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: 1N6GZ

Calculation Name: 3BCV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3BCV

Chain ID: A

ChEMBL ID:

UniProt ID: Q5LBM4

Base Structure: X-ray

Registration Date: 2023-09-22

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 196
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2240992.99514
FMO2-HF: Nuclear repulsion 2161846.381178
FMO2-HF: Total energy -79146.613962
FMO2-MP2: Total energy -79373.116766


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:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-0.890.8560-0.719-1.0260
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.030
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].
3A5PRO00.0150.0163.514-1.5890.0150.001-0.714-0.8910.000
4A6LYS10.8890.9475.4620.6220.6220.0000.0000.0000.000
5A7VAL0-0.006-0.0147.5030.0980.0980.0000.0000.0000.000
6A8SER0-0.034-0.03410.606-0.008-0.0080.0000.0000.0000.000
7A9VAL0-0.005-0.01012.2810.0130.0130.0000.0000.0000.000
8A10ILE0-0.042-0.00615.5910.0250.0250.0000.0000.0000.000
9A11VAL00.0300.01218.3240.0040.0040.0000.0000.0000.000
10A12PRO0-0.053-0.01021.4230.0090.0090.0000.0000.0000.000
11A13ILE00.023-0.00923.1990.0070.0070.0000.0000.0000.000
12A14TYR0-0.003-0.02026.8360.0020.0020.0000.0000.0000.000
13A15ASN0-0.045-0.02130.649-0.001-0.0010.0000.0000.0000.000
14A16VAL00.0360.01228.349-0.001-0.0010.0000.0000.0000.000
15A17GLU-1-0.845-0.94530.1680.0030.0030.0000.0000.0000.000
16A18LYS10.8800.94031.1190.0110.0110.0000.0000.0000.000
17A19TYR0-0.040-0.02329.4270.0010.0010.0000.0000.0000.000
18A20LEU00.0510.02224.075-0.001-0.0010.0000.0000.0000.000
19A21ASP-1-0.831-0.90424.8450.0180.0180.0000.0000.0000.000
20A22GLN0-0.015-0.01724.5300.0060.0060.0000.0000.0000.000
21A23CYS0-0.0270.00823.316-0.002-0.0020.0000.0000.0000.000
22A24VAL00.0430.00019.220-0.007-0.0070.0000.0000.0000.000
23A25GLN0-0.014-0.00519.5690.0110.0110.0000.0000.0000.000
24A26ALA0-0.0100.00220.7550.0070.0070.0000.0000.0000.000
25A27LEU0-0.043-0.03116.850-0.012-0.0120.0000.0000.0000.000
26A28LEU0-0.055-0.02315.511-0.001-0.0010.0000.0000.0000.000
27A29ALA0-0.036-0.00516.4450.0250.0250.0000.0000.0000.000
28A30GLN0-0.076-0.02414.932-0.030-0.0300.0000.0000.0000.000
29A31THR00.0260.00615.3920.0130.0130.0000.0000.0000.000
30A32LEU0-0.119-0.04410.4540.0030.0030.0000.0000.0000.000
31A33SER00.016-0.0027.233-0.033-0.0330.0000.0000.0000.000
32A34ASP-1-0.862-0.9394.7240.6660.808-0.001-0.005-0.1350.000
33A35ILE00.0630.0426.881-0.368-0.3680.0000.0000.0000.000
34A36GLU-1-0.792-0.8579.057-0.374-0.3740.0000.0000.0000.000
35A37ILE00.0250.01410.650-0.055-0.0550.0000.0000.0000.000
36A38ILE0-0.028-0.00814.0190.0220.0220.0000.0000.0000.000
37A39LEU00.0290.01516.729-0.003-0.0030.0000.0000.0000.000
38A40ILE0-0.028-0.01620.0940.0030.0030.0000.0000.0000.000
39A41ASP-1-0.727-0.84122.963-0.018-0.0180.0000.0000.0000.000
40A42ASP-1-0.797-0.88326.253-0.050-0.0500.0000.0000.0000.000
41A43GLU-1-0.913-0.96928.880-0.021-0.0210.0000.0000.0000.000
42A44SER0-0.029-0.02429.928-0.001-0.0010.0000.0000.0000.000
