FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 37JLL

Calculation Name: 2OPT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OPT

Chain ID: A

ChEMBL ID:

UniProt ID: Q53901

Base Structure: X-ray

Registration Date: 2023-09-27

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2084092.382258
FMO2-HF: Nuclear repulsion 2004329.651024
FMO2-HF: Total energy -79762.731234
FMO2-MP2: Total energy -79994.002992


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:27:ALA)


Summations of interaction energy for fragment #1(A:27:ALA)
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.
-0.7260.816-0.001-0.712-0.829-0.001
Interaction energy analysis for fragmet #1(A:27:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.018 / q_NPA : -0.030
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].
3A29ALA00.0430.0373.771-0.6800.862-0.001-0.712-0.829-0.001
4A30PRO0-0.005-0.0166.5340.3600.3600.0000.0000.0000.000
5A31LEU0-0.0030.0039.741-0.107-0.1070.0000.0000.0000.000
6A32THR00.0280.01611.5500.0270.0270.0000.0000.0000.000
7A33GLN00.0530.00514.3210.0020.0020.0000.0000.0000.000
8A34ASP-1-0.875-0.93315.420-0.315-0.3150.0000.0000.0000.000
9A35ARG10.9520.9919.4570.4980.4980.0000.0000.0000.000
10A36ILE0-0.006-0.00813.1480.0280.0280.0000.0000.0000.000
11A37VAL00.0390.02314.6170.0250.0250.0000.0000.0000.000
12A38VAL00.0280.02814.7840.0120.0120.0000.0000.0000.000
13A39THR0-0.075-0.05812.2940.0030.0030.0000.0000.0000.000
14A40ALA0-0.006-0.01314.6410.0260.0260.0000.0000.0000.000
15A41LEU00.0260.02117.9390.0160.0160.0000.0000.0000.000
16A42GLY00.0320.02617.1390.0070.0070.0000.0000.0000.000
17A43ILE0-0.058-0.03415.8460.0150.0150.0000.0000.0000.000
18A44LEU00.0260.01419.1160.0110.0110.0000.0000.0000.000
19A45ASP-1-0.802-0.88121.373-0.088-0.0880.0000.0000.0000.000
20A46ALA0-0.057-0.02220.4000.0060.0060.0000.0000.0000.000
21A47GLU-1-0.903-0.94019.5980.0040.0040.0000.0000.0000.000
22A48GLY0-0.025-0.01623.7470.0080.0080.0000.0000.0000.000
23A49LEU00.015-0.00524.6780.0020.0020.0000.0000.0000.000
24A50ASP-1-0.908-0.93826.016-0.007-0.0070.0000.0000.0000.000
25A51ALA0-0.0090.01222.5320.0070.0070.0000.0000.0000.000
26A52LEU00.0070.02519.7440.0070.0070.0000.0000.0000.000
27A53SER00.0190.01521.4120.0040.0040.0000.0000.0000.000
28A54MET00.0770.03119.9330.0000.0000.0000.0000.0000.000
29A55ARG10.9330.96618.313-0.094-0.0940.0000.0000.0000.000
30A56ARG10.7630.86516.1460.0070.0070.0000.0000.0000.000
31A57LEU00.0650.03815.0040.0090.0090.0000.0000.0000.000
32A58ALA0-0.001-0.00913.996-0.009-0.0090.0000.0000.0000.000
33A59GLN0-0.009-0.01112.6290.0170.0170.0000.0000.0000.000
