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: N2R1Q

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 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 181
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -594678.348529
FMO2-HF: Nuclear repulsion 557005.752336
FMO2-HF: Total energy -37672.596193
FMO2-MP2: Total energy -37783.011751


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.
-4.255-1.202-0.014-1.684-1.3550.006
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 : 0.127 / q_NPA : 0.039
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].
4A2ARG10.8391.0233.7751.0641.5990.007-0.245-0.2960.000
5A3ASP00.078-0.0903.808-2.2800.087-0.021-1.415-0.9320.006
6A3ASP-1-1.000-0.8437.442-2.572-2.5720.0000.0000.0000.000
7A4TYR00.102-0.0747.1100.3230.3230.0000.0000.0000.000
8A4TYR0-0.1270.0683.9410.1150.2660.000-0.024-0.1270.000
9A5SER00.015-0.0978.8020.1610.1610.0000.0000.0000.000
10A5SER0-0.0220.06611.7670.0040.0040.0000.0000.0000.000
11A6GLU00.087-0.12012.2630.0490.0490.0000.0000.0000.000
12A6GLU-1-0.894-0.8279.289-1.026-1.0260.0000.0000.0000.000
13A7LEU00.068-0.08410.8010.1210.1210.0000.0000.0000.000
14A7LEU0-0.1420.08910.021-0.012-0.0120.0000.0000.0000.000
15A8GLU0-0.016-0.11511.803-0.014-0.0140.0000.0000.0000.000
16A8GLU-1-0.841-0.78914.939-0.194-0.1940.0000.0000.0000.000
17A9ILE00.116-0.05314.2540.0250.0250.0000.0000.0000.000
18A9ILE0-0.1310.06012.7420.0080.0080.0000.0000.0000.000
19A10PHE00.049-0.09015.6270.0400.0400.0000.0000.0000.000
20A10PHE0-0.0890.05115.4360.0050.0050.0000.0000.0000.000
21A11GLU00.097-0.08818.568-0.019-0.0190.0000.0000.0000.000
22A11GLU-1-1.038-0.84821.105-0.112-0.1120.0000.0000.0000.000
23A12GLY00.050-0.07920.831-0.022-0.0220.0000.0000.0000.000
24A13ASN00.093-0.04921.6580.0160.0160.0000.0000.0000.000
25A13ASN0-0.1240.10325.0680.0120.0120.0000.0000.0000.000
26A14PRO00.012-0.10924.534-0.008-0.0080.0000.0000.0000.000
27A15LEU00.064-0.02125.5450.0020.0020.0000.0000.0000.000
28A15LEU0-0.0310.12929.3550.0010.0010.0000.0000.0000.000
29A16ASP00.129-0.10325.7590.0060.0060.0000.0000.0000.000
30A16ASP-1-0.927-0.79924.910-0.113-0.1130.0000.0000.0000.000
31A17LYS00.099-0.07623.062-0.012-0.0120.0000.0000.0000.000
32A17LYS10.7450.99218.5750.1630.1630.0000.0000.0000.000
33A18TRP00.119-0.09224.137-0.001-0.0010.0000.0000.0000.000
34A18TRP0-0.0920.06627.9790.0000.0000.0000.0000.0000.000
35A19ASN00.107-0.06027.2680.0050.0050.0000.0000.0000.000
36A19ASN0-0.1090.06727.9590.0070.0070.0000.0000.0000.000
37A20ASP00.045-0.13024.4110.0060.0060.0000.0000.0000.000
38A20ASP-1-0.949-0.82423.424-0.163-0.1630.0000.0000.0000.000
39A21ILE00.022-0.09125.398-0.008-0.0080.0000.0000.0000.000
40A21ILE0-0.0830.09422.0360.0020.0020.0000.0000.0000.000
