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: 3Q66L

Calculation Name: 2QVA-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QVA

Chain ID: A

ChEMBL ID:

UniProt ID: Q7JVK6

Base Structure: X-ray

Registration Date: 2023-06-20

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1907041.290387
FMO2-HF: Nuclear repulsion 1834410.835193
FMO2-HF: Total energy -72630.455194
FMO2-MP2: Total energy -72844.886573


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:5:VAL)


Summations of interaction energy for fragment #1(A:5:VAL)
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.
-0.1081.287-0.008-0.483-0.9030.001
Interaction energy analysis for fragmet #1(A:5:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.013
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].
3A7LEU00.0920.0353.8620.0861.352-0.007-0.475-0.7840.001
4A8ASP-1-0.827-0.8946.4410.2730.2730.0000.0000.0000.000
5A9ILE0-0.064-0.0354.914-0.005-0.0050.0000.0000.0000.000
6A10PHE00.0040.0044.417-0.175-0.046-0.001-0.008-0.1190.000
7A11SER0-0.034-0.0299.391-0.107-0.1070.0000.0000.0000.000
8A12ASN0-0.046-0.02311.301-0.035-0.0350.0000.0000.0000.000
9A13TYR00.0220.00410.974-0.096-0.0960.0000.0000.0000.000
10A14GLN0-0.055-0.01813.870-0.045-0.0450.0000.0000.0000.000
11A15LYS11.0160.99715.689-0.123-0.1230.0000.0000.0000.000
12A16TYR0-0.0030.02217.038-0.010-0.0100.0000.0000.0000.000
13A17ILE00.0330.00714.834-0.014-0.0140.0000.0000.0000.000
14A18ASP-1-0.852-0.91518.9560.0410.0410.0000.0000.0000.000
15A19ASN0-0.027-0.03021.525-0.014-0.0140.0000.0000.0000.000
16A20GLU-1-0.786-0.84721.8140.1300.1300.0000.0000.0000.000
17A21GLN0-0.035-0.02122.266-0.005-0.0050.0000.0000.0000.000
18A22GLU-1-0.928-0.95624.7800.0510.0510.0000.0000.0000.000
19A23VAL00.0210.01827.025-0.007-0.0070.0000.0000.0000.000
20A24ARG10.8540.92224.266-0.105-0.1050.0000.0000.0000.000
21A25GLU-1-0.820-0.87528.8870.0320.0320.0000.0000.0000.000
22A26ASN0-0.046-0.03930.718-0.009-0.0090.0000.0000.0000.000
23A27ILE00.0060.01031.882-0.004-0.0040.0000.0000.0000.000
24A28ARG10.8260.87928.289-0.047-0.0470.0000.0000.0000.000
25A29ILE0-0.033-0.02934.267-0.005-0.0050.0000.0000.0000.000
26A30VAL00.0320.01636.863-0.003-0.0030.0000.0000.0000.000
27A31VAL00.0240.01236.091-0.002-0.0020.0000.0000.0000.000
28A32ARG10.9210.97137.918-0.028-0.0280.0000.0000.0000.000
29A33GLU-1-0.859-0.91340.0770.0250.0250.0000.0000.0000.000
30A34ILE00.0270.02041.050-0.002-0.0020.0000.0000.0000.000
31A35GLU-1-0.850-0.88441.5480.0240.0240.0000.0000.0000.000
32A36HIS00.0620.02143.648-0.001-0.0010.0000.0000.0000.000
33A37LEU0-0.021-0.01346.229-0.002-0.0020.0000.0000.0000.000
34A38SER00.052-0.00146.246-0.001-0.0010.0000.0000.0000.000
35A39LYS10.8260.92146.767-0.021-0.0210.0000.0000.0000.000
36A40GLU-1-0.832-0.89749.1370.0150.0150.0000.0000.0000.000
37A41ALA00.0320.01351.751-0.001-0.0010.0000.0000.0000.000
