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: 2J6YR

Calculation Name: 2HQ1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HQ1

Chain ID: A

ChEMBL ID:

UniProt ID: A3DDY9

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 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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2437283.489244
FMO2-HF: Nuclear repulsion 2354610.587984
FMO2-HF: Total energy -82672.90126
FMO2-MP2: Total energy -82911.782275


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-21.57-14.9838.906-4.327-11.166-0.025
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.027 / q_NPA : -0.023
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].
3A3LEU0-0.035-0.0263.405-0.2551.553-0.005-0.750-1.0520.001
4A4LYS10.8960.9642.381-12.372-9.7531.920-1.649-2.8900.014
5A5GLY0-0.007-0.0014.153-1.258-1.0990.004-0.074-0.0900.000
6A6LYS10.8610.9577.131-1.189-1.1890.0000.0000.0000.000
7A7THR0-0.013-0.0078.8750.1890.1890.0000.0000.0000.000
8A8ALA0-0.017-0.01211.145-0.109-0.1090.0000.0000.0000.000
9A9ILE00.0240.01212.781-0.013-0.0130.0000.0000.0000.000
10A10VAL0-0.0110.00614.043-0.037-0.0370.0000.0000.0000.000
11A11THR00.0530.03317.0380.0000.0000.0000.0000.0000.000
12A12GLY00.0160.01520.349-0.030-0.0300.0000.0000.0000.000
13A13SER0-0.022-0.03717.068-0.029-0.0290.0000.0000.0000.000
14A14SER00.0050.01118.040-0.031-0.0310.0000.0000.0000.000
15A15ARG10.9280.94420.1280.1040.1040.0000.0000.0000.000
16A16GLY00.0400.02520.6840.0130.0130.0000.0000.0000.000
17A17LEU00.0560.02018.623-0.035-0.0350.0000.0000.0000.000
18A18GLY00.0720.03517.564-0.031-0.0310.0000.0000.0000.000
19A19LYS10.7730.87015.6640.3550.3550.0000.0000.0000.000
20A20ALA00.0520.02414.120-0.053-0.0530.0000.0000.0000.000
21A21ILE0-0.002-0.01212.770-0.105-0.1050.0000.0000.0000.000
22A22ALA00.0060.00011.811-0.031-0.0310.0000.0000.0000.000
23A23TRP00.0380.0249.3600.0050.0050.0000.0000.0000.000
24A24LYS10.8910.9567.3781.2991.2990.0000.0000.0000.000
25A25LEU00.022-0.0117.012-0.214-0.2140.0000.0000.0000.000
26A26GLY00.0260.0086.4380.3840.3840.0000.0000.0000.000
27A27ASN0-0.044-0.0323.956-0.2960.1540.002-0.060-0.3930.000
28A28MET0-0.0760.0032.541-4.789-2.8181.979-1.344-2.605-0.016
29A29GLY0-0.022-0.0302.377-2.524-1.2484.843-2.385-3.734-0.025
30A30ALA00.0250.0263.3321.629-0.0670.1631.935-0.4020.001
31A31ASN0-0.003-0.0076.724-0.048-0.0480.0000.0000.0000.000
32A32ILE00.004-0.0049.773-0.146-0.1460.0000.0000.0000.000
33A33VAL00.0120.00812.403-0.005-0.0050.0000.0000.0000.000
34A34LEU00.0080.00814.585-0.043-0.0430.0000.0000.0000.000
35A35ASN00.015-0.00117.3930.0150.0150.0000.0000.0000.000
36A36GLY0-0.033-0.02021.091-0.036-0.0360.0000.0000.0000.000
