FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: RYR88

Calculation Name: 2EPI-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EPI

Chain ID: A

ChEMBL ID:

UniProt ID: Q58452

Base Structure: X-ray

Registration Date: 2025-07-10

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 190
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -688858.416928
FMO2-HF: Nuclear repulsion 650851.147593
FMO2-HF: Total energy -38007.269335
FMO2-MP2: Total energy -38118.943381


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:2:ILE)


Summations of interaction energy for fragment #1(A:2:ILE)
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.
-3.278-0.6720.026-1.192-1.4390.001
Interaction energy analysis for fragmet #1(A:2:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.083 / q_NPA : 0.023
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].
4A3PHE0-0.0480.0854.511-1.228-0.8340.003-0.101-0.2960.000
5A4MET00.231-0.0602.917-1.6370.3590.026-1.070-0.9510.001
6A4MET0-0.1570.0944.633-0.149-0.098-0.001-0.006-0.0430.000
7A5ARG00.100-0.0834.5380.2480.413-0.002-0.015-0.1490.000
8A5ARG10.7170.9525.581-0.299-0.2990.0000.0000.0000.000
9A6LYS00.098-0.0935.810-0.295-0.2950.0000.0000.0000.000
10A6LYS10.7290.9788.244-0.914-0.9140.0000.0000.0000.000
11A7VAL0-0.015-0.1138.6140.0080.0080.0000.0000.0000.000
12A7VAL0-0.0580.11310.451-0.024-0.0240.0000.0000.0000.000
13A8VAL00.145-0.07112.0090.0340.0340.0000.0000.0000.000
14A8VAL0-0.1130.07715.246-0.006-0.0060.0000.0000.0000.000
15A9ALA00.075-0.10315.635-0.015-0.0150.0000.0000.0000.000
16A9ALA0-0.0520.10016.377-0.003-0.0030.0000.0000.0000.000
17A10GLU00.096-0.11217.9680.0150.0150.0000.0000.0000.000
18A10GLU-1-0.950-0.80122.2720.1370.1370.0000.0000.0000.000
19A11VAL00.031-0.11621.597-0.009-0.0090.0000.0000.0000.000
20A11VAL0-0.0450.11920.830-0.002-0.0020.0000.0000.0000.000
21A12SER00.057-0.09323.5050.0060.0060.0000.0000.0000.000
22A12SER0-0.0030.10227.7750.0010.0010.0000.0000.0000.000
23A13ILE00.022-0.10327.293-0.005-0.0050.0000.0000.0000.000
24A13ILE0-0.0490.10725.3950.0000.0000.0000.0000.0000.000
25A14ILE00.074-0.11529.2820.0030.0030.0000.0000.0000.000
26A14ILE0-0.0830.11831.6660.0000.0000.0000.0000.0000.000
27A15PRO00.014-0.10533.023-0.005-0.0050.0000.0000.0000.000
28A16LEU00.037-0.00935.0480.0030.0030.0000.0000.0000.000
29A16LEU0-0.1330.08736.201-0.001-0.0010.0000.0000.0000.000
30A17GLY00.118-0.06738.238-0.004-0.0040.0000.0000.0000.000
31A18LYS0-0.037-0.06740.7230.0010.0010.0000.0000.0000.000
32A18LYS10.9011.10744.347-0.014-0.0140.0000.0000.0000.000
33A19GLY00.067-0.08643.814-0.001-0.0010.0000.0000.0000.000
34A20ALA00.0950.01543.5120.0000.0000.0000.0000.0000.000
35A20ALA0-0.0640.11745.7630.0000.0000.0000.0000.0000.000
36A21SER00.058-0.09040.8250.0020.0020.0000.0000.0000.000
37A21SER0-0.0240.05440.2530.0010.0010.0000.0000.0000.000
38A22VAL0-0.053-0.11136.667-0.004-0.0040.0000.0000.0000.000
39A22VAL00.0420.15735.6520.0000.0000.0000.0000.0000.000
