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: MN3KZ

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 OptH
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 -1694836.775563
FMO2-HF: Nuclear repulsion 1627314.914609
FMO2-HF: Total energy -67521.860954
FMO2-MP2: Total energy -67717.877787


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.
0.1891.7080.001-0.8-0.720.001
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 : 0.002 / q_NPA : -0.011
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].
3A13PRO00.0160.0053.562-0.1901.3290.001-0.800-0.7200.001
4A14MET00.0410.0385.449-0.219-0.2190.0000.0000.0000.000
5A15SER00.0010.0007.5260.0280.0280.0000.0000.0000.000
6A16ILE00.0610.00911.2060.0470.0470.0000.0000.0000.000
7A17ALA00.0140.00414.0920.0250.0250.0000.0000.0000.000
8A18ALA00.0040.0139.7770.0080.0080.0000.0000.0000.000
9A19GLN0-0.0070.0009.9730.1130.1130.0000.0000.0000.000
10A20LYS10.8690.93911.729-0.021-0.0210.0000.0000.0000.000
11A21ASN0-0.020-0.02213.5250.0220.0220.0000.0000.0000.000
12A22ASP-1-0.815-0.90111.0870.2590.2590.0000.0000.0000.000
13A23ASP-1-0.848-0.92913.2130.2100.2100.0000.0000.0000.000
14A24ASP-1-0.840-0.92115.8670.0380.0380.0000.0000.0000.000
15A25ARG10.6680.82010.661-0.157-0.1570.0000.0000.0000.000
16A26GLN00.0250.01713.168-0.029-0.0290.0000.0000.0000.000
17A27ALA0-0.0110.00417.689-0.006-0.0060.0000.0000.0000.000
18A28ARG10.9410.95417.759-0.020-0.0200.0000.0000.0000.000
19A29ALA00.0520.04019.266-0.005-0.0050.0000.0000.0000.000
20A30LEU0-0.028-0.02820.282-0.005-0.0050.0000.0000.0000.000
21A31ALA0-0.050-0.02323.402-0.006-0.0060.0000.0000.0000.000
22A32ALA00.0400.01624.688-0.005-0.0050.0000.0000.0000.000
23A33LEU0-0.030-0.00724.851-0.003-0.0030.0000.0000.0000.000
24A34ALA00.0150.01727.0780.0000.0000.0000.0000.0000.000
25A35GLU-1-0.953-0.95230.2720.0220.0220.0000.0000.0000.000
26A36LYS10.7760.87128.018-0.058-0.0580.0000.0000.0000.000
27A37PRO0-0.057-0.03430.5280.0020.0020.0000.0000.0000.000
28A38ASP-1-0.761-0.92531.7140.0260.0260.0000.0000.0000.000
29A39GLY0-0.014-0.03433.282-0.002-0.0020.0000.0000.0000.000
30A40ILE00.0160.00332.4450.0000.0000.0000.0000.0000.000
31A41VAL0-0.018-0.01731.523-0.003-0.0030.0000.0000.0000.000
32A42GLU-1-0.895-0.90428.7280.0140.0140.0000.0000.0000.000
33A43ALA00.017-0.02424.5660.0000.0000.0000.0000.0000.000
34A44ILE00.0380.00624.6580.0010.0010.0000.0000.0000.000
35A45ALA00.002-0.01625.447-0.003-0.0030.0000.0000.0000.000
36A46ALA0-0.0150.02524.877-0.003-0.0030.0000.0000.0000.000
37A47LYS10.9130.96822.5700.0020.0020.0000.0000.0000.000
38A48ALA0-0.056-0.02323.208-0.008-0.0080.0000.0000.0000.000
39A49GLU-1-0.940-0.97718.6760.0300.0300.0000.0000.0000.000
40A50VAL0-0.073-0.03214.492-0.016-0.0160.0000.0000.0000.000
