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: 43YGN

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 OptHSide
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 -2378674.80175
FMO2-HF: Nuclear repulsion 2297790.361537
FMO2-HF: Total energy -80884.440213
FMO2-MP2: Total energy -81119.062804


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.
-6.876-1.3263.667-2.6-6.6150.015
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 : 0.023 / q_NPA : 0.006
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-1SER0-0.023-0.0192.491-5.098-0.2483.027-3.001-4.8750.013
4A0HIS10.8100.8713.5070.223-0.0720.0560.723-0.4840.002
5A1MET00.0110.0686.645-0.313-0.3130.0000.0000.0000.000
6A2THR00.003-0.0069.065-0.053-0.0530.0000.0000.0000.000
7A3ILE0-0.007-0.00411.3560.0780.0780.0000.0000.0000.000
8A4LEU0-0.026-0.01214.9220.0110.0110.0000.0000.0000.000
9A5VAL00.0310.03417.7940.0180.0180.0000.0000.0000.000
10A6VAL0-0.002-0.00721.3580.0040.0040.0000.0000.0000.000
11A7THR00.001-0.01123.6130.0120.0120.0000.0000.0000.000
12A8GLY00.0310.00627.0890.0020.0020.0000.0000.0000.000
13A9THR0-0.027-0.02430.209-0.001-0.0010.0000.0000.0000.000
14A10GLY00.0300.01332.8050.0030.0030.0000.0000.0000.000
15A11THR0-0.005-0.01034.361-0.004-0.0040.0000.0000.0000.000
16A12GLY0-0.0100.00535.3430.0020.0020.0000.0000.0000.000
17A13VAL0-0.0070.00531.1710.0030.0030.0000.0000.0000.000
18A14GLY00.0190.00931.5740.0010.0010.0000.0000.0000.000
19A15LYS10.7930.87027.8930.0970.0970.0000.0000.0000.000
20A16THR00.0390.02126.729-0.005-0.0050.0000.0000.0000.000
21A17VAL00.0330.01426.699-0.003-0.0030.0000.0000.0000.000
22A18VAL00.0040.00523.9210.0010.0010.0000.0000.0000.000
23A19CYS0-0.054-0.02522.461-0.010-0.0100.0000.0000.0000.000
24A20ALA00.0390.02821.926-0.007-0.0070.0000.0000.0000.000
25A21ALA00.0390.01922.8690.0030.0030.0000.0000.0000.000
26A22LEU0-0.016-0.01617.2010.0060.0060.0000.0000.0000.000
27A23ALA00.0060.00318.286-0.003-0.0030.0000.0000.0000.000
28A24SER00.0340.01018.3360.0060.0060.0000.0000.0000.000
29A25ALA0-0.018-0.00219.0590.0170.0170.0000.0000.0000.000
30A26ALA00.023-0.00714.2610.0230.0230.0000.0000.0000.000
31A27ARG10.9020.96014.4740.0670.0670.0000.0000.0000.000
32A28GLN0-0.102-0.05316.2170.0370.0370.0000.0000.0000.000
33A29ALA0-0.071-0.02713.5030.0310.0310.0000.0000.0000.000
34A30GLY0-0.0110.00312.5030.0500.0500.0000.0000.0000.000
35A31ILE0-0.040-0.0079.959-0.015-0.0150.0000.0000.0000.000
36A32ASP-1-0.797-0.88110.430-0.193-0.1930.0000.0000.0000.000
37A33VAL0-0.028-0.01211.897-0.072-0.0720.0000.0000.0000.000
38A34ALA0-0.016-0.00214.6320.0320.0320.0000.0000.0000.000
39A35VAL0-0.022-0.00916.336-0.013-0.0130.0000.0000.0000.000
