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: YN5J2

Calculation Name: 4J4U-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4J4U

Chain ID: A

ChEMBL ID:

UniProt ID: I6WJ72

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
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 465
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2899079.300886
FMO2-HF: Nuclear repulsion 2803637.198344
FMO2-HF: Total energy -95442.102542
FMO2-MP2: Total energy -95716.755958


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:0:ALA)


Summations of interaction energy for fragment #1(A:0:ALA)
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.
-20.54-28.51525.471-10.537-6.9610.058
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.241 / q_NPA : 0.082
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].
4A1MET0-0.0810.0963.925-0.944-0.4150.005-0.251-0.2830.001
5A2SER00.031-0.0553.586-2.732-0.8380.003-1.021-0.8760.002
6A2SER0-0.0090.0516.3460.6830.6830.0000.0000.0000.000
7A3GLU00.099-0.0873.9951.4401.6400.003-0.056-0.1470.000
8A3GLU-1-0.938-0.8207.9520.8780.8780.0000.0000.0000.000
9A4TRP00.100-0.0836.0770.2030.2030.0000.0000.0000.000
10A4TRP0-0.0900.0658.0670.0230.0230.0000.0000.0000.000
11A5SER00.127-0.0633.515-2.207-3.469-0.0051.669-0.4020.006
12A5SER0-0.1400.0001.786-13.155-24.04022.161-8.453-2.8230.051
13A6ARG00.053-0.1062.9100.1531.8990.453-0.989-1.211-0.003
14A6ARG10.8051.0372.271-0.307-0.8322.732-1.361-0.8460.002
15A7ILE00.101-0.0523.367-1.139-1.2070.0670.068-0.0670.000
16A7ILE0-0.1070.0827.632-0.076-0.0760.0000.0000.0000.000
17A8ALA00.112-0.0806.520-0.941-0.9410.0000.0000.0000.000
18A8ALA0-0.1030.0785.6460.0870.0870.0000.0000.0000.000
19A9VAL00.025-0.0924.660-0.357-0.322-0.002-0.008-0.0250.000
20A9VAL0-0.0960.0732.925-0.575-0.2140.054-0.135-0.281-0.001
21A10GLU00.120-0.0845.842-0.411-0.4110.0000.0000.0000.000
22A10GLU-1-0.955-0.8436.3950.2280.2280.0000.0000.0000.000
23A11PHE00.101-0.0968.537-0.257-0.2570.0000.0000.0000.000
24A11PHE0-0.1120.08210.2370.0130.0130.0000.0000.0000.000
25A12GLY0-0.048-0.1229.346-0.089-0.0890.0000.0000.0000.000
26A13GLU00.088-0.00410.195-0.069-0.0690.0000.0000.0000.000
27A13GLU-1-1.005-0.8548.650-0.715-0.7150.0000.0000.0000.000
28A14GLN00.030-0.10911.801-0.108-0.1080.0000.0000.0000.000
29A14GLN0-0.1330.06413.299-0.029-0.0290.0000.0000.0000.000
30A15GLN00.064-0.09714.8050.0120.0120.0000.0000.0000.000
31A15GLN0-0.1430.07415.638-0.011-0.0110.0000.0000.0000.000
32A16LEU00.071-0.12018.1180.0190.0190.0000.0000.0000.000
33A16LEU0-0.0840.10317.056-0.002-0.0020.0000.0000.0000.000
34A17ASN00.128-0.06620.183-0.031-0.0310.0000.0000.0000.000
35A17ASN0-0.1270.04523.442-0.015-0.0150.0000.0000.0000.000