41A51ALA0-0.0040.01215.921-0.005-0.0050.0000.0000.0000.000
42A52PRO00.0390.01317.8370.0160.0160.0000.0000.0000.000
43A53ALA00.007-0.00616.1820.0080.0080.0000.0000.0000.000
44A54GLU-1-0.791-0.91314.4320.0800.0800.0000.0000.0000.000
45A55ILE00.0390.02817.0940.0130.0130.0000.0000.0000.000
46A56LEU0-0.036-0.02920.3210.0030.0030.0000.0000.0000.000
47A57ALA0-0.051-0.01517.0930.0020.0020.0000.0000.0000.000
48A58ILE00.0050.00317.8550.0140.0140.0000.0000.0000.000
49A59LEU0-0.072-0.02121.177-0.009-0.0090.0000.0000.0000.000
50A60PRO0-0.009-0.00324.0890.0080.0080.0000.0000.0000.000
51A61GLN00.0710.02824.445-0.004-0.0040.0000.0000.0000.000
52A62GLY0-0.068-0.04325.321-0.007-0.0070.0000.0000.0000.000
53A63ALA0-0.0070.00926.602-0.005-0.0050.0000.0000.0000.000
54A64ALA00.0280.01522.574-0.008-0.0080.0000.0000.0000.000
55A65VAL0-0.0230.00922.7930.0120.0120.0000.0000.0000.000
56A66SER00.0120.01119.581-0.014-0.0140.0000.0000.0000.000
57A67ALA00.0070.02621.6120.0070.0070.0000.0000.0000.000
58A68PRO00.005-0.00219.1590.0000.0000.0000.0000.0000.000
59A69ALA00.0870.03418.846-0.008-0.0080.0000.0000.0000.000
60A70ASP-1-0.885-0.92820.5740.0580.0580.0000.0000.0000.000
61A71ARG10.8600.91222.488-0.053-0.0530.0000.0000.0000.000
62A72PHE00.014-0.00224.370-0.003-0.0030.0000.0000.0000.000
63A73ASP-1-0.821-0.90426.1010.0160.0160.0000.0000.0000.000
64A74ALA0-0.041-0.01528.825-0.001-0.0010.0000.0000.0000.000
65A75ILE00.0300.01225.902-0.001-0.0010.0000.0000.0000.000
66A76TRP00.011-0.00129.978-0.001-0.0010.0000.0000.0000.000
67A77ASN0-0.031-0.03031.688-0.003-0.0030.0000.0000.0000.000
68A78GLU-1-0.931-0.95732.9830.0320.0320.0000.0000.0000.000
69A79MET0-0.031-0.02330.404-0.001-0.0010.0000.0000.0000.000
70A80ARG10.8740.95634.971-0.016-0.0160.0000.0000.0000.000
71A81GLY0-0.0140.01437.661-0.001-0.0010.0000.0000.0000.000
72A82TRP0-0.056-0.04732.4310.0000.0000.0000.0000.0000.000
73A83GLY00.0030.02639.4690.0000.0000.0000.0000.0000.000
74A84GLU-1-0.861-0.92940.4940.0110.0110.0000.0000.0000.000
75A85ILE00.0110.01135.9050.0010.0010.0000.0000.0000.000
76A86LEU00.013-0.01136.508-0.002-0.0020.0000.0000.0000.000
77A87MET0-0.0150.00731.2400.0020.0020.0000.0000.0000.000
78A88ILE0-0.0020.00131.835-0.001-0.0010.0000.0000.0000.000
79A89VAL00.0190.00929.5790.0010.0010.0000.0000.0000.000
80A90GLN0-0.037-0.01628.9180.0020.0020.0000.0000.0000.000
81A91THR0-0.038-0.00828.239-0.002-0.0020.0000.0000.0000.000
82A92GLY0-0.026-0.02629.1360.0020.0020.0000.0000.0000.000
83A93ASP-1-0.893-0.93930.244-0.019-0.0190.0000.0000.0000.000
84A94ILE0-0.057-0.03432.8720.0010.0010.0000.0000.0000.000
85A95VAL00.0350.02032.6850.0000.0000.0000.0000.0000.000
86A96LEU0-0.032-0.01234.1520.0000.0000.0000.0000.0000.000
