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: 2N7YR

Calculation Name: 2QKO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QKO

Chain ID: A

ChEMBL ID:

UniProt ID: Q0S912

Base Structure: X-ray

Registration Date: 2023-09-20

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 174
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1699438.349807
FMO2-HF: Nuclear repulsion 1632164.708015
FMO2-HF: Total energy -67273.641792
FMO2-MP2: Total energy -67472.48798


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:PRO)


Summations of interaction energy for fragment #1(A:5:PRO)
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.
-16.045-14.6559.474-5.007-5.8560.025
Interaction energy analysis for fragmet #1(A:5:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.017 / q_NPA : 0.004
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].
3A7ARG10.9450.9682.976-1.5260.6470.013-0.978-1.2080.000
4A8ARG10.9290.9752.893-2.911-1.4060.112-0.492-1.1250.002
5A9ALA00.0390.0195.009-0.861-0.702-0.001-0.021-0.1360.000
6A10ALA0-0.0090.0056.943-0.049-0.0490.0000.0000.0000.000
7A11LEU00.002-0.0067.365-0.093-0.0930.0000.0000.0000.000
8A12VAL00.0100.0048.668-0.139-0.1390.0000.0000.0000.000
9A13ASN0-0.003-0.00110.748-0.137-0.1370.0000.0000.0000.000
10A14ALA00.0490.03512.813-0.046-0.0460.0000.0000.0000.000
11A15ALA0-0.017-0.01813.626-0.048-0.0480.0000.0000.0000.000
12A16ILE00.002-0.00113.925-0.056-0.0560.0000.0000.0000.000
13A17GLU-1-0.753-0.86716.7870.1020.1020.0000.0000.0000.000
14A18VAL00.0100.00318.409-0.020-0.0200.0000.0000.0000.000
15A19LEU0-0.075-0.04117.468-0.026-0.0260.0000.0000.0000.000
16A20ALA00.0060.00420.884-0.023-0.0230.0000.0000.0000.000
17A21ARG10.7140.85021.294-0.243-0.2430.0000.0000.0000.000
18A22GLU-1-0.836-0.90323.7190.2070.2070.0000.0000.0000.000
19A23GLY00.0100.01223.560-0.013-0.0130.0000.0000.0000.000
20A24ALA0-0.034-0.03122.1440.0250.0250.0000.0000.0000.000
21A25ARG10.7490.83822.941-0.143-0.1430.0000.0000.0000.000
22A26GLY00.0220.01924.0640.0030.0030.0000.0000.0000.000
23A27LEU00.0180.02416.3910.0330.0330.0000.0000.0000.000
24A28THR0-0.020-0.01519.4540.0210.0210.0000.0000.0000.000
25A29PHE00.0390.01714.5610.0020.0020.0000.0000.0000.000
26A30ARG10.9640.97616.968-0.311-0.3110.0000.0000.0000.000
27A31ALA00.0490.03819.571-0.013-0.0130.0000.0000.0000.000
28A32VAL00.0100.00113.205-0.003-0.0030.0000.0000.0000.000
29A33ASP-1-0.741-0.88614.1030.8920.8920.0000.0000.0000.000
30A34VAL0-0.045-0.02015.619-0.028-0.0280.0000.0000.0000.000
31A35GLU-1-0.822-0.88116.8240.2210.2210.0000.0000.0000.000
32A36ALA0-0.034-0.00112.0940.0000.0000.0000.0000.0000.000
33A37ASN0-0.015-0.02311.051-0.005-0.0050.0000.0000.0000.000
34A38VAL0-0.051-0.0399.203-0.027-0.0270.0000.0000.0000.000
35A39PRO00.0580.04212.6090.1250.1250.0000.0000.0000.000
