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: J2149

Calculation Name: 5B3D-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 5B3D

Chain ID: A

ChEMBL ID:

UniProt ID: P0A1J7

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 223
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -737017.113799
FMO2-HF: Nuclear repulsion 690798.230508
FMO2-HF: Total energy -46218.883291
FMO2-MP2: Total energy -46353.737174


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:2:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-9.495-6.9770.009-0.927-1.5990
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.069 / q_NPA : 0.051
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].
4A3ARG10.7451.0054.4971.4111.644-0.001-0.103-0.1290.000
5A4LEU00.100-0.1083.869-2.728-1.021-0.006-0.871-0.8290.002
6A4LEU0-0.0770.1035.1180.3250.385-0.001-0.004-0.0540.000
7A5SER00.049-0.0843.637-0.552-0.1560.006-0.176-0.2260.001
8A5SER0-0.0560.0603.645-0.0150.1310.012-0.063-0.0950.000
9A6GLU00.105-0.0854.5040.2680.368-0.002-0.032-0.0670.000
10A6GLU-1-0.862-0.8043.532-7.711-7.8350.0010.322-0.199-0.003
11A7ILE00.045-0.0746.5580.0730.0730.0000.0000.0000.000
12A7ILE0-0.1170.0797.9910.0300.0300.0000.0000.0000.000
13A8LEU00.085-0.0878.274-0.075-0.0750.0000.0000.0000.000
14A8LEU0-0.0440.1058.2970.0390.0390.0000.0000.0000.000
15A9ASP00.102-0.0758.7550.1280.1280.0000.0000.0000.000
16A9ASP-1-0.924-0.8277.295-0.745-0.7450.0000.0000.0000.000
17A10GLN00.114-0.07010.3590.0230.0230.0000.0000.0000.000
18A10GLN0-0.0760.08110.619-0.138-0.1380.0000.0000.0000.000
19A11MET00.087-0.09612.314-0.007-0.0070.0000.0000.0000.000
20A11MET0-0.1050.08013.0850.0540.0540.0000.0000.0000.000
21A12THR00.005-0.08913.4660.0210.0210.0000.0000.0000.000
22A12THR0-0.0530.05712.764-0.022-0.0220.0000.0000.0000.000
23A13THR00.011-0.07414.6860.0390.0390.0000.0000.0000.000
24A13THR0-0.0610.05514.169-0.023-0.0230.0000.0000.0000.000
25A14VAL00.135-0.06016.5970.0130.0130.0000.0000.0000.000
26A14VAL0-0.0940.08316.945-0.002-0.0020.0000.0000.0000.000
27A15LEU00.071-0.10218.0130.0020.0020.0000.0000.0000.000
28A15LEU0-0.0690.10017.0310.0090.0090.0000.0000.0000.000
29A16ASN00.090-0.06119.4340.0220.0220.0000.0000.0000.000
30A16ASN0-0.1280.04918.1770.0180.0180.0000.0000.0000.000
31A17ASP00.147-0.08321.0110.0140.0140.0000.0000.0000.000
32A17ASP-1-1.011-0.85320.785-0.176-0.1760.0000.0000.0000.000
33A18LEU00.050-0.12722.4510.0000.0000.0000.0000.0000.000
34A18LEU0-0.0820.10521.5490.0030.0030.0000.0000.0000.000
35A19LYS00.093-0.07823.7580.0080.0080.0000.0000.0000.000
36A19LYS10.7230.97924.259-0.008-0.0080.0000.0000.0000.000
37A20THR00.041-0.08625.4870.0110.0110.0000.0000.0000.000
38A20THR0-0.0600.05625.106-0.003-0.0030.0000.0000.0000.000
