FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: GQ9K1

Calculation Name: 3FGN-A-Xray307

Preferred Name: ATP-dependent dethiobiotin synthetase BioD

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3FGN

Chain ID: A

ChEMBL ID: CHEMBL4105930

UniProt ID: P9WPQ5

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2383618.36419
FMO2-HF: Nuclear repulsion 2302583.701523
FMO2-HF: Total energy -81034.662667
FMO2-MP2: Total energy -81269.689818


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:-4:ACE )


Summations of interaction energy for fragment #1(A:-4:ACE )
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.
-0.5980.33-0.005-0.416-0.5070
Interaction energy analysis for fragmet #1(A:-4:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.014
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].
3A-2GLN 00.0530.0483.8600.8851.813-0.005-0.416-0.5070.000
4A-1SER 0-0.026-0.0217.0670.0660.0660.0000.0000.0000.000
5A0HIS 10.7800.8669.5480.4290.4290.0000.0000.0000.000
6A1MET 00.0220.08911.366-0.100-0.1000.0000.0000.0000.000
7A2THR 00.012-0.00212.2240.0240.0240.0000.0000.0000.000
8A3ILE 0-0.008-0.00314.3980.0140.0140.0000.0000.0000.000
9A4LEU 0-0.020-0.01518.1270.0210.0210.0000.0000.0000.000
10A5VAL 00.0250.03320.4900.0000.0000.0000.0000.0000.000
11A6VAL 0-0.004-0.00724.1870.0040.0040.0000.0000.0000.000
12A7THR 0-0.002-0.01526.3090.0050.0050.0000.0000.0000.000
13A8GLY 00.0270.00229.592-0.001-0.0010.0000.0000.0000.000
14A9THR 0-0.046-0.03032.5780.0030.0030.0000.0000.0000.000
15A10GLY 00.0300.01234.8460.0040.0040.0000.0000.0000.000
16A11THR 0-0.008-0.01236.853-0.004-0.0040.0000.0000.0000.000
17A12GLY 0-0.0110.00338.1300.0010.0010.0000.0000.0000.000
18A13VAL 0-0.0080.00533.7050.0010.0010.0000.0000.0000.000
19A14GLY 00.0230.00934.211-0.001-0.0010.0000.0000.0000.000
20A15LYS 10.9100.94830.3220.0650.0650.0000.0000.0000.000
21A16THR 00.0600.04129.682-0.005-0.0050.0000.0000.0000.000
22A17VAL 00.0400.01929.987-0.007-0.0070.0000.0000.0000.000
23A18VAL 00.000-0.00226.494-0.005-0.0050.0000.0000.0000.000
24A19CYS 0-0.031-0.00125.503-0.011-0.0110.0000.0000.0000.000
25A20ALA 00.0360.02525.111-0.014-0.0140.0000.0000.0000.000
26A21ALA 00.0380.01426.004-0.009-0.0090.0000.0000.0000.000
27A22LEU 0-0.018-0.01819.691-0.006-0.0060.0000.0000.0000.000
28A23ALA 00.0100.00621.288-0.021-0.0210.0000.0000.0000.000
29A24SER 00.0350.00921.603-0.022-0.0220.0000.0000.0000.000
30A25ALA 0-0.019-0.01021.204-0.006-0.0060.0000.0000.0000.000
31A26ALA 00.012-0.00817.366-0.012-0.0120.0000.0000.0000.000
32A27ARG 10.9530.97917.4780.1520.1520.0000.0000.0000.000
33A28GLN 0-0.126-0.07119.293-0.008-0.0080.0000.0000.0000.000
34A29ALA 0-0.068-0.02515.5780.0110.0110.0000.0000.0000.000
35A30GLY 0-0.0090.00214.803-0.043-0.0430.0000.0000.0000.000
