Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 535GZ

Calculation Name: 3FGN-A-Xray372

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: 2023-03-14

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2383240.901369
FMO2-HF: Nuclear repulsion 2302356.193798
FMO2-HF: Total energy -80884.707571
FMO2-MP2: Total energy -81119.295479


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:-3:PHE)


Summations of interaction energy for fragment #1(A:-3:PHE)
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.
-6.509-1.3554.084-2.561-6.6760.006
Interaction energy analysis for fragmet #1(A:-3:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.030 / q_NPA : 0.015
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-1SER0-0.035-0.0222.360-5.288-0.5823.226-3.261-4.6720.006
4A0HIS10.8180.8743.4201.0670.4990.0461.037-0.5140.002
5A1MET00.0120.0746.050-0.472-0.4720.0000.0000.0000.000
6A2THR0-0.001-0.0068.653-0.033-0.0330.0000.0000.0000.000
7A3ILE00.000-0.00310.9900.0840.0840.0000.0000.0000.000
8A4LEU0-0.021-0.01114.5520.0160.0160.0000.0000.0000.000
9A5VAL00.0220.02317.7620.0220.0220.0000.0000.0000.000
10A6VAL0-0.015-0.01021.1300.0070.0070.0000.0000.0000.000
11A7THR00.029-0.00523.5690.0170.0170.0000.0000.0000.000
12A8GLY00.014-0.00327.0450.0030.0030.0000.0000.0000.000
13A9THR0-0.032-0.01130.1360.0000.0000.0000.0000.0000.000
14A10GLY00.0330.00732.8880.0060.0060.0000.0000.0000.000
15A11THR00.0290.00534.347-0.006-0.0060.0000.0000.0000.000
16A12GLY00.0010.00535.2380.0030.0030.0000.0000.0000.000
17A13VAL0-0.057-0.01531.2940.0020.0020.0000.0000.0000.000
18A14GLY00.0800.03631.2730.0010.0010.0000.0000.0000.000
19A15LYS10.7630.87027.8640.1330.1330.0000.0000.0000.000
20A16THR00.0640.02526.756-0.007-0.0070.0000.0000.0000.000
21A17VAL00.0320.01926.627-0.006-0.0060.0000.0000.0000.000
22A18VAL0-0.007-0.00523.7620.0000.0000.0000.0000.0000.000
23A19CYS0-0.064-0.04322.414-0.017-0.0170.0000.0000.0000.000
24A20ALA00.0340.02821.840-0.013-0.0130.0000.0000.0000.000
25A21ALA00.0350.01422.7390.0000.0000.0000.0000.0000.000
26A22LEU0-0.022-0.00817.2840.0050.0050.0000.0000.0000.000
27A23ALA00.0230.00517.972-0.013-0.0130.0000.0000.0000.000
28A24SER00.0180.00918.1010.0030.0030.0000.0000.0000.000
29A25ALA0-0.018-0.00319.1450.0160.0160.0000.0000.0000.000
30A26ALA00.0380.01214.1280.0220.0220.0000.0000.0000.000
31A27ARG10.8860.95014.4290.1410.1410.0000.0000.0000.000
32A28GLN0-0.092-0.05116.0080.0420.0420.0000.0000.0000.000
33A29ALA0-0.063-0.02513.4750.0350.0350.0000.0000.0000.000
34A30GLY0-0.019-0.00412.4380.0440.0440.0000.0000.0000.000
35A31ILE0-0.044-0.0049.786-0.021-0.0210.0000.0000.0000.000
36A32ASP-1-0.778-0.87810.499-0.299-0.2990.0000.0000.0000.000