40A23SER00.105-0.06935.2270.0020.0020.0000.0000.0000.000
41A23SER0-0.0230.07936.468-0.001-0.0010.0000.0000.0000.000
42A24LYS00.100-0.07134.4680.0060.0060.0000.0000.0000.000
43A24LYS10.8611.06636.446-0.027-0.0270.0000.0000.0000.000
44A25TYR00.029-0.11933.2510.0010.0010.0000.0000.0000.000
45A25TYR0-0.0780.09533.2670.0000.0000.0000.0000.0000.000
46A26VAL00.147-0.05530.592-0.001-0.0010.0000.0000.0000.000
47A26VAL0-0.0730.10130.1590.0000.0000.0000.0000.0000.000
48A27LYS00.126-0.07529.5230.0080.0080.0000.0000.0000.000
49A27LYS10.8671.06131.579-0.058-0.0580.0000.0000.0000.000
50A28LYS00.064-0.08329.4840.0070.0070.0000.0000.0000.000
51A28LYS10.7000.96230.416-0.020-0.0200.0000.0000.0000.000
52A29ALA00.131-0.09226.795-0.003-0.0030.0000.0000.0000.000
53A29ALA0-0.0870.10426.3730.0000.0000.0000.0000.0000.000
54A30ILE00.118-0.06825.2470.0050.0050.0000.0000.0000.000
55A30ILE0-0.1300.07326.2230.0010.0010.0000.0000.0000.000
56A31GLU00.030-0.11325.3300.0170.0170.0000.0000.0000.000
57A31GLU-1-0.920-0.82328.0460.0900.0900.0000.0000.0000.000
58A32VAL00.052-0.09624.4440.0060.0060.0000.0000.0000.000
59A32VAL0-0.0970.09422.698-0.002-0.0020.0000.0000.0000.000
60A33PHE00.066-0.09620.885-0.005-0.0050.0000.0000.0000.000
61A33PHE0-0.0130.09221.0460.0010.0010.0000.0000.0000.000
62A34LYS00.059-0.08620.0200.0220.0220.0000.0000.0000.000
63A34LYS10.7340.97223.326-0.116-0.1160.0000.0000.0000.000
64A35LYS00.034-0.08120.9590.0150.0150.0000.0000.0000.000
65A35LYS10.7670.97621.269-0.025-0.0250.0000.0000.0000.000
66A36TYR00.030-0.09016.829-0.027-0.0270.0000.0000.0000.000
67A36TYR0-0.1480.02915.899-0.010-0.0100.0000.0000.0000.000
68A37ASP00.124-0.07913.549-0.026-0.0260.0000.0000.0000.000
69A37ASP-1-1.021-0.85412.0280.6170.6170.0000.0000.0000.000
70A38LEU00.017-0.13313.3690.0950.0950.0000.0000.0000.000
71A38LEU0-0.0840.08613.823-0.010-0.0100.0000.0000.0000.000
72A39LYS00.117-0.06415.816-0.027-0.0270.0000.0000.0000.000
73A39LYS10.7620.99315.300-0.507-0.5070.0000.0000.0000.000
74A40VAL00.016-0.09818.1300.0030.0030.0000.0000.0000.000
75A40VAL0-0.1110.07719.933-0.006-0.0060.0000.0000.0000.000
76A41GLU00.162-0.06121.305-0.019-0.0190.0000.0000.0000.000
77A41GLU-1-1.011-0.87021.3050.2410.2410.0000.0000.0000.000
78A42THR00.062-0.07823.730-0.003-0.0030.0000.0000.0000.000
79A42THR0-0.0450.05626.7140.0020.0020.0000.0000.0000.000
80A43ASN00.054-0.04226.6850.0020.0020.0000.0000.0000.000
81A43ASN0-0.0730.05426.179-0.010-0.0100.0000.0000.0000.000
82A44ALA00.136-0.09929.099-0.003-0.0030.0000.0000.0000.000
83A44ALA0-0.0790.09933.393-0.001-0.0010.0000.0000.0000.000
84A45MET0-0.026-0.14130.514-0.008-0.0080.0000.0000.0000.000
85A45MET0-0.0810.10430.393-0.002-0.0020.0000.0000.0000.000
86A46GLY00.009-0.10927.223-0.007-0.0070.0000.0000.0000.000
87A47THR0-0.033-0.00224.3800.0010.0010.0000.0000.0000.000
88A47THR0-0.0200.07822.444-0.007-0.0070.0000.0000.0000.000
89A48VAL00.117-0.07321.562-0.007-0.0070.0000.0000.0000.000
90A48VAL0-0.0990.08720.0600.0020.0020.0000.0000.0000.000