36A18LEU00.072-0.12523.5370.0250.0250.0000.0000.0000.000
37A18LEU0-0.0790.10223.353-0.002-0.0020.0000.0000.0000.000
38A19THR00.025-0.04025.4100.0090.0090.0000.0000.0000.000
39A19THR0-0.0410.03928.684-0.004-0.0040.0000.0000.0000.000
40A20GLU00.150-0.04826.410-0.004-0.0040.0000.0000.0000.000
41A20GLU-1-0.925-0.81724.2440.1940.1940.0000.0000.0000.000
42A21LEU00.054-0.10623.9990.0110.0110.0000.0000.0000.000
43A21LEU0-0.0860.09020.9160.0030.0030.0000.0000.0000.000
44A22GLU00.151-0.06925.0650.0180.0180.0000.0000.0000.000
45A22GLU-1-1.002-0.84128.4990.1170.1170.0000.0000.0000.000
46A23ASP00.035-0.13028.4390.0000.0000.0000.0000.0000.000
47A23ASP-1-0.913-0.79729.8890.1190.1190.0000.0000.0000.000
48A24PHE00.103-0.09426.624-0.008-0.0080.0000.0000.0000.000
49A24PHE0-0.0830.08123.9380.0070.0070.0000.0000.0000.000
50A25ALA00.087-0.10127.8510.0120.0120.0000.0000.0000.000
51A25ALA0-0.0940.10627.222-0.001-0.0010.0000.0000.0000.000
52A26ARG00.005-0.11128.6790.0000.0000.0000.0000.0000.000
53A26ARG10.6800.93132.595-0.120-0.1200.0000.0000.0000.000
54A27GLU00.028-0.14731.398-0.009-0.0090.0000.0000.0000.000
55A27GLU-1-1.001-0.84630.3870.1830.1830.0000.0000.0000.000
56A28LEU00.007-0.10729.104-0.005-0.0050.0000.0000.0000.000
57A28LEU0-0.0910.09226.6060.0070.0070.0000.0000.0000.000
58A29ALA00.093-0.10430.6350.0130.0130.0000.0000.0000.000
59A29ALA0-0.0720.12132.983-0.003-0.0030.0000.0000.0000.000
60A30TYR00.051-0.09532.8540.0020.0020.0000.0000.0000.000
61A30TYR0-0.0780.06934.857-0.004-0.0040.0000.0000.0000.000
62A31GLU00.068-0.13835.429-0.009-0.0090.0000.0000.0000.000
63A31GLU-1-0.873-0.71937.8820.1310.1310.0000.0000.0000.000
64A32GLY0-0.012-0.10438.7440.0030.0030.0000.0000.0000.000
65A33LEU00.0570.00341.8940.0020.0020.0000.0000.0000.000
66A33LEU0-0.1060.06344.552-0.001-0.0010.0000.0000.0000.000
67A34ASP00.133-0.07743.3400.0000.0000.0000.0000.0000.000
68A34ASP-1-0.851-0.76043.2370.1050.1050.0000.0000.0000.000
69A35PRO00.017-0.11244.839-0.002-0.0020.0000.0000.0000.000
70A36ALA00.1260.01647.366-0.004-0.0040.0000.0000.0000.000
71A36ALA0-0.0490.12147.0950.0000.0000.0000.0000.0000.000
72A37LEU00.085-0.11746.819-0.005-0.0050.0000.0000.0000.000
73A37LEU0-0.1110.11544.7410.0010.0010.0000.0000.0000.000
74A38ILE00.076-0.08648.194-0.001-0.0010.0000.0000.0000.000
75A38ILE0-0.0920.09547.3920.0000.0000.0000.0000.0000.000
76A39ILE00.095-0.10650.359-0.002-0.0020.0000.0000.0000.000
77A39ILE0-0.1080.09152.193-0.001-0.0010.0000.0000.0000.000
78A40LYS00.097-0.07351.797-0.004-0.0040.0000.0000.0000.000
79A40LYS10.7400.98549.944-0.080-0.0800.0000.0000.0000.000
80A41LYS00.114-0.09651.835-0.003-0.0030.0000.0000.0000.000
81A41LYS10.7851.04151.106-0.083-0.0830.0000.0000.0000.000