38A42GLN00.0500.02949.3810.0000.0000.0000.0000.0000.000
39A43ILE0-0.039-0.02652.699-0.001-0.0010.0000.0000.0000.000
40A44LYS10.8160.90454.560-0.016-0.0160.0000.0000.0000.000
41A45LEU00.0400.01455.027-0.001-0.0010.0000.0000.0000.000
42A46GLN0-0.051-0.02054.5850.0000.0000.0000.0000.0000.000
43A47ILE00.0250.01757.997-0.001-0.0010.0000.0000.0000.000
44A48ILE00.0210.01859.721-0.001-0.0010.0000.0000.0000.000
45A49HIS0-0.079-0.04257.997-0.001-0.0010.0000.0000.0000.000
46A50SER0-0.083-0.05163.138-0.001-0.0010.0000.0000.0000.000
47A51ASP-1-0.757-0.86065.7110.0110.0110.0000.0000.0000.000
48A52LEU0-0.003-0.01066.7630.0010.0010.0000.0000.0000.000
49A53SER0-0.088-0.05968.4980.0000.0000.0000.0000.0000.000
50A54GLN0-0.031-0.02865.0460.0010.0010.0000.0000.0000.000
51A55ILE0-0.0010.01464.0880.0010.0010.0000.0000.0000.000
52A56SER00.0490.01463.8050.0010.0010.0000.0000.0000.000
53A57ALA0-0.0010.00864.5310.0010.0010.0000.0000.0000.000
54A58ALA00.002-0.00360.4020.0000.0000.0000.0000.0000.000
55A59CYS0-0.0130.00859.5910.0010.0010.0000.0000.0000.000
56A60GLY00.0380.02659.6950.0010.0010.0000.0000.0000.000
57A61LEU0-0.036-0.01957.8270.0010.0010.0000.0000.0000.000
58A62ALA00.016-0.00355.6670.0010.0010.0000.0000.0000.000
59A63ARG10.8260.88255.039-0.022-0.0220.0000.0000.0000.000
60A64LYS10.9290.96754.893-0.019-0.0190.0000.0000.0000.000
61A65GLN0-0.053-0.03352.3110.0010.0010.0000.0000.0000.000
62A66VAL00.005-0.00251.2770.0010.0010.0000.0000.0000.000
63A67GLU-1-0.860-0.93350.9510.0250.0250.0000.0000.0000.000
64A68LEU0-0.053-0.01950.5360.0010.0010.0000.0000.0000.000
65A69CYS0-0.065-0.03446.6570.0010.0010.0000.0000.0000.000
66A70ALA00.0700.04346.4470.0020.0020.0000.0000.0000.000
67A71GLN0-0.051-0.02947.0520.0020.0020.0000.0000.0000.000
68A72LYS10.7830.88243.659-0.027-0.0270.0000.0000.0000.000
69A73TYR00.0620.02341.1780.0010.0010.0000.0000.0000.000
70A74GLN0-0.066-0.02942.2030.0040.0040.0000.0000.0000.000
71A75LYS10.8140.89239.742-0.040-0.0400.0000.0000.0000.000
72A76LEU0-0.026-0.01336.6290.0020.0020.0000.0000.0000.000
73A77ALA00.0090.00237.4510.0050.0050.0000.0000.0000.000
74A78GLU-1-0.865-0.91637.7550.0510.0510.0000.0000.0000.000
75A79LEU0-0.026-0.00734.2190.0030.0030.0000.0000.0000.000
76A80VAL0-0.0100.00732.9170.0060.0060.0000.0000.0000.000
77A81PRO0-0.0140.00428.9580.0000.0000.0000.0000.0000.000
78A82ALA00.0310.00331.1240.0090.0090.0000.0000.0000.000
79A83GLY00.0040.01532.802-0.004-0.0040.0000.0000.0000.000
80A84GLN0-0.065-0.05626.8890.0170.0170.0000.0000.0000.000
81A85TYR00.0360.01031.1690.0000.0000.0000.0000.0000.000
82A86TYR0-0.034-0.06531.8890.0000.0000.0000.0000.0000.000
83A87ARG10.7720.89322.084-0.161-0.1610.0000.0000.0000.000
84A88TYR0-0.047-0.06226.1610.0010.0010.0000.0000.0000.000
85A89SER00.0810.04531.235-0.004-0.0040.0000.0000.0000.000
86A90ASP-1-0.903-0.93231.6490.0740.0740.0000.0000.0000.000
87A91HIS0-0.072-0.03629.6080.0000.0000.0000.0000.0000.000