34A60GLU-1-0.832-0.92111.6900.0760.0760.0000.0000.0000.000
35A61LEU0-0.0120.0059.554-0.022-0.0220.0000.0000.0000.000
36A62LYS10.7470.8907.022-0.130-0.1300.0000.0000.0000.000
37A63THR00.0220.0239.0610.1090.1090.0000.0000.0000.000
38A64GLY0-0.007-0.00411.3330.0040.0040.0000.0000.0000.000
39A65HIS00.043-0.01514.703-0.027-0.0270.0000.0000.0000.000
40A66ALA0-0.0120.00917.894-0.019-0.0190.0000.0000.0000.000
41A67SER00.0460.01813.429-0.012-0.0120.0000.0000.0000.000
42A68LEU00.0110.01115.317-0.031-0.0310.0000.0000.0000.000
43A69TYR00.0020.00216.830-0.016-0.0160.0000.0000.0000.000
44A70ALA0-0.036-0.02818.885-0.008-0.0080.0000.0000.0000.000
45A71HIS0-0.058-0.02215.302-0.037-0.0370.0000.0000.0000.000
46A72VAL0-0.017-0.02418.458-0.015-0.0150.0000.0000.0000.000
47A73GLY00.0370.06121.0570.0010.0010.0000.0000.0000.000
48A74ASN0-0.065-0.08622.6820.0080.0080.0000.0000.0000.000
49A75ARG10.8890.91924.0350.0060.0060.0000.0000.0000.000
50A76ASP-1-0.859-0.94025.076-0.024-0.0240.0000.0000.0000.000
51A77GLU-1-0.806-0.86825.533-0.025-0.0250.0000.0000.0000.000
52A78LEU0-0.024-0.01519.413-0.010-0.0100.0000.0000.0000.000
53A79LEU00.005-0.01623.274-0.011-0.0110.0000.0000.0000.000
54A80ASP-1-0.802-0.87725.562-0.049-0.0490.0000.0000.0000.000
55A81LEU0-0.047-0.03221.589-0.008-0.0080.0000.0000.0000.000
56A82VAL0-0.056-0.02821.133-0.012-0.0120.0000.0000.0000.000
57A83PHE00.0220.00323.493-0.005-0.0050.0000.0000.0000.000
58A84ASP-1-0.759-0.88726.032-0.099-0.0990.0000.0000.0000.000
59A85ILE0-0.021-0.00619.755-0.006-0.0060.0000.0000.0000.000
60A86VAL00.0240.00324.078-0.008-0.0080.0000.0000.0000.000
61A87LEU0-0.0030.00025.7150.0030.0030.0000.0000.0000.000
62A88THR0-0.036-0.00424.2870.0000.0000.0000.0000.0000.000
63A89GLU-1-0.897-0.93125.155-0.113-0.1130.0000.0000.0000.000
64A90VAL0-0.091-0.03528.7590.0060.0060.0000.0000.0000.000
65A91GLU-1-0.922-0.95231.435-0.103-0.1030.0000.0000.0000.000
66A92VAL0-0.037-0.01634.2300.0060.0060.0000.0000.0000.000
67A93PRO00.0230.01537.364-0.003-0.0030.0000.0000.0000.000
68A94GLU-1-0.838-0.91239.354-0.066-0.0660.0000.0000.0000.000
69A95PRO00.0090.00541.1730.0010.0010.0000.0000.0000.000
70A96GLU-1-0.810-0.86743.590-0.056-0.0560.0000.0000.0000.000
71A97PRO0-0.009-0.02346.9680.0020.0020.0000.0000.0000.000
72A98GLY0-0.025-0.01350.7610.0000.0000.0000.0000.0000.000
73A99ARG10.7370.83542.8090.0550.0550.0000.0000.0000.000
74A100TRP00.0050.00747.8870.0000.0000.0000.0000.0000.000
75A101ALA00.0470.01447.492-0.001-0.0010.0000.0000.0000.000
76A102GLU-1-0.801-0.92246.601-0.042-0.0420.0000.0000.0000.000
77A103GLN00.0160.01943.3780.0000.0000.0000.0000.0000.000
78A104VAL00.0490.03242.694-0.002-0.0020.0000.0000.0000.000
