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

tag_button

FMODB ID: 3J6VL

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1866347.529979
FMO2-HF: Nuclear repulsion 1791024.268362
FMO2-HF: Total energy -75323.261618
FMO2-MP2: Total energy -75540.354615


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.
-8.844-2.0145.893-4.172-8.549-0.014
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 : 0.000 / q_NPA : 0.008
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].
3A3LEU0-0.003-0.0133.770-0.6591.803-0.009-1.239-1.2140.005
4A4PHE00.0020.0165.6330.1180.1180.0000.0000.0000.000
5A5TYR0-0.015-0.0519.4020.2800.2800.0000.0000.0000.000
6A6ASN00.0280.00411.913-0.032-0.0320.0000.0000.0000.000
7A7LYS10.8420.92615.682-0.050-0.0500.0000.0000.0000.000
8A8GLU-1-0.855-0.94218.020-0.118-0.1180.0000.0000.0000.000
9A9ALA00.0190.02418.9400.0070.0070.0000.0000.0000.000
10A10VAL00.0490.01015.6370.0110.0110.0000.0000.0000.000
11A11GLY00.0890.04417.9930.0310.0310.0000.0000.0000.000
12A12ASP-1-0.912-0.91916.4120.1270.1270.0000.0000.0000.000
13A13VAL0-0.019-0.01612.6850.0740.0740.0000.0000.0000.000
14A14ALA0-0.0200.0048.711-0.105-0.1050.0000.0000.0000.000
15A15PHE00.000-0.0098.4180.2080.2080.0000.0000.0000.000
16A16LEU00.0150.0042.927-2.078-1.2261.831-0.544-2.1390.002
17A17GLN00.0150.0093.639-0.1560.1890.002-0.080-0.2670.000
18A18ILE0-0.006-0.0252.403-5.729-2.7784.059-2.290-4.719-0.021
19A19ASN00.0090.0163.589-1.127-0.9070.010-0.019-0.2100.000
20A20PRO00.001-0.0055.5290.5460.5460.0000.0000.0000.000
21A21THR0-0.031-0.0218.672-0.020-0.0200.0000.0000.0000.000
22A22GLU-1-0.894-0.91610.9520.0790.0790.0000.0000.0000.000
23A23GLY00.0180.02213.3970.0130.0130.0000.0000.0000.000
24A24GLU-1-0.956-0.97416.6860.1080.1080.0000.0000.0000.000
25A25TYR0-0.094-0.08013.490-0.039-0.0390.0000.0000.0000.000
26A26ASN0-0.052-0.01920.0430.0000.0000.0000.0000.0000.000
27A27TYR00.001-0.01820.206-0.008-0.0080.0000.0000.0000.000
28A28VAL00.0310.02625.5630.0050.0050.0000.0000.0000.000
29A29THR0-0.047-0.02028.542-0.010-0.0100.0000.0000.0000.000
30A30GLN0-0.010-0.01230.6130.0090.0090.0000.0000.0000.000
31A31GLY00.0080.00833.047-0.005-0.0050.0000.0000.0000.000
32A32ASP-1-0.795-0.89232.388-0.077-0.0770.0000.0000.0000.000
33A33VAL0-0.046-0.00728.720-0.010-0.0100.0000.0000.0000.000
34A34VAL0-0.011-0.01325.8270.0090.0090.0000.0000.0000.000
35A35GLU-1-0.773-0.86024.772-0.061-0.0610.0000.0000.0000.000
36A36ILE0-0.038-0.00718.8210.0100.0100.0000.0000.0000.000
37A37GLN00.000-0.02220.553-0.003-0.0030.0000.0000.0000.000
38A38ASN00.0060.01216.4310.0160.0160.0000.0000.0000.000
39A39ASP-1-0.906-0.95317.8100.1250.1250.0000.0000.0000.000
40A40GLY0-0.036-0.02220.832-0.009-0.0090.0000.0000.0000.000
41A41GLU-1-0.940-0.95618.824-0.027-0.0270.0000.0000.0000.000
42A42VAL0-0.036-0.01820.4070.0020.0020.0000.0000.0000.000
43A43VAL0-0.034-0.02316.042-0.008-0.0080.0000.0000.0000.000
44A44GLY0-0.013-0.01017.368-0.037-0.0370.0000.0000.0000.000
45A45TYR0-0.049-0.06219.9670.0170.0170.0000.0000.0000.000
46A46ASN0-0.0270.00822.044-0.025-0.0250.0000.0000.0000.000
