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: M3J7Z

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 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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2787228.190322
FMO2-HF: Nuclear repulsion 2699977.968315
FMO2-HF: Total energy -87250.222006
FMO2-MP2: Total energy -87506.334805


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.
-0.5313.0160.428-1.057-2.920.003
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 : 0.011 / q_NPA : 0.018
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].
3A3THR0-0.089-0.0552.439-0.7112.4560.428-1.001-2.5940.003
4A4TRP00.0200.0115.006-0.380-0.320-0.001-0.012-0.0480.000
5A5LYS10.9630.9578.6530.7940.7940.0000.0000.0000.000
6A6VAL00.0390.03711.1480.0290.0290.0000.0000.0000.000
7A7GLY00.0580.02214.6590.0610.0610.0000.0000.0000.000
8A8PRO0-0.083-0.04714.144-0.083-0.0830.0000.0000.0000.000
9A9VAL0-0.021-0.01012.7550.0150.0150.0000.0000.0000.000
10A10GLU-1-0.879-0.9055.832-1.790-1.7900.0000.0000.0000.000
11A11LEU0-0.0200.0029.0200.2080.2080.0000.0000.0000.000
12A12LYS10.8900.9134.637-0.777-0.643-0.001-0.013-0.1200.000
13A13SER0-0.020-0.0046.2460.2840.2840.0000.0000.0000.000
14A14ARG10.8590.9165.7950.5030.5030.0000.0000.0000.000
15A15LEU00.0050.0009.784-0.118-0.1180.0000.0000.0000.000
16A16ILE0-0.027-0.00212.5920.0540.0540.0000.0000.0000.000
17A17LEU00.0680.03715.719-0.020-0.0200.0000.0000.0000.000
18A18GLY0-0.016-0.01518.755-0.017-0.0170.0000.0000.0000.000
19A19SER00.0300.00622.5210.0040.0040.0000.0000.0000.000
20A20GLY0-0.072-0.03225.348-0.005-0.0050.0000.0000.0000.000
21A21LYS10.9160.91827.234-0.021-0.0210.0000.0000.0000.000
22A22TYR00.0230.01922.1010.0020.0020.0000.0000.0000.000
23A23GLU-1-0.945-0.96028.5380.0660.0660.0000.0000.0000.000
24A24ASP-1-0.815-0.90830.0630.1070.1070.0000.0000.0000.000
25A25PHE00.010-0.02128.1490.0070.0070.0000.0000.0000.000
26A26GLY0-0.0210.00227.0980.0160.0160.0000.0000.0000.000
27A27VAL00.0890.03326.0340.0180.0180.0000.0000.0000.000
28A28MET0-0.071-0.01424.0990.0040.0040.0000.0000.0000.000
29A29ARG10.9480.96422.695-0.184-0.1840.0000.0000.0000.000
30A30GLU-1-0.950-0.96421.5580.2080.2080.0000.0000.0000.000
31A31ALA0-0.0090.00520.3850.0300.0300.0000.0000.0000.000
32A32ILE00.024-0.01017.8100.0280.0280.0000.0000.0000.000
33A33ALA0-0.0200.00016.6830.0550.0550.0000.0000.0000.000
34A34ALA0-0.0140.00215.8220.0750.0750.0000.0000.0000.000
35A35ALA0-0.035-0.02414.4000.0350.0350.0000.0000.0000.000
36A36LYS10.8720.93010.147-0.890-0.8900.0000.0000.0000.000
37A37ALA0-0.0090.01011.6650.1010.1010.0000.0000.0000.000
38A38GLU-1-0.739-0.8519.5330.6860.6860.0000.0000.0000.000