82A42LEU00.067-0.08653.101-0.001-0.0010.0000.0000.0000.000
83A42LEU0-0.1060.06654.3580.0000.0000.0000.0000.0000.000
84A43LYS00.111-0.07456.113-0.002-0.0020.0000.0000.0000.000
85A43LYS10.7901.03256.911-0.058-0.0580.0000.0000.0000.000
86A44GLU00.060-0.12856.458-0.004-0.0040.0000.0000.0000.000
87A44GLU-1-0.869-0.76453.9780.0760.0760.0000.0000.0000.000
88A45THR0-0.034-0.09957.103-0.002-0.0020.0000.0000.0000.000
89A45THR0-0.0740.04755.9360.0020.0020.0000.0000.0000.000
90A46GLY0-0.022-0.09858.481-0.002-0.0020.0000.0000.0000.000
91A47GLY00.0370.01961.4620.0000.0000.0000.0000.0000.000
92A48ASP00.1060.01063.0450.0000.0000.0000.0000.0000.000
93A48ASP-1-0.954-0.82467.1480.0480.0480.0000.0000.0000.000
94A49ASP00.039-0.13164.7130.0020.0020.0000.0000.0000.000
95A49ASP-1-0.893-0.78366.5660.0480.0480.0000.0000.0000.000
96A50TRP00.127-0.12861.1650.0000.0000.0000.0000.0000.000
97A50TRP0-0.0200.14657.4670.0010.0010.0000.0000.0000.000
98A51VAL00.065-0.09561.4220.0020.0020.0000.0000.0000.000
99A51VAL0-0.0660.11562.5760.0000.0000.0000.0000.0000.000
100A52LYS00.056-0.11763.2660.0000.0000.0000.0000.0000.000
101A52LYS10.8411.01866.497-0.047-0.0470.0000.0000.0000.000
102A53ASP00.011-0.10762.431-0.001-0.0010.0000.0000.0000.000
103A53ASP-1-0.819-0.72761.5950.0590.0590.0000.0000.0000.000
104A54THR00.084-0.07259.0420.0010.0010.0000.0000.0000.000
105A54THR0-0.0290.06257.4110.0010.0010.0000.0000.0000.000
106A55LYS00.103-0.07759.5840.0020.0020.0000.0000.0000.000
107A55LYS10.8481.07562.349-0.050-0.0500.0000.0000.0000.000
108A56PHE00.133-0.06561.9130.0000.0000.0000.0000.0000.000
109A56PHE0-0.1150.06662.552-0.001-0.0010.0000.0000.0000.000
110A57ILE00.058-0.10058.3930.0000.0000.0000.0000.0000.000
111A57ILE0-0.0860.09756.3620.0000.0000.0000.0000.0000.000
112A58ILE00.082-0.07757.3510.0030.0030.0000.0000.0000.000
113A58ILE0-0.0990.09056.5080.0000.0000.0000.0000.0000.000
114A59VAL00.122-0.08458.3960.0010.0010.0000.0000.0000.000
115A59VAL0-0.0830.09962.7340.0000.0000.0000.0000.0000.000
116A60PHE00.115-0.06160.041-0.001-0.0010.0000.0000.0000.000
117A60PHE0-0.0970.07756.525-0.001-0.0010.0000.0000.0000.000
118A61ALA00.080-0.10855.7140.0000.0000.0000.0000.0000.000
119A61ALA0-0.0620.10054.7110.0000.0000.0000.0000.0000.000
120A62LEU0-0.008-0.14456.0790.0030.0030.0000.0000.0000.000
121A62LEU0-0.0850.12156.8460.0000.0000.0000.0000.0000.000
122A63THR00.024-0.08358.0130.0000.0000.0000.0000.0000.000
123A63THR0-0.0640.06761.5430.0000.0000.0000.0000.0000.000
124A64ARG0-0.047-0.15358.606-0.001-0.0010.0000.0000.0000.000
125A64ARG10.7971.02858.896-0.063-0.0630.0000.0000.0000.000
126A65GLY00.020-0.07254.4120.0020.0020.0000.0000.0000.000
127A66ASN00.054-0.00251.396-0.002-0.0020.0000.0000.0000.000
