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: Q83RY

Calculation Name: 2HTM-A-Xray311

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 237
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2797725.053421
FMO2-HF: Nuclear repulsion 2710284.797568
FMO2-HF: Total energy -87440.255852
FMO2-MP2: Total energy -87696.998905


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.
-0.4153.0930.425-1.065-2.8670.003
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 : 0.013 / q_NPA : 0.019
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].
3A3THR 0-0.090-0.0542.470-0.7052.4280.422-1.009-2.5460.003
4A4TRP 00.0210.0105.006-0.338-0.2830.000-0.011-0.0440.000
5A5LYS 10.9630.9578.7280.7940.7940.0000.0000.0000.000
6A6VAL 00.0390.03611.2170.0390.0390.0000.0000.0000.000
7A7GLY 00.0600.02314.7160.0620.0620.0000.0000.0000.000
8A8PRO 0-0.083-0.04614.214-0.082-0.0820.0000.0000.0000.000
9A9VAL 0-0.023-0.01012.7690.0130.0130.0000.0000.0000.000
10A10GLU -1-0.877-0.9055.893-1.833-1.8330.0000.0000.0000.000
11A11LEU 0-0.0210.0039.0210.2000.2000.0000.0000.0000.000
12A12LYS 10.8900.9124.637-0.626-0.4940.000-0.014-0.1180.000
13A13SER 0-0.019-0.0046.2460.2880.2880.0000.0000.0000.000
14A14ARG 10.8560.9155.7950.5360.5360.0000.0000.0000.000
15A15LEU 00.0010.0009.784-0.110-0.1100.0000.0000.0000.000
16A16ILE 0-0.021-0.00112.5920.0530.0530.0000.0000.0000.000
17A17LEU 00.0660.03615.719-0.018-0.0180.0000.0000.0000.000
18A18GLY 0-0.014-0.01318.755-0.016-0.0160.0000.0000.0000.000
19A19SER 00.0270.00422.5210.0040.0040.0000.0000.0000.000
20A20GLY 0-0.067-0.02925.348-0.004-0.0040.0000.0000.0000.000
21A21LYS 10.9120.91627.234-0.009-0.0090.0000.0000.0000.000
22A22TYR 00.0240.01922.1010.0020.0020.0000.0000.0000.000
23A23GLU -1-0.944-0.95928.5380.0550.0550.0000.0000.0000.000
24A24ASP -1-0.813-0.90830.0630.0940.0940.0000.0000.0000.000
25A25PHE 00.011-0.02228.1490.0060.0060.0000.0000.0000.000
26A26GLY 0-0.0190.00327.0980.0150.0150.0000.0000.0000.000
27A27VAL 00.0890.03326.0340.0170.0170.0000.0000.0000.000
28A28MET 0-0.073-0.01524.0990.0030.0030.0000.0000.0000.000
29A29ARG 10.9460.96422.695-0.165-0.1650.0000.0000.0000.000
30A30GLU -1-0.946-0.96321.5580.1890.1890.0000.0000.0000.000
31A31ALA 0-0.0060.00520.3850.0280.0280.0000.0000.0000.000
32A32ILE 00.016-0.01317.8100.0260.0260.0000.0000.0000.000
33A33ALA 0-0.0160.00216.6830.0520.0520.0000.0000.0000.000
34A34ALA 0-0.0120.00315.8220.0710.0710.0000.0000.0000.000
35A35ALA 0-0.032-0.02314.4000.0320.0320.0000.0000.0000.000
36A36LYS 10.8670.92910.147-0.825-0.8250.0000.0000.0000.000
37A37ALA 0-0.0090.01011.6650.0910.0910.0000.0000.0000.000
38A38GLU -1-0.739-0.8529.5330.5870.5870.0000.0000.0000.000
39A39VAL 0-0.026-0.00113.744-0.057-0.0570.0000.0000.0000.000
