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: 72L9K

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 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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2435024.67333
FMO2-HF: Nuclear repulsion 2352352.426383
FMO2-HF: Total energy -82672.246948
FMO2-MP2: Total energy -82911.080329


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.
-19.406-14.9211.516-3.931-12.073-0.02
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 : -0.026 / q_NPA : -0.012
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].
3A3LEU0-0.033-0.0173.291-1.1380.970-0.001-0.922-1.1850.002
4A4LYS10.8940.9652.587-13.237-10.5621.767-1.551-2.8920.018
5A5GLY0-0.010-0.0044.570-1.850-1.6950.003-0.079-0.0790.000
6A6LYS10.9370.9887.565-1.870-1.8700.0000.0000.0000.000
7A7THR0-0.0070.0009.2400.2420.2420.0000.0000.0000.000
8A8ALA0-0.022-0.01511.097-0.121-0.1210.0000.0000.0000.000
9A9ILE00.0280.01312.913-0.030-0.0300.0000.0000.0000.000
10A10VAL0-0.0120.00513.986-0.028-0.0280.0000.0000.0000.000
11A11THR00.0470.01916.979-0.014-0.0140.0000.0000.0000.000
12A12GLY00.0050.00420.298-0.019-0.0190.0000.0000.0000.000
13A13SER0-0.020-0.02517.288-0.030-0.0300.0000.0000.0000.000
14A14SER00.0020.01018.409-0.023-0.0230.0000.0000.0000.000
15A15ARG10.9230.93720.548-0.007-0.0070.0000.0000.0000.000
16A16GLY00.0370.02421.3190.0170.0170.0000.0000.0000.000
17A17LEU00.0600.02218.465-0.016-0.0160.0000.0000.0000.000
18A18GLY00.0650.03317.629-0.004-0.0040.0000.0000.0000.000
19A19LYS10.9390.98216.1360.2190.2190.0000.0000.0000.000
20A20ALA00.0400.01814.811-0.012-0.0120.0000.0000.0000.000
21A21ILE00.001-0.00713.238-0.040-0.0400.0000.0000.0000.000
22A22ALA00.0120.00211.7710.0400.0400.0000.0000.0000.000
23A23TRP00.0370.0229.6950.1290.1290.0000.0000.0000.000
24A24LYS10.9250.9767.1960.9250.9250.0000.0000.0000.000
25A25LEU00.014-0.0126.9910.0230.0230.0000.0000.0000.000
26A26GLY00.0340.0136.3980.5760.5760.0000.0000.0000.000
27A27ASN0-0.035-0.0274.520-0.3100.1590.003-0.103-0.3690.000
28A28MET0-0.092-0.0142.520-1.480-0.7013.134-1.113-2.800-0.014
29A29GLY0-0.023-0.0302.373-1.782-1.3086.393-2.524-4.343-0.027
30A30ALA00.0310.0253.4501.830-0.3440.2172.361-0.4050.001
31A31ASN00.004-0.0016.987-0.225-0.2250.0000.0000.0000.000
32A32ILE00.006-0.0049.801-0.112-0.1120.0000.0000.0000.000
33A33VAL00.0050.00712.391-0.057-0.0570.0000.0000.0000.000
34A34LEU00.0030.00314.868-0.028-0.0280.0000.0000.0000.000
35A35ASN00.001-0.01017.589-0.001-0.0010.0000.0000.0000.000
36A36GLY0-0.034-0.02221.275-0.027-0.0270.0000.0000.0000.000
37A37SER00.0810.04824.1250.0080.0080.0000.0000.0000.000
38A38PRO00.0610.01526.663-0.004-0.0040.0000.0000.0000.000