36A40LYS10.8970.94714.417-0.422-0.4220.0000.0000.0000.000
37A41GLY00.0020.01414.959-0.066-0.0660.0000.0000.0000.000
38A42THR0-0.065-0.0438.9290.0610.0610.0000.0000.0000.000
39A43ALA00.0180.00110.6810.3040.3040.0000.0000.0000.000
40A44SER0-0.033-0.02711.8390.0770.0770.0000.0000.0000.000
41A45ASN0-0.073-0.03510.781-0.165-0.1650.0000.0000.0000.000
42A46TYR0-0.046-0.0371.985-11.018-13.4659.350-3.516-3.3870.023
43A47PHE0-0.0070.0028.2700.2250.2250.0000.0000.0000.000
44A48PRO00.0100.01510.789-0.169-0.1690.0000.0000.0000.000
45A49SER00.0220.01213.932-0.136-0.1360.0000.0000.0000.000
46A50ARG10.9120.93615.421-0.270-0.2700.0000.0000.0000.000
47A51ASP-1-0.837-0.90817.3400.3080.3080.0000.0000.0000.000
48A52ASP-1-0.885-0.94311.8800.9560.9560.0000.0000.0000.000
49A53LEU00.0100.00612.5020.0290.0290.0000.0000.0000.000
50A54PHE0-0.021-0.02113.583-0.034-0.0340.0000.0000.0000.000
51A55ASP-1-0.837-0.89414.5550.2600.2600.0000.0000.0000.000
52A56GLN00.0250.0157.555-0.031-0.0310.0000.0000.0000.000
53A57VAL0-0.010-0.01011.637-0.087-0.0870.0000.0000.0000.000
54A58GLY00.0230.00713.618-0.080-0.0800.0000.0000.0000.000
55A59LYS10.8370.91712.326-0.068-0.0680.0000.0000.0000.000
56A60ARG10.7870.8496.7620.2230.2230.0000.0000.0000.000
57A61ILE0-0.0170.00312.264-0.056-0.0560.0000.0000.0000.000
58A62HIS00.019-0.01315.612-0.030-0.0300.0000.0000.0000.000
59A63GLU-1-0.809-0.84811.190-0.320-0.3200.0000.0000.0000.000
60A64ARG10.7470.85215.347-0.108-0.1080.0000.0000.0000.000
61A65LEU0-0.0160.01417.2470.0100.0100.0000.0000.0000.000
62A81ASN0-0.016-0.03337.209-0.001-0.0010.0000.0000.0000.000
63A82LEU00.0090.00738.451-0.002-0.0020.0000.0000.0000.000
64A83GLU-1-0.839-0.92439.388-0.041-0.0410.0000.0000.0000.000
65A84LEU00.0560.03833.7340.0000.0000.0000.0000.0000.000
66A85ALA0-0.007-0.00234.690-0.002-0.0020.0000.0000.0000.000
67A86ILE0-0.029-0.01335.1790.0030.0030.0000.0000.0000.000
68A87GLU-1-0.884-0.94435.606-0.048-0.0480.0000.0000.0000.000
69A88TYR0-0.053-0.01726.771-0.003-0.0030.0000.0000.0000.000
70A89MET0-0.014-0.00831.2190.0020.0020.0000.0000.0000.000
71A90GLN0-0.005-0.01932.7180.0020.0020.0000.0000.0000.000
72A91GLY00.0270.01731.6780.0030.0030.0000.0000.0000.000
73A92LEU0-0.069-0.03725.721-0.001-0.0010.0000.0000.0000.000
74A93PHE0-0.012-0.01528.7400.0050.0050.0000.0000.0000.000
75A94GLY00.0390.02331.3610.0060.0060.0000.0000.0000.000
76A95ARG10.7650.85621.7620.0740.0740.0000.0000.0000.000
77A96ILE00.0150.02426.5420.0040.0040.0000.0000.0000.000
78A97THR00.007-0.00926.9170.0100.0100.0000.0000.0000.000
79A98ARG10.9010.96322.2830.0500.0500.0000.0000.0000.000
80A99ASP-1-0.801-0.88322.197-0.031-0.0310.0000.0000.0000.000
81A100ARG10.9070.96622.851-0.047-0.0470.0000.0000.0000.000
82A101THR0-0.017-0.00319.357-0.001-0.0010.0000.0000.0000.000
