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: Y9Y12

Calculation Name: 4J2C-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4J2C

Chain ID: A

ChEMBL ID:

UniProt ID: O43752

Base Structure: X-ray

Registration Date: 2025-07-11

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 OptHSide
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 210
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -803724.972674
FMO2-HF: Nuclear repulsion 759812.406639
FMO2-HF: Total energy -43912.566035
FMO2-MP2: Total energy -44040.090794


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:1:GLY)


Summations of interaction energy for fragment #1(A:1:GLY)
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.
-0.3630.6620.004-0.45-0.580.001
Interaction energy analysis for fragmet #1(A:1:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / 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].
3A2ALA0-0.0650.0974.6630.4640.632-0.001-0.068-0.1000.000
4A3MET00.091-0.0973.814-0.966-0.1090.005-0.382-0.4800.001
5A3MET0-0.1140.0815.8600.1150.1150.0000.0000.0000.000
6A4GLU00.076-0.1286.2690.2980.2980.0000.0000.0000.000
7A4GLU-1-0.981-0.8359.642-0.195-0.1950.0000.0000.0000.000
8A5ASP00.067-0.1139.737-0.116-0.1160.0000.0000.0000.000
9A5ASP-1-0.866-0.77712.749-0.309-0.3090.0000.0000.0000.000
10A6PRO00.001-0.09512.4390.0800.0800.0000.0000.0000.000
11A7PHE00.1850.04215.0960.0380.0380.0000.0000.0000.000
12A7PHE0-0.1020.08417.4850.0090.0090.0000.0000.0000.000
13A8PHE00.069-0.10517.9490.0170.0170.0000.0000.0000.000
14A8PHE0-0.0780.08615.2920.0110.0110.0000.0000.0000.000
15A9VAL00.040-0.11218.1750.0320.0320.0000.0000.0000.000
16A9VAL0-0.0770.10816.377-0.002-0.0020.0000.0000.0000.000
17A10VAL00.123-0.09219.4080.0250.0250.0000.0000.0000.000
18A10VAL0-0.0420.13018.945-0.002-0.0020.0000.0000.0000.000
19A11LYS00.115-0.07921.3960.0150.0150.0000.0000.0000.000
20A11LYS10.8121.05222.7230.0850.0850.0000.0000.0000.000
21A12GLY0-0.022-0.11322.9820.0140.0140.0000.0000.0000.000
22A13GLU00.049-0.03523.8610.0180.0180.0000.0000.0000.000
23A13GLU-1-0.861-0.78122.864-0.105-0.1050.0000.0000.0000.000
24A14VAL00.133-0.06425.5080.0090.0090.0000.0000.0000.000
25A14VAL0-0.0900.12125.4820.0000.0000.0000.0000.0000.000
26A15GLN00.097-0.07627.4690.0070.0070.0000.0000.0000.000
27A15GLN0-0.0900.06227.516-0.002-0.0020.0000.0000.0000.000
28A16LYS00.086-0.07928.4000.0080.0080.0000.0000.0000.000
29A16LYS10.7240.99425.8910.0860.0860.0000.0000.0000.000
30A17ALA00.105-0.10729.6090.0090.0090.0000.0000.0000.000
31A17ALA0-0.0310.12629.894-0.001-0.0010.0000.0000.0000.000
32A18VAL00.072-0.12931.4460.0040.0040.0000.0000.0000.000
