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: 76G8K

Calculation Name: 2HQV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HQV

Chain ID: A

ChEMBL ID:

UniProt ID: Q7CX01

Base Structure: X-ray

Registration Date: 2023-09-21

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1693425.171231
FMO2-HF: Nuclear repulsion 1625902.208224
FMO2-HF: Total energy -67522.963006
FMO2-MP2: Total energy -67718.854362


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:11:ALA)


Summations of interaction energy for fragment #1(A:11: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.
0.1561.555-0.005-0.759-0.6340.002
Interaction energy analysis for fragmet #1(A:11:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.000 / 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].
3A13PRO00.0140.0033.664-0.9330.466-0.005-0.759-0.6340.002
4A14MET00.0360.0355.3030.8340.8340.0000.0000.0000.000
5A15SER0-0.009-0.0077.454-0.080-0.0800.0000.0000.0000.000
6A16ILE00.0610.00811.2460.0350.0350.0000.0000.0000.000
7A17ALA00.0160.00813.9690.0170.0170.0000.0000.0000.000
8A18ALA00.0100.01310.2220.0300.0300.0000.0000.0000.000
9A19GLN0-0.040-0.0329.506-0.006-0.0060.0000.0000.0000.000
10A20LYS10.8550.92411.655-0.022-0.0220.0000.0000.0000.000
11A21ASN0-0.028-0.02814.011-0.024-0.0240.0000.0000.0000.000
12A22ASP-1-0.811-0.86510.8790.2040.2040.0000.0000.0000.000
13A23ASP-1-0.819-0.91413.359-0.040-0.0400.0000.0000.0000.000
14A24ASP-1-0.813-0.90015.7550.0580.0580.0000.0000.0000.000
15A25ARG10.7320.83310.474-0.385-0.3850.0000.0000.0000.000
16A26GLN00.001-0.01513.071-0.030-0.0300.0000.0000.0000.000
17A27ALA0-0.0210.00217.709-0.012-0.0120.0000.0000.0000.000
18A28ARG10.9130.96018.456-0.178-0.1780.0000.0000.0000.000
19A29ALA00.0530.04619.529-0.006-0.0060.0000.0000.0000.000
20A30LEU0-0.016-0.02420.251-0.009-0.0090.0000.0000.0000.000
21A31ALA0-0.059-0.02923.369-0.006-0.0060.0000.0000.0000.000
22A32ALA00.0410.01624.925-0.005-0.0050.0000.0000.0000.000
23A33LEU0-0.030-0.00524.975-0.006-0.0060.0000.0000.0000.000
24A34ALA00.0060.01227.178-0.008-0.0080.0000.0000.0000.000
25A35GLU-1-0.954-0.95330.3300.0570.0570.0000.0000.0000.000
26A36LYS10.8060.88227.954-0.041-0.0410.0000.0000.0000.000
27A37PRO0-0.045-0.01630.5610.0030.0030.0000.0000.0000.000
28A38ASP-1-0.730-0.88631.7870.0550.0550.0000.0000.0000.000
29A39GLY0-0.018-0.02133.6390.0020.0020.0000.0000.0000.000
30A40ILE00.0130.01032.7470.0050.0050.0000.0000.0000.000
31A41VAL0-0.034-0.02631.5020.0050.0050.0000.0000.0000.000
32A42GLU-1-0.852-0.88828.8080.1060.1060.0000.0000.0000.000
33A43ALA00.012-0.02324.7250.0030.0030.0000.0000.0000.000
34A44ILE00.0300.00024.6890.0100.0100.0000.0000.0000.000
35A45ALA0-0.001-0.01125.6950.0090.0090.0000.0000.0000.000
36A46ALA0-0.0090.03125.2630.0020.0020.0000.0000.0000.000
