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: 376KL

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 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 223
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -734444.006513
FMO2-HF: Nuclear repulsion 688227.556305
FMO2-HF: Total energy -46216.450207
FMO2-MP2: Total energy -46351.369715


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.
-7.848-4.860.759-1.589-2.1580.004
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 : 0.149 / q_NPA : 0.026
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].
4A3ARG10.8641.0724.560-0.475-0.236-0.001-0.108-0.1310.000
5A4LEU00.101-0.1143.390-3.770-1.7850.012-1.050-0.9480.004
6A4LEU0-0.0780.1183.7500.1770.3000.001-0.023-0.0990.000
7A5SER00.036-0.0893.199-0.418-0.3240.0820.241-0.4180.000
8A5SER0-0.0140.0742.611-0.1210.0210.666-0.493-0.3150.000
9A6GLU00.084-0.1034.313-0.1400.0700.000-0.100-0.1100.000
10A6GLU-1-1.018-0.8554.483-2.757-2.562-0.001-0.056-0.1370.000
11A7ILE00.078-0.0876.2760.0130.0130.0000.0000.0000.000
12A7ILE0-0.1200.0697.6540.0740.0740.0000.0000.0000.000
13A8LEU00.041-0.1107.860-0.072-0.0720.0000.0000.0000.000
14A8LEU0-0.0390.1138.0920.0150.0150.0000.0000.0000.000
15A9ASP00.136-0.1128.4670.0820.0820.0000.0000.0000.000
16A9ASP-1-0.981-0.8207.928-0.641-0.6410.0000.0000.0000.000
17A10GLN00.083-0.10010.209-0.011-0.0110.0000.0000.0000.000
18A10GLN0-0.1210.06910.4470.0120.0120.0000.0000.0000.000
19A11MET00.093-0.08612.125-0.016-0.0160.0000.0000.0000.000
20A11MET0-0.1160.08312.8360.0540.0540.0000.0000.0000.000
21A12THR00.032-0.08313.3170.0180.0180.0000.0000.0000.000
22A12THR0-0.0400.07512.779-0.020-0.0200.0000.0000.0000.000
23A13THR00.014-0.07114.6710.0150.0150.0000.0000.0000.000
24A13THR0-0.0310.07514.371-0.023-0.0230.0000.0000.0000.000
25A14VAL00.085-0.07816.436-0.008-0.0080.0000.0000.0000.000
26A14VAL0-0.0800.09116.8070.0040.0040.0000.0000.0000.000
27A15LEU00.040-0.12117.7490.0000.0000.0000.0000.0000.000
28A15LEU0-0.0670.10816.8230.0040.0040.0000.0000.0000.000
29A16ASN00.090-0.07819.0470.0120.0120.0000.0000.0000.000
30A16ASN0-0.1220.06018.0710.0180.0180.0000.0000.0000.000
31A17ASP00.138-0.11420.7300.0020.0020.0000.0000.0000.000
32A17ASP-1-1.023-0.83920.945-0.094-0.0940.0000.0000.0000.000
33A18LEU00.044-0.14222.240-0.003-0.0030.0000.0000.0000.000
34A18LEU0-0.0890.11721.4870.0030.0030.0000.0000.0000.000
35A19LYS00.100-0.08323.6200.0060.0060.0000.0000.0000.000
36A19LYS10.7701.03624.1030.0020.0020.0000.0000.0000.000
37A20THR00.028-0.07925.3850.0050.0050.0000.0000.0000.000
38A20THR0-0.0440.06525.258-0.003-0.0030.0000.0000.0000.000
39A21VAL00.064-0.10126.914-0.001-0.0010.0000.0000.0000.000