37A37SER00.0870.04723.8580.0160.0160.0000.0000.0000.000
38A38PRO00.0690.02326.394-0.008-0.0080.0000.0000.0000.000
39A39ALA00.0050.01028.256-0.003-0.0030.0000.0000.0000.000
40A40SER0-0.112-0.05024.681-0.018-0.0180.0000.0000.0000.000
41A41THR00.0660.02926.1170.0040.0040.0000.0000.0000.000
42A42SER00.003-0.00421.9790.0030.0030.0000.0000.0000.000
43A43LEU0-0.028-0.00819.453-0.021-0.0210.0000.0000.0000.000
44A44ASP-1-0.769-0.86119.422-0.024-0.0240.0000.0000.0000.000
45A45ALA00.0260.02119.134-0.003-0.0030.0000.0000.0000.000
46A46THR00.013-0.00315.793-0.045-0.0450.0000.0000.0000.000
47A47ALA00.0000.00214.959-0.043-0.0430.0000.0000.0000.000
48A48GLU-1-0.892-0.94214.338-0.069-0.0690.0000.0000.0000.000
49A49GLU-1-0.864-0.91114.016-0.411-0.4110.0000.0000.0000.000
50A50PHE0-0.027-0.03210.579-0.136-0.1360.0000.0000.0000.000
51A51LYS10.9170.9659.564-0.339-0.3390.0000.0000.0000.000
52A52ALA00.0000.00210.649-0.006-0.0060.0000.0000.0000.000
53A53ALA0-0.037-0.0107.896-0.060-0.0600.0000.0000.0000.000
54A54GLY0-0.0100.0006.341-0.498-0.4980.0000.0000.0000.000
55A55ILE0-0.066-0.0156.0860.3950.3950.0000.0000.0000.000
56A56ASN0-0.047-0.0237.505-0.262-0.2620.0000.0000.0000.000
57A57VAL0-0.018-0.00710.2330.0550.0550.0000.0000.0000.000
58A58VAL00.0220.03013.051-0.014-0.0140.0000.0000.0000.000
59A59VAL0-0.008-0.01916.764-0.032-0.0320.0000.0000.0000.000
60A60ALA00.0140.02219.4300.0120.0120.0000.0000.0000.000
61A61LYS10.8270.86622.345-0.028-0.0280.0000.0000.0000.000
62A62GLY00.0410.02225.1910.0110.0110.0000.0000.0000.000
63A63ASP-1-0.964-0.99327.037-0.030-0.0300.0000.0000.0000.000
64A64VAL00.005-0.01124.2750.0080.0080.0000.0000.0000.000
65A65LYS10.8750.93927.7480.0310.0310.0000.0000.0000.000
66A66ASN0-0.042-0.03330.9350.0050.0050.0000.0000.0000.000
67A67PRO00.000-0.01230.7630.0050.0050.0000.0000.0000.000
68A68GLU-1-0.832-0.90630.6410.0690.0690.0000.0000.0000.000
69A69ASP-1-0.802-0.89228.4750.0570.0570.0000.0000.0000.000
70A70VAL0-0.080-0.03525.8870.0120.0120.0000.0000.0000.000
71A71GLU-1-0.826-0.91425.7020.1610.1610.0000.0000.0000.000
72A72ASN0-0.0170.00425.9560.0270.0270.0000.0000.0000.000
73A73MET00.0060.00421.4630.0130.0130.0000.0000.0000.000
74A74VAL0-0.009-0.00721.6630.0330.0330.0000.0000.0000.000
75A75LYS10.8150.88521.857-0.180-0.1800.0000.0000.0000.000
76A76THR00.0150.00321.4460.0270.0270.0000.0000.0000.000
77A77ALA0-0.0020.00217.6790.0370.0370.0000.0000.0000.000
78A78MET0-0.055-0.01517.8580.0760.0760.0000.0000.0000.000
79A79ASP-1-0.818-0.89319.8200.2910.2910.0000.0000.0000.000
80A80ALA0-0.053-0.00816.8710.0220.0220.0000.0000.0000.000
81A81PHE0-0.015-0.03313.4600.0890.0890.0000.0000.0000.000
82A82GLY0-0.0090.01315.4990.0810.0810.0000.0000.0000.000
83A83ARG10.8020.86212.446-0.834-0.8340.0000.0000.0000.000
