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: 7G5RK

Calculation Name: 2HTM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HTM

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SKG7

Base Structure: X-ray

Registration Date: 2023-06-19

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2787562.933217
FMO2-HF: Nuclear repulsion 2700310.732537
FMO2-HF: Total energy -87252.20068
FMO2-MP2: Total energy -87508.251098


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.
-1.1421.520.147-0.179-2.630.005
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 : 0.034 / q_NPA : 0.039
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].
3A3THR0-0.062-0.0412.581-0.6971.6330.147-0.135-2.3420.005
4A4TRP00.006-0.0025.224-0.433-0.397-0.001-0.007-0.0280.000
5A5LYS10.8930.9298.7600.5090.5090.0000.0000.0000.000
6A6VAL00.0360.03611.2470.0250.0250.0000.0000.0000.000
7A7GLY00.0570.02714.7410.0380.0380.0000.0000.0000.000
8A8PRO0-0.044-0.02714.243-0.069-0.0690.0000.0000.0000.000
9A9VAL0-0.001-0.00312.802-0.004-0.0040.0000.0000.0000.000
10A10GLU-1-0.820-0.8785.257-1.496-1.4960.0000.0000.0000.000
11A11LEU0-0.0220.0169.2630.1220.1220.0000.0000.0000.000
12A12LYS10.8080.8614.701-0.408-0.285-0.001-0.010-0.1120.000
13A13SER00.0040.0106.4400.4720.4720.0000.0000.0000.000
14A14ARG10.8140.8976.466-0.219-0.2190.0000.0000.0000.000
15A15LEU0-0.002-0.00110.227-0.130-0.1300.0000.0000.0000.000
16A16ILE0-0.0210.00212.9860.0330.0330.0000.0000.0000.000
17A17LEU00.0510.02216.150-0.023-0.0230.0000.0000.0000.000
18A18GLY0-0.002-0.00619.151-0.014-0.0140.0000.0000.0000.000
19A19SER00.000-0.01022.9250.0010.0010.0000.0000.0000.000
20A20GLY0-0.050-0.02225.692-0.006-0.0060.0000.0000.0000.000
21A21LYS10.8100.86427.583-0.035-0.0350.0000.0000.0000.000
22A22TYR00.0410.02222.1120.0040.0040.0000.0000.0000.000
23A23GLU-1-0.953-0.96328.8520.0590.0590.0000.0000.0000.000
24A24ASP-1-0.795-0.89230.3530.0950.0950.0000.0000.0000.000
25A25PHE0-0.016-0.03728.4410.0060.0060.0000.0000.0000.000
26A26GLY0-0.0110.00027.3690.0130.0130.0000.0000.0000.000
27A27VAL00.0870.03226.3120.0150.0150.0000.0000.0000.000
28A28MET0-0.066-0.01924.1520.0060.0060.0000.0000.0000.000
29A29ARG10.9370.96422.951-0.146-0.1460.0000.0000.0000.000
30A30GLU-1-0.947-0.96321.8340.1710.1710.0000.0000.0000.000
31A31ALA0-0.0050.00720.5910.0260.0260.0000.0000.0000.000
32A32ILE00.008-0.01318.3040.0280.0280.0000.0000.0000.000
33A33ALA0-0.0060.00716.9460.0490.0490.0000.0000.0000.000
34A34ALA0-0.0060.00516.0910.0600.0600.0000.0000.0000.000
35A35ALA0-0.029-0.02014.6330.0280.0280.0000.0000.0000.000
36A36LYS10.8720.92910.427-0.618-0.6180.0000.0000.0000.000
37A37ALA0-0.0130.00811.9310.1030.1030.0000.0000.0000.000