47A47ILE00.0000.00624.5880.0130.0130.0000.0000.0000.000
48A48PHE00.010-0.00526.792-0.012-0.0120.0000.0000.0000.000
49A49ASN0-0.035-0.04530.0700.0020.0020.0000.0000.0000.000
50A50ALA00.0620.02028.6800.0030.0030.0000.0000.0000.000
51A51SER00.0030.00430.7480.0010.0010.0000.0000.0000.000
52A52ASN0-0.031-0.01732.9780.0000.0000.0000.0000.0000.000
53A53LYS10.7590.87732.3760.0930.0930.0000.0000.0000.000
54A54ALA00.0310.01930.5990.0000.0000.0000.0000.0000.000
55A55THR0-0.020-0.00932.6600.0020.0020.0000.0000.0000.000
56A56LEU00.0280.00626.872-0.008-0.0080.0000.0000.0000.000
57A57THR0-0.028-0.00529.550-0.009-0.0090.0000.0000.0000.000
58A58GLY00.0190.01830.660-0.010-0.0100.0000.0000.0000.000
59A59ASN0-0.050-0.04329.275-0.007-0.0070.0000.0000.0000.000
60A60GLY00.0460.02527.1740.0020.0020.0000.0000.0000.000
61A61HIS0-0.028-0.01422.372-0.022-0.0220.0000.0000.0000.000
62A62ILE00.0310.01622.225-0.018-0.0180.0000.0000.0000.000
63A63LYS10.9510.98120.4030.3390.3390.0000.0000.0000.000
64A64LEU00.0160.01220.2550.0250.0250.0000.0000.0000.000
65A65THR00.0460.01623.7300.0000.0000.0000.0000.0000.000
66A66GLU-1-0.858-0.92926.762-0.119-0.1190.0000.0000.0000.000
67A67THR0-0.015-0.00428.5360.0080.0080.0000.0000.0000.000
68A68LEU0-0.023-0.01426.5520.0070.0070.0000.0000.0000.000
69A69VAL00.0410.01824.5150.0060.0060.0000.0000.0000.000
70A70GLN0-0.0110.00427.2650.0130.0130.0000.0000.0000.000
71A71ALA0-0.041-0.01330.8680.0090.0090.0000.0000.0000.000
72A72PHE00.023-0.00925.4540.0060.0060.0000.0000.0000.000
73A73GLN00.0180.02328.3810.0020.0020.0000.0000.0000.000
74A74LYS10.9550.96829.8260.0850.0850.0000.0000.0000.000
75A75ALA0-0.045-0.02331.0240.0070.0070.0000.0000.0000.000
76A76ILE00.0310.00226.9310.0060.0060.0000.0000.0000.000
77A77GLU-1-0.780-0.86130.749-0.061-0.0610.0000.0000.0000.000
78A78ALA0-0.091-0.03033.4400.0060.0060.0000.0000.0000.000
79A79ALA0-0.046-0.01732.4980.0040.0040.0000.0000.0000.000
80A80GLY0-0.024-0.01434.6470.0050.0050.0000.0000.0000.000
81A81PHE0-0.0150.00029.3770.0040.0040.0000.0000.0000.000
82A82THR0-0.009-0.02430.896-0.003-0.0030.0000.0000.0000.000
83A83TYR00.0390.03621.488-0.005-0.0050.0000.0000.0000.000
84A84LYS10.7710.85926.7100.0670.0670.0000.0000.0000.000
85A85LEU00.000-0.00823.664-0.003-0.0030.0000.0000.0000.000
86A86ASP-1-0.901-0.93321.042-0.160-0.1600.0000.0000.0000.000
87A87ALA0-0.012-0.02523.408-0.013-0.0130.0000.0000.0000.000
88A88ASP-1-0.768-0.83324.036-0.138-0.1380.0000.0000.0000.000
89A89PHE0-0.054-0.03124.084-0.022-0.0220.0000.0000.0000.000
90A90THR0-0.036-0.03426.1540.0000.0000.0000.0000.0000.000
91A91PRO0-0.016-0.01525.090-0.017-0.0170.0000.0000.0000.000
92A92LYS10.8470.91520.8610.1900.1900.0000.0000.0000.000
93A93PHE0-0.0030.00618.7610.0040.0040.0000.0000.0000.000
94A94VAL00.0120.00624.1700.0090.0090.0000.0000.0000.000
95A95VAL00.0000.02227.327-0.003-0.0030.0000.0000.0000.000
96A96GLY00.0220.00829.1840.0050.0050.0000.0000.0000.000
97A97TYR0-0.021-0.01130.136-0.001-0.0010.0000.0000.0000.000
98A98VAL0-0.0080.00429.0000.0030.0030.0000.0000.0000.000