84A84ILE00.010-0.01315.3910.0040.0040.0000.0000.0000.000
85A85ASP-1-0.785-0.83112.0530.8050.8050.0000.0000.0000.000
86A86ILE00.015-0.00110.139-0.084-0.0840.0000.0000.0000.000
87A87LEU0-0.0080.01314.5030.0250.0250.0000.0000.0000.000
88A88VAL0-0.003-0.01114.524-0.034-0.0340.0000.0000.0000.000
89A89ASN0-0.018-0.01917.5790.0110.0110.0000.0000.0000.000
90A90ASN0-0.045-0.03119.905-0.039-0.0390.0000.0000.0000.000
91A91ALA00.0280.01621.8100.0130.0130.0000.0000.0000.000
92A107TRP00.0540.00039.4040.0000.0000.0000.0000.0000.000
93A108ASP-1-0.875-0.93338.534-0.015-0.0150.0000.0000.0000.000
94A109ASP-1-0.898-0.95735.864-0.035-0.0350.0000.0000.0000.000
95A110VAL0-0.026-0.01034.249-0.002-0.0020.0000.0000.0000.000
96A111LEU00.0180.00933.323-0.002-0.0020.0000.0000.0000.000
97A112ASN00.010-0.01033.3730.0090.0090.0000.0000.0000.000
98A113THR00.0140.01229.7510.0070.0070.0000.0000.0000.000
99A114ASN0-0.0060.02326.5730.0010.0010.0000.0000.0000.000
100A115LEU00.0200.00728.1620.0050.0050.0000.0000.0000.000
101A116LYS10.9190.96229.7090.0030.0030.0000.0000.0000.000
102A117SER00.0520.01326.9210.0130.0130.0000.0000.0000.000
103A118ALA00.0240.02625.2680.0130.0130.0000.0000.0000.000
104A119TYR00.0070.02526.1130.0190.0190.0000.0000.0000.000
105A120LEU0-0.025-0.01328.5640.0140.0140.0000.0000.0000.000
106A121CYS00.0110.01723.3260.0160.0160.0000.0000.0000.000
107A122THR0-0.001-0.01723.8160.0210.0210.0000.0000.0000.000
108A123LYS10.9130.96024.861-0.049-0.0490.0000.0000.0000.000
109A124ALA00.0000.00025.6230.0120.0120.0000.0000.0000.000
110A125VAL00.0390.01019.6540.0190.0190.0000.0000.0000.000
111A126SER0-0.030-0.01522.3220.0270.0270.0000.0000.0000.000
112A127LYS10.8220.91324.163-0.138-0.1380.0000.0000.0000.000
113A128ILE0-0.004-0.01119.8150.0070.0070.0000.0000.0000.000
114A129MET0-0.0130.01717.1860.0120.0120.0000.0000.0000.000
115A130LEU0-0.009-0.00420.9720.0100.0100.0000.0000.0000.000
116A131LYS10.8780.94323.219-0.245-0.2450.0000.0000.0000.000
117A132GLN0-0.038-0.02717.0800.0410.0410.0000.0000.0000.000
118A133LYS10.9360.98319.982-0.224-0.2240.0000.0000.0000.000
119A134SER00.0070.00316.3930.0250.0250.0000.0000.0000.000
120A135GLY00.0300.00016.4720.0210.0210.0000.0000.0000.000
121A136LYS10.8160.91813.176-0.062-0.0620.0000.0000.0000.000
122A137ILE00.0170.01016.6350.0100.0100.0000.0000.0000.000
123A138ILE00.006-0.00214.078-0.023-0.0230.0000.0000.0000.000
124A139ASN0-0.002-0.00918.4800.0100.0100.0000.0000.0000.000
125A140ILE00.0380.01217.820-0.021-0.0210.0000.0000.0000.000
126A141THR0-0.035-0.01221.9420.0150.0150.0000.0000.0000.000
127A142SER00.0550.03124.939-0.017-0.0170.0000.0000.0000.000
128A152GLN00.0490.01236.0030.0000.0000.0000.0000.0000.000