87A97GLU-1-0.922-0.97635.0760.0100.0100.0000.0000.0000.000
88A98VAL0-0.016-0.01337.173-0.001-0.0010.0000.0000.0000.000
89A99PRO0-0.047-0.00538.3970.0010.0010.0000.0000.0000.000
90A100GLY00.0730.00540.416-0.001-0.0010.0000.0000.0000.000
91A101HIS00.0360.02539.7680.0020.0020.0000.0000.0000.000
92A102LEU00.0240.01933.666-0.001-0.0010.0000.0000.0000.000
93A103PRO00.0140.02036.8700.0010.0010.0000.0000.0000.000
94A104GLU-1-0.923-0.97236.7670.0110.0110.0000.0000.0000.000
95A105GLY00.0220.00234.127-0.001-0.0010.0000.0000.0000.000
96A106THR0-0.061-0.01334.5440.0000.0000.0000.0000.0000.000
97A107GLU-1-0.833-0.92626.6840.0050.0050.0000.0000.0000.000
98A108SER0-0.026-0.00930.192-0.001-0.0010.0000.0000.0000.000
99A109HIS0-0.064-0.04627.012-0.002-0.0020.0000.0000.0000.000
100A110GLY00.0750.04624.503-0.003-0.0030.0000.0000.0000.000
101A111TRP0-0.036-0.01225.2300.0010.0010.0000.0000.0000.000
102A112PHE00.0290.01028.0300.0010.0010.0000.0000.0000.000
103A113ASN00.0220.00830.127-0.002-0.0020.0000.0000.0000.000
104A114ILE0-0.0080.00933.2490.0020.0020.0000.0000.0000.000
105A115HIS00.0380.00235.700-0.001-0.0010.0000.0000.0000.000
106A116GLY00.011-0.00139.4590.0010.0010.0000.0000.0000.000
107A117ASP-1-0.962-0.96242.3250.0050.0050.0000.0000.0000.000
108A118SER0-0.010-0.03040.4590.0010.0010.0000.0000.0000.000
109A119PRO0-0.0220.00241.859-0.001-0.0010.0000.0000.0000.000
110A120ILE0-0.048-0.01236.023-0.001-0.0010.0000.0000.0000.000
111A121GLY00.0460.01537.5380.0010.0010.0000.0000.0000.000
112A122GLY0-0.037-0.01435.132-0.001-0.0010.0000.0000.0000.000
113A123HIS0-0.075-0.06631.4040.0000.0000.0000.0000.0000.000
114A124ILE00.0350.02826.810-0.002-0.0020.0000.0000.0000.000
115A125LYS10.9120.97921.7540.0380.0380.0000.0000.0000.000
116A126LYS10.8470.88923.534-0.014-0.0140.0000.0000.0000.000
117A127ASP-1-0.913-0.95420.893-0.018-0.0180.0000.0000.0000.000
118A128ASN0-0.001-0.00219.075-0.006-0.0060.0000.0000.0000.000
119A129CYS0-0.111-0.04418.8530.0020.0020.0000.0000.0000.000
120A130ALA0-0.009-0.00615.0440.0000.0000.0000.0000.0000.000
121A131ALA0-0.026-0.02116.8120.0170.0170.0000.0000.0000.000
122A132ILE00.0230.02819.024-0.011-0.0110.0000.0000.0000.000
123A133THR0-0.025-0.02520.6850.0060.0060.0000.0000.0000.000
124A134PHE0-0.003-0.00523.259-0.009-0.0090.0000.0000.0000.000
125A135VAL0-0.015-0.01325.1000.0060.0060.0000.0000.0000.000
126A136ASP-1-0.833-0.88427.5800.0420.0420.0000.0000.0000.000
127A137ARG10.9320.96027.919-0.039-0.0390.0000.0000.0000.000
128A138GLY0-0.0010.00231.480-0.004-0.0040.0000.0000.0000.000
129A139PHE00.004-0.02530.4020.0010.0010.0000.0000.0000.000
130A140HIS00.0030.05134.665-0.003-0.0030.0000.0000.0000.000
131A141GLY0-0.0040.00937.223-0.002-0.0020.0000.0000.0000.000