39A39VAL0-0.026-0.00213.744-0.059-0.0590.0000.0000.0000.000
40A40VAL00.0290.01716.4780.0000.0000.0000.0000.0000.000
41A41THR0-0.050-0.02619.997-0.018-0.0180.0000.0000.0000.000
42A42VAL0-0.001-0.00722.7540.0090.0090.0000.0000.0000.000
43A43SER0-0.016-0.02326.251-0.012-0.0120.0000.0000.0000.000
44A44VAL00.0110.02129.6310.0070.0070.0000.0000.0000.000
45A45ARG10.9340.95732.391-0.023-0.0230.0000.0000.0000.000
46A46ARG10.9410.96135.639-0.003-0.0030.0000.0000.0000.000
47A47VAL00.0240.01437.9550.0020.0020.0000.0000.0000.000
48A48GLU-1-0.958-0.96039.8170.0240.0240.0000.0000.0000.000
49A56GLY00.0420.01232.476-0.003-0.0030.0000.0000.0000.000
50A57LEU00.008-0.00527.5190.0080.0080.0000.0000.0000.000
51A58LEU0-0.009-0.02526.8690.0100.0100.0000.0000.0000.000
52A59GLU-1-0.902-0.94226.5620.1250.1250.0000.0000.0000.000
53A60ALA0-0.061-0.01526.4680.0160.0160.0000.0000.0000.000
54A61LEU0-0.024-0.02922.4690.0110.0110.0000.0000.0000.000
55A62GLU-1-0.944-0.95821.9300.2220.2220.0000.0000.0000.000
56A63GLY0-0.0050.00018.9410.0170.0170.0000.0000.0000.000
57A64VAL0-0.066-0.02616.7600.0520.0520.0000.0000.0000.000
58A65ARG10.9010.94216.112-0.103-0.1030.0000.0000.0000.000
59A66LEU00.0300.01418.402-0.005-0.0050.0000.0000.0000.000
60A67LEU0-0.0030.00819.430-0.017-0.0170.0000.0000.0000.000
61A68PRO00.0250.03721.8620.0040.0040.0000.0000.0000.000
62A69ASN00.0710.03625.349-0.010-0.0100.0000.0000.0000.000
63A70THR0-0.010-0.02027.1040.0020.0020.0000.0000.0000.000
64A71ALA00.0410.04329.792-0.004-0.0040.0000.0000.0000.000
65A72GLY0-0.054-0.03031.5660.0040.0040.0000.0000.0000.000
66A73ALA0-0.033-0.00833.9820.0000.0000.0000.0000.0000.000
67A74ARG10.8520.92635.5340.0160.0160.0000.0000.0000.000
68A75THR00.002-0.00637.945-0.003-0.0030.0000.0000.0000.000
69A76ALA00.0450.00335.3530.0010.0010.0000.0000.0000.000
70A77GLU-1-0.946-0.96136.036-0.026-0.0260.0000.0000.0000.000
71A78GLU-1-0.821-0.91637.768-0.019-0.0190.0000.0000.0000.000
72A79ALA00.0530.02732.5590.0040.0040.0000.0000.0000.000
73A80VAL00.017-0.00832.9840.0030.0030.0000.0000.0000.000
74A81ARG10.8300.93534.0660.0210.0210.0000.0000.0000.000
75A82LEU0-0.003-0.00832.5630.0050.0050.0000.0000.0000.000
76A83ALA00.0420.03129.7050.0060.0060.0000.0000.0000.000
77A84ARG10.8060.88330.2740.0360.0360.0000.0000.0000.000
78A85LEU0-0.015-0.01332.0970.0050.0050.0000.0000.0000.000
79A86GLY00.0640.02329.3840.0070.0070.0000.0000.0000.000
80A87ARG10.8970.95727.3160.0420.0420.0000.0000.0000.000
81A88LEU0-0.044-0.01728.1530.0070.0070.0000.0000.0000.000
82A89LEU0-0.028-0.01330.0870.0070.0070.0000.0000.0000.000
83A90THR0-0.031-0.00924.7450.0080.0080.0000.0000.0000.000
84A91GLY0-0.039-0.01225.2890.0100.0100.0000.0000.0000.000
