Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: 53L4Z

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:


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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1860028.474401
FMO2-HF: Nuclear repulsion 1791442.532531
FMO2-HF: Total energy -68585.94187
FMO2-MP2: Total energy -68785.761491


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.
-15.476-13.53817.719-9.656-10.003-0.009
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 : 0.029 / q_NPA : 0.046
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].
3A3LYS10.9530.9833.039-1.9140.8090.131-1.454-1.4010.000
4A4ILE00.0370.0255.2820.1230.193-0.001-0.004-0.0650.000
5A5ALA00.0060.0168.0980.1410.1410.0000.0000.0000.000
6A6LEU00.0010.00811.309-0.001-0.0010.0000.0000.0000.000
7A7CYS0-0.033-0.01613.6600.0190.0190.0000.0000.0000.000
8A8ILE00.0250.01916.905-0.001-0.0010.0000.0000.0000.000
9A9THR0-0.053-0.09519.822-0.001-0.0010.0000.0000.0000.000
10A10GLY00.003-0.02123.4070.0030.0030.0000.0000.0000.000
11A11ALA0-0.028-0.01826.379-0.002-0.0020.0000.0000.0000.000
12A12SER0-0.030-0.00926.9850.0020.0020.0000.0000.0000.000
13A13GLY00.0340.00526.355-0.001-0.0010.0000.0000.0000.000
14A14VAL0-0.024-0.02023.2460.0010.0010.0000.0000.0000.000
15A15ILE00.0320.01821.8010.0040.0040.0000.0000.0000.000
16A16TYR00.0140.00120.8740.0050.0050.0000.0000.0000.000
17A17GLY00.0410.02218.0960.0000.0000.0000.0000.0000.000
18A18ILE0-0.062-0.02216.8130.0110.0110.0000.0000.0000.000
19A19LYS10.9540.97716.520-0.035-0.0350.0000.0000.0000.000
20A20LEU00.0280.01313.2410.0090.0090.0000.0000.0000.000
21A21LEU0-0.015-0.01011.670-0.008-0.0080.0000.0000.0000.000
22A22GLN0-0.028-0.02811.6390.0360.0360.0000.0000.0000.000
23A23VAL00.0780.04311.7020.0290.0290.0000.0000.0000.000
24A24LEU0-0.023-0.0108.289-0.020-0.0200.0000.0000.0000.000
25A25GLU-1-0.782-0.8707.0270.4350.4350.0000.0000.0000.000
26A26GLU-1-0.984-0.9857.6600.1930.1930.0000.0000.0000.000
27A27LEU0-0.082-0.0307.590-0.009-0.0090.0000.0000.0000.000
28A28ASP-1-0.927-0.9453.729-0.415-0.0340.014-0.133-0.2630.000
29A29PHE0-0.045-0.0342.304-6.986-4.2722.848-2.572-2.990-0.032
30A30SER0-0.058-0.0602.248-3.381-8.56714.546-4.959-4.4010.024
31A31VAL0-0.005-0.0024.047-1.774-1.5330.030-0.141-0.1300.002
32A32ASP-1-0.755-0.8147.657-0.025-0.0250.0000.0000.0000.000
33A33LEU00.012-0.01010.351-0.051-0.0510.0000.0000.0000.000
34A34VAL00.0020.00713.545-0.010-0.0100.0000.0000.0000.000
35A35ILE0-0.001-0.00617.0870.0010.0010.0000.0000.0000.000
36A36SER00.0070.01819.976-0.004-0.0040.0000.0000.0000.000
37A37ARG11.0090.97423.5020.0130.0130.0000.0000.0000.000
38A38ASN0-0.041-0.02826.5030.0000.0000.0000.0000.0000.000
39A39ALA00.0310.01123.1690.0010.0010.0000.0000.0000.000