43A45PRO0-0.034-0.01731.8990.0040.0040.0000.0000.0000.000
44A46ASP-1-0.785-0.85832.275-0.009-0.0090.0000.0000.0000.000
45A47ASN0-0.049-0.03632.1740.0040.0040.0000.0000.0000.000
46A48CYS0-0.020-0.00528.0160.0040.0040.0000.0000.0000.000
47A49PRO0-0.0080.01027.2280.0030.0030.0000.0000.0000.000
48A50LYS11.0230.98826.656-0.023-0.0230.0000.0000.0000.000
49A51ILE00.0490.05525.4570.0060.0060.0000.0000.0000.000
50A52CYS0-0.039-0.02422.9310.0020.0020.0000.0000.0000.000
51A53ASP-1-0.885-0.94422.1220.0330.0330.0000.0000.0000.000
52A54ASP-1-0.929-0.96522.6100.0630.0630.0000.0000.0000.000
53A55TYR0-0.065-0.04719.9420.0170.0170.0000.0000.0000.000
54A56ALA0-0.015-0.02018.1070.0200.0200.0000.0000.0000.000
55A57ALA0-0.068-0.02018.1120.0240.0240.0000.0000.0000.000
56A58GLN0-0.081-0.05019.6490.0210.0210.0000.0000.0000.000
57A59TYR0-0.0060.00015.7640.0230.0230.0000.0000.0000.000
58A60PRO0-0.012-0.00411.711-0.009-0.0090.0000.0000.0000.000
59A61ASN0-0.064-0.03610.5550.0590.0590.0000.0000.0000.000
60A62ILE00.0240.01811.994-0.089-0.0890.0000.0000.0000.000
61A63LYS10.9140.96810.8410.2570.2570.0000.0000.0000.000
62A64VAL00.0380.01815.989-0.014-0.0140.0000.0000.0000.000
63A65ILE0-0.034-0.01118.9570.0010.0010.0000.0000.0000.000
64A66HIS10.7620.86422.0650.0010.0010.0000.0000.0000.000
65A67LYS10.8650.93624.9990.0740.0740.0000.0000.0000.000
66A68LYS10.9610.98927.9160.0290.0290.0000.0000.0000.000
67A69ASN00.0240.00831.038-0.006-0.0060.0000.0000.0000.000
68A70ALA0-0.120-0.07230.3120.0010.0010.0000.0000.0000.000
69A71GLY0-0.052-0.01231.549-0.002-0.0020.0000.0000.0000.000
70A72LEU00.0780.01928.042-0.004-0.0040.0000.0000.0000.000
71A73GLY00.0760.05826.732-0.009-0.0090.0000.0000.0000.000
72A74MET0-0.011-0.02026.457-0.011-0.0110.0000.0000.0000.000
73A75ALA0-0.045-0.01825.269-0.004-0.0040.0000.0000.0000.000
74A76CYS00.0260.00822.403-0.009-0.0090.0000.0000.0000.000
75A77ASN00.0390.01221.423-0.031-0.0310.0000.0000.0000.000
76A78SER00.0130.01321.332-0.008-0.0080.0000.0000.0000.000
77A79GLY00.0320.00218.882-0.008-0.0080.0000.0000.0000.000
78A80LEU0-0.017-0.02417.198-0.037-0.0370.0000.0000.0000.000
79A81ASP-1-0.916-0.94616.790-0.194-0.1940.0000.0000.0000.000
80A82VAL0-0.073-0.03115.238-0.012-0.0120.0000.0000.0000.000
81A83ALA0-0.033-0.00813.226-0.040-0.0400.0000.0000.0000.000
82A84THR0-0.111-0.0798.429-0.129-0.1290.0000.0000.0000.000
83A85GLY00.0050.0108.041-0.274-0.2740.0000.0000.0000.000
84A86GLU-1-0.977-0.9768.283-0.728-0.7280.0000.0000.0000.000
85A87TYR0-0.073-0.0529.9150.2150.2150.0000.0000.0000.000
86A88VAL0-0.028-0.01312.130-0.051-0.0510.0000.0000.0000.000
87A89ALA00.0390.00614.8380.0220.0220.0000.0000.0000.000
88A90PHE00.0230.01817.654-0.005-0.0050.0000.0000.0000.000
89A91CYS0-0.020-0.00620.4570.0030.0030.0000.0000.0000.000
90A92ASP-1-0.853-0.91822.104-0.076-0.0760.0000.0000.0000.000
91A93SER00.045-0.01525.2270.0060.0060.0000.0000.0000.000
92A94ASP-1-1.064-1.02626.374-0.040-0.0400.0000.0000.0000.000
93A95ASP-1-0.876-0.92625.634-0.059-0.0590.0000.0000.0000.000
94A96TYR0-0.060-0.02924.277-0.001-0.0010.0000.0000.0000.000
