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: K3VQ3

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 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 230
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2378208.489538
FMO2-HF: Nuclear repulsion 2297324.840174
FMO2-HF: Total energy -80883.649364
FMO2-MP2: Total energy -81118.26434


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.
-5.057-0.524.344-2.284-6.5980.015
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 : -0.014 / q_NPA : -0.028
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-1SER0-0.015-0.0162.461-3.8080.0323.143-2.346-4.6370.011
4A0HIS10.7920.8733.738-0.496-0.6140.0430.547-0.4730.002
5A1MET00.0180.0866.713-0.177-0.1770.0000.0000.0000.000
6A2THR00.007-0.0069.1760.0490.0490.0000.0000.0000.000
7A3ILE0-0.0010.00111.333-0.018-0.0180.0000.0000.0000.000
8A4LEU0-0.025-0.01615.0260.0320.0320.0000.0000.0000.000
9A5VAL00.0300.03517.773-0.014-0.0140.0000.0000.0000.000
10A6VAL0-0.004-0.00921.3460.0120.0120.0000.0000.0000.000
11A7THR0-0.002-0.01423.593-0.008-0.0080.0000.0000.0000.000
12A8GLY00.0280.00227.0700.0050.0050.0000.0000.0000.000
13A9THR0-0.041-0.02830.192-0.002-0.0020.0000.0000.0000.000
14A10GLY00.0270.01132.788-0.001-0.0010.0000.0000.0000.000
15A11THR0-0.007-0.01134.343-0.001-0.0010.0000.0000.0000.000
16A12GLY0-0.0090.00435.3270.0010.0010.0000.0000.0000.000
17A13VAL0-0.0070.00531.2170.0010.0010.0000.0000.0000.000
18A14GLY00.0220.00931.5590.0030.0030.0000.0000.0000.000
19A15LYS10.9100.94827.591-0.003-0.0030.0000.0000.0000.000
20A16THR00.0610.04226.7120.0020.0020.0000.0000.0000.000
21A17VAL00.0460.02126.641-0.001-0.0010.0000.0000.0000.000
22A18VAL0-0.008-0.00523.8780.0030.0030.0000.0000.0000.000
23A19CYS0-0.028-0.00122.4420.0040.0040.0000.0000.0000.000
24A20ALA00.0380.02621.866-0.003-0.0030.0000.0000.0000.000
25A21ALA00.0390.01622.835-0.001-0.0010.0000.0000.0000.000
26A22LEU0-0.023-0.02017.3280.0060.0060.0000.0000.0000.000
27A23ALA00.0050.00418.1910.0030.0030.0000.0000.0000.000
28A24SER00.0430.01318.208-0.006-0.0060.0000.0000.0000.000
29A25ALA0-0.024-0.01118.9550.0020.0020.0000.0000.0000.000
30A26ALA00.011-0.01014.2160.0150.0150.0000.0000.0000.000
31A27ARG10.9530.97814.4660.0430.0430.0000.0000.0000.000
32A28GLN0-0.121-0.06816.1930.0000.0000.0000.0000.0000.000
33A29ALA0-0.068-0.02513.5070.0130.0130.0000.0000.0000.000
34A30GLY0-0.0120.00012.4550.0300.0300.0000.0000.0000.000
35A31ILE0-0.033-0.0049.806-0.062-0.0620.0000.0000.0000.000
36A32ASP-1-0.796-0.89010.249-0.221-0.2210.0000.0000.0000.000
37A33VAL0-0.021-0.01011.802-0.012-0.0120.0000.0000.0000.000
38A34ALA0-0.021-0.00614.542-0.001-0.0010.0000.0000.0000.000
39A35VAL0-0.012-0.00316.3010.0140.0140.0000.0000.0000.000