79A105LYS10.8620.92842.8760.0370.0370.0000.0000.0000.000
80A106GLU-1-0.874-0.93239.522-0.062-0.0620.0000.0000.0000.000
81A107MET00.0410.02538.463-0.003-0.0030.0000.0000.0000.000
82A108CYS0-0.060-0.02437.992-0.001-0.0010.0000.0000.0000.000
83A109ARG10.7520.83638.5900.0460.0460.0000.0000.0000.000
84A110SER0-0.004-0.00633.506-0.002-0.0020.0000.0000.0000.000
85A111LEU00.0300.02733.662-0.004-0.0040.0000.0000.0000.000
86A112ARG10.7850.86534.0120.0440.0440.0000.0000.0000.000
87A113ARG10.9170.95831.7790.0730.0730.0000.0000.0000.000
88A114MET00.0090.03028.775-0.002-0.0020.0000.0000.0000.000
89A115PHE00.032-0.00929.559-0.001-0.0010.0000.0000.0000.000
90A116LEU0-0.066-0.02230.9410.0020.0020.0000.0000.0000.000
91A117ALA0-0.054-0.00527.2750.0010.0010.0000.0000.0000.000
92A118HIS10.7590.83723.4950.0980.0980.0000.0000.0000.000
93A119ARG10.9641.00626.0570.0370.0370.0000.0000.0000.000
94A120ASP-1-0.828-0.93027.162-0.030-0.0300.0000.0000.0000.000
95A121LEU00.0280.02026.9750.0030.0030.0000.0000.0000.000
96A122ALA00.0310.00729.4220.0000.0000.0000.0000.0000.000
97A123ARG10.7520.85030.6510.0210.0210.0000.0000.0000.000
98A124ILE0-0.031-0.01326.5080.0020.0020.0000.0000.0000.000
99A125ALA00.0230.00330.8880.0010.0010.0000.0000.0000.000
100A126ILE0-0.0370.00032.8960.0010.0010.0000.0000.0000.000
101A127ASP-1-0.905-0.94334.032-0.027-0.0270.0000.0000.0000.000
102A128ARG10.7440.86329.7320.0350.0350.0000.0000.0000.000
103A129VAL00.0210.00734.6210.0000.0000.0000.0000.0000.000
104A130PRO0-0.0090.00832.588-0.003-0.0030.0000.0000.0000.000
105A131LEU0-0.022-0.03233.228-0.001-0.0010.0000.0000.0000.000
106A132GLY00.0280.03629.1740.0010.0010.0000.0000.0000.000
107A133PRO0-0.035-0.02526.4860.0030.0030.0000.0000.0000.000
108A134ASN0-0.015-0.03225.2440.0000.0000.0000.0000.0000.000
109A135GLY00.0040.00429.4910.0040.0040.0000.0000.0000.000
110A136MET0-0.037-0.02632.2140.0040.0040.0000.0000.0000.000
111A137VAL0-0.0050.00831.6720.0030.0030.0000.0000.0000.000
112A138GLY00.0410.02533.6210.0030.0030.0000.0000.0000.000
113A139MET0-0.0010.00935.1000.0050.0050.0000.0000.0000.000
114A140GLU-1-0.910-0.95337.623-0.051-0.0510.0000.0000.0000.000
115A141ARG10.7750.87035.4050.0770.0770.0000.0000.0000.000
116A142THR0-0.007-0.02438.4190.0030.0030.0000.0000.0000.000
117A143MET0-0.049-0.02040.8830.0040.0040.0000.0000.0000.000
118A144ASN0-0.0200.00042.3010.0050.0050.0000.0000.0000.000
119A145LEU00.0140.00642.4620.0020.0020.0000.0000.0000.000
120A146LEU0-0.0070.01644.4720.0030.0030.0000.0000.0000.000
121A147ARG10.9280.93847.0480.0400.0400.0000.0000.0000.000
122A148SER0-0.090-0.03847.4780.0010.0010.0000.0000.0000.000
