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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: YZYM2

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1879823.830781
FMO2-HF: Nuclear repulsion 1808397.368897
FMO2-HF: Total energy -71426.461884
FMO2-MP2: Total energy -71626.97821


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.
-0.6632.2110.456-1.093-2.2350.002
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 : -0.006 / q_NPA : -0.015
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].
3A13PHE0-0.027-0.0183.686-1.3510.7820.000-0.913-1.2190.002
4A14LEU00.0610.0385.5430.1340.1340.0000.0000.0000.000
5A15ARG10.7600.8778.1310.2390.2390.0000.0000.0000.000
6A16THR0-0.003-0.01712.3500.0330.0330.0000.0000.0000.000
7A17ASP-1-0.880-0.95915.746-0.066-0.0660.0000.0000.0000.000
8A18ASP-1-0.832-0.90211.378-0.060-0.0600.0000.0000.0000.000
9A19GLU-1-0.847-0.91015.0950.0730.0730.0000.0000.0000.000
10A20VAL0-0.062-0.03612.6970.0460.0460.0000.0000.0000.000
11A21VAL00.0300.02614.840-0.025-0.0250.0000.0000.0000.000
12A22LEU00.0170.00214.8720.0170.0170.0000.0000.0000.000
13A23GLN00.001-0.01314.3130.0390.0390.0000.0000.0000.000
14A24CYS00.0150.01716.241-0.009-0.0090.0000.0000.0000.000
15A25SER00.0270.00618.1510.0270.0270.0000.0000.0000.000
16A26ALA00.0150.01720.164-0.014-0.0140.0000.0000.0000.000
17A27THR0-0.033-0.03523.783-0.008-0.0080.0000.0000.0000.000
18A28VAL0-0.0010.00923.3800.0030.0030.0000.0000.0000.000
19A29LEU00.0130.01318.5620.0040.0040.0000.0000.0000.000
20A30LYS10.9230.96511.051-0.256-0.2560.0000.0000.0000.000
21A31GLU-1-0.938-0.97412.9860.4150.4150.0000.0000.0000.000
22A32GLN0-0.085-0.04416.0110.0040.0040.0000.0000.0000.000
23A33LEU0-0.019-0.01019.555-0.007-0.0070.0000.0000.0000.000
24A34LYS10.8510.92512.933-0.345-0.3450.0000.0000.0000.000
25A35LEU0-0.0130.00019.210-0.008-0.0080.0000.0000.0000.000
26A36CYS0-0.0010.00918.9100.0180.0180.0000.0000.0000.000
27A37LEU00.007-0.00519.944-0.015-0.0150.0000.0000.0000.000
28A38ALA00.0080.00521.9100.0070.0070.0000.0000.0000.000
29A39ALA00.015-0.00524.689-0.010-0.0100.0000.0000.0000.000
30A40GLU-1-0.862-0.92727.8000.0650.0650.0000.0000.0000.000
31A41GLY00.027-0.01730.5580.0000.0000.0000.0000.0000.000
32A42PHE0-0.044-0.02531.163-0.004-0.0040.0000.0000.0000.000
33A43GLY00.003-0.00235.326-0.001-0.0010.0000.0000.0000.000
34A44ASN0-0.027-0.00832.950-0.007-0.0070.0000.0000.0000.000
35A45ARG10.8030.86932.752-0.024-0.0240.0000.0000.0000.000
36A46LEU00.0090.01431.437-0.001-0.0010.0000.0000.0000.000
37A47CYS0-0.048-0.01026.3900.0020.0020.0000.0000.0000.000
38A48PHE0-0.039-0.01627.253-0.004-0.0040.0000.0000.0000.000
39A49LEU0-0.038-0.02422.9730.0050.0050.0000.0000.0000.000
40A50GLU-1-0.836-0.92723.2100.1120.1120.0000.0000.0000.000