40A40VAL 00.0300.01516.4780.0000.0000.0000.0000.0000.000
41A41THR 0-0.052-0.02719.997-0.017-0.0170.0000.0000.0000.000
42A42VAL 0-0.001-0.00622.7540.0100.0100.0000.0000.0000.000
43A43SER 0-0.017-0.02426.251-0.012-0.0120.0000.0000.0000.000
44A44VAL 00.0100.02129.6310.0070.0070.0000.0000.0000.000
45A45ARG 10.9340.95732.391-0.014-0.0140.0000.0000.0000.000
46A46ARG 10.9400.96035.6390.0030.0030.0000.0000.0000.000
47A47VAL 00.0220.01037.9550.0020.0020.0000.0000.0000.000
48A48GLU -1-0.945-0.95239.8170.0160.0160.0000.0000.0000.000
49A49NME 0-0.012-0.00442.0060.0030.0030.0000.0000.0000.000
50A55ACE 0-0.016-0.02134.141-0.001-0.0010.0000.0000.0000.000
51A56GLY 00.0710.02532.346-0.002-0.0020.0000.0000.0000.000
52A57LEU 0-0.009-0.00127.5210.0080.0080.0000.0000.0000.000
53A58LEU 0-0.010-0.02426.8700.0090.0090.0000.0000.0000.000
54A59GLU -1-0.898-0.93826.5620.1120.1120.0000.0000.0000.000
55A60ALA 0-0.055-0.01226.4690.0150.0150.0000.0000.0000.000
56A61LEU 0-0.030-0.03122.4680.0100.0100.0000.0000.0000.000
57A62GLU -1-0.942-0.95721.9300.2000.2000.0000.0000.0000.000
58A63GLY 0-0.0030.00018.9410.0180.0180.0000.0000.0000.000
59A64VAL 0-0.068-0.02616.7600.0470.0470.0000.0000.0000.000
60A65ARG 10.9020.94116.092-0.072-0.0720.0000.0000.0000.000
61A66LEU 00.0290.01518.402-0.005-0.0050.0000.0000.0000.000
62A67LEU 0-0.0010.00819.435-0.018-0.0180.0000.0000.0000.000
63A68PRO 00.0300.03821.8620.0050.0050.0000.0000.0000.000
64A69ASN 00.0680.03625.349-0.010-0.0100.0000.0000.0000.000
65A70THR 0-0.013-0.02227.1040.0030.0030.0000.0000.0000.000
66A71ALA 00.0440.04429.792-0.003-0.0030.0000.0000.0000.000
67A72GLY 0-0.054-0.03031.5660.0050.0050.0000.0000.0000.000
68A73ALA 0-0.036-0.00833.9800.0010.0010.0000.0000.0000.000
69A74ARG 10.8560.92735.5340.0210.0210.0000.0000.0000.000
70A75THR 00.000-0.00837.946-0.003-0.0030.0000.0000.0000.000
71A76ALA 00.0450.00235.3540.0010.0010.0000.0000.0000.000
72A77GLU -1-0.945-0.96036.036-0.031-0.0310.0000.0000.0000.000
73A78GLU -1-0.817-0.91537.768-0.024-0.0240.0000.0000.0000.000
74A79ALA 00.0500.02532.5590.0030.0030.0000.0000.0000.000
75A80VAL 00.006-0.01232.9840.0020.0020.0000.0000.0000.000
76A81ARG 10.8390.93934.0660.0260.0260.0000.0000.0000.000
77A82LEU 0-0.005-0.00932.5630.0050.0050.0000.0000.0000.000
78A83ALA 00.0440.03229.7060.0050.0050.0000.0000.0000.000
79A84ARG 10.8100.88430.2740.0410.0410.0000.0000.0000.000
80A85LEU 0-0.018-0.01432.1080.0050.0050.0000.0000.0000.000
81A86GLY 00.0670.02329.3850.0070.0070.0000.0000.0000.000
82A87ARG 10.8970.95727.3310.0490.0490.0000.0000.0000.000
83A88LEU 0-0.046-0.01728.1520.0060.0060.0000.0000.0000.000
84A89LEU 0-0.030-0.01330.0870.0070.0070.0000.0000.0000.000
85A90THR 0-0.032-0.01024.7450.0070.0070.0000.0000.0000.000