33A18VAL0-0.0960.11331.8080.0000.0000.0000.0000.0000.000
34A19ASN00.123-0.06733.0990.0040.0040.0000.0000.0000.000
35A19ASN0-0.1590.04632.6660.0000.0000.0000.0000.0000.000
36A20THR00.009-0.09834.2070.0050.0050.0000.0000.0000.000
37A20THR0-0.0530.06933.4000.0010.0010.0000.0000.0000.000
38A21ALA00.100-0.07435.5340.0040.0040.0000.0000.0000.000
39A21ALA0-0.0580.10435.938-0.001-0.0010.0000.0000.0000.000
40A22GLN00.087-0.10137.4060.0020.0020.0000.0000.0000.000
41A22GLN0-0.0970.09937.5180.0020.0020.0000.0000.0000.000
42A23GLY0-0.019-0.11539.0080.0030.0030.0000.0000.0000.000
43A24LEU00.075-0.00540.1170.0040.0040.0000.0000.0000.000
44A24LEU0-0.1070.10938.6340.0000.0000.0000.0000.0000.000
45A25PHE00.149-0.09141.5890.0020.0020.0000.0000.0000.000
46A25PHE0-0.0840.10141.975-0.001-0.0010.0000.0000.0000.000
47A26GLN00.123-0.08543.4470.0010.0010.0000.0000.0000.000
48A26GLN0-0.1310.06444.428-0.001-0.0010.0000.0000.0000.000
49A27ARG00.061-0.08944.8660.0020.0020.0000.0000.0000.000
50A27ARG10.7391.00344.9990.0270.0270.0000.0000.0000.000
51A28TRP00.105-0.08645.7650.0020.0020.0000.0000.0000.000
52A28TRP0-0.0820.08445.605-0.001-0.0010.0000.0000.0000.000
53A29THR00.003-0.09547.4580.0010.0010.0000.0000.0000.000
54A29THR0-0.0560.05247.2340.0000.0000.0000.0000.0000.000
55A30GLU00.079-0.13749.4680.0010.0010.0000.0000.0000.000
56A30GLU-1-0.880-0.78348.924-0.026-0.0260.0000.0000.0000.000
57A31LEU00.032-0.07950.5380.0020.0020.0000.0000.0000.000
58A31LEU0-0.1490.06248.5830.0000.0000.0000.0000.0000.000
59A32LEU00.048-0.11351.4950.0010.0010.0000.0000.0000.000
60A32LEU0-0.0950.10550.0920.0000.0000.0000.0000.0000.000
61A33GLN00.072-0.06153.2220.0000.0000.0000.0000.0000.000
62A33GLN0-0.1180.06354.0310.0000.0000.0000.0000.0000.000
63A34ASP00.045-0.12855.3970.0010.0010.0000.0000.0000.000
64A34ASP-1-0.916-0.78756.567-0.020-0.0200.0000.0000.0000.000
65A35PRO00.008-0.11156.6810.0000.0000.0000.0000.0000.000
66A36SER00.0040.00658.2670.0000.0000.0000.0000.0000.000
67A36SER0-0.0850.02059.6560.0000.0000.0000.0000.0000.000
68A37THR0-0.023-0.11355.9160.0000.0000.0000.0000.0000.000
69A37THR0-0.0390.07454.1380.0000.0000.0000.0000.0000.000
70A38ALA00.131-0.09153.9460.0000.0000.0000.0000.0000.000
71A38ALA0-0.1230.13353.7060.0000.0000.0000.0000.0000.000
72A39THR00.041-0.05954.3610.0000.0000.0000.0000.0000.000
73A39THR0-0.0840.04252.9830.0000.0000.0000.0000.0000.000
74A40ARG00.169-0.05852.967-0.001-0.0010.0000.0000.0000.000
75A40ARG10.7340.97152.2640.0310.0310.0000.0000.0000.000
76A41GLU00.124-0.09250.841-0.002-0.0020.0000.0000.0000.000
77A41GLU-1-0.957-0.80550.735-0.029-0.0290.0000.0000.0000.000