85A92GLU-1-0.923-0.95820.1370.0480.0480.0000.0000.0000.000
86A93ARG10.9080.94020.9140.1010.1010.0000.0000.0000.000
87A94TRP0-0.049-0.03215.549-0.027-0.0270.0000.0000.0000.000
88A95VAL00.0330.00422.2410.0200.0200.0000.0000.0000.000
89A96LYS10.9060.97122.9280.0190.0190.0000.0000.0000.000
90A97LEU0-0.040-0.00424.4930.0100.0100.0000.0000.0000.000
91A98GLU-1-0.855-0.95227.429-0.032-0.0320.0000.0000.0000.000
92A99VAL00.0010.00529.8380.0060.0060.0000.0000.0000.000
93A100ILE0-0.0090.01030.575-0.004-0.0040.0000.0000.0000.000
94A101PRO00.0120.01034.7420.0060.0060.0000.0000.0000.000
95A102ASP-1-0.830-0.91838.001-0.025-0.0250.0000.0000.0000.000
96A103PRO0-0.058-0.06036.039-0.002-0.0020.0000.0000.0000.000
97A104THR0-0.022-0.00336.3840.0040.0040.0000.0000.0000.000
98A105TYR0-0.029-0.01734.4450.0010.0010.0000.0000.0000.000
99A106LEU0-0.029-0.00630.893-0.002-0.0020.0000.0000.0000.000
100A107LEU0-0.0030.00131.286-0.005-0.0050.0000.0000.0000.000
101A108PRO00.0200.01629.1440.0040.0040.0000.0000.0000.000
102A109ASP-1-0.857-0.91832.418-0.067-0.0670.0000.0000.0000.000
103A110PRO00.026-0.00233.034-0.005-0.0050.0000.0000.0000.000
104A111LEU00.0270.01733.907-0.005-0.0050.0000.0000.0000.000
105A112GLU-1-0.838-0.92935.974-0.055-0.0550.0000.0000.0000.000
106A113THR00.006-0.01229.6670.0020.0020.0000.0000.0000.000
107A114LEU0-0.010-0.00231.049-0.007-0.0070.0000.0000.0000.000
108A115LYS10.8980.93832.6290.0590.0590.0000.0000.0000.000
109A116ALA0-0.041-0.02232.4940.0020.0020.0000.0000.0000.000
110A117ALA00.0170.00128.4650.0010.0010.0000.0000.0000.000
111A118GLU-1-0.926-0.94929.428-0.098-0.0980.0000.0000.0000.000
112A119ARG10.9840.98131.6100.0520.0520.0000.0000.0000.000
113A120LEU0-0.034-0.01028.5500.0040.0040.0000.0000.0000.000
114A121ILE0-0.019-0.00625.5910.0030.0030.0000.0000.0000.000
115A122GLU-1-0.927-0.95528.215-0.070-0.0700.0000.0000.0000.000
116A123GLU-1-0.888-0.90730.833-0.035-0.0350.0000.0000.0000.000
117A124ASP-1-0.938-0.97226.409-0.072-0.0720.0000.0000.0000.000
118A125PHE0-0.040-0.01625.6850.0030.0030.0000.0000.0000.000
119A126LEU0-0.023-0.01918.808-0.020-0.0200.0000.0000.0000.000
120A127VAL0-0.017-0.00722.6740.0110.0110.0000.0000.0000.000
121A128LEU0-0.006-0.02018.203-0.021-0.0210.0000.0000.0000.000
122A129PRO0-0.008-0.00522.5690.0200.0200.0000.0000.0000.000
123A130TYR0-0.019-0.00624.618-0.010-0.0100.0000.0000.0000.000
124A131MET0-0.044-0.02625.085-0.002-0.0020.0000.0000.0000.000
125A132GLY00.0860.03526.6040.0020.0020.0000.0000.0000.000
126A133PRO00.0050.01025.975-0.012-0.0120.0000.0000.0000.000
127A134ASP-1-0.851-0.92427.043-0.133-0.1330.0000.0000.0000.000
