FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: VKGN1

Calculation Name: 3Q4H-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3Q4H

Chain ID: A

ChEMBL ID:

UniProt ID: A0QQ43

Base Structure: X-ray

Registration Date: 2025-07-09

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 176
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -450062.191832
FMO2-HF: Nuclear repulsion 417396.639879
FMO2-HF: Total energy -32665.551953
FMO2-MP2: Total energy -32759.446298


3D Structure
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:5:ASP)


Summations of interaction energy for fragment #1(A:5:ASP)
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.
-6.938-2.9750.16-2-2.1220.012
Interaction energy analysis for fragmet #1(A:5:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.187 / q_NPA : 0.070
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].
4A6ALA0-0.0750.1174.750-0.0380.115-0.001-0.065-0.0870.000
5A7HIS00.035-0.0972.911-2.261-0.5790.046-0.821-0.9060.004
6A7HIS0-0.0650.0973.356-1.355-0.4520.069-0.535-0.4380.004
7A8ILE00.016-0.1043.857-1.894-1.4240.002-0.185-0.2870.001
8A8ILE0-0.0470.1313.558-0.861-0.1060.044-0.394-0.4040.003
9A9PRO00.072-0.1104.973-0.866-0.8660.0000.0000.0000.000
10A10GLN00.0670.0087.539-0.249-0.2490.0000.0000.0000.000
11A10GLN0-0.0990.0666.812-0.022-0.0220.0000.0000.0000.000
12A11LEU00.092-0.0708.376-0.516-0.5160.0000.0000.0000.000
13A11LEU0-0.1120.1058.5160.1830.1830.0000.0000.0000.000
14A12ILE00.158-0.0739.804-0.256-0.2560.0000.0000.0000.000
15A12ILE0-0.1010.1028.679-0.033-0.0330.0000.0000.0000.000
16A13ALA00.134-0.09311.626-0.152-0.1520.0000.0000.0000.000
17A13ALA0-0.0850.11112.614-0.032-0.0320.0000.0000.0000.000
18A14SER0-0.011-0.11313.043-0.183-0.1830.0000.0000.0000.000
19A14SER0-0.0710.05512.695-0.032-0.0320.0000.0000.0000.000
20A15GLU00.048-0.12214.174-0.144-0.1440.0000.0000.0000.000
21A15GLU-1-0.959-0.81912.9901.3311.3310.0000.0000.0000.000
22A16ALA00.159-0.08115.723-0.081-0.0810.0000.0000.0000.000
23A16ALA0-0.0610.12916.336-0.010-0.0100.0000.0000.0000.000
24A17ASN00.046-0.09717.485-0.074-0.0740.0000.0000.0000.000
25A17ASN0-0.1960.02117.077-0.055-0.0550.0000.0000.0000.000
26A18PHE00.039-0.11818.793-0.076-0.0760.0000.0000.0000.000
27A18PHE0-0.0670.11319.2940.0010.0010.0000.0000.0000.000
28A19GLY00.048-0.09920.075-0.044-0.0440.0000.0000.0000.000
29A20ALA00.1140.00421.758-0.034-0.0340.0000.0000.0000.000
30A20ALA0-0.0830.11222.466-0.005-0.0050.0000.0000.0000.000
31A21LYS00.043-0.10523.523-0.036-0.0360.0000.0000.0000.000
32A21LYS10.8791.06622.086-0.300-0.3000.0000.0000.0000.000
33A22ALA00.107-0.10624.593-0.034-0.0340.0000.0000.0000.000
34A22ALA0-0.0760.11624.7120.0060.0060.0000.0000.0000.000
35A23ALA00.085-0.11126.191-0.014-0.0140.0000.0000.0000.000
