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: 8J1LY

Calculation Name: 2QH9-A-Xray316

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QH9

Chain ID: A

ChEMBL ID:

UniProt ID: O28839

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 179
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1943447.137753
FMO2-HF: Nuclear repulsion 1871783.897029
FMO2-HF: Total energy -71663.240724
FMO2-MP2: Total energy -71867.736726


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:-2:GLY )


Summations of interaction energy for fragment #1(A:-2:GLY )
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.
-8.687-5.0593.505-3.014-4.1180.011
Interaction energy analysis for fragmet #1(A:-2:GLY )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.045 / q_NPA : 0.021
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].
3A0ALA 0-0.019-0.0103.265-2.567-0.2580.187-1.223-1.2730.009
4A1MET 00.0260.0292.161-6.174-5.2813.304-1.714-2.4820.002
5A2LYS 10.9820.9993.5811.0601.4470.014-0.067-0.3340.000
6A3LYS 10.9300.9656.167-0.552-0.5520.0000.0000.0000.000
7A4TRP 0-0.026-0.0076.215-0.006-0.0060.0000.0000.0000.000
8A5ARG 10.8250.8898.868-0.182-0.1820.0000.0000.0000.000
9A6PHE 00.0160.0157.0630.0020.0020.0000.0000.0000.000
10A7LEU 00.0050.01013.1800.0240.0240.0000.0000.0000.000
11A8GLY 00.008-0.00216.509-0.024-0.0240.0000.0000.0000.000
12A9ILE 0-0.031-0.01818.0510.0210.0210.0000.0000.0000.000
13A10ASP -1-0.835-0.92921.590-0.135-0.1350.0000.0000.0000.000
14A11ASP -1-0.849-0.92524.245-0.073-0.0730.0000.0000.0000.000
15A12SER 0-0.0060.00228.018-0.005-0.0050.0000.0000.0000.000
16A13PHE 00.003-0.01931.2110.0030.0030.0000.0000.0000.000
17A14ASP -1-0.811-0.89434.667-0.044-0.0440.0000.0000.0000.000
18A15ASP -1-0.935-0.97038.177-0.037-0.0370.0000.0000.0000.000
19A16ARG 10.8910.94440.4890.0330.0330.0000.0000.0000.000
20A17LYS 10.8820.95036.3180.0370.0370.0000.0000.0000.000
21A18CYS 00.0100.04332.284-0.004-0.0040.0000.0000.0000.000
22A19CYS 0-0.080-0.01531.6600.0020.0020.0000.0000.0000.000
23A20VAL 00.0370.01126.394-0.006-0.0060.0000.0000.0000.000
24A21VAL 0-0.013-0.00624.5940.0070.0070.0000.0000.0000.000
25A22GLY 00.001-0.00822.186-0.011-0.0110.0000.0000.0000.000
26A23CYS 0-0.025-0.00220.0980.0080.0080.0000.0000.0000.000
27A24VAL 00.0300.00716.539-0.016-0.0160.0000.0000.0000.000
28A25THR 0-0.0020.00114.560-0.009-0.0090.0000.0000.0000.000
29A26CYS 0-0.0080.01611.8650.0230.0230.0000.0000.0000.000
30A27GLY 00.0370.01710.7510.0230.0230.0000.0000.0000.000
31A28GLY 0-0.028-0.01711.701-0.014-0.0140.0000.0000.0000.000
32A29TYR 0-0.026-0.00114.4110.0140.0140.0000.0000.0000.000
33A30VAL 00.0430.00517.0810.0060.0060.0000.0000.0000.000
34A31GLU -1-0.859-0.93016.9410.0480.0480.0000.0000.0000.000
35A32GLY 0-0.028-0.01520.2810.0130.0130.0000.0000.0000.000
36A33PHE 00.0070.00321.820-0.013-0.0130.0000.0000.0000.000
