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: VK6M1

Calculation Name: 3F3H-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F3H

Chain ID: A

ChEMBL ID:

UniProt ID: P14945

Base Structure: X-ray

Registration Date: 2025-07-08

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 208
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -824923.814713
FMO2-HF: Nuclear repulsion 782436.983307
FMO2-HF: Total energy -42486.831406
FMO2-MP2: Total energy -42613.827883


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:2:SER)


Summations of interaction energy for fragment #1(A:2:SER)
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.
2.985.8260.23-0.999-2.0740.003
Interaction energy analysis for fragmet #1(A:2:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.095 / q_NPA : 0.043
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].
4A3ASP-1-0.952-0.8074.733-2.291-1.894-0.001-0.112-0.2830.000
5A4THR0-0.009-0.0723.345-0.1011.356-0.005-0.659-0.7930.004
6A4THR0-0.0300.0513.792-0.150-0.0830.0050.020-0.0910.000
7A5ALA00.125-0.0723.2831.6641.7140.0070.175-0.232-0.001
8A5ALA0-0.0950.0912.5390.2350.6070.225-0.255-0.3410.000
9A6LEU00.009-0.1333.9231.3131.524-0.002-0.055-0.1540.000
10A6LEU0-0.0530.1173.552-0.0720.2200.001-0.113-0.1800.000
11A7ILE00.086-0.0795.7150.7940.7940.0000.0000.0000.000
12A7ILE0-0.0690.0977.2720.0430.0430.0000.0000.0000.000
13A8PHE00.066-0.0967.9780.4370.4370.0000.0000.0000.000
14A8PHE0-0.0750.0877.9750.0120.0120.0000.0000.0000.000
15A9ARG00.142-0.0678.1610.3230.3230.0000.0000.0000.000
16A9ARG10.8611.0657.9780.4990.4990.0000.0000.0000.000
17A10LEU00.141-0.0979.6150.2260.2260.0000.0000.0000.000
18A10LEU0-0.0850.10810.665-0.006-0.0060.0000.0000.0000.000
19A11ALA00.074-0.11211.6690.1660.1660.0000.0000.0000.000
20A11ALA0-0.0880.11212.870-0.011-0.0110.0000.0000.0000.000
21A12TRP00.015-0.11312.9520.1070.1070.0000.0000.0000.000
22A12TRP0-0.0570.09813.2560.0060.0060.0000.0000.0000.000
23A13ASP00.089-0.10114.0650.0860.0860.0000.0000.0000.000
24A13ASP-1-1.023-0.85313.708-0.479-0.4790.0000.0000.0000.000
25A14VAL00.002-0.11315.6430.0700.0700.0000.0000.0000.000
26A14VAL0-0.0290.11215.281-0.001-0.0010.0000.0000.0000.000
27A15LYS00.056-0.09216.8830.0330.0330.0000.0000.0000.000
28A15LYS10.7451.00917.8800.3950.3950.0000.0000.0000.000
29A16LYS00.141-0.09618.233-0.041-0.0410.0000.0000.0000.000
30A16LYS10.8051.04521.1690.3050.3050.0000.0000.0000.000
31A17LEU00.073-0.13017.3820.0500.0500.0000.0000.0000.000
32A17LEU0-0.0470.13915.225-0.009-0.0090.0000.0000.0000.000
33A18SER00.046-0.09418.126-0.048-0.0480.0000.0000.0000.000