36A31ILE 0-0.0220.00212.926-0.057-0.0570.0000.0000.0000.000
37A32ASP -1-0.799-0.89215.030-0.244-0.2440.0000.0000.0000.000
38A33VAL 0-0.020-0.00816.841-0.011-0.0110.0000.0000.0000.000
39A34ALA 0-0.025-0.00819.4960.0190.0190.0000.0000.0000.000
40A35VAL 0-0.012-0.00221.8030.0000.0000.0000.0000.0000.000
41A36CYS 0-0.021-0.00224.6310.0080.0080.0000.0000.0000.000
42A37LYS 10.8020.89726.5680.0780.0780.0000.0000.0000.000
43A38PRO 0-0.0020.00028.7030.0040.0040.0000.0000.0000.000
44A39VAL 00.0270.01331.3140.0040.0040.0000.0000.0000.000
45A40GLN 00.0240.01034.716-0.006-0.0060.0000.0000.0000.000
46A41THR 0-0.033-0.00836.6100.0010.0010.0000.0000.0000.000
47A42GLY 00.0670.03339.982-0.002-0.0020.0000.0000.0000.000
48A43THR 0-0.0160.00039.8090.0000.0000.0000.0000.0000.000
49A44ALA 0-0.043-0.02042.3410.0000.0000.0000.0000.0000.000
50A45ARG 10.7760.87942.0800.0480.0480.0000.0000.0000.000
51A46GLY 0-0.014-0.00643.2640.0000.0000.0000.0000.0000.000
52A47ASP -1-0.846-0.89939.326-0.053-0.0530.0000.0000.0000.000
53A48ASP -1-0.847-0.95735.354-0.077-0.0770.0000.0000.0000.000
54A49ASP -1-0.802-0.89932.551-0.072-0.0720.0000.0000.0000.000
55A50LEU 0-0.012-0.00729.110-0.005-0.0050.0000.0000.0000.000
56A51ALA 0-0.0080.00131.496-0.005-0.0050.0000.0000.0000.000
57A52GLU -1-0.974-0.98833.747-0.072-0.0720.0000.0000.0000.000
58A53VAL 00.027-0.00227.134-0.002-0.0020.0000.0000.0000.000
59A54GLY 0-0.0160.00329.432-0.006-0.0060.0000.0000.0000.000
60A55ARG 10.8960.94330.4640.0710.0710.0000.0000.0000.000
61A56LEU 0-0.0420.00331.021-0.001-0.0010.0000.0000.0000.000
62A57ALA 0-0.022-0.01625.998-0.002-0.0020.0000.0000.0000.000
63A58GLY 0-0.0100.00626.779-0.010-0.0100.0000.0000.0000.000
64A59VAL 0-0.080-0.04323.932-0.011-0.0110.0000.0000.0000.000
65A60THR 00.0000.00124.6330.0100.0100.0000.0000.0000.000
66A61GLN 0-0.048-0.03120.9780.0090.0090.0000.0000.0000.000
67A62LEU 00.0040.00524.981-0.005-0.0050.0000.0000.0000.000
68A63ALA 00.0210.01126.5340.0060.0060.0000.0000.0000.000
69A64GLY 00.0390.01228.3900.0020.0020.0000.0000.0000.000
70A65LEU 0-0.038-0.02431.659-0.001-0.0010.0000.0000.0000.000
71A66ALA 0-0.0040.01733.7060.0040.0040.0000.0000.0000.000
72A67ARG 10.9070.93536.3180.0650.0650.0000.0000.0000.000
73A68TYR 00.001-0.02438.7630.0010.0010.0000.0000.0000.000
74A69PRO 00.0130.00142.314-0.001-0.0010.0000.0000.0000.000
75A70GLN 00.0980.03645.063-0.001-0.0010.0000.0000.0000.000
76A71PRO 00.0030.00543.420-0.002-0.0020.0000.0000.0000.000
77A72MET 0-0.053-0.01043.8740.0020.0020.0000.0000.0000.000
78A73ALA 00.0310.00041.256-0.003-0.0030.0000.0000.0000.000
79A74PRO 00.0280.00737.6130.0010.0010.0000.0000.0000.000
80A75ALA 00.0780.05140.6090.0000.0000.0000.0000.0000.000
81A76ALA 00.0400.02442.9250.0010.0010.0000.0000.0000.000
82A77ALA 0-0.055-0.03342.8480.0010.0010.0000.0000.0000.000
