-0.0010.0000.0000.0000.000
104A133PHE0-0.0160.00131.103-0.001-0.0010.0000.0000.0000.000
105A134ASP-1-0.778-0.88230.5790.0270.0270.0000.0000.0000.000
106A135VAL0-0.011-0.00925.113-0.004-0.0040.0000.0000.0000.000
107A136GLY00.027-0.01428.1740.0040.0040.0000.0000.0000.000
108A137LEU0-0.042-0.00826.648-0.004-0.0040.0000.0000.0000.000
109A138GLN00.005-0.00129.343-0.002-0.0020.0000.0000.0000.000
110A139GLU-1-0.971-0.99930.3780.0120.0120.0000.0000.0000.000
111A140ASP-1-0.836-0.90331.804-0.007-0.0070.0000.0000.0000.000
112A141ALA00.006-0.00427.8630.0010.0010.0000.0000.0000.000
113A142THR0-0.049-0.03929.574-0.004-0.0040.0000.0000.0000.000
114A143GLY0-0.020-0.00931.5940.0030.0030.0000.0000.0000.000
115A144GLU-1-0.908-0.97828.712-0.025-0.0250.0000.0000.0000.000
116A145ALA0-0.026-0.01227.707-0.001-0.0010.0000.0000.0000.000
117A146CYS0-0.056-0.00826.3120.0020.0020.0000.0000.0000.000
118A147TRP00.0290.01721.795-0.006-0.0060.0000.0000.0000.000
119A148TRP0-0.007-0.01420.0000.0060.0060.0000.0000.0000.000
120A149THR0-0.015-0.01419.268-0.007-0.0070.0000.0000.0000.000
121A150MET0-0.0280.00813.4370.0090.0090.0000.0000.0000.000
122A151HIS00.0300.03416.116-0.011-0.0110.0000.0000.0000.000
123A152PRO00.0120.00213.2640.0120.0120.0000.0000.0000.000
124A153ALA00.0350.04113.4430.0090.0090.0000.0000.0000.000
125A154SER0-0.022-0.02613.422-0.001-0.0010.0000.0000.0000.000
126A155LYS10.9550.95714.6980.0500.0500.0000.0000.0000.000
127A156GLN0-0.0240.00110.048-0.034-0.0340.0000.0000.0000.000
128A157ARG10.7900.9044.5260.1070.176-0.001-0.002-0.0660.000
129A158SER00.0290.00311.2200.0290.0290.0000.0000.0000.000
130A159GLU-1-0.879-0.95013.494-0.108-0.1080.0000.0000.0000.000
131A160GLY00.0030.00514.931-0.003-0.0030.0000.0000.0000.000
132A161GLU-1-0.945-0.9739.638-0.263-0.2630.0000.0000.0000.000
133A162LYS10.9430.9626.8420.5640.5640.0000.0000.0000.000
134A163VAL00.0570.0517.7610.0080.0080.0000.0000.0000.000
135A164ARG10.8070.8912.684-0.3940.1181.152-0.279-1.3860.001
136A165VAL00.0350.0224.118-0.0040.170-0.001-0.019-0.1540.000
137A166GLY0-0.016-0.0114.9820.0000.119-0.001-0.002-0.1150.000
138A167ASP-1-0.753-0.8175.795-0.193-0.1930.0000.0000.0000.000
139A168ASP-1-0.879-0.9248.0910.1680.1680.0000.0000.0000.000
140A169LEU0-0.044-0.03010.737-0.034-0.0340.0000.0000.0000.000
141A170ILE0-0.023-0.01913.6410.0210.0210.0000.0000.0000.000
142A171LEU00.0200.01016.231-0.013-0.0130.0000.0000.0000.000
143A172VAL00.0150.01419.0510.0090.0090.0000.0000.0000.000
144A173SER00.0130.01122.310-0.006-0.0060.0000.0000.0000.000
145A174VAL00.0150.00623.914-0.002-0.0020.0000.0000.0000.000
146A175SER00.0160.01326.3160.0010.0010.0000.0000.0000.000
147A176SER0-0.031-0.02828.7540.0000.0000.0000.0000.0000.000
148A177GLU-1-0.922-0.96027.010-0.021-0.0210.0000.0000.0000.000
149A178ARG10.8140.94127.237-0.004-0.0040.0000.0000.0000.000
150A179TYR00.017-0.00921.744-0.001-0.0010.0000.0000.0000.000
151A180LEU00.0000.02319.6230.0040.0040.0000.0000.0000.000
152A181HIS10.7830.86821.934-0.031-0.0310.0000.0000.0000.000
153A182LEU00.0360.03823.4250.0010.0010.0000.0000.0000.000
154A183SER0-0.074-0.03825.201-0.003-0.0030.0000.0000.0000.000
155A184THR00.0490.02328.4740.0030.0030.0000.0000.0000.000
156A185ALA0-0.032-0.03030.533-0.004-0.0040.0000.0000.0000.000
157A186SER0-0.035-0.01333.8050.0020.0020.0000.0000.0000.000
158A187GLY00.0420.01634.293-0.004-0.0040.0000.0000.0000.000
159A188GLU-1-0.970-0.99733.2790.0470.0470.0000.0000.0000.000
160A189LEU0-0.0550.00226.6290.0040.0040.0000.0000.0000.000
161A190GLN00.0240.00329.2750.0000.0000.0000.0000.0000.000
162A191VAL00.023-0.00624.1910.0030.0030.0000.0000.0000.000
163A192ASP-1-0.819-0.89626.7000.0300.0300.0000.0000.0000.000
164A193ALA00.0590.04526.2310.0010.0010.0000.0000.0000.000
165A194SER0-0.022-0.02727.108-0.002-0.0020.0000.0000.0000.000
166A195PHE00.0560.00527.409-0.002-0.0020.0000.0000.0000.000
167A196MET0-0.036-0.00927.099-0.001-0.0010.0000.0000.0000.000
168A197GLN00.0380.00921.442-0.004-0.0040.0000.0000.0000.000
169A198THR0-0.010-0.00519.8510.0040.0040.0000.0000.0000.000
170A199LEU0-0.038-0.00415.521-0.008-0.0080.0000.0000.0000.000
171A200TRP00.006-0.01415.5130.0190.0190.0000.0000.0000.000
172A201ASN0-0.051-0.03110.9690.0220.0220.0000.0000.0000.000
173A202MET00.0340.02310.691-0.005-0.0050.0000.0000.0000.000
174A203ASN0-0.028-0.0238.844-0.060-0.0600.0000.0000.0000.000
175A204PRO00.0570.0168.712-0.039-0.0390.0000.0000.0000.000
176A205ILE0-0.0140.01311.6660.0960.0960.0000.0000.0000.000