FMODB

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

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: RYRL8

Calculation Name: 2XTC-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2XTC

Chain ID: A

ChEMBL ID:

UniProt ID: O60907

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 OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 140
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -369234.026482
FMO2-HF: Nuclear repulsion 341448.917104
FMO2-HF: Total energy -27785.109378
FMO2-MP2: Total energy -27867.759208


3D Structure Molmil
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:SER)


Summations of interaction energy for fragment #1(A: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.
0.9971.7210.037-0.145-0.6160
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.101 / q_NPA : 0.040
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].
4A3ILE0-0.0970.0533.5480.1280.4790.022-0.161-0.2120.000
5A4THR00.076-0.0763.710-0.826-0.4530.0150.016-0.4040.000
6A4THR0-0.0380.0685.2470.2270.2270.0000.0000.0000.000
7A5SER00.087-0.0626.8350.5140.5140.0000.0000.0000.000
8A5SER0-0.0280.06911.245-0.073-0.0730.0000.0000.0000.000
9A6ASP00.151-0.09510.3210.1810.1810.0000.0000.0000.000
10A6ASP-1-1.013-0.83510.542-0.394-0.3940.0000.0000.0000.000
11A7GLU00.058-0.1298.1970.1080.1080.0000.0000.0000.000
12A7GLU-1-0.942-0.8185.4111.0871.0870.0000.0000.0000.000
13A8VAL00.001-0.0839.3140.2740.2740.0000.0000.0000.000
14A8VAL0-0.0400.0968.0310.0050.0050.0000.0000.0000.000
15A9ASN00.132-0.09810.4750.0970.0970.0000.0000.0000.000
16A9ASN0-0.0480.09713.942-0.003-0.0030.0000.0000.0000.000
17A10PHE00.157-0.05713.2050.0100.0100.0000.0000.0000.000
18A10PHE0-0.0710.09213.2190.0280.0280.0000.0000.0000.000
19A11LEU00.005-0.14512.479-0.003-0.0030.0000.0000.0000.000
20A11LEU0-0.1140.1029.8340.0240.0240.0000.0000.0000.000
21A12VAL00.112-0.08513.7780.0390.0390.0000.0000.0000.000
22A12VAL0-0.0450.09913.914-0.008-0.0080.0000.0000.0000.000
23A13TYR00.121-0.09216.039-0.008-0.0080.0000.0000.0000.000
24A13TYR0-0.0990.08917.791-0.010-0.0100.0000.0000.0000.000
25A14ARG00.039-0.10217.455-0.034-0.0340.0000.0000.0000.000
26A14ARG10.6980.99017.037-0.378-0.3780.0000.0000.0000.000
27A15TYR00.098-0.07217.7910.0020.0020.0000.0000.0000.000
28A15TYR0-0.0430.08617.575-0.004-0.0040.0000.0000.0000.000
29A16LEU00.030-0.10519.302-0.002-0.0020.0000.0000.0000.000
30A16LEU0-0.0770.08920.228-0.007-0.0070.0000.0000.0000.000
31A17GLN00.069-0.09121.839-0.019-0.0190.0000.0000.0000.000
32A17GLN0-0.0960.07422.0050.0210.0210.0000.0000.0000.000
33A18GLU00.036-0.10222.339-0.025-0.0250.0000.0000.0000.000
34A18GLU-1-0.829-0.75920.1690.3870.3870.0000.0000.0000.000
35A19SER0-0.042-0.11423.5590.0020.0020.0000.0000.0000.000
36A19SER0-0.0660.04722.4840.0040.0040.0000.0000.0000.000
37A20GLY0-0.007-0.09625.126-0.015-0.0150.0000.0000.0000.000
38A21PHE00.056-0.01125.745-0.015-0.0150.0000.0000.0000.000
39A21PHE0-0.1180.10023.731-0.004-0.0040.0000.0000.0000.000