83A78ALA 0-0.002-0.00842.3670.0000.0000.0000.0000.0000.000
84A79GLU -1-0.916-0.94444.381-0.027-0.0270.0000.0000.0000.000
85A80HIS 0-0.044-0.02847.7110.0010.0010.0000.0000.0000.000
86A81ALA 0-0.064-0.03546.2650.0010.0010.0000.0000.0000.000
87A82GLY 0-0.0020.00948.4280.0000.0000.0000.0000.0000.000
88A83MET 0-0.106-0.04942.254-0.001-0.0010.0000.0000.0000.000
89A84ALA 00.0610.03742.4190.0010.0010.0000.0000.0000.000
90A85LEU 00.0090.02038.601-0.003-0.0030.0000.0000.0000.000
91A86PRO 0-0.037-0.00434.8000.0000.0000.0000.0000.0000.000
92A87ALA 00.0480.01535.5080.0020.0020.0000.0000.0000.000
93A88ARG 10.9020.91629.5750.0430.0430.0000.0000.0000.000
94A89ASP -1-0.873-0.94130.456-0.060-0.0600.0000.0000.0000.000
95A90GLN 0-0.022-0.00729.984-0.005-0.0050.0000.0000.0000.000
96A91ILE 0-0.0050.01028.316-0.008-0.0080.0000.0000.0000.000
97A92VAL 00.0300.01224.991-0.010-0.0100.0000.0000.0000.000
98A93ARG 10.9340.96725.3430.0750.0750.0000.0000.0000.000
99A94LEU 0-0.034-0.00726.111-0.009-0.0090.0000.0000.0000.000
100A95ILE 0-0.002-0.00721.730-0.012-0.0120.0000.0000.0000.000
101A96ALA 00.0200.00421.301-0.021-0.0210.0000.0000.0000.000
102A97ASP -1-0.889-0.93521.300-0.137-0.1370.0000.0000.0000.000
103A98LEU 0-0.095-0.05221.168-0.012-0.0120.0000.0000.0000.000
104A99ASP -1-0.764-0.87915.850-0.348-0.3480.0000.0000.0000.000
105A100ARG 10.8520.91815.5620.2700.2700.0000.0000.0000.000
106A101PRO 0-0.004-0.00710.226-0.003-0.0030.0000.0000.0000.000
107A102GLY 00.0460.03610.338-0.030-0.0300.0000.0000.0000.000
108A103ARG 10.7700.89010.8600.3510.3510.0000.0000.0000.000
109A104LEU 00.0140.00614.261-0.001-0.0010.0000.0000.0000.000
110A105THR 0-0.019-0.06316.3020.0230.0230.0000.0000.0000.000
111A106LEU 0-0.038-0.00419.4550.0140.0140.0000.0000.0000.000
112A107VAL 00.024-0.00422.3000.0060.0060.0000.0000.0000.000
113A108GLU -1-0.821-0.90625.055-0.079-0.0790.0000.0000.0000.000
114A109GLY 00.0130.00128.2640.0040.0040.0000.0000.0000.000
115A110ALA 0-0.012-0.01330.927-0.001-0.0010.0000.0000.0000.000
116A111GLY 00.005-0.01234.6670.0030.0030.0000.0000.0000.000
117A112GLY 00.0320.02334.4200.0040.0040.0000.0000.0000.000
118A113LEU 0-0.034-0.01729.332-0.002-0.0020.0000.0000.0000.000
119A114LEU 00.006-0.01832.818-0.001-0.0010.0000.0000.0000.000
120A115VAL 0-0.0330.00935.6380.0030.0030.0000.0000.0000.000
121A116GLU -1-0.838-0.92535.710-0.039-0.0390.0000.0000.0000.000
122A117LEU 0-0.092-0.06131.780-0.002-0.0020.0000.0000.0000.000
123A118ALA 00.0270.00434.679-0.002-0.0020.0000.0000.0000.000
124A119GLU -1-0.923-0.92236.654-0.033-0.0330.0000.0000.0000.000
125A120PRO 0-0.083-0.04438.169-0.001-0.0010.0000.0000.0000.000
126A121GLY 00.011-0.02138.8260.0010.0010.0000.0000.0000.000
127A122VAL 0-0.0160.00832.7620.0000.0000.0000.0000.0000.000
128A123THR 0-0.015-0.00932.851-0.003-0.0030.0000.0000.0000.000
