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: 372QL

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 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 181
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -594833.600534
FMO2-HF: Nuclear repulsion 557163.021514
FMO2-HF: Total energy -37670.57902
FMO2-MP2: Total energy -37781.083012


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.
-4.644-1.3010.023-1.872-1.4930.007
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 : 0.093 / q_NPA : 0.017
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].
4A2ARG10.8961.0793.3130.9131.6450.041-0.345-0.4270.001
5A3ASP00.108-0.1083.808-2.487-0.051-0.019-1.489-0.9280.006
6A3ASP-1-1.009-0.8397.357-2.610-2.6100.0000.0000.0000.000
7A4TYR00.093-0.0826.9850.3210.3210.0000.0000.0000.000
8A4TYR0-0.1410.0573.8180.1890.3640.001-0.038-0.1380.000
9A5SER0-0.018-0.1068.7890.1750.1750.0000.0000.0000.000
10A5SER0-0.0120.08111.0900.0540.0540.0000.0000.0000.000
11A6GLU00.135-0.10212.3750.0620.0620.0000.0000.0000.000
12A6GLU-1-0.977-0.8699.345-1.122-1.1220.0000.0000.0000.000
13A7LEU00.063-0.08810.7730.1330.1330.0000.0000.0000.000
14A7LEU0-0.1480.08310.006-0.013-0.0130.0000.0000.0000.000
15A8GLU0-0.013-0.11511.808-0.017-0.0170.0000.0000.0000.000
16A8GLU-1-0.863-0.80615.178-0.224-0.2240.0000.0000.0000.000
17A9ILE00.137-0.06914.2500.0290.0290.0000.0000.0000.000
18A9ILE0-0.1350.06412.8660.0070.0070.0000.0000.0000.000
19A10PHE00.046-0.08515.6260.0440.0440.0000.0000.0000.000
20A10PHE0-0.0810.06216.0170.0040.0040.0000.0000.0000.000
21A11GLU00.051-0.10418.562-0.019-0.0190.0000.0000.0000.000
22A11GLU-1-1.031-0.85020.873-0.133-0.1330.0000.0000.0000.000
23A12GLY00.073-0.05920.829-0.023-0.0230.0000.0000.0000.000
24A13ASN00.096-0.04921.6590.0190.0190.0000.0000.0000.000
25A13ASN0-0.0730.13225.1320.0120.0120.0000.0000.0000.000
26A14PRO00.005-0.10824.540-0.008-0.0080.0000.0000.0000.000
27A15LEU00.074-0.03925.5530.0020.0020.0000.0000.0000.000
28A15LEU0-0.0360.13129.3780.0020.0020.0000.0000.0000.000
29A16ASP00.131-0.09725.7520.0080.0080.0000.0000.0000.000
30A16ASP-1-0.969-0.82024.887-0.130-0.1300.0000.0000.0000.000
31A17LYS00.091-0.10223.222-0.012-0.0120.0000.0000.0000.000
32A17LYS10.7791.02418.9780.1660.1660.0000.0000.0000.000
33A18TRP00.096-0.09224.148-0.001-0.0010.0000.0000.0000.000
34A18TRP0-0.0990.07127.9980.0000.0000.0000.0000.0000.000
35A19ASN00.097-0.07227.2810.0060.0060.0000.0000.0000.000
36A19ASN0-0.1040.07828.2090.0090.0090.0000.0000.0000.000
37A20ASP00.084-0.13224.4240.0080.0080.0000.0000.0000.000
38A20ASP-1-0.978-0.83923.271-0.178-0.1780.0000.0000.0000.000
39A21ILE0-0.015-0.10825.395-0.009-0.0090.0000.0000.0000.000
40A21ILE0-0.0670.09922.2380.0020.0020.0000.0000.0000.000