99A99GLU-1-0.860-0.90731.485-0.028-0.0280.0000.0000.0000.000
100A100THR0-0.021-0.01532.2530.0020.0020.0000.0000.0000.000
101A101LYS10.8290.89528.8760.0100.0100.0000.0000.0000.000
102A102ASP-1-0.896-0.93829.6410.0110.0110.0000.0000.0000.000
103A103LYS10.8530.91628.518-0.055-0.0550.0000.0000.0000.000
104A104HIS0-0.035-0.00821.308-0.006-0.0060.0000.0000.0000.000
105A105PRO0-0.002-0.00825.8740.0040.0040.0000.0000.0000.000
106A106ASP-1-0.866-0.92623.5340.1530.1530.0000.0000.0000.000
107A107ALA00.0280.01321.7750.0220.0220.0000.0000.0000.000
108A108ASP-1-0.931-0.96323.2970.0820.0820.0000.0000.0000.000
109A109LYS10.9420.96920.760-0.130-0.1300.0000.0000.0000.000
110A110LEU0-0.0080.00819.224-0.008-0.0080.0000.0000.0000.000
111A111SER0-0.019-0.01323.6670.0060.0060.0000.0000.0000.000
112A112VAL0-0.008-0.00524.288-0.004-0.0040.0000.0000.0000.000
113A113LEU00.007-0.00325.595-0.001-0.0010.0000.0000.0000.000
114A114SER00.0070.02526.9280.0000.0000.0000.0000.0000.000
115A115VAL0-0.020-0.03626.667-0.002-0.0020.0000.0000.0000.000
116A116ASP-1-0.823-0.88029.279-0.054-0.0540.0000.0000.0000.000
117A117VAL00.026-0.01727.459-0.008-0.0080.0000.0000.0000.000
118A118ALA0-0.0010.01230.571-0.007-0.0070.0000.0000.0000.000
119A119THR0-0.082-0.06529.8670.0030.0030.0000.0000.0000.000
120A120GLU-1-0.792-0.87026.996-0.082-0.0820.0000.0000.0000.000
121A121LYS10.7740.86830.3600.0310.0310.0000.0000.0000.000
122A122LEU0-0.027-0.00224.1560.0030.0030.0000.0000.0000.000
123A123GLN0-0.0040.00223.9590.0030.0030.0000.0000.0000.000
124A124ILE0-0.044-0.01420.720-0.002-0.0020.0000.0000.0000.000
125A125VAL00.0100.00220.0040.0090.0090.0000.0000.0000.000
126A126CYS0-0.054-0.01820.359-0.020-0.0200.0000.0000.0000.000
127A127GLY00.0590.00321.1280.0180.0180.0000.0000.0000.000
128A128ALA0-0.0110.01122.4370.0030.0030.0000.0000.0000.000
129A129PRO0-0.075-0.03824.0030.0080.0080.0000.0000.0000.000
130A130ASN0-0.059-0.03927.0840.0060.0060.0000.0000.0000.000
131A131VAL00.0260.03626.275-0.003-0.0030.0000.0000.0000.000
132A132GLU-1-0.831-0.92628.935-0.006-0.0060.0000.0000.0000.000
133A133ALA0-0.0070.01032.104-0.007-0.0070.0000.0000.0000.000
134A134GLY0-0.017-0.01633.8900.0010.0010.0000.0000.0000.000
135A135GLN0-0.009-0.00330.844-0.008-0.0080.0000.0000.0000.000
136A136LYS10.8230.91332.5740.0670.0670.0000.0000.0000.000
137A137VAL0-0.006-0.01626.593-0.004-0.0040.0000.0000.0000.000
138A138VAL00.0550.02724.7920.0020.0020.0000.0000.0000.000
139A139VAL0-0.028-0.01623.555-0.009-0.0090.0000.0000.0000.000
140A140ALA00.0070.00319.094-0.005-0.0050.0000.0000.0000.000
141A141LYS10.8720.91020.1410.1170.1170.0000.0000.0000.000
142A142VAL00.013-0.00417.821-0.038-0.0380.0000.0000.0000.000
143A143GLY0-0.0010.00317.1540.0200.0200.0000.0000.0000.000
144A144ALA0-0.032-0.00917.358-0.034-0.0340.0000.0000.0000.000
145A145VAL0-0.008-0.00914.488-0.039-0.0390.0000.0000.0000.000
146A146MET0-0.0020.00613.7340.0730.0730.0000.0000.0000.000
147A147PRO00.0330.01414.296-0.108-0.1080.0000.0000.0000.000
148A148SER0-0.074-0.03812.179-0.050-0.0500.0000.0000.0000.000