86A91GLY 0-0.037-0.01225.2900.0090.0090.0000.0000.0000.000
87A92GLU -1-0.924-0.95920.1330.0250.0250.0000.0000.0000.000
88A93ARG 10.9090.94020.9660.1100.1100.0000.0000.0000.000
89A94TRP 0-0.047-0.03115.549-0.026-0.0260.0000.0000.0000.000
90A95VAL 00.0300.00222.2690.0200.0200.0000.0000.0000.000
91A96LYS 10.9020.97022.9290.0330.0330.0000.0000.0000.000
92A97LEU 0-0.039-0.00324.4930.0110.0110.0000.0000.0000.000
93A98GLU -1-0.851-0.95027.429-0.043-0.0430.0000.0000.0000.000
94A99VAL 00.0030.00529.8380.0060.0060.0000.0000.0000.000
95A100ILE 0-0.0060.01130.574-0.004-0.0040.0000.0000.0000.000
96A101PRO 00.0080.00734.7420.0060.0060.0000.0000.0000.000
97A102ASP -1-0.828-0.91838.001-0.029-0.0290.0000.0000.0000.000
98A103PRO 0-0.059-0.06036.039-0.002-0.0020.0000.0000.0000.000
99A104THR 0-0.022-0.00336.3840.0030.0030.0000.0000.0000.000
100A105TYR 0-0.028-0.01734.4450.0010.0010.0000.0000.0000.000
101A106LEU 0-0.030-0.00730.894-0.002-0.0020.0000.0000.0000.000
102A107LEU 0-0.0040.00131.286-0.005-0.0050.0000.0000.0000.000
103A108PRO 00.0230.01729.1440.0040.0040.0000.0000.0000.000
104A109ASP -1-0.857-0.91832.418-0.071-0.0710.0000.0000.0000.000
105A110PRO 00.024-0.00333.034-0.005-0.0050.0000.0000.0000.000
106A111LEU 00.0280.01733.908-0.005-0.0050.0000.0000.0000.000
107A112GLU -1-0.840-0.92935.974-0.059-0.0590.0000.0000.0000.000
108A113THR 00.011-0.01029.6670.0020.0020.0000.0000.0000.000
109A114LEU 0-0.012-0.00331.128-0.007-0.0070.0000.0000.0000.000
110A115LYS 10.8980.93832.7020.0630.0630.0000.0000.0000.000
111A116ALA 0-0.038-0.02132.4950.0020.0020.0000.0000.0000.000
112A117ALA 00.011-0.00228.5340.0010.0010.0000.0000.0000.000
113A118GLU -1-0.924-0.94829.495-0.100-0.1000.0000.0000.0000.000
114A119ARG 10.9850.98231.6790.0560.0560.0000.0000.0000.000
115A120LEU 0-0.034-0.01128.5930.0040.0040.0000.0000.0000.000
116A121ILE 0-0.023-0.00725.6590.0020.0020.0000.0000.0000.000
117A122GLU -1-0.923-0.95428.279-0.073-0.0730.0000.0000.0000.000
118A123GLU -1-0.887-0.90730.889-0.040-0.0400.0000.0000.0000.000
119A124ASP -1-0.937-0.97226.459-0.078-0.0780.0000.0000.0000.000
120A125PHE 0-0.040-0.01625.7300.0020.0020.0000.0000.0000.000
121A126LEU 0-0.023-0.01918.852-0.020-0.0200.0000.0000.0000.000
122A127VAL 0-0.017-0.00722.7200.0100.0100.0000.0000.0000.000
123A128LEU 0-0.008-0.02018.203-0.021-0.0210.0000.0000.0000.000
124A129PRO 0-0.009-0.00722.5690.0200.0200.0000.0000.0000.000
125A130TYR 0-0.019-0.00524.618-0.010-0.0100.0000.0000.0000.000
126A131MET 0-0.045-0.02625.085-0.001-0.0010.0000.0000.0000.000
127A132GLY 00.0880.03526.6040.0010.0010.0000.0000.0000.000
128A133PRO 00.0070.01225.975-0.012-0.0120.0000.0000.0000.000
129A134ASP -1-0.851-0.92527.043-0.135-0.1350.0000.0000.0000.000
