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: LN139

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 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 198
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1866852.773178
FMO2-HF: Nuclear repulsion 1791528.957294
FMO2-HF: Total energy -75323.815884
FMO2-MP2: Total energy -75540.88242


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.
-9.777-3.9299.155-4.62-10.382-0.018
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 : -0.003 / 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].
3A3LEU0-0.015-0.0183.545-1.0901.4040.017-1.297-1.2130.004
4A4PHE00.0170.0215.6240.1030.1030.0000.0000.0000.000
5A5TYR0-0.004-0.0409.4140.2970.2970.0000.0000.0000.000
6A6ASN00.0150.00711.997-0.028-0.0280.0000.0000.0000.000
7A7LYS10.8890.93315.777-0.025-0.0250.0000.0000.0000.000
8A8GLU-1-0.831-0.92117.943-0.144-0.1440.0000.0000.0000.000
9A9ALA00.0050.00619.5210.0050.0050.0000.0000.0000.000
10A10VAL00.0210.00015.3480.0000.0000.0000.0000.0000.000
11A11GLY00.0760.03518.1700.0370.0370.0000.0000.0000.000
12A12ASP-1-0.878-0.90316.6560.0970.0970.0000.0000.0000.000
13A13VAL0-0.018-0.01013.0400.0750.0750.0000.0000.0000.000
14A14ALA0-0.036-0.0059.070-0.117-0.1170.0000.0000.0000.000
15A15PHE00.012-0.0058.5890.2780.2780.0000.0000.0000.000
16A16LEU00.010-0.0012.738-2.132-1.3682.127-0.612-2.2790.002
17A17GLN0-0.0040.0003.323-0.2080.2510.008-0.114-0.3520.000
18A18ILE0-0.005-0.0142.443-6.036-3.9046.952-2.982-6.103-0.024
19A19ASN00.0210.0153.142-1.183-1.2370.0520.386-0.3840.000
20A20PRO0-0.0010.0045.2060.4490.502-0.001-0.001-0.0510.000
21A21THR0-0.038-0.0248.4940.0260.0260.0000.0000.0000.000
22A22GLU-1-0.878-0.90610.6950.1240.1240.0000.0000.0000.000
23A23GLY00.0240.01213.3130.0300.0300.0000.0000.0000.000
24A24GLU-1-0.972-0.99116.9230.1220.1220.0000.0000.0000.000
25A25TYR0-0.095-0.06913.044-0.047-0.0470.0000.0000.0000.000
26A26ASN0-0.060-0.02719.603-0.009-0.0090.0000.0000.0000.000
27A27TYR0-0.003-0.01320.139-0.010-0.0100.0000.0000.0000.000
28A28VAL00.0110.01725.1940.0070.0070.0000.0000.0000.000
29A29THR0-0.040-0.02328.139-0.011-0.0110.0000.0000.0000.000
30A30GLN0-0.029-0.01730.5340.0100.0100.0000.0000.0000.000
31A31GLY00.010-0.00133.157-0.005-0.0050.0000.0000.0000.000
32A32ASP-1-0.773-0.87132.976-0.085-0.0850.0000.0000.0000.000
33A33VAL0-0.056-0.01828.514-0.011-0.0110.0000.0000.0000.000
34A34VAL0-0.005-0.01025.5600.0100.0100.0000.0000.0000.000
35A35GLU-1-0.778-0.84524.219-0.057-0.0570.0000.0000.0000.000
36A36ILE0-0.025-0.00618.4370.0100.0100.0000.0000.0000.000
37A37GLN0-0.015-0.02320.128-0.002-0.0020.0000.0000.0000.000
38A38ASN00.0280.01016.3130.0210.0210.0000.0000.0000.000
39A39ASP-1-0.875-0.93517.5250.1700.1700.0000.0000.0000.000
40A40GLY0-0.057-0.03820.569-0.007-0.0070.0000.0000.0000.000
41A41GLU-1-0.945-0.95518.825-0.014-0.0140.0000.0000.0000.000
42A42VAL0-0.046-0.01919.8040.0010.0010.0000.0000.0000.000
43A43VAL0-0.015-0.01315.685-0.007-0.0070.0000.0000.0000.000
44A44GLY0-0.022-0.01216.940-0.046-0.0460.0000.0000.0000.000