39A39ALA00.0020.00728.486-0.005-0.0050.0000.0000.0000.000
40A40SER0-0.083-0.03024.974-0.016-0.0160.0000.0000.0000.000
41A41THR00.0620.02826.4390.0030.0030.0000.0000.0000.000
42A42SER00.0230.00422.303-0.003-0.0030.0000.0000.0000.000
43A43LEU0-0.036-0.01320.142-0.011-0.0110.0000.0000.0000.000
44A44ASP-1-0.837-0.91119.7250.0570.0570.0000.0000.0000.000
45A45ALA00.0100.01119.424-0.002-0.0020.0000.0000.0000.000
46A46THR0-0.006-0.01016.138-0.034-0.0340.0000.0000.0000.000
47A47ALA0-0.007-0.00915.321-0.018-0.0180.0000.0000.0000.000
48A48GLU-1-0.900-0.94614.584-0.018-0.0180.0000.0000.0000.000
49A49GLU-1-0.949-0.98214.566-0.236-0.2360.0000.0000.0000.000
50A50PHE0-0.046-0.03810.956-0.102-0.1020.0000.0000.0000.000
51A51LYS10.9220.9769.845-0.276-0.2760.0000.0000.0000.000
52A52ALA00.003-0.00310.805-0.051-0.0510.0000.0000.0000.000
53A53ALA0-0.039-0.0108.328-0.087-0.0870.0000.0000.0000.000
54A54GLY0-0.0120.0006.582-0.436-0.4360.0000.0000.0000.000
55A55ILE0-0.060-0.0116.2960.2610.2610.0000.0000.0000.000
56A56ASN0-0.074-0.0407.621-0.354-0.3540.0000.0000.0000.000
57A57VAL0-0.016-0.00410.1600.1300.1300.0000.0000.0000.000
58A58VAL00.0310.03513.095-0.046-0.0460.0000.0000.0000.000
59A59VAL0-0.003-0.01916.784-0.007-0.0070.0000.0000.0000.000
60A60ALA00.0110.01819.5390.0000.0000.0000.0000.0000.000
61A61LYS10.9050.93422.440-0.098-0.0980.0000.0000.0000.000
62A62GLY00.0350.01925.3480.0050.0050.0000.0000.0000.000
63A63ASP-1-0.928-0.97027.1990.0600.0600.0000.0000.0000.000
64A64VAL00.009-0.00824.2300.0040.0040.0000.0000.0000.000
65A65LYS10.9260.96527.687-0.051-0.0510.0000.0000.0000.000
66A66ASN0-0.052-0.04830.868-0.001-0.0010.0000.0000.0000.000
67A67PRO0-0.002-0.01330.8630.0090.0090.0000.0000.0000.000
68A68GLU-1-0.828-0.89730.9380.1280.1280.0000.0000.0000.000
69A69ASP-1-0.800-0.88728.5200.1270.1270.0000.0000.0000.000
70A70VAL0-0.083-0.04025.9880.0190.0190.0000.0000.0000.000
71A71GLU-1-0.834-0.91526.0000.2380.2380.0000.0000.0000.000
72A72ASN0-0.023-0.01026.1710.0260.0260.0000.0000.0000.000
73A73MET00.0110.00821.7030.0180.0180.0000.0000.0000.000
74A74VAL0-0.012-0.01321.9410.0420.0420.0000.0000.0000.000
75A75LYS10.8510.90422.184-0.212-0.2120.0000.0000.0000.000
76A76THR0-0.0090.00321.3120.0270.0270.0000.0000.0000.000
77A77ALA00.0110.00417.9750.0360.0360.0000.0000.0000.000
78A78MET0-0.063-0.02118.1690.0810.0810.0000.0000.0000.000
79A79ASP-1-0.821-0.89420.1500.3400.3400.0000.0000.0000.000
80A80ALA0-0.058-0.01117.0900.0110.0110.0000.0000.0000.000
81A81PHE0-0.018-0.03213.5210.0870.0870.0000.0000.0000.000
82A82GLY0-0.0100.01015.8590.0840.0840.0000.0000.0000.000
83A83ARG10.8110.86912.975-1.003-1.0030.0000.0000.0000.000