41A22ILE00.083-0.11825.9860.0030.0030.0000.0000.0000.000
42A22ILE0-0.1140.11029.6600.0010.0010.0000.0000.0000.000
43A23PHE00.039-0.12629.0570.0080.0080.0000.0000.0000.000
44A23PHE0-0.1050.08829.3180.0000.0000.0000.0000.0000.000
45A24HIS00.027-0.11725.8110.0000.0000.0000.0000.0000.000
46A24HIS0-0.1090.08524.0000.0020.0020.0000.0000.0000.000
47A25ALA00.117-0.08026.883-0.006-0.0060.0000.0000.0000.000
48A25ALA0-0.0360.10827.2780.0030.0030.0000.0000.0000.000
49A26SER00.085-0.07427.870-0.005-0.0050.0000.0000.0000.000
50A26SER0-0.0630.05229.8730.0020.0020.0000.0000.0000.000
51A27LYS00.056-0.09430.4730.0050.0050.0000.0000.0000.000
52A27LYS10.8641.06831.0370.0880.0880.0000.0000.0000.000
53A28LYS00.103-0.06733.7640.0020.0020.0000.0000.0000.000
54A28LYS10.8631.04834.2610.0150.0150.0000.0000.0000.000
55A29LEU0-0.013-0.14131.7270.0050.0050.0000.0000.0000.000
56A29LEU0-0.0600.11129.515-0.001-0.0010.0000.0000.0000.000
57A30SER00.138-0.04432.6470.0080.0080.0000.0000.0000.000
58A30SER0-0.0030.11331.5600.0000.0000.0000.0000.0000.000
59A31LYS00.079-0.08733.2650.0020.0020.0000.0000.0000.000
60A31LYS10.6960.95937.4660.0250.0250.0000.0000.0000.000
61A32LYS00.145-0.05936.4740.0010.0010.0000.0000.0000.000
62A32LYS10.8501.04035.537-0.004-0.0040.0000.0000.0000.000
63A33GLU00.027-0.09534.1090.0040.0040.0000.0000.0000.000
64A33GLU-1-0.787-0.70232.489-0.004-0.0040.0000.0000.0000.000
65A34LEU00.066-0.11735.6290.0040.0040.0000.0000.0000.000
66A34LEU0-0.0670.10534.469-0.001-0.0010.0000.0000.0000.000
67A35GLU00.142-0.08737.4740.0000.0000.0000.0000.0000.000
68A35GLU-1-0.890-0.78340.551-0.021-0.0210.0000.0000.0000.000
69A36ARG00.156-0.04638.7480.0010.0010.0000.0000.0000.000
70A36ARG10.7080.96234.458-0.002-0.0020.0000.0000.0000.000
71A37LEU00.012-0.12738.1970.0040.0040.0000.0000.0000.000
72A37LEU0-0.1110.08234.7390.0000.0000.0000.0000.0000.000
73A38LEU00.134-0.06939.3660.0020.0020.0000.0000.0000.000
74A38LEU0-0.1040.09142.003-0.001-0.0010.0000.0000.0000.000
75A39GLU00.096-0.10642.5320.0000.0000.0000.0000.0000.000
76A39GLU-1-1.027-0.85943.602-0.001-0.0010.0000.0000.0000.000
77A40LEU00.097-0.08041.9820.0010.0010.0000.0000.0000.000
78A40LEU0-0.1380.06639.7720.0010.0010.0000.0000.0000.000
79A41LEU00.104-0.09942.9500.0030.0030.0000.0000.0000.000
80A41LEU0-0.0910.10242.593-0.001-0.0010.0000.0000.0000.000
81A42ALA00.176-0.06544.2620.0010.0010.0000.0000.0000.000
82A42ALA0-0.0940.09747.5270.0000.0000.0000.0000.0000.000
83A43LEU00.044-0.08146.7430.0000.0000.0000.0000.0000.000
84A43LEU0-0.1310.06646.3200.0010.0010.0000.0000.0000.000
85A44LEU00.064-0.10646.0000.0020.0020.0000.0000.0000.000
86A44LEU0-0.1090.06842.8120.0000.0000.0000.0000.0000.000
87A45GLU00.083-0.10947.3700.0020.0020.0000.0000.0000.000
88A45GLU-1-0.995-0.84247.195-0.013-0.0130.0000.0000.0000.000