149A149GLY0-0.0040.00310.200-0.294-0.2940.0000.0000.0000.000
150A150MET0-0.036-0.0119.3310.0560.0560.0000.0000.0000.000
151A151VAL00.0270.01410.2920.1590.1590.0000.0000.0000.000
152A152ILE0-0.027-0.00612.3120.0410.0410.0000.0000.0000.000
153A153LYS10.9180.93613.0830.1250.1250.0000.0000.0000.000
154A154ASP-1-0.811-0.89315.193-0.064-0.0640.0000.0000.0000.000
155A155ALA0-0.034-0.01114.5100.0320.0320.0000.0000.0000.000
156A156GLU-1-0.878-0.95415.5150.1730.1730.0000.0000.0000.000
157A157LEU0-0.041-0.00515.5020.0380.0380.0000.0000.0000.000
158A158ARG10.8020.87517.121-0.233-0.2330.0000.0000.0000.000
159A159GLY00.0520.03419.051-0.015-0.0150.0000.0000.0000.000
160A160VAL0-0.0180.01021.267-0.011-0.0110.0000.0000.0000.000
161A161ALA00.0530.01320.2060.0030.0030.0000.0000.0000.000
162A162SER00.0100.00618.244-0.003-0.0030.0000.0000.0000.000
163A163SER0-0.016-0.01118.717-0.004-0.0040.0000.0000.0000.000
164A164GLY00.0390.01619.005-0.005-0.0050.0000.0000.0000.000
165A165MET0-0.039-0.02014.3510.0060.0060.0000.0000.0000.000
166A166ILE00.0080.01419.622-0.011-0.0110.0000.0000.0000.000
167A167CYS0-0.037-0.00721.237-0.025-0.0250.0000.0000.0000.000
168A168SER00.059-0.01320.6530.0260.0260.0000.0000.0000.000
169A169MET00.023-0.00522.896-0.016-0.0160.0000.0000.0000.000
170A170LYS10.7760.88519.0210.1950.1950.0000.0000.0000.000
171A171GLU-1-0.793-0.85717.146-0.366-0.3660.0000.0000.0000.000
172A172LEU0-0.025-0.00519.589-0.030-0.0300.0000.0000.0000.000
173A173GLY00.0080.00620.8230.0020.0020.0000.0000.0000.000
174A174LEU0-0.065-0.02421.8230.0100.0100.0000.0000.0000.000
175A175PRO0-0.012-0.00822.377-0.015-0.0150.0000.0000.0000.000
176A176ASN0-0.028-0.01322.500-0.020-0.0200.0000.0000.0000.000
177A177ALA00.0260.01122.1950.0020.0020.0000.0000.0000.000
178A178PRO00.0390.02923.7230.0170.0170.0000.0000.0000.000
179A179GLN00.0110.00225.960-0.001-0.0010.0000.0000.0000.000
180A180GLU-1-0.877-0.94427.823-0.078-0.0780.0000.0000.0000.000
181A181LYS10.7960.88422.3030.1150.1150.0000.0000.0000.000
182A182GLY00.0650.05823.094-0.009-0.0090.0000.0000.0000.000
183A183ILE0-0.022-0.02022.861-0.022-0.0220.0000.0000.0000.000
184A184MET0-0.020-0.01925.2040.0100.0100.0000.0000.0000.000
185A185VAL0-0.040-0.00827.827-0.001-0.0010.0000.0000.0000.000
186A186LEU0-0.041-0.00830.049-0.002-0.0020.0000.0000.0000.000
187A187SER00.0230.00733.1560.0060.0060.0000.0000.0000.000
188A188ASP-1-0.840-0.93436.613-0.061-0.0610.0000.0000.0000.000
189A189ASP-1-0.989-0.97438.553-0.080-0.0800.0000.0000.0000.000
190A190TYR00.0280.01032.403-0.001-0.0010.0000.0000.0000.000
191A191THR00.008-0.00235.7420.0080.0080.0000.0000.0000.000
192A192VAL0-0.009-0.01632.723-0.007-0.0070.0000.0000.0000.000
193A193GLY00.002-0.00131.6540.0050.0050.0000.0000.0000.000
194A194GLN0-0.052-0.01731.6890.0000.0000.0000.0000.0000.000
195A195SER0-0.017-0.02828.708-0.009-0.0090.0000.0000.0000.000
196A196PHE0-0.004-0.01626.5850.0070.0070.0000.0000.0000.000
197A197PHE0-0.041-0.01723.0710.0020.0020.0000.0000.0000.000
198A198GLU-1-0.937-0.95328.499-0.132-0.1320.0000.0000.0000.000