91A49LEU00.089-0.09018.063-0.002-0.0020.0000.0000.0000.000
92A49LEU0-0.0690.10017.241-0.003-0.0030.0000.0000.0000.000
93A50GLU00.078-0.11514.723-0.009-0.0090.0000.0000.0000.000
94A50GLU-1-0.831-0.77513.3450.5970.5970.0000.0000.0000.000
95A51GLY00.061-0.06311.430-0.006-0.0060.0000.0000.0000.000
96A52ASP00.1420.0238.6010.0710.0710.0000.0000.0000.000
97A52ASP-1-0.854-0.7896.4820.3380.3380.0000.0000.0000.000
98A53LEU00.087-0.0979.288-0.103-0.1030.0000.0000.0000.000
99A53LEU0-0.0910.07810.2100.0000.0000.0000.0000.0000.000
100A54ASP00.059-0.11410.0300.0050.0050.0000.0000.0000.000
101A54ASP-1-0.924-0.8039.545-0.320-0.3200.0000.0000.0000.000
102A55GLU00.035-0.13811.309-0.072-0.0720.0000.0000.0000.000
103A55GLU-1-0.844-0.78510.866-0.064-0.0640.0000.0000.0000.000
104A56ILE00.106-0.07713.161-0.027-0.0270.0000.0000.0000.000
105A56ILE0-0.1030.09113.150-0.004-0.0040.0000.0000.0000.000
106A57LEU00.057-0.12614.674-0.003-0.0030.0000.0000.0000.000
107A57LEU0-0.1060.10113.605-0.006-0.0060.0000.0000.0000.000
108A58LYS00.029-0.12915.738-0.010-0.0100.0000.0000.0000.000
109A58LYS10.7160.99111.5050.2270.2270.0000.0000.0000.000
110A59ALA00.113-0.08417.217-0.020-0.0200.0000.0000.0000.000
111A59ALA0-0.0290.12317.8020.0080.0080.0000.0000.0000.000
112A60PHE00.051-0.08718.971-0.003-0.0030.0000.0000.0000.000
113A60PHE0-0.0920.08519.7130.0010.0010.0000.0000.0000.000
114A61LYS00.099-0.08920.4380.0020.0020.0000.0000.0000.000
115A61LYS10.8731.07520.6590.0720.0720.0000.0000.0000.000
116A62GLU00.098-0.12421.651-0.007-0.0070.0000.0000.0000.000
117A62GLU-1-0.849-0.70921.9450.0060.0060.0000.0000.0000.000
118A63ALA00.087-0.08323.118-0.007-0.0070.0000.0000.0000.000
119A63ALA0-0.0380.12023.7000.0030.0030.0000.0000.0000.000
120A64HIS00.090-0.08324.9050.0010.0010.0000.0000.0000.000
121A64HIS0-0.0490.12025.5060.0070.0070.0000.0000.0000.000
122A65SER0-0.016-0.12226.2280.0020.0020.0000.0000.0000.000
123A65SER0-0.0650.05025.542-0.005-0.0050.0000.0000.0000.000
124A66THR00.039-0.07427.450-0.005-0.0050.0000.0000.0000.000
125A66THR0-0.0560.05826.6200.0000.0000.0000.0000.0000.000
126A67VAL00.051-0.08129.175-0.001-0.0010.0000.0000.0000.000
127A67VAL0-0.0860.09029.4800.0010.0010.0000.0000.0000.000
128A68LEU00.129-0.10230.7760.0010.0010.0000.0000.0000.000
129A68LEU0-0.1290.08630.6560.0000.0000.0000.0000.0000.000
130A69ASN00.107-0.06532.030-0.003-0.0030.0000.0000.0000.000
131A69ASN0-0.1950.03131.943-0.004-0.0040.0000.0000.0000.000
132A70ASP00.048-0.08733.732-0.003-0.0030.0000.0000.0000.000
133A70ASP-1-0.921-0.84235.3080.0170.0170.0000.0000.0000.000
134A71VAL00.007-0.11236.2130.0010.0010.0000.0000.0000.000
135A71VAL0-0.0620.07035.3890.0010.0010.0000.0000.0000.000
136A72ASP00.120-0.07936.472-0.001-0.0010.0000.0000.0000.000
137A72ASP-1-0.954-0.83940.0630.0030.0030.0000.0000.0000.000
138A73ARG00.104-0.07735.681-0.003-0.0030.0000.0000.0000.000
139A73ARG10.8261.04935.940-0.010-0.0100.0000.0000.0000.000
140A74VAL00.055-0.13432.2560.0030.0030.0000.0000.0000.000
