FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37478

Number of unique PDB entries: 7783

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FMODB ID: VR4J1

Calculation Name: 2EJB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2EJB

Chain ID: A

ChEMBL ID:

UniProt ID: O66811

Base Structure: X-ray

Registration Date: 2023-06-21

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


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 176
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1866604.146822
FMO2-HF: Nuclear repulsion 1798016.489247
FMO2-HF: Total energy -68587.657575
FMO2-MP2: Total energy -68787.307632


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.
-16.4-17.30424.699-11.232-12.562-0.001
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 : 0.039 / q_NPA : 0.064
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].
3A3LYS10.9630.9913.318-1.1770.9980.039-1.102-1.1130.002
4A4ILE00.0090.0116.005-0.074-0.0740.0000.0000.0000.000
5A5ALA0-0.0050.0118.5540.1290.1290.0000.0000.0000.000
6A6LEU00.0010.00611.852-0.025-0.0250.0000.0000.0000.000
7A7CYS0-0.023-0.00414.090-0.014-0.0140.0000.0000.0000.000
8A8ILE00.0430.03116.877-0.006-0.0060.0000.0000.0000.000
9A9THR0-0.050-0.04520.178-0.015-0.0150.0000.0000.0000.000
10A10GLY00.024-0.00323.8280.0010.0010.0000.0000.0000.000
11A11ALA0-0.036-0.02426.490-0.004-0.0040.0000.0000.0000.000
12A12SER0-0.040-0.03426.8860.0030.0030.0000.0000.0000.000
13A13GLY00.039-0.00126.2040.0020.0020.0000.0000.0000.000
14A14VAL0-0.031-0.02523.0780.0090.0090.0000.0000.0000.000
15A15ILE00.0200.01221.5270.0110.0110.0000.0000.0000.000
16A16TYR00.0260.00620.6380.0070.0070.0000.0000.0000.000
17A17GLY00.0360.02517.7600.0120.0120.0000.0000.0000.000
18A18ILE0-0.048-0.02716.4550.0240.0240.0000.0000.0000.000
19A19LYS10.8490.90616.431-0.062-0.0620.0000.0000.0000.000
20A20LEU00.0160.00713.2470.0120.0120.0000.0000.0000.000
21A21LEU0-0.027-0.02211.1850.0310.0310.0000.0000.0000.000
22A22GLN0-0.0080.01111.2680.0590.0590.0000.0000.0000.000
23A23VAL00.0790.03611.4740.0370.0370.0000.0000.0000.000
24A24LEU0-0.014-0.0148.237-0.011-0.0110.0000.0000.0000.000
25A25GLU-1-0.818-0.8976.9000.4430.4430.0000.0000.0000.000
26A26GLU-1-0.940-0.9837.8030.0940.0940.0000.0000.0000.000
27A27LEU0-0.054-0.0167.938-0.059-0.0590.0000.0000.0000.000
28A28ASP-1-0.897-0.9333.5850.1010.4700.008-0.110-0.2670.000
29A29PHE0-0.027-0.0152.537-5.263-2.6713.103-2.469-3.226-0.026
30A30SER0-0.050-0.0722.152-4.531-12.28119.956-6.926-5.2790.032
31A31VAL0-0.015-0.0054.070-1.833-2.2320.0830.538-0.2220.005
32A32ASP-1-0.759-0.7937.758-0.021-0.0210.0000.0000.0000.000
33A33LEU00.003-0.00610.490-0.030-0.0300.0000.0000.0000.000
34A34VAL00.0110.00513.516-0.044-0.0440.0000.0000.0000.000
35A35ILE00.0200.00516.5570.0050.0050.0000.0000.0000.000