34A18SER0-0.0810.06320.3690.0230.0230.0000.0000.0000.000
35A19PHE0-0.032-0.07817.9620.0450.0450.0000.0000.0000.000
36A19PHE0-0.0460.07812.836-0.008-0.0080.0000.0000.0000.000
37A20ASP00.140-0.13517.994-0.056-0.0560.0000.0000.0000.000
38A20ASP-1-0.914-0.76719.156-0.351-0.3510.0000.0000.0000.000
39A21TYR00.022-0.09217.3930.0460.0460.0000.0000.0000.000
40A21TYR0-0.0400.11616.763-0.009-0.0090.0000.0000.0000.000
41A22THR00.073-0.11218.1310.0110.0110.0000.0000.0000.000
42A22THR0-0.0560.06218.394-0.006-0.0060.0000.0000.0000.000
43A23PRO0-0.014-0.09318.0670.0240.0240.0000.0000.0000.000
44A24ASN00.0640.00021.3760.0050.0050.0000.0000.0000.000
45A24ASN0-0.1380.08223.1430.0150.0150.0000.0000.0000.000
46A25TRP00.067-0.10824.8100.0020.0020.0000.0000.0000.000
47A25TRP0-0.0530.10121.8410.0050.0050.0000.0000.0000.000
48A26GLY00.002-0.09026.8930.0010.0010.0000.0000.0000.000
49A27ARG00.031-0.01830.6330.0030.0030.0000.0000.0000.000
50A27ARG10.7390.99428.6610.0600.0600.0000.0000.0000.000
51A28GLY00.050-0.07833.027-0.003-0.0030.0000.0000.0000.000
52A29ASN00.055-0.00736.4110.0000.0000.0000.0000.0000.000
53A29ASN0-0.1640.06940.4930.0030.0030.0000.0000.0000.000
54A30PRO00.068-0.08539.6720.0020.0020.0000.0000.0000.000
55A31ASN00.1240.05836.1530.0000.0000.0000.0000.0000.000
56A31ASN0-0.0720.06235.2200.0030.0030.0000.0000.0000.000
57A32ASN00.124-0.04934.125-0.006-0.0060.0000.0000.0000.000
58A32ASN0-0.0780.07135.1490.0000.0000.0000.0000.0000.000
59A33PHE00.047-0.10433.8090.0030.0030.0000.0000.0000.000
60A33PHE0-0.0860.10335.6040.0020.0020.0000.0000.0000.000
61A34ILE00.124-0.09030.185-0.004-0.0040.0000.0000.0000.000
62A34ILE0-0.1000.10027.884-0.001-0.0010.0000.0000.0000.000
63A35ASP00.124-0.12531.6350.0040.0040.0000.0000.0000.000
64A35ASP-1-0.953-0.83233.844-0.058-0.0580.0000.0000.0000.000
65A36THR0-0.066-0.08830.3530.0020.0020.0000.0000.0000.000
66A36THR0-0.0250.04030.549-0.004-0.0040.0000.0000.0000.000
67A37VAL00.066-0.06225.6430.0060.0060.0000.0000.0000.000
68A37VAL0-0.0350.10023.6400.0000.0000.0000.0000.0000.000
69A38THR00.014-0.08126.0180.0020.0020.0000.0000.0000.000
70A38THR0-0.0060.06726.7740.0040.0040.0000.0000.0000.000
71A39PHE00.058-0.08622.5640.0000.0000.0000.0000.0000.000
72A39PHE0-0.0950.09720.4750.0000.0000.0000.0000.0000.000
73A40PRO00.048-0.09021.5840.0120.0120.0000.0000.0000.000
74A41LYS00.1670.05222.4110.0180.0180.0000.0000.0000.000
75A41LYS10.7771.03421.7210.3090.3090.0000.0000.0000.000
76A42VAL00.053-0.08721.262-0.049-0.0490.0000.0000.0000.000
77A42VAL0-0.0600.10722.3480.0020.0020.0000.0000.0000.000
