Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: JQ199

Calculation Name: 3BU2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BU2

Chain ID: A

ChEMBL ID:

UniProt ID: Q49YH3

Base Structure: X-ray

Registration Date: 2023-09-24

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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1867752.18267
FMO2-HF: Nuclear repulsion 1792430.332851
FMO2-HF: Total energy -75321.849819
FMO2-MP2: Total energy -75539.081127


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-8.699-1.6485.008-4.078-7.979-0.014
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : 0.007
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].
3A3LEU00.002-0.0093.801-0.3252.213-0.009-1.267-1.2610.005
4A4PHE0-0.0050.0155.640-0.016-0.0160.0000.0000.0000.000
5A5TYR0-0.056-0.1139.4320.2790.2790.0000.0000.0000.000
6A6ASN00.0240.00112.017-0.041-0.0410.0000.0000.0000.000
7A7LYS10.9630.99715.773-0.074-0.0740.0000.0000.0000.000
8A8GLU-1-0.917-0.97718.179-0.037-0.0370.0000.0000.0000.000
9A9ALA0-0.0250.00518.9050.0010.0010.0000.0000.0000.000
10A10VAL00.0590.01815.7120.0060.0060.0000.0000.0000.000
11A11GLY00.0820.03918.1530.0250.0250.0000.0000.0000.000
12A12ASP-1-0.972-0.91716.3340.2080.2080.0000.0000.0000.000
13A13VAL0-0.006-0.01012.7640.0650.0650.0000.0000.0000.000
14A14ALA0-0.0140.0058.718-0.095-0.0950.0000.0000.0000.000
15A15PHE0-0.016-0.0168.5500.1610.1610.0000.0000.0000.000
16A16LEU00.0160.0023.127-1.995-1.0431.268-0.426-1.7940.003
17A17GLN0-0.010-0.0023.706-0.335-0.0260.001-0.072-0.2380.000
18A18ILE00.016-0.0112.343-5.546-2.6373.738-2.264-4.382-0.022
19A19ASN00.0130.0143.487-1.415-1.0720.010-0.049-0.3040.000
20A20PRO0-0.016-0.0135.4050.6180.6180.0000.0000.0000.000
21A21THR0-0.025-0.0208.589-0.035-0.0350.0000.0000.0000.000
22A22GLU-1-0.912-0.94410.7270.0780.0780.0000.0000.0000.000
23A23GLY00.0140.01913.2690.0090.0090.0000.0000.0000.000
24A24GLU-1-0.945-0.96616.3210.1110.1110.0000.0000.0000.000
25A25TYR0-0.049-0.04013.293-0.037-0.0370.0000.0000.0000.000
26A26ASN0-0.076-0.03919.6490.0020.0020.0000.0000.0000.000
27A27TYR0-0.018-0.02219.461-0.007-0.0070.0000.0000.0000.000
28A28VAL00.0280.02825.1540.0050.0050.0000.0000.0000.000
29A29THR0-0.063-0.02928.124-0.010-0.0100.0000.0000.0000.000
30A30GLN0-0.004-0.01030.1990.0100.0100.0000.0000.0000.000
31A31GLY00.0040.00732.634-0.005-0.0050.0000.0000.0000.000
32A32ASP-1-0.795-0.88732.019-0.080-0.0800.0000.0000.0000.000
33A33VAL0-0.042-0.00628.208-0.011-0.0110.0000.0000.0000.000
34A34VAL0-0.011-0.01325.0740.0090.0090.0000.0000.0000.000
35A35GLU-1-0.806-0.89924.580-0.065-0.0650.0000.0000.0000.000
36A36ILE0-0.027-0.00318.0210.0110.0110.0000.0000.0000.000
37A37GLN00.023-0.00120.370-0.003-0.0030.0000.0000.0000.000
38A38ASN00.0220.02115.7940.0090.0090.0000.0000.0000.000
39A39ASP-1-0.918-0.94718.0170.1290.1290.0000.0000.0000.000
40A40GLY0-0.044-0.03020.707-0.010-0.0100.0000.0000.0000.000
41A41GLU-1-0.931-0.95018.548-0.021-0.0210.0000.0000.0000.000
42A42VAL0-0.017-0.01520.2570.0010.0010.0000.0000.0000.000
43A43VAL0-0.052-0.02816.073-0.007-0.0070.0000.0000.0000.000
