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: 2281R

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 OptAll
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 -2789221.245241
FMO2-HF: Nuclear repulsion 2701968.146103
FMO2-HF: Total energy -87253.099138
FMO2-MP2: Total energy -87509.004316


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.
-2.7370.1210.248-0.713-2.3910.003
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 : 0.057 / 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].
3A3THR0-0.082-0.0392.843-1.4870.9640.246-0.661-2.0360.003
4A4TRP0-0.015-0.0274.6950.1070.178-0.001-0.012-0.0580.000
5A5LYS10.8710.9158.5470.5620.5620.0000.0000.0000.000
6A6VAL00.0370.04911.6980.0600.0600.0000.0000.0000.000
7A7GLY00.0490.01514.9130.0220.0220.0000.0000.0000.000
8A8PRO0-0.028-0.01714.409-0.065-0.0650.0000.0000.0000.000
9A9VAL00.0130.02213.121-0.054-0.0540.0000.0000.0000.000
10A10GLU-1-0.850-0.9185.925-1.746-1.7460.0000.0000.0000.000
11A11LEU0-0.0430.0028.6080.0440.0440.0000.0000.0000.000
12A12LYS10.8340.8764.4990.1770.317-0.001-0.011-0.1270.000
13A13SER00.0150.0215.9450.7090.7090.0000.0000.0000.000
14A14ARG10.7730.8776.655-0.700-0.7000.0000.0000.0000.000
15A15LEU0-0.008-0.00310.584-0.062-0.0620.0000.0000.0000.000
16A16ILE0-0.0180.00413.691-0.014-0.0140.0000.0000.0000.000
17A17LEU00.0440.01816.0270.0050.0050.0000.0000.0000.000
18A18GLY00.0320.01919.464-0.011-0.0110.0000.0000.0000.000
19A19SER0-0.009-0.02623.0180.0040.0040.0000.0000.0000.000
20A20GLY0-0.0160.00025.615-0.001-0.0010.0000.0000.0000.000
21A21LYS10.8090.86128.080-0.007-0.0070.0000.0000.0000.000
22A22TYR00.0180.02022.8110.0020.0020.0000.0000.0000.000
23A23GLU-1-0.924-0.95229.5310.0060.0060.0000.0000.0000.000
24A24ASP-1-0.832-0.90730.6530.0050.0050.0000.0000.0000.000
25A25PHE00.017-0.02428.6530.0010.0010.0000.0000.0000.000
26A26GLY0-0.025-0.00727.4370.0000.0000.0000.0000.0000.000
27A27VAL00.0930.03226.3870.0010.0010.0000.0000.0000.000
28A28MET0-0.064-0.01224.3750.0030.0030.0000.0000.0000.000
29A29ARG10.9090.96122.8370.0000.0000.0000.0000.0000.000
30A30GLU-1-0.932-0.96021.3730.0140.0140.0000.0000.0000.000
31A31ALA00.0000.00520.2740.0050.0050.0000.0000.0000.000
32A32ILE00.006-0.00918.2250.0110.0110.0000.0000.0000.000
33A33ALA0-0.018-0.00616.9270.0110.0110.0000.0000.0000.000
34A34ALA00.0090.01415.5970.0070.0070.0000.0000.0000.000
35A35ALA0-0.009-0.01014.7360.0130.0130.0000.0000.0000.000
36A36LYS10.7940.8948.691-0.014-0.0140.0000.0000.0000.000
37A37ALA0-0.0070.01312.1440.0280.0280.0000.0000.0000.000
38A38GLU-1-0.728-0.8679.267-0.067-0.0670.0000.0000.0000.000
39A39VAL0-0.046-0.01513.440-0.030-0.0300.0000.0000.0000.000
40A40VAL00.0400.02016.3150.0200.0200.0000.0000.0000.000
