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: J2839

Calculation Name: 2BO3-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BO3

Chain ID: A

ChEMBL ID:

UniProt ID: O25025

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 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 181
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -595633.366197
FMO2-HF: Nuclear repulsion 557960.373162
FMO2-HF: Total energy -37672.993035
FMO2-MP2: Total energy -37783.301456


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-4.291-1.373-0.01-1.642-1.2670.004
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.129 / q_NPA : 0.021
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].
4A2ARG10.8321.0253.9931.0231.4390.003-0.183-0.2360.000
5A3ASP00.115-0.0983.879-2.0220.262-0.015-1.397-0.8720.004
6A3ASP-1-0.990-0.8407.782-2.544-2.5440.0000.0000.0000.000
7A4TYR00.083-0.0737.0670.3280.3280.0000.0000.0000.000
8A4TYR0-0.1210.0743.644-0.463-0.2450.002-0.062-0.1590.000
9A5SER00.007-0.0998.3340.1740.1740.0000.0000.0000.000
10A5SER0-0.0370.04911.6750.0000.0000.0000.0000.0000.000
11A6GLU00.044-0.10010.8840.0790.0790.0000.0000.0000.000
12A6GLU-1-0.859-0.8099.146-0.910-0.9100.0000.0000.0000.000
13A7LEU00.090-0.09410.8930.1180.1180.0000.0000.0000.000
14A7LEU0-0.1490.0789.771-0.005-0.0050.0000.0000.0000.000
15A8GLU00.065-0.10611.810-0.005-0.0050.0000.0000.0000.000
16A8GLU-1-0.859-0.75814.715-0.140-0.1400.0000.0000.0000.000
17A9ILE00.018-0.11114.1150.0170.0170.0000.0000.0000.000
18A9ILE0-0.1030.07312.3800.0110.0110.0000.0000.0000.000
19A10PHE00.041-0.10415.5340.0470.0470.0000.0000.0000.000
20A10PHE0-0.0730.06415.1090.0050.0050.0000.0000.0000.000
21A11GLU00.090-0.07818.566-0.020-0.0200.0000.0000.0000.000
22A11GLU-1-1.022-0.84521.267-0.076-0.0760.0000.0000.0000.000
23A12GLY00.044-0.08820.551-0.021-0.0210.0000.0000.0000.000
24A13ASN00.098-0.03321.3860.0190.0190.0000.0000.0000.000
25A13ASN0-0.1180.09224.9800.0120.0120.0000.0000.0000.000
26A14PRO00.002-0.11024.162-0.007-0.0070.0000.0000.0000.000
27A15LEU00.0700.00125.2620.0020.0020.0000.0000.0000.000
28A15LEU0-0.0520.11329.0450.0000.0000.0000.0000.0000.000
29A16ASP00.132-0.10425.7060.0050.0050.0000.0000.0000.000
30A16ASP-1-0.924-0.80224.819-0.080-0.0800.0000.0000.0000.000
31A17LYS00.100-0.07822.777-0.012-0.0120.0000.0000.0000.000
32A17LYS10.7290.98618.5760.1190.1190.0000.0000.0000.000
33A18TRP00.107-0.08323.9010.0020.0020.0000.0000.0000.000
34A18TRP0-0.1000.05927.769-0.001-0.0010.0000.0000.0000.000
35A19ASN00.121-0.05627.0710.0040.0040.0000.0000.0000.000
36A19ASN0-0.1210.05927.4240.0040.0040.0000.0000.0000.000
37A20ASP00.062-0.13424.0680.0020.0020.0000.0000.0000.000
38A20ASP-1-0.940-0.82322.987-0.124-0.1240.0000.0000.0000.000
39A21ILE00.007-0.08724.997-0.009-0.0090.0000.0000.0000.000