37A33VAL0-0.043-0.02911.752-0.091-0.0910.0000.0000.0000.000
38A34ALA0-0.0120.00614.3830.0440.0440.0000.0000.0000.000
39A35VAL0-0.016-0.01216.180-0.017-0.0170.0000.0000.0000.000
40A36CYS0-0.037-0.00719.3500.0160.0160.0000.0000.0000.000
41A37LYS10.7750.89121.1910.1350.1350.0000.0000.0000.000
42A38PRO00.0280.00223.6610.0110.0110.0000.0000.0000.000
43A39VAL00.0190.01226.0730.0090.0090.0000.0000.0000.000
44A40GLN0-0.016-0.00529.634-0.009-0.0090.0000.0000.0000.000
45A41THR0-0.019-0.00231.5140.0040.0040.0000.0000.0000.000
46A42GLY00.0410.00935.027-0.001-0.0010.0000.0000.0000.000
47A43THR0-0.048-0.03334.1100.0050.0050.0000.0000.0000.000
48A44ALA0-0.033-0.01136.8640.0030.0030.0000.0000.0000.000
49A45ARG10.7960.88938.1500.0730.0730.0000.0000.0000.000
50A46GLY00.0100.00737.5130.0020.0020.0000.0000.0000.000
51A47ASP-1-0.861-0.91334.671-0.075-0.0750.0000.0000.0000.000
52A48ASP-1-0.785-0.88929.500-0.106-0.1060.0000.0000.0000.000
53A49ASP-1-0.785-0.86927.855-0.108-0.1080.0000.0000.0000.000
54A50LEU00.0160.01223.698-0.003-0.0030.0000.0000.0000.000
55A51ALA00.0090.00026.1110.0010.0010.0000.0000.0000.000
56A52GLU-1-0.850-0.90228.722-0.068-0.0680.0000.0000.0000.000
57A53VAL0-0.011-0.02122.3910.0030.0030.0000.0000.0000.000
58A54GLY0-0.021-0.00824.5200.0000.0000.0000.0000.0000.000
59A55ARG10.7970.88025.5180.0800.0800.0000.0000.0000.000
60A56LEU0-0.0170.00427.0200.0060.0060.0000.0000.0000.000
61A57ALA00.0080.01022.2790.0050.0050.0000.0000.0000.000
62A58GLY00.0220.01922.354-0.002-0.0020.0000.0000.0000.000
63A59VAL0-0.055-0.03118.944-0.003-0.0030.0000.0000.0000.000
64A60THR00.0390.00319.0740.0080.0080.0000.0000.0000.000
65A61GLN0-0.104-0.04614.033-0.001-0.0010.0000.0000.0000.000
66A62LEU00.0150.00919.101-0.021-0.0210.0000.0000.0000.000
67A63ALA00.0350.01619.7050.0130.0130.0000.0000.0000.000
68A64GLY00.0370.01121.811-0.007-0.0070.0000.0000.0000.000
69A65LEU0-0.024-0.01325.203-0.002-0.0020.0000.0000.0000.000
70A66ALA00.0140.02027.1920.0100.0100.0000.0000.0000.000
71A67ARG10.8300.88629.6730.0980.0980.0000.0000.0000.000
72A68TYR00.031-0.00833.2390.0010.0010.0000.0000.0000.000
73A69PRO00.0110.01836.7260.0000.0000.0000.0000.0000.000
74A70GLN00.0970.04539.8050.0010.0010.0000.0000.0000.000
75A71PRO00.003-0.00238.858-0.005-0.0050.0000.0000.0000.000
76A72MET0-0.069-0.02339.2330.0030.0030.0000.0000.0000.000
77A73ALA00.0390.01037.182-0.004-0.0040.0000.0000.0000.000
78A74PRO00.004-0.00333.3260.0040.0040.0000.0000.0000.000
79A75ALA00.0780.05135.9820.0030.0030.0000.0000.0000.000
80A76ALA00.0590.03338.3800.0030.0030.0000.0000.0000.000
81A77ALA0-0.068-0.04337.9130.0040.0040.0000.0000.0000.000
82A78ALA00.0080.00637.0700.0020.0020.0000.0000.0000.000
83A79GLU-1-0.912-0.95239.063-0.063-0.0630.0000.0000.0000.000