41A41THR00.002-0.00419.839-0.007-0.0070.0000.0000.0000.000
42A42VAL0-0.0080.01322.6990.0050.0050.0000.0000.0000.000
43A43SER0-0.003-0.02026.166-0.002-0.0020.0000.0000.0000.000
44A44VAL0-0.0050.01029.4750.0010.0010.0000.0000.0000.000
45A45ARG10.9340.96132.1760.0120.0120.0000.0000.0000.000
46A46ARG10.9410.96235.4480.0130.0130.0000.0000.0000.000
47A47VAL00.0310.01837.6940.0010.0010.0000.0000.0000.000
48A48GLU-1-0.969-0.96839.717-0.006-0.0060.0000.0000.0000.000
49A56GLY0-0.012-0.02532.2590.0000.0000.0000.0000.0000.000
50A57LEU0-0.023-0.01427.5160.0010.0010.0000.0000.0000.000
51A58LEU0-0.015-0.01827.1020.0000.0000.0000.0000.0000.000
52A59GLU-1-0.783-0.88826.126-0.011-0.0110.0000.0000.0000.000
53A60ALA0-0.084-0.03426.3580.0020.0020.0000.0000.0000.000
54A61LEU0-0.037-0.03622.4300.0040.0040.0000.0000.0000.000
55A62GLU-1-0.926-0.94321.925-0.019-0.0190.0000.0000.0000.000
56A63GLY0-0.036-0.02118.9470.0050.0050.0000.0000.0000.000
57A64VAL0-0.056-0.01916.429-0.001-0.0010.0000.0000.0000.000
58A65ARG10.8420.90214.9390.1290.1290.0000.0000.0000.000
59A66LEU00.0520.02818.3230.0100.0100.0000.0000.0000.000
60A67LEU00.0120.00518.879-0.009-0.0090.0000.0000.0000.000
61A68PRO00.0100.02021.7370.0090.0090.0000.0000.0000.000
62A69ASN00.0230.00925.037-0.004-0.0040.0000.0000.0000.000
63A70THR0-0.028-0.02427.0440.0000.0000.0000.0000.0000.000
64A71ALA00.0070.01029.9200.0010.0010.0000.0000.0000.000
65A72GLY0-0.015-0.01531.5870.0010.0010.0000.0000.0000.000
66A73ALA0-0.061-0.01333.8380.0000.0000.0000.0000.0000.000
67A74ARG10.8180.87635.4040.0150.0150.0000.0000.0000.000
68A75THR0-0.003-0.01937.6900.0000.0000.0000.0000.0000.000
69A76ALA00.0700.01635.113-0.001-0.0010.0000.0000.0000.000
70A77GLU-1-0.829-0.88235.756-0.024-0.0240.0000.0000.0000.000
71A78GLU-1-0.814-0.86537.320-0.018-0.0180.0000.0000.0000.000
72A79ALA00.0310.01632.146-0.001-0.0010.0000.0000.0000.000
73A80VAL0-0.0010.00132.644-0.001-0.0010.0000.0000.0000.000
74A81ARG10.8010.89333.9720.0210.0210.0000.0000.0000.000
75A82LEU0-0.009-0.01332.5440.0000.0000.0000.0000.0000.000
76A83ALA00.0510.02929.4490.0000.0000.0000.0000.0000.000
77A84ARG10.7590.84130.0440.0350.0350.0000.0000.0000.000
78A85LEU0-0.012-0.00532.135-0.001-0.0010.0000.0000.0000.000
79A86GLY00.0650.01728.9170.0000.0000.0000.0000.0000.000
80A87ARG10.8600.94926.8030.0650.0650.0000.0000.0000.000
81A88LEU0-0.039-0.02028.323-0.001-0.0010.0000.0000.0000.000
82A89LEU0-0.040-0.02030.1830.0020.0020.0000.0000.0000.000
83A90THR0-0.043-0.03524.6260.0000.0000.0000.0000.0000.000
84A91GLY0-0.0180.00625.125-0.002-0.0020.0000.0000.0000.000
85A92GLU-1-0.833-0.89619.244-0.111-0.1110.0000.0000.0000.000
86A93ARG10.7780.85021.5900.1220.1220.0000.0000.0000.000