38A38GLU-1-0.729-0.8569.6990.6310.6310.0000.0000.0000.000
39A39VAL0-0.040-0.01013.868-0.059-0.0590.0000.0000.0000.000
40A40VAL00.0320.01416.6570.0050.0050.0000.0000.0000.000
41A41THR00.0040.00120.175-0.015-0.0150.0000.0000.0000.000
42A42VAL0-0.038-0.02722.9670.0050.0050.0000.0000.0000.000
43A43SER0-0.011-0.01626.450-0.008-0.0080.0000.0000.0000.000
44A44VAL00.0280.02229.8460.0040.0040.0000.0000.0000.000
45A45ARG10.9390.96232.605-0.033-0.0330.0000.0000.0000.000
46A46ARG10.9380.96035.846-0.014-0.0140.0000.0000.0000.000
47A47VAL00.0260.01438.0340.0010.0010.0000.0000.0000.000
48A48GLU-1-0.962-0.96239.9870.0280.0280.0000.0000.0000.000
49A56GLY00.0360.00932.549-0.003-0.0030.0000.0000.0000.000
50A57LEU0-0.002-0.01027.7600.0070.0070.0000.0000.0000.000
51A58LEU0-0.014-0.02727.3110.0090.0090.0000.0000.0000.000
52A59GLU-1-0.884-0.93126.6340.1040.1040.0000.0000.0000.000
53A60ALA0-0.059-0.02126.4970.0120.0120.0000.0000.0000.000
54A61LEU0-0.030-0.02822.7490.0100.0100.0000.0000.0000.000
55A62GLU-1-0.947-0.95722.0090.1810.1810.0000.0000.0000.000
56A63GLY0-0.008-0.00318.9440.0120.0120.0000.0000.0000.000
57A64VAL0-0.067-0.02216.6450.0440.0440.0000.0000.0000.000
58A65ARG10.8470.89415.452-0.121-0.1210.0000.0000.0000.000
59A66LEU00.0220.01018.5420.0000.0000.0000.0000.0000.000
60A67LEU0-0.009-0.00319.511-0.014-0.0140.0000.0000.0000.000
61A68PRO00.0200.04522.0840.0020.0020.0000.0000.0000.000
62A69ASN00.0330.00425.603-0.006-0.0060.0000.0000.0000.000
63A70THR0-0.021-0.00927.3610.0000.0000.0000.0000.0000.000
64A71ALA00.0450.03130.284-0.004-0.0040.0000.0000.0000.000
65A72GLY0-0.065-0.03531.8300.0020.0020.0000.0000.0000.000
66A73ALA0-0.0270.00034.331-0.001-0.0010.0000.0000.0000.000
67A74ARG10.8110.87035.854-0.001-0.0010.0000.0000.0000.000
68A75THR0-0.002-0.01238.273-0.003-0.0030.0000.0000.0000.000
69A76ALA00.0780.02335.6060.0020.0020.0000.0000.0000.000
70A77GLU-1-0.863-0.90836.201-0.007-0.0070.0000.0000.0000.000
71A78GLU-1-0.801-0.86538.0210.0000.0000.0000.0000.0000.000
72A79ALA00.0430.02132.7760.0030.0030.0000.0000.0000.000
73A80VAL0-0.010-0.01933.0530.0030.0030.0000.0000.0000.000
74A81ARG10.8000.89734.1220.0040.0040.0000.0000.0000.000
75A82LEU0-0.003-0.00832.9390.0030.0030.0000.0000.0000.000
76A83ALA00.0420.03129.7160.0050.0050.0000.0000.0000.000
77A84ARG10.7780.85630.3340.0150.0150.0000.0000.0000.000
78A85LEU0-0.009-0.00832.1150.0030.0030.0000.0000.0000.000
79A86GLY00.0650.02129.6110.0050.0050.0000.0000.0000.000
80A87ARG10.8460.93726.8300.0210.0210.0000.0000.0000.000
81A88LEU0-0.040-0.01128.1540.0050.0050.0000.0000.0000.000
82A89LEU0-0.029-0.01230.4260.0050.0050.0000.0000.0000.000
83A90THR0-0.027-0.01624.8430.0060.0060.0000.0000.0000.000
84A91GLY0-0.051-0.02025.3160.0080.0080.0000.0000.0000.000