37A34LEU 0-0.090-0.03922.3700.0100.0100.0000.0000.0000.000
38A35TYR 00.017-0.02525.757-0.008-0.0080.0000.0000.0000.000
39A36THR 0-0.041-0.03428.6750.0080.0080.0000.0000.0000.000
40A37GLU -1-0.797-0.86230.917-0.039-0.0390.0000.0000.0000.000
41A38ILE 0-0.097-0.04930.3730.0020.0020.0000.0000.0000.000
42A39ASP -1-0.848-0.91933.916-0.035-0.0350.0000.0000.0000.000
43A40ILE 00.004-0.00635.611-0.003-0.0030.0000.0000.0000.000
44A41ASP -1-0.856-0.92135.675-0.048-0.0480.0000.0000.0000.000
45A42GLY 00.0010.01236.2340.0020.0020.0000.0000.0000.000
46A43LEU 0-0.012-0.02935.125-0.002-0.0020.0000.0000.0000.000
47A44ASP -1-0.741-0.84534.187-0.040-0.0400.0000.0000.0000.000
48A45ALA 00.0190.01929.1660.0000.0000.0000.0000.0000.000
49A46THR 00.000-0.00326.997-0.003-0.0030.0000.0000.0000.000
50A47ASP -1-0.816-0.90528.186-0.032-0.0320.0000.0000.0000.000
51A48LYS 10.7840.87629.9510.0380.0380.0000.0000.0000.000
52A49LEU 00.0190.00723.6120.0010.0010.0000.0000.0000.000
53A50ILE 0-0.0150.00425.1370.0010.0010.0000.0000.0000.000
54A51SER 0-0.037-0.02526.2710.0060.0060.0000.0000.0000.000
55A52MET 0-0.033-0.01024.1170.0060.0060.0000.0000.0000.000
56A53VAL 00.0220.01421.2250.0040.0040.0000.0000.0000.000
57A54ARG 10.8960.93423.8870.0160.0160.0000.0000.0000.000
58A55ARG 10.9581.00126.0610.0330.0330.0000.0000.0000.000
59A56SER 0-0.0110.01520.9470.0060.0060.0000.0000.0000.000
60A57LYS 10.9570.97123.3080.0000.0000.0000.0000.0000.000
61A58PHE 00.021-0.00518.3950.0080.0080.0000.0000.0000.000
62A59ARG 10.9570.99018.518-0.005-0.0050.0000.0000.0000.000
63A60GLU -1-0.902-0.94318.6910.0540.0540.0000.0000.0000.000
64A61GLN 0-0.067-0.04915.5290.0130.0130.0000.0000.0000.000
65A62ILE 0-0.064-0.02114.0700.0120.0120.0000.0000.0000.000
66A63LYS 10.9100.9529.714-0.178-0.1780.0000.0000.0000.000
67A64CYS 0-0.016-0.00210.911-0.050-0.0500.0000.0000.0000.000
68A65ILE 00.0190.01612.9380.0100.0100.0000.0000.0000.000
69A66PHE 0-0.050-0.03310.329-0.022-0.0220.0000.0000.0000.000
70A67LEU 00.0440.01016.4470.0220.0220.0000.0000.0000.000
71A68PRO 00.0200.02019.374-0.024-0.0240.0000.0000.0000.000
72A69GLY 00.037-0.00221.6680.0030.0030.0000.0000.0000.000
73A70ILE 0-0.008-0.01123.464-0.003-0.0030.0000.0000.0000.000
74A71THR 0-0.051-0.02925.4470.0100.0100.0000.0000.0000.000
75A72LEU 0-0.008-0.00725.288-0.008-0.0080.0000.0000.0000.000
76A73GLY 00.031-0.02729.1900.0050.0050.0000.0000.0000.000
77A74GLY 00.0350.04131.8590.0040.0040.0000.0000.0000.000
78A75PHE 0-0.042-0.01432.284-0.005-0.0050.0000.0000.0000.000
79A76ASN 0-0.022-0.00931.9340.0030.0030.0000.0000.0000.000
80A77LEU 0-0.0100.01429.745-0.005-0.0050.0000.0000.0000.000
81A78VAL 0-0.027-0.03124.3980.0040.0040.0000.0000.0000.000
82A79ASP -1-0.828-0.92726.319-0.064-0.0640.0000.0000.0000.000
83A80ILE 00.022-0.01220.3220.0030.0030.0000.0000.0000.000
84A81GLN 00.0280.01421.1820.0060.0060.0000.0000.0000.000
85A82ARG 10.8050.90123.5490.0430.0430.0000.0000.0000.000