40A36CYS0-0.020-0.00119.437-0.003-0.0030.0000.0000.0000.000
41A37LYS10.8000.89621.2510.0190.0190.0000.0000.0000.000
42A38PRO00.0010.00123.657-0.001-0.0010.0000.0000.0000.000
43A39VAL00.0280.01325.8510.0000.0000.0000.0000.0000.000
44A40GLN00.0230.01029.5830.0010.0010.0000.0000.0000.000
45A41THR0-0.035-0.00931.489-0.001-0.0010.0000.0000.0000.000
46A42GLY00.0670.03435.2250.0000.0000.0000.0000.0000.000
47A43THR0-0.012-0.00134.0160.0000.0000.0000.0000.0000.000
48A44ALA0-0.047-0.02136.8760.0000.0000.0000.0000.0000.000
49A45ARG10.7790.88138.1670.0030.0030.0000.0000.0000.000
50A46GLY0-0.015-0.00638.0120.0010.0010.0000.0000.0000.000
51A47ASP-1-0.844-0.89934.802-0.005-0.0050.0000.0000.0000.000
52A48ASP-1-0.847-0.95629.887-0.027-0.0270.0000.0000.0000.000
53A49ASP-1-0.800-0.89728.288-0.007-0.0070.0000.0000.0000.000
54A50LEU0-0.015-0.00923.8490.0000.0000.0000.0000.0000.000
55A51ALA0-0.0080.00026.304-0.002-0.0020.0000.0000.0000.000
56A52GLU-1-0.969-0.98628.707-0.001-0.0010.0000.0000.0000.000
57A53VAL00.023-0.00322.6530.0020.0020.0000.0000.0000.000
58A54GLY0-0.0160.00224.3140.0000.0000.0000.0000.0000.000
59A55ARG10.8970.94425.3530.0120.0120.0000.0000.0000.000
60A56LEU0-0.0410.00427.1080.0010.0010.0000.0000.0000.000
61A57ALA0-0.021-0.01522.1040.0030.0030.0000.0000.0000.000
62A58GLY0-0.0090.00722.518-0.002-0.0020.0000.0000.0000.000
63A59VAL0-0.080-0.04418.873-0.009-0.0090.0000.0000.0000.000
64A60THR00.0000.00218.7230.0020.0020.0000.0000.0000.000
65A61GLN0-0.049-0.03214.950-0.007-0.0070.0000.0000.0000.000
66A62LEU00.0030.00418.6850.0010.0010.0000.0000.0000.000
67A63ALA00.0220.01219.7090.0000.0000.0000.0000.0000.000
68A64GLY00.0380.01121.7880.0060.0060.0000.0000.0000.000
69A65LEU0-0.039-0.02424.838-0.004-0.0040.0000.0000.0000.000
70A66ALA00.0000.01927.0370.0010.0010.0000.0000.0000.000
71A67ARG10.9050.93430.2110.0260.0260.0000.0000.0000.000
72A68TYR00.003-0.02133.0760.0000.0000.0000.0000.0000.000
73A69PRO00.0120.00036.5740.0010.0010.0000.0000.0000.000
74A70GLN00.1040.03739.4220.0000.0000.0000.0000.0000.000
75A71PRO0-0.0010.00439.0400.0000.0000.0000.0000.0000.000
76A72MET0-0.050-0.00939.4800.0020.0020.0000.0000.0000.000
77A73ALA00.0320.00137.513-0.001-0.0010.0000.0000.0000.000
78A74PRO00.0170.00333.497-0.001-0.0010.0000.0000.0000.000
79A75ALA00.0880.05536.075-0.001-0.0010.0000.0000.0000.000
80A76ALA00.0370.02338.3550.0000.0000.0000.0000.0000.000
81A77ALA0-0.055-0.03437.8860.0000.0000.0000.0000.0000.000
82A78ALA00.002-0.00636.945-0.001-0.0010.0000.0000.0000.000
83A79GLU-1-0.921-0.94638.874-0.008-0.0080.0000.0000.0000.000
84A80HIS0-0.041-0.02842.3130.0000.0000.0000.0000.0000.000
85A81ALA0-0.063-0.03540.2570.0000.0000.0000.0000.0000.000
86A82GLY0-0.0020.00942.348-0.001-0.0010.0000.0000.0000.000