129A124LEU 00.035-0.01227.596-0.002-0.0020.0000.0000.0000.000
130A125ARG 10.8990.93628.1470.0290.0290.0000.0000.0000.000
131A126ASP -1-0.814-0.90227.916-0.042-0.0420.0000.0000.0000.000
132A127VAL 00.0050.00825.900-0.002-0.0020.0000.0000.0000.000
133A128ALA 0-0.016-0.01624.053-0.008-0.0080.0000.0000.0000.000
134A129VAL 0-0.013-0.00223.153-0.004-0.0040.0000.0000.0000.000
135A130ASP -1-0.839-0.90123.769-0.058-0.0580.0000.0000.0000.000
136A131VAL 0-0.069-0.04321.221-0.004-0.0040.0000.0000.0000.000
137A132ALA 0-0.0160.00518.334-0.017-0.0170.0000.0000.0000.000
138A133ALA 0-0.0290.00318.388-0.015-0.0150.0000.0000.0000.000
139A134ALA 00.0010.00618.9030.0180.0180.0000.0000.0000.000
140A135ALA 0-0.006-0.02020.573-0.009-0.0090.0000.0000.0000.000
141A136LEU 0-0.0170.00322.3080.0060.0060.0000.0000.0000.000
142A137VAL 0-0.003-0.01124.3380.0020.0020.0000.0000.0000.000
143A138VAL 0-0.0080.00528.0480.0010.0010.0000.0000.0000.000
144A139VAL 0-0.004-0.00930.4080.0040.0040.0000.0000.0000.000
145A140THR 00.0710.03933.346-0.002-0.0020.0000.0000.0000.000
146A141ALA 00.0450.01736.1020.0010.0010.0000.0000.0000.000
147A142ASP -1-0.854-0.91637.752-0.030-0.0300.0000.0000.0000.000
148A143LEU 0-0.001-0.02340.7280.0000.0000.0000.0000.0000.000
149A144GLY 00.0210.01742.269-0.001-0.0010.0000.0000.0000.000
150A145THR 0-0.046-0.02436.1090.0000.0000.0000.0000.0000.000
151A146LEU 00.000-0.00736.309-0.001-0.0010.0000.0000.0000.000
152A147ASN 00.0060.00037.1900.0010.0010.0000.0000.0000.000
153A148HIS 00.0750.03937.3050.0000.0000.0000.0000.0000.000
154A149THR 00.0160.00031.832-0.003-0.0030.0000.0000.0000.000
155A150LYS 10.9490.96533.2060.0120.0120.0000.0000.0000.000
156A151LEU 00.0270.02934.6300.0010.0010.0000.0000.0000.000
157A152THR 0-0.018-0.01130.622-0.001-0.0010.0000.0000.0000.000
158A153LEU 0-0.010-0.02728.665-0.002-0.0020.0000.0000.0000.000
159A154GLU -1-0.943-0.95730.271-0.013-0.0130.0000.0000.0000.000
160A155ALA 00.0090.00532.3280.0010.0010.0000.0000.0000.000
161A156LEU 0-0.025-0.01126.377-0.001-0.0010.0000.0000.0000.000
162A157ALA 00.0310.02127.8220.0000.0000.0000.0000.0000.000
163A158ALA 0-0.029-0.00328.8830.0030.0030.0000.0000.0000.000
164A159GLN 0-0.051-0.02329.0500.0040.0040.0000.0000.0000.000
165A160GLN 0-0.040-0.02124.785-0.001-0.0010.0000.0000.0000.000
166A161VAL 00.0110.02623.547-0.004-0.0040.0000.0000.0000.000
167A162SER 00.003-0.00219.7540.0040.0040.0000.0000.0000.000
168A163CYS 0-0.0100.00222.474-0.012-0.0120.0000.0000.0000.000
169A164ALA 00.0370.01919.8690.0030.0030.0000.0000.0000.000
170A165GLY 00.002-0.00921.078-0.002-0.0020.0000.0000.0000.000
171A166LEU 0-0.015-0.01723.936-0.003-0.0030.0000.0000.0000.000
172A167VAL 00.0310.01525.597-0.004-0.0040.0000.0000.0000.000
173A168ILE 0-0.035-0.01528.1720.0040.0040.0000.0000.0000.000