86A83VAL 00.0300.01621.0310.0070.0070.0000.0000.0000.000
87A84TYR 0-0.0160.02117.3090.0070.0070.0000.0000.0000.000
88A85ARG 10.9110.95020.7990.0520.0520.0000.0000.0000.000
89A86GLU -1-0.887-0.94723.559-0.020-0.0200.0000.0000.0000.000
90A87THR 0-0.079-0.05020.5710.0060.0060.0000.0000.0000.000
91A88LYS 10.9190.96719.630-0.003-0.0030.0000.0000.0000.000
92A89ILE 0-0.0200.00415.1120.0070.0070.0000.0000.0000.000
93A90PRO 0-0.018-0.00412.812-0.003-0.0030.0000.0000.0000.000
94A91VAL 00.0280.01115.504-0.008-0.0080.0000.0000.0000.000
95A92VAL 0-0.014-0.01712.210-0.015-0.0150.0000.0000.0000.000
96A93VAL 0-0.0080.01515.6880.0030.0030.0000.0000.0000.000
97A94VAL 0-0.016-0.02214.757-0.022-0.0220.0000.0000.0000.000
98A95MET 00.0510.03717.8330.0190.0190.0000.0000.0000.000
99A96ARG 10.8780.90418.9370.1780.1780.0000.0000.0000.000
100A97ARG 10.9010.94721.2420.1340.1340.0000.0000.0000.000
101A98LYS 10.9800.98924.5180.0970.0970.0000.0000.0000.000
102A99PRO 00.0280.02224.6620.0060.0060.0000.0000.0000.000
103A100ASP -1-0.814-0.90627.751-0.070-0.0700.0000.0000.0000.000
104A101MET 0-0.030-0.04128.8420.0000.0000.0000.0000.0000.000
105A102GLU -1-0.922-0.94931.682-0.053-0.0530.0000.0000.0000.000
106A103GLU -1-0.937-0.96234.580-0.061-0.0610.0000.0000.0000.000
107A104PHE 0-0.0010.03031.9020.0030.0030.0000.0000.0000.000
108A105ASP -1-0.808-0.88734.582-0.046-0.0460.0000.0000.0000.000
109A106SER 0-0.120-0.10336.5870.0040.0040.0000.0000.0000.000
110A107ALA 0-0.0020.00437.4560.0030.0030.0000.0000.0000.000
111A108MET 0-0.022-0.00434.1000.0020.0020.0000.0000.0000.000
112A109ARG 10.9360.96938.0610.0420.0420.0000.0000.0000.000
113A110ASN 0-0.063-0.02641.0650.0040.0040.0000.0000.0000.000
114A111LEU 0-0.0120.01037.7620.0010.0010.0000.0000.0000.000
115A112GLU -1-0.916-0.95841.349-0.028-0.0280.0000.0000.0000.000
116A113ASN 0-0.011-0.02039.332-0.002-0.0020.0000.0000.0000.000
117A114TYR 00.020-0.01537.671-0.001-0.0010.0000.0000.0000.000
118A115GLU -1-0.877-0.94537.882-0.037-0.0370.0000.0000.0000.000
119A116LEU 0-0.063-0.01933.817-0.002-0.0020.0000.0000.0000.000
120A117ARG 10.8260.88633.9630.0410.0410.0000.0000.0000.000
121A118ARG 11.0141.00633.0410.0360.0360.0000.0000.0000.000
122A119LYS 10.9840.99732.0680.0340.0340.0000.0000.0000.000
123A120ILE 0-0.059-0.03228.386-0.003-0.0030.0000.0000.0000.000
124A121VAL 00.0180.00128.337-0.007-0.0070.0000.0000.0000.000
125A122GLU -1-0.942-0.96428.244-0.054-0.0540.0000.0000.0000.000
126A123VAL 0-0.080-0.04126.690-0.004-0.0040.0000.0000.0000.000
127A124ALA 0-0.066-0.02923.972-0.005-0.0050.0000.0000.0000.000
128A125GLY 00.0060.00922.876-0.012-0.0120.0000.0000.0000.000
129A126GLU -1-0.941-0.97322.032-0.110-0.1100.0000.0000.0000.000
130A127ILE 0-0.017-0.00621.875-0.013-0.0130.0000.0000.0000.000
131A128HIS 00.0130.00117.866-0.001-0.0010.0000.0000.0000.000
132A129ARG 10.9400.97718.8660.1320.1320.0000.0000.0000.000