40A21VAL0-0.0760.09926.8430.0000.0000.0000.0000.0000.000
41A22MET00.102-0.09028.118-0.002-0.0020.0000.0000.0000.000
42A22MET0-0.0980.09227.3460.0040.0040.0000.0000.0000.000
43A23ASP00.127-0.09229.5820.0050.0050.0000.0000.0000.000
44A23ASP-1-0.940-0.81229.4910.0010.0010.0000.0000.0000.000
45A24ALA00.107-0.11731.4320.0010.0010.0000.0000.0000.000
46A24ALA0-0.0990.10932.349-0.001-0.0010.0000.0000.0000.000
47A25GLU00.045-0.18032.689-0.003-0.0030.0000.0000.0000.000
48A25GLU-1-1.000-0.80832.4640.0310.0310.0000.0000.0000.000
49A26GLN00.119-0.11733.9450.0020.0020.0000.0000.0000.000
50A26GLN0-0.0650.14334.220-0.001-0.0010.0000.0000.0000.000
51A27GLN00.037-0.09335.8020.0020.0020.0000.0000.0000.000
52A27GLN0-0.1030.08534.950-0.002-0.0020.0000.0000.0000.000
53A28GLN00.035-0.13237.362-0.002-0.0020.0000.0000.0000.000
54A28GLN0-0.1020.09737.2190.0010.0010.0000.0000.0000.000
55A29LEU00.054-0.12438.534-0.002-0.0020.0000.0000.0000.000
56A29LEU0-0.0810.12336.9840.0000.0000.0000.0000.0000.000
57A30SER00.004-0.07540.2690.0030.0030.0000.0000.0000.000
58A30SER0-0.0900.02239.1900.0000.0000.0000.0000.0000.000
59A31VAL00.055-0.11441.736-0.002-0.0020.0000.0000.0000.000
60A31VAL0-0.0730.10645.0200.0000.0000.0000.0000.0000.000
61A32GLY00.015-0.08745.4090.0010.0010.0000.0000.0000.000
62A33GLN00.023-0.02243.2510.0000.0000.0000.0000.0000.000
63A33GLN0-0.0860.09441.470-0.001-0.0010.0000.0000.0000.000
64A34ILE00.123-0.06744.4260.0000.0000.0000.0000.0000.000
65A34ILE0-0.0930.08644.4240.0000.0000.0000.0000.0000.000
66A35ASN00.062-0.08242.7640.0000.0000.0000.0000.0000.000
67A35ASN0-0.1420.06241.8150.0000.0000.0000.0000.0000.000
68A36GLY00.065-0.07742.1730.0000.0000.0000.0000.0000.000
69A37SER00.0610.00641.740-0.004-0.0040.0000.0000.0000.000
70A37SER0-0.0130.09940.8770.0000.0000.0000.0000.0000.000
71A38GLN00.051-0.11942.7390.0000.0000.0000.0000.0000.000
72A38GLN0-0.0770.09943.5390.0010.0010.0000.0000.0000.000
73A39LEU00.162-0.11043.5010.0000.0000.0000.0000.0000.000
74A39LEU0-0.0470.15742.2640.0000.0000.0000.0000.0000.000
75A40GLN00.112-0.07844.4910.0020.0020.0000.0000.0000.000
76A40GLN0-0.0840.11644.5980.0010.0010.0000.0000.0000.000
77A41ARG00.093-0.09146.1270.0010.0010.0000.0000.0000.000
78A41ARG10.8331.05044.7440.0100.0100.0000.0000.0000.000
79A42ILE00.099-0.08048.2680.0000.0000.0000.0000.0000.000
80A42ILE0-0.1050.08947.0110.0000.0000.0000.0000.0000.000
81A43THR0-0.013-0.10348.4570.0010.0010.0000.0000.0000.000
82A43THR0-0.0470.05846.9830.0010.0010.0000.0000.0000.000
83A44GLU00.072-0.11449.6700.0020.0020.0000.0000.0000.000
84A44GLU-1-0.930-0.81949.1830.0020.0020.0000.0000.0000.000
85A45GLU00.116-0.13351.9510.0010.0010.0000.0000.0000.000
86A45GLU-1-0.997-0.81853.588-0.002-0.0020.0000.0000.0000.000