83A102GLY00.0380.02119.4190.0220.0220.0000.0000.0000.000
84A103TYR00.0590.00420.2940.0140.0140.0000.0000.0000.000
85A104LEU00.0060.00623.6620.0060.0060.0000.0000.0000.000
86A105ALA00.0160.01019.1370.0110.0110.0000.0000.0000.000
87A106LEU0-0.008-0.00120.8220.0170.0170.0000.0000.0000.000
88A107GLN00.0290.01821.8180.0010.0010.0000.0000.0000.000
89A108GLU-1-0.736-0.84623.0400.1690.1690.0000.0000.0000.000
90A109LEU0-0.011-0.00617.4740.0140.0140.0000.0000.0000.000
91A110ARG10.8790.94221.874-0.056-0.0560.0000.0000.0000.000
92A111LEU00.0150.00425.028-0.001-0.0010.0000.0000.0000.000
93A112GLU-1-0.819-0.89922.1920.2260.2260.0000.0000.0000.000
94A113ALA00.0100.01923.1520.0050.0050.0000.0000.0000.000
95A114VAL0-0.020-0.00124.469-0.008-0.0080.0000.0000.0000.000
96A115ARG10.8320.90026.501-0.169-0.1690.0000.0000.0000.000
97A116ARG10.7950.88920.670-0.281-0.2810.0000.0000.0000.000
98A117PRO00.003-0.00823.432-0.005-0.0050.0000.0000.0000.000
99A118GLU-1-0.818-0.88918.7130.1640.1640.0000.0000.0000.000
100A119LEU00.0180.01918.141-0.010-0.0100.0000.0000.0000.000
101A120ARG10.8670.92919.972-0.141-0.1410.0000.0000.0000.000
102A121THR0-0.016-0.01021.068-0.026-0.0260.0000.0000.0000.000
103A122THR0-0.056-0.06015.561-0.049-0.0490.0000.0000.0000.000
104A123LEU00.0150.01618.934-0.025-0.0250.0000.0000.0000.000
105A124THR0-0.037-0.03020.311-0.025-0.0250.0000.0000.0000.000
106A125ARG10.8930.97019.133-0.113-0.1130.0000.0000.0000.000
107A126THR00.0370.01217.233-0.028-0.0280.0000.0000.0000.000
108A127ILE0-0.0040.00719.531-0.021-0.0210.0000.0000.0000.000
109A128SER0-0.032-0.02622.926-0.012-0.0120.0000.0000.0000.000
110A129GLU-1-0.922-0.96218.645-0.055-0.0550.0000.0000.0000.000
111A130ASN0-0.049-0.03121.152-0.026-0.0260.0000.0000.0000.000
112A131LEU00.0590.04023.057-0.006-0.0060.0000.0000.0000.000
113A132LYS10.9160.95725.2000.0380.0380.0000.0000.0000.000
114A133ARG10.8590.92218.9780.0970.0970.0000.0000.0000.000
115A134ASP-1-0.818-0.90225.701-0.061-0.0610.0000.0000.0000.000
116A135ILE0-0.055-0.03827.9410.0010.0010.0000.0000.0000.000
117A136GLY0-0.015-0.00329.4480.0010.0010.0000.0000.0000.000
118A137PHE00.0410.01627.745-0.001-0.0010.0000.0000.0000.000
119A138HIS0-0.022-0.02629.825-0.001-0.0010.0000.0000.0000.000
120A139LEU0-0.052-0.01433.0900.0020.0020.0000.0000.0000.000
121A140ASP-1-0.912-0.95730.929-0.077-0.0770.0000.0000.0000.000
122A141SER0-0.101-0.06032.886-0.001-0.0010.0000.0000.0000.000
123A142GLY0-0.021-0.00834.3710.0000.0000.0000.0000.0000.000
124A143LEU0-0.057-0.01634.8730.0040.0040.0000.0000.0000.000
125A144PRO0-0.0020.01038.5340.0010.0010.0000.0000.0000.000
126A145GLY00.0720.03139.3690.0000.0000.0000.0000.0000.000
127A146ASP-1-0.775-0.87538.716-0.020-0.0200.0000.0000.0000.000
128A147ARG10.9390.96133.0830.0160.0160.0000.0000.0000.000
