FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: JQ6N9

Calculation Name: 2OO2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2OO2

Chain ID: A

ChEMBL ID:

UniProt ID: O28492

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptHSide
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 76
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -528202.189818
FMO2-HF: Nuclear repulsion 496312.459532
FMO2-HF: Total energy -31889.730286
FMO2-MP2: Total energy -31983.810337


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-9.799-4.9233.99-4.026-4.8410.013
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.032 / q_NPA : 0.001
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].
3A2GLU-1-0.861-0.9182.972-0.0602.8110.358-1.415-1.8140.008
4A3GLU-1-0.872-0.9302.195-5.981-4.5653.624-2.346-2.6940.004
5A4GLU-1-0.932-0.9513.606-3.298-2.7090.008-0.265-0.3330.001
6A5LEU00.020-0.0055.4960.6550.6550.0000.0000.0000.000
7A6ARG10.8810.9425.478-1.686-1.6860.0000.0000.0000.000
8A7ARG10.8380.9055.0500.4170.4170.0000.0000.0000.000
9A8GLU-1-0.780-0.8729.361-0.381-0.3810.0000.0000.0000.000
10A9THR00.011-0.02211.3640.0480.0480.0000.0000.0000.000
11A10LEU00.0110.00711.5410.0210.0210.0000.0000.0000.000
12A11LYS10.7870.90712.4630.3360.3360.0000.0000.0000.000
13A12TRP00.004-0.02314.9320.0410.0410.0000.0000.0000.000
14A13LEU00.0400.02516.9610.0100.0100.0000.0000.0000.000
15A14GLU-1-0.901-0.95916.796-0.015-0.0150.0000.0000.0000.000
16A15ARG10.8270.92718.5970.1220.1220.0000.0000.0000.000
17A16ILE00.0210.01221.3950.0070.0070.0000.0000.0000.000
18A17GLU-1-0.847-0.90622.393-0.001-0.0010.0000.0000.0000.000
19A18GLU-1-0.826-0.90624.495-0.013-0.0130.0000.0000.0000.000
20A19ARG10.7920.89625.5710.0530.0530.0000.0000.0000.000
21A20VAL0-0.021-0.02327.2400.0020.0020.0000.0000.0000.000
22A21LYS10.7500.85328.0540.0180.0180.0000.0000.0000.000
23A22GLU-1-0.928-0.94429.657-0.037-0.0370.0000.0000.0000.000
24A23ILE0-0.0160.00730.695-0.001-0.0010.0000.0000.0000.000
25A24GLU-1-0.889-0.92233.836-0.019-0.0190.0000.0000.0000.000
26A25GLY00.026-0.01136.635-0.002-0.0020.0000.0000.0000.000
27A26ASP-1-0.856-0.91937.309-0.026-0.0260.0000.0000.0000.000
28A27GLU-1-0.728-0.84936.511-0.020-0.0200.0000.0000.0000.000
29A28GLY0-0.0190.00436.1700.0010.0010.0000.0000.0000.000
30A29PHE0-0.013-0.01032.823-0.001-0.0010.0000.0000.0000.000
31A30MET00.0490.03031.851-0.003-0.0030.0000.0000.0000.000
32A31ARG10.7310.83331.7740.0190.0190.0000.0000.0000.000
33A32ASN0-0.010-0.00729.9120.0040.0040.0000.0000.0000.000
34A33ILE00.0150.01726.973-0.001-0.0010.0000.0000.0000.000
35A34GLU-1-0.826-0.89726.576-0.016-0.0160.0000.0000.0000.000
36A35ALA0-0.0220.01127.2580.0040.0040.0000.0000.0000.000
37A36TYR00.000-0.01723.5490.0040.0040.0000.0000.0000.000
38A37ILE00.0150.00422.7760.0010.0010.0000.0000.0000.000
39A38SER0-0.014-0.00522.5920.0090.0090.0000.0000.0000.000
40A39ASP-1-0.900-0.95122.634-0.001-0.0010.0000.0000.0000.000
41A40SER0-0.117-0.07717.7320.0130.0130.0000.0000.0000.000
42A41ARG10.8430.88618.1240.0230.0230.0000.0000.0000.000
43A42TYR0-0.0230.00219.1760.0240.0240.0000.0000.0000.000
44A43PHE0-0.024-0.04217.0070.0180.0180.0000.0000.0000.000
45A44LEU0-0.027-0.01612.8540.0430.0430.0000.0000.0000.000
46A45GLU-1-0.969-0.96814.7180.1370.1370.0000.0000.0000.000
47A46LYS10.8090.92116.560-0.066-0.0660.0000.0000.0000.000
48A47GLY0-0.015-0.00712.8050.0150.0150.0000.0000.0000.000
49A48ASP-1-0.914-0.95612.7260.0960.0960.0000.0000.0000.000
50A49LEU00.034-0.0027.969-0.024-0.0240.0000.0000.0000.000
51A50VAL00.0140.01511.926-0.081-0.0810.0000.0000.0000.000
52A51ARG10.8440.90913.5520.0230.0230.0000.0000.0000.000
53A52ALA00.0380.02414.164-0.018-0.0180.0000.0000.0000.000
54A53PHE00.0210.01312.932-0.038-0.0380.0000.0000.0000.000
55A54GLU-1-0.846-0.90215.081-0.103-0.1030.0000.0000.0000.000
56A55CYS0-0.032-0.01617.9530.0010.0010.0000.0000.0000.000
57A56VAL00.0470.02816.3570.0010.0010.0000.0000.0000.000
58A57VAL0-0.0350.00217.2810.0000.0000.0000.0000.0000.000
59A58TRP0-0.012-0.00720.0570.0060.0060.0000.0000.0000.000
60A59ALA0-0.007-0.00922.6630.0070.0070.0000.0000.0000.000
61A60TRP0-0.021-0.03820.2910.0050.0050.0000.0000.0000.000
62A61ALA0-0.0360.00823.8520.0040.0040.0000.0000.0000.000
63A62TRP0-0.018-0.01625.6030.0080.0080.0000.0000.0000.000
64A63LEU00.0050.00426.3740.0060.0060.0000.0000.0000.000
65A64GLU-1-0.879-0.97425.303-0.068-0.0680.0000.0000.0000.000
66A65ILE0-0.0020.00427.6840.0040.0040.0000.0000.0000.000
67A66GLY00.012-0.01130.5900.0040.0040.0000.0000.0000.000
68A67LEU0-0.022-0.00429.9670.0040.0040.0000.0000.0000.000
69A68GLU-1-0.964-0.96631.737-0.051-0.0510.0000.0000.0000.000
70A69VAL0-0.115-0.06133.7280.0030.0030.0000.0000.0000.000
71A70GLY0-0.0010.01336.3730.0030.0030.0000.0000.0000.000
72A71LYS10.7750.87436.1250.0330.0330.0000.0000.0000.000
73A72LEU0-0.100-0.03932.1290.0020.0020.0000.0000.0000.000
74A73HIS00.0130.00735.988-0.002-0.0020.0000.0000.0000.000
75A74GLU-1-0.815-0.89032.116-0.042-0.0420.0000.0000.0000.000
76A75THR0-0.119-0.06735.7190.0010.0010.0000.0000.0000.000