36A23ALA0-0.0600.12226.677-0.001-0.0010.0000.0000.0000.000
37A24LEU00.045-0.12827.885-0.019-0.0190.0000.0000.0000.000
38A24LEU0-0.0760.11427.115-0.002-0.0020.0000.0000.0000.000
39A25MET00.149-0.07129.288-0.023-0.0230.0000.0000.0000.000
40A25MET0-0.1040.11229.698-0.003-0.0030.0000.0000.0000.000
41A26ARG00.072-0.11430.872-0.015-0.0150.0000.0000.0000.000
42A26ARG10.7170.97827.622-0.261-0.2610.0000.0000.0000.000
43A27SER00.076-0.04332.316-0.011-0.0110.0000.0000.0000.000
44A27SER0-0.0490.05932.684-0.004-0.0040.0000.0000.0000.000
45A28THR00.000-0.09433.753-0.013-0.0130.0000.0000.0000.000
46A28THR0-0.0670.04833.227-0.002-0.0020.0000.0000.0000.000
47A29ILE00.081-0.07135.296-0.013-0.0130.0000.0000.0000.000
48A29ILE0-0.1000.08634.1240.0020.0020.0000.0000.0000.000
49A30ALA00.137-0.08836.821-0.008-0.0080.0000.0000.0000.000
50A30ALA0-0.0860.09937.2880.0000.0000.0000.0000.0000.000
51A31GLN00.082-0.10238.283-0.007-0.0070.0000.0000.0000.000
52A31GLN0-0.1080.08235.847-0.007-0.0070.0000.0000.0000.000
53A32ALA00.104-0.09639.708-0.010-0.0100.0000.0000.0000.000
54A32ALA0-0.0990.09840.1500.0010.0010.0000.0000.0000.000
55A33GLU00.097-0.09141.236-0.006-0.0060.0000.0000.0000.000
56A33GLU-1-0.927-0.80741.8370.1070.1070.0000.0000.0000.000
57A34GLN00.062-0.10242.829-0.005-0.0050.0000.0000.0000.000
58A34GLN0-0.0850.09141.7640.0020.0020.0000.0000.0000.000
59A35ALA00.116-0.06844.259-0.007-0.0070.0000.0000.0000.000
60A35ALA0-0.0690.10744.6420.0000.0000.0000.0000.0000.000
61A36ALA00.075-0.07945.665-0.006-0.0060.0000.0000.0000.000
62A36ALA0-0.0650.10645.9990.0010.0010.0000.0000.0000.000
63A37MET00.031-0.13147.215-0.004-0.0040.0000.0000.0000.000
64A37MET0-0.0950.09046.7810.0010.0010.0000.0000.0000.000
65A38SER0-0.007-0.09948.853-0.003-0.0030.0000.0000.0000.000
66A38SER0-0.0770.05748.242-0.001-0.0010.0000.0000.0000.000
67A39SER0-0.011-0.09950.540-0.005-0.0050.0000.0000.0000.000
68A39SER0-0.0680.05249.5010.0010.0010.0000.0000.0000.000
69A40GLN00.159-0.09551.978-0.002-0.0020.0000.0000.0000.000
70A40GLN0-0.1050.08152.3600.0030.0030.0000.0000.0000.000
71A41ALA00.081-0.11653.705-0.001-0.0010.0000.0000.0000.000
72A41ALA0-0.0700.11055.7260.0000.0000.0000.0000.0000.000
73A42PHE0-0.002-0.10856.585-0.002-0.0020.0000.0000.0000.000
74A42PHE0-0.1200.07954.412-0.001-0.0010.0000.0000.0000.000
75A43HIS00.072-0.07457.887-0.003-0.0030.0000.0000.0000.000
76A43HIS0-0.1080.09153.999-0.002-0.0020.0000.0000.0000.000
77A44MET00.142-0.10559.1560.0000.0000.0000.0000.0000.000
78A44MET0-0.0690.10963.163-0.001-0.0010.0000.0000.0000.000
79A45GLY0-0.045-0.12561.6340.0000.0000.0000.0000.0000.000
80A46GLU00.1620.00760.6400.0030.0030.0000.0000.0000.000
81A46GLU-1-1.019-0.83860.9780.0570.0570.0000.0000.0000.000
82A47ALA00.101-0.10758.5570.0030.0030.0000.0000.0000.000