87A83MET0-0.107-0.04935.721-0.001-0.0010.0000.0000.0000.000
88A84ALA00.0630.03936.0210.0010.0010.0000.0000.0000.000
89A85LEU00.0130.02133.426-0.001-0.0010.0000.0000.0000.000
90A86PRO0-0.040-0.00628.780-0.001-0.0010.0000.0000.0000.000
91A87ALA00.0480.01629.2640.0020.0020.0000.0000.0000.000
92A88ARG10.9020.91726.1490.0140.0140.0000.0000.0000.000
93A89ASP-1-0.875-0.94224.617-0.039-0.0390.0000.0000.0000.000
94A90GLN0-0.021-0.00723.622-0.004-0.0040.0000.0000.0000.000
95A91ILE00.0000.01123.250-0.005-0.0050.0000.0000.0000.000
96A92VAL00.0220.01019.694-0.005-0.0050.0000.0000.0000.000
97A93ARG10.9400.96919.1780.0590.0590.0000.0000.0000.000
98A94LEU0-0.032-0.00718.901-0.010-0.0100.0000.0000.0000.000
99A95ILE0-0.006-0.00816.274-0.010-0.0100.0000.0000.0000.000
100A96ALA00.0230.00514.809-0.020-0.0200.0000.0000.0000.000
101A97ASP-1-0.889-0.93513.883-0.124-0.1240.0000.0000.0000.000
102A98LEU0-0.093-0.05014.039-0.018-0.0180.0000.0000.0000.000
103A99ASP-1-0.763-0.8809.011-0.310-0.3100.0000.0000.0000.000
104A100ARG10.8570.9217.4550.2940.2940.0000.0000.0000.000
105A101PRO0-0.003-0.0062.275-0.756-0.2381.160-0.458-1.2200.002
106A102GLY00.0280.0264.414-0.348-0.189-0.001-0.022-0.1350.000
107A103ARG10.7780.8935.6610.5310.5310.0000.0000.0000.000
108A104LEU00.0080.0029.1800.0530.0530.0000.0000.0000.000
109A105THR0-0.017-0.06112.255-0.007-0.0070.0000.0000.0000.000
110A106LEU0-0.036-0.00414.9840.0260.0260.0000.0000.0000.000
111A107VAL00.023-0.00418.524-0.008-0.0080.0000.0000.0000.000
112A108GLU-1-0.820-0.90621.1350.0050.0050.0000.0000.0000.000
113A109GLY00.0120.00124.568-0.004-0.0040.0000.0000.0000.000
114A110ALA0-0.009-0.01227.4940.0000.0000.0000.0000.0000.000
115A111GLY00.003-0.01231.0660.0000.0000.0000.0000.0000.000
116A112GLY00.0340.02431.6990.0010.0010.0000.0000.0000.000
117A113LEU0-0.036-0.01727.230-0.002-0.0020.0000.0000.0000.000
118A114LEU00.007-0.01930.494-0.002-0.0020.0000.0000.0000.000
119A115VAL0-0.0320.01132.847-0.001-0.0010.0000.0000.0000.000
120A116GLU-1-0.841-0.92632.486-0.008-0.0080.0000.0000.0000.000
121A117LEU0-0.087-0.05927.667-0.001-0.0010.0000.0000.0000.000
122A118ALA00.0230.00229.865-0.003-0.0030.0000.0000.0000.000
123A119GLU-1-0.918-0.91931.828-0.011-0.0110.0000.0000.0000.000
124A120PRO0-0.084-0.04333.366-0.002-0.0020.0000.0000.0000.000
125A121GLY00.011-0.02135.0590.0010.0010.0000.0000.0000.000
126A122VAL0-0.0130.00828.6990.0020.0020.0000.0000.0000.000
127A123THR0-0.018-0.01030.2550.0010.0010.0000.0000.0000.000
128A124LEU00.037-0.01124.429-0.002-0.0020.0000.0000.0000.000
129A125ARG10.8970.93425.497-0.014-0.0140.0000.0000.0000.000
130A126ASP-1-0.814-0.90225.8120.0000.0000.0000.0000.0000.000
131A127VAL00.0100.01022.078-0.002-0.0020.0000.0000.0000.000