133A130ILE 00.0110.00013.1550.0020.0020.0000.0000.0000.000
134A131GLY 0-0.021-0.00715.517-0.024-0.0240.0000.0000.0000.000
135A132ASP -1-0.920-0.96416.373-0.154-0.1540.0000.0000.0000.000
136A133ILE 0-0.108-0.04714.1920.0090.0090.0000.0000.0000.000
137A134TYR 00.008-0.00818.3340.0040.0040.0000.0000.0000.000
138A135ILE 0-0.010-0.01614.137-0.012-0.0120.0000.0000.0000.000
139A136GLN 00.0300.02018.1170.0140.0140.0000.0000.0000.000
140A137THR 0-0.056-0.02815.337-0.019-0.0190.0000.0000.0000.000
141A138ALA 00.0470.03317.3970.0220.0220.0000.0000.0000.000
142A139GLY 00.009-0.00616.907-0.008-0.0080.0000.0000.0000.000
143A140LEU 0-0.042-0.01611.032-0.010-0.0100.0000.0000.0000.000
144A141THR 00.0180.00212.862-0.001-0.0010.0000.0000.0000.000
145A142PRO 00.0870.03013.393-0.046-0.0460.0000.0000.0000.000
146A143SER 00.0130.01311.045-0.054-0.0540.0000.0000.0000.000
147A144GLU -1-0.877-0.9458.821-0.315-0.3150.0000.0000.0000.000
148A145ALA 00.0370.0258.791-0.142-0.1420.0000.0000.0000.000
149A146GLU -1-0.847-0.9129.302-0.470-0.4700.0000.0000.0000.000
150A147LYS 10.8870.9335.0020.4330.4330.0000.0000.0000.000
151A148LEU 00.0500.0045.731-0.453-0.4530.0000.0000.0000.000
152A149VAL 00.0310.0277.5850.0020.0020.0000.0000.0000.000
153A150LYS 10.8250.9156.1050.5840.5840.0000.0000.0000.000
154A151ALA 0-0.063-0.0304.388-0.140-0.1010.000-0.010-0.0290.000
155A152SER 00.006-0.0066.0080.2510.2510.0000.0000.0000.000
156A153LEU 0-0.042-0.0039.3180.1460.1460.0000.0000.0000.000
157A154ILE 00.0120.01710.466-0.052-0.0520.0000.0000.0000.000
158A155LYS 10.9540.96713.1550.1600.1600.0000.0000.0000.000
159A156GLY 00.0070.00515.9650.0150.0150.0000.0000.0000.000
160A157ASN 00.0580.03414.694-0.027-0.0270.0000.0000.0000.000
161A158MET 0-0.0120.00715.237-0.015-0.0150.0000.0000.0000.000
162A159PRO 00.0240.01313.192-0.008-0.0080.0000.0000.0000.000
163A160GLU -1-0.759-0.84913.584-0.166-0.1660.0000.0000.0000.000
164A161PRO 0-0.051-0.01914.4550.0330.0330.0000.0000.0000.000
165A162VAL 00.0300.01517.1130.0200.0200.0000.0000.0000.000
166A163ARG 10.8080.89018.3850.1910.1910.0000.0000.0000.000
167A164ILE 0-0.007-0.01518.9340.0190.0190.0000.0000.0000.000
168A165SER 0-0.004-0.01921.4320.0170.0170.0000.0000.0000.000
169A166HIS 00.0360.03022.9640.0060.0060.0000.0000.0000.000
170A167LEU 0-0.052-0.02223.6980.0090.0090.0000.0000.0000.000
171A168VAL 0-0.021-0.00925.6720.0090.0090.0000.0000.0000.000
172A169ALA 00.0400.01327.4230.0070.0070.0000.0000.0000.000
173A170SER 0-0.007-0.02328.4370.0060.0060.0000.0000.0000.000
174A171ALA 0-0.027-0.00230.5700.0040.0040.0000.0000.0000.000
175A172ILE 0-0.042-0.02530.8660.0050.0050.0000.0000.0000.000
176A173ILE 0-0.023-0.00933.5170.0040.0040.0000.0000.0000.000
177A174HIS 0-0.049-0.02132.9610.0050.0050.0000.0000.0000.000
178A175GLY 0-0.023-0.01736.2240.0000.0000.0000.0000.0000.000
179A176NME 0-0.0500.00136.9310.0030.0030.0000.0000.0000.000