37A47LYS10.8970.95722.972-0.130-0.1300.0000.0000.0000.000
38A48ALA0-0.050-0.01723.8110.0070.0070.0000.0000.0000.000
39A49GLU-1-0.936-0.99219.0910.1730.1730.0000.0000.0000.000
40A50VAL0-0.045-0.01615.1900.0380.0380.0000.0000.0000.000
41A51ALA00.0100.01816.057-0.024-0.0240.0000.0000.0000.000
42A52PRO00.0500.01818.032-0.019-0.0190.0000.0000.0000.000
43A53ALA00.000-0.00516.342-0.022-0.0220.0000.0000.0000.000
44A54GLU-1-0.843-0.92914.2190.3720.3720.0000.0000.0000.000
45A55ILE00.0210.01917.171-0.029-0.0290.0000.0000.0000.000
46A56LEU0-0.035-0.02620.390-0.021-0.0210.0000.0000.0000.000
47A57ALA0-0.046-0.01417.078-0.019-0.0190.0000.0000.0000.000
48A58ILE0-0.006-0.00318.139-0.021-0.0210.0000.0000.0000.000
49A59LEU0-0.062-0.01321.142-0.012-0.0120.0000.0000.0000.000
50A60PRO0-0.009-0.00624.019-0.007-0.0070.0000.0000.0000.000
51A61GLN00.0550.01623.6730.0050.0050.0000.0000.0000.000
52A62GLY0-0.048-0.03125.225-0.002-0.0020.0000.0000.0000.000
53A63ALA0-0.0130.00726.6590.0020.0020.0000.0000.0000.000
54A64ALA00.0220.01222.6460.0070.0070.0000.0000.0000.000
55A65VAL0-0.0180.01122.751-0.004-0.0040.0000.0000.0000.000
56A66SER00.0120.00919.2160.0100.0100.0000.0000.0000.000
57A67ALA00.0080.02721.604-0.013-0.0130.0000.0000.0000.000
58A68PRO00.0130.00019.1160.0160.0160.0000.0000.0000.000
59A69ALA00.0780.03218.853-0.005-0.0050.0000.0000.0000.000
60A70ASP-1-0.845-0.90220.5780.0570.0570.0000.0000.0000.000
61A71ARG10.8130.88522.408-0.058-0.0580.0000.0000.0000.000
62A72PHE00.0370.00524.297-0.003-0.0030.0000.0000.0000.000
63A73ASP-1-0.819-0.90926.0560.0760.0760.0000.0000.0000.000
64A74ALA0-0.032-0.01128.748-0.004-0.0040.0000.0000.0000.000
65A75ILE00.0260.01025.982-0.004-0.0040.0000.0000.0000.000
66A76TRP00.0170.00030.0460.0000.0000.0000.0000.0000.000
67A77ASN0-0.038-0.02931.800-0.003-0.0030.0000.0000.0000.000
68A78GLU-1-0.935-0.95833.0250.0320.0320.0000.0000.0000.000
69A79MET0-0.017-0.01630.545-0.001-0.0010.0000.0000.0000.000
70A80ARG10.8190.92435.049-0.048-0.0480.0000.0000.0000.000
71A81GLY0-0.0170.01137.771-0.002-0.0020.0000.0000.0000.000
72A82TRP0-0.050-0.03732.450-0.001-0.0010.0000.0000.0000.000
73A83GLY00.0090.02639.547-0.001-0.0010.0000.0000.0000.000
74A84GLU-1-0.837-0.89040.6150.0450.0450.0000.0000.0000.000
75A85ILE00.0300.03235.994-0.001-0.0010.0000.0000.0000.000
76A86LEU00.010-0.00936.840-0.001-0.0010.0000.0000.0000.000
77A87MET0-0.0140.00831.3450.0030.0030.0000.0000.0000.000
78A88ILE0-0.015-0.00732.216-0.001-0.0010.0000.0000.0000.000
79A89VAL00.0120.00529.7010.0080.0080.0000.0000.0000.000
80A90GLN0-0.051-0.03729.082-0.004-0.0040.0000.0000.0000.000
81A91THR0-0.029-0.01828.5060.0100.0100.0000.0000.0000.000
82A92GLY0-0.022-0.01629.398-0.005-0.0050.0000.0000.0000.000
83A93ASP-1-0.896-0.94430.5790.1170.1170.0000.0000.0000.000