36A36SER0-0.0030.00319.848-0.015-0.0150.0000.0000.0000.000
37A37ARG10.9150.92123.574-0.019-0.0190.0000.0000.0000.000
38A38ASN00.008-0.00326.021-0.002-0.0020.0000.0000.0000.000
39A39ALA00.0540.03222.995-0.001-0.0010.0000.0000.0000.000
40A40LYS10.8010.90021.038-0.019-0.0190.0000.0000.0000.000
41A41VAL0-0.031-0.00424.790-0.006-0.0060.0000.0000.0000.000
42A42VAL00.0710.03627.228-0.001-0.0010.0000.0000.0000.000
43A43LEU0-0.021-0.01321.7310.0010.0010.0000.0000.0000.000
44A44LYS10.8480.92525.983-0.012-0.0120.0000.0000.0000.000
45A45GLU-1-0.930-0.96728.6190.0150.0150.0000.0000.0000.000
46A46GLU-1-0.849-0.88127.7350.0440.0440.0000.0000.0000.000
47A54VAL0-0.020-0.02319.2060.0040.0040.0000.0000.0000.000
48A55LEU00.0120.00917.8070.0000.0000.0000.0000.0000.000
49A56LYS10.8890.93414.293-0.049-0.0490.0000.0000.0000.000
50A57GLY00.0200.01113.629-0.019-0.0190.0000.0000.0000.000
51A58LEU0-0.028-0.00310.264-0.029-0.0290.0000.0000.0000.000
52A59LYS10.8290.8915.713-0.403-0.4030.0000.0000.0000.000
53A60ASN0-0.015-0.0192.868-4.169-2.1961.511-1.151-2.333-0.014
54A61VAL00.0150.0234.5470.6420.778-0.001-0.012-0.1220.000
55A62ARG10.8370.8818.070-0.204-0.2040.0000.0000.0000.000
56A63ILE0-0.003-0.0059.7410.0380.0380.0000.0000.0000.000
57A64HIS0-0.0060.00111.757-0.075-0.0750.0000.0000.0000.000
58A65GLU-1-0.765-0.89116.2820.0220.0220.0000.0000.0000.000
59A66GLU-1-0.812-0.88219.9570.0290.0290.0000.0000.0000.000
60A67ASN0-0.011-0.00822.2640.0030.0030.0000.0000.0000.000
61A68ASP-1-0.808-0.88118.727-0.029-0.0290.0000.0000.0000.000
62A69PHE0-0.021-0.02920.4400.0050.0050.0000.0000.0000.000
63A70THR0-0.078-0.05320.754-0.003-0.0030.0000.0000.0000.000
64A71SER00.0330.02015.623-0.008-0.0080.0000.0000.0000.000
65A72PRO0-0.053-0.05312.7930.0020.0020.0000.0000.0000.000
66A73LEU00.0390.02112.5180.0050.0050.0000.0000.0000.000
67A74ALA00.0090.01915.7990.0070.0070.0000.0000.0000.000
68A75SER0-0.010-0.00717.272-0.005-0.0050.0000.0000.0000.000
69A76GLY00.0730.03317.035-0.002-0.0020.0000.0000.0000.000
70A77SER0-0.006-0.00617.0540.0030.0030.0000.0000.0000.000
71A78ARG10.8930.95013.3570.0750.0750.0000.0000.0000.000
72A79LEU00.0530.01212.641-0.009-0.0090.0000.0000.0000.000
73A80VAL00.0340.00713.5440.0070.0070.0000.0000.0000.000
74A81HIS0-0.089-0.0219.8000.0360.0360.0000.0000.0000.000
75A82TYR0-0.112-0.0858.874-0.149-0.1490.0000.0000.0000.000
76A83ARG10.8330.9157.631-0.233-0.2330.0000.0000.0000.000
77A84GLY00.0270.00110.2430.0220.0220.0000.0000.0000.000
78A85VAL0-0.034-0.01611.7990.0120.0120.0000.0000.0000.000
79A86TYR00.009-0.01711.708-0.008-0.0080.0000.0000.0000.000
80A87VAL0-0.017-0.02715.8920.0020.0020.0000.0000.0000.000
81A88VAL00.0070.02617.478-0.008-0.0080.0000.0000.0000.000
82A89PRO00.0490.02219.5240.0080.0080.0000.0000.0000.000
83A90CYS0-0.0270.00222.645-0.001-0.0010.0000.0000.0000.000