132A128ALA0-0.023-0.01921.464-0.005-0.0050.0000.0000.0000.000
133A129VAL0-0.014-0.00321.0030.0020.0020.0000.0000.0000.000
134A130ASP-1-0.834-0.89821.445-0.022-0.0220.0000.0000.0000.000
135A131VAL0-0.068-0.04217.055-0.007-0.0070.0000.0000.0000.000
136A132ALA0-0.0180.00316.244-0.005-0.0050.0000.0000.0000.000
137A133ALA0-0.0310.00116.3960.0090.0090.0000.0000.0000.000
138A134ALA0-0.0020.00417.1640.0100.0100.0000.0000.0000.000
139A135ALA0-0.006-0.01818.760-0.014-0.0140.0000.0000.0000.000
140A136LEU0-0.0210.00020.2360.0120.0120.0000.0000.0000.000
141A137VAL00.000-0.00922.301-0.010-0.0100.0000.0000.0000.000
142A138VAL0-0.0080.00426.1030.0050.0050.0000.0000.0000.000
143A139VAL00.000-0.00728.278-0.004-0.0040.0000.0000.0000.000
144A140THR00.0690.03831.4840.0010.0010.0000.0000.0000.000
145A141ALA00.0390.01534.5290.0030.0030.0000.0000.0000.000
146A142ASP-1-0.851-0.91536.2620.0240.0240.0000.0000.0000.000
147A143LEU00.000-0.02339.2360.0020.0020.0000.0000.0000.000
148A144GLY00.0230.01840.780-0.001-0.0010.0000.0000.0000.000
149A145THR0-0.042-0.02234.5890.0000.0000.0000.0000.0000.000
150A146LEU0-0.005-0.00935.3860.0010.0010.0000.0000.0000.000
151A147ASN00.0090.00136.1230.0020.0020.0000.0000.0000.000
152A148HIS00.0750.03935.5530.0010.0010.0000.0000.0000.000
153A149THR00.0160.00030.5280.0000.0000.0000.0000.0000.000
154A150LYS10.9460.96431.953-0.038-0.0380.0000.0000.0000.000
155A151LEU00.0290.03033.6050.0000.0000.0000.0000.0000.000
156A152THR0-0.018-0.01128.964-0.002-0.0020.0000.0000.0000.000
157A153LEU0-0.012-0.02927.6250.0000.0000.0000.0000.0000.000
158A154GLU-1-0.942-0.95629.2980.0310.0310.0000.0000.0000.000
159A155ALA00.0120.00731.353-0.001-0.0010.0000.0000.0000.000
160A156LEU0-0.024-0.01124.924-0.003-0.0030.0000.0000.0000.000
161A157ALA00.0240.01727.0540.0000.0000.0000.0000.0000.000
162A158ALA0-0.025-0.00228.091-0.001-0.0010.0000.0000.0000.000
163A159GLN0-0.049-0.02127.631-0.002-0.0020.0000.0000.0000.000
164A160GLN0-0.040-0.02224.1460.0070.0070.0000.0000.0000.000
165A161VAL00.0120.02621.8290.0030.0030.0000.0000.0000.000
166A162SER00.001-0.00319.1430.0010.0010.0000.0000.0000.000
167A163CYS0-0.0080.00321.375-0.007-0.0070.0000.0000.0000.000
168A164ALA00.0310.01618.2930.0140.0140.0000.0000.0000.000
169A165GLY00.003-0.00919.7950.0180.0180.0000.0000.0000.000
170A166LEU0-0.016-0.01522.786-0.010-0.0100.0000.0000.0000.000
171A167VAL00.0310.01423.5030.0080.0080.0000.0000.0000.000
172A168ILE0-0.031-0.01226.398-0.006-0.0060.0000.0000.0000.000
173A169GLY00.0260.01229.5490.0010.0010.0000.0000.0000.000
174A170SER0-0.021-0.01130.535-0.002-0.0020.0000.0000.0000.000
175A171TRP0-0.010-0.01632.7030.0020.0020.0000.0000.0000.000
176A172PRO0-0.016-0.01434.571-0.001-0.0010.0000.0000.0000.000
