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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: 5238Z

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1876936.721437
FMO2-HF: Nuclear repulsion 1805510.95327
FMO2-HF: Total energy -71425.768167
FMO2-MP2: Total energy -71626.312978


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.
-1.3172.140.675-1.245-2.8910.001
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 : -0.014 / 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].
3A13PHE0-0.040-0.0323.615-1.8750.5510.005-1.002-1.4300.001
4A14LEU00.0650.0395.3020.1340.171-0.001-0.002-0.0350.000
5A15ARG10.8590.9227.7470.3960.3960.0000.0000.0000.000
6A16THR0-0.017-0.01711.8890.0270.0270.0000.0000.0000.000
7A17ASP-1-0.891-0.96715.447-0.052-0.0520.0000.0000.0000.000
8A18ASP-1-0.876-0.91311.202-0.054-0.0540.0000.0000.0000.000
9A19GLU-1-0.868-0.92514.8660.0670.0670.0000.0000.0000.000
10A20VAL0-0.067-0.05312.5430.0420.0420.0000.0000.0000.000
11A21VAL00.0320.03314.539-0.020-0.0200.0000.0000.0000.000
12A22LEU00.013-0.00314.8070.0080.0080.0000.0000.0000.000
13A23GLN00.0290.01214.5860.0230.0230.0000.0000.0000.000
14A24CYS00.0090.01815.783-0.011-0.0110.0000.0000.0000.000
15A25SER00.022-0.00117.8710.0220.0220.0000.0000.0000.000
16A26ALA00.0130.01219.710-0.013-0.0130.0000.0000.0000.000
17A27THR0-0.045-0.05123.482-0.007-0.0070.0000.0000.0000.000
18A28VAL00.0360.00422.688-0.002-0.0020.0000.0000.0000.000
19A29LEU00.0010.03318.8930.0060.0060.0000.0000.0000.000
20A30LYS10.8910.94111.302-0.142-0.1420.0000.0000.0000.000
21A31GLU-1-0.917-0.96113.2510.3220.3220.0000.0000.0000.000
22A32GLN0-0.067-0.02916.3370.0040.0040.0000.0000.0000.000
23A33LEU0-0.0140.00519.9980.0000.0000.0000.0000.0000.000
24A34LYS10.8220.92313.327-0.259-0.2590.0000.0000.0000.000
25A35LEU0-0.010-0.00119.617-0.002-0.0020.0000.0000.0000.000
26A36CYS0-0.029-0.01019.3120.0150.0150.0000.0000.0000.000
27A37LEU0-0.001-0.00720.037-0.010-0.0100.0000.0000.0000.000
28A38ALA00.0180.00921.9130.0080.0080.0000.0000.0000.000
29A39ALA00.0270.00724.649-0.010-0.0100.0000.0000.0000.000
30A40GLU-1-0.885-0.93327.6590.0550.0550.0000.0000.0000.000
31A41GLY00.032-0.00830.4040.0010.0010.0000.0000.0000.000
32A42PHE0-0.045-0.02331.145-0.003-0.0030.0000.0000.0000.000
33A43GLY00.0150.01035.2890.0000.0000.0000.0000.0000.000
34A44ASN0-0.058-0.03533.148-0.006-0.0060.0000.0000.0000.000
35A45ARG10.8230.88332.190-0.015-0.0150.0000.0000.0000.000
36A46LEU00.0250.03430.757-0.001-0.0010.0000.0000.0000.000
37A47CYS0-0.025-0.00326.1210.0020.0020.0000.0000.0000.000
38A48PHE0-0.048-0.01727.177-0.004-0.0040.0000.0000.0000.000
39A49LEU0-0.053-0.03323.1470.0040.0040.0000.0000.0000.000
40A50GLU-1-0.835-0.92423.2930.1000.1000.0000.0000.0000.000