44A44GLY0-0.012-0.01217.119-0.040-0.0400.0000.0000.0000.000
45A45TYR0-0.068-0.06219.6380.0200.0200.0000.0000.0000.000
46A46ASN0-0.0040.02421.685-0.033-0.0330.0000.0000.0000.000
47A47ILE00.0100.01724.1910.0140.0140.0000.0000.0000.000
48A48PHE00.009-0.01626.479-0.012-0.0120.0000.0000.0000.000
49A49ASN0-0.024-0.02029.6920.0020.0020.0000.0000.0000.000
50A50ALA00.0620.01628.3230.0030.0030.0000.0000.0000.000
51A51SER0-0.005-0.00330.3880.0010.0010.0000.0000.0000.000
52A52ASN0-0.007-0.00732.640-0.001-0.0010.0000.0000.0000.000
53A53LYS10.7300.85031.8970.0990.0990.0000.0000.0000.000
54A54ALA00.0250.01330.2410.0000.0000.0000.0000.0000.000
55A55THR0-0.019-0.00432.3180.0030.0030.0000.0000.0000.000
56A56LEU00.011-0.00126.641-0.008-0.0080.0000.0000.0000.000
57A57THR0-0.0330.00029.268-0.009-0.0090.0000.0000.0000.000
58A58GLY0-0.001-0.00230.403-0.008-0.0080.0000.0000.0000.000
59A59ASN0-0.025-0.02529.079-0.021-0.0210.0000.0000.0000.000
60A60GLY00.0490.02226.9750.0020.0020.0000.0000.0000.000
61A61HIS0-0.026-0.01522.179-0.017-0.0170.0000.0000.0000.000
62A62ILE0-0.0060.00621.909-0.015-0.0150.0000.0000.0000.000
63A63LYS10.9920.99520.1540.3590.3590.0000.0000.0000.000
64A64LEU00.0200.01220.1340.0250.0250.0000.0000.0000.000
65A65THR00.0410.02223.5540.0010.0010.0000.0000.0000.000
66A66GLU-1-0.849-0.93426.614-0.121-0.1210.0000.0000.0000.000
67A67THR0-0.005-0.01028.3820.0110.0110.0000.0000.0000.000
68A68LEU0-0.032-0.01926.0410.0070.0070.0000.0000.0000.000
69A69VAL00.0360.01824.5100.0050.0050.0000.0000.0000.000
70A70GLN00.0020.00827.1030.0120.0120.0000.0000.0000.000
71A71ALA0-0.033-0.00630.5030.0090.0090.0000.0000.0000.000
72A72PHE00.016-0.01425.0700.0060.0060.0000.0000.0000.000
73A73GLN00.0700.05328.2960.0010.0010.0000.0000.0000.000
74A74LYS10.9710.97729.6590.0870.0870.0000.0000.0000.000
75A75ALA0-0.052-0.02930.6680.0070.0070.0000.0000.0000.000
76A76ILE00.0120.00427.2730.0050.0050.0000.0000.0000.000
77A77GLU-1-0.913-0.95830.542-0.063-0.0630.0000.0000.0000.000
78A78ALA0-0.100-0.03433.2730.0060.0060.0000.0000.0000.000
79A79ALA0-0.049-0.01432.1800.0040.0040.0000.0000.0000.000
80A80GLY0-0.030-0.01934.3300.0050.0050.0000.0000.0000.000
81A81PHE0-0.023-0.00429.2470.0030.0030.0000.0000.0000.000
82A82THR0-0.004-0.01930.737-0.003-0.0030.0000.0000.0000.000
83A83TYR00.0370.03321.212-0.006-0.0060.0000.0000.0000.000
84A84LYS10.9250.94426.5390.0650.0650.0000.0000.0000.000
85A85LEU0-0.021-0.01223.572-0.002-0.0020.0000.0000.0000.000
86A86ASP-1-0.913-0.93521.150-0.163-0.1630.0000.0000.0000.000
87A87ALA0-0.015-0.02723.243-0.013-0.0130.0000.0000.0000.000
88A88ASP-1-0.817-0.86123.840-0.132-0.1320.0000.0000.0000.000
89A89PHE0-0.038-0.01923.855-0.022-0.0220.0000.0000.0000.000
90A90THR0-0.061-0.05325.8810.0010.0010.0000.0000.0000.000
91A91PRO0-0.017-0.01424.958-0.017-0.0170.0000.0000.0000.000
92A92LYS10.8920.95120.5500.1920.1920.0000.0000.0000.000
93A93PHE00.0000.00618.7270.0050.0050.0000.0000.0000.000
94A94VAL00.0070.00424.0750.0070.0070.0000.0000.0000.000
95A95VAL0-0.0040.02027.249-0.002-0.0020.0000.0000.0000.000
96A96GLY00.0200.00529.2390.0040.0040.0000.0000.0000.000