45A45TYR0-0.042-0.05819.6450.0200.0200.0000.0000.0000.000
46A46ASN0-0.036-0.00521.619-0.023-0.0230.0000.0000.0000.000
47A47ILE00.0020.00124.2910.0150.0150.0000.0000.0000.000
48A48PHE00.0210.00726.735-0.013-0.0130.0000.0000.0000.000
49A49ASN0-0.045-0.05029.7970.0000.0000.0000.0000.0000.000
50A50ALA00.0520.02928.5070.0030.0030.0000.0000.0000.000
51A51SER00.0070.00330.5740.0000.0000.0000.0000.0000.000
52A52ASN0-0.044-0.01732.9420.0000.0000.0000.0000.0000.000
53A53LYS10.7530.86131.8280.1020.1020.0000.0000.0000.000
54A54ALA00.0470.02629.9690.0010.0010.0000.0000.0000.000
55A55THR0-0.003-0.00131.9930.0010.0010.0000.0000.0000.000
56A56LEU0-0.015-0.00126.358-0.009-0.0090.0000.0000.0000.000
57A57THR00.008-0.00329.323-0.005-0.0050.0000.0000.0000.000
58A58GLY00.0060.01630.218-0.013-0.0130.0000.0000.0000.000
59A59ASN0-0.069-0.05328.797-0.009-0.0090.0000.0000.0000.000
60A60GLY00.0600.03226.9840.0040.0040.0000.0000.0000.000
61A61HIS0-0.028-0.01422.603-0.024-0.0240.0000.0000.0000.000
62A62ILE00.0310.02622.116-0.023-0.0230.0000.0000.0000.000
63A63LYS10.9270.95520.1210.3720.3720.0000.0000.0000.000
64A64LEU00.0320.02419.7850.0290.0290.0000.0000.0000.000
65A65THR00.0300.00623.146-0.003-0.0030.0000.0000.0000.000
66A66GLU-1-0.822-0.90426.178-0.126-0.1260.0000.0000.0000.000
67A67THR0-0.0140.00228.2300.0080.0080.0000.0000.0000.000
68A68LEU0-0.013-0.01326.4640.0080.0080.0000.0000.0000.000
69A69VAL00.0320.01724.1390.0050.0050.0000.0000.0000.000
70A70GLN0-0.045-0.03026.9560.0130.0130.0000.0000.0000.000
71A71ALA0-0.041-0.01430.4680.0100.0100.0000.0000.0000.000
72A72PHE00.014-0.01224.8750.0070.0070.0000.0000.0000.000
73A73GLN00.0110.00927.9690.0020.0020.0000.0000.0000.000
74A74LYS10.9600.97429.3330.0910.0910.0000.0000.0000.000
75A75ALA0-0.043-0.02330.2350.0080.0080.0000.0000.0000.000
76A76ILE00.0220.01426.6150.0070.0070.0000.0000.0000.000
77A77GLU-1-0.774-0.85530.436-0.061-0.0610.0000.0000.0000.000
78A78ALA0-0.089-0.04133.2860.0060.0060.0000.0000.0000.000
79A79ALA0-0.034-0.00732.2920.0040.0040.0000.0000.0000.000
80A80GLY0-0.0090.00434.4450.0050.0050.0000.0000.0000.000
81A81PHE0-0.011-0.01528.7760.0040.0040.0000.0000.0000.000
82A82THR0-0.016-0.02630.991-0.005-0.0050.0000.0000.0000.000
83A83TYR00.0450.03621.426-0.004-0.0040.0000.0000.0000.000
84A84LYS10.7500.85726.4090.0680.0680.0000.0000.0000.000
85A85LEU00.018-0.00123.321-0.002-0.0020.0000.0000.0000.000
86A86ASP-1-0.870-0.92620.620-0.170-0.1700.0000.0000.0000.000
87A87ALA0-0.015-0.02423.067-0.013-0.0130.0000.0000.0000.000
88A88ASP-1-0.764-0.83323.504-0.146-0.1460.0000.0000.0000.000
89A89PHE0-0.055-0.03723.569-0.022-0.0220.0000.0000.0000.000
90A90THR0-0.036-0.03525.728-0.003-0.0030.0000.0000.0000.000
91A91PRO0-0.023-0.01224.836-0.018-0.0180.0000.0000.0000.000
92A92LYS10.8500.92520.5480.2070.2070.0000.0000.0000.000
93A93PHE00.000-0.00318.212-0.003-0.0030.0000.0000.0000.000
94A94VAL00.0010.00623.7550.0090.0090.0000.0000.0000.000
95A95VAL0-0.0020.00926.985-0.005-0.0050.0000.0000.0000.000
96A96GLY00.0380.01928.7700.0050.0050.0000.0000.0000.000
97A97TYR0-0.040-0.02729.699-0.001-0.0010.0000.0000.0000.000