84A91SER00.020-0.00324.374-0.005-0.0050.0000.0000.0000.000
85A92THR00.042-0.00227.8290.0010.0010.0000.0000.0000.000
86A93ASN0-0.017-0.00930.1800.0000.0000.0000.0000.0000.000
87A94THR00.0550.03224.043-0.001-0.0010.0000.0000.0000.000
88A95LEU00.0090.00926.9820.0010.0010.0000.0000.0000.000
89A96SER0-0.0040.00127.9010.0000.0000.0000.0000.0000.000
90A97CYS0-0.077-0.02828.189-0.003-0.0030.0000.0000.0000.000
91A98ILE00.0280.01322.633-0.001-0.0010.0000.0000.0000.000
92A99ALA0-0.0030.01526.7280.0000.0000.0000.0000.0000.000
93A100ASN0-0.093-0.06029.179-0.002-0.0020.0000.0000.0000.000
94A101GLY00.0360.03928.584-0.003-0.0030.0000.0000.0000.000
95A102ILE0-0.025-0.00629.670-0.003-0.0030.0000.0000.0000.000
96A103ASN0-0.021-0.04026.3630.0050.0050.0000.0000.0000.000
97A104LYS10.9450.97628.252-0.021-0.0210.0000.0000.0000.000
98A105ASN0-0.035-0.03724.807-0.001-0.0010.0000.0000.0000.000
99A106LEU00.0230.01517.9060.0030.0030.0000.0000.0000.000
100A107ILE00.008-0.00720.1890.0040.0040.0000.0000.0000.000
101A108HIS0-0.030-0.02021.5760.0010.0010.0000.0000.0000.000
102A109ARG10.8580.92921.540-0.017-0.0170.0000.0000.0000.000
103A110VAL00.004-0.00916.3420.0000.0000.0000.0000.0000.000
104A111GLY00.0250.01519.5440.0050.0050.0000.0000.0000.000
105A112GLU-1-0.818-0.89221.6180.0290.0290.0000.0000.0000.000
106A113VAL0-0.018-0.01618.5010.0000.0000.0000.0000.0000.000
107A114ALA00.0070.00018.0110.0010.0010.0000.0000.0000.000
108A115LEU00.0180.00519.3930.0030.0030.0000.0000.0000.000
109A116LYS10.8040.89822.803-0.032-0.0320.0000.0000.0000.000
110A117GLU-1-0.863-0.93018.8610.0410.0410.0000.0000.0000.000
111A118ARG10.8500.93719.999-0.060-0.0600.0000.0000.0000.000
112A119VAL00.0020.02814.3800.0100.0100.0000.0000.0000.000
113A120PRO00.0220.00814.885-0.006-0.0060.0000.0000.0000.000
114A121LEU00.0200.01616.0230.0010.0010.0000.0000.0000.000
115A122VAL0-0.015-0.00316.877-0.005-0.0050.0000.0000.0000.000
116A123LEU0-0.001-0.00618.9370.0040.0040.0000.0000.0000.000
117A124LEU0-0.0030.00921.038-0.002-0.0020.0000.0000.0000.000
118A125VAL0-0.0030.00422.739-0.004-0.0040.0000.0000.0000.000
119A126ARG10.8960.94426.453-0.040-0.0400.0000.0000.0000.000
120A127GLU-1-0.864-0.92928.7050.0340.0340.0000.0000.0000.000
121A128ALA0-0.0220.00432.3870.0010.0010.0000.0000.0000.000
122A129PRO00.0250.00535.678-0.001-0.0010.0000.0000.0000.000
123A130TYR0-0.0050.00231.1750.0010.0010.0000.0000.0000.000
124A131ASN00.0400.00736.642-0.001-0.0010.0000.0000.0000.000
125A132GLU-1-0.860-0.94137.2450.0290.0290.0000.0000.0000.000
126A133ILE00.0460.02935.7000.0020.0020.0000.0000.0000.000
127A134HIS00.0130.00733.1950.0030.0030.0000.0000.0000.000
128A135LEU00.0280.00832.7920.0030.0030.0000.0000.0000.000
129A136GLU-1-0.906-0.95033.6120.0370.0370.0000.0000.0000.000
130A137ASN0-0.028-0.02030.8210.0020.0020.0000.0000.0000.000