177A173ASP-1-0.936-0.91937.8150.0350.0350.0000.0000.0000.000
178A174PRO00.032-0.00339.467-0.002-0.0020.0000.0000.0000.000
179A175PRO0-0.008-0.00737.879-0.001-0.0010.0000.0000.0000.000
180A176GLY00.0530.01440.093-0.001-0.0010.0000.0000.0000.000
181A177LEU00.033-0.00241.7630.0020.0020.0000.0000.0000.000
182A178VAL00.0000.00141.6500.0020.0020.0000.0000.0000.000
183A179ALA00.0550.03238.1610.0020.0020.0000.0000.0000.000
184A180ALA00.0340.01437.4840.0030.0030.0000.0000.0000.000
185A181SER0-0.027-0.01437.5780.0040.0040.0000.0000.0000.000
186A182ASN0-0.013-0.03837.0130.0030.0030.0000.0000.0000.000
187A183ARG10.9741.00429.235-0.058-0.0580.0000.0000.0000.000
188A184SER0-0.022-0.00732.9720.0050.0050.0000.0000.0000.000
189A185ALA0-0.072-0.04034.0660.0030.0030.0000.0000.0000.000
190A186LEU00.003-0.00931.1560.0020.0020.0000.0000.0000.000
191A187ALA00.0060.00729.3680.0040.0040.0000.0000.0000.000
192A188ARG10.8980.95929.715-0.046-0.0460.0000.0000.0000.000
193A189ILE0-0.065-0.02630.3780.0000.0000.0000.0000.0000.000
194A190ALA00.0120.00525.9830.0010.0010.0000.0000.0000.000
195A191MET00.0160.02322.132-0.003-0.0030.0000.0000.0000.000
196A192VAL00.0070.00224.654-0.004-0.0040.0000.0000.0000.000
197A193ARG10.8210.91119.593-0.147-0.1470.0000.0000.0000.000
198A194ALA00.0650.03623.0990.0040.0040.0000.0000.0000.000
199A195ALA0-0.067-0.03725.514-0.004-0.0040.0000.0000.0000.000
200A196LEU00.0030.01025.7330.0010.0010.0000.0000.0000.000
201A197PRO00.0570.02629.625-0.002-0.0020.0000.0000.0000.000
202A198ALA00.0310.01432.934-0.003-0.0030.0000.0000.0000.000
203A199GLY00.0210.00535.6850.0000.0000.0000.0000.0000.000
204A200ALA00.0030.00230.315-0.002-0.0020.0000.0000.0000.000
205A201ALA0-0.011-0.01531.879-0.001-0.0010.0000.0000.0000.000
206A202SER0-0.072-0.03232.903-0.003-0.0030.0000.0000.0000.000
207A203LEU0-0.033-0.00331.0300.0000.0000.0000.0000.0000.000
208A204ASP-1-0.841-0.91332.7840.0050.0050.0000.0000.0000.000
209A205ALA00.011-0.00228.3350.0020.0020.0000.0000.0000.000
210A206GLY0-0.021-0.00927.9940.0010.0010.0000.0000.0000.000
211A207ASP-1-0.850-0.93628.8620.0220.0220.0000.0000.0000.000
212A208PHE00.0050.00025.1190.0050.0050.0000.0000.0000.000
213A209ALA00.0030.01024.6610.0050.0050.0000.0000.0000.000
214A210ALA00.0370.03324.5480.0070.0070.0000.0000.0000.000
215A211MET0-0.042-0.00226.3660.0090.0090.0000.0000.0000.000
216A212SER0-0.020-0.03922.7670.0060.0060.0000.0000.0000.000
217A213ALA0-0.067-0.03821.4790.0100.0100.0000.0000.0000.000
218A214ALA0-0.0080.00122.3960.0130.0130.0000.0000.0000.000
219A215ALA0-0.042-0.00424.6050.0050.0050.0000.0000.0000.000
220A216PHE0-0.027-0.01719.7870.0040.0040.0000.0000.0000.000
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