40A36CYS0-0.024-0.00219.5060.0110.0110.0000.0000.0000.000
41A37LYS10.8120.92421.4100.0900.0900.0000.0000.0000.000
42A38PRO00.0090.00223.5550.0090.0090.0000.0000.0000.000
43A39VAL00.0250.01525.9530.0070.0070.0000.0000.0000.000
44A40GLN0-0.015-0.00429.692-0.006-0.0060.0000.0000.0000.000
45A41THR0-0.026-0.00831.6400.0030.0030.0000.0000.0000.000
46A42GLY00.0530.01935.3130.0000.0000.0000.0000.0000.000
47A43THR0-0.013-0.01034.2160.0030.0030.0000.0000.0000.000
48A44ALA0-0.047-0.01737.0710.0020.0020.0000.0000.0000.000
49A45ARG10.7840.88338.3160.0490.0490.0000.0000.0000.000
50A46GLY0-0.006-0.00238.1020.0020.0020.0000.0000.0000.000
51A47ASP-1-0.851-0.90234.835-0.050-0.0500.0000.0000.0000.000
52A48ASP-1-0.794-0.90029.974-0.065-0.0650.0000.0000.0000.000
53A49ASP-1-0.809-0.89828.161-0.073-0.0730.0000.0000.0000.000
54A50LEU00.0390.01124.0220.0000.0000.0000.0000.0000.000
55A51ALA0-0.0060.00126.3680.0020.0020.0000.0000.0000.000
56A52GLU-1-0.862-0.92528.796-0.039-0.0390.0000.0000.0000.000
57A53VAL00.005-0.01122.7600.0030.0030.0000.0000.0000.000
58A54GLY0-0.0130.00424.4250.0020.0020.0000.0000.0000.000
59A55ARG10.8180.90025.4610.0480.0480.0000.0000.0000.000
60A56LEU0-0.0310.00927.1280.0050.0050.0000.0000.0000.000
61A57ALA0-0.011-0.01122.2780.0050.0050.0000.0000.0000.000
62A58GLY00.0150.01122.6820.0050.0050.0000.0000.0000.000
63A59VAL0-0.079-0.03918.9640.0010.0010.0000.0000.0000.000
64A60THR00.0300.01218.7220.0040.0040.0000.0000.0000.000
65A61GLN0-0.045-0.03614.1920.0000.0000.0000.0000.0000.000
66A62LEU00.0010.00518.944-0.017-0.0170.0000.0000.0000.000
67A63ALA00.0230.01219.8790.0080.0080.0000.0000.0000.000
68A64GLY00.0380.01121.978-0.004-0.0040.0000.0000.0000.000
69A65LEU0-0.027-0.02424.980-0.002-0.0020.0000.0000.0000.000
70A66ALA00.0090.02527.1560.0070.0070.0000.0000.0000.000
71A67ARG10.8270.88630.0880.0620.0620.0000.0000.0000.000
72A68TYR00.032-0.01333.1980.0010.0010.0000.0000.0000.000
73A69PRO00.0220.00836.7090.0000.0000.0000.0000.0000.000
74A70GLN00.0900.03539.5830.0010.0010.0000.0000.0000.000
75A71PRO0-0.0010.00039.083-0.003-0.0030.0000.0000.0000.000
76A72MET0-0.056-0.01439.5950.0020.0020.0000.0000.0000.000
77A73ALA00.0340.00937.533-0.003-0.0030.0000.0000.0000.000
78A74PRO00.0270.00633.5430.0030.0030.0000.0000.0000.000
79A75ALA00.0740.04836.1540.0020.0020.0000.0000.0000.000
80A76ALA00.0420.02338.4010.0020.0020.0000.0000.0000.000
81A77ALA0-0.057-0.03538.0000.0030.0030.0000.0000.0000.000
82A78ALA00.003-0.00636.9730.0020.0020.0000.0000.0000.000
83A79GLU-1-0.915-0.94638.950-0.047-0.0470.0000.0000.0000.000
84A80HIS0-0.041-0.02942.3730.0020.0020.0000.0000.0000.000
85A81ALA0-0.062-0.03340.3770.0020.0020.0000.0000.0000.000
86A82GLY0-0.0040.00942.4420.0010.0010.0000.0000.0000.000