131A138MET0-0.014-0.00328.8200.0040.0040.0000.0000.0000.000
132A139LEU00.0120.01529.0900.0040.0040.0000.0000.0000.000
133A140LYS10.8700.93530.702-0.036-0.0360.0000.0000.0000.000
134A141ILE00.013-0.00224.4900.0020.0020.0000.0000.0000.000
135A142THR0-0.037-0.02326.1190.0040.0040.0000.0000.0000.000
136A143ARG10.9090.94827.301-0.044-0.0440.0000.0000.0000.000
137A144MET0-0.065-0.02126.689-0.001-0.0010.0000.0000.0000.000
138A145GLY00.0010.01524.2240.0020.0020.0000.0000.0000.000
139A146GLY0-0.0110.00721.6900.0070.0070.0000.0000.0000.000
140A147VAL0-0.028-0.02620.682-0.001-0.0010.0000.0000.0000.000
141A148VAL00.001-0.00422.2870.0010.0010.0000.0000.0000.000
142A149VAL00.0040.00221.0930.0000.0000.0000.0000.0000.000
143A150PRO00.0210.02024.228-0.001-0.0010.0000.0000.0000.000
144A151ALA0-0.004-0.00925.6250.0030.0030.0000.0000.0000.000
145A152SER0-0.053-0.03626.611-0.004-0.0040.0000.0000.0000.000
146A153PRO0-0.0010.00826.7540.0030.0030.0000.0000.0000.000
147A154ALA0-0.0090.00227.912-0.004-0.0040.0000.0000.0000.000
148A155PHE00.045-0.00229.3610.0010.0010.0000.0000.0000.000
149A156TYR0-0.029-0.01028.754-0.001-0.0010.0000.0000.0000.000
150A157HIS00.023-0.00224.152-0.005-0.0050.0000.0000.0000.000
151A158LYS10.9130.96729.406-0.040-0.0400.0000.0000.0000.000
152A159PRO0-0.0120.01528.680-0.001-0.0010.0000.0000.0000.000
153A160GLN00.0240.00830.185-0.001-0.0010.0000.0000.0000.000
154A161SER0-0.036-0.02628.210-0.002-0.0020.0000.0000.0000.000
155A162ILE00.040-0.00927.4610.0030.0030.0000.0000.0000.000
156A163ASP-1-0.778-0.86222.9610.0640.0640.0000.0000.0000.000
157A164ASP-1-0.779-0.86823.9050.0510.0510.0000.0000.0000.000
158A165MET0-0.032-0.01624.8000.0050.0050.0000.0000.0000.000
159A166ILE0-0.004-0.00421.0100.0050.0050.0000.0000.0000.000
160A167ASN00.0240.00120.1420.0160.0160.0000.0000.0000.000
161A168PHE00.0120.01320.3460.0080.0080.0000.0000.0000.000
162A169VAL0-0.013-0.00521.4880.0060.0060.0000.0000.0000.000
163A170VAL0-0.004-0.00815.9720.0060.0060.0000.0000.0000.000
164A171GLY00.0540.02616.9120.0110.0110.0000.0000.0000.000
165A172LYS10.8660.92817.790-0.090-0.0900.0000.0000.0000.000
166A173LEU0-0.004-0.00316.7590.0020.0020.0000.0000.0000.000
167A174LEU00.0090.03211.5860.0070.0070.0000.0000.0000.000
168A175ASP-1-0.791-0.88514.5980.1280.1280.0000.0000.0000.000
169A176VAL0-0.069-0.01817.2120.0060.0060.0000.0000.0000.000
170A177LEU00.0010.01011.7050.0020.0020.0000.0000.0000.000
171A178ARG10.8840.92612.680-0.127-0.1270.0000.0000.0000.000
172A179ILE0-0.051-0.0139.2560.0290.0290.0000.0000.0000.000
173A180GLU-1-0.924-0.95910.3110.2750.2750.0000.0000.0000.000
174A181HIS0-0.010-0.02711.696-0.010-0.0100.0000.0000.0000.000
175A182ASN0-0.007-0.00414.328-0.002-0.0020.0000.0000.0000.000
176A183LEU0-0.043-0.00416.188-0.013-0.0130.0000.0000.0000.000