41A51PRO0-0.038-0.01322.5540.0160.0160.0000.0000.0000.000
42A52THR00.0110.00119.4380.0140.0140.0000.0000.0000.000
43A61ASP-1-0.810-0.91321.7700.1950.1950.0000.0000.0000.000
44A62LEU00.011-0.01018.672-0.012-0.0120.0000.0000.0000.000
45A63ALA0-0.052-0.02622.270-0.010-0.0100.0000.0000.0000.000
46A64ILE0-0.013-0.01124.932-0.012-0.0120.0000.0000.0000.000
47A65CYS0-0.0110.00420.498-0.006-0.0060.0000.0000.0000.000
48A66CYS0-0.0390.00019.4970.0120.0120.0000.0000.0000.000
49A67PHE0-0.017-0.01819.117-0.020-0.0200.0000.0000.0000.000
50A68THR0-0.007-0.01718.4160.0110.0110.0000.0000.0000.000
51A69LEU0-0.030-0.01713.818-0.010-0.0100.0000.0000.0000.000
52A70GLU-1-0.790-0.88217.969-0.009-0.0090.0000.0000.0000.000
53A71GLN0-0.011-0.00720.176-0.020-0.0200.0000.0000.0000.000
54A72SER00.028-0.00616.4240.0030.0030.0000.0000.0000.000
55A73LEU0-0.050-0.00218.613-0.015-0.0150.0000.0000.0000.000
56A74SER00.0570.02820.9670.0060.0060.0000.0000.0000.000
57A75VAL00.0730.02821.8770.0050.0050.0000.0000.0000.000
58A76ARG10.8320.91624.7260.0530.0530.0000.0000.0000.000
59A77ALA00.0360.01624.2320.0040.0040.0000.0000.0000.000
60A78LEU00.0100.01724.8680.0030.0030.0000.0000.0000.000
61A79GLN00.0340.00426.7380.0010.0010.0000.0000.0000.000
62A80GLU-1-0.856-0.91629.469-0.050-0.0500.0000.0000.0000.000
63A81MET0-0.0020.00726.2830.0030.0030.0000.0000.0000.000
64A82LEU0-0.0050.00629.6510.0040.0040.0000.0000.0000.000
65A83ALA0-0.037-0.01732.4150.0030.0030.0000.0000.0000.000
66A84ASN0-0.116-0.06033.8290.0020.0020.0000.0000.0000.000
67A85THR0-0.050-0.01833.3900.0020.0020.0000.0000.0000.000
68A97GLY00.0370.01519.754-0.003-0.0030.0000.0000.0000.000
69A98HIS00.0350.05114.894-0.031-0.0310.0000.0000.0000.000
70A99ARG10.8810.93014.5110.0980.0980.0000.0000.0000.000
71A100THR0-0.035-0.0238.9470.0030.0030.0000.0000.0000.000
72A101LEU00.0380.03010.8400.0220.0220.0000.0000.0000.000
73A102LEU0-0.064-0.03910.621-0.066-0.0660.0000.0000.0000.000
74A103TYR0-0.017-0.0338.9230.0460.0460.0000.0000.0000.000
75A104GLY00.0360.02214.392-0.011-0.0110.0000.0000.0000.000
76A105HIS0-0.079-0.03815.6160.0180.0180.0000.0000.0000.000
77A106ALA00.0330.01218.3720.0080.0080.0000.0000.0000.000
78A107ILE0-0.045-0.04116.191-0.008-0.0080.0000.0000.0000.000
79A108LEU00.0100.01719.6790.0080.0080.0000.0000.0000.000
80A109LEU00.008-0.01017.5900.0000.0000.0000.0000.0000.000
81A110ARG10.9210.98421.650-0.016-0.0160.0000.0000.0000.000
82A111HIS00.0170.03323.0240.0020.0020.0000.0000.0000.000
83A112ALA00.0230.00122.234-0.006-0.0060.0000.0000.0000.000
84A113HIS0-0.038-0.00224.356-0.005-0.0050.0000.0000.0000.000
85A114SER00.007-0.02527.556-0.008-0.0080.0000.0000.0000.000
86A115ARG10.7980.89527.645-0.053-0.0530.0000.0000.0000.000