83A47ALA0-0.0620.11758.8130.0000.0000.0000.0000.0000.000
84A48SER00.078-0.07556.8580.0030.0030.0000.0000.0000.000
85A48SER0-0.0620.06657.629-0.001-0.0010.0000.0000.0000.000
86A49ALA00.097-0.08355.9010.0030.0030.0000.0000.0000.000
87A49ALA0-0.0900.09558.1590.0000.0000.0000.0000.0000.000
88A50ALA00.082-0.11654.9730.0040.0040.0000.0000.0000.000
89A50ALA0-0.0920.11355.1760.0000.0000.0000.0000.0000.000
90A51PHE00.072-0.10352.3570.0050.0050.0000.0000.0000.000
91A51PHE0-0.0830.11050.2930.0000.0000.0000.0000.0000.000
92A52GLN00.089-0.09051.1450.0050.0050.0000.0000.0000.000
93A52GLN0-0.0660.10853.692-0.002-0.0020.0000.0000.0000.000
94A53ALA00.098-0.08850.9770.0040.0040.0000.0000.0000.000
95A53ALA0-0.0850.09952.2480.0000.0000.0000.0000.0000.000
96A54ALA00.060-0.12948.6210.0060.0060.0000.0000.0000.000
97A54ALA0-0.0820.11748.6040.0000.0000.0000.0000.0000.000
98A55HIS00.065-0.09246.8890.0070.0070.0000.0000.0000.000
99A55HIS0-0.1390.04446.289-0.003-0.0030.0000.0000.0000.000
100A56ALA00.155-0.07946.0580.0060.0060.0000.0000.0000.000
101A56ALA0-0.0900.09748.730-0.001-0.0010.0000.0000.0000.000
102A57ARG00.080-0.10245.5530.0060.0060.0000.0000.0000.000
103A57ARG10.7461.00943.135-0.129-0.1290.0000.0000.0000.000
104A58PHE00.078-0.10842.6560.0090.0090.0000.0000.0000.000
105A58PHE0-0.0800.10639.9150.0000.0000.0000.0000.0000.000
106A59VAL00.098-0.08841.2960.0110.0110.0000.0000.0000.000
107A59VAL0-0.0560.12742.4740.0000.0000.0000.0000.0000.000
108A60GLU00.113-0.08940.9660.0090.0090.0000.0000.0000.000
109A60GLU-1-0.891-0.77042.6220.1350.1350.0000.0000.0000.000
110A61VAL00.019-0.15139.4670.0090.0090.0000.0000.0000.000
111A61VAL0-0.0940.11338.2340.0000.0000.0000.0000.0000.000
112A62SER00.066-0.10937.1830.0150.0150.0000.0000.0000.000
113A62SER0-0.0390.08538.0130.0000.0000.0000.0000.0000.000
114A63ALA00.107-0.07136.0450.0130.0130.0000.0000.0000.000
115A63ALA0-0.0650.11338.386-0.001-0.0010.0000.0000.0000.000
116A64LYS00.055-0.09235.4140.0120.0120.0000.0000.0000.000
117A64LYS10.7720.99736.217-0.155-0.1550.0000.0000.0000.000
118A65VAL00.071-0.10833.0300.0170.0170.0000.0000.0000.000
119A65VAL0-0.0770.10332.299-0.001-0.0010.0000.0000.0000.000
120A66ASN00.083-0.06131.4230.0200.0200.0000.0000.0000.000
121A66ASN0-0.1190.04633.0740.0040.0040.0000.0000.0000.000
122A67ALA00.225-0.04430.4780.0200.0200.0000.0000.0000.000
123A67ALA0-0.0960.09332.698-0.003-0.0030.0000.0000.0000.000
124A68LEU00.017-0.13229.5420.0210.0210.0000.0000.0000.000
125A68LEU0-0.1000.09429.765-0.001-0.0010.0000.0000.0000.000
126A69LEU00.089-0.09226.9370.0340.0340.0000.0000.0000.000
127A69LEU0-0.1190.08126.954-0.001-0.0010.0000.0000.0000.000
128A70ASP00.071-0.09425.8850.0340.0340.0000.0000.0000.000
129A70ASP-1-0.884-0.79328.2930.2630.2630.0000.0000.0000.000