97A97TYR0-0.025-0.00230.186-0.001-0.0010.0000.0000.0000.000
98A98VAL0-0.0090.00729.1680.0030.0030.0000.0000.0000.000
99A99GLU-1-0.854-0.91331.570-0.022-0.0220.0000.0000.0000.000
100A100THR0-0.005-0.00732.2680.0010.0010.0000.0000.0000.000
101A101LYS10.8810.93828.699-0.003-0.0030.0000.0000.0000.000
102A102ASP-1-0.898-0.92929.7720.0200.0200.0000.0000.0000.000
103A103LYS10.8900.93627.943-0.064-0.0640.0000.0000.0000.000
104A104HIS0-0.038-0.02121.484-0.007-0.0070.0000.0000.0000.000
105A105PRO0-0.019-0.01425.9290.0030.0030.0000.0000.0000.000
106A106ASP-1-0.932-0.97423.7760.1430.1430.0000.0000.0000.000
107A107ALA00.0090.00521.9960.0190.0190.0000.0000.0000.000
108A108ASP-1-0.978-0.99623.4400.0990.0990.0000.0000.0000.000
109A109LYS10.9290.96521.434-0.142-0.1420.0000.0000.0000.000
110A110LEU0-0.0090.00719.384-0.007-0.0070.0000.0000.0000.000
111A111SER0-0.031-0.02123.8110.0040.0040.0000.0000.0000.000
112A112VAL00.0100.01024.420-0.002-0.0020.0000.0000.0000.000
113A113LEU0-0.003-0.01525.717-0.002-0.0020.0000.0000.0000.000
114A114SER00.0090.03027.0400.0000.0000.0000.0000.0000.000
115A115VAL0-0.012-0.03426.671-0.002-0.0020.0000.0000.0000.000
116A116ASP-1-0.883-0.93129.363-0.049-0.0490.0000.0000.0000.000
117A117VAL00.027-0.00427.284-0.008-0.0080.0000.0000.0000.000
118A118ALA0-0.0200.00330.583-0.007-0.0070.0000.0000.0000.000
119A119THR0-0.047-0.03629.8760.0020.0020.0000.0000.0000.000
120A120GLU-1-0.948-0.97727.161-0.064-0.0640.0000.0000.0000.000
121A121LYS10.8500.92230.4310.0260.0260.0000.0000.0000.000
122A122LEU00.0000.01224.2190.0020.0020.0000.0000.0000.000
123A123GLN00.0020.01324.1850.0010.0010.0000.0000.0000.000
124A124ILE0-0.040-0.00921.069-0.001-0.0010.0000.0000.0000.000
125A125VAL00.0120.00020.1550.0080.0080.0000.0000.0000.000
126A126CYS0-0.074-0.02620.474-0.017-0.0170.0000.0000.0000.000
127A127GLY00.0500.00021.2360.0150.0150.0000.0000.0000.000
128A128ALA0-0.0200.00422.5580.0030.0030.0000.0000.0000.000
129A129PRO0-0.069-0.03524.1470.0050.0050.0000.0000.0000.000
130A130ASN0-0.007-0.01227.1340.0050.0050.0000.0000.0000.000
131A131VAL0-0.0130.01726.539-0.004-0.0040.0000.0000.0000.000
132A132GLU-1-0.880-0.97129.0270.0030.0030.0000.0000.0000.000
133A133ALA0-0.0030.01132.203-0.006-0.0060.0000.0000.0000.000
134A134GLY0-0.002-0.01933.9890.0010.0010.0000.0000.0000.000
135A135GLN00.0000.00130.811-0.008-0.0080.0000.0000.0000.000
136A136LYS10.9120.97632.6120.0590.0590.0000.0000.0000.000
137A137VAL00.015-0.00126.418-0.003-0.0030.0000.0000.0000.000
138A138VAL00.0370.02124.5260.0010.0010.0000.0000.0000.000
139A139VAL0-0.018-0.01223.488-0.007-0.0070.0000.0000.0000.000
140A140ALA00.003-0.00118.992-0.007-0.0070.0000.0000.0000.000
141A141LYS10.9770.97120.1050.1220.1220.0000.0000.0000.000
142A142VAL00.0480.01617.724-0.037-0.0370.0000.0000.0000.000
143A143GLY0-0.010-0.00517.0370.0180.0180.0000.0000.0000.000
144A144ALA0-0.042-0.01817.228-0.035-0.0350.0000.0000.0000.000
145A145VAL0-0.005-0.00114.361-0.034-0.0340.0000.0000.0000.000
146A146MET0-0.0020.00313.6660.0700.0700.0000.0000.0000.000
147A147PRO00.0250.01114.233-0.111-0.1110.0000.0000.0000.000