123A149GLY0-0.013-0.01649.3890.0010.0010.0000.0000.0000.000
124A150GLY0-0.049-0.02351.4120.0020.0020.0000.0000.0000.000
125A151LEU0-0.042-0.01249.5770.0020.0020.0000.0000.0000.000
126A152HIS00.0340.01752.377-0.001-0.0010.0000.0000.0000.000
127A153ASP-1-0.800-0.91451.182-0.033-0.0330.0000.0000.0000.000
128A154GLU-1-0.938-0.96650.418-0.025-0.0250.0000.0000.0000.000
129A155LEU0-0.0200.00350.9730.0000.0000.0000.0000.0000.000
130A156ALA0-0.035-0.01548.239-0.001-0.0010.0000.0000.0000.000
131A157ALA00.0210.00246.202-0.002-0.0020.0000.0000.0000.000
132A158TYR00.0170.00345.994-0.001-0.0010.0000.0000.0000.000
133A159GLY00.0340.01447.0750.0000.0000.0000.0000.0000.000
134A160GLY00.0330.00143.823-0.001-0.0010.0000.0000.0000.000
135A161ASP-1-0.933-0.95242.592-0.035-0.0350.0000.0000.0000.000
136A162LEU0-0.0140.00443.1920.0000.0000.0000.0000.0000.000
137A163LEU0-0.013-0.02242.7470.0000.0000.0000.0000.0000.000
138A164SER0-0.033-0.01038.677-0.001-0.0010.0000.0000.0000.000
139A165THR00.0330.01739.6800.0000.0000.0000.0000.0000.000
140A166PHE0-0.034-0.00841.7660.0010.0010.0000.0000.0000.000
141A167VAL0-0.002-0.01137.5390.0000.0000.0000.0000.0000.000
142A168THR0-0.020-0.02035.881-0.002-0.0020.0000.0000.0000.000
143A169ALA0-0.016-0.00638.0130.0010.0010.0000.0000.0000.000
144A170GLU-1-0.807-0.88440.597-0.028-0.0280.0000.0000.0000.000
145A171ALA00.0070.01835.3430.0010.0010.0000.0000.0000.000
146A172LEU0-0.0010.00035.6670.0010.0010.0000.0000.0000.000
147A173GLU-1-0.813-0.88637.255-0.023-0.0230.0000.0000.0000.000
148A174GLN00.0430.02437.3570.0010.0010.0000.0000.0000.000
149A175SER0-0.028-0.01734.045-0.001-0.0010.0000.0000.0000.000
150A176SER0-0.092-0.05035.9540.0030.0030.0000.0000.0000.000
151A177ARG10.7600.88637.5630.0290.0290.0000.0000.0000.000
152A188ALA00.0280.01041.5520.0010.0010.0000.0000.0000.000
153A189GLY00.0320.00043.5720.0000.0000.0000.0000.0000.000
154A190VAL00.0170.00945.7590.0010.0010.0000.0000.0000.000
155A191PHE00.008-0.00546.5230.0000.0000.0000.0000.0000.000
156A192ALA00.0720.03747.9540.0010.0010.0000.0000.0000.000
157A193ASP-1-0.834-0.92449.686-0.015-0.0150.0000.0000.0000.000
158A194GLN0-0.089-0.03450.9810.0010.0010.0000.0000.0000.000
159A195LEU00.0140.01451.5350.0010.0010.0000.0000.0000.000
160A196HIS0-0.0170.00053.4820.0000.0000.0000.0000.0000.000
161A197GLY00.0100.00855.2990.0000.0000.0000.0000.0000.000
162A198TYR0-0.0100.00356.7750.0010.0010.0000.0000.0000.000
163A199LEU0-0.004-0.00456.1830.0000.0000.0000.0000.0000.000
164A200LYS10.9540.97159.1000.0120.0120.0000.0000.0000.000
165A201SER0-0.122-0.07461.0050.0000.0000.0000.0000.0000.000