40A21ILE0-0.0820.09221.7530.0020.0020.0000.0000.0000.000
41A22ILE00.108-0.11625.6550.0030.0030.0000.0000.0000.000
42A22ILE0-0.1110.11729.3840.0010.0010.0000.0000.0000.000
43A23PHE00.085-0.11728.6970.0060.0060.0000.0000.0000.000
44A23PHE0-0.1100.09728.942-0.001-0.0010.0000.0000.0000.000
45A24HIS00.046-0.12525.1520.0000.0000.0000.0000.0000.000
46A24HIS0-0.1180.08423.6870.0000.0000.0000.0000.0000.000
47A25ALA00.103-0.08526.310-0.007-0.0070.0000.0000.0000.000
48A25ALA0-0.0360.11626.6250.0030.0030.0000.0000.0000.000
49A26SER00.042-0.08727.196-0.007-0.0070.0000.0000.0000.000
50A26SER0-0.0580.05929.1390.0010.0010.0000.0000.0000.000
51A27LYS00.080-0.08629.8420.0070.0070.0000.0000.0000.000
52A27LYS10.8671.06130.3110.0690.0690.0000.0000.0000.000
53A28LYS00.098-0.05633.1240.0020.0020.0000.0000.0000.000
54A28LYS10.8681.05033.722-0.001-0.0010.0000.0000.0000.000
55A29LEU0-0.022-0.13230.9710.0040.0040.0000.0000.0000.000
56A29LEU0-0.0690.10128.680-0.001-0.0010.0000.0000.0000.000
57A30SER00.107-0.05831.9190.0080.0080.0000.0000.0000.000
58A30SER0-0.0240.10030.8550.0000.0000.0000.0000.0000.000
59A31LYS00.107-0.06432.6560.0010.0010.0000.0000.0000.000
60A31LYS10.6880.94236.8380.0100.0100.0000.0000.0000.000
61A32LYS00.139-0.05635.9850.0000.0000.0000.0000.0000.000
62A32LYS10.8571.04334.455-0.025-0.0250.0000.0000.0000.000
63A33GLU00.060-0.08733.5350.0030.0030.0000.0000.0000.000
64A33GLU-1-0.785-0.68731.9390.0190.0190.0000.0000.0000.000
65A34LEU00.072-0.10935.0620.0040.0040.0000.0000.0000.000
66A34LEU0-0.0790.09534.148-0.001-0.0010.0000.0000.0000.000
67A35GLU00.127-0.09036.9770.0000.0000.0000.0000.0000.000
68A35GLU-1-0.885-0.77839.772-0.006-0.0060.0000.0000.0000.000
69A36ARG00.158-0.05537.9300.0000.0000.0000.0000.0000.000
70A36ARG10.7020.95134.012-0.024-0.0240.0000.0000.0000.000
71A37LEU00.024-0.12437.6670.0040.0040.0000.0000.0000.000
72A37LEU0-0.1200.08434.2350.0000.0000.0000.0000.0000.000
73A38LEU00.129-0.06938.7710.0010.0010.0000.0000.0000.000
74A38LEU0-0.1130.08541.542-0.001-0.0010.0000.0000.0000.000
75A39GLU00.114-0.10342.050-0.001-0.0010.0000.0000.0000.000
76A39GLU-1-1.039-0.86342.7430.0140.0140.0000.0000.0000.000
77A40LEU00.093-0.08541.3200.0000.0000.0000.0000.0000.000
78A40LEU0-0.1370.06639.1000.0010.0010.0000.0000.0000.000
79A41LEU00.095-0.10042.5140.0030.0030.0000.0000.0000.000
80A41LEU0-0.1120.09742.2460.0000.0000.0000.0000.0000.000
81A42ALA00.194-0.06443.8640.0010.0010.0000.0000.0000.000
82A42ALA0-0.0940.10046.9590.0000.0000.0000.0000.0000.000
83A43LEU00.059-0.08746.366-0.001-0.0010.0000.0000.0000.000
84A43LEU0-0.1230.07445.7390.0010.0010.0000.0000.0000.000
85A44LEU00.053-0.09945.6530.0010.0010.0000.0000.0000.000
86A44LEU0-0.1150.06942.5230.0010.0010.0000.0000.0000.000
87A45GLU00.086-0.10447.0290.0020.0020.0000.0000.0000.000