128A135LEU00.0540.01524.738-0.006-0.0060.0000.0000.0000.000
129A136VAL00.001-0.00327.417-0.011-0.0110.0000.0000.0000.000
130A137LEU0-0.020-0.02429.822-0.002-0.0020.0000.0000.0000.000
131A138ALA0-0.011-0.00124.698-0.001-0.0010.0000.0000.0000.000
132A139LYS10.9220.94825.9830.2350.2350.0000.0000.0000.000
133A140ARG10.8970.95627.3940.1220.1220.0000.0000.0000.000
134A141LEU00.027-0.00126.0110.0020.0020.0000.0000.0000.000
135A142ALA00.003-0.01023.430-0.003-0.0030.0000.0000.0000.000
136A143ALA0-0.055-0.02124.565-0.008-0.0080.0000.0000.0000.000
137A144LEU0-0.028-0.01127.1560.0070.0070.0000.0000.0000.000
138A145GLY0-0.0020.01924.0820.0080.0080.0000.0000.0000.000
139A146THR0-0.053-0.00422.0820.0140.0140.0000.0000.0000.000
140A147ALA00.007-0.00517.949-0.030-0.0300.0000.0000.0000.000
141A148THR0-0.084-0.05417.693-0.030-0.0300.0000.0000.0000.000
142A149VAL00.0180.01019.6340.0240.0240.0000.0000.0000.000
143A150MET0-0.017-0.00720.209-0.016-0.0160.0000.0000.0000.000
144A151PRO0-0.0140.01620.6170.0180.0180.0000.0000.0000.000
145A152LEU00.0290.01322.1690.0010.0010.0000.0000.0000.000
146A153ALA00.001-0.00321.770-0.009-0.0090.0000.0000.0000.000
147A154ALA0-0.084-0.04823.792-0.001-0.0010.0000.0000.0000.000
148A155PRO00.0800.03427.2880.0020.0020.0000.0000.0000.000
149A156ILE00.0700.07127.1320.0060.0060.0000.0000.0000.000
150A157GLY0-0.139-0.04127.0310.0050.0050.0000.0000.0000.000
151A158SER0-0.009-0.03728.4560.0030.0030.0000.0000.0000.000
152A159GLY00.0250.02125.8090.0050.0050.0000.0000.0000.000
153A160TRP0-0.040-0.03926.867-0.005-0.0050.0000.0000.0000.000
154A161GLY00.0490.01623.9890.0000.0000.0000.0000.0000.000
155A162VAL00.0010.00620.601-0.001-0.0010.0000.0000.0000.000
156A163ARG10.8950.95023.7170.0490.0490.0000.0000.0000.000
157A164THR00.0010.01025.2950.0000.0000.0000.0000.0000.000
158A165ARG10.9270.97421.8730.1660.1660.0000.0000.0000.000
159A166ALA00.0290.00624.335-0.014-0.0140.0000.0000.0000.000
160A167LEU0-0.002-0.00126.610-0.009-0.0090.0000.0000.0000.000
161A168LEU00.0270.00620.662-0.014-0.0140.0000.0000.0000.000
162A169GLU-1-0.901-0.95621.208-0.217-0.2170.0000.0000.0000.000
163A170LEU0-0.051-0.02822.488-0.023-0.0230.0000.0000.0000.000
164A171PHE00.0270.01420.640-0.013-0.0130.0000.0000.0000.000
165A172ALA00.0160.01718.407-0.032-0.0320.0000.0000.0000.000
166A173ARG10.8760.93719.0080.1880.1880.0000.0000.0000.000
167A174GLU-1-0.903-0.94521.700-0.287-0.2870.0000.0000.0000.000
168A175LYS10.9780.99514.1460.5650.5650.0000.0000.0000.000
169A176ALA0-0.036-0.01718.195-0.026-0.0260.0000.0000.0000.000
170A177SER0-0.101-0.04619.1420.0170.0170.0000.0000.0000.000
171A178LEU0-0.032-0.01020.2060.0370.0370.0000.0000.0000.000