129A153ALA00.0260.00937.603-0.001-0.0010.0000.0000.0000.000
130A154ASN00.0700.04437.877-0.002-0.0020.0000.0000.0000.000
131A155TYR00.0430.02133.4220.0040.0040.0000.0000.0000.000
132A156ALA00.0030.00833.444-0.002-0.0020.0000.0000.0000.000
133A157ALA00.0210.00834.5730.0000.0000.0000.0000.0000.000
134A158SER0-0.004-0.01932.2510.0060.0060.0000.0000.0000.000
135A159LYS10.9370.97327.3370.1310.1310.0000.0000.0000.000
136A160ALA0-0.001-0.00429.9980.0000.0000.0000.0000.0000.000
137A161GLY00.0300.01532.1010.0050.0050.0000.0000.0000.000
138A162LEU00.0050.00025.1010.0080.0080.0000.0000.0000.000
139A163ILE00.0180.02527.1350.0050.0050.0000.0000.0000.000
140A164GLY0-0.0050.00028.5450.0050.0050.0000.0000.0000.000
141A165PHE00.001-0.00626.1300.0090.0090.0000.0000.0000.000
142A166THR00.013-0.01523.5600.0100.0100.0000.0000.0000.000
143A167LYS10.9290.97526.1030.0580.0580.0000.0000.0000.000
144A168SER0-0.0110.00228.1980.0070.0070.0000.0000.0000.000
145A169ILE00.0080.00224.7540.0090.0090.0000.0000.0000.000
146A170ALA0-0.0060.00724.7270.0140.0140.0000.0000.0000.000
147A171LYS10.9470.96725.704-0.017-0.0170.0000.0000.0000.000
148A172GLU-1-0.949-0.96629.0400.0830.0830.0000.0000.0000.000
149A173PHE00.000-0.02425.0290.0160.0160.0000.0000.0000.000
150A174ALA00.0620.05124.7800.0170.0170.0000.0000.0000.000
151A175ALA0-0.030-0.01725.3250.0120.0120.0000.0000.0000.000
152A176LYS10.8000.90125.280-0.108-0.1080.0000.0000.0000.000
153A177GLY00.0330.02521.7260.0260.0260.0000.0000.0000.000
154A178ILE0-0.072-0.02220.1520.0120.0120.0000.0000.0000.000
155A179TYR00.0160.01417.516-0.042-0.0420.0000.0000.0000.000
156A180CYS0-0.073-0.02420.1610.0040.0040.0000.0000.0000.000
157A181ASN00.026-0.00118.480-0.012-0.0120.0000.0000.0000.000
158A182ALA00.0160.00520.8110.0070.0070.0000.0000.0000.000
159A183VAL00.0320.02117.560-0.014-0.0140.0000.0000.0000.000
160A184ALA0-0.041-0.03221.0040.0140.0140.0000.0000.0000.000
161A185PRO0-0.0070.00021.588-0.007-0.0070.0000.0000.0000.000
162A186GLY0-0.017-0.00424.0180.0220.0220.0000.0000.0000.000
163A187ILE0-0.016-0.00826.695-0.001-0.0010.0000.0000.0000.000
164A188ILE0-0.029-0.00222.031-0.016-0.0160.0000.0000.0000.000
165A189LYS10.8270.88422.4900.3260.3260.0000.0000.0000.000
166A190THR0-0.031-0.02723.555-0.009-0.0090.0000.0000.0000.000
167A191ASP-1-0.858-0.93925.743-0.201-0.2010.0000.0000.0000.000
168A192MET00.0260.01427.6420.0090.0090.0000.0000.0000.000
169A193THR00.0520.01128.0980.0030.0030.0000.0000.0000.000
170A194ASP-1-0.842-0.90126.581-0.268-0.2680.0000.0000.0000.000
171A195VAL0-0.030-0.00929.8480.0040.0040.0000.0000.0000.000
172A196LEU0-0.043-0.00432.7130.0120.0120.0000.0000.0000.000
173A197PRO00.0330.00734.968-0.004-0.0040.0000.0000.0000.000