40A40LYS10.9320.97722.467-0.011-0.0110.0000.0000.0000.000
41A41VAL0-0.010-0.01025.6330.0020.0020.0000.0000.0000.000
42A42VAL00.0360.03327.0720.0010.0010.0000.0000.0000.000
43A43LEU0-0.011-0.00522.4630.0010.0010.0000.0000.0000.000
44A44LYS10.8670.94026.546-0.008-0.0080.0000.0000.0000.000
45A45GLU-1-0.980-0.99629.1720.0050.0050.0000.0000.0000.000
46A46GLU-1-0.805-0.88228.6420.0120.0120.0000.0000.0000.000
47A54VAL00.007-0.00120.2760.0040.0040.0000.0000.0000.000
48A55LEU00.009-0.00219.1600.0090.0090.0000.0000.0000.000
49A56LYS10.9220.95815.348-0.089-0.0890.0000.0000.0000.000
50A57GLY00.0160.01615.196-0.005-0.0050.0000.0000.0000.000
51A58LEU0-0.049-0.04311.201-0.028-0.0280.0000.0000.0000.000
52A59LYS10.9320.9497.207-0.297-0.2970.0000.0000.0000.000
53A60ASN0-0.025-0.0163.514-2.032-1.0370.151-0.393-0.753-0.003
54A61VAL00.0350.0276.3030.3520.3520.0000.0000.0000.000
55A62ARG10.8340.9059.291-0.027-0.0270.0000.0000.0000.000
56A63ILE00.000-0.01011.122-0.024-0.0240.0000.0000.0000.000
57A64HIS0-0.044-0.01712.003-0.042-0.0420.0000.0000.0000.000
58A65GLU-1-0.858-0.92916.943-0.004-0.0040.0000.0000.0000.000
59A66GLU-1-0.873-0.94120.712-0.015-0.0150.0000.0000.0000.000
60A67ASN0-0.002-0.01622.131-0.001-0.0010.0000.0000.0000.000
61A68ASP-1-0.807-0.87419.893-0.062-0.0620.0000.0000.0000.000
62A69PHE0-0.038-0.02720.851-0.005-0.0050.0000.0000.0000.000
63A70THR0-0.083-0.05921.039-0.007-0.0070.0000.0000.0000.000
64A71SER00.015-0.01016.158-0.019-0.0190.0000.0000.0000.000
65A72PRO0-0.031-0.03213.528-0.011-0.0110.0000.0000.0000.000
66A73LEU00.0270.01411.678-0.011-0.0110.0000.0000.0000.000
67A74ALA00.0000.01615.2620.0060.0060.0000.0000.0000.000
68A75SER0-0.029-0.02017.4020.0130.0130.0000.0000.0000.000
69A76GLY00.0400.01416.852-0.019-0.0190.0000.0000.0000.000
70A77SER0-0.002-0.00516.950-0.014-0.0140.0000.0000.0000.000
71A78ARG10.9030.94813.4640.1930.1930.0000.0000.0000.000
72A79LEU00.045-0.00112.569-0.055-0.0550.0000.0000.0000.000
73A80VAL00.0070.00813.142-0.027-0.0270.0000.0000.0000.000
74A81HIS0-0.045-0.0099.8890.0310.0310.0000.0000.0000.000
75A82TYR0-0.149-0.0838.664-0.201-0.2010.0000.0000.0000.000
76A83ARG10.8920.9716.9750.1930.1930.0000.0000.0000.000
77A84GLY00.007-0.01310.0020.0980.0980.0000.0000.0000.000
78A85VAL0-0.039-0.01611.658-0.044-0.0440.0000.0000.0000.000
79A86TYR00.007-0.00511.7380.0140.0140.0000.0000.0000.000
80A87VAL0-0.010-0.00815.7550.0050.0050.0000.0000.0000.000
81A88VAL0-0.0140.02617.8330.0030.0030.0000.0000.0000.000
82A89PRO00.0550.01919.4240.0060.0060.0000.0000.0000.000
83A90CYS00.0250.05122.536-0.003-0.0030.0000.0000.0000.000
84A91SER0-0.0010.00524.0100.0010.0010.0000.0000.0000.000
85A92THR00.0970.03327.483-0.002-0.0020.0000.0000.0000.000