41A22ILE00.050-0.12226.0020.0040.0040.0000.0000.0000.000
42A22ILE0-0.0690.10129.3930.0010.0010.0000.0000.0000.000
43A23PHE0-0.006-0.11029.0680.0090.0090.0000.0000.0000.000
44A23PHE0-0.1090.07329.2980.0000.0000.0000.0000.0000.000
45A24HIS00.046-0.13025.8490.0000.0000.0000.0000.0000.000
46A24HIS0-0.0770.12423.9350.0050.0050.0000.0000.0000.000
47A25ALA00.106-0.08526.931-0.007-0.0070.0000.0000.0000.000
48A25ALA0-0.0300.11027.3960.0030.0030.0000.0000.0000.000
49A26SER00.071-0.07327.911-0.004-0.0040.0000.0000.0000.000
50A26SER0-0.0720.05430.0280.0020.0020.0000.0000.0000.000
51A27LYS00.057-0.11230.5180.0040.0040.0000.0000.0000.000
52A27LYS10.9121.09131.8260.0970.0970.0000.0000.0000.000
53A28LYS00.106-0.07133.7890.0020.0020.0000.0000.0000.000
54A28LYS10.8631.05934.2760.0230.0230.0000.0000.0000.000
55A29LEU0-0.020-0.14331.7770.0050.0050.0000.0000.0000.000
56A29LEU0-0.0710.11729.526-0.001-0.0010.0000.0000.0000.000
57A30SER00.131-0.04632.7360.0080.0080.0000.0000.0000.000
58A30SER00.0030.10231.7080.0000.0000.0000.0000.0000.000
59A31LYS00.110-0.07833.2980.0020.0020.0000.0000.0000.000
60A31LYS10.7491.01137.4180.0350.0350.0000.0000.0000.000
61A32LYS00.142-0.05136.5030.0020.0020.0000.0000.0000.000
62A32LYS10.8471.03535.5150.0060.0060.0000.0000.0000.000
63A33GLU00.020-0.10734.1360.0050.0050.0000.0000.0000.000
64A33GLU-1-0.761-0.73132.581-0.015-0.0150.0000.0000.0000.000
65A34LEU00.043-0.11735.6490.0040.0040.0000.0000.0000.000
66A34LEU0-0.0750.11134.742-0.001-0.0010.0000.0000.0000.000
67A35GLU00.142-0.09737.4920.0010.0010.0000.0000.0000.000
68A35GLU-1-0.943-0.81640.515-0.028-0.0280.0000.0000.0000.000
69A36ARG00.115-0.07638.7160.0020.0020.0000.0000.0000.000
70A36ARG10.7180.96534.7210.0080.0080.0000.0000.0000.000
71A37LEU00.022-0.10838.2440.0050.0050.0000.0000.0000.000
72A37LEU0-0.1010.07934.8480.0000.0000.0000.0000.0000.000
73A38LEU00.132-0.07239.3840.0020.0020.0000.0000.0000.000
74A38LEU0-0.1010.10042.208-0.001-0.0010.0000.0000.0000.000
75A39GLU00.093-0.10542.5480.0000.0000.0000.0000.0000.000
76A39GLU-1-1.014-0.85743.605-0.007-0.0070.0000.0000.0000.000
77A40LEU00.099-0.08942.0140.0020.0020.0000.0000.0000.000
78A40LEU0-0.1350.07139.8140.0010.0010.0000.0000.0000.000
79A41LEU00.098-0.10442.9670.0030.0030.0000.0000.0000.000
80A41LEU0-0.0870.10542.364-0.001-0.0010.0000.0000.0000.000
81A42ALA00.151-0.06744.2780.0010.0010.0000.0000.0000.000
82A42ALA0-0.0740.09747.6120.0000.0000.0000.0000.0000.000
83A43LEU00.059-0.10246.7640.0000.0000.0000.0000.0000.000
84A43LEU0-0.1390.08046.0780.0010.0010.0000.0000.0000.000
85A44LEU00.053-0.10446.0320.0020.0020.0000.0000.0000.000
86A44LEU0-0.1060.07242.8120.0000.0000.0000.0000.0000.000
87A45GLU00.086-0.10547.3860.0020.0020.0000.0000.0000.000
88A45GLU-1-1.007-0.84047.236-0.019-0.0190.0000.0000.0000.000