41A51PRO0-0.018-0.00722.4370.0120.0120.0000.0000.0000.000
42A52THR00.0160.00219.1680.0100.0100.0000.0000.0000.000
43A61ASP-1-0.849-0.94521.8390.1760.1760.0000.0000.0000.000
44A62LEU00.0440.01418.852-0.009-0.0090.0000.0000.0000.000
45A63ALA0-0.064-0.02022.457-0.009-0.0090.0000.0000.0000.000
46A64ILE00.000-0.00925.015-0.010-0.0100.0000.0000.0000.000
47A65CYS00.0000.00620.235-0.007-0.0070.0000.0000.0000.000
48A66CYS0-0.056-0.01619.2990.0070.0070.0000.0000.0000.000
49A67PHE0-0.011-0.01518.875-0.019-0.0190.0000.0000.0000.000
50A68THR0-0.006-0.02718.2170.0120.0120.0000.0000.0000.000
51A69LEU0-0.047-0.01813.285-0.014-0.0140.0000.0000.0000.000
52A70GLU-1-0.812-0.88717.434-0.017-0.0170.0000.0000.0000.000
53A71GLN00.0140.00819.669-0.020-0.0200.0000.0000.0000.000
54A72SER00.0350.00116.074-0.001-0.0010.0000.0000.0000.000
55A73LEU0-0.067-0.01818.162-0.011-0.0110.0000.0000.0000.000
56A74SER00.0590.04420.4070.0040.0040.0000.0000.0000.000
57A75VAL00.1000.03421.3940.0060.0060.0000.0000.0000.000
58A76ARG10.8470.92124.1970.0640.0640.0000.0000.0000.000
59A77ALA00.0190.01023.8150.0050.0050.0000.0000.0000.000
60A78LEU0-0.0010.00524.2040.0050.0050.0000.0000.0000.000
61A79GLN00.024-0.01126.1670.0020.0020.0000.0000.0000.000
62A80GLU-1-0.853-0.90829.036-0.058-0.0580.0000.0000.0000.000
63A81MET0-0.027-0.00825.9670.0040.0040.0000.0000.0000.000
64A82LEU00.0010.00529.0000.0040.0040.0000.0000.0000.000
65A83ALA0-0.035-0.01031.9500.0030.0030.0000.0000.0000.000
66A84ASN0-0.136-0.06733.4920.0040.0040.0000.0000.0000.000
67A85THR0-0.0100.00433.3510.0010.0010.0000.0000.0000.000
68A97GLY00.017-0.00719.454-0.004-0.0040.0000.0000.0000.000
69A98HIS00.0110.04414.504-0.018-0.0180.0000.0000.0000.000
70A99ARG10.9140.95314.0500.1100.1100.0000.0000.0000.000
71A100THR0-0.038-0.0208.428-0.011-0.0110.0000.0000.0000.000
72A101LEU00.0280.02110.7380.0230.0230.0000.0000.0000.000
73A102LEU0-0.037-0.03710.498-0.071-0.0710.0000.0000.0000.000
74A103TYR0-0.024-0.0378.5730.0480.0480.0000.0000.0000.000
75A104GLY00.0480.02513.972-0.007-0.0070.0000.0000.0000.000
76A105HIS0-0.085-0.04215.4140.0210.0210.0000.0000.0000.000
77A106ALA00.020-0.00917.8690.0070.0070.0000.0000.0000.000
78A107ILE0-0.039-0.03715.695-0.008-0.0080.0000.0000.0000.000
79A108LEU0-0.0020.01819.1290.0090.0090.0000.0000.0000.000
80A109LEU00.007-0.01117.2420.0000.0000.0000.0000.0000.000
81A110ARG10.9430.99321.224-0.010-0.0100.0000.0000.0000.000
82A111HIS00.0130.04522.5410.0030.0030.0000.0000.0000.000
83A112ALA00.0140.01422.279-0.005-0.0050.0000.0000.0000.000
84A113HIS0-0.023-0.00924.373-0.003-0.0030.0000.0000.0000.000
85A114SER00.011-0.02227.270-0.007-0.0070.0000.0000.0000.000
86A115ARG10.8220.91227.377-0.046-0.0460.0000.0000.0000.000