86A93ASN0-0.027-0.01529.841-0.002-0.0020.0000.0000.0000.000
87A94THR00.0380.01923.472-0.002-0.0020.0000.0000.0000.000
88A95LEU00.0000.00726.548-0.003-0.0030.0000.0000.0000.000
89A96SER0-0.017-0.01127.491-0.001-0.0010.0000.0000.0000.000
90A97CYS0-0.062-0.03027.7540.0000.0000.0000.0000.0000.000
91A98ILE00.0420.02022.389-0.002-0.0020.0000.0000.0000.000
92A99ALA0-0.037-0.00826.458-0.001-0.0010.0000.0000.0000.000
93A100ASN0-0.087-0.05429.0220.0020.0020.0000.0000.0000.000
94A101GLY00.0030.02128.1040.0000.0000.0000.0000.0000.000
95A102ILE0-0.046-0.00729.191-0.001-0.0010.0000.0000.0000.000
96A103ASN00.008-0.01625.3680.0010.0010.0000.0000.0000.000
97A104LYS10.9330.96427.9070.0130.0130.0000.0000.0000.000
98A105ASN0-0.012-0.00524.027-0.002-0.0020.0000.0000.0000.000
99A106LEU00.0460.02517.856-0.002-0.0020.0000.0000.0000.000
100A107ILE00.021-0.00819.612-0.006-0.0060.0000.0000.0000.000
101A108HIS00.0150.01620.937-0.005-0.0050.0000.0000.0000.000
102A109ARG10.8950.94121.1760.0550.0550.0000.0000.0000.000
103A110VAL0-0.011-0.01816.037-0.004-0.0040.0000.0000.0000.000
104A111GLY00.0200.01918.836-0.007-0.0070.0000.0000.0000.000
105A112GLU-1-0.831-0.90320.878-0.039-0.0390.0000.0000.0000.000
106A113VAL0-0.058-0.03718.2060.0030.0030.0000.0000.0000.000
107A114ALA00.0430.01317.514-0.001-0.0010.0000.0000.0000.000
108A115LEU00.0130.01618.7100.0060.0060.0000.0000.0000.000
109A116LYS10.7950.89522.0880.0660.0660.0000.0000.0000.000
110A117GLU-1-0.859-0.92418.509-0.063-0.0630.0000.0000.0000.000
111A118ARG10.8750.94819.2410.0150.0150.0000.0000.0000.000
112A119VAL0-0.0090.01414.0530.0060.0060.0000.0000.0000.000
113A120PRO00.0180.00414.4630.0070.0070.0000.0000.0000.000
114A121LEU00.0270.02115.868-0.022-0.0220.0000.0000.0000.000
115A122VAL0-0.017-0.00916.6940.0140.0140.0000.0000.0000.000
116A123LEU00.008-0.01618.882-0.002-0.0020.0000.0000.0000.000
117A124LEU00.0210.02121.2020.0040.0040.0000.0000.0000.000
118A125VAL00.0020.00022.9760.0000.0000.0000.0000.0000.000
119A126ARG10.9670.98326.679-0.005-0.0050.0000.0000.0000.000
120A127GLU-1-0.913-0.95028.9140.0020.0020.0000.0000.0000.000
121A128ALA0-0.109-0.04032.5620.0010.0010.0000.0000.0000.000
122A129PRO00.0530.00935.9250.0000.0000.0000.0000.0000.000
123A130TYR00.0040.00531.295-0.001-0.0010.0000.0000.0000.000
124A131ASN00.0420.02836.9470.0000.0000.0000.0000.0000.000
125A132GLU-1-0.850-0.96237.5710.0020.0020.0000.0000.0000.000
126A133ILE00.0540.03135.1320.0000.0000.0000.0000.0000.000
127A134HIS0-0.036-0.02133.3820.0000.0000.0000.0000.0000.000
128A135LEU00.0230.00532.6930.0000.0000.0000.0000.0000.000
129A136GLU-1-0.898-0.94933.6460.0000.0000.0000.0000.0000.000
130A137ASN0-0.010-0.00530.594-0.001-0.0010.0000.0000.0000.000
131A138MET0-0.032-0.01028.781-0.002-0.0020.0000.0000.0000.000