87A46LYS00.076-0.10653.2410.0000.0000.0000.0000.0000.000
88A46LYS10.8311.06151.454-0.013-0.0130.0000.0000.0000.000
89A47SER0-0.017-0.11753.9410.0000.0000.0000.0000.0000.000
90A47SER0-0.0330.08953.1750.0000.0000.0000.0000.0000.000
91A48SER00.036-0.09155.4230.0010.0010.0000.0000.0000.000
92A48SER0-0.0430.08856.256-0.001-0.0010.0000.0000.0000.000
93A49LEU00.054-0.13657.7700.0000.0000.0000.0000.0000.000
94A49LEU0-0.0770.12557.4080.0000.0000.0000.0000.0000.000
95A50LEU00.049-0.12758.4130.0000.0000.0000.0000.0000.000
96A50LEU0-0.0820.10956.0840.0000.0000.0000.0000.0000.000
97A51ALA00.135-0.08859.7060.0010.0010.0000.0000.0000.000
98A51ALA0-0.0710.12559.9310.0000.0000.0000.0000.0000.000
99A52THR00.003-0.10561.4450.0000.0000.0000.0000.0000.000
100A52THR0-0.0600.07262.4080.0000.0000.0000.0000.0000.000
101A53LEU00.094-0.08963.1310.0000.0000.0000.0000.0000.000
102A53LEU0-0.1080.09362.5180.0000.0000.0000.0000.0000.000
103A54ASP00.073-0.11763.6660.0000.0000.0000.0000.0000.000
104A54ASP-1-0.984-0.84063.1320.0120.0120.0000.0000.0000.000
105A55TYR00.108-0.08365.1240.0000.0000.0000.0000.0000.000
106A55TYR0-0.1010.08266.6740.0000.0000.0000.0000.0000.000
107A56LEU00.055-0.13167.5570.0000.0000.0000.0000.0000.000
108A56LEU0-0.0830.10267.3340.0000.0000.0000.0000.0000.000
109A57GLU00.096-0.10268.2280.0000.0000.0000.0000.0000.000
110A57GLU-1-0.873-0.75567.8790.0100.0100.0000.0000.0000.000
111A58GLN00.024-0.15069.4860.0000.0000.0000.0000.0000.000
112A58GLN0-0.0610.12667.2030.0000.0000.0000.0000.0000.000
113A59GLN00.075-0.11471.2640.0000.0000.0000.0000.0000.000
114A59GLN0-0.1070.09971.8530.0000.0000.0000.0000.0000.000
115A60ARG00.165-0.06972.9030.0000.0000.0000.0000.0000.000
116A60ARG10.7150.98471.878-0.009-0.0090.0000.0000.0000.000
117A61ARG00.025-0.09673.8180.0000.0000.0000.0000.0000.000
118A61ARG10.8091.02670.120-0.011-0.0110.0000.0000.0000.000
119A62LEU00.016-0.13075.4520.0000.0000.0000.0000.0000.000
120A62LEU0-0.0790.10875.3390.0000.0000.0000.0000.0000.000
121A63GLU00.029-0.11677.6980.0000.0000.0000.0000.0000.000
122A63GLU-1-1.018-0.85177.9470.0050.0050.0000.0000.0000.000
123A64GLN00.119-0.10779.6670.0000.0000.0000.0000.0000.000
124A64GLN0-0.1560.07477.3490.0000.0000.0000.0000.0000.000
125A65ASN00.036-0.09880.9450.0000.0000.0000.0000.0000.000
126A65ASN0-0.0690.07583.0470.0000.0000.0000.0000.0000.000
127A66ALA00.062-0.12983.3200.0000.0000.0000.0000.0000.000
128A66ALA0-0.0220.16482.9270.0000.0000.0000.0000.0000.000
129A67GLN00.047-0.09584.7430.0000.0000.0000.0000.0000.000
130A67GLN0-0.1220.06688.6190.0000.0000.0000.0000.0000.000
131A68ARG00.130-0.05185.4310.0000.0000.0000.0000.0000.000
132A68ARG10.8721.04785.694-0.005-0.0050.0000.0000.0000.000