87A83MET0-0.115-0.05335.9680.0000.0000.0000.0000.0000.000
88A84ALA00.0600.03836.0650.0000.0000.0000.0000.0000.000
89A85LEU0-0.0010.01733.471-0.001-0.0010.0000.0000.0000.000
90A86PRO0-0.050-0.01128.8060.0000.0000.0000.0000.0000.000
91A87ALA00.0480.01229.2130.0000.0000.0000.0000.0000.000
92A88ARG10.8310.85325.9540.1410.1410.0000.0000.0000.000
93A89ASP-1-0.869-0.93924.544-0.134-0.1340.0000.0000.0000.000
94A90GLN0-0.0030.00423.578-0.007-0.0070.0000.0000.0000.000
95A91ILE0-0.0070.00723.343-0.006-0.0060.0000.0000.0000.000
96A92VAL00.0240.01019.686-0.013-0.0130.0000.0000.0000.000
97A93ARG10.8600.91919.1530.1100.1100.0000.0000.0000.000
98A94LEU0-0.047-0.01218.921-0.008-0.0080.0000.0000.0000.000
99A95ILE00.001-0.00816.396-0.009-0.0090.0000.0000.0000.000
100A96ALA00.0290.01314.801-0.029-0.0290.0000.0000.0000.000
101A97ASP-1-0.824-0.89813.888-0.183-0.1830.0000.0000.0000.000
102A98LEU0-0.058-0.02514.1660.0070.0070.0000.0000.0000.000
103A99ASP-1-0.784-0.8828.944-0.589-0.5890.0000.0000.0000.000
104A100ARG10.8440.9057.5910.3760.3760.0000.0000.0000.000
105A101PRO00.001-0.0042.438-0.898-0.1780.586-0.301-1.0050.000
106A102GLY00.0260.0284.604-0.1250.006-0.001-0.016-0.1130.000
107A103ARG10.7580.8835.6990.6670.6670.0000.0000.0000.000
108A104LEU00.0080.0019.212-0.063-0.0630.0000.0000.0000.000
109A105THR00.000-0.04112.2720.0670.0670.0000.0000.0000.000
110A106LEU0-0.028-0.00214.956-0.004-0.0040.0000.0000.0000.000
111A107VAL00.021-0.00618.5030.0170.0170.0000.0000.0000.000
112A108GLU-1-0.762-0.86521.074-0.094-0.0940.0000.0000.0000.000
113A109GLY00.0290.01124.5280.0030.0030.0000.0000.0000.000
114A110ALA00.007-0.00427.4260.0060.0060.0000.0000.0000.000
115A111GLY00.0170.00131.0020.0030.0030.0000.0000.0000.000
116A112GLY00.0260.01931.6650.0050.0050.0000.0000.0000.000
117A113LEU0-0.043-0.02127.386-0.002-0.0020.0000.0000.0000.000
118A114LEU00.011-0.01730.514-0.005-0.0050.0000.0000.0000.000
119A115VAL0-0.0310.01032.8220.0050.0050.0000.0000.0000.000
120A116GLU-1-0.844-0.91632.508-0.084-0.0840.0000.0000.0000.000
121A117LEU0-0.076-0.05527.9310.0020.0020.0000.0000.0000.000
122A118ALA00.0230.00029.8470.0000.0000.0000.0000.0000.000
123A119GLU-1-0.899-0.91431.820-0.070-0.0700.0000.0000.0000.000
124A120PRO0-0.070-0.04133.308-0.003-0.0030.0000.0000.0000.000
125A121GLY00.018-0.02334.985-0.003-0.0030.0000.0000.0000.000
126A122VAL0-0.0280.00028.702-0.006-0.0060.0000.0000.0000.000
127A123THR0-0.015-0.01930.2390.0010.0010.0000.0000.0000.000
128A124LEU00.039-0.00724.455-0.007-0.0070.0000.0000.0000.000
129A125ARG10.9060.94825.4280.1080.1080.0000.0000.0000.000
130A126ASP-1-0.805-0.87625.826-0.139-0.1390.0000.0000.0000.000