40A22SER00.131-0.05426.139-0.005-0.0050.0000.0000.0000.000
41A22SER0-0.0600.05730.1690.0000.0000.0000.0000.0000.000
42A23HIS00.074-0.08128.312-0.003-0.0030.0000.0000.0000.000
43A23HIS0-0.0870.08829.844-0.002-0.0020.0000.0000.0000.000
44A24SER00.099-0.08225.150-0.016-0.0160.0000.0000.0000.000
45A24SER0-0.0100.08924.1940.0050.0050.0000.0000.0000.000
46A25ALA00.101-0.07623.204-0.020-0.0200.0000.0000.0000.000
47A25ALA0-0.0590.09824.2570.0040.0040.0000.0000.0000.000
48A26PHE00.073-0.07223.954-0.005-0.0050.0000.0000.0000.000
49A26PHE0-0.1000.07428.236-0.001-0.0010.0000.0000.0000.000
50A27THR00.026-0.08825.962-0.007-0.0070.0000.0000.0000.000
51A27THR0-0.0470.06225.666-0.001-0.0010.0000.0000.0000.000
52A28PHE00.077-0.05721.539-0.024-0.0240.0000.0000.0000.000
53A28PHE0-0.0830.08416.3020.0040.0040.0000.0000.0000.000
54A29GLY00.001-0.10321.212-0.018-0.0180.0000.0000.0000.000
55A30ILE00.0320.00022.022-0.011-0.0110.0000.0000.0000.000
56A30ILE0-0.0600.08725.7880.0000.0000.0000.0000.0000.000
57A31GLU00.078-0.14322.845-0.017-0.0170.0000.0000.0000.000
58A31GLU-1-1.042-0.83722.093-0.119-0.1190.0000.0000.0000.000
59A32SER0-0.018-0.08318.344-0.043-0.0430.0000.0000.0000.000
60A32SER0-0.0650.03117.2930.0120.0120.0000.0000.0000.000
61A33HIS00.065-0.05218.078-0.021-0.0210.0000.0000.0000.000
62A33HIS0-0.1000.05619.2170.0060.0060.0000.0000.0000.000
63A34ILE00.069-0.07117.900-0.027-0.0270.0000.0000.0000.000
64A34ILE0-0.0510.08016.4280.0110.0110.0000.0000.0000.000
65A35SER00.016-0.10518.4600.0260.0260.0000.0000.0000.000
66A35SER0-0.0410.07522.540-0.002-0.0020.0000.0000.0000.000
67A36GLN00.017-0.09619.2980.0270.0270.0000.0000.0000.000
68A36GLN0-0.0780.09518.8250.0160.0160.0000.0000.0000.000
69A37SER00.028-0.06715.252-0.055-0.0550.0000.0000.0000.000
70A37SER0-0.0170.06114.2120.0300.0300.0000.0000.0000.000
71A38ASN00.094-0.03513.9010.0400.0400.0000.0000.0000.000
72A38ASN0-0.1210.04813.2740.0160.0160.0000.0000.0000.000
73A39ILE00.109-0.11413.3980.0420.0420.0000.0000.0000.000
74A39ILE0-0.0760.12310.8020.0250.0250.0000.0000.0000.000
75A40ASN00.121-0.08014.059-0.053-0.0530.0000.0000.0000.000
76A40ASN0-0.0870.09516.232-0.017-0.0170.0000.0000.0000.000
77A41GLY00.047-0.09816.4060.0700.0700.0000.0000.0000.000
78A42THR0-0.0260.00718.0290.0390.0390.0000.0000.0000.000
79A42THR0-0.0240.05620.3240.0010.0010.0000.0000.0000.000
80A43LEU00.065-0.08416.591-0.022-0.0220.0000.0000.0000.000
81A43LEU0-0.0810.09515.8280.0050.0050.0000.0000.0000.000
82A44VAL00.068-0.11815.2630.1270.1270.0000.0000.0000.000
83A44VAL0-0.1130.11113.7530.0040.0040.0000.0000.0000.000
84A45PRO00.009-0.08015.075-0.093-0.0930.0000.0000.0000.000
85A46PRO00.033-0.01317.6190.0090.0090.0000.0000.0000.000
86A47ALA00.094-0.00118.7350.0460.0460.0000.0000.0000.000
87A47ALA0-0.0640.11319.473-0.008-0.0080.0000.0000.0000.000
88A48ALA00.111-0.10114.6100.0200.0200.0000.0000.0000.000
89A48ALA0-0.0590.12913.5660.0090.0090.0000.0000.0000.000
90A49LEU00.098-0.09813.0510.1690.1690.0000.0000.0000.000