87A116MET0-0.0030.03628.997-0.004-0.0040.0000.0000.0000.000
88A117TYR0-0.044-0.05225.2100.0040.0040.0000.0000.0000.000
89A118LEU00.0150.01321.6200.0000.0000.0000.0000.0000.000
90A119SER0-0.035-0.01625.393-0.007-0.0070.0000.0000.0000.000
91A120CYS00.0030.02027.6310.0050.0050.0000.0000.0000.000
92A121LEU0-0.033-0.00229.179-0.003-0.0030.0000.0000.0000.000
93A122THR00.029-0.00132.808-0.001-0.0010.0000.0000.0000.000
94A123THR0-0.073-0.05435.787-0.001-0.0010.0000.0000.0000.000
95A124SER00.013-0.02435.4290.0010.0010.0000.0000.0000.000
96A125ARG10.8150.91536.242-0.028-0.0280.0000.0000.0000.000
97A126SER00.0170.01236.2680.0040.0040.0000.0000.0000.000
98A127MET0-0.0350.00638.1390.0000.0000.0000.0000.0000.000
99A128THR00.000-0.01540.594-0.001-0.0010.0000.0000.0000.000
100A129ASP-1-0.863-0.92939.7500.0200.0200.0000.0000.0000.000
101A130LYS10.8810.93231.873-0.035-0.0350.0000.0000.0000.000
102A131LEU0-0.0020.00135.292-0.001-0.0010.0000.0000.0000.000
103A132ALA0-0.070-0.03531.318-0.001-0.0010.0000.0000.0000.000
104A133PHE00.0070.01331.601-0.002-0.0020.0000.0000.0000.000
105A134ASP-1-0.747-0.85431.0720.0320.0320.0000.0000.0000.000
106A135VAL0-0.007-0.00525.662-0.003-0.0030.0000.0000.0000.000
107A136GLY00.0390.00528.8700.0050.0050.0000.0000.0000.000
108A137LEU0-0.0350.00627.116-0.002-0.0020.0000.0000.0000.000
109A138GLN00.0240.01229.799-0.001-0.0010.0000.0000.0000.000
110A139GLU-1-0.826-0.90830.9320.0210.0210.0000.0000.0000.000
111A140ASP-1-0.847-0.90632.3840.0010.0010.0000.0000.0000.000
112A141ALA00.009-0.00328.2300.0010.0010.0000.0000.0000.000
113A142THR0-0.050-0.04029.691-0.004-0.0040.0000.0000.0000.000
114A143GLY00.0080.00132.2250.0030.0030.0000.0000.0000.000
115A144GLU-1-0.902-0.97328.941-0.019-0.0190.0000.0000.0000.000
116A145ALA0-0.0100.00028.1630.0000.0000.0000.0000.0000.000
117A146CYS0-0.050-0.01626.8390.0030.0030.0000.0000.0000.000
118A147TRP00.0000.00522.700-0.004-0.0040.0000.0000.0000.000
119A148TRP0-0.004-0.01620.6160.0040.0040.0000.0000.0000.000
120A149THR0-0.028-0.01719.773-0.004-0.0040.0000.0000.0000.000
121A150MET0-0.0230.02014.2340.0130.0130.0000.0000.0000.000
122A151HIS0-0.006-0.01416.213-0.012-0.0120.0000.0000.0000.000
123A152PRO0-0.010-0.00913.3000.0140.0140.0000.0000.0000.000
124A153ALA00.0480.04413.4410.0090.0090.0000.0000.0000.000
125A154SER0-0.036-0.02513.262-0.003-0.0030.0000.0000.0000.000
126A155LYS10.9700.96514.1150.0580.0580.0000.0000.0000.000
127A156GLN0-0.0060.01510.064-0.043-0.0430.0000.0000.0000.000
128A157ARG10.7900.8945.4290.1940.1940.0000.0000.0000.000
129A158SER0-0.005-0.01311.4590.0280.0280.0000.0000.0000.000
130A159GLU-1-0.773-0.89613.728-0.103-0.1030.0000.0000.0000.000
131A160GLY0-0.023-0.00915.517-0.007-0.0070.0000.0000.0000.000