84A84ILE00.007-0.00915.7810.0170.0170.0000.0000.0000.000
85A85ASP-1-0.817-0.86012.4701.0671.0670.0000.0000.0000.000
86A86ILE00.0170.00510.167-0.084-0.0840.0000.0000.0000.000
87A87LEU0-0.0110.01114.4010.0200.0200.0000.0000.0000.000
88A88VAL0-0.006-0.01114.431-0.035-0.0350.0000.0000.0000.000
89A89ASN0-0.011-0.01517.494-0.001-0.0010.0000.0000.0000.000
90A90ASN0-0.018-0.00719.740-0.039-0.0390.0000.0000.0000.000
91A91ALA00.0240.01221.7440.0050.0050.0000.0000.0000.000
92A107TRP00.0480.00039.4180.0000.0000.0000.0000.0000.000
93A108ASP-1-0.872-0.93638.4610.0380.0380.0000.0000.0000.000
94A109ASP-1-0.939-0.96836.0470.0320.0320.0000.0000.0000.000
95A110VAL0-0.033-0.01734.2630.0020.0020.0000.0000.0000.000
96A111LEU00.0190.00633.2520.0030.0030.0000.0000.0000.000
97A112ASN0-0.017-0.03233.2920.0120.0120.0000.0000.0000.000
98A113THR00.0130.01829.8510.0100.0100.0000.0000.0000.000
99A114ASN0-0.0200.01126.7040.0050.0050.0000.0000.0000.000
100A115LEU00.0180.00728.0820.0110.0110.0000.0000.0000.000
101A116LYS10.9380.98629.620-0.056-0.0560.0000.0000.0000.000
102A117SER00.042-0.00326.9280.0110.0110.0000.0000.0000.000
103A118ALA00.0230.02725.1770.0180.0180.0000.0000.0000.000
104A119TYR00.0060.02026.0190.0200.0200.0000.0000.0000.000
105A120LEU0-0.030-0.01728.4680.0130.0130.0000.0000.0000.000
106A121CYS00.0210.02323.2380.0160.0160.0000.0000.0000.000
107A122THR00.000-0.01123.7160.0290.0290.0000.0000.0000.000
108A123LYS10.9140.96524.761-0.117-0.1170.0000.0000.0000.000
109A124ALA0-0.002-0.00725.8030.0090.0090.0000.0000.0000.000
110A125VAL00.0380.01019.8010.0160.0160.0000.0000.0000.000
111A126SER0-0.029-0.01622.6970.0260.0260.0000.0000.0000.000
112A127LYS10.8380.92024.331-0.215-0.2150.0000.0000.0000.000
113A128ILE0-0.004-0.00320.294-0.002-0.0020.0000.0000.0000.000
114A129MET0-0.0110.01617.3360.0070.0070.0000.0000.0000.000
115A130LEU0-0.009-0.00921.4200.0060.0060.0000.0000.0000.000
116A131LYS10.8950.95323.738-0.307-0.3070.0000.0000.0000.000
117A132GLN0-0.043-0.02417.3950.0310.0310.0000.0000.0000.000
118A133LYS10.9340.97920.289-0.277-0.2770.0000.0000.0000.000
119A134SER00.0050.00516.6760.0320.0320.0000.0000.0000.000
120A135GLY00.0450.00216.5270.0200.0200.0000.0000.0000.000
121A136LYS10.8560.95013.121-0.352-0.3520.0000.0000.0000.000
122A137ILE00.0140.00916.5170.0230.0230.0000.0000.0000.000
123A138ILE00.005-0.00114.050-0.033-0.0330.0000.0000.0000.000
124A139ASN0-0.005-0.00918.3770.0160.0160.0000.0000.0000.000
125A140ILE00.0280.00917.773-0.019-0.0190.0000.0000.0000.000
126A141THR0-0.045-0.01521.8620.0020.0020.0000.0000.0000.000
127A142SER00.0370.01524.870-0.011-0.0110.0000.0000.0000.000
128A152GLN00.0520.01636.1200.0000.0000.0000.0000.0000.000