130A135LEU 00.0550.01524.738-0.006-0.0060.0000.0000.0000.000
131A136VAL 00.001-0.00227.417-0.010-0.0100.0000.0000.0000.000
132A137LEU 0-0.022-0.02429.822-0.002-0.0020.0000.0000.0000.000
133A138ALA 0-0.013-0.00124.698-0.002-0.0020.0000.0000.0000.000
134A139LYS 10.9220.94826.0760.2320.2320.0000.0000.0000.000
135A140ARG 10.8990.95627.4290.1240.1240.0000.0000.0000.000
136A141LEU 00.0290.00026.0920.0020.0020.0000.0000.0000.000
137A142ALA 00.003-0.01023.531-0.003-0.0030.0000.0000.0000.000
138A143ALA 0-0.056-0.02124.663-0.008-0.0080.0000.0000.0000.000
139A144LEU 0-0.025-0.01027.2570.0080.0080.0000.0000.0000.000
140A145GLY 0-0.0040.01824.1710.0070.0070.0000.0000.0000.000
141A146THR 0-0.055-0.00522.1640.0130.0130.0000.0000.0000.000
142A147ALA 00.008-0.00518.014-0.030-0.0300.0000.0000.0000.000
143A148THR 0-0.085-0.05417.693-0.032-0.0320.0000.0000.0000.000
144A149VAL 00.0170.01019.6340.0260.0260.0000.0000.0000.000
145A150MET 0-0.019-0.00820.209-0.017-0.0170.0000.0000.0000.000
146A151PRO 0-0.0100.01620.6170.0190.0190.0000.0000.0000.000
147A152LEU 00.0270.01222.1690.0010.0010.0000.0000.0000.000
148A153ALA 0-0.004-0.00421.770-0.008-0.0080.0000.0000.0000.000
149A154ALA 0-0.082-0.04723.7920.0010.0010.0000.0000.0000.000
150A155PRO 00.0840.03427.2880.0020.0020.0000.0000.0000.000
151A156ILE 00.0730.07327.1320.0060.0060.0000.0000.0000.000
152A157GLY 0-0.145-0.04427.0310.0050.0050.0000.0000.0000.000
153A158SER 0-0.005-0.03628.4560.0030.0030.0000.0000.0000.000
154A159GLY 00.0220.02025.8090.0050.0050.0000.0000.0000.000
155A160TRP 0-0.038-0.03826.867-0.005-0.0050.0000.0000.0000.000
156A161GLY 00.0500.01623.9890.0000.0000.0000.0000.0000.000
157A162VAL 00.0010.00520.601-0.001-0.0010.0000.0000.0000.000
158A163ARG 10.8960.95023.7170.0570.0570.0000.0000.0000.000
159A164THR 0-0.0030.00825.2950.0010.0010.0000.0000.0000.000
160A165ARG 10.9260.97421.8730.1710.1710.0000.0000.0000.000
161A166ALA 00.0310.00724.335-0.014-0.0140.0000.0000.0000.000
162A167LEU 0-0.001-0.00126.610-0.009-0.0090.0000.0000.0000.000
163A168LEU 00.0250.00420.662-0.014-0.0140.0000.0000.0000.000
164A169GLU -1-0.899-0.95421.208-0.220-0.2200.0000.0000.0000.000
165A170LEU 0-0.051-0.02822.488-0.022-0.0220.0000.0000.0000.000
166A171PHE 00.0240.01320.640-0.013-0.0130.0000.0000.0000.000
167A172ALA 00.0160.01718.407-0.032-0.0320.0000.0000.0000.000
168A173ARG 10.8800.93819.0080.1880.1880.0000.0000.0000.000
169A174GLU -1-0.907-0.94721.700-0.282-0.2820.0000.0000.0000.000
170A175LYS 10.9820.99714.1460.5590.5590.0000.0000.0000.000
171A176ALA 0-0.037-0.01718.195-0.026-0.0260.0000.0000.0000.000
172A177SER 0-0.103-0.04719.1420.0190.0190.0000.0000.0000.000
173A178LEU 0-0.034-0.01220.2060.0370.0370.0000.0000.0000.000