39A21VAL00.057-0.09926.9810.0010.0010.0000.0000.0000.000
40A21VAL0-0.1000.09227.036-0.001-0.0010.0000.0000.0000.000
41A22MET00.132-0.09428.254-0.002-0.0020.0000.0000.0000.000
42A22MET0-0.1000.09727.9330.0050.0050.0000.0000.0000.000
43A23ASP00.098-0.08529.7710.0080.0080.0000.0000.0000.000
44A23ASP-1-0.910-0.79229.421-0.002-0.0020.0000.0000.0000.000
45A24ALA00.131-0.08831.5820.0050.0050.0000.0000.0000.000
46A24ALA0-0.0880.10632.338-0.002-0.0020.0000.0000.0000.000
47A25GLU00.033-0.14932.726-0.002-0.0020.0000.0000.0000.000
48A25GLU-1-0.973-0.82732.1810.0080.0080.0000.0000.0000.000
49A26GLN00.099-0.10034.0090.0010.0010.0000.0000.0000.000
50A26GLN0-0.0680.11534.3900.0030.0030.0000.0000.0000.000
51A27GLN00.045-0.10535.8210.0040.0040.0000.0000.0000.000
52A27GLN0-0.0990.08335.694-0.004-0.0040.0000.0000.0000.000
53A28GLN00.068-0.10837.3720.0000.0000.0000.0000.0000.000
54A28GLN0-0.1080.08037.2420.0010.0010.0000.0000.0000.000
55A29LEU00.061-0.10038.552-0.002-0.0020.0000.0000.0000.000
56A29LEU0-0.0670.11136.9440.0000.0000.0000.0000.0000.000
57A30SER00.030-0.05740.2860.0040.0040.0000.0000.0000.000
58A30SER0-0.0700.02639.3750.0010.0010.0000.0000.0000.000
59A31VAL00.028-0.11241.822-0.003-0.0030.0000.0000.0000.000
60A31VAL0-0.0750.09945.0360.0000.0000.0000.0000.0000.000
61A32GLY00.015-0.09545.4670.0020.0020.0000.0000.0000.000
62A33GLN00.014-0.02043.6490.0010.0010.0000.0000.0000.000
63A33GLN0-0.0840.08541.963-0.001-0.0010.0000.0000.0000.000
64A34ILE00.105-0.07145.054-0.001-0.0010.0000.0000.0000.000
65A34ILE0-0.0730.08745.0200.0000.0000.0000.0000.0000.000
66A35ASN00.055-0.07442.748-0.001-0.0010.0000.0000.0000.000
67A35ASN0-0.1400.05541.3270.0000.0000.0000.0000.0000.000
68A36GLY00.077-0.07442.516-0.002-0.0020.0000.0000.0000.000
69A37SER00.0590.02242.180-0.005-0.0050.0000.0000.0000.000
70A37SER0-0.0390.09141.3250.0000.0000.0000.0000.0000.000
71A38GLN00.076-0.10443.0970.0020.0020.0000.0000.0000.000
72A38GLN0-0.0550.10343.9640.0000.0000.0000.0000.0000.000
73A39LEU00.122-0.09143.7960.0000.0000.0000.0000.0000.000
74A39LEU0-0.0590.13542.1500.0000.0000.0000.0000.0000.000
75A40GLN00.133-0.08244.6770.0030.0030.0000.0000.0000.000
76A40GLN0-0.1420.09444.8710.0000.0000.0000.0000.0000.000
77A41ARG00.079-0.08846.3820.0030.0030.0000.0000.0000.000
78A41ARG10.7791.00944.9050.0240.0240.0000.0000.0000.000
79A42ILE00.142-0.05748.6320.0010.0010.0000.0000.0000.000
80A42ILE0-0.1130.08147.3200.0000.0000.0000.0000.0000.000
81A43THR00.008-0.09548.9600.0010.0010.0000.0000.0000.000
82A43THR0-0.0640.05347.5490.0010.0010.0000.0000.0000.000
83A44GLU00.100-0.07250.2130.0020.0020.0000.0000.0000.000
84A44GLU-1-0.865-0.80049.241-0.005-0.0050.0000.0000.0000.000
85A45GLU00.117-0.09852.3250.0020.0020.0000.0000.0000.000