85A92GLU-1-0.839-0.90219.6210.0600.0600.0000.0000.0000.000
86A93ARG10.7830.85520.9850.0570.0570.0000.0000.0000.000
87A94TRP0-0.040-0.02315.439-0.020-0.0200.0000.0000.0000.000
88A95VAL00.022-0.00322.2830.0140.0140.0000.0000.0000.000
89A96LYS10.8310.92523.243-0.020-0.0200.0000.0000.0000.000
90A97LEU0-0.036-0.00324.7800.0050.0050.0000.0000.0000.000
91A98GLU-1-0.799-0.90627.7370.0080.0080.0000.0000.0000.000
92A99VAL00.0050.00830.1380.0030.0030.0000.0000.0000.000
93A100ILE0-0.0090.01230.954-0.003-0.0030.0000.0000.0000.000
94A101PRO00.0100.01035.1910.0030.0030.0000.0000.0000.000
95A102ASP-1-0.794-0.87738.428-0.006-0.0060.0000.0000.0000.000
96A103PRO0-0.043-0.04336.361-0.001-0.0010.0000.0000.0000.000
97A104THR0-0.056-0.04036.7810.0030.0030.0000.0000.0000.000
98A105TYR0-0.035-0.02434.8530.0010.0010.0000.0000.0000.000
99A106LEU0-0.030-0.01231.6950.0000.0000.0000.0000.0000.000
100A107LEU00.0250.02131.572-0.002-0.0020.0000.0000.0000.000
101A108PRO00.0090.01829.6590.0020.0020.0000.0000.0000.000
102A109ASP-1-0.850-0.91932.856-0.036-0.0360.0000.0000.0000.000
103A110PRO00.0260.01233.475-0.002-0.0020.0000.0000.0000.000
104A111LEU00.0420.02134.219-0.004-0.0040.0000.0000.0000.000
105A112GLU-1-0.797-0.89736.137-0.028-0.0280.0000.0000.0000.000
106A113THR0-0.013-0.02729.9930.0020.0020.0000.0000.0000.000
107A114LEU0-0.008-0.00531.080-0.004-0.0040.0000.0000.0000.000
108A115LYS10.8410.89432.7330.0310.0310.0000.0000.0000.000
109A116ALA0-0.042-0.02332.6080.0010.0010.0000.0000.0000.000
110A117ALA00.0150.00028.4990.0010.0010.0000.0000.0000.000
111A118GLU-1-0.934-0.95529.523-0.061-0.0610.0000.0000.0000.000
112A119ARG10.9670.98631.7080.0260.0260.0000.0000.0000.000
113A120LEU0-0.025-0.01028.5690.0030.0030.0000.0000.0000.000
114A121ILE0-0.005-0.00225.8650.0020.0020.0000.0000.0000.000
115A122GLU-1-0.924-0.95328.306-0.042-0.0420.0000.0000.0000.000
116A123GLU-1-0.840-0.87730.895-0.014-0.0140.0000.0000.0000.000
117A124ASP-1-0.813-0.87126.155-0.044-0.0440.0000.0000.0000.000
118A125PHE0-0.040-0.02825.7020.0040.0040.0000.0000.0000.000
119A126LEU0-0.021-0.01719.012-0.015-0.0150.0000.0000.0000.000
120A127VAL0-0.006-0.00422.7400.0110.0110.0000.0000.0000.000
121A128LEU0-0.010-0.02618.408-0.012-0.0120.0000.0000.0000.000
122A129PRO0-0.012-0.00222.8740.0140.0140.0000.0000.0000.000
123A130TYR0-0.017-0.03125.076-0.005-0.0050.0000.0000.0000.000
124A131MET0-0.050-0.02825.583-0.005-0.0050.0000.0000.0000.000
125A132GLY00.0820.03427.0210.0030.0030.0000.0000.0000.000
126A133PRO00.0040.01326.419-0.007-0.0070.0000.0000.0000.000
127A134ASP-1-0.847-0.94027.414-0.082-0.0820.0000.0000.0000.000
128A135LEU00.0570.02125.126-0.004-0.0040.0000.0000.0000.000
129A136VAL00.0080.00027.783-0.008-0.0080.0000.0000.0000.000