166A202LEU00.0270.02161.5980.0010.0010.0000.0000.0000.000
167A203PRO00.001-0.00864.4800.0000.0000.0000.0000.0000.000
168A204ALA00.0430.02167.7330.0000.0000.0000.0000.0000.000
169A205THR0-0.031-0.01768.6870.0000.0000.0000.0000.0000.000
170A206SER0-0.031-0.01068.4690.0000.0000.0000.0000.0000.000
171A207PHE00.006-0.00764.2800.0000.0000.0000.0000.0000.000
172A208PRO00.0370.03365.2330.0000.0000.0000.0000.0000.000
173A209ASN00.002-0.01563.4200.0000.0000.0000.0000.0000.000
174A210LEU00.0370.02059.660-0.001-0.0010.0000.0000.0000.000
175A211VAL00.0140.01160.6020.0000.0000.0000.0000.0000.000
176A212HIS0-0.073-0.03261.9140.0000.0000.0000.0000.0000.000
177A213LEU0-0.014-0.01958.588-0.001-0.0010.0000.0000.0000.000
178A214ALA00.0270.03757.363-0.001-0.0010.0000.0000.0000.000
179A215GLY00.0610.03255.2640.0000.0000.0000.0000.0000.000
180A216PRO00.004-0.00353.710-0.001-0.0010.0000.0000.0000.000
181A217ILE0-0.013-0.00952.765-0.001-0.0010.0000.0000.0000.000
182A218THR0-0.026-0.02451.1320.0000.0000.0000.0000.0000.000
183A219SER0-0.114-0.04449.8850.0000.0000.0000.0000.0000.000
184A220LEU0-0.025-0.02348.483-0.001-0.0010.0000.0000.0000.000
185A221ASP-1-0.833-0.89245.133-0.030-0.0300.0000.0000.0000.000
186A222SER00.0580.00041.3700.0000.0000.0000.0000.0000.000
187A223ASP-1-0.802-0.86641.326-0.043-0.0430.0000.0000.0000.000
188A224ARG10.8320.92743.7890.0290.0290.0000.0000.0000.000
189A225ARG10.7140.81845.3980.0270.0270.0000.0000.0000.000
190A226PHE00.0520.01640.7030.0000.0000.0000.0000.0000.000
191A227GLU-1-0.775-0.87644.047-0.042-0.0420.0000.0000.0000.000
192A228LEU0-0.031-0.00446.8300.0010.0010.0000.0000.0000.000
193A229GLY00.010-0.00247.8440.0010.0010.0000.0000.0000.000
194A230LEU00.0060.00643.9270.0000.0000.0000.0000.0000.000
195A231GLU-1-0.918-0.96147.231-0.031-0.0310.0000.0000.0000.000
196A232ILE0-0.045-0.01950.7160.0010.0010.0000.0000.0000.000
197A233ILE00.0170.01246.9900.0010.0010.0000.0000.0000.000
198A234ILE00.0150.01346.4770.0000.0000.0000.0000.0000.000
199A235ALA0-0.025-0.01350.6090.0000.0000.0000.0000.0000.000
200A236GLY0-0.0050.00353.6750.0010.0010.0000.0000.0000.000
201A237LEU00.007-0.00148.4790.0010.0010.0000.0000.0000.000
202A238LEU0-0.002-0.00853.0130.0000.0000.0000.0000.0000.000
203A239ALA0-0.060-0.02155.1530.0010.0010.0000.0000.0000.000
204A240GLY00.0540.02756.6420.0010.0010.0000.0000.0000.000
205A241ALA0-0.032-0.02754.8550.0000.0000.0000.0000.0000.000
206A242GLY0-0.019-0.01956.9600.0000.0000.0000.0000.0000.000
207A243GLU-1-0.987-0.98460.165-0.021-0.0210.0000.0000.0000.000
208A244ALA0-0.043-0.01558.9350.0000.0000.0000.0000.0000.000
209A245ALA0-0.090-0.02660.1520.0010.0010.0000.0000.0000.000