174A169GLY 00.0270.01331.654-0.003-0.0030.0000.0000.0000.000
175A170SER 0-0.015-0.00932.758-0.001-0.0010.0000.0000.0000.000
176A171TRP 0-0.015-0.01834.3600.0050.0050.0000.0000.0000.000
177A172PRO 0-0.016-0.01636.326-0.001-0.0010.0000.0000.0000.000
178A173ASP -1-0.939-0.91939.320-0.032-0.0320.0000.0000.0000.000
179A174PRO 00.033-0.00441.0340.0000.0000.0000.0000.0000.000
180A175PRO 0-0.006-0.00538.8770.0000.0000.0000.0000.0000.000
181A176GLY 00.0500.01241.3210.0020.0020.0000.0000.0000.000
182A177LEU 00.031-0.00342.7660.0000.0000.0000.0000.0000.000
183A178VAL 00.0010.00142.8750.0000.0000.0000.0000.0000.000
184A179ALA 00.0550.03239.4890.0000.0000.0000.0000.0000.000
185A180ALA 00.0370.01638.512-0.001-0.0010.0000.0000.0000.000
186A181SER 0-0.029-0.01538.2130.0010.0010.0000.0000.0000.000
187A182ASN 0-0.013-0.03838.1100.0020.0020.0000.0000.0000.000
188A183ARG 10.9771.00530.1020.0390.0390.0000.0000.0000.000
189A184SER 0-0.024-0.00733.5840.0000.0000.0000.0000.0000.000
190A185ALA 0-0.070-0.04034.3020.0020.0020.0000.0000.0000.000
191A186LEU 0-0.005-0.01232.0830.0010.0010.0000.0000.0000.000
192A187ALA 00.0130.01129.778-0.001-0.0010.0000.0000.0000.000
193A188ARG 10.8970.95929.7660.0130.0130.0000.0000.0000.000
194A189ILE 0-0.069-0.02831.0350.0030.0030.0000.0000.0000.000
195A190ALA 00.0160.00626.697-0.001-0.0010.0000.0000.0000.000
196A191MET 00.0170.02422.2240.0030.0030.0000.0000.0000.000
197A192VAL 00.001-0.00125.292-0.006-0.0060.0000.0000.0000.000
198A193ARG 10.8210.91219.9460.0750.0750.0000.0000.0000.000
199A194ALA 00.0690.03824.300-0.004-0.0040.0000.0000.0000.000
200A195ALA 0-0.068-0.03927.0020.0050.0050.0000.0000.0000.000
201A196LEU 00.0040.01127.9550.0000.0000.0000.0000.0000.000
202A197PRO 00.0550.02531.6560.0040.0040.0000.0000.0000.000
203A198ALA 00.0310.01434.952-0.002-0.0020.0000.0000.0000.000
204A199GLY 00.0180.00337.9010.0000.0000.0000.0000.0000.000
205A200ALA 00.0050.00332.910-0.001-0.0010.0000.0000.0000.000
206A201ALA 0-0.011-0.01534.694-0.003-0.0030.0000.0000.0000.000
207A202SER 0-0.073-0.03235.8550.0000.0000.0000.0000.0000.000
208A203LEU 0-0.033-0.00333.6060.0020.0020.0000.0000.0000.000
209A204ASP -1-0.844-0.91536.024-0.063-0.0630.0000.0000.0000.000
210A205ALA 00.014-0.00132.214-0.004-0.0040.0000.0000.0000.000
211A206GLY 0-0.022-0.00931.211-0.006-0.0060.0000.0000.0000.000
212A207ASP -1-0.851-0.93831.437-0.066-0.0660.0000.0000.0000.000
213A208PHE 00.0030.00028.177-0.001-0.0010.0000.0000.0000.000
214A209ALA 00.0040.01127.361-0.005-0.0050.0000.0000.0000.000
215A210ALA 00.0370.03427.006-0.007-0.0070.0000.0000.0000.000
216A211MET 0-0.044-0.00428.4060.0010.0010.0000.0000.0000.000
217A212SER 0-0.021-0.03925.3500.0000.0000.0000.0000.0000.000
218A213ALA 0-0.061-0.03523.510-0.006-0.0060.0000.0000.0000.000
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