88A92TRP00.028-0.00334.246-0.005-0.0050.0000.0000.0000.000
89A93THR00.0140.01037.334-0.002-0.0020.0000.0000.0000.000
90A94PHE00.004-0.00335.640-0.003-0.0030.0000.0000.0000.000
91A95ILE0-0.042-0.02340.027-0.003-0.0030.0000.0000.0000.000
92A96THR00.0240.00541.977-0.001-0.0010.0000.0000.0000.000
93A97GLN00.0160.00741.513-0.001-0.0010.0000.0000.0000.000
94A98ARG10.7940.88844.470-0.030-0.0300.0000.0000.0000.000
95A99LEU00.0210.00345.575-0.002-0.0020.0000.0000.0000.000
96A100ILE0-0.0090.01945.688-0.001-0.0010.0000.0000.0000.000
97A101PHE0-0.051-0.01649.326-0.002-0.0020.0000.0000.0000.000
98A102ILE0-0.026-0.01249.761-0.002-0.0020.0000.0000.0000.000
99A103ILE00.0140.00250.748-0.001-0.0010.0000.0000.0000.000
100A104ALA00.009-0.00253.606-0.001-0.0010.0000.0000.0000.000
101A105LEU0-0.017-0.00955.235-0.001-0.0010.0000.0000.0000.000
102A106VAL0-0.010-0.01056.848-0.001-0.0010.0000.0000.0000.000
103A107ILE00.0240.00857.982-0.001-0.0010.0000.0000.0000.000
104A108TYR0-0.028-0.00259.490-0.001-0.0010.0000.0000.0000.000
105A109LEU0-0.042-0.03660.220-0.001-0.0010.0000.0000.0000.000
106A110GLU-1-0.837-0.89161.7960.0210.0210.0000.0000.0000.000
107A111ALA0-0.045-0.02563.949-0.001-0.0010.0000.0000.0000.000
108A112GLY00.0020.01864.3760.0000.0000.0000.0000.0000.000
109A113PHE0-0.055-0.03360.3240.0000.0000.0000.0000.0000.000
110A114LEU00.008-0.00155.1750.0000.0000.0000.0000.0000.000
111A115VAL00.0160.02254.0150.0000.0000.0000.0000.0000.000
112A116THR00.0630.04854.7860.0010.0010.0000.0000.0000.000
113A117ARG10.8070.88845.929-0.049-0.0490.0000.0000.0000.000
114A118GLU-1-0.800-0.91450.6490.0420.0420.0000.0000.0000.000
115A119THR00.0150.00752.2690.0000.0000.0000.0000.0000.000
116A120VAL0-0.020-0.01249.340-0.001-0.0010.0000.0000.0000.000
117A121ALA0-0.010-0.00848.3720.0000.0000.0000.0000.0000.000
118A122GLU-1-0.956-0.96949.4270.0330.0330.0000.0000.0000.000
119A123MET0-0.046-0.03152.252-0.001-0.0010.0000.0000.0000.000
120A124LEU0-0.022-0.00746.768-0.001-0.0010.0000.0000.0000.000
121A125GLY0-0.0120.00647.7450.0010.0010.0000.0000.0000.000
122A126LEU0-0.042-0.01643.5980.0020.0020.0000.0000.0000.000
123A127LYS10.8030.87844.110-0.054-0.0540.0000.0000.0000.000
124A128ILE00.0430.01845.8360.0000.0000.0000.0000.0000.000
125A129SER0-0.069-0.05744.3220.0010.0010.0000.0000.0000.000
126A130GLN00.0640.01836.6200.0030.0030.0000.0000.0000.000
127A131SER0-0.019-0.00840.1370.0040.0040.0000.0000.0000.000
128A132GLU-1-0.760-0.86042.0000.0540.0540.0000.0000.0000.000
129A133GLY0-0.0040.00841.234-0.003-0.0030.0000.0000.0000.000
130A134PHE00.0400.03237.4860.0020.0020.0000.0000.0000.000
131A135HIS0-0.046-0.01738.424-0.004-0.0040.0000.0000.0000.000
132A136LEU00.0340.03541.9350.0010.0010.0000.0000.0000.000
133A137ASP-1-0.742-0.84239.3770.0660.0660.0000.0000.0000.000
134A138VAL0-0.005-0.01342.926-0.004-0.0040.0000.0000.0000.000
135A139GLU-1-0.871-0.93540.9080.0550.0550.0000.0000.0000.000