86A45GLU-1-1.032-0.84753.499-0.014-0.0140.0000.0000.0000.000
87A46LYS00.078-0.10453.5020.0010.0010.0000.0000.0000.000
88A46LYS10.8141.03451.5960.0010.0010.0000.0000.0000.000
89A47SER0-0.011-0.11054.1780.0000.0000.0000.0000.0000.000
90A47SER0-0.0540.06453.4350.0010.0010.0000.0000.0000.000
91A48SER00.049-0.08555.6710.0020.0020.0000.0000.0000.000
92A48SER0-0.0500.07156.446-0.001-0.0010.0000.0000.0000.000
93A49LEU00.073-0.10858.0720.0010.0010.0000.0000.0000.000
94A49LEU0-0.0670.11557.4980.0000.0000.0000.0000.0000.000
95A50LEU00.057-0.11058.6190.0000.0000.0000.0000.0000.000
96A50LEU0-0.0880.09656.3130.0000.0000.0000.0000.0000.000
97A51ALA00.134-0.09159.8240.0010.0010.0000.0000.0000.000
98A51ALA0-0.0760.11460.0830.0000.0000.0000.0000.0000.000
99A52THR0-0.007-0.10861.6450.0010.0010.0000.0000.0000.000
100A52THR0-0.0830.05462.2840.0000.0000.0000.0000.0000.000
101A53LEU00.095-0.08563.2730.0000.0000.0000.0000.0000.000
102A53LEU0-0.1190.08562.6020.0000.0000.0000.0000.0000.000
103A54ASP00.062-0.10363.9190.0000.0000.0000.0000.0000.000
104A54ASP-1-0.947-0.82863.5540.0060.0060.0000.0000.0000.000
105A55TYR00.106-0.08365.4570.0010.0010.0000.0000.0000.000
106A55TYR0-0.0960.07866.9730.0000.0000.0000.0000.0000.000
107A56LEU00.068-0.11267.7830.0000.0000.0000.0000.0000.000
108A56LEU0-0.0810.10067.3370.0000.0000.0000.0000.0000.000
109A57GLU00.108-0.08068.5400.0000.0000.0000.0000.0000.000
110A57GLU-1-0.854-0.73668.1150.0020.0020.0000.0000.0000.000
111A58GLN00.038-0.14469.5930.0000.0000.0000.0000.0000.000
112A58GLN0-0.1190.07567.1690.0000.0000.0000.0000.0000.000
113A59GLN00.084-0.10671.3960.0010.0010.0000.0000.0000.000
114A59GLN0-0.0770.12072.3950.0000.0000.0000.0000.0000.000
115A60ARG00.147-0.07073.1430.0000.0000.0000.0000.0000.000
116A60ARG10.7270.97272.289-0.001-0.0010.0000.0000.0000.000
117A61ARG00.029-0.10874.0040.0000.0000.0000.0000.0000.000
118A61ARG10.7801.00470.326-0.005-0.0050.0000.0000.0000.000
119A62LEU00.047-0.10875.5630.0010.0010.0000.0000.0000.000
120A62LEU0-0.0800.10175.6610.0000.0000.0000.0000.0000.000
121A63GLU00.064-0.10277.8370.0000.0000.0000.0000.0000.000
122A63GLU-1-1.010-0.86077.8030.0000.0000.0000.0000.0000.000
123A64GLN00.079-0.10679.651-0.001-0.0010.0000.0000.0000.000
124A64GLN0-0.1490.06577.6430.0000.0000.0000.0000.0000.000
125A65ASN00.003-0.05880.8220.0000.0000.0000.0000.0000.000
126A65ASN0-0.0880.03683.6070.0000.0000.0000.0000.0000.000
127A66ALA00.087-0.12283.3290.0000.0000.0000.0000.0000.000
128A66ALA0-0.0270.14782.9970.0000.0000.0000.0000.0000.000
129A67GLN00.007-0.10584.8510.0000.0000.0000.0000.0000.000
130A67GLN0-0.0640.08788.7530.0000.0000.0000.0000.0000.000
131A68ARG00.114-0.06285.5450.0000.0000.0000.0000.0000.000