133A69SER0-0.022-0.12385.7450.0000.0000.0000.0000.0000.000
134A69SER0-0.0100.09285.7420.0000.0000.0000.0000.0000.000
135A70ALA00.109-0.05786.8480.0000.0000.0000.0000.0000.000
136A70ALA0-0.1040.09588.9630.0000.0000.0000.0000.0000.000
137A71ASN00.076-0.08487.2970.0000.0000.0000.0000.0000.000
138A71ASN0-0.1120.05484.6900.0000.0000.0000.0000.0000.000
139A72ASP00.153-0.12583.5900.0000.0000.0000.0000.0000.000
140A72ASP-1-1.001-0.83082.0130.0030.0030.0000.0000.0000.000
141A73ASP00.040-0.11779.9980.0010.0010.0000.0000.0000.000
142A73ASP-1-0.859-0.79078.4680.0020.0020.0000.0000.0000.000
143A74ILE00.022-0.12778.3200.0000.0000.0000.0000.0000.000
144A74ILE0-0.0740.11778.2580.0000.0000.0000.0000.0000.000
145A75ALA00.175-0.09477.2300.0000.0000.0000.0000.0000.000
146A75ALA0-0.0770.10679.5220.0000.0000.0000.0000.0000.000
147A76GLU00.072-0.15076.7560.0010.0010.0000.0000.0000.000
148A76GLU-1-1.012-0.81776.2120.0030.0030.0000.0000.0000.000
149A77ARG00.065-0.11874.0940.0000.0000.0000.0000.0000.000
150A77ARG10.8101.05874.337-0.003-0.0030.0000.0000.0000.000
151A78TRP00.063-0.10472.6880.0000.0000.0000.0000.0000.000
152A78TRP0-0.0670.09271.0330.0000.0000.0000.0000.0000.000
153A79GLN00.082-0.09672.0700.0010.0010.0000.0000.0000.000
154A79GLN0-0.1010.08471.1050.0000.0000.0000.0000.0000.000
155A80ALA00.175-0.08570.1640.0010.0010.0000.0000.0000.000
156A80ALA0-0.0870.11070.1070.0000.0000.0000.0000.0000.000
157A81ILE0-0.003-0.12468.3060.0000.0000.0000.0000.0000.000
158A81ILE0-0.0720.10468.1530.0000.0000.0000.0000.0000.000
159A82THR00.043-0.11067.1400.0000.0000.0000.0000.0000.000
160A82THR0-0.0270.08569.2670.0000.0000.0000.0000.0000.000
161A83GLU00.045-0.12566.6100.0010.0010.0000.0000.0000.000
162A83GLU-1-0.967-0.79666.8240.0060.0060.0000.0000.0000.000
163A84LYS00.085-0.09063.8190.0010.0010.0000.0000.0000.000
164A84LYS10.8751.06163.922-0.004-0.0040.0000.0000.0000.000
165A85THR0-0.004-0.09362.3810.0000.0000.0000.0000.0000.000
166A85THR0-0.0610.06464.1710.0000.0000.0000.0000.0000.000
167A86GLN00.088-0.09361.9160.0010.0010.0000.0000.0000.000
168A86GLN0-0.0770.11061.5870.0000.0000.0000.0000.0000.000
169A87HIS00.129-0.08060.3390.0010.0010.0000.0000.0000.000
170A87HIS0-0.1020.08957.7160.0000.0000.0000.0000.0000.000
171A88LEU00.057-0.11857.9320.0010.0010.0000.0000.0000.000
172A88LEU0-0.0830.10457.6120.0000.0000.0000.0000.0000.000
173A89ARG00.084-0.09657.0700.0010.0010.0000.0000.0000.000
174A89ARG10.8131.06159.135-0.014-0.0140.0000.0000.0000.000
175A90ASP00.119-0.12156.7280.0020.0020.0000.0000.0000.000
176A90ASP-1-0.966-0.81656.9160.0160.0160.0000.0000.0000.000
177A91LEU00.112-0.10053.9340.0020.0020.0000.0000.0000.000
178A91LEU0-0.1290.10352.2100.0000.0000.0000.0000.0000.000