84A80HIS0-0.047-0.03142.4780.0030.0030.0000.0000.0000.000
85A81ALA0-0.055-0.03240.3950.0030.0030.0000.0000.0000.000
86A82GLY0-0.0190.00542.5050.0010.0010.0000.0000.0000.000
87A83MET0-0.119-0.05836.0490.0000.0000.0000.0000.0000.000
88A84ALA00.0690.04736.4190.0010.0010.0000.0000.0000.000
89A85LEU0-0.031-0.00733.243-0.002-0.0020.0000.0000.0000.000
90A86PRO0-0.042-0.01128.7930.0010.0010.0000.0000.0000.000
91A87ALA00.0480.01329.0030.0000.0000.0000.0000.0000.000
92A88ARG10.8110.85126.1480.1730.1730.0000.0000.0000.000
93A89ASP-1-0.849-0.93224.537-0.173-0.1730.0000.0000.0000.000
94A90GLN0-0.016-0.00323.569-0.010-0.0100.0000.0000.0000.000
95A91ILE0-0.0090.00823.464-0.011-0.0110.0000.0000.0000.000
96A92VAL00.0090.00419.862-0.020-0.0200.0000.0000.0000.000
97A93ARG10.8360.88519.2420.1670.1670.0000.0000.0000.000
98A94LEU0-0.066-0.02018.823-0.017-0.0170.0000.0000.0000.000
99A95ILE00.0150.00416.401-0.012-0.0120.0000.0000.0000.000
100A96ALA00.0290.01414.893-0.044-0.0440.0000.0000.0000.000
101A97ASP-1-0.793-0.87813.918-0.278-0.2780.0000.0000.0000.000
102A98LEU0-0.044-0.01214.1770.0030.0030.0000.0000.0000.000
103A99ASP-1-0.762-0.8708.929-0.911-0.9110.0000.0000.0000.000
104A100ARG10.8240.8927.5080.5680.5680.0000.0000.0000.000
105A101PRO0-0.023-0.0212.380-0.869-0.1210.814-0.303-1.258-0.002
106A102GLY00.0230.0304.463-0.0400.148-0.001-0.032-0.1560.000
107A103ARG10.7550.8845.2850.9190.999-0.001-0.002-0.0760.000
108A104LEU00.0260.0138.864-0.087-0.0870.0000.0000.0000.000
109A105THR0-0.010-0.04911.9870.0800.0800.0000.0000.0000.000
110A106LEU0-0.0180.00614.6790.0020.0020.0000.0000.0000.000
111A107VAL00.0290.00218.2440.0150.0150.0000.0000.0000.000
112A108GLU-1-0.752-0.86020.832-0.134-0.1340.0000.0000.0000.000
113A109GLY00.0350.01824.3630.0050.0050.0000.0000.0000.000
114A110ALA0-0.022-0.01427.5230.0070.0070.0000.0000.0000.000
115A111GLY00.0350.00631.0640.0070.0070.0000.0000.0000.000
116A112GLY0-0.0040.00031.6880.0060.0060.0000.0000.0000.000
117A113LEU0-0.028-0.00727.166-0.004-0.0040.0000.0000.0000.000
118A114LEU00.018-0.00829.959-0.007-0.0070.0000.0000.0000.000
119A115VAL0-0.0380.00132.4180.0070.0070.0000.0000.0000.000
120A116GLU-1-0.840-0.91731.847-0.111-0.1110.0000.0000.0000.000
121A117LEU0-0.056-0.04627.4370.0020.0020.0000.0000.0000.000
122A118ALA00.0230.00429.575-0.001-0.0010.0000.0000.0000.000
123A119GLU-1-0.845-0.89231.560-0.092-0.0920.0000.0000.0000.000
124A120PRO0-0.080-0.03533.184-0.005-0.0050.0000.0000.0000.000
125A121GLY00.017-0.02634.887-0.003-0.0030.0000.0000.0000.000
126A122VAL0-0.031-0.00128.636-0.005-0.0050.0000.0000.0000.000
127A123THR0-0.019-0.03330.055-0.002-0.0020.0000.0000.0000.000
128A124LEU00.019-0.00824.376-0.008-0.0080.0000.0000.0000.000