89A46THR00.157-0.06849.6090.0000.0000.0000.0000.0000.000
90A46THR0-0.1130.04151.1780.0000.0000.0000.0000.0000.000
91A47PHE00.072-0.08950.9400.0010.0010.0000.0000.0000.000
92A47PHE0-0.1530.04750.1690.0010.0010.0000.0000.0000.000
93A48ILE00.071-0.07951.2470.0020.0020.0000.0000.0000.000
94A48ILE0-0.1100.07448.4520.0000.0000.0000.0000.0000.000
95A49GLU00.084-0.10852.5230.0010.0010.0000.0000.0000.000
96A49GLU-1-1.022-0.84354.150-0.011-0.0110.0000.0000.0000.000
97A50LYS00.123-0.02755.4800.0000.0000.0000.0000.0000.000
98A50LYS10.7360.97654.972-0.003-0.0030.0000.0000.0000.000
99A51GLU00.001-0.13355.3990.0010.0010.0000.0000.0000.000
100A51GLU-1-1.011-0.87354.4950.0050.0050.0000.0000.0000.000
101A52ASP00.123-0.08456.7570.0010.0010.0000.0000.0000.000
102A52ASP-1-1.053-0.86659.649-0.003-0.0030.0000.0000.0000.000
103A53LEU00.027-0.12954.2940.0000.0000.0000.0000.0000.000
104A53LEU0-0.1660.05652.9850.0000.0000.0000.0000.0000.000
105A54GLU00.086-0.15153.9050.0000.0000.0000.0000.0000.000
106A54GLU-1-0.856-0.76455.110-0.007-0.0070.0000.0000.0000.000
107A55GLU00.114-0.10054.110-0.001-0.0010.0000.0000.0000.000
108A55GLU-1-0.980-0.83757.754-0.007-0.0070.0000.0000.0000.000
109A56LYS00.037-0.12254.379-0.001-0.0010.0000.0000.0000.000
110A56LYS10.8721.08253.282-0.001-0.0010.0000.0000.0000.000
111A57PHE00.075-0.11850.3880.0010.0010.0000.0000.0000.000
112A57PHE0-0.0280.11145.7820.0000.0000.0000.0000.0000.000
113A58GLU00.060-0.12649.925-0.001-0.0010.0000.0000.0000.000
114A58GLU-1-0.979-0.81052.640-0.014-0.0140.0000.0000.0000.000
115A59SER0-0.011-0.10251.453-0.002-0.0020.0000.0000.0000.000
116A59SER0-0.0530.05853.4340.0000.0000.0000.0000.0000.000
117A60PHE00.090-0.06749.111-0.001-0.0010.0000.0000.0000.000
118A60PHE0-0.1160.07143.8760.0010.0010.0000.0000.0000.000
119A61ALA00.054-0.14046.4800.0010.0010.0000.0000.0000.000
120A61ALA0-0.0480.14247.0660.0000.0000.0000.0000.0000.000
121A62LYS0-0.058-0.19647.019-0.003-0.0030.0000.0000.0000.000
122A62LYS10.8501.10847.8630.0210.0210.0000.0000.0000.000
123A63ALA00.032-0.12248.968-0.002-0.0020.0000.0000.0000.000
124A63ALA0-0.0540.10949.0260.0010.0010.0000.0000.0000.000
125A64LEU00.096-0.12144.4840.0020.0020.0000.0000.0000.000
126A64LEU0-0.0870.13241.1900.0000.0000.0000.0000.0000.000
127A65ARG00.148-0.04243.984-0.001-0.0010.0000.0000.0000.000
128A65ARG10.7760.99145.8170.0200.0200.0000.0000.0000.000
129A66ILE00.004-0.10044.848-0.002-0.0020.0000.0000.0000.000
130A66ILE0-0.0690.04548.2100.0000.0000.0000.0000.0000.000
131A67ASP00.123-0.03745.0550.0010.0010.0000.0000.0000.000
132A67ASP-1-0.887-0.81243.9330.0000.0000.0000.0000.0000.000
133A68GLU00.020-0.12341.160-0.004-0.0040.0000.0000.0000.000
134A68GLU-1-0.981-0.84940.640-0.010-0.0100.0000.0000.0000.000
135A69GLU00.105-0.12839.342-0.002-0.0020.0000.0000.0000.000