87A116MET0-0.0230.00928.668-0.005-0.0050.0000.0000.0000.000
88A117TYR0-0.023-0.04224.8690.0040.0040.0000.0000.0000.000
89A118LEU00.0240.01921.5820.0010.0010.0000.0000.0000.000
90A119SER0-0.042-0.02225.210-0.007-0.0070.0000.0000.0000.000
91A120CYS00.0090.02327.3310.0050.0050.0000.0000.0000.000
92A121LEU0-0.045-0.01228.800-0.002-0.0020.0000.0000.0000.000
93A122THR00.014-0.01232.360-0.001-0.0010.0000.0000.0000.000
94A123THR0-0.089-0.05535.458-0.001-0.0010.0000.0000.0000.000
95A124SER00.026-0.01435.4170.0000.0000.0000.0000.0000.000
96A125ARG10.8780.95536.415-0.020-0.0200.0000.0000.0000.000
97A126SER00.0580.02036.3550.0020.0020.0000.0000.0000.000
98A127MET0-0.058-0.00838.0420.0000.0000.0000.0000.0000.000
99A128THR0-0.040-0.02640.301-0.001-0.0010.0000.0000.0000.000
100A129ASP-1-0.875-0.93339.2540.0100.0100.0000.0000.0000.000
101A130LYS10.8810.92931.737-0.018-0.0180.0000.0000.0000.000
102A131LEU0-0.017-0.01334.912-0.001-0.0010.0000.0000.0000.000
103A132ALA0-0.049-0.01530.779-0.002-0.0020.0000.0000.0000.000
104A133PHE00.0100.01431.0420.0000.0000.0000.0000.0000.000
105A134ASP-1-0.764-0.86730.5070.0200.0200.0000.0000.0000.000
106A135VAL0-0.003-0.00425.101-0.004-0.0040.0000.0000.0000.000
107A136GLY00.025-0.01028.2400.0050.0050.0000.0000.0000.000
108A137LEU0-0.038-0.00626.773-0.003-0.0030.0000.0000.0000.000
109A138GLN0-0.005-0.00629.544-0.001-0.0010.0000.0000.0000.000
110A139GLU-1-0.860-0.92830.6270.0130.0130.0000.0000.0000.000
111A140ASP-1-0.829-0.89032.037-0.005-0.0050.0000.0000.0000.000
112A141ALA0-0.008-0.00227.8280.0000.0000.0000.0000.0000.000
113A142THR0-0.037-0.04629.715-0.005-0.0050.0000.0000.0000.000
114A143GLY0-0.010-0.00431.7970.0030.0030.0000.0000.0000.000
115A144GLU-1-0.904-0.97628.900-0.030-0.0300.0000.0000.0000.000
116A145ALA0-0.026-0.01127.885-0.001-0.0010.0000.0000.0000.000
117A146CYS0-0.038-0.00126.5050.0020.0020.0000.0000.0000.000
118A147TRP00.0240.01221.801-0.006-0.0060.0000.0000.0000.000
119A148TRP0-0.002-0.00920.2230.0040.0040.0000.0000.0000.000
120A149THR0-0.013-0.00919.394-0.006-0.0060.0000.0000.0000.000
121A150MET0-0.0380.01014.1170.0070.0070.0000.0000.0000.000
122A151HIS00.0150.00416.052-0.009-0.0090.0000.0000.0000.000
123A152PRO00.0080.00913.0560.0100.0100.0000.0000.0000.000
124A153ALA00.0310.03713.1570.0130.0130.0000.0000.0000.000
125A154SER0-0.020-0.02813.2940.0010.0010.0000.0000.0000.000
126A155LYS10.9660.96614.5230.0850.0850.0000.0000.0000.000
127A156GLN0-0.032-0.0039.840-0.044-0.0440.0000.0000.0000.000
128A157ARG10.7920.9005.0170.3110.3110.0000.0000.0000.000
129A158SER00.021-0.00711.1020.0350.0350.0000.0000.0000.000
130A159GLU-1-0.827-0.91913.498-0.138-0.1380.0000.0000.0000.000
131A160GLY00.0030.00415.020-0.001-0.0010.0000.0000.0000.000