129A125ARG10.8840.93825.2810.1310.1310.0000.0000.0000.000
130A126ASP-1-0.814-0.87025.620-0.171-0.1710.0000.0000.0000.000
131A127VAL00.0450.02122.284-0.014-0.0140.0000.0000.0000.000
132A128ALA0-0.033-0.02221.181-0.024-0.0240.0000.0000.0000.000
133A129VAL0-0.012-0.00720.650-0.029-0.0290.0000.0000.0000.000
134A130ASP-1-0.819-0.87221.274-0.234-0.2340.0000.0000.0000.000
135A131VAL0-0.054-0.02916.869-0.011-0.0110.0000.0000.0000.000
136A132ALA0-0.023-0.00816.388-0.057-0.0570.0000.0000.0000.000
137A133ALA0-0.0210.01316.718-0.044-0.0440.0000.0000.0000.000
138A134ALA00.0040.00716.8640.0380.0380.0000.0000.0000.000
139A135ALA0-0.003-0.01818.5050.0040.0040.0000.0000.0000.000
140A136LEU0-0.022-0.00120.2110.0100.0100.0000.0000.0000.000
141A137VAL0-0.011-0.01622.3430.0080.0080.0000.0000.0000.000
142A138VAL0-0.011-0.00126.1670.0070.0070.0000.0000.0000.000
143A139VAL0-0.018-0.01528.2400.0030.0030.0000.0000.0000.000
144A140THR00.028-0.01531.4380.0010.0010.0000.0000.0000.000
145A141ALA00.0400.02634.428-0.002-0.0020.0000.0000.0000.000
146A142ASP-1-0.817-0.87336.385-0.052-0.0520.0000.0000.0000.000
147A143LEU0-0.016-0.02839.407-0.003-0.0030.0000.0000.0000.000
148A144GLY00.0640.03240.5380.0000.0000.0000.0000.0000.000
149A145THR0-0.036-0.02334.569-0.006-0.0060.0000.0000.0000.000
150A146LEU00.0090.01235.174-0.006-0.0060.0000.0000.0000.000
151A147ASN0-0.039-0.01635.782-0.003-0.0030.0000.0000.0000.000
152A148HIS00.0840.05235.661-0.005-0.0050.0000.0000.0000.000
153A149THR00.009-0.00530.260-0.009-0.0090.0000.0000.0000.000
154A150LYS10.9420.97331.6270.0670.0670.0000.0000.0000.000
155A151LEU00.0460.02933.015-0.005-0.0050.0000.0000.0000.000
156A152THR0-0.015-0.02228.790-0.006-0.0060.0000.0000.0000.000
157A153LEU00.001-0.02027.278-0.010-0.0100.0000.0000.0000.000
158A154GLU-1-0.952-0.96129.075-0.104-0.1040.0000.0000.0000.000
159A155ALA00.0140.00731.206-0.005-0.0050.0000.0000.0000.000
160A156LEU0-0.020-0.02024.727-0.006-0.0060.0000.0000.0000.000
161A157ALA00.0080.00726.945-0.011-0.0110.0000.0000.0000.000
162A158ALA0-0.021-0.00628.022-0.004-0.0040.0000.0000.0000.000
163A159GLN0-0.053-0.02927.0180.0120.0120.0000.0000.0000.000
164A160GLN0-0.031-0.01823.714-0.019-0.0190.0000.0000.0000.000
165A161VAL00.0170.02521.970-0.022-0.0220.0000.0000.0000.000
166A162SER00.0090.00418.8450.0280.0280.0000.0000.0000.000
167A163CYS0-0.027-0.00220.664-0.008-0.0080.0000.0000.0000.000
168A164ALA00.0350.02117.9830.0000.0000.0000.0000.0000.000
169A165GLY0-0.003-0.01819.3760.0130.0130.0000.0000.0000.000
170A166LEU0-0.0160.00022.404-0.005-0.0050.0000.0000.0000.000
171A167VAL00.0190.00323.4960.0030.0030.0000.0000.0000.000
172A168ILE0-0.024-0.00526.4440.0010.0010.0000.0000.0000.000
173A169GLY00.0220.00829.5210.0020.0020.0000.0000.0000.000