136A69GLU-1-1.000-0.83340.5460.0130.0130.0000.0000.0000.000
137A70LEU00.055-0.14939.5040.0030.0030.0000.0000.0000.000
138A70LEU0-0.0790.13241.7160.0000.0000.0000.0000.0000.000
139A71GLN00.066-0.11839.2440.0000.0000.0000.0000.0000.000
140A71GLN0-0.0960.08138.803-0.004-0.0040.0000.0000.0000.000
141A72GLN00.134-0.08135.299-0.003-0.0030.0000.0000.0000.000
142A72GLN0-0.0790.11331.923-0.003-0.0030.0000.0000.0000.000
143A73LYS00.086-0.09534.8840.0020.0020.0000.0000.0000.000
144A73LYS10.8291.05938.125-0.012-0.0120.0000.0000.0000.000
145A74ILE0-0.009-0.12536.2390.0040.0040.0000.0000.0000.000
146A74ILE0-0.0340.09937.0250.0000.0000.0000.0000.0000.000
147A75GLU00.103-0.11333.908-0.002-0.0020.0000.0000.0000.000
148A75GLU-1-0.958-0.81632.476-0.032-0.0320.0000.0000.0000.000
149A76SER00.026-0.12131.628-0.005-0.0050.0000.0000.0000.000
150A76SER0-0.0160.07932.6470.0040.0040.0000.0000.0000.000
151A77ARG00.130-0.07932.2400.0040.0040.0000.0000.0000.000
152A77ARG10.8151.07636.198-0.011-0.0110.0000.0000.0000.000
153A78LYS00.028-0.10933.3850.0030.0030.0000.0000.0000.000
154A78LYS10.8411.07032.8790.0380.0380.0000.0000.0000.000
155A79THR00.013-0.07829.246-0.006-0.0060.0000.0000.0000.000
156A79THR0-0.0330.08227.392-0.002-0.0020.0000.0000.0000.000
157A80ASP00.092-0.12029.1950.0000.0000.0000.0000.0000.000
158A80ASP-1-0.940-0.83431.5070.0220.0220.0000.0000.0000.000
159A81ILE00.048-0.12531.0560.0050.0050.0000.0000.0000.000
160A81ILE0-0.1030.10933.5970.0000.0000.0000.0000.0000.000
161A82VAL00.082-0.10529.0240.0010.0010.0000.0000.0000.000
162A82VAL0-0.0860.12626.989-0.001-0.0010.0000.0000.0000.000
163A83ILE00.083-0.07726.926-0.008-0.0080.0000.0000.0000.000
164A83ILE0-0.0550.09525.6420.0020.0020.0000.0000.0000.000
165A84GLN00.114-0.09227.8800.0040.0040.0000.0000.0000.000
166A84GLN0-0.1020.08032.3140.0010.0010.0000.0000.0000.000
167A85SER0-0.015-0.08530.8720.0040.0040.0000.0000.0000.000
168A85SER0-0.0440.06830.037-0.005-0.0050.0000.0000.0000.000
169A86MET00.012-0.14026.196-0.003-0.0030.0000.0000.0000.000
170A86MET0-0.0810.10223.6180.0020.0020.0000.0000.0000.000
171A87ALA00.119-0.09626.844-0.004-0.0040.0000.0000.0000.000
172A87ALA0-0.0440.13427.6810.0030.0030.0000.0000.0000.000
173A88ASN00.087-0.09427.8450.0070.0070.0000.0000.0000.000
174A88ASN0-0.1470.06131.9290.0060.0060.0000.0000.0000.000
175A89ILE00.018-0.10728.8230.0050.0050.0000.0000.0000.000
176A89ILE0-0.0510.10327.163-0.002-0.0020.0000.0000.0000.000
177A90LEU00.010-0.14425.497-0.008-0.0080.0000.0000.0000.000
178A90LEU0-0.0980.11522.4800.0000.0000.0000.0000.0000.000
179A91SER00.036-0.06726.4050.0050.0050.0000.0000.0000.000
180A91SER0-0.1080.04229.9540.0020.0020.0000.0000.0000.000
181A92GLY0-0.090-0.12729.0790.0010.0010.0000.0000.0000.000