128A66ASN0-0.0430.09149.218-0.002-0.0020.0000.0000.0000.000
129A67LYS00.160-0.01952.9290.0020.0020.0000.0000.0000.000
130A67LYS10.8221.03950.420-0.096-0.0960.0000.0000.0000.000
131A68ILE00.142-0.11754.723-0.003-0.0030.0000.0000.0000.000
132A68ILE0-0.0740.12354.4220.0000.0000.0000.0000.0000.000
133A69VAL00.140-0.08556.523-0.004-0.0040.0000.0000.0000.000
134A69VAL0-0.0540.13056.2300.0000.0000.0000.0000.0000.000
135A70LYS00.106-0.06757.243-0.003-0.0030.0000.0000.0000.000
136A70LYS10.8641.05256.294-0.075-0.0750.0000.0000.0000.000
137A71ALA00.038-0.12458.811-0.002-0.0020.0000.0000.0000.000
138A71ALA0-0.0430.11459.1690.0000.0000.0000.0000.0000.000
139A72SER00.003-0.12160.670-0.003-0.0030.0000.0000.0000.000
140A72SER0-0.0100.09761.2600.0000.0000.0000.0000.0000.000
141A73GLY00.000-0.06862.580-0.003-0.0030.0000.0000.0000.000
142A74LYS0-0.011-0.02364.005-0.002-0.0020.0000.0000.0000.000
143A74LYS10.8431.05662.957-0.062-0.0620.0000.0000.0000.000
144A75MET00.169-0.04565.0740.0000.0000.0000.0000.0000.000
145A75MET0-0.1150.08362.6360.0000.0000.0000.0000.0000.000
146A76SER00.121-0.03966.9580.0000.0000.0000.0000.0000.000
147A76SER0-0.0140.07969.9410.0000.0000.0000.0000.0000.000
148A77ASN00.180-0.04068.8660.0020.0020.0000.0000.0000.000
149A77ASN0-0.1060.07971.7220.0010.0010.0000.0000.0000.000
150A78SER00.022-0.08669.7420.0010.0010.0000.0000.0000.000
151A78SER0-0.0200.07571.7440.0000.0000.0000.0000.0000.000
152A79GLY00.011-0.09567.4470.0010.0010.0000.0000.0000.000
153A80SER00.1490.04564.9930.0020.0020.0000.0000.0000.000
154A80SER0-0.0930.04865.7000.0000.0000.0000.0000.0000.000
155A81LYS00.092-0.08464.9350.0020.0020.0000.0000.0000.000
156A81LYS10.8601.06068.874-0.050-0.0500.0000.0000.0000.000
157A82ARG00.088-0.06265.9560.0010.0010.0000.0000.0000.000
158A82ARG10.7540.98865.104-0.055-0.0550.0000.0000.0000.000
159A83LEU00.101-0.10462.1100.0010.0010.0000.0000.0000.000
160A83LEU0-0.1130.10059.1650.0000.0000.0000.0000.0000.000
161A84MET00.094-0.10760.9290.0030.0030.0000.0000.0000.000
162A84MET0-0.0920.10859.3210.0000.0000.0000.0000.0000.000
163A85ALA00.164-0.06461.3430.0030.0030.0000.0000.0000.000
164A85ALA0-0.0930.09765.007-0.001-0.0010.0000.0000.0000.000
165A86LEU00.023-0.10861.0600.0000.0000.0000.0000.0000.000
166A86LEU0-0.1410.07760.1990.0000.0000.0000.0000.0000.000
167A87GLN00.100-0.07057.3130.0020.0020.0000.0000.0000.000
168A87GLN0-0.1430.04654.772-0.002-0.0020.0000.0000.0000.000
169A88GLU00.088-0.13057.1620.0040.0040.0000.0000.0000.000
170A88GLU-1-1.020-0.83960.1080.0680.0680.0000.0000.0000.000
171A89LYS00.073-0.08258.6780.0020.0020.0000.0000.0000.000
172A89LYS10.7731.00960.687-0.061-0.0610.0000.0000.0000.000
173A90TYR0-0.010-0.13356.7920.0000.0000.0000.0000.0000.000