87A94TRP0-0.034-0.02715.166-0.009-0.0090.0000.0000.0000.000
88A95VAL00.014-0.00322.2330.0090.0090.0000.0000.0000.000
89A96LYS10.8090.91322.4320.0060.0060.0000.0000.0000.000
90A97LEU0-0.039-0.00624.1190.0050.0050.0000.0000.0000.000
91A98GLU-1-0.791-0.90126.920-0.011-0.0110.0000.0000.0000.000
92A99VAL00.0010.01329.3010.0000.0000.0000.0000.0000.000
93A100ILE0-0.0060.00931.0380.0010.0010.0000.0000.0000.000
94A101PRO00.0000.00234.9600.0000.0000.0000.0000.0000.000
95A102ASP-1-0.802-0.88737.915-0.006-0.0060.0000.0000.0000.000
96A103PRO0-0.021-0.03636.8930.0010.0010.0000.0000.0000.000
97A104THR0-0.070-0.03737.6320.0010.0010.0000.0000.0000.000
98A105TYR0-0.029-0.01736.0000.0020.0020.0000.0000.0000.000
99A106LEU0-0.018-0.00532.4840.0010.0010.0000.0000.0000.000
100A107LEU00.0390.03832.3180.0000.0000.0000.0000.0000.000
101A108PRO00.0050.00729.790-0.001-0.0010.0000.0000.0000.000
102A109ASP-1-0.827-0.90732.910-0.020-0.0200.0000.0000.0000.000
103A110PRO00.008-0.00432.978-0.003-0.0030.0000.0000.0000.000
104A111LEU00.0140.01133.476-0.004-0.0040.0000.0000.0000.000
105A112GLU-1-0.787-0.89135.788-0.028-0.0280.0000.0000.0000.000
106A113THR0-0.005-0.01629.331-0.002-0.0020.0000.0000.0000.000
107A114LEU0-0.007-0.00530.945-0.004-0.0040.0000.0000.0000.000
108A115LYS10.8530.90132.2070.0250.0250.0000.0000.0000.000
109A116ALA0-0.028-0.00731.911-0.001-0.0010.0000.0000.0000.000
110A117ALA00.005-0.00927.993-0.003-0.0030.0000.0000.0000.000
111A118GLU-1-0.933-0.96229.386-0.050-0.0500.0000.0000.0000.000
112A119ARG10.9600.98231.6790.0340.0340.0000.0000.0000.000
113A120LEU0-0.032-0.01628.4470.0000.0000.0000.0000.0000.000
114A121ILE00.0100.00726.015-0.003-0.0030.0000.0000.0000.000
115A122GLU-1-0.953-0.96328.517-0.050-0.0500.0000.0000.0000.000
116A123GLU-1-0.806-0.87231.508-0.043-0.0430.0000.0000.0000.000
117A124ASP-1-0.783-0.85626.669-0.093-0.0930.0000.0000.0000.000
118A125PHE0-0.057-0.03925.640-0.006-0.0060.0000.0000.0000.000
119A126LEU0-0.043-0.02519.010-0.008-0.0080.0000.0000.0000.000
120A127VAL00.0220.00522.3870.0070.0070.0000.0000.0000.000
121A128LEU00.0140.00317.708-0.010-0.0100.0000.0000.0000.000
122A129PRO0-0.015-0.00522.0080.0090.0090.0000.0000.0000.000
123A130TYR0-0.013-0.03824.3540.0030.0030.0000.0000.0000.000
124A131MET0-0.052-0.02525.298-0.005-0.0050.0000.0000.0000.000
125A132GLY00.0830.03827.4000.0050.0050.0000.0000.0000.000
126A133PRO0-0.006-0.00727.267-0.003-0.0030.0000.0000.0000.000
127A134ASP-1-0.843-0.92428.297-0.025-0.0250.0000.0000.0000.000
128A135LEU00.0530.01125.445-0.004-0.0040.0000.0000.0000.000
129A136VAL0-0.007-0.00328.193-0.006-0.0060.0000.0000.0000.000
130A137LEU0-0.003-0.00429.593-0.005-0.0050.0000.0000.0000.000