91A49LEU0-0.0610.11912.430-0.010-0.0100.0000.0000.0000.000
92A50ILE00.113-0.09513.8830.0470.0470.0000.0000.0000.000
93A50ILE0-0.0810.10018.060-0.009-0.0090.0000.0000.0000.000
94A51SER00.028-0.07815.486-0.029-0.0290.0000.0000.0000.000
95A51SER0-0.0820.03715.016-0.010-0.0100.0000.0000.0000.000
96A52ILE00.055-0.11810.669-0.033-0.0330.0000.0000.0000.000
97A52ILE0-0.0620.1058.5260.0360.0360.0000.0000.0000.000
98A53LEU00.067-0.13211.3490.1210.1210.0000.0000.0000.000
99A53LEU0-0.1150.08712.175-0.022-0.0220.0000.0000.0000.000
100A54GLN00.0290.01913.178-0.032-0.0320.0000.0000.0000.000
101A54GLN0-0.0710.04816.500-0.008-0.0080.0000.0000.0000.000
102A55LYS00.153-0.12313.104-0.108-0.1080.0000.0000.0000.000
103A55LYS10.8501.07012.344-1.060-1.0600.0000.0000.0000.000
104A56GLY0-0.005-0.08611.3030.0560.0560.0000.0000.0000.000
105A57LEU00.052-0.01412.016-0.054-0.0540.0000.0000.0000.000
106A57LEU0-0.0990.09815.282-0.012-0.0120.0000.0000.0000.000
107A58GLN00.187-0.04115.597-0.061-0.0610.0000.0000.0000.000
108A58GLN0-0.1000.06515.9540.0690.0690.0000.0000.0000.000
109A59TYR00.081-0.07612.683-0.087-0.0870.0000.0000.0000.000
110A59TYR0-0.1450.06011.7320.1480.1480.0000.0000.0000.000
111A60VAL00.108-0.06914.206-0.023-0.0230.0000.0000.0000.000
112A60VAL0-0.0910.07513.261-0.008-0.0080.0000.0000.0000.000
113A61GLU00.083-0.11415.427-0.060-0.0600.0000.0000.0000.000
114A61GLU-1-1.033-0.86618.8450.3160.3160.0000.0000.0000.000
115A62ALA00.111-0.08517.722-0.061-0.0610.0000.0000.0000.000
116A62ALA0-0.1000.08417.0420.0140.0140.0000.0000.0000.000
117A63GLU00.023-0.14616.362-0.018-0.0180.0000.0000.0000.000
118A63GLU-1-1.015-0.86613.5670.2920.2920.0000.0000.0000.000
119A64ILE00.007-0.07017.562-0.042-0.0420.0000.0000.0000.000
120A64ILE0-0.0830.05819.065-0.006-0.0060.0000.0000.0000.000
121A65SER00.109-0.04820.622-0.030-0.0300.0000.0000.0000.000
122A65SER0-0.0560.05822.5880.0090.0090.0000.0000.0000.000
123A66ILE00.049-0.10421.585-0.017-0.0170.0000.0000.0000.000
124A66ILE0-0.1360.07419.3910.0030.0030.0000.0000.0000.000
125A67ASN00.018-0.06622.860-0.010-0.0100.0000.0000.0000.000
126A67ASN0-0.1380.02421.222-0.007-0.0070.0000.0000.0000.000
127A68GLU00.099-0.11724.414-0.024-0.0240.0000.0000.0000.000
128A68GLU-1-1.029-0.85125.4150.1370.1370.0000.0000.0000.000
129A69ASP00.080-0.11826.532-0.013-0.0130.0000.0000.0000.000
130A69ASP-1-1.039-0.85729.9310.1080.1080.0000.0000.0000.000
131A70GLY0-0.024-0.08828.451-0.013-0.0130.0000.0000.0000.000
132A71THR0-0.0040.00429.7620.0120.0120.0000.0000.0000.000
133A71THR0-0.0600.02730.396-0.001-0.0010.0000.0000.0000.000
134A72VAL00.071-0.08432.584-0.007-0.0070.0000.0000.0000.000
135A72VAL0-0.0870.09136.1980.0010.0010.0000.0000.0000.000
136A73PHE00.020-0.10035.024-0.004-0.0040.0000.0000.0000.000
137A73PHE0-0.1240.04534.8860.0010.0010.0000.0000.0000.000
138A74ASP00.108-0.11633.221-0.006-0.0060.0000.0000.0000.000
139A74ASP-1-0.894-0.76931.5400.0320.0320.0000.0000.0000.000
140A75GLY0-0.092-0.13333.962-0.003-0.0030.0000.0000.0000.000