174A90TYR0-0.1500.02755.858-0.001-0.0010.0000.0000.0000.000
175A91GLY00.071-0.08353.6370.0030.0030.0000.0000.0000.000
176A92LEU00.083-0.00552.4160.0050.0050.0000.0000.0000.000
177A92LEU0-0.1080.08454.413-0.001-0.0010.0000.0000.0000.000
178A93VAL00.037-0.11550.228-0.002-0.0020.0000.0000.0000.000
179A93VAL0-0.0620.13948.3960.0010.0010.0000.0000.0000.000
180A94GLU00.096-0.12750.902-0.001-0.0010.0000.0000.0000.000
181A94GLU-1-0.927-0.83050.7620.0900.0900.0000.0000.0000.000
182A95ARG00.003-0.12946.593-0.001-0.0010.0000.0000.0000.000
183A95ARG10.7901.02144.189-0.122-0.1220.0000.0000.0000.000
184A96ALA00.162-0.07944.596-0.001-0.0010.0000.0000.0000.000
185A96ALA0-0.1010.09643.990-0.001-0.0010.0000.0000.0000.000
186A97GLU00.075-0.11941.5840.0040.0040.0000.0000.0000.000
187A97GLU-1-0.929-0.81042.0660.1310.1310.0000.0000.0000.000
188A98THR00.025-0.06440.2380.0100.0100.0000.0000.0000.000
189A98THR00.0050.07040.532-0.003-0.0030.0000.0000.0000.000
190A99ARG00.124-0.05840.763-0.006-0.0060.0000.0000.0000.000
191A99ARG10.7800.97338.472-0.129-0.1290.0000.0000.0000.000
192A100LEU00.069-0.09542.310-0.006-0.0060.0000.0000.0000.000
193A100LEU0-0.0430.11442.9840.0000.0000.0000.0000.0000.000
194A101SER00.022-0.08244.902-0.007-0.0070.0000.0000.0000.000
195A101SER0-0.1060.06044.4490.0010.0010.0000.0000.0000.000
196A102ILE00.050-0.10946.7610.0020.0020.0000.0000.0000.000
197A102ILE0-0.0350.13048.968-0.001-0.0010.0000.0000.0000.000
198A103THR00.092-0.05949.047-0.003-0.0030.0000.0000.0000.000
199A103THR0-0.0520.07247.709-0.001-0.0010.0000.0000.0000.000
200A104PRO00.018-0.08750.541-0.002-0.0020.0000.0000.0000.000
201A105VAL00.1210.01251.075-0.004-0.0040.0000.0000.0000.000
202A105VAL0-0.0990.08849.5890.0000.0000.0000.0000.0000.000
203A106ARG00.116-0.09348.741-0.002-0.0020.0000.0000.0000.000
204A106ARG10.7351.00142.268-0.120-0.1200.0000.0000.0000.000
205A107VAL00.105-0.06249.6410.0000.0000.0000.0000.0000.000
206A107VAL0-0.0870.08852.9230.0000.0000.0000.0000.0000.000
207A108ALA00.095-0.09152.968-0.002-0.0020.0000.0000.0000.000
208A108ALA0-0.0810.09553.4480.0000.0000.0000.0000.0000.000
209A109GLN00.080-0.10749.370-0.005-0.0050.0000.0000.0000.000
210A109GLN0-0.0990.08346.5810.0030.0030.0000.0000.0000.000
211A110SER00.076-0.07150.1190.0010.0010.0000.0000.0000.000
212A110SER0-0.0570.06050.3420.0010.0010.0000.0000.0000.000
213A111LEU0-0.067-0.10451.399-0.001-0.0010.0000.0000.0000.000
214A111LEU0-0.0780.09554.335-0.001-0.0010.0000.0000.0000.000
215A112PRO00.154-0.06951.402-0.003-0.0030.0000.0000.0000.000
216A113THR00.0520.02354.220-0.001-0.0010.0000.0000.0000.000
217A113THR0-0.0180.07855.7950.0000.0000.0000.0000.0000.000
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