95A97VAL0-0.003-0.01419.928-0.001-0.0010.0000.0000.0000.000
96A98ASP-1-0.824-0.92522.546-0.051-0.0510.0000.0000.0000.000
97A99SER00.0310.00719.528-0.012-0.0120.0000.0000.0000.000
98A100ASP-1-0.861-0.91618.369-0.059-0.0590.0000.0000.0000.000
99A101MET0-0.051-0.01019.072-0.021-0.0210.0000.0000.0000.000
100A102TYR00.044-0.00414.593-0.029-0.0290.0000.0000.0000.000
101A103MET0-0.0190.02313.137-0.044-0.0440.0000.0000.0000.000
102A104THR0-0.010-0.00715.740-0.021-0.0210.0000.0000.0000.000
103A105MET0-0.007-0.00917.672-0.012-0.0120.0000.0000.0000.000
104A106TYR00.0400.0218.806-0.005-0.0050.0000.0000.0000.000
105A107ASN00.001-0.02414.714-0.052-0.0520.0000.0000.0000.000
106A108VAL0-0.046-0.01816.0950.0050.0050.0000.0000.0000.000
107A109ALA00.019-0.01015.6870.0120.0120.0000.0000.0000.000
108A110GLN00.0480.03510.5560.0380.0380.0000.0000.0000.000
109A111LYS10.8610.95715.4210.1580.1580.0000.0000.0000.000
110A112TYR0-0.050-0.05418.6710.0220.0220.0000.0000.0000.000
111A113THR0-0.0130.00716.6060.0120.0120.0000.0000.0000.000
112A114CYS0-0.083-0.01418.2120.0210.0210.0000.0000.0000.000
113A115ASP-1-0.731-0.87218.003-0.258-0.2580.0000.0000.0000.000
114A116ALA00.011-0.00519.703-0.012-0.0120.0000.0000.0000.000
115A117VAL0-0.033-0.01319.1710.0140.0140.0000.0000.0000.000
116A118PHE00.034-0.00121.653-0.002-0.0020.0000.0000.0000.000
117A119THR00.0020.01424.6990.0080.0080.0000.0000.0000.000
118A140PHE0-0.007-0.00924.7360.0020.0020.0000.0000.0000.000
119A141LYS10.9240.96928.6390.0830.0830.0000.0000.0000.000
120A142LEU00.0220.01324.737-0.007-0.0070.0000.0000.0000.000
121A143TYR0-0.016-0.00627.1370.0090.0090.0000.0000.0000.000
122A144LYS10.9610.97126.6710.0940.0940.0000.0000.0000.000
123A145ASN00.0540.03826.958-0.001-0.0010.0000.0000.0000.000
124A146LYS11.0300.99926.8250.1310.1310.0000.0000.0000.000
125A147ASN0-0.079-0.02029.7890.0060.0060.0000.0000.0000.000
126A148GLU-1-0.840-0.94431.189-0.093-0.0930.0000.0000.0000.000
127A149ILE00.0040.00826.7300.0040.0040.0000.0000.0000.000
128A150HIS0-0.008-0.01131.2570.0050.0050.0000.0000.0000.000
129A151THR0-0.046-0.03534.0360.0060.0060.0000.0000.0000.000
130A152LEU0-0.0120.00930.9540.0050.0050.0000.0000.0000.000
131A153LEU00.0360.00931.3270.0030.0030.0000.0000.0000.000
132A154LYS10.9140.96535.2230.0670.0670.0000.0000.0000.000
133A155ASP-1-0.880-0.93338.056-0.061-0.0610.0000.0000.0000.000
134A156LEU0-0.014-0.01334.3890.0030.0030.0000.0000.0000.000
135A157ILE0-0.035-0.00239.0680.0020.0020.0000.0000.0000.000
136A158ALA00.0010.02841.9730.0030.0030.0000.0000.0000.000
137A159SER00.020-0.00544.4300.0000.0000.0000.0000.0000.000
138A160ASP-1-0.868-0.94945.292-0.044-0.0440.0000.0000.0000.000
139A161PRO0-0.016-0.00944.569-0.002-0.0020.0000.0000.0000.000
140A162TYR00.0590.03143.417-0.002-0.0020.0000.0000.0000.000
141A163ALA00.0740.05641.365-0.002-0.0020.0000.0000.0000.000
142A164ARG10.7920.88239.6750.0470.0470.0000.0000.0000.000
143A165GLU-1-0.979-0.99338.844-0.050-0.0500.0000.0000.0000.000
144A166GLU-1-0.924-0.96037.194-0.063-0.0630.0000.0000.0000.000
145A167ARG10.8780.93334.2620.0690.0690.0000.0000.0000.000