130A71ILE00.096-0.08925.3170.0320.0320.0000.0000.0000.000
131A71ILE0-0.0930.09525.397-0.001-0.0010.0000.0000.0000.000
132A72ALA00.129-0.07923.0710.0490.0490.0000.0000.0000.000
133A72ALA0-0.1040.09023.418-0.006-0.0060.0000.0000.0000.000
134A73GLN00.056-0.09521.3960.0650.0650.0000.0000.0000.000
135A73GLN0-0.0300.09222.4380.0290.0290.0000.0000.0000.000
136A74LEU00.017-0.11520.5310.0540.0540.0000.0000.0000.000
137A74LEU0-0.0750.09822.591-0.006-0.0060.0000.0000.0000.000
138A75ASN00.032-0.07819.0460.0420.0420.0000.0000.0000.000
139A75ASN0-0.1750.01719.9800.0170.0170.0000.0000.0000.000
140A76ILE00.082-0.07616.8490.1120.1120.0000.0000.0000.000
141A76ILE0-0.0970.08017.115-0.009-0.0090.0000.0000.0000.000
142A77GLY00.011-0.10617.914-0.017-0.0170.0000.0000.0000.000
143A78ASP00.1650.05017.8140.0950.0950.0000.0000.0000.000
144A78ASP-1-1.036-0.88821.0860.3850.3850.0000.0000.0000.000
145A79ALA00.160-0.05118.1630.0430.0430.0000.0000.0000.000
146A79ALA0-0.0840.08420.950-0.011-0.0110.0000.0000.0000.000
147A80ALA00.081-0.10916.698-0.011-0.0110.0000.0000.0000.000
148A80ALA0-0.0780.12515.8000.0020.0020.0000.0000.0000.000
149A81SER00.097-0.06213.6220.1400.1400.0000.0000.0000.000
150A81SER0-0.1030.03614.411-0.045-0.0450.0000.0000.0000.000
151A82SER00.089-0.06313.5570.0860.0860.0000.0000.0000.000
152A82SER0-0.0840.06117.676-0.018-0.0180.0000.0000.0000.000
153A83TYR00.079-0.08815.157-0.053-0.0530.0000.0000.0000.000
154A83TYR0-0.1530.04613.396-0.077-0.0770.0000.0000.0000.000
155A84VAL00.054-0.11511.142-0.069-0.0690.0000.0000.0000.000
156A84VAL0-0.0790.1089.1770.0780.0780.0000.0000.0000.000
157A85ALA00.128-0.0909.8650.2830.2830.0000.0000.0000.000
158A85ALA0-0.0910.09012.299-0.040-0.0400.0000.0000.0000.000
159A86GLN00.041-0.10211.148-0.064-0.0640.0000.0000.0000.000
160A86GLN0-0.1320.05414.912-0.070-0.0700.0000.0000.0000.000
161A87ASP00.060-0.10211.668-0.199-0.1990.0000.0000.0000.000
162A87ASP-1-0.959-0.81110.3721.3741.3740.0000.0000.0000.000
163A88ALA00.148-0.0897.617-0.125-0.1250.0000.0000.0000.000
164A88ALA0-0.0810.1056.7670.0830.0830.0000.0000.0000.000
165A89ALA00.088-0.0788.383-0.228-0.2280.0000.0000.0000.000
166A89ALA0-0.0860.09811.818-0.019-0.0190.0000.0000.0000.000
167A90ALA00.093-0.09110.983-0.180-0.1800.0000.0000.0000.000
168A90ALA0-0.0790.09713.1220.0010.0010.0000.0000.0000.000
169A91ALA00.052-0.1359.339-0.222-0.2220.0000.0000.0000.000
170A91ALA0-0.0750.1158.5930.0740.0740.0000.0000.0000.000
171A92SER0-0.022-0.1218.938-0.103-0.1030.0000.0000.0000.000
172A92SER0-0.0660.0517.719-0.115-0.1150.0000.0000.0000.000
173A93THR0-0.052-0.0839.495-0.174-0.1740.0000.0000.0000.000
174A93THR0-0.0890.03412.935-0.022-0.0220.0000.0000.0000.000
175A94TYR0-0.092-0.12013.136-0.083-0.0830.0000.0000.0000.000
176A94TYR00.0110.01513.7510.0110.0110.0000.0000.0000.000