78A43LEU00.084-0.13121.3670.0010.0010.0000.0000.0000.000
79A43LEU0-0.0950.10818.057-0.008-0.0080.0000.0000.0000.000
80A44THR00.021-0.07322.3890.0170.0170.0000.0000.0000.000
81A44THR0-0.0410.06125.786-0.004-0.0040.0000.0000.0000.000
82A45ASP00.018-0.09523.9530.0230.0230.0000.0000.0000.000
83A45ASP-1-0.864-0.81122.191-0.289-0.2890.0000.0000.0000.000
84A46LYS00.008-0.11025.0170.0130.0130.0000.0000.0000.000
85A46LYS10.8571.05521.3630.2240.2240.0000.0000.0000.000
86A47ALA00.131-0.07626.164-0.010-0.0100.0000.0000.0000.000
87A47ALA0-0.1000.10229.8300.0030.0030.0000.0000.0000.000
88A48TYR00.045-0.13024.6700.0180.0180.0000.0000.0000.000
89A48TYR0-0.1520.04721.312-0.006-0.0060.0000.0000.0000.000
90A49THR0-0.012-0.07125.8960.0020.0020.0000.0000.0000.000
91A49THR0-0.0350.06827.4580.0050.0050.0000.0000.0000.000
92A50TYR00.102-0.08925.130-0.013-0.0130.0000.0000.0000.000
93A50TYR0-0.1000.07922.913-0.007-0.0070.0000.0000.0000.000
94A51ARG00.213-0.06724.8950.0120.0120.0000.0000.0000.000
95A51ARG10.7290.99522.2990.0600.0600.0000.0000.0000.000
96A52VAL00.039-0.09025.044-0.011-0.0110.0000.0000.0000.000
97A52VAL0-0.0770.09826.9870.0000.0000.0000.0000.0000.000
98A53ALA00.121-0.10026.0860.0070.0070.0000.0000.0000.000
99A53ALA0-0.0910.10825.1990.0020.0020.0000.0000.0000.000
100A54VAL00.053-0.10726.654-0.005-0.0050.0000.0000.0000.000
101A54VAL0-0.0620.11729.1670.0000.0000.0000.0000.0000.000
102A55SER0-0.047-0.11627.8640.0050.0050.0000.0000.0000.000
103A55SER0-0.0660.05129.9530.0000.0000.0000.0000.0000.000
104A56GLY00.051-0.09326.8200.0070.0070.0000.0000.0000.000
105A57ARG00.013-0.02327.8400.0040.0040.0000.0000.0000.000
106A57ARG10.9061.08831.6940.0000.0000.0000.0000.0000.000
107A58ASN00.157-0.05028.694-0.006-0.0060.0000.0000.0000.000
108A58ASN0-0.0810.07628.439-0.006-0.0060.0000.0000.0000.000
109A59LEU0-0.023-0.13129.5590.0060.0060.0000.0000.0000.000
110A59LEU0-0.0540.11530.863-0.001-0.0010.0000.0000.0000.000
111A60GLY00.010-0.09929.939-0.002-0.0020.0000.0000.0000.000
112A61VAL00.111-0.02829.061-0.005-0.0050.0000.0000.0000.000
113A61VAL0-0.0410.14127.6550.0010.0010.0000.0000.0000.000
114A62LYS0-0.023-0.14129.8200.0070.0070.0000.0000.0000.000
115A62LYS10.9051.10031.8570.0650.0650.0000.0000.0000.000
116A63PRO00.024-0.08630.005-0.008-0.0080.0000.0000.0000.000
117A64SER00.0730.04429.7910.0100.0100.0000.0000.0000.000
118A64SER0-0.0730.05429.077-0.006-0.0060.0000.0000.0000.000
119A65TYR00.034-0.11131.1250.0030.0030.0000.0000.0000.000
120A65TYR0-0.0740.11132.6760.0010.0010.0000.0000.0000.000
121A66ALA00.126-0.08031.208-0.010-0.0100.0000.0000.0000.000