78A42GLU00.079-0.14148.784-0.002-0.0020.0000.0000.0000.000
79A42GLU-1-0.899-0.80948.690-0.028-0.0280.0000.0000.0000.000
80A43ILE00.056-0.09547.923-0.002-0.0020.0000.0000.0000.000
81A43ILE0-0.0340.12949.8720.0000.0000.0000.0000.0000.000
82A44ASP00.083-0.09247.647-0.002-0.0020.0000.0000.0000.000
83A44ASP-1-0.939-0.83248.067-0.035-0.0350.0000.0000.0000.000
84A45TRP00.100-0.07644.845-0.003-0.0030.0000.0000.0000.000
85A45TRP0-0.0700.09840.7950.0010.0010.0000.0000.0000.000
86A46THR0-0.022-0.12343.308-0.003-0.0030.0000.0000.0000.000
87A46THR0-0.0400.08144.1980.0000.0000.0000.0000.0000.000
88A47THR00.044-0.08342.878-0.003-0.0030.0000.0000.0000.000
89A47THR0-0.0650.05444.7760.0000.0000.0000.0000.0000.000
90A48ASN00.051-0.07442.173-0.003-0.0030.0000.0000.0000.000
91A48ASN0-0.1630.03841.898-0.002-0.0020.0000.0000.0000.000
92A49GLU00.113-0.12038.910-0.005-0.0050.0000.0000.0000.000
93A49GLU-1-0.921-0.79137.564-0.058-0.0580.0000.0000.0000.000
94A50LEU00.117-0.10937.930-0.005-0.0050.0000.0000.0000.000
95A50LEU0-0.0940.13839.0410.0000.0000.0000.0000.0000.000
96A51ARG00.066-0.10538.263-0.003-0.0030.0000.0000.0000.000
97A51ARG10.8481.05039.2880.0540.0540.0000.0000.0000.000
98A52ASN00.045-0.10135.844-0.005-0.0050.0000.0000.0000.000
99A52ASN0-0.1290.05434.563-0.005-0.0050.0000.0000.0000.000
100A53ASN00.053-0.09033.488-0.006-0.0060.0000.0000.0000.000
101A53ASN0-0.1210.05333.907-0.001-0.0010.0000.0000.0000.000
102A54LEU00.102-0.08333.103-0.007-0.0070.0000.0000.0000.000
103A54LEU0-0.0800.09836.0310.0010.0010.0000.0000.0000.000
104A55ARG00.150-0.05733.597-0.003-0.0030.0000.0000.0000.000
105A55ARG10.7771.02932.4600.0770.0770.0000.0000.0000.000
106A56SER00.056-0.09529.651-0.006-0.0060.0000.0000.0000.000
107A56SER0-0.0290.08028.1930.0010.0010.0000.0000.0000.000
108A57ILE00.050-0.07528.686-0.011-0.0110.0000.0000.0000.000
109A57ILE0-0.1380.07830.4370.0010.0010.0000.0000.0000.000
110A58GLU00.113-0.07629.512-0.007-0.0070.0000.0000.0000.000
111A58GLU-1-0.897-0.78732.481-0.076-0.0760.0000.0000.0000.000
112A59TRP00.096-0.06128.164-0.003-0.0030.0000.0000.0000.000
113A59TRP0-0.1240.05823.8270.0070.0070.0000.0000.0000.000
114A60ASP00.052-0.11724.982-0.012-0.0120.0000.0000.0000.000
115A60ASP-1-0.954-0.85825.095-0.139-0.1390.0000.0000.0000.000
116A61LEU00.093-0.11024.854-0.017-0.0170.0000.0000.0000.000
117A61LEU0-0.1110.08227.5390.0020.0020.0000.0000.0000.000
118A62GLU00.021-0.12626.538-0.002-0.0020.0000.0000.0000.000
119A62GLU-1-0.974-0.84127.155-0.121-0.1210.0000.0000.0000.000
120A63ASP00.129-0.09922.668-0.002-0.0020.0000.0000.0000.000
121A63ASP-1-0.979-0.82721.595-0.207-0.2070.0000.0000.0000.000