174A179PRO 00.0140.02118.097-0.047-0.0470.0000.0000.0000.000
175A180PRO 0-0.005-0.00713.9830.0010.0010.0000.0000.0000.000
176A181VAL 0-0.008-0.01915.9700.0730.0730.0000.0000.0000.000
177A182VAL 0-0.042-0.02915.408-0.010-0.0100.0000.0000.0000.000
178A183VAL 00.0100.00516.7970.0170.0170.0000.0000.0000.000
179A184ASP -1-0.799-0.90818.577-0.074-0.0740.0000.0000.0000.000
180A185ALA 0-0.0030.00021.122-0.004-0.0040.0000.0000.0000.000
181A186GLY 00.0480.02424.254-0.010-0.0100.0000.0000.0000.000
182A187LEU 0-0.044-0.02118.1980.0010.0010.0000.0000.0000.000
183A188GLY 00.038-0.00222.2260.0130.0130.0000.0000.0000.000
184A189LEU 0-0.012-0.00821.4880.0120.0120.0000.0000.0000.000
185A190PRO 00.0550.02316.263-0.016-0.0160.0000.0000.0000.000
186A191SER 0-0.011-0.00816.544-0.019-0.0190.0000.0000.0000.000
187A192HIS 00.0710.05818.407-0.018-0.0180.0000.0000.0000.000
188A193ALA 00.0340.01614.526-0.022-0.0220.0000.0000.0000.000
189A194ALA 00.0180.01013.359-0.036-0.0360.0000.0000.0000.000
190A195GLU -1-0.846-0.91514.424-0.187-0.1870.0000.0000.0000.000
191A196VAL 0-0.028-0.03115.210-0.031-0.0310.0000.0000.0000.000
192A197MET 0-0.068-0.00710.737-0.042-0.0420.0000.0000.0000.000
193A198GLU -1-0.926-0.96912.252-0.328-0.3280.0000.0000.0000.000
194A199LEU 0-0.102-0.04413.972-0.026-0.0260.0000.0000.0000.000
195A200GLY 0-0.031-0.02712.731-0.019-0.0190.0000.0000.0000.000
196A201LEU 0-0.060-0.02613.729-0.039-0.0390.0000.0000.0000.000
197A202ASP -1-0.868-0.91011.649-0.705-0.7050.0000.0000.0000.000
198A203ALA 0-0.015-0.01810.7840.0170.0170.0000.0000.0000.000
199A204VAL 0-0.0160.00712.779-0.006-0.0060.0000.0000.0000.000
200A205LEU 0-0.008-0.00115.1850.0380.0380.0000.0000.0000.000
201A206VAL 0-0.008-0.01117.123-0.013-0.0130.0000.0000.0000.000
202A207ASN 0-0.016-0.02419.5600.0210.0210.0000.0000.0000.000
203A208THR 00.0820.00522.8490.0080.0080.0000.0000.0000.000
204A209ALA 00.0120.03921.5680.0040.0040.0000.0000.0000.000
205A210ILE 0-0.026-0.00617.9570.0050.0050.0000.0000.0000.000
206A211ALA 00.0040.00622.4490.0060.0060.0000.0000.0000.000
207A212GLU -1-0.935-0.97625.6350.0170.0170.0000.0000.0000.000
208A213ALA 0-0.063-0.01324.929-0.004-0.0040.0000.0000.0000.000
209A214GLN 00.022-0.00726.8940.0010.0010.0000.0000.0000.000
210A215ASP -1-0.871-0.93425.0620.1210.1210.0000.0000.0000.000
211A216PRO 00.0070.00423.8970.0100.0100.0000.0000.0000.000
212A217PRO 00.0340.00921.3490.0120.0120.0000.0000.0000.000
213A218ALA 00.0560.04219.8670.0210.0210.0000.0000.0000.000
214A219MET 0-0.034-0.01319.3990.0010.0010.0000.0000.0000.000
215A220ALA 00.015-0.01018.007-0.007-0.0070.0000.0000.0000.000
216A221GLU -1-0.917-0.94915.0240.2990.2990.0000.0000.0000.000
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