132A161GLU-1-0.852-0.9128.818-0.451-0.4510.0000.0000.0000.000
133A162LYS10.9380.9706.9440.5860.5860.0000.0000.0000.000
134A163VAL00.0380.0307.803-0.016-0.0160.0000.0000.0000.000
135A164ARG10.7130.8272.778-0.3390.3750.673-0.221-1.1670.000
136A165VAL00.0290.0164.364-0.0050.154-0.001-0.016-0.1430.000
137A166GLY0-0.011-0.0074.790-0.0250.096-0.001-0.004-0.1160.000
138A167ASP-1-0.747-0.8175.925-0.337-0.3370.0000.0000.0000.000
139A168ASP-1-0.883-0.9237.7920.1170.1170.0000.0000.0000.000
140A169LEU0-0.053-0.03310.737-0.036-0.0360.0000.0000.0000.000
141A170ILE0-0.008-0.01213.4490.0240.0240.0000.0000.0000.000
142A171LEU00.0290.01416.329-0.012-0.0120.0000.0000.0000.000
143A172VAL00.0100.01219.0100.0090.0090.0000.0000.0000.000
144A173SER00.0030.00622.294-0.005-0.0050.0000.0000.0000.000
145A174VAL00.0110.00124.036-0.002-0.0020.0000.0000.0000.000
146A175SER00.0110.01826.4290.0010.0010.0000.0000.0000.000
147A176SER0-0.043-0.05428.8160.0000.0000.0000.0000.0000.000
148A177GLU-1-0.930-0.96026.969-0.031-0.0310.0000.0000.0000.000
149A178ARG10.7820.91427.1600.0040.0040.0000.0000.0000.000
150A179TYR00.006-0.00921.817-0.001-0.0010.0000.0000.0000.000
151A180LEU00.0020.02019.6270.0050.0050.0000.0000.0000.000
152A181HIS10.7930.87321.770-0.019-0.0190.0000.0000.0000.000
153A182LEU00.0440.03422.7870.0020.0020.0000.0000.0000.000
154A183SER0-0.058-0.03024.962-0.005-0.0050.0000.0000.0000.000
155A184THR00.0260.00228.2250.0030.0030.0000.0000.0000.000
156A185ALA0-0.018-0.01130.295-0.003-0.0030.0000.0000.0000.000
157A186SER0-0.022-0.00733.5660.0020.0020.0000.0000.0000.000
158A187GLY00.0380.01034.099-0.003-0.0030.0000.0000.0000.000
159A188GLU-1-0.979-0.99932.9560.0390.0390.0000.0000.0000.000
160A189LEU0-0.061-0.00326.5300.0040.0040.0000.0000.0000.000
161A190GLN00.0350.01329.1650.0000.0000.0000.0000.0000.000
162A191VAL00.033-0.00124.2170.0020.0020.0000.0000.0000.000
163A192ASP-1-0.786-0.87726.5070.0180.0180.0000.0000.0000.000
164A193ALA00.0800.05126.1110.0000.0000.0000.0000.0000.000
165A194SER0-0.003-0.01126.969-0.002-0.0020.0000.0000.0000.000
166A195PHE00.0820.02127.248-0.002-0.0020.0000.0000.0000.000
167A196MET0-0.037-0.00926.835-0.003-0.0030.0000.0000.0000.000
168A197GLN00.0280.01021.188-0.003-0.0030.0000.0000.0000.000
169A198THR0-0.023-0.01819.7440.0050.0050.0000.0000.0000.000
170A199LEU0-0.0240.00815.248-0.008-0.0080.0000.0000.0000.000
171A200TRP00.017-0.01015.3040.0210.0210.0000.0000.0000.000
172A201ASN0-0.050-0.03010.7710.0130.0130.0000.0000.0000.000
173A202MET00.0330.02410.6420.0030.0030.0000.0000.0000.000
174A203ASN0-0.013-0.0208.908-0.067-0.0670.0000.0000.0000.000
175A204PRO00.0560.0168.740-0.036-0.0360.0000.0000.0000.000
176A205ILE0-0.0200.01311.6650.0910.0910.0000.0000.0000.000