88A45GLU-1-0.981-0.84547.0810.0000.0000.0000.0000.0000.000
89A46THR00.104-0.07249.3450.0000.0000.0000.0000.0000.000
90A46THR0-0.0880.02750.7590.0000.0000.0000.0000.0000.000
91A47PHE00.059-0.05750.4780.0000.0000.0000.0000.0000.000
92A47PHE0-0.1660.03849.0940.0010.0010.0000.0000.0000.000
93A48ILE00.112-0.06850.8900.0010.0010.0000.0000.0000.000
94A48ILE0-0.1450.05548.0420.0000.0000.0000.0000.0000.000
95A49GLU00.104-0.10252.2760.0010.0010.0000.0000.0000.000
96A49GLU-1-1.016-0.86353.6230.0030.0030.0000.0000.0000.000
97A50LYS00.056-0.05855.043-0.001-0.0010.0000.0000.0000.000
98A50LYS10.6680.92054.555-0.016-0.0160.0000.0000.0000.000
99A51GLU00.018-0.08655.5500.0000.0000.0000.0000.0000.000
100A51GLU-1-0.949-0.85454.8870.0190.0190.0000.0000.0000.000
101A52ASP00.124-0.04756.8520.0010.0010.0000.0000.0000.000
102A52ASP-1-1.037-0.88059.7910.0100.0100.0000.0000.0000.000
103A53LEU00.068-0.10654.0930.0000.0000.0000.0000.0000.000
104A53LEU0-0.1450.05852.5890.0010.0010.0000.0000.0000.000
105A54GLU00.052-0.16353.5020.0010.0010.0000.0000.0000.000
106A54GLU-1-0.848-0.77254.3400.0060.0060.0000.0000.0000.000
107A55GLU00.142-0.09953.5930.0000.0000.0000.0000.0000.000
108A55GLU-1-0.963-0.82957.4860.0050.0050.0000.0000.0000.000
109A56LYS00.040-0.09354.127-0.001-0.0010.0000.0000.0000.000
110A56LYS10.8771.08752.315-0.016-0.0160.0000.0000.0000.000
111A57PHE00.093-0.11750.0650.0010.0010.0000.0000.0000.000
112A57PHE0-0.0680.12145.7940.0000.0000.0000.0000.0000.000
113A58GLU00.061-0.15249.5370.0000.0000.0000.0000.0000.000
114A58GLU-1-0.993-0.81951.843-0.001-0.0010.0000.0000.0000.000
115A59SER00.008-0.12250.871-0.002-0.0020.0000.0000.0000.000
116A59SER0-0.0720.05853.3200.0000.0000.0000.0000.0000.000
117A60PHE00.063-0.07048.762-0.001-0.0010.0000.0000.0000.000
118A60PHE0-0.1170.07643.5680.0010.0010.0000.0000.0000.000
119A61ALA00.129-0.10546.2580.0010.0010.0000.0000.0000.000
120A61ALA0-0.0600.12546.9010.0000.0000.0000.0000.0000.000
121A62LYS0-0.079-0.15346.930-0.003-0.0030.0000.0000.0000.000
122A62LYS10.8371.04847.4570.0040.0040.0000.0000.0000.000
123A63ALA00.163-0.08348.508-0.002-0.0020.0000.0000.0000.000
124A63ALA0-0.0800.10848.5510.0010.0010.0000.0000.0000.000
125A64LEU00.124-0.08744.3490.0010.0010.0000.0000.0000.000
126A64LEU0-0.1010.10141.3370.0000.0000.0000.0000.0000.000
127A65ARG00.067-0.07843.6030.0000.0000.0000.0000.0000.000
128A65ARG10.7971.01845.5080.0040.0040.0000.0000.0000.000
129A66ILE0-0.026-0.10845.531-0.003-0.0030.0000.0000.0000.000
130A66ILE0-0.0940.05048.2300.0000.0000.0000.0000.0000.000
131A67ASP00.135-0.05944.6780.0000.0000.0000.0000.0000.000
132A67ASP-1-0.900-0.82243.3040.0210.0210.0000.0000.0000.000
133A68GLU00.018-0.13940.787-0.004-0.0040.0000.0000.0000.000
134A68GLU-1-0.980-0.83340.1490.0120.0120.0000.0000.0000.000