131A127VAL00.0350.02122.111-0.010-0.0100.0000.0000.0000.000
132A128ALA0-0.027-0.02021.390-0.018-0.0180.0000.0000.0000.000
133A129VAL0-0.011-0.00220.966-0.024-0.0240.0000.0000.0000.000
134A130ASP-1-0.823-0.87121.306-0.188-0.1880.0000.0000.0000.000
135A131VAL0-0.065-0.04116.971-0.011-0.0110.0000.0000.0000.000
136A132ALA0-0.0180.00216.192-0.043-0.0430.0000.0000.0000.000
137A133ALA0-0.0290.00516.417-0.042-0.0420.0000.0000.0000.000
138A134ALA00.0010.00417.1560.0220.0220.0000.0000.0000.000
139A135ALA0-0.006-0.01818.7770.0070.0070.0000.0000.0000.000
140A136LEU0-0.0200.00020.2350.0070.0070.0000.0000.0000.000
141A137VAL0-0.007-0.01222.3170.0080.0080.0000.0000.0000.000
142A138VAL0-0.007-0.00126.1180.0060.0060.0000.0000.0000.000
143A139VAL00.007-0.00528.2930.0020.0020.0000.0000.0000.000
144A140THR00.0390.02531.4970.0020.0020.0000.0000.0000.000
145A141ALA00.0370.02234.540-0.002-0.0020.0000.0000.0000.000
146A142ASP-1-0.846-0.92136.272-0.037-0.0370.0000.0000.0000.000
147A143LEU00.011-0.01439.247-0.003-0.0030.0000.0000.0000.000
148A144GLY00.0320.02140.7930.0000.0000.0000.0000.0000.000
149A145THR0-0.034-0.02634.759-0.005-0.0050.0000.0000.0000.000
150A146LEU0-0.0140.00035.525-0.005-0.0050.0000.0000.0000.000
151A147ASN0-0.016-0.00736.134-0.004-0.0040.0000.0000.0000.000
152A148HIS00.0930.04235.751-0.005-0.0050.0000.0000.0000.000
153A149THR00.0180.00430.553-0.007-0.0070.0000.0000.0000.000
154A150LYS10.9470.96431.9660.0570.0570.0000.0000.0000.000
155A151LEU00.0320.03133.618-0.004-0.0040.0000.0000.0000.000
156A152THR0-0.026-0.02229.041-0.005-0.0050.0000.0000.0000.000
157A153LEU0-0.014-0.03127.702-0.008-0.0080.0000.0000.0000.000
158A154GLU-1-0.945-0.95729.312-0.092-0.0920.0000.0000.0000.000
159A155ALA00.0160.01031.319-0.005-0.0050.0000.0000.0000.000
160A156LEU0-0.021-0.01924.934-0.005-0.0050.0000.0000.0000.000
161A157ALA00.0230.01626.879-0.010-0.0100.0000.0000.0000.000
162A158ALA0-0.023-0.00127.929-0.004-0.0040.0000.0000.0000.000
163A159GLN0-0.059-0.02827.5930.0090.0090.0000.0000.0000.000
164A160GLN0-0.041-0.02223.832-0.018-0.0180.0000.0000.0000.000
165A161VAL00.0130.02721.965-0.020-0.0200.0000.0000.0000.000
166A162SER00.005-0.00119.0510.0250.0250.0000.0000.0000.000
167A163CYS0-0.0140.00721.3900.0020.0020.0000.0000.0000.000
168A164ALA00.0320.01418.329-0.004-0.0040.0000.0000.0000.000
169A165GLY0-0.007-0.01919.8070.0100.0100.0000.0000.0000.000
170A166LEU0-0.016-0.01622.795-0.003-0.0030.0000.0000.0000.000
171A167VAL00.0220.00823.5380.0030.0030.0000.0000.0000.000
172A168ILE0-0.030-0.01326.4090.0010.0010.0000.0000.0000.000
173A169GLY00.0300.01529.5610.0030.0030.0000.0000.0000.000
174A170SER0-0.021-0.01230.5470.0040.0040.0000.0000.0000.000