122A66ALA0-0.0600.10133.6380.0010.0010.0000.0000.0000.000
123A67VAL00.036-0.10329.4250.0040.0040.0000.0000.0000.000
124A67VAL0-0.0730.08627.852-0.002-0.0020.0000.0000.0000.000
125A68GLU00.048-0.11530.2880.0080.0080.0000.0000.0000.000
126A68GLU-1-1.027-0.85430.991-0.124-0.1240.0000.0000.0000.000
127A69SER00.067-0.05831.183-0.011-0.0110.0000.0000.0000.000
128A69SER0-0.0750.03634.6990.0010.0010.0000.0000.0000.000
129A70ASP0-0.028-0.13930.662-0.004-0.0040.0000.0000.0000.000
130A70ASP-1-0.856-0.76730.020-0.168-0.1680.0000.0000.0000.000
131A71GLY0-0.057-0.12527.328-0.016-0.0160.0000.0000.0000.000
132A72SER00.0490.02926.188-0.021-0.0210.0000.0000.0000.000
133A72SER0-0.0650.03327.2440.0060.0060.0000.0000.0000.000
134A73GLN00.136-0.10226.4640.0120.0120.0000.0000.0000.000
135A73GLN0-0.0690.12726.118-0.017-0.0170.0000.0000.0000.000
136A74LYS00.102-0.07926.641-0.011-0.0110.0000.0000.0000.000
137A74LYS10.8471.06329.7910.1100.1100.0000.0000.0000.000
138A75VAL00.077-0.12227.8290.0040.0040.0000.0000.0000.000
139A75VAL0-0.0500.12826.0980.0000.0000.0000.0000.0000.000
140A76ASN00.106-0.08329.0440.0000.0000.0000.0000.0000.000
141A76ASN0-0.1000.07233.3900.0020.0020.0000.0000.0000.000
142A77PHE00.113-0.10431.5030.0020.0020.0000.0000.0000.000
143A77PHE0-0.0630.10626.3220.0000.0000.0000.0000.0000.000
144A78LEU00.097-0.09432.1230.0060.0060.0000.0000.0000.000
145A78LEU0-0.1070.12035.1300.0000.0000.0000.0000.0000.000
146A79GLU00.064-0.13235.1670.0070.0070.0000.0000.0000.000
147A79GLU-1-0.957-0.83934.360-0.080-0.0800.0000.0000.0000.000
148A80TYR00.037-0.10432.6280.0030.0030.0000.0000.0000.000
149A80TYR0-0.1570.05229.213-0.001-0.0010.0000.0000.0000.000
150A81ASN00.036-0.06934.1370.0050.0050.0000.0000.0000.000
151A81ASN0-0.1340.05133.8920.0030.0030.0000.0000.0000.000
152A82SER0-0.018-0.11935.7110.0010.0010.0000.0000.0000.000
153A82SER0-0.0300.07938.7490.0020.0020.0000.0000.0000.000
154A83GLY00.037-0.08538.4200.0030.0030.0000.0000.0000.000
155A84TYR00.002-0.04438.311-0.002-0.0020.0000.0000.0000.000
156A84TYR0-0.0770.11938.7490.0010.0010.0000.0000.0000.000
157A85GLY00.102-0.05834.710-0.002-0.0020.0000.0000.0000.000
158A86ILE00.007-0.05331.9070.0060.0060.0000.0000.0000.000
159A86ILE0-0.0700.11530.5860.0010.0010.0000.0000.0000.000
160A87ALA00.176-0.05632.636-0.006-0.0060.0000.0000.0000.000
161A87ALA0-0.1030.09634.5560.0010.0010.0000.0000.0000.000
162A88ASP00.072-0.09030.2620.0030.0030.0000.0000.0000.000
163A88ASP-1-0.865-0.80929.779-0.035-0.0350.0000.0000.0000.000
164A89THR00.075-0.05829.470-0.001-0.0010.0000.0000.0000.000
165A89THR0-0.0550.04932.340-0.001-0.0010.0000.0000.0000.000