146A168ALA00.0070.00734.000-0.006-0.0060.0000.0000.0000.000
147A169ILE00.0120.00833.719-0.004-0.0040.0000.0000.0000.000
148A170GLN0-0.055-0.02731.004-0.007-0.0070.0000.0000.0000.000
149A171VAL0-0.060-0.04329.710-0.007-0.0070.0000.0000.0000.000
150A172SER0-0.0020.00229.216-0.008-0.0080.0000.0000.0000.000
151A173ALA0-0.040-0.00527.4110.0030.0030.0000.0000.0000.000
152A174LYS11.0381.01126.8090.0570.0570.0000.0000.0000.000
153A175VAL00.0140.01421.719-0.009-0.0090.0000.0000.0000.000
154A176VAL00.0060.00121.5070.0000.0000.0000.0000.0000.000
155A177LEU0-0.052-0.00414.431-0.012-0.0120.0000.0000.0000.000
156A178TYR00.013-0.03017.6140.0020.0020.0000.0000.0000.000
157A179ARG10.9210.95814.6280.2780.2780.0000.0000.0000.000
158A180ARG10.9500.97210.0180.6950.6950.0000.0000.0000.000
159A181ASN0-0.018-0.02713.6320.0680.0680.0000.0000.0000.000
160A182LEU0-0.054-0.00815.4300.0340.0340.0000.0000.0000.000
161A183ILE00.0610.02318.4300.0250.0250.0000.0000.0000.000
162A184GLU-1-0.850-0.92715.381-0.250-0.2500.0000.0000.0000.000
163A185LYS10.8450.92017.1730.2830.2830.0000.0000.0000.000
164A186LYS10.8660.93719.9860.1750.1750.0000.0000.0000.000
165A187HIS0-0.0120.00821.8760.0110.0110.0000.0000.0000.000
166A188LEU0-0.0380.00022.6200.0110.0110.0000.0000.0000.000
167A189ARG10.8000.88419.1710.1830.1830.0000.0000.0000.000
168A190PHE00.0290.02623.0870.0070.0070.0000.0000.0000.000
169A191VAL0-0.0100.00027.5580.0040.0040.0000.0000.0000.000
170A192SER00.0350.00231.1540.0020.0020.0000.0000.0000.000
171A193GLU-1-0.714-0.87631.615-0.062-0.0620.0000.0000.0000.000
172A194ARG10.7590.87034.0710.0490.0490.0000.0000.0000.000
173A195ILE0-0.070-0.02135.5970.0030.0030.0000.0000.0000.000
174A196LEU0-0.001-0.02434.6720.0030.0030.0000.0000.0000.000
175A197PRO00.0340.02034.860-0.004-0.0040.0000.0000.0000.000
176A198SER0-0.031-0.00334.9890.0000.0000.0000.0000.0000.000
177A199GLU-1-0.881-0.96729.136-0.090-0.0900.0000.0000.0000.000
178A200ASP-1-0.840-0.90727.177-0.113-0.1130.0000.0000.0000.000
179A201LEU0-0.035-0.00428.900-0.006-0.0060.0000.0000.0000.000
180A202ILE0-0.046-0.03930.764-0.004-0.0040.0000.0000.0000.000
181A203PHE00.0510.04722.066-0.008-0.0080.0000.0000.0000.000
182A204ASN00.0720.02525.701-0.022-0.0220.0000.0000.0000.000
183A205VAL0-0.044-0.02727.347-0.006-0.0060.0000.0000.0000.000
184A206ASP-1-0.898-0.93627.146-0.115-0.1150.0000.0000.0000.000
185A207VAL0-0.0020.00922.821-0.007-0.0070.0000.0000.0000.000
186A208LEU0-0.0110.02225.344-0.005-0.0050.0000.0000.0000.000
187A209ALA0-0.051-0.02627.4640.0010.0010.0000.0000.0000.000
188A210ASN0-0.130-0.07625.5240.0060.0060.0000.0000.0000.000
189A211SER0-0.049-0.04623.822-0.020-0.0200.0000.0000.0000.000
190A212ASN0-0.153-0.09223.3180.0280.0280.0000.0000.0000.000
191A213ILE00.0080.01021.4500.0150.0150.0000.0000.0000.000
192A214VAL00.0340.02922.859-0.015-0.0150.0000.0000.0000.000
193A215CYS0-0.036-0.01822.7290.0120.0120.0000.0000.0000.000
194A216VAL00.0060.01924.674-0.006-0.0060.0000.0000.0000.000
195A217LEU00.002-0.01421.9950.0060.0060.0000.0000.0000.000
196A218PRO00.0060.01526.2770.0060.0060.0000.0000.0000.000