174A198ASP-1-0.761-0.87437.031-0.131-0.1310.0000.0000.0000.000
175A199LYS10.8670.91438.1030.1160.1160.0000.0000.0000.000
176A200VAL00.0080.00137.3650.0010.0010.0000.0000.0000.000
177A201LYS10.8530.93931.8730.1830.1830.0000.0000.0000.000
178A202GLU-1-0.873-0.94235.147-0.163-0.1630.0000.0000.0000.000
179A203MET0-0.054-0.00437.3690.0010.0010.0000.0000.0000.000
180A204TYR00.014-0.00333.7320.0030.0030.0000.0000.0000.000
181A205LEU00.0200.01730.681-0.005-0.0050.0000.0000.0000.000
182A206ASN00.0240.00334.018-0.008-0.0080.0000.0000.0000.000
183A207ASN0-0.059-0.02736.0850.0080.0080.0000.0000.0000.000
184A208ILE0-0.0030.01229.4050.0010.0010.0000.0000.0000.000
185A209PRO0-0.0090.01331.423-0.005-0.0050.0000.0000.0000.000
186A210LEU0-0.021-0.01125.663-0.004-0.0040.0000.0000.0000.000
187A211LYS10.7900.89929.7690.1460.1460.0000.0000.0000.000
188A212ARG10.9320.97224.3970.2860.2860.0000.0000.0000.000
189A213PHE0-0.022-0.01326.7970.0090.0090.0000.0000.0000.000
190A214GLY00.0580.03123.388-0.017-0.0170.0000.0000.0000.000
191A215THR0-0.025-0.03719.154-0.001-0.0010.0000.0000.0000.000
192A216PRO00.030-0.00517.7830.0030.0030.0000.0000.0000.000
193A217GLU-1-0.844-0.93414.064-0.582-0.5820.0000.0000.0000.000
194A218GLU-1-0.874-0.90314.683-0.482-0.4820.0000.0000.0000.000
195A219VAL00.0070.00016.1980.0050.0050.0000.0000.0000.000
196A220ALA00.0030.00012.8820.0250.0250.0000.0000.0000.000
197A221ASN00.0170.00011.283-0.183-0.1830.0000.0000.0000.000
198A222VAL00.0070.02112.212-0.002-0.0020.0000.0000.0000.000
199A223VAL0-0.010-0.01012.8040.0460.0460.0000.0000.0000.000
200A224GLY00.017-0.0029.5390.0530.0530.0000.0000.0000.000
201A225PHE00.0150.0079.5770.0330.0330.0000.0000.0000.000
202A226LEU0-0.015-0.01111.7350.0680.0680.0000.0000.0000.000
203A227ALA0-0.015-0.0019.8610.0830.0830.0000.0000.0000.000
204A228SER0-0.048-0.0168.2720.1150.1150.0000.0000.0000.000
205A229ASP-1-0.815-0.9229.4970.3690.3690.0000.0000.0000.000
206A230ASP-1-0.867-0.9239.504-0.532-0.5320.0000.0000.0000.000
207A231SER0-0.045-0.01812.3870.0430.0430.0000.0000.0000.000
208A232ASN0-0.034-0.03313.6030.0270.0270.0000.0000.0000.000
209A233TYR0-0.019-0.01716.600-0.023-0.0230.0000.0000.0000.000
210A234ILE0-0.0010.02917.762-0.008-0.0080.0000.0000.0000.000
211A235THR00.0360.00719.7950.0090.0090.0000.0000.0000.000
212A236GLY00.0190.01422.384-0.005-0.0050.0000.0000.0000.000
213A237GLN0-0.071-0.03822.248-0.014-0.0140.0000.0000.0000.000
214A238VAL0-0.013-0.02123.0310.0030.0030.0000.0000.0000.000
215A239ILE00.0200.01818.110-0.002-0.0020.0000.0000.0000.000
216A240ASN0-0.004-0.00522.170-0.002-0.0020.0000.0000.0000.000
217A241ILE00.0100.00919.051-0.010-0.0100.0000.0000.0000.000
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