130A137LEU0-0.010-0.00930.313-0.002-0.0020.0000.0000.0000.000
131A138ALA00.0020.00225.055-0.001-0.0010.0000.0000.0000.000
132A139LYS10.8490.88725.8070.1610.1610.0000.0000.0000.000
133A140ARG10.9030.95827.5350.0760.0760.0000.0000.0000.000
134A141LEU00.025-0.00126.2910.0000.0000.0000.0000.0000.000
135A142ALA0-0.003-0.01023.630-0.002-0.0020.0000.0000.0000.000
136A143ALA0-0.051-0.02224.704-0.008-0.0080.0000.0000.0000.000
137A144LEU0-0.026-0.00727.2990.0040.0040.0000.0000.0000.000
138A145GLY0-0.0050.01724.2090.0050.0050.0000.0000.0000.000
139A146THR0-0.055-0.01822.4000.0100.0100.0000.0000.0000.000
140A147ALA00.000-0.00518.073-0.022-0.0220.0000.0000.0000.000
141A148THR0-0.072-0.04517.830-0.012-0.0120.0000.0000.0000.000
142A149VAL00.0340.02119.7820.0100.0100.0000.0000.0000.000
143A150MET0-0.020-0.00520.469-0.001-0.0010.0000.0000.0000.000
144A151PRO0-0.0310.01421.0110.0090.0090.0000.0000.0000.000
145A152LEU00.0380.01322.5630.0040.0040.0000.0000.0000.000
146A153ALA00.0070.00022.104-0.009-0.0090.0000.0000.0000.000
147A154ALA0-0.075-0.02724.125-0.005-0.0050.0000.0000.0000.000
148A155PRO00.0560.02427.6170.0030.0030.0000.0000.0000.000
149A156ILE00.0680.04527.0780.0050.0050.0000.0000.0000.000
150A157GLY0-0.045-0.01027.3830.0010.0010.0000.0000.0000.000
151A158SER0-0.027-0.03428.7960.0010.0010.0000.0000.0000.000
152A159GLY00.0140.01426.0850.0020.0020.0000.0000.0000.000
153A160TRP0-0.061-0.04827.139-0.004-0.0040.0000.0000.0000.000
154A161GLY00.0410.01824.231-0.001-0.0010.0000.0000.0000.000
155A162VAL00.0000.00520.6890.0010.0010.0000.0000.0000.000
156A163ARG10.9200.95723.9660.0170.0170.0000.0000.0000.000
157A164THR0-0.011-0.01525.599-0.003-0.0030.0000.0000.0000.000
158A165ARG10.8470.89721.7640.1010.1010.0000.0000.0000.000
159A166ALA00.000-0.01124.580-0.010-0.0100.0000.0000.0000.000
160A167LEU00.0120.00626.899-0.007-0.0070.0000.0000.0000.000
161A168LEU00.0280.00921.172-0.010-0.0100.0000.0000.0000.000
162A169GLU-1-0.805-0.87721.492-0.145-0.1450.0000.0000.0000.000
163A170LEU0-0.049-0.02822.730-0.017-0.0170.0000.0000.0000.000
164A171PHE00.0200.01021.050-0.010-0.0100.0000.0000.0000.000
165A172ALA00.0140.01918.607-0.021-0.0210.0000.0000.0000.000
166A173ARG10.8450.92019.3200.1200.1200.0000.0000.0000.000
167A174GLU-1-0.873-0.91221.996-0.196-0.1960.0000.0000.0000.000
168A175LYS10.9230.96114.5210.3410.3410.0000.0000.0000.000
169A176ALA0-0.021-0.00618.163-0.017-0.0170.0000.0000.0000.000
170A177SER0-0.082-0.02319.2120.0100.0100.0000.0000.0000.000
171A178LEU0-0.038-0.00920.7270.0240.0240.0000.0000.0000.000
172A179PRO00.0130.01918.133-0.034-0.0340.0000.0000.0000.000
173A180PRO00.006-0.00214.0420.0090.0090.0000.0000.0000.000