132A139LEU00.0290.02329.1260.0000.0000.0000.0000.0000.000
133A140LYS10.9500.98630.1810.0090.0090.0000.0000.0000.000
134A141ILE00.0060.00124.469-0.001-0.0010.0000.0000.0000.000
135A142THR0-0.026-0.02726.122-0.001-0.0010.0000.0000.0000.000
136A143ARG10.9060.95526.979-0.003-0.0030.0000.0000.0000.000
137A144MET0-0.077-0.02826.1580.0010.0010.0000.0000.0000.000
138A145GLY0-0.0080.00723.777-0.002-0.0020.0000.0000.0000.000
139A146GLY0-0.0230.00221.761-0.002-0.0020.0000.0000.0000.000
140A147VAL0-0.004-0.01120.5400.0070.0070.0000.0000.0000.000
141A148VAL0-0.001-0.01122.249-0.005-0.0050.0000.0000.0000.000
142A149VAL0-0.025-0.01320.9570.0040.0040.0000.0000.0000.000
143A150PRO00.0160.02924.131-0.002-0.0020.0000.0000.0000.000
144A151ALA00.005-0.00725.5070.0010.0010.0000.0000.0000.000
145A152SER0-0.058-0.04126.4340.0000.0000.0000.0000.0000.000
146A153PRO0-0.013-0.00526.8320.0010.0010.0000.0000.0000.000
147A154ALA00.0130.01827.801-0.001-0.0010.0000.0000.0000.000
148A155PHE00.029-0.01129.4640.0010.0010.0000.0000.0000.000
149A156TYR0-0.030-0.01628.2790.0000.0000.0000.0000.0000.000
150A157HIS00.004-0.01124.6670.0000.0000.0000.0000.0000.000
151A158LYS10.9140.97329.256-0.023-0.0230.0000.0000.0000.000
152A159PRO0-0.0050.01728.7220.0000.0000.0000.0000.0000.000
153A160GLN00.0200.00230.0350.0000.0000.0000.0000.0000.000
154A161SER0-0.0120.00328.257-0.001-0.0010.0000.0000.0000.000
155A162ILE00.011-0.02027.5360.0000.0000.0000.0000.0000.000
156A163ASP-1-0.915-0.96523.5380.0340.0340.0000.0000.0000.000
157A164ASP-1-0.732-0.86124.0540.0280.0280.0000.0000.0000.000
158A165MET0-0.071-0.04025.1140.0000.0000.0000.0000.0000.000
159A166ILE0-0.027-0.01721.125-0.001-0.0010.0000.0000.0000.000
160A167ASN00.0760.02720.120-0.001-0.0010.0000.0000.0000.000
161A168PHE0-0.0050.02320.273-0.001-0.0010.0000.0000.0000.000
162A169VAL0-0.024-0.01721.524-0.001-0.0010.0000.0000.0000.000
163A170VAL0-0.011-0.01116.079-0.004-0.0040.0000.0000.0000.000
164A171GLY00.0560.02816.890-0.007-0.0070.0000.0000.0000.000
165A172LYS10.9510.97517.882-0.026-0.0260.0000.0000.0000.000
166A173LEU0-0.022-0.01416.715-0.002-0.0020.0000.0000.0000.000
167A174LEU00.0220.02811.454-0.016-0.0160.0000.0000.0000.000
168A175ASP-1-0.837-0.89714.4310.0360.0360.0000.0000.0000.000
169A176VAL0-0.087-0.04016.8990.0100.0100.0000.0000.0000.000
170A177LEU0-0.030-0.01612.1940.0060.0060.0000.0000.0000.000
171A178ARG10.8610.92612.355-0.048-0.0480.0000.0000.0000.000
172A179ILE0-0.059-0.0178.8390.0310.0310.0000.0000.0000.000
173A180GLU-1-0.932-0.95710.0730.2180.2180.0000.0000.0000.000
174A181HIS0-0.009-0.03311.537-0.024-0.0240.0000.0000.0000.000
175A182ASN00.020-0.00114.0070.0140.0140.0000.0000.0000.000
176A183LEU0-0.047-0.00115.102-0.002-0.0020.0000.0000.0000.000