132A142ARG10.8990.94238.608-0.020-0.0200.0000.0000.0000.000
133A143ARG10.7720.85734.418-0.041-0.0410.0000.0000.0000.000
134A144SER0-0.044-0.00232.978-0.003-0.0030.0000.0000.0000.000
135A145CYS00.0410.02432.2830.0030.0030.0000.0000.0000.000
136A146SER00.0130.01329.875-0.004-0.0040.0000.0000.0000.000
137A147VAL00.0200.00427.2670.0050.0050.0000.0000.0000.000
138A148TRP00.006-0.02523.330-0.006-0.0060.0000.0000.0000.000
139A149PHE00.0650.04323.5150.0070.0070.0000.0000.0000.000
140A150MET00.0060.01618.744-0.009-0.0090.0000.0000.0000.000
141A151ASN00.0830.04018.139-0.001-0.0010.0000.0000.0000.000
142A152ALA00.035-0.00713.5560.0080.0080.0000.0000.0000.000
143A153ALA0-0.053-0.02213.418-0.009-0.0090.0000.0000.0000.000
144A154GLY00.0450.02915.3650.0040.0040.0000.0000.0000.000
145A155GLY00.0200.00516.4530.0070.0070.0000.0000.0000.000
146A156ALA0-0.018-0.02420.0740.0030.0030.0000.0000.0000.000
147A157MET0-0.097-0.04222.053-0.005-0.0050.0000.0000.0000.000
148A158PHE00.0170.00224.446-0.003-0.0030.0000.0000.0000.000
149A159LYS10.8470.94726.328-0.017-0.0170.0000.0000.0000.000
150A160ILE00.0270.02729.155-0.003-0.0030.0000.0000.0000.000
151A161PHE0-0.014-0.02131.0970.0040.0040.0000.0000.0000.000
152A162VAL00.0080.00934.169-0.002-0.0020.0000.0000.0000.000
153A163ARG10.8130.92336.780-0.015-0.0150.0000.0000.0000.000
154A164ARG10.8470.91137.905-0.022-0.0220.0000.0000.0000.000
155A165ASP-1-0.802-0.91342.7850.0170.0170.0000.0000.0000.000
156A166GLU-1-0.890-0.94046.5130.0120.0120.0000.0000.0000.000
157A167ASN0-0.012-0.00149.121-0.001-0.0010.0000.0000.0000.000
158A168LYS10.8090.89845.336-0.013-0.0130.0000.0000.0000.000
159A169GLU-1-0.949-0.96443.6890.0230.0230.0000.0000.0000.000
160A170LEU0-0.059-0.03337.670-0.001-0.0010.0000.0000.0000.000
161A171LEU00.0560.02141.5160.0000.0000.0000.0000.0000.000
162A172ALA00.0530.02641.8020.0010.0010.0000.0000.0000.000
163A173GLY00.006-0.00142.2960.0010.0010.0000.0000.0000.000
164A174GLN0-0.018-0.02538.2430.0020.0020.0000.0000.0000.000
165A175LEU00.010-0.00136.7990.0020.0020.0000.0000.0000.000
166A176ALA00.0340.01837.3560.0030.0030.0000.0000.0000.000
167A177LYS10.9670.99237.425-0.022-0.0220.0000.0000.0000.000
168A178PHE0-0.023-0.00630.3670.0020.0020.0000.0000.0000.000
169A179GLU-1-0.876-0.95432.9330.0430.0430.0000.0000.0000.000
170A180GLU-1-0.904-0.93933.3570.0400.0400.0000.0000.0000.000
171A181LEU00.0050.00130.1120.0030.0030.0000.0000.0000.000
172A182ARG10.8540.93928.127-0.052-0.0520.0000.0000.0000.000
173A183ASP-1-0.951-0.99028.6680.0620.0620.0000.0000.0000.000
174A184GLY0-0.0310.00029.8020.0050.0050.0000.0000.0000.000
175A185PHE0-0.024-0.02224.7780.0030.0030.0000.0000.0000.000
176A186ARG10.8990.96424.730-0.065-0.0650.0000.0000.0000.000