131A138ALA00.0070.00824.650-0.005-0.0050.0000.0000.0000.000
132A139LYS10.8460.89525.5850.0500.0500.0000.0000.0000.000
133A140ARG10.9060.95827.5370.0360.0360.0000.0000.0000.000
134A141LEU00.0280.00925.918-0.003-0.0030.0000.0000.0000.000
135A142ALA0-0.005-0.01223.726-0.007-0.0070.0000.0000.0000.000
136A143ALA0-0.049-0.02324.832-0.008-0.0080.0000.0000.0000.000
137A144LEU0-0.029-0.00727.6020.0000.0000.0000.0000.0000.000
138A145GLY00.0040.01824.038-0.001-0.0010.0000.0000.0000.000
139A146THR0-0.066-0.03222.124-0.006-0.0060.0000.0000.0000.000
140A147ALA00.0200.00718.471-0.014-0.0140.0000.0000.0000.000
141A148THR0-0.073-0.04717.261-0.018-0.0180.0000.0000.0000.000
142A149VAL0-0.0050.00119.0140.0070.0070.0000.0000.0000.000
143A150MET0-0.0040.00019.9640.0070.0070.0000.0000.0000.000
144A151PRO0-0.0450.00321.5070.0010.0010.0000.0000.0000.000
145A152LEU00.0220.01023.4230.0080.0080.0000.0000.0000.000
146A153ALA00.0180.01023.2650.0010.0010.0000.0000.0000.000
147A154ALA0-0.056-0.02125.269-0.001-0.0010.0000.0000.0000.000
148A155PRO00.0560.02928.823-0.001-0.0010.0000.0000.0000.000
149A156ILE00.0440.02827.9070.0040.0040.0000.0000.0000.000
150A157GLY0-0.017-0.00328.369-0.001-0.0010.0000.0000.0000.000
151A158SER0-0.035-0.03129.6600.0020.0020.0000.0000.0000.000
152A159GLY00.0320.01927.0670.0000.0000.0000.0000.0000.000
153A160TRP0-0.028-0.02727.7540.0020.0020.0000.0000.0000.000
154A161GLY00.0130.00124.7170.0000.0000.0000.0000.0000.000
155A162VAL0-0.0040.01421.279-0.004-0.0040.0000.0000.0000.000
156A163ARG10.9000.94524.537-0.020-0.0200.0000.0000.0000.000
157A164THR00.001-0.01026.461-0.004-0.0040.0000.0000.0000.000
158A165ARG10.8210.88122.579-0.038-0.0380.0000.0000.0000.000
159A166ALA00.002-0.00525.1410.0000.0000.0000.0000.0000.000
160A167LEU00.0190.00727.481-0.002-0.0020.0000.0000.0000.000
161A168LEU00.0260.01122.141-0.004-0.0040.0000.0000.0000.000
162A169GLU-1-0.777-0.86622.3200.0200.0200.0000.0000.0000.000
163A170LEU0-0.057-0.02423.605-0.004-0.0040.0000.0000.0000.000
164A171PHE00.0230.00721.493-0.007-0.0070.0000.0000.0000.000
165A172ALA0-0.0120.00219.397-0.008-0.0080.0000.0000.0000.000
166A173ARG10.8010.89719.883-0.005-0.0050.0000.0000.0000.000
167A174GLU-1-0.819-0.90022.133-0.054-0.0540.0000.0000.0000.000
168A175LYS10.8320.93415.535-0.029-0.0290.0000.0000.0000.000
169A176ALA0-0.008-0.00118.056-0.019-0.0190.0000.0000.0000.000
170A177SER0-0.085-0.04119.109-0.009-0.0090.0000.0000.0000.000
171A178LEU0-0.023-0.01020.2590.0110.0110.0000.0000.0000.000
172A179PRO00.0090.02017.859-0.021-0.0210.0000.0000.0000.000
173A180PRO00.0160.00313.7390.0250.0250.0000.0000.0000.000
174A181VAL00.0000.00515.7520.0140.0140.0000.0000.0000.000