129A153ALA00.0270.00937.5330.0010.0010.0000.0000.0000.000
130A154ASN00.0660.04137.7740.0000.0000.0000.0000.0000.000
131A155TYR00.0480.02633.3660.0040.0040.0000.0000.0000.000
132A156ALA00.0010.00533.3670.0030.0030.0000.0000.0000.000
133A157ALA00.0230.00834.4880.0030.0030.0000.0000.0000.000
134A158SER0-0.012-0.01932.1280.0070.0070.0000.0000.0000.000
135A159LYS10.9800.99328.3450.0290.0290.0000.0000.0000.000
136A160ALA0-0.005-0.00729.9070.0050.0050.0000.0000.0000.000
137A161GLY00.0270.01532.0020.0050.0050.0000.0000.0000.000
138A162LEU00.0100.00424.9510.0090.0090.0000.0000.0000.000
139A163ILE00.0180.02126.9890.0110.0110.0000.0000.0000.000
140A164GLY0-0.006-0.00228.4430.0060.0060.0000.0000.0000.000
141A165PHE0-0.001-0.00426.2510.0060.0060.0000.0000.0000.000
142A166THR00.023-0.00923.5890.0140.0140.0000.0000.0000.000
143A167LYS10.9310.96925.988-0.027-0.0270.0000.0000.0000.000
144A168SER0-0.0130.00228.0820.0020.0020.0000.0000.0000.000
145A169ILE00.0140.00624.5990.0060.0060.0000.0000.0000.000
146A170ALA0-0.0200.00224.5980.0140.0140.0000.0000.0000.000
147A171LYS10.9400.96425.582-0.077-0.0770.0000.0000.0000.000
148A172GLU-1-0.969-0.97328.9370.1510.1510.0000.0000.0000.000
149A173PHE0-0.027-0.03624.8490.0110.0110.0000.0000.0000.000
150A174ALA00.0610.04224.6530.0200.0200.0000.0000.0000.000
151A175ALA0-0.029-0.01625.1990.0130.0130.0000.0000.0000.000
152A176LYS10.8610.93325.487-0.187-0.1870.0000.0000.0000.000
153A177GLY00.0300.02421.7250.0280.0280.0000.0000.0000.000
154A178ILE0-0.064-0.01620.0270.0270.0270.0000.0000.0000.000
155A179TYR00.0140.01117.224-0.053-0.0530.0000.0000.0000.000
156A180CYS0-0.069-0.01820.0410.0090.0090.0000.0000.0000.000
157A181ASN00.0260.00018.379-0.037-0.0370.0000.0000.0000.000
158A182ALA00.0080.00320.7050.0130.0130.0000.0000.0000.000
159A183VAL00.0290.01717.446-0.013-0.0130.0000.0000.0000.000
160A184ALA0-0.031-0.02620.9160.0090.0090.0000.0000.0000.000
161A185PRO0-0.011-0.00521.574-0.013-0.0130.0000.0000.0000.000
162A186GLY0-0.011-0.00123.9550.0120.0120.0000.0000.0000.000
163A187ILE0-0.028-0.01226.6470.0020.0020.0000.0000.0000.000
164A188ILE0-0.0240.00222.062-0.013-0.0130.0000.0000.0000.000
165A189LYS10.8610.90723.3600.2070.2070.0000.0000.0000.000
166A190THR0-0.046-0.03124.2140.0000.0000.0000.0000.0000.000
167A191ASP-1-0.821-0.92226.557-0.107-0.1070.0000.0000.0000.000
168A192MET0-0.0020.00228.4220.0020.0020.0000.0000.0000.000
169A193THR00.0420.00128.7160.0000.0000.0000.0000.0000.000
170A194ASP-1-0.856-0.91427.248-0.167-0.1670.0000.0000.0000.000
171A195VAL0-0.039-0.01630.625-0.001-0.0010.0000.0000.0000.000
172A196LEU0-0.042-0.00333.1320.0080.0080.0000.0000.0000.000
173A197PRO00.0290.00835.735-0.005-0.0050.0000.0000.0000.000