98A98VAL00.0030.00728.6190.0040.0040.0000.0000.0000.000
99A99GLU-1-0.836-0.89031.123-0.030-0.0300.0000.0000.0000.000
100A100THR0-0.059-0.04931.6880.0020.0020.0000.0000.0000.000
101A101LYS10.8310.89428.6620.0160.0160.0000.0000.0000.000
102A102ASP-1-0.869-0.90929.5270.0100.0100.0000.0000.0000.000
103A103LYS10.8390.91328.479-0.052-0.0520.0000.0000.0000.000
104A104HIS0-0.023-0.01021.454-0.006-0.0060.0000.0000.0000.000
105A105PRO0-0.014-0.00325.6070.0020.0020.0000.0000.0000.000
106A106ASP-1-0.825-0.91022.9800.1810.1810.0000.0000.0000.000
107A107ALA00.0030.00121.4390.0240.0240.0000.0000.0000.000
108A108ASP-1-0.914-0.95323.1430.0730.0730.0000.0000.0000.000
109A109LYS10.8760.93220.473-0.136-0.1360.0000.0000.0000.000
110A110LEU0-0.0060.00319.431-0.012-0.0120.0000.0000.0000.000
111A111SER0-0.023-0.01423.8350.0060.0060.0000.0000.0000.000
112A112VAL0-0.0030.00024.216-0.005-0.0050.0000.0000.0000.000
113A113LEU00.0120.00225.094-0.003-0.0030.0000.0000.0000.000
114A114SER0-0.0180.00226.839-0.001-0.0010.0000.0000.0000.000
115A115VAL0-0.009-0.01926.368-0.004-0.0040.0000.0000.0000.000
116A116ASP-1-0.812-0.87828.964-0.060-0.0600.0000.0000.0000.000
117A117VAL00.012-0.01627.290-0.010-0.0100.0000.0000.0000.000
118A118ALA00.0130.01930.455-0.007-0.0070.0000.0000.0000.000
119A119THR0-0.089-0.07429.5750.0030.0030.0000.0000.0000.000
120A120GLU-1-0.791-0.86426.742-0.090-0.0900.0000.0000.0000.000
121A121LYS10.7660.85430.1280.0350.0350.0000.0000.0000.000
122A122LEU0-0.031-0.01123.9990.0040.0040.0000.0000.0000.000
123A123GLN0-0.006-0.00123.5560.0020.0020.0000.0000.0000.000
124A124ILE0-0.039-0.02320.727-0.005-0.0050.0000.0000.0000.000
125A125VAL00.003-0.00119.9210.0110.0110.0000.0000.0000.000
126A126CYS0-0.0430.00120.163-0.021-0.0210.0000.0000.0000.000
127A127GLY00.0430.00521.1040.0210.0210.0000.0000.0000.000
128A128ALA0-0.056-0.01422.5850.0000.0000.0000.0000.0000.000
129A129PRO0-0.043-0.02724.0180.0100.0100.0000.0000.0000.000
130A130ASN0-0.034-0.03427.0110.0070.0070.0000.0000.0000.000
131A131VAL00.0340.03925.983-0.003-0.0030.0000.0000.0000.000
132A132GLU-1-0.846-0.93228.707-0.010-0.0100.0000.0000.0000.000
133A133ALA00.0060.01231.849-0.007-0.0070.0000.0000.0000.000
134A134GLY0-0.015-0.00733.8220.0000.0000.0000.0000.0000.000
135A135GLN0-0.015-0.01330.593-0.009-0.0090.0000.0000.0000.000
136A136LYS10.8500.92732.1880.0750.0750.0000.0000.0000.000
137A137VAL00.003-0.00726.673-0.002-0.0020.0000.0000.0000.000
138A138VAL00.0190.02324.5660.0010.0010.0000.0000.0000.000
139A139VAL0-0.037-0.02723.266-0.004-0.0040.0000.0000.0000.000
140A140ALA00.0170.01318.788-0.008-0.0080.0000.0000.0000.000
141A141LYS10.8680.90920.2400.1380.1380.0000.0000.0000.000
142A142VAL00.000-0.01117.975-0.043-0.0430.0000.0000.0000.000
143A143GLY00.0130.00517.0210.0190.0190.0000.0000.0000.000
144A144ALA0-0.0320.00017.610-0.027-0.0270.0000.0000.0000.000
145A145VAL0-0.010-0.00913.827-0.050-0.0500.0000.0000.0000.000
146A146MET0-0.0120.00413.6000.0840.0840.0000.0000.0000.000
147A147PRO00.0170.00414.177-0.118-0.1180.0000.0000.0000.000
148A148SER0-0.057-0.02711.932-0.040-0.0400.0000.0000.0000.000