129A148SER0-0.043-0.05035.5790.0020.0020.0000.0000.0000.000
130A149THR00.0000.00536.7770.0020.0020.0000.0000.0000.000
131A150VAL00.0270.02131.1340.0020.0020.0000.0000.0000.000
132A151LEU0-0.047-0.02332.4110.0030.0030.0000.0000.0000.000
133A152MET0-0.0110.00934.1580.0040.0040.0000.0000.0000.000
134A153LEU00.0380.01633.5050.0030.0030.0000.0000.0000.000
135A154TYR00.0290.01625.8590.0070.0070.0000.0000.0000.000
136A155LEU0-0.023-0.01231.1730.0060.0060.0000.0000.0000.000
137A156ALA00.0090.01333.2610.0050.0050.0000.0000.0000.000
138A157MET00.0390.02031.1450.0040.0040.0000.0000.0000.000
139A158ASN0-0.079-0.05627.7410.0110.0110.0000.0000.0000.000
140A159ALA0-0.011-0.00130.4460.0060.0060.0000.0000.0000.000
141A160LEU00.0240.01733.6420.0040.0040.0000.0000.0000.000
142A161ILE00.008-0.00627.4180.0020.0020.0000.0000.0000.000
143A162VAL0-0.012-0.02328.9070.0060.0060.0000.0000.0000.000
144A163GLU-1-0.865-0.92231.0350.0390.0390.0000.0000.0000.000
145A164HIS00.0370.01632.1390.0030.0030.0000.0000.0000.000
146A165LEU0-0.058-0.03027.0490.0030.0030.0000.0000.0000.000
147A166THR0-0.105-0.07130.7200.0080.0080.0000.0000.0000.000
148A167LEU0-0.0140.00333.0370.0030.0030.0000.0000.0000.000
149A168PRO00.0340.01934.950-0.004-0.0040.0000.0000.0000.000
150A169GLY00.0280.02037.418-0.004-0.0040.0000.0000.0000.000
151A170VAL0-0.043-0.02239.663-0.003-0.0030.0000.0000.0000.000
152A171LEU0-0.035-0.03536.722-0.003-0.0030.0000.0000.0000.000
153A172GLU-1-0.958-0.95840.8030.0180.0180.0000.0000.0000.000
154A173GLY0-0.019-0.00442.665-0.002-0.0020.0000.0000.0000.000
155A174VAL0-0.068-0.03341.958-0.002-0.0020.0000.0000.0000.000
156A175ASP-1-0.793-0.88742.405-0.008-0.0080.0000.0000.0000.000
157A176THR00.012-0.01238.020-0.002-0.0020.0000.0000.0000.000
158A177GLU-1-0.926-0.94639.041-0.022-0.0220.0000.0000.0000.000
159A178ARG10.8720.92140.0830.0030.0030.0000.0000.0000.000
160A179LEU0-0.027-0.00139.763-0.001-0.0010.0000.0000.0000.000
161A180VAL00.014-0.00135.7460.0000.0000.0000.0000.0000.000
162A181ALA00.0510.03238.675-0.002-0.0020.0000.0000.0000.000
163A182ASP-1-0.799-0.87741.225-0.009-0.0090.0000.0000.0000.000
164A183LEU0-0.051-0.02036.2810.0000.0000.0000.0000.0000.000
165A184VAL00.013-0.00136.5820.0000.0000.0000.0000.0000.000
166A185THR0-0.025-0.03239.336-0.002-0.0020.0000.0000.0000.000
167A186ARG10.7850.87342.9720.0070.0070.0000.0000.0000.000
168A187ALA00.0010.00138.7560.0010.0010.0000.0000.0000.000
169A188VAL0-0.0080.00539.170-0.001-0.0010.0000.0000.0000.000
170A189ALA0-0.0260.00541.424-0.001-0.0010.0000.0000.0000.000
171A190THR0-0.019-0.01842.7540.0010.0010.0000.0000.0000.000
172A191PRO0-0.025-0.00345.4500.0000.0000.0000.0000.0000.000
173A192ASP-1-0.878-0.94247.961-0.011-0.0110.0000.0000.0000.000
174A193ALA0-0.107-0.04747.3630.0030.0030.0000.0000.0000.000