84A94ILE0-0.041-0.01933.167-0.009-0.0090.0000.0000.0000.000
85A95VAL00.0310.01832.8710.0080.0080.0000.0000.0000.000
86A96LEU0-0.031-0.00834.403-0.006-0.0060.0000.0000.0000.000
87A97GLU-1-0.903-0.96835.3060.0710.0710.0000.0000.0000.000
88A98VAL0-0.015-0.01437.377-0.004-0.0040.0000.0000.0000.000
89A99PRO0-0.0120.00538.5880.0010.0010.0000.0000.0000.000
90A100GLY00.049-0.00440.572-0.001-0.0010.0000.0000.0000.000
91A101HIS00.0440.02539.9270.0010.0010.0000.0000.0000.000
92A102LEU00.0390.03733.7790.0020.0020.0000.0000.0000.000
93A103PRO00.0090.01736.989-0.003-0.0030.0000.0000.0000.000
94A104GLU-1-0.857-0.93036.7140.0460.0460.0000.0000.0000.000
95A105GLY00.0290.00034.0810.0020.0020.0000.0000.0000.000
96A106THR0-0.055-0.01434.508-0.002-0.0020.0000.0000.0000.000
97A107GLU-1-0.841-0.91926.6410.1000.1000.0000.0000.0000.000
98A108SER0-0.020-0.00930.177-0.004-0.0040.0000.0000.0000.000
99A109HIS0-0.046-0.03727.0020.0050.0050.0000.0000.0000.000
100A110GLY00.0520.03324.4970.0080.0080.0000.0000.0000.000
101A111TRP0-0.0130.00325.2170.0100.0100.0000.0000.0000.000
102A112PHE00.0270.00628.014-0.008-0.0080.0000.0000.0000.000
103A113ASN0-0.006-0.00130.0950.0070.0070.0000.0000.0000.000
104A114ILE0-0.0080.00933.312-0.005-0.0050.0000.0000.0000.000
105A115HIS00.028-0.00135.664-0.002-0.0020.0000.0000.0000.000
106A116GLY00.007-0.00439.424-0.002-0.0020.0000.0000.0000.000
107A117ASP-1-0.959-0.95742.2820.0410.0410.0000.0000.0000.000
108A118SER0-0.017-0.04840.719-0.001-0.0010.0000.0000.0000.000
109A119PRO0-0.0240.00142.1900.0010.0010.0000.0000.0000.000
110A120ILE0-0.057-0.01236.2610.0040.0040.0000.0000.0000.000
111A121GLY00.0490.01937.521-0.002-0.0020.0000.0000.0000.000
112A122GLY0-0.029-0.01035.1120.0040.0040.0000.0000.0000.000
113A123HIS0-0.070-0.06231.321-0.005-0.0050.0000.0000.0000.000
114A124ILE00.0470.03126.8710.0070.0070.0000.0000.0000.000
115A125LYS10.8000.89421.246-0.207-0.2070.0000.0000.0000.000
116A126LYS10.8280.88023.507-0.076-0.0760.0000.0000.0000.000
117A127ASP-1-0.840-0.89320.8340.1920.1920.0000.0000.0000.000
118A128ASN0-0.015-0.00619.0460.0260.0260.0000.0000.0000.000
119A129CYS0-0.094-0.03518.8170.0190.0190.0000.0000.0000.000
120A130ALA0-0.007-0.00415.1980.0030.0030.0000.0000.0000.000
121A131ALA0-0.026-0.01716.916-0.015-0.0150.0000.0000.0000.000
122A132ILE00.0200.02619.1230.0060.0060.0000.0000.0000.000
123A133THR0-0.033-0.02520.776-0.005-0.0050.0000.0000.0000.000
124A134PHE00.009-0.00123.3130.0030.0030.0000.0000.0000.000
125A135VAL0-0.008-0.00925.161-0.004-0.0040.0000.0000.0000.000
126A136ASP-1-0.795-0.85927.6180.0340.0340.0000.0000.0000.000
127A137ARG10.8960.93228.130-0.071-0.0710.0000.0000.0000.000
128A138GLY00.0020.00731.4930.0000.0000.0000.0000.0000.000
129A139PHE00.013-0.02430.3740.0050.0050.0000.0000.0000.000
130A140HIS0-0.0210.00834.7320.0000.0000.0000.0000.0000.000