136A140ASP-1-0.800-0.89440.8420.0510.0510.0000.0000.0000.000
137A141TYR0-0.038-0.05343.598-0.003-0.0030.0000.0000.0000.000
138A142LEU00.0140.00546.675-0.003-0.0030.0000.0000.0000.000
139A143LEU00.0140.00042.260-0.003-0.0030.0000.0000.0000.000
140A144GLY00.0240.01546.577-0.002-0.0020.0000.0000.0000.000
141A145ILE0-0.012-0.01448.415-0.003-0.0030.0000.0000.0000.000
142A146LEU0-0.0080.00647.487-0.002-0.0020.0000.0000.0000.000
143A147GLN0-0.043-0.02346.920-0.001-0.0010.0000.0000.0000.000
144A148LEU00.0180.02850.551-0.002-0.0020.0000.0000.0000.000
145A149ALA00.0550.03353.884-0.002-0.0020.0000.0000.0000.000
146A150SER0-0.064-0.03352.449-0.002-0.0020.0000.0000.0000.000
147A151GLU-1-0.780-0.88254.3970.0180.0180.0000.0000.0000.000
148A152LEU00.0150.00056.042-0.001-0.0010.0000.0000.0000.000
149A153SER00.0160.00157.765-0.001-0.0010.0000.0000.0000.000
150A154ARG10.8210.91252.388-0.022-0.0220.0000.0000.0000.000
151A155PHE00.0410.01359.737-0.001-0.0010.0000.0000.0000.000
152A156ALA00.0260.02562.005-0.001-0.0010.0000.0000.0000.000
153A157THR0-0.016-0.00262.386-0.001-0.0010.0000.0000.0000.000
154A158ASN0-0.023-0.03761.380-0.001-0.0010.0000.0000.0000.000
155A159SER0-0.022-0.02065.281-0.001-0.0010.0000.0000.0000.000
156A160VAL0-0.033-0.00767.846-0.001-0.0010.0000.0000.0000.000
157A161THR0-0.041-0.01766.449-0.001-0.0010.0000.0000.0000.000
158A162MET0-0.059-0.00266.203-0.001-0.0010.0000.0000.0000.000
159A163GLY0-0.0100.00970.9750.0000.0000.0000.0000.0000.000
160A164ASP-1-0.804-0.88970.5220.0140.0140.0000.0000.0000.000
161A165TYR00.025-0.01670.9500.0010.0010.0000.0000.0000.000
162A166GLU-1-0.919-0.95371.9230.0140.0140.0000.0000.0000.000
163A167ARG10.8950.94466.749-0.014-0.0140.0000.0000.0000.000
164A168SER0-0.031-0.02667.2860.0010.0010.0000.0000.0000.000
165A169LEU0-0.0100.00567.2590.0010.0010.0000.0000.0000.000
166A170ASN0-0.028-0.02868.3020.0010.0010.0000.0000.0000.000
167A171ILE0-0.024-0.00362.4440.0010.0010.0000.0000.0000.000
168A172SER0-0.032-0.03563.4760.0010.0010.0000.0000.0000.000
169A173HIS0-0.019-0.00664.2580.0010.0010.0000.0000.0000.000
170A174PHE00.0460.03158.9730.0010.0010.0000.0000.0000.000
171A175ILE0-0.013-0.00658.8790.0010.0010.0000.0000.0000.000
172A176GLY00.0040.00859.7240.0010.0010.0000.0000.0000.000
173A177ASP-1-0.888-0.93461.0690.0240.0240.0000.0000.0000.000
174A178LEU0-0.030-0.01555.9640.0010.0010.0000.0000.0000.000
175A179ASN0-0.001-0.01056.1420.0020.0020.0000.0000.0000.000
176A180THR0-0.056-0.04456.7600.0010.0010.0000.0000.0000.000
177A181GLY00.0220.01256.2740.0010.0010.0000.0000.0000.000
178A182PHE00.016-0.00450.1280.0010.0010.0000.0000.0000.000
179A183ARG10.8750.94452.542-0.025-0.0250.0000.0000.0000.000
180A184LEU0-0.037-0.01054.5100.0000.0000.0000.0000.0000.000
181A185LEU0-0.058-0.00648.4470.0010.0010.0000.0000.0000.000
182A186ASN0-0.063-0.02947.9550.0020.0020.0000.0000.0000.000