132A68ARG10.8431.03585.5350.0010.0010.0000.0000.0000.000
133A69SER0-0.062-0.10385.7420.0000.0000.0000.0000.0000.000
134A69SER0-0.0080.05684.6000.0000.0000.0000.0000.0000.000
135A70ALA00.125-0.08287.368-0.001-0.0010.0000.0000.0000.000
136A70ALA0-0.1070.08288.7850.0000.0000.0000.0000.0000.000
137A71ASN00.080-0.08587.3350.0000.0000.0000.0000.0000.000
138A71ASN0-0.1320.06284.4910.0000.0000.0000.0000.0000.000
139A72ASP00.172-0.09983.7120.0000.0000.0000.0000.0000.000
140A72ASP-1-0.932-0.78182.059-0.004-0.0040.0000.0000.0000.000
141A73ASP00.025-0.08280.3450.0010.0010.0000.0000.0000.000
142A73ASP-1-0.815-0.75978.614-0.006-0.0060.0000.0000.0000.000
143A74ILE00.037-0.12578.3560.0000.0000.0000.0000.0000.000
144A74ILE0-0.0790.10578.3740.0000.0000.0000.0000.0000.000
145A75ALA00.186-0.08277.2340.0000.0000.0000.0000.0000.000
146A75ALA0-0.0770.09579.4200.0000.0000.0000.0000.0000.000
147A76GLU00.070-0.12876.5580.0000.0000.0000.0000.0000.000
148A76GLU-1-1.005-0.82676.139-0.007-0.0070.0000.0000.0000.000
149A77ARG00.075-0.10773.9740.0000.0000.0000.0000.0000.000
150A77ARG10.7060.94974.3470.0050.0050.0000.0000.0000.000
151A78TRP00.070-0.07672.6150.0000.0000.0000.0000.0000.000
152A78TRP0-0.0680.08570.8450.0000.0000.0000.0000.0000.000
153A79GLN00.115-0.07371.9850.0000.0000.0000.0000.0000.000
154A79GLN0-0.1330.06271.3110.0010.0010.0000.0000.0000.000
155A80ALA00.159-0.07570.1290.0000.0000.0000.0000.0000.000
156A80ALA0-0.0900.09670.2500.0000.0000.0000.0000.0000.000
157A81ILE00.058-0.10968.295-0.001-0.0010.0000.0000.0000.000
158A81ILE0-0.0700.10568.1910.0000.0000.0000.0000.0000.000
159A82THR00.004-0.08567.2210.0000.0000.0000.0000.0000.000
160A82THR0-0.0580.06169.2500.0000.0000.0000.0000.0000.000
161A83GLU00.101-0.12766.5350.0010.0010.0000.0000.0000.000
162A83GLU-1-0.905-0.80266.575-0.007-0.0070.0000.0000.0000.000
163A84LYS00.099-0.04563.7150.0000.0000.0000.0000.0000.000
164A84LYS10.7761.04264.0180.0080.0080.0000.0000.0000.000
165A85THR0-0.013-0.12162.471-0.001-0.0010.0000.0000.0000.000
166A85THR0-0.0680.05364.3340.0000.0000.0000.0000.0000.000
167A86GLN00.115-0.07362.1180.0010.0010.0000.0000.0000.000
168A86GLN0-0.1030.07661.9730.0010.0010.0000.0000.0000.000
169A87HIS00.118-0.08660.2450.0010.0010.0000.0000.0000.000
170A87HIS0-0.1120.09057.6170.0000.0000.0000.0000.0000.000
171A88LEU00.049-0.11658.0650.0000.0000.0000.0000.0000.000
172A88LEU0-0.0680.10657.8860.0000.0000.0000.0000.0000.000
173A89ARG00.096-0.09757.2240.0000.0000.0000.0000.0000.000
174A89ARG10.7581.01658.851-0.002-0.0020.0000.0000.0000.000
175A90ASP00.099-0.09256.7630.0020.0020.0000.0000.0000.000
176A90ASP-1-0.915-0.79357.5580.0000.0000.0000.0000.0000.000
177A91LEU00.137-0.09854.1490.0010.0010.0000.0000.0000.000