175A171TRP00.008-0.00732.664-0.003-0.0030.0000.0000.0000.000
176A172PRO0-0.014-0.02034.5790.0030.0030.0000.0000.0000.000
177A173ASP-1-0.939-0.91837.768-0.009-0.0090.0000.0000.0000.000
178A174PRO00.031-0.00139.4720.0010.0010.0000.0000.0000.000
179A175PRO0-0.014-0.01337.918-0.002-0.0020.0000.0000.0000.000
180A176GLY00.0500.01540.0980.0020.0020.0000.0000.0000.000
181A177LEU00.0410.00041.767-0.001-0.0010.0000.0000.0000.000
182A178VAL00.0030.00241.676-0.001-0.0010.0000.0000.0000.000
183A179ALA00.0500.03038.235-0.002-0.0020.0000.0000.0000.000
184A180ALA00.0390.01737.490-0.003-0.0030.0000.0000.0000.000
185A181SER0-0.009-0.00537.582-0.002-0.0020.0000.0000.0000.000
186A182ASN0-0.012-0.03537.012-0.003-0.0030.0000.0000.0000.000
187A183ARG10.9591.00029.5400.0290.0290.0000.0000.0000.000
188A184SER00.0040.00232.977-0.003-0.0030.0000.0000.0000.000
189A185ALA0-0.067-0.03334.069-0.002-0.0020.0000.0000.0000.000
190A186LEU00.013-0.00231.181-0.004-0.0040.0000.0000.0000.000
191A187ALA0-0.0100.00129.367-0.006-0.0060.0000.0000.0000.000
192A188ARG10.8370.92329.6280.0420.0420.0000.0000.0000.000
193A189ILE0-0.051-0.01830.623-0.002-0.0020.0000.0000.0000.000
194A190ALA00.0200.01025.986-0.010-0.0100.0000.0000.0000.000
195A191MET00.0100.01922.0500.0100.0100.0000.0000.0000.000
196A192VAL00.002-0.00224.661-0.008-0.0080.0000.0000.0000.000
197A193ARG10.8470.92919.7060.1390.1390.0000.0000.0000.000
198A194ALA00.0570.03423.1050.0080.0080.0000.0000.0000.000
199A195ALA0-0.073-0.04125.520-0.005-0.0050.0000.0000.0000.000
200A196LEU00.0130.01725.6910.0060.0060.0000.0000.0000.000
201A197PRO00.0520.02129.633-0.001-0.0010.0000.0000.0000.000
202A198ALA00.0260.01232.942-0.002-0.0020.0000.0000.0000.000
203A199GLY00.0230.00535.6940.0030.0030.0000.0000.0000.000
204A200ALA00.001-0.00330.3350.0020.0020.0000.0000.0000.000
205A201ALA0-0.016-0.02031.8910.0010.0010.0000.0000.0000.000
206A202SER0-0.030-0.00932.9160.0000.0000.0000.0000.0000.000
207A203LEU0-0.069-0.01530.9240.0030.0030.0000.0000.0000.000
208A204ASP-1-0.819-0.90732.941-0.001-0.0010.0000.0000.0000.000
209A205ALA00.0300.01828.553-0.002-0.0020.0000.0000.0000.000
210A206GLY0-0.026-0.01428.1860.0010.0010.0000.0000.0000.000
211A207ASP-1-0.872-0.95128.8670.0090.0090.0000.0000.0000.000
212A208PHE00.000-0.00425.192-0.002-0.0020.0000.0000.0000.000
213A209ALA00.0180.02524.644-0.005-0.0050.0000.0000.0000.000
214A210ALA00.0450.02724.5530.0020.0020.0000.0000.0000.000
215A211MET0-0.050-0.00926.369-0.001-0.0010.0000.0000.0000.000
216A212SER0-0.028-0.04822.735-0.007-0.0070.0000.0000.0000.000
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218A214ALA0-0.015-0.00222.3970.0040.0040.0000.0000.0000.000
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