149A149GLY00.0040.00510.099-0.318-0.3180.0000.0000.0000.000
150A150MET0-0.042-0.0119.168-0.037-0.0370.0000.0000.0000.000
151A151VAL00.0420.0229.8260.2010.2010.0000.0000.0000.000
152A152ILE0-0.016-0.01411.7040.0280.0280.0000.0000.0000.000
153A153LYS10.8800.91313.1490.1000.1000.0000.0000.0000.000
154A154ASP-1-0.799-0.86715.222-0.060-0.0600.0000.0000.0000.000
155A155ALA0-0.0070.00913.9210.0260.0260.0000.0000.0000.000
156A156GLU-1-0.887-0.94215.0740.2220.2220.0000.0000.0000.000
157A157LEU0-0.020-0.00515.4130.0390.0390.0000.0000.0000.000
158A158ARG10.8070.88517.309-0.258-0.2580.0000.0000.0000.000
159A159GLY00.0480.02219.242-0.026-0.0260.0000.0000.0000.000
160A160VAL0-0.036-0.00920.948-0.018-0.0180.0000.0000.0000.000
161A161ALA00.0320.00819.7350.0040.0040.0000.0000.0000.000
162A162SER00.0120.00617.995-0.006-0.0060.0000.0000.0000.000
163A163SER0-0.015-0.02218.371-0.006-0.0060.0000.0000.0000.000
164A164GLY00.0340.00619.175-0.011-0.0110.0000.0000.0000.000
165A165MET0-0.031-0.00614.1440.0040.0040.0000.0000.0000.000
166A166ILE00.0410.03019.381-0.013-0.0130.0000.0000.0000.000
167A167CYS0-0.043-0.00620.817-0.033-0.0330.0000.0000.0000.000
168A168SER00.018-0.01920.6340.0250.0250.0000.0000.0000.000
169A169MET00.020-0.01822.634-0.019-0.0190.0000.0000.0000.000
170A170LYS10.7380.86218.5410.2270.2270.0000.0000.0000.000
171A171GLU-1-0.761-0.85117.312-0.415-0.4150.0000.0000.0000.000
172A172LEU0-0.022-0.00319.390-0.026-0.0260.0000.0000.0000.000
173A173GLY00.0050.01020.3530.0030.0030.0000.0000.0000.000
174A174LEU0-0.028-0.01121.3240.0110.0110.0000.0000.0000.000
175A175PRO0-0.024-0.01522.432-0.015-0.0150.0000.0000.0000.000
176A176ASN0-0.046-0.02123.071-0.007-0.0070.0000.0000.0000.000
177A177ALA00.0380.01322.0610.0040.0040.0000.0000.0000.000
178A178PRO00.0240.03323.7010.0200.0200.0000.0000.0000.000
179A179GLN00.0200.00526.179-0.002-0.0020.0000.0000.0000.000
180A180GLU-1-0.793-0.88527.663-0.099-0.0990.0000.0000.0000.000
181A181LYS10.7630.86322.7160.1330.1330.0000.0000.0000.000
182A182GLY00.0570.03822.823-0.016-0.0160.0000.0000.0000.000
183A183ILE0-0.059-0.03322.861-0.022-0.0220.0000.0000.0000.000
184A184MET0-0.004-0.00725.1520.0120.0120.0000.0000.0000.000
185A185VAL0-0.022-0.00727.6300.0000.0000.0000.0000.0000.000
186A186LEU0-0.063-0.01529.728-0.005-0.0050.0000.0000.0000.000
187A187SER00.010-0.00432.8840.0070.0070.0000.0000.0000.000
188A188ASP-1-0.835-0.93136.338-0.068-0.0680.0000.0000.0000.000
189A189ASP-1-0.986-0.97438.296-0.090-0.0900.0000.0000.0000.000
190A190TYR00.0130.01131.895-0.001-0.0010.0000.0000.0000.000
191A191THR00.008-0.00135.7710.0080.0080.0000.0000.0000.000
192A192VAL0-0.001-0.02032.307-0.008-0.0080.0000.0000.0000.000
193A193GLY00.0030.01130.7990.0050.0050.0000.0000.0000.000
194A194GLN0-0.046-0.01430.884-0.001-0.0010.0000.0000.0000.000
195A195SER0-0.014-0.03428.415-0.011-0.0110.0000.0000.0000.000
196A196PHE0-0.008-0.01826.3330.0090.0090.0000.0000.0000.000
197A197PHE0-0.041-0.01222.935-0.001-0.0010.0000.0000.0000.000
198A198GLU-1-0.936-0.94828.419-0.149-0.1490.0000.0000.0000.000