179A92ASN00.051-0.09552.4570.0010.0010.0000.0000.0000.000
180A92ASN0-0.0880.07253.582-0.001-0.0010.0000.0000.0000.000
181A93GLN00.107-0.09551.9520.0010.0010.0000.0000.0000.000
182A93GLN0-0.0950.10852.983-0.001-0.0010.0000.0000.0000.000
183A94HIS00.103-0.08350.4910.0020.0020.0000.0000.0000.000
184A94HIS0-0.0900.09448.0600.0010.0010.0000.0000.0000.000
185A95ASN00.088-0.08548.0270.0020.0020.0000.0000.0000.000
186A95ASN0-0.0980.06448.7840.0000.0000.0000.0000.0000.000
187A96GLY00.003-0.09447.0260.0010.0010.0000.0000.0000.000
188A97TRP00.1590.02746.6430.0020.0020.0000.0000.0000.000
189A97TRP0-0.0990.09347.308-0.001-0.0010.0000.0000.0000.000
190A98LEU00.049-0.12144.1340.0030.0030.0000.0000.0000.000
191A98LEU0-0.1370.08143.931-0.001-0.0010.0000.0000.0000.000
192A99LEU00.026-0.11942.5250.0010.0010.0000.0000.0000.000
193A99LEU0-0.0880.10343.2960.0000.0000.0000.0000.0000.000
194A100GLU00.086-0.13341.8760.0020.0020.0000.0000.0000.000
195A100GLU-1-0.945-0.80443.8060.0380.0380.0000.0000.0000.000
196A101GLY00.020-0.09240.4700.0040.0040.0000.0000.0000.000
197A102GLN00.016-0.03838.0540.0040.0040.0000.0000.0000.000
198A102GLN0-0.0630.09737.9250.0010.0010.0000.0000.0000.000
199A103ILE00.094-0.09037.0320.0020.0020.0000.0000.0000.000
200A103ILE0-0.0950.09839.0050.0000.0000.0000.0000.0000.000
201A104GLU00.124-0.11036.9060.0050.0050.0000.0000.0000.000
202A104GLU-1-1.018-0.84536.5980.0580.0580.0000.0000.0000.000
203A105ARG00.041-0.11933.9880.0080.0080.0000.0000.0000.000
204A105ARG10.8571.06733.647-0.038-0.0380.0000.0000.0000.000
205A106ASN00.100-0.06032.4680.0050.0050.0000.0000.0000.000
206A106ASN0-0.1120.07733.7740.0030.0030.0000.0000.0000.000
207A107GLN00.094-0.11232.2550.0050.0050.0000.0000.0000.000
208A107GLN0-0.0660.11534.4620.0010.0010.0000.0000.0000.000
209A108GLN00.060-0.11231.1770.0110.0110.0000.0000.0000.000
210A108GLN0-0.1010.08330.908-0.001-0.0010.0000.0000.0000.000
211A109ALA00.099-0.11228.3480.0140.0140.0000.0000.0000.000
212A109ALA0-0.0800.11828.824-0.002-0.0020.0000.0000.0000.000
213A110LEU00.079-0.12127.4020.0080.0080.0000.0000.0000.000
214A110LEU0-0.1100.11128.906-0.001-0.0010.0000.0000.0000.000
215A111GLU00.052-0.13727.3520.0090.0090.0000.0000.0000.000
216A111GLU-1-0.997-0.84628.1090.1340.1340.0000.0000.0000.000
217A112VAL00.002-0.13324.1820.0220.0220.0000.0000.0000.000
218A112VAL0-0.0970.09522.727-0.001-0.0010.0000.0000.0000.000
219A113LEU00.012-0.11822.7100.0230.0230.0000.0000.0000.000
220A113LEU0-0.0590.11722.959-0.003-0.0030.0000.0000.0000.000
221A114LYS00.029-0.07923.7190.0020.0020.0000.0000.0000.000
222A114LYS10.8681.07024.859-0.197-0.1970.0000.0000.0000.000
223A115PRO0-0.029-0.12320.9720.0190.0190.0000.0000.0000.000