135A69GLU00.114-0.10138.8720.0000.0000.0000.0000.0000.000
136A69GLU-1-0.931-0.80839.9070.0360.0360.0000.0000.0000.000
137A70LEU00.081-0.13238.8300.0040.0040.0000.0000.0000.000
138A70LEU0-0.1040.11841.1700.0000.0000.0000.0000.0000.000
139A71GLN00.065-0.10838.8810.0010.0010.0000.0000.0000.000
140A71GLN0-0.0840.09038.366-0.003-0.0030.0000.0000.0000.000
141A72GLN00.156-0.07334.910-0.002-0.0020.0000.0000.0000.000
142A72GLN0-0.0780.10831.288-0.003-0.0030.0000.0000.0000.000
143A73LYS00.118-0.06734.5520.0040.0040.0000.0000.0000.000
144A73LYS10.7381.01137.906-0.036-0.0360.0000.0000.0000.000
145A74ILE00.028-0.13236.1010.0050.0050.0000.0000.0000.000
146A74ILE0-0.0790.10836.853-0.001-0.0010.0000.0000.0000.000
147A75GLU00.094-0.11533.469-0.001-0.0010.0000.0000.0000.000
148A75GLU-1-0.846-0.74831.576-0.002-0.0020.0000.0000.0000.000
149A76SER00.038-0.09331.296-0.001-0.0010.0000.0000.0000.000
150A76SER0-0.0840.04332.2690.0030.0030.0000.0000.0000.000
151A77ARG00.092-0.06831.9320.0050.0050.0000.0000.0000.000
152A77ARG10.7731.01135.313-0.048-0.0480.0000.0000.0000.000
153A78LYS00.084-0.12033.2840.0030.0030.0000.0000.0000.000
154A78LYS10.7490.99832.5960.0000.0000.0000.0000.0000.000
155A79THR00.009-0.07829.054-0.005-0.0050.0000.0000.0000.000
156A79THR0-0.0450.07127.0620.0000.0000.0000.0000.0000.000
157A80ASP00.085-0.11329.0610.0040.0040.0000.0000.0000.000
158A80ASP-1-0.912-0.82231.5900.0600.0600.0000.0000.0000.000
159A81ILE00.053-0.09231.0270.0060.0060.0000.0000.0000.000
160A81ILE0-0.0920.10733.4330.0000.0000.0000.0000.0000.000
161A82VAL00.082-0.11028.7100.0000.0000.0000.0000.0000.000
162A82VAL0-0.1100.11526.637-0.001-0.0010.0000.0000.0000.000
163A83ILE00.129-0.08326.616-0.006-0.0060.0000.0000.0000.000
164A83ILE0-0.0830.10125.3710.0030.0030.0000.0000.0000.000
165A84GLN00.128-0.09027.5820.0050.0050.0000.0000.0000.000
166A84GLN0-0.1100.08231.4840.0030.0030.0000.0000.0000.000
167A85SER0-0.010-0.09730.4330.0030.0030.0000.0000.0000.000
168A85SER0-0.0400.05229.991-0.005-0.0050.0000.0000.0000.000
169A86MET00.053-0.11925.678-0.007-0.0070.0000.0000.0000.000
170A86MET0-0.1090.09023.6950.0060.0060.0000.0000.0000.000
171A87ALA00.108-0.10626.586-0.002-0.0020.0000.0000.0000.000
172A87ALA0-0.0650.12927.4550.0020.0020.0000.0000.0000.000
173A88ASN00.075-0.10227.5830.0050.0050.0000.0000.0000.000
174A88ASN0-0.1680.04531.5340.0050.0050.0000.0000.0000.000
175A89ILE00.052-0.09328.2480.0010.0010.0000.0000.0000.000
176A89ILE0-0.0720.10426.613-0.002-0.0020.0000.0000.0000.000
177A90LEU0-0.008-0.13324.784-0.008-0.0080.0000.0000.0000.000
178A90LEU0-0.0780.11221.6790.0010.0010.0000.0000.0000.000
179A91SER00.056-0.09725.8340.0060.0060.0000.0000.0000.000
180A91SER0-0.0290.07829.0360.0020.0020.0000.0000.0000.000
181A92GLY0-0.164-0.15228.377-0.004-0.0040.0000.0000.0000.000