122A64LEU00.042-0.13221.776-0.026-0.0260.0000.0000.0000.000
123A64LEU0-0.0900.09721.0660.0020.0020.0000.0000.0000.000
124A65ASP00.116-0.09522.560-0.013-0.0130.0000.0000.0000.000
125A65ASP-1-0.843-0.76726.552-0.120-0.1200.0000.0000.0000.000
126A66GLU00.031-0.16822.8910.0070.0070.0000.0000.0000.000
127A66GLU-1-0.971-0.79722.109-0.201-0.2010.0000.0000.0000.000
128A67THR0-0.023-0.11919.070-0.010-0.0100.0000.0000.0000.000
129A67THR0-0.0820.03718.147-0.007-0.0070.0000.0000.0000.000
130A68ILE00.059-0.09419.446-0.025-0.0250.0000.0000.0000.000
131A68ILE0-0.0860.11022.1620.0040.0040.0000.0000.0000.000
132A69SER00.043-0.10221.9820.0030.0030.0000.0000.0000.000
133A69SER0-0.0180.09523.2270.0070.0070.0000.0000.0000.000
134A70ILE00.045-0.07818.4980.0170.0170.0000.0000.0000.000
135A70ILE0-0.1010.08216.488-0.013-0.0130.0000.0000.0000.000
136A71VAL00.028-0.15017.510-0.024-0.0240.0000.0000.0000.000
137A71VAL0-0.0780.09916.6810.0000.0000.0000.0000.0000.000
138A72GLU00.065-0.11718.5330.0030.0030.0000.0000.0000.000
139A72GLU-1-0.886-0.76522.728-0.113-0.1130.0000.0000.0000.000
140A73ALA00.070-0.11021.0590.0220.0220.0000.0000.0000.000
141A73ALA0-0.0790.11320.646-0.001-0.0010.0000.0000.0000.000
142A74ASN00.001-0.09716.8820.0140.0140.0000.0000.0000.000
143A74ASN0-0.1430.05114.6310.0070.0070.0000.0000.0000.000
144A75PRO00.098-0.06816.149-0.037-0.0370.0000.0000.0000.000
145A76ARG00.0860.02015.7610.0000.0000.0000.0000.0000.000
146A76ARG10.8401.04814.0870.0530.0530.0000.0000.0000.000
147A77LYS00.096-0.09611.8590.0440.0440.0000.0000.0000.000
148A77LYS10.8421.05410.0430.7500.7500.0000.0000.0000.000
149A78PHE00.036-0.08211.212-0.078-0.0780.0000.0000.0000.000
150A78PHE0-0.0750.09012.435-0.029-0.0290.0000.0000.0000.000
151A79ASN00.151-0.04313.4460.0020.0020.0000.0000.0000.000
152A79ASN0-0.1860.04213.2330.0260.0260.0000.0000.0000.000
153A80LEU00.063-0.12115.0520.0230.0230.0000.0000.0000.000
154A80LEU0-0.0730.11415.773-0.002-0.0020.0000.0000.0000.000
155A81ASP00.125-0.09117.6270.0080.0080.0000.0000.0000.000
156A81ASP-1-0.867-0.82320.577-0.026-0.0260.0000.0000.0000.000
157A82ALA00.124-0.08120.709-0.017-0.0170.0000.0000.0000.000
158A82ALA0-0.0860.10823.8990.0020.0020.0000.0000.0000.000
159A83THR0-0.021-0.11523.738-0.009-0.0090.0000.0000.0000.000
160A83THR0-0.0080.07725.8250.0020.0020.0000.0000.0000.000
161A84GLU00.090-0.09422.0150.0000.0000.0000.0000.0000.000
162A84GLU-1-0.898-0.78719.151-0.120-0.1200.0000.0000.0000.000
163A85LEU00.115-0.09222.551-0.008-0.0080.0000.0000.0000.000
164A85LEU0-0.0990.10921.104-0.001-0.0010.0000.0000.0000.000
165A86SER00.038-0.10323.229-0.009-0.0090.0000.0000.0000.000