174A170SER0-0.019-0.01230.4730.0040.0040.0000.0000.0000.000
175A171TRP00.016-0.00132.658-0.003-0.0030.0000.0000.0000.000
176A172PRO00.001-0.01434.6080.0030.0030.0000.0000.0000.000
177A173ASP-1-0.911-0.93437.560-0.023-0.0230.0000.0000.0000.000
178A174PRO00.0410.02139.4060.0010.0010.0000.0000.0000.000
179A175PRO0-0.044-0.01537.623-0.002-0.0020.0000.0000.0000.000
180A176GLY00.0540.02139.9740.0020.0020.0000.0000.0000.000
181A177LEU00.021-0.00941.460-0.003-0.0030.0000.0000.0000.000
182A178VAL0-0.0050.00141.336-0.001-0.0010.0000.0000.0000.000
183A179ALA00.0610.04037.948-0.003-0.0030.0000.0000.0000.000
184A180ALA00.0320.01237.090-0.003-0.0030.0000.0000.0000.000
185A181SER0-0.0140.00737.185-0.003-0.0030.0000.0000.0000.000
186A182ASN00.004-0.02636.657-0.003-0.0030.0000.0000.0000.000
187A183ARG10.9530.99329.4340.0470.0470.0000.0000.0000.000
188A184SER00.010-0.01032.644-0.003-0.0030.0000.0000.0000.000
189A185ALA0-0.075-0.01734.240-0.001-0.0010.0000.0000.0000.000
190A186LEU00.0230.00530.700-0.004-0.0040.0000.0000.0000.000
191A187ALA00.001-0.00229.069-0.007-0.0070.0000.0000.0000.000
192A188ARG10.8430.91029.7400.0530.0530.0000.0000.0000.000
193A189ILE0-0.066-0.02530.4680.0010.0010.0000.0000.0000.000
194A190ALA00.0180.00825.582-0.009-0.0090.0000.0000.0000.000
195A191MET00.0170.00921.7930.0110.0110.0000.0000.0000.000
196A192VAL0-0.011-0.00624.017-0.012-0.0120.0000.0000.0000.000
197A193ARG10.8590.94219.2820.1760.1760.0000.0000.0000.000
198A194ALA00.0550.03322.9060.0070.0070.0000.0000.0000.000
199A195ALA0-0.074-0.05025.262-0.003-0.0030.0000.0000.0000.000
200A196LEU00.0270.02925.7810.0070.0070.0000.0000.0000.000
201A197PRO00.0390.00929.6160.0000.0000.0000.0000.0000.000
202A198ALA0-0.008-0.00333.032-0.004-0.0040.0000.0000.0000.000
203A199GLY00.0410.02435.8020.0040.0040.0000.0000.0000.000
204A200ALA00.0090.00730.5590.0010.0010.0000.0000.0000.000
205A201ALA0-0.030-0.02731.5330.0000.0000.0000.0000.0000.000
206A202SER0-0.058-0.03332.5560.0010.0010.0000.0000.0000.000
207A203LEU0-0.035-0.00330.7650.0040.0040.0000.0000.0000.000
208A204ASP-1-0.819-0.90332.426-0.025-0.0250.0000.0000.0000.000
209A205ALA00.0390.01328.235-0.003-0.0030.0000.0000.0000.000
210A206GLY0-0.028-0.01227.812-0.001-0.0010.0000.0000.0000.000
211A207ASP-1-0.884-0.95428.522-0.014-0.0140.0000.0000.0000.000
212A208PHE00.0080.00225.009-0.004-0.0040.0000.0000.0000.000
213A209ALA00.0200.02924.269-0.008-0.0080.0000.0000.0000.000
214A210ALA00.0540.02524.589-0.001-0.0010.0000.0000.0000.000
215A211MET0-0.063-0.01426.484-0.001-0.0010.0000.0000.0000.000
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217A213ALA0-0.059-0.02421.681-0.009-0.0090.0000.0000.0000.000
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