141A74VAL0-0.0620.14230.6360.0000.0000.0000.0000.0000.000
142A75VAL00.033-0.10931.527-0.006-0.0060.0000.0000.0000.000
143A75VAL0-0.0910.10231.5220.0000.0000.0000.0000.0000.000
144A76SER00.011-0.09427.5020.0050.0050.0000.0000.0000.000
145A76SER00.0010.05726.5530.0020.0020.0000.0000.0000.000
146A77SER0-0.009-0.08425.668-0.008-0.0080.0000.0000.0000.000
147A77SER00.0000.06426.2060.0010.0010.0000.0000.0000.000
148A78LEU00.089-0.09221.2660.0060.0060.0000.0000.0000.000
149A78LEU0-0.0910.10517.931-0.001-0.0010.0000.0000.0000.000
150A79LYS00.079-0.10221.254-0.014-0.0140.0000.0000.0000.000
151A79LYS10.7711.01721.597-0.126-0.1260.0000.0000.0000.000
152A80ILE00.038-0.11816.9320.0130.0130.0000.0000.0000.000
153A80ILE0-0.0570.11514.9090.0010.0010.0000.0000.0000.000
154A81ASP00.123-0.07516.628-0.028-0.0280.0000.0000.0000.000
155A81ASP-1-0.963-0.81717.8130.2650.2650.0000.0000.0000.000
156A82GLU00.156-0.10613.3510.0510.0510.0000.0000.0000.000
157A82GLU-1-0.894-0.74710.1490.3540.3540.0000.0000.0000.000
158A83ARG0-0.014-0.09613.643-0.048-0.0480.0000.0000.0000.000
159A83ARG10.7430.97014.752-0.307-0.3070.0000.0000.0000.000
160A84LYS00.124-0.06611.8440.0820.0820.0000.0000.0000.000
161A84LYS10.8921.05311.868-0.265-0.2650.0000.0000.0000.000
162A85ASP00.071-0.06912.7640.0240.0240.0000.0000.0000.000
163A85ASP-1-0.809-0.77816.8650.2980.2980.0000.0000.0000.000
164A86LYS00.014-0.09614.678-0.007-0.0070.0000.0000.0000.000
165A86LYS10.8341.01116.589-0.285-0.2850.0000.0000.0000.000
166A87GLU00.124-0.09012.0830.0070.0070.0000.0000.0000.000
167A87GLU-1-0.824-0.72911.5350.8090.8090.0000.0000.0000.000
168A88ASN00.031-0.07711.839-0.111-0.1110.0000.0000.0000.000
169A88ASN0-0.0970.09010.498-0.083-0.0830.0000.0000.0000.000
170A89THR00.078-0.07213.3610.0350.0350.0000.0000.0000.000
171A89THR0-0.1010.01813.812-0.028-0.0280.0000.0000.0000.000
172A90ILE00.111-0.10315.594-0.035-0.0350.0000.0000.0000.000
173A90ILE0-0.0330.13017.7640.0010.0010.0000.0000.0000.000
174A91GLU00.122-0.10618.826-0.038-0.0380.0000.0000.0000.000
175A91GLU-1-0.948-0.79518.9920.3740.3740.0000.0000.0000.000
176A92ARG00.123-0.08518.524-0.037-0.0370.0000.0000.0000.000
177A92ARG10.7701.01516.313-0.389-0.3890.0000.0000.0000.000
178A93LYS00.008-0.10019.644-0.020-0.0200.0000.0000.0000.000
179A93LYS10.7530.96918.557-0.260-0.2600.0000.0000.0000.000
180A94LEU00.080-0.08321.251-0.019-0.0190.0000.0000.0000.000
181A94LEU0-0.0390.10523.2300.0000.0000.0000.0000.0000.000
182A95LYS00.122-0.06223.332-0.023-0.0230.0000.0000.0000.000
183A95LYS10.7680.98922.228-0.288-0.2880.0000.0000.0000.000
184A96ALA00.105-0.07123.373-0.017-0.0170.0000.0000.0000.000
185A96ALA0-0.1510.05222.6570.0040.0040.0000.0000.0000.000
186A97ILE0-0.003-0.11324.647-0.011-0.0110.0000.0000.0000.000
187A97ILE0-0.1070.08925.1260.0000.0000.0000.0000.0000.000
188A98GLY00.005-0.10527.347-0.014-0.0140.0000.0000.0000.000
189A99GLU0-0.116-0.06327.3200.0000.0000.0000.0000.0000.000
190A99GLU-1-0.914-0.94527.5520.1420.1420.0000.0000.0000.000