172A179PRO00.0120.02017.998-0.047-0.0470.0000.0000.0000.000
173A180PRO0-0.005-0.00713.8960.0020.0020.0000.0000.0000.000
174A181VAL0-0.010-0.02015.9700.0720.0720.0000.0000.0000.000
175A182VAL0-0.036-0.02815.409-0.010-0.0100.0000.0000.0000.000
176A183VAL00.0010.00316.7970.0140.0140.0000.0000.0000.000
177A184ASP-1-0.794-0.90718.577-0.060-0.0600.0000.0000.0000.000
178A185ALA0-0.0040.00021.122-0.006-0.0060.0000.0000.0000.000
179A186GLY00.0450.02124.254-0.011-0.0110.0000.0000.0000.000
180A187LEU0-0.042-0.02018.1980.0000.0000.0000.0000.0000.000
181A188GLY00.035-0.00222.2260.0120.0120.0000.0000.0000.000
182A189LEU0-0.010-0.00621.4880.0120.0120.0000.0000.0000.000
183A190PRO00.0600.02516.262-0.016-0.0160.0000.0000.0000.000
184A191SER0-0.005-0.00616.544-0.016-0.0160.0000.0000.0000.000
185A192HIS00.0580.05218.407-0.018-0.0180.0000.0000.0000.000
186A193ALA00.0350.01714.525-0.022-0.0220.0000.0000.0000.000
187A194ALA00.0200.01013.359-0.034-0.0340.0000.0000.0000.000
188A195GLU-1-0.850-0.91714.424-0.178-0.1780.0000.0000.0000.000
189A196VAL0-0.027-0.03115.211-0.032-0.0320.0000.0000.0000.000
190A197MET0-0.061-0.00510.737-0.039-0.0390.0000.0000.0000.000
191A198GLU-1-0.932-0.97112.252-0.315-0.3150.0000.0000.0000.000
192A199LEU0-0.099-0.04413.972-0.029-0.0290.0000.0000.0000.000
193A200GLY0-0.032-0.02612.731-0.019-0.0190.0000.0000.0000.000
194A201LEU0-0.058-0.02513.729-0.041-0.0410.0000.0000.0000.000
195A202ASP-1-0.868-0.91111.649-0.697-0.6970.0000.0000.0000.000
196A203ALA0-0.012-0.01710.7840.0210.0210.0000.0000.0000.000
197A204VAL0-0.0170.00712.779-0.012-0.0120.0000.0000.0000.000
198A205LEU0-0.012-0.00215.1850.0400.0400.0000.0000.0000.000
199A206VAL0-0.001-0.00817.123-0.016-0.0160.0000.0000.0000.000
200A207ASN0-0.022-0.02619.5600.0210.0210.0000.0000.0000.000
201A208THR00.0850.00622.8490.0080.0080.0000.0000.0000.000
202A209ALA00.0130.03921.5690.0040.0040.0000.0000.0000.000
203A210ILE0-0.025-0.00617.9570.0050.0050.0000.0000.0000.000
204A211ALA00.0010.00422.4490.0060.0060.0000.0000.0000.000
205A212GLU-1-0.931-0.97425.6350.0280.0280.0000.0000.0000.000
206A213ALA0-0.067-0.01524.929-0.005-0.0050.0000.0000.0000.000
207A214GLN00.022-0.00726.8940.0010.0010.0000.0000.0000.000
208A215ASP-1-0.872-0.93325.0620.1370.1370.0000.0000.0000.000
209A216PRO00.0090.00423.8970.0110.0110.0000.0000.0000.000
210A217PRO00.0320.00821.3490.0130.0130.0000.0000.0000.000
211A218ALA00.0570.04219.8670.0240.0240.0000.0000.0000.000
212A219MET0-0.034-0.01219.3990.0040.0040.0000.0000.0000.000
213A220ALA00.008-0.01218.007-0.006-0.0060.0000.0000.0000.000
214A221GLU-1-0.913-0.94815.0240.3330.3330.0000.0000.0000.000
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