166A86SER0-0.0460.07226.9900.0020.0020.0000.0000.0000.000
167A87ILE00.072-0.08226.1300.0010.0010.0000.0000.0000.000
168A87ILE0-0.1240.08525.5430.0010.0010.0000.0000.0000.000
169A88ARG00.043-0.10823.3280.0060.0060.0000.0000.0000.000
170A88ARG10.6660.93516.7140.1980.1980.0000.0000.0000.000
171A89LYS00.150-0.07224.729-0.005-0.0050.0000.0000.0000.000
172A89LYS10.7320.98525.7030.1090.1090.0000.0000.0000.000
173A90ALA00.102-0.08827.389-0.001-0.0010.0000.0000.0000.000
174A90ALA0-0.0700.10629.8590.0020.0020.0000.0000.0000.000
175A91PHE00.035-0.07227.5050.0080.0080.0000.0000.0000.000
176A91PHE0-0.0580.08225.9520.0010.0010.0000.0000.0000.000
177A92ILE00.145-0.08127.8500.0060.0060.0000.0000.0000.000
178A92ILE0-0.0970.14924.5140.0000.0000.0000.0000.0000.000
179A93THR00.027-0.11228.8610.0010.0010.0000.0000.0000.000
180A93THR0-0.0820.05430.9570.0010.0010.0000.0000.0000.000
181A94SER00.021-0.09032.2610.0030.0030.0000.0000.0000.000
182A94SER0-0.0620.05031.9820.0010.0010.0000.0000.0000.000
183A95THR0-0.027-0.10631.3800.0070.0070.0000.0000.0000.000
184A95THR0-0.0190.06930.3920.0000.0000.0000.0000.0000.000
185A96ARG00.095-0.06732.5760.0020.0020.0000.0000.0000.000
186A96ARG10.7330.97729.1980.1070.1070.0000.0000.0000.000
187A97GLN00.138-0.07034.0440.0010.0010.0000.0000.0000.000
188A97GLN0-0.1390.05437.540-0.002-0.0020.0000.0000.0000.000
189A98VAL00.117-0.06436.3850.0030.0030.0000.0000.0000.000
190A98VAL0-0.1120.08235.5490.0000.0000.0000.0000.0000.000
191A99VAL00.090-0.12135.7710.0050.0050.0000.0000.0000.000
192A99VAL0-0.0880.10133.9020.0000.0000.0000.0000.0000.000
193A100ARG00.085-0.10337.0340.0020.0020.0000.0000.0000.000
194A100ARG10.8391.06338.2470.0590.0590.0000.0000.0000.000
195A101ASP00.057-0.12139.3130.0010.0010.0000.0000.0000.000
196A101ASP-1-0.927-0.81041.110-0.046-0.0460.0000.0000.0000.000
197A102MET00.083-0.07540.5190.0040.0040.0000.0000.0000.000
198A102MET0-0.1120.07937.1380.0000.0000.0000.0000.0000.000
199A103LYS00.089-0.08440.8790.0030.0030.0000.0000.0000.000
200A103LYS10.7240.95737.2370.0700.0700.0000.0000.0000.000
201A104ASP00.129-0.08442.1990.0010.0010.0000.0000.0000.000
202A104ASP-1-1.016-0.84444.204-0.048-0.0480.0000.0000.0000.000
203A105GLN00.010-0.13845.1360.0020.0020.0000.0000.0000.000
204A105GLN0-0.0870.08645.7760.0000.0000.0000.0000.0000.000
205A106MET00.084-0.07445.2520.0030.0030.0000.0000.0000.000
206A106MET0-0.1600.05643.331-0.001-0.0010.0000.0000.0000.000
207A107SER0-0.030-0.09845.6270.0020.0020.0000.0000.0000.000
208A107SER0-0.0470.05744.409-0.001-0.0010.0000.0000.0000.000
209A108THR0-0.168-0.17447.0470.0010.0010.0000.0000.0000.000
210A108THR00.0640.06049.4140.0010.0010.0000.0000.0000.000