174A198ASP-1-0.757-0.86837.621-0.083-0.0830.0000.0000.0000.000
175A199LYS10.8640.90938.7000.0740.0740.0000.0000.0000.000
176A200VAL00.0110.00137.7730.0010.0010.0000.0000.0000.000
177A201LYS10.8590.94232.5100.1170.1170.0000.0000.0000.000
178A202GLU-1-0.881-0.94235.350-0.103-0.1030.0000.0000.0000.000
179A203MET0-0.056-0.01137.5570.0010.0010.0000.0000.0000.000
180A204TYR00.014-0.00133.7470.0040.0040.0000.0000.0000.000
181A205LEU00.0120.00930.819-0.001-0.0010.0000.0000.0000.000
182A206ASN00.004-0.00333.954-0.006-0.0060.0000.0000.0000.000
183A207ASN0-0.083-0.04536.0350.0060.0060.0000.0000.0000.000
184A208ILE0-0.0140.00429.3190.0030.0030.0000.0000.0000.000
185A209PRO0-0.033-0.00531.271-0.007-0.0070.0000.0000.0000.000
186A210LEU0-0.023-0.01725.581-0.006-0.0060.0000.0000.0000.000
187A211LYS10.8440.94929.6590.0870.0870.0000.0000.0000.000
188A212ARG10.9650.98224.2370.1910.1910.0000.0000.0000.000
189A213PHE0-0.022-0.00826.9480.0090.0090.0000.0000.0000.000
190A214GLY00.0630.03123.293-0.015-0.0150.0000.0000.0000.000
191A215THR00.0050.00119.0350.0010.0010.0000.0000.0000.000
192A216PRO00.0470.00218.3970.0130.0130.0000.0000.0000.000
193A217GLU-1-0.863-0.94214.559-0.323-0.3230.0000.0000.0000.000
194A218GLU-1-0.912-0.94214.659-0.280-0.2800.0000.0000.0000.000
195A219VAL00.0110.00216.1520.0140.0140.0000.0000.0000.000
196A220ALA0-0.004-0.00612.8010.0380.0380.0000.0000.0000.000
197A221ASN00.005-0.01111.406-0.025-0.0250.0000.0000.0000.000
198A222VAL0-0.0070.01212.1440.0080.0080.0000.0000.0000.000
199A223VAL0-0.008-0.00812.6880.0420.0420.0000.0000.0000.000
200A224GLY00.014-0.0049.4510.0780.0780.0000.0000.0000.000
201A225PHE00.0110.0079.4740.0660.0660.0000.0000.0000.000
202A226LEU0-0.012-0.01311.6370.0590.0590.0000.0000.0000.000
203A227ALA0-0.009-0.0029.7660.0590.0590.0000.0000.0000.000
204A228SER0-0.065-0.0238.0920.1370.1370.0000.0000.0000.000
205A229ASP-1-0.880-0.9689.3710.6250.6250.0000.0000.0000.000
206A230ASP-1-0.909-0.9459.783-0.270-0.2700.0000.0000.0000.000
207A231SER0-0.076-0.03512.2570.0070.0070.0000.0000.0000.000
208A232ASN0-0.016-0.02213.7870.0380.0380.0000.0000.0000.000
209A233TYR0-0.029-0.02416.476-0.036-0.0360.0000.0000.0000.000
210A234ILE00.0000.03217.511-0.020-0.0200.0000.0000.0000.000
211A235THR00.023-0.00119.6720.0270.0270.0000.0000.0000.000
212A236GLY00.0200.01122.261-0.015-0.0150.0000.0000.0000.000
213A237GLN0-0.070-0.03522.098-0.026-0.0260.0000.0000.0000.000
214A238VAL0-0.011-0.01922.9220.0110.0110.0000.0000.0000.000
215A239ILE00.0160.01518.176-0.009-0.0090.0000.0000.0000.000
216A240ASN0-0.030-0.01322.0780.0070.0070.0000.0000.0000.000
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