174A181VAL0-0.020-0.01016.3530.0440.0440.0000.0000.0000.000
175A182VAL0-0.019-0.01815.7190.0080.0080.0000.0000.0000.000
176A183VAL0-0.005-0.00117.201-0.001-0.0010.0000.0000.0000.000
177A184ASP-1-0.803-0.90818.9680.0170.0170.0000.0000.0000.000
178A185ALA00.0200.01621.525-0.010-0.0100.0000.0000.0000.000
179A186GLY00.0490.02324.608-0.009-0.0090.0000.0000.0000.000
180A187LEU0-0.041-0.02018.387-0.003-0.0030.0000.0000.0000.000
181A188GLY00.0360.00222.5130.0090.0090.0000.0000.0000.000
182A189LEU0-0.023-0.01021.6670.0070.0070.0000.0000.0000.000
183A190PRO00.0590.02316.513-0.008-0.0080.0000.0000.0000.000
184A191SER0-0.002-0.00516.695-0.007-0.0070.0000.0000.0000.000
185A192HIS00.0680.04518.538-0.010-0.0100.0000.0000.0000.000
186A193ALA00.0370.01914.808-0.014-0.0140.0000.0000.0000.000
187A194ALA00.0180.01213.514-0.014-0.0140.0000.0000.0000.000
188A195GLU-1-0.815-0.89014.566-0.104-0.1040.0000.0000.0000.000
189A196VAL0-0.027-0.02915.947-0.023-0.0230.0000.0000.0000.000
190A197MET0-0.048-0.00810.938-0.010-0.0100.0000.0000.0000.000
191A198GLU-1-0.942-0.97212.439-0.200-0.2000.0000.0000.0000.000
192A199LEU0-0.078-0.03314.087-0.030-0.0300.0000.0000.0000.000
193A200GLY0-0.018-0.03112.947-0.022-0.0220.0000.0000.0000.000
194A201LEU0-0.075-0.03913.991-0.026-0.0260.0000.0000.0000.000
195A202ASP-1-0.841-0.91612.027-0.383-0.3830.0000.0000.0000.000
196A203ALA00.006-0.01211.2120.0760.0760.0000.0000.0000.000
197A204VAL0-0.0220.00713.203-0.040-0.0400.0000.0000.0000.000
198A205LEU0-0.008-0.00715.6000.0360.0360.0000.0000.0000.000
199A206VAL0-0.008-0.00517.393-0.021-0.0210.0000.0000.0000.000
200A207ASN0-0.014-0.02719.9190.0080.0080.0000.0000.0000.000
201A208THR00.0350.02523.2050.0000.0000.0000.0000.0000.000
202A209ALA00.0020.02221.8320.0010.0010.0000.0000.0000.000
203A210ILE0-0.029-0.01518.1660.0010.0010.0000.0000.0000.000
204A211ALA00.0170.01922.7090.0020.0020.0000.0000.0000.000
205A212GLU-1-0.823-0.91225.9160.0350.0350.0000.0000.0000.000
206A213ALA0-0.062-0.01425.110-0.006-0.0060.0000.0000.0000.000
207A214GLN00.013-0.01127.0950.0010.0010.0000.0000.0000.000
208A215ASP-1-0.868-0.92824.8710.1160.1160.0000.0000.0000.000
209A216PRO00.0230.01524.0550.0100.0100.0000.0000.0000.000
210A217PRO00.0360.00721.5270.0140.0140.0000.0000.0000.000
211A218ALA00.0460.03320.0130.0210.0210.0000.0000.0000.000
212A219MET0-0.044-0.01219.5030.0050.0050.0000.0000.0000.000
213A220ALA00.009-0.00918.2880.0010.0010.0000.0000.0000.000
214A221GLU-1-0.847-0.90014.7200.3100.3100.0000.0000.0000.000
215A222ALA0-0.032-0.01414.6410.0070.0070.0000.0000.0000.000
216A223PHE00.033-0.01914.928-0.015-0.0150.0000.0000.0000.000
217A224ARG10.7530.8639.670-0.460-0.4600.0000.0000.0000.000
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