89A46THR00.117-0.06849.5950.0000.0000.0000.0000.0000.000
90A46THR0-0.0940.02651.1270.0000.0000.0000.0000.0000.000
91A47PHE00.065-0.06150.9250.0000.0000.0000.0000.0000.000
92A47PHE0-0.1640.04149.8180.0010.0010.0000.0000.0000.000
93A48ILE00.098-0.07151.2270.0010.0010.0000.0000.0000.000
94A48ILE0-0.1220.06748.2490.0000.0000.0000.0000.0000.000
95A49GLU00.083-0.10752.5090.0010.0010.0000.0000.0000.000
96A49GLU-1-0.988-0.85553.900-0.007-0.0070.0000.0000.0000.000
97A50LYS00.128-0.00555.4610.0000.0000.0000.0000.0000.000
98A50LYS10.6720.91855.149-0.006-0.0060.0000.0000.0000.000
99A51GLU0-0.018-0.09955.4090.0010.0010.0000.0000.0000.000
100A51GLU-1-0.960-0.85754.6750.0090.0090.0000.0000.0000.000
101A52ASP00.077-0.08456.7420.0010.0010.0000.0000.0000.000
102A52ASP-1-1.028-0.87659.6610.0010.0010.0000.0000.0000.000
103A53LEU00.064-0.11254.2850.0000.0000.0000.0000.0000.000
104A53LEU0-0.1620.04353.0630.0000.0000.0000.0000.0000.000
105A54GLU00.067-0.18053.8840.0000.0000.0000.0000.0000.000
106A54GLU-1-0.812-0.76354.788-0.003-0.0030.0000.0000.0000.000
107A55GLU00.081-0.07854.100-0.001-0.0010.0000.0000.0000.000
108A55GLU-1-0.975-0.84057.754-0.003-0.0030.0000.0000.0000.000
109A56LYS00.066-0.09554.370-0.001-0.0010.0000.0000.0000.000
110A56LYS10.8711.08253.052-0.005-0.0050.0000.0000.0000.000
111A57PHE00.074-0.12950.3670.0010.0010.0000.0000.0000.000
112A57PHE0-0.0520.11945.9390.0000.0000.0000.0000.0000.000
113A58GLU00.075-0.14049.917-0.001-0.0010.0000.0000.0000.000
114A58GLU-1-0.976-0.80552.365-0.010-0.0100.0000.0000.0000.000
115A59SER0-0.029-0.10551.447-0.002-0.0020.0000.0000.0000.000
116A59SER0-0.0760.04853.3940.0000.0000.0000.0000.0000.000
117A60PHE00.101-0.06849.141-0.001-0.0010.0000.0000.0000.000
118A60PHE0-0.1180.07243.9710.0010.0010.0000.0000.0000.000
119A61ALA00.062-0.12846.4750.0010.0010.0000.0000.0000.000
120A61ALA0-0.0500.12847.0530.0000.0000.0000.0000.0000.000
121A62LYS0-0.090-0.18347.014-0.003-0.0030.0000.0000.0000.000
122A62LYS10.9151.09347.4310.0170.0170.0000.0000.0000.000
123A63ALA00.034-0.11248.963-0.002-0.0020.0000.0000.0000.000
124A63ALA0-0.0760.10849.0670.0010.0010.0000.0000.0000.000
125A64LEU00.109-0.10644.5730.0020.0020.0000.0000.0000.000
126A64LEU0-0.0960.10841.4210.0000.0000.0000.0000.0000.000
127A65ARG00.130-0.05543.9810.0000.0000.0000.0000.0000.000
128A65ARG10.7981.01345.5890.0160.0160.0000.0000.0000.000
129A66ILE00.000-0.09844.848-0.002-0.0020.0000.0000.0000.000
130A66ILE0-0.0850.05248.3350.0000.0000.0000.0000.0000.000
131A67ASP00.128-0.03845.0520.0000.0000.0000.0000.0000.000
132A67ASP-1-0.884-0.81643.7440.0050.0050.0000.0000.0000.000
133A68GLU00.008-0.15241.157-0.003-0.0030.0000.0000.0000.000
134A68GLU-1-0.985-0.83540.537-0.003-0.0030.0000.0000.0000.000
135A69GLU00.113-0.11839.329-0.002-0.0020.0000.0000.0000.000