175A182VAL0-0.006-0.01315.0980.0270.0270.0000.0000.0000.000
176A183VAL0-0.0110.01217.575-0.010-0.0100.0000.0000.0000.000
177A184ASP-1-0.767-0.90019.5850.0140.0140.0000.0000.0000.000
178A185ALA00.007-0.00222.1850.0000.0000.0000.0000.0000.000
179A186GLY00.0420.02825.686-0.001-0.0010.0000.0000.0000.000
180A187LEU0-0.028-0.01819.2500.0000.0000.0000.0000.0000.000
181A188GLY00.0130.00523.288-0.003-0.0030.0000.0000.0000.000
182A189LEU0-0.014-0.01122.334-0.002-0.0020.0000.0000.0000.000
183A190PRO00.0430.02417.2000.0050.0050.0000.0000.0000.000
184A191SER00.0130.00117.2830.0140.0140.0000.0000.0000.000
185A192HIS00.0640.03918.8250.0050.0050.0000.0000.0000.000
186A193ALA00.0330.01515.5680.0000.0000.0000.0000.0000.000
187A194ALA0-0.0040.01114.0610.0230.0230.0000.0000.0000.000
188A195GLU-1-0.798-0.89615.0400.0590.0590.0000.0000.0000.000
189A196VAL0-0.014-0.02116.353-0.004-0.0040.0000.0000.0000.000
190A197MET0-0.051-0.00711.5090.0340.0340.0000.0000.0000.000
191A198GLU-1-0.926-0.96212.9860.1230.1230.0000.0000.0000.000
192A199LEU0-0.064-0.02614.819-0.016-0.0160.0000.0000.0000.000
193A200GLY00.024-0.01113.269-0.029-0.0290.0000.0000.0000.000
194A201LEU0-0.065-0.02414.040-0.031-0.0310.0000.0000.0000.000
195A202ASP-1-0.838-0.92411.673-0.017-0.0170.0000.0000.0000.000
196A203ALA0-0.005-0.00711.4070.1010.1010.0000.0000.0000.000
197A204VAL0-0.021-0.00213.612-0.038-0.0380.0000.0000.0000.000
198A205LEU0-0.011-0.00516.1320.0060.0060.0000.0000.0000.000
199A206VAL0-0.003-0.00318.262-0.009-0.0090.0000.0000.0000.000
200A207ASN0-0.021-0.04920.778-0.006-0.0060.0000.0000.0000.000
201A208THR00.0020.01624.0610.0000.0000.0000.0000.0000.000
202A209ALA0-0.0160.00522.921-0.001-0.0010.0000.0000.0000.000
203A210ILE0-0.024-0.00319.1270.0020.0020.0000.0000.0000.000
204A211ALA00.009-0.00223.649-0.002-0.0020.0000.0000.0000.000
205A212GLU-1-0.800-0.89226.8300.0100.0100.0000.0000.0000.000
206A213ALA0-0.063-0.01725.5400.0000.0000.0000.0000.0000.000
207A214GLN0-0.014-0.02727.541-0.002-0.0020.0000.0000.0000.000
208A215ASP-1-0.839-0.90824.8130.0180.0180.0000.0000.0000.000
209A216PRO00.0230.02024.2960.0040.0040.0000.0000.0000.000
210A217PRO00.0410.01021.4140.0060.0060.0000.0000.0000.000
211A218ALA00.0230.01020.0910.0060.0060.0000.0000.0000.000
212A219MET0-0.036-0.00920.0330.0070.0070.0000.0000.0000.000
213A220ALA00.003-0.00318.3140.0100.0100.0000.0000.0000.000
214A221GLU-1-0.806-0.87814.3480.0550.0550.0000.0000.0000.000
215A222ALA0-0.012-0.00415.0560.0130.0130.0000.0000.0000.000
216A223PHE00.015-0.02615.7380.0110.0110.0000.0000.0000.000
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218A225LEU0-0.024-0.00311.0690.0530.0530.0000.0000.0000.000
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