178A91LEU0-0.1130.10852.5450.0000.0000.0000.0000.0000.000
179A92ASN00.069-0.06252.719-0.001-0.0010.0000.0000.0000.000
180A92ASN0-0.0850.07453.593-0.001-0.0010.0000.0000.0000.000
181A93GLN00.110-0.08552.1590.0010.0010.0000.0000.0000.000
182A93GLN0-0.0840.09453.028-0.001-0.0010.0000.0000.0000.000
183A94HIS00.079-0.08450.6490.0020.0020.0000.0000.0000.000
184A94HIS0-0.0840.08848.3490.0010.0010.0000.0000.0000.000
185A95ASN00.068-0.08448.1950.0000.0000.0000.0000.0000.000
186A95ASN0-0.1510.02548.729-0.001-0.0010.0000.0000.0000.000
187A96GLY00.028-0.08947.3140.0000.0000.0000.0000.0000.000
188A97TRP00.1490.03246.6940.0020.0020.0000.0000.0000.000
189A97TRP0-0.1050.08447.105-0.001-0.0010.0000.0000.0000.000
190A98LEU00.053-0.09744.1040.0020.0020.0000.0000.0000.000
191A98LEU0-0.1200.07744.095-0.001-0.0010.0000.0000.0000.000
192A99LEU00.054-0.09842.628-0.001-0.0010.0000.0000.0000.000
193A99LEU0-0.0820.09643.3060.0000.0000.0000.0000.0000.000
194A100GLU00.079-0.12742.1150.0020.0020.0000.0000.0000.000
195A100GLU-1-0.967-0.83444.1020.0190.0190.0000.0000.0000.000
196A101GLY00.016-0.10440.7490.0030.0030.0000.0000.0000.000
197A102GLN00.0620.00438.1670.0010.0010.0000.0000.0000.000
198A102GLN0-0.0700.08837.706-0.001-0.0010.0000.0000.0000.000
199A103ILE00.105-0.07137.2060.0010.0010.0000.0000.0000.000
200A103ILE0-0.0910.09039.1200.0010.0010.0000.0000.0000.000
201A104GLU00.116-0.06937.0020.0070.0070.0000.0000.0000.000
202A104GLU-1-0.897-0.79137.0250.0110.0110.0000.0000.0000.000
203A105ARG00.082-0.11634.2240.0070.0070.0000.0000.0000.000
204A105ARG10.6950.99233.980-0.004-0.0040.0000.0000.0000.000
205A106ASN00.146-0.05632.7770.0020.0020.0000.0000.0000.000
206A106ASN0-0.1460.06133.8220.0060.0060.0000.0000.0000.000
207A107GLN00.081-0.10932.4540.0060.0060.0000.0000.0000.000
208A107GLN0-0.0960.08935.0140.0000.0000.0000.0000.0000.000
209A108GLN00.068-0.10231.4110.0130.0130.0000.0000.0000.000
210A108GLN0-0.1390.05030.882-0.005-0.0050.0000.0000.0000.000
211A109ALA00.113-0.08128.3130.0100.0100.0000.0000.0000.000
212A109ALA0-0.0830.10728.833-0.002-0.0020.0000.0000.0000.000
213A110LEU00.096-0.10327.6290.0090.0090.0000.0000.0000.000
214A110LEU0-0.1070.10029.4230.0000.0000.0000.0000.0000.000
215A111GLU00.052-0.12728.1570.0160.0160.0000.0000.0000.000
216A111GLU-1-0.918-0.80429.0360.1200.1200.0000.0000.0000.000
217A112VAL00.036-0.10724.9000.0240.0240.0000.0000.0000.000
218A112VAL0-0.0870.09123.199-0.003-0.0030.0000.0000.0000.000
219A113LEU00.041-0.10023.4650.0190.0190.0000.0000.0000.000
220A113LEU0-0.0730.10523.442-0.002-0.0020.0000.0000.0000.000
221A114LYS00.059-0.08424.2220.0130.0130.0000.0000.0000.000
222A114LYS10.7430.98625.981-0.147-0.1470.0000.0000.0000.000
223A115PRO0-0.100-0.14421.9500.0310.0310.0000.0000.0000.000