131A141GLY0-0.0040.00537.296-0.002-0.0020.0000.0000.0000.000
132A142ARG10.8960.94138.671-0.045-0.0450.0000.0000.0000.000
133A143ARG10.7510.83334.363-0.027-0.0270.0000.0000.0000.000
134A144SER0-0.030-0.00133.209-0.001-0.0010.0000.0000.0000.000
135A145CYS00.0200.01632.335-0.001-0.0010.0000.0000.0000.000
136A146SER00.0230.01630.1190.0030.0030.0000.0000.0000.000
137A147VAL00.008-0.00127.2980.0000.0000.0000.0000.0000.000
138A148TRP0-0.013-0.02823.7020.0100.0100.0000.0000.0000.000
139A149PHE00.0760.04723.6500.0010.0010.0000.0000.0000.000
140A150MET00.0030.01418.9520.0020.0020.0000.0000.0000.000
141A151ASN00.0740.02918.5970.0220.0220.0000.0000.0000.000
142A152ALA00.034-0.00313.6600.0040.0040.0000.0000.0000.000
143A153ALA0-0.047-0.01713.6760.0700.0700.0000.0000.0000.000
144A154GLY00.0450.02815.645-0.003-0.0030.0000.0000.0000.000
145A155GLY00.0210.00616.658-0.030-0.0300.0000.0000.0000.000
146A156ALA0-0.017-0.02220.300-0.001-0.0010.0000.0000.0000.000
147A157MET0-0.094-0.04322.2940.0050.0050.0000.0000.0000.000
148A158PHE00.0190.00424.684-0.006-0.0060.0000.0000.0000.000
149A159LYS10.8680.95126.823-0.113-0.1130.0000.0000.0000.000
150A160ILE00.0250.02429.321-0.003-0.0030.0000.0000.0000.000
151A161PHE0-0.010-0.01831.163-0.001-0.0010.0000.0000.0000.000
152A162VAL00.0100.01134.287-0.002-0.0020.0000.0000.0000.000
153A163ARG10.7690.86836.868-0.046-0.0460.0000.0000.0000.000
154A164ARG10.8360.90938.163-0.044-0.0440.0000.0000.0000.000
155A165ASP-1-0.776-0.90842.8760.0290.0290.0000.0000.0000.000
156A166GLU-1-0.851-0.90946.6010.0310.0310.0000.0000.0000.000
157A167ASN0-0.085-0.03048.8980.0000.0000.0000.0000.0000.000
158A168LYS10.7680.86745.397-0.032-0.0320.0000.0000.0000.000
159A169GLU-1-0.900-0.93743.7290.0260.0260.0000.0000.0000.000
160A170LEU0-0.052-0.02937.6020.0010.0010.0000.0000.0000.000
161A171LEU00.0390.01241.567-0.003-0.0030.0000.0000.0000.000
162A172ALA00.0420.02041.8420.0010.0010.0000.0000.0000.000
163A173GLY00.0050.00042.3090.0000.0000.0000.0000.0000.000
164A174GLN0-0.029-0.03338.4110.0020.0020.0000.0000.0000.000
165A175LEU00.0150.00336.7320.0020.0020.0000.0000.0000.000
166A176ALA00.0240.01537.3600.0000.0000.0000.0000.0000.000
167A177LYS10.9580.98337.356-0.032-0.0320.0000.0000.0000.000
168A178PHE0-0.031-0.01130.4430.0010.0010.0000.0000.0000.000
169A179GLU-1-0.848-0.91732.9280.0250.0250.0000.0000.0000.000
170A180GLU-1-0.917-0.94733.3100.0200.0200.0000.0000.0000.000
171A181LEU0-0.009-0.00730.137-0.001-0.0010.0000.0000.0000.000
172A182ARG10.8190.90428.195-0.029-0.0290.0000.0000.0000.000
173A183ASP-1-0.892-0.96428.6080.0150.0150.0000.0000.0000.000
174A184GLY0-0.039-0.00729.700-0.005-0.0050.0000.0000.0000.000
175A185PHE0-0.028-0.02624.726-0.001-0.0010.0000.0000.0000.000
176A186ARG10.8870.96424.630-0.017-0.0170.0000.0000.0000.000