166A90ASN00.015-0.07129.7870.0080.0080.0000.0000.0000.000
167A90ASN0-0.0970.06429.8660.0050.0050.0000.0000.0000.000
168A91THR00.110-0.06925.471-0.007-0.0070.0000.0000.0000.000
169A91THR0-0.0780.07723.5150.0050.0050.0000.0000.0000.000
170A92ILE00.035-0.10125.0230.0060.0060.0000.0000.0000.000
171A92ILE0-0.0530.09925.747-0.001-0.0010.0000.0000.0000.000
172A93GLN00.081-0.10122.315-0.009-0.0090.0000.0000.0000.000
173A93GLN0-0.1210.07520.2550.0040.0040.0000.0000.0000.000
174A94VAL00.093-0.06521.7430.0130.0130.0000.0000.0000.000
175A94VAL0-0.0620.08122.258-0.001-0.0010.0000.0000.0000.000
176A95PHE00.072-0.09320.461-0.020-0.0200.0000.0000.0000.000
177A95PHE0-0.0910.07619.4520.0100.0100.0000.0000.0000.000
178A96VAL00.134-0.06720.1760.0210.0210.0000.0000.0000.000
179A96VAL0-0.0920.11019.038-0.005-0.0050.0000.0000.0000.000
180A97VAL00.103-0.12220.823-0.012-0.0120.0000.0000.0000.000
181A97VAL0-0.0930.10624.4220.0030.0030.0000.0000.0000.000
182A98ASP00.142-0.08821.634-0.006-0.0060.0000.0000.0000.000
183A98ASP-1-0.947-0.84020.713-0.207-0.2070.0000.0000.0000.000
184A99PRO0-0.067-0.12022.7950.0170.0170.0000.0000.0000.000
185A100ASP00.130-0.01424.8140.0180.0180.0000.0000.0000.000
186A100ASP-1-1.009-0.84023.812-0.161-0.1610.0000.0000.0000.000
187A101THR0-0.071-0.11722.6770.0120.0120.0000.0000.0000.000
188A101THR0-0.0390.05321.2600.0010.0010.0000.0000.0000.000
189A102ASN00.003-0.05224.2000.0120.0120.0000.0000.0000.000
190A102ASN0-0.1250.04926.245-0.002-0.0020.0000.0000.0000.000
191A103ASN00.157-0.06920.1780.0180.0180.0000.0000.0000.000
192A103ASN0-0.1150.06119.2380.0170.0170.0000.0000.0000.000
193A104ASP00.176-0.06620.415-0.020-0.0200.0000.0000.0000.000
194A104ASP-1-0.938-0.81520.540-0.091-0.0910.0000.0000.0000.000
195A105PHE0-0.012-0.12416.8150.0180.0180.0000.0000.0000.000
196A105PHE0-0.0780.10114.928-0.017-0.0170.0000.0000.0000.000
197A106ILE00.118-0.08716.558-0.009-0.0090.0000.0000.0000.000
198A106ILE0-0.1120.08915.0680.0080.0080.0000.0000.0000.000
199A107ILE0-0.015-0.11815.978-0.042-0.0420.0000.0000.0000.000
200A107ILE0-0.0590.11416.055-0.002-0.0020.0000.0000.0000.000
201A108ALA00.175-0.11417.879-0.023-0.0230.0000.0000.0000.000
202A108ALA0-0.0990.10620.8220.0020.0020.0000.0000.0000.000
203A109GLN00.110-0.09519.4730.0120.0120.0000.0000.0000.000
204A109GLN0-0.1100.10018.8710.0000.0000.0000.0000.0000.000
205A110TRP00.021-0.11220.595-0.007-0.0070.0000.0000.0000.000
206A110TRP0-0.1140.07324.357-0.005-0.0050.0000.0000.0000.000
207A111ASN0-0.026-0.09721.3560.0120.0120.0000.0000.0000.000
208A111ASN00.0360.01825.1810.0040.0040.0000.0000.0000.000