148A148SER0-0.066-0.03712.021-0.064-0.0640.0000.0000.0000.000
149A149GLY00.0020.00810.127-0.279-0.2790.0000.0000.0000.000
150A150MET0-0.037-0.0089.2740.0610.0610.0000.0000.0000.000
151A151VAL00.0340.01910.2010.1600.1600.0000.0000.0000.000
152A152ILE0-0.023-0.00512.2080.0490.0490.0000.0000.0000.000
153A153LYS10.9820.97712.7080.1220.1220.0000.0000.0000.000
154A154ASP-1-0.865-0.92215.126-0.037-0.0370.0000.0000.0000.000
155A155ALA0-0.055-0.02214.5990.0300.0300.0000.0000.0000.000
156A156GLU-1-0.912-0.96515.6460.1560.1560.0000.0000.0000.000
157A157LEU0-0.033-0.00915.1850.0400.0400.0000.0000.0000.000
158A158ARG10.9120.95017.190-0.273-0.2730.0000.0000.0000.000
159A159GLY00.0740.04219.226-0.014-0.0140.0000.0000.0000.000
160A160VAL00.0000.02121.437-0.010-0.0100.0000.0000.0000.000
161A161ALA00.0470.01620.3400.0050.0050.0000.0000.0000.000
162A162SER00.016-0.00518.382-0.004-0.0040.0000.0000.0000.000
163A163SER0-0.010-0.01318.819-0.003-0.0030.0000.0000.0000.000
164A164GLY00.0210.00819.089-0.008-0.0080.0000.0000.0000.000
165A165MET0-0.043-0.02114.4390.0090.0090.0000.0000.0000.000
166A166ILE0-0.0020.01319.673-0.013-0.0130.0000.0000.0000.000
167A167CYS0-0.0220.00521.268-0.021-0.0210.0000.0000.0000.000
168A168SER00.042-0.02620.4370.0210.0210.0000.0000.0000.000
169A169MET00.026-0.00422.822-0.018-0.0180.0000.0000.0000.000
170A170LYS10.8650.93618.9870.1610.1610.0000.0000.0000.000
171A171GLU-1-0.808-0.87017.146-0.322-0.3220.0000.0000.0000.000
172A172LEU0-0.024-0.00919.487-0.032-0.0320.0000.0000.0000.000
173A173GLY00.0110.01020.762-0.001-0.0010.0000.0000.0000.000
174A174LEU0-0.067-0.02921.7760.0080.0080.0000.0000.0000.000
175A175PRO0-0.013-0.00622.203-0.013-0.0130.0000.0000.0000.000
176A176ASN0-0.004-0.00122.311-0.021-0.0210.0000.0000.0000.000
177A177ALA00.008-0.00122.1060.0020.0020.0000.0000.0000.000
178A178PRO00.0130.01023.6630.0160.0160.0000.0000.0000.000
179A179GLN0-0.009-0.00125.9300.0030.0030.0000.0000.0000.000
180A180GLU-1-0.897-0.94227.839-0.053-0.0530.0000.0000.0000.000
181A181LYS10.8400.89821.8270.0960.0960.0000.0000.0000.000
182A182GLY00.0640.05623.138-0.006-0.0060.0000.0000.0000.000
183A183ILE0-0.049-0.03322.989-0.021-0.0210.0000.0000.0000.000
184A184MET0-0.015-0.00625.2400.0090.0090.0000.0000.0000.000
185A185VAL0-0.022-0.00427.8110.0010.0010.0000.0000.0000.000
186A186LEU0-0.049-0.01930.180-0.003-0.0030.0000.0000.0000.000
187A187SER00.0210.00833.1890.0060.0060.0000.0000.0000.000
188A188ASP-1-0.926-0.98536.645-0.052-0.0520.0000.0000.0000.000
189A189ASP-1-0.997-0.98638.466-0.073-0.0730.0000.0000.0000.000
190A190TYR00.0310.01232.584-0.001-0.0010.0000.0000.0000.000
191A191THR00.0170.00135.6620.0080.0080.0000.0000.0000.000
192A192VAL00.006-0.01032.704-0.007-0.0070.0000.0000.0000.000
193A193GLY00.002-0.00331.5580.0040.0040.0000.0000.0000.000
194A194GLN0-0.044-0.02231.5850.0000.0000.0000.0000.0000.000
195A195SER0-0.040-0.03328.572-0.008-0.0080.0000.0000.0000.000
196A196PHE0-0.008-0.01126.4350.0070.0070.0000.0000.0000.000
197A197PHE0-0.035-0.01623.1880.0000.0000.0000.0000.0000.000
198A198GLU-1-0.940-0.95528.404-0.129-0.1290.0000.0000.0000.000