132A161GLU-1-0.831-0.8938.580-0.423-0.4230.0000.0000.0000.000
133A162LYS10.9350.9717.3550.5090.5090.0000.0000.0000.000
134A163VAL00.0310.0248.089-0.004-0.0040.0000.0000.0000.000
135A164ARG10.7160.8152.652-0.3550.2930.457-0.179-0.9260.000
136A165VAL00.002-0.0034.8670.1340.1340.0000.0000.0000.000
137A166GLY00.0010.0035.0950.1470.240-0.001-0.001-0.0900.000
138A167ASP-1-0.736-0.8206.226-0.222-0.2220.0000.0000.0000.000
139A168ASP-1-0.864-0.9027.9370.2130.2130.0000.0000.0000.000
140A169LEU0-0.081-0.04210.838-0.045-0.0450.0000.0000.0000.000
141A170ILE00.0180.00413.5650.0210.0210.0000.0000.0000.000
142A171LEU00.0150.00516.311-0.012-0.0120.0000.0000.0000.000
143A172VAL0-0.007-0.00119.1780.0080.0080.0000.0000.0000.000
144A173SER0-0.0010.00622.645-0.006-0.0060.0000.0000.0000.000
145A174VAL00.009-0.01924.338-0.003-0.0030.0000.0000.0000.000
146A175SER0-0.0140.00026.7150.0000.0000.0000.0000.0000.000
147A176SER0-0.047-0.04629.0260.0010.0010.0000.0000.0000.000
148A177GLU-1-0.936-0.95727.437-0.015-0.0150.0000.0000.0000.000
149A178ARG10.7970.92327.387-0.010-0.0100.0000.0000.0000.000
150A179TYR0-0.011-0.00722.036-0.001-0.0010.0000.0000.0000.000
151A180LEU00.0310.02420.0230.0030.0030.0000.0000.0000.000
152A181HIS10.7970.88422.251-0.038-0.0380.0000.0000.0000.000
153A182LEU00.0400.02623.2730.0020.0020.0000.0000.0000.000
154A183SER0-0.075-0.02625.398-0.007-0.0070.0000.0000.0000.000
155A184THR00.021-0.01428.6860.0050.0050.0000.0000.0000.000
156A185ALA0-0.023-0.00530.709-0.005-0.0050.0000.0000.0000.000
157A186SER0-0.022-0.00233.9580.0020.0020.0000.0000.0000.000
158A187GLY00.0380.01034.196-0.004-0.0040.0000.0000.0000.000
159A188GLU-1-0.954-0.99632.8690.0520.0520.0000.0000.0000.000
160A189LEU0-0.0310.00526.7450.0030.0030.0000.0000.0000.000
161A190GLN00.0310.01429.0050.0030.0030.0000.0000.0000.000
162A191VAL00.0320.01424.8220.0030.0030.0000.0000.0000.000
163A192ASP-1-0.813-0.88827.0750.0340.0340.0000.0000.0000.000
164A193ALA00.0780.04426.6100.0020.0020.0000.0000.0000.000
165A194SER00.009-0.00627.371-0.003-0.0030.0000.0000.0000.000
166A195PHE00.0860.02627.564-0.001-0.0010.0000.0000.0000.000
167A196MET0-0.040-0.00827.226-0.002-0.0020.0000.0000.0000.000
168A197GLN00.0330.01421.580-0.001-0.0010.0000.0000.0000.000
169A198THR0-0.031-0.02920.1170.0060.0060.0000.0000.0000.000
170A199LEU0-0.0230.00915.575-0.009-0.0090.0000.0000.0000.000
171A200TRP00.014-0.01315.7410.0200.0200.0000.0000.0000.000
172A201ASN0-0.042-0.03411.1340.0230.0230.0000.0000.0000.000
173A202MET00.0190.01711.192-0.014-0.0140.0000.0000.0000.000
174A203ASN00.009-0.0139.007-0.054-0.0540.0000.0000.0000.000
175A204PRO00.0360.0169.253-0.039-0.0390.0000.0000.0000.000
176A205ILE0-0.0250.00712.0810.0890.0890.0000.0000.0000.000