136A69GLU-1-0.917-0.79640.4380.0190.0190.0000.0000.0000.000
137A70LEU00.077-0.13239.4990.0040.0040.0000.0000.0000.000
138A70LEU0-0.0950.11841.5560.0000.0000.0000.0000.0000.000
139A71GLN00.036-0.10739.2400.0010.0010.0000.0000.0000.000
140A71GLN0-0.0760.08338.702-0.003-0.0030.0000.0000.0000.000
141A72GLN00.145-0.07735.302-0.003-0.0030.0000.0000.0000.000
142A72GLN0-0.0720.11031.733-0.003-0.0030.0000.0000.0000.000
143A73LYS00.122-0.06934.8780.0020.0020.0000.0000.0000.000
144A73LYS10.7351.00938.106-0.018-0.0180.0000.0000.0000.000
145A74ILE00.049-0.13336.2310.0040.0040.0000.0000.0000.000
146A74ILE0-0.0720.10936.8280.0000.0000.0000.0000.0000.000
147A75GLU00.078-0.12033.934-0.001-0.0010.0000.0000.0000.000
148A75GLU-1-0.870-0.76132.110-0.025-0.0250.0000.0000.0000.000
149A76SER00.014-0.11331.621-0.004-0.0040.0000.0000.0000.000
150A76SER0-0.0540.06532.4560.0030.0030.0000.0000.0000.000
151A77ARG00.117-0.06932.2290.0040.0040.0000.0000.0000.000
152A77ARG10.7661.02735.675-0.023-0.0230.0000.0000.0000.000
153A78LYS00.059-0.12433.3740.0030.0030.0000.0000.0000.000
154A78LYS10.7631.01532.7730.0240.0240.0000.0000.0000.000
155A79THR00.018-0.08529.251-0.005-0.0050.0000.0000.0000.000
156A79THR0-0.0390.08327.196-0.001-0.0010.0000.0000.0000.000
157A80ASP00.067-0.12729.1820.0010.0010.0000.0000.0000.000
158A80ASP-1-0.880-0.82331.8070.0320.0320.0000.0000.0000.000
159A81ILE00.046-0.08231.0400.0050.0050.0000.0000.0000.000
160A81ILE0-0.0960.10933.6670.0000.0000.0000.0000.0000.000
161A82VAL00.098-0.11129.0380.0010.0010.0000.0000.0000.000
162A82VAL0-0.1120.11626.965-0.001-0.0010.0000.0000.0000.000
163A83ILE00.108-0.08126.917-0.007-0.0070.0000.0000.0000.000
164A83ILE0-0.0790.10025.5510.0020.0020.0000.0000.0000.000
165A84GLN00.123-0.08227.8630.0050.0050.0000.0000.0000.000
166A84GLN0-0.1110.07832.2360.0020.0020.0000.0000.0000.000
167A85SER00.000-0.08730.8530.0040.0040.0000.0000.0000.000
168A85SER0-0.0530.04630.201-0.005-0.0050.0000.0000.0000.000
169A86MET00.038-0.14426.176-0.003-0.0030.0000.0000.0000.000
170A86MET0-0.0840.10123.9570.0030.0030.0000.0000.0000.000
171A87ALA00.115-0.09626.834-0.003-0.0030.0000.0000.0000.000
172A87ALA0-0.0540.13427.6870.0020.0020.0000.0000.0000.000
173A88ASN00.066-0.10827.8420.0070.0070.0000.0000.0000.000
174A88ASN0-0.1530.04831.8620.0050.0050.0000.0000.0000.000
175A89ILE00.045-0.08628.8680.0040.0040.0000.0000.0000.000
176A89ILE0-0.0580.10627.302-0.002-0.0020.0000.0000.0000.000
177A90LEU00.005-0.13225.414-0.008-0.0080.0000.0000.0000.000
178A90LEU0-0.0740.10722.2120.0010.0010.0000.0000.0000.000
179A91SER00.005-0.06726.3900.0050.0050.0000.0000.0000.000
180A91SER0-0.0810.05129.805-0.001-0.0010.0000.0000.0000.000
181A92GLY0-0.116-0.15229.149-0.001-0.0010.0000.0000.0000.000