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: 3J3LL

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 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 76
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -529870.304974
FMO2-HF: Nuclear repulsion 497980.040113
FMO2-HF: Total energy -31890.264861
FMO2-MP2: Total energy -31984.134828


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.
-7.355-2.6161.41-2.698-3.4520.002
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 : 0.037 / q_NPA : 0.013
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-1-0.810-0.8953.352-0.2902.1650.051-1.197-1.3100.005
4A3GLU-1-0.854-0.9122.426-3.989-2.2571.359-1.268-1.823-0.004
5A4GLU-1-0.946-0.9683.943-3.266-2.7690.001-0.232-0.2660.001
6A5LEU00.0320.0135.8860.6570.6570.0000.0000.0000.000
7A6ARG10.8410.9166.178-1.051-1.0510.0000.0000.0000.000
8A7ARG10.8560.9104.6630.4630.518-0.001-0.001-0.0530.000
9A8GLU-1-0.796-0.8769.601-0.375-0.3750.0000.0000.0000.000
10A9THR00.004-0.02411.6490.0760.0760.0000.0000.0000.000
11A10LEU0-0.0110.00711.5260.0330.0330.0000.0000.0000.000
12A11LYS10.8150.89711.9740.3700.3700.0000.0000.0000.000
13A12TRP0-0.031-0.04114.3730.0510.0510.0000.0000.0000.000
14A13LEU00.0580.04417.1510.0140.0140.0000.0000.0000.000
15A14GLU-1-0.909-0.96816.621-0.059-0.0590.0000.0000.0000.000
16A15ARG10.8490.93318.2670.1410.1410.0000.0000.0000.000
17A16ILE00.0070.01121.4650.0080.0080.0000.0000.0000.000
18A17GLU-1-0.828-0.91222.812-0.027-0.0270.0000.0000.0000.000
19A18GLU-1-0.834-0.89424.727-0.025-0.0250.0000.0000.0000.000
20A19ARG10.7320.85825.6400.0660.0660.0000.0000.0000.000
21A20VAL0-0.011-0.01627.3850.0030.0030.0000.0000.0000.000
22A21LYS10.7340.84627.9730.0340.0340.0000.0000.0000.000
23A22GLU-1-0.925-0.94529.526-0.047-0.0470.0000.0000.0000.000
24A23ILE0-0.019-0.00530.4750.0000.0000.0000.0000.0000.000
25A24GLU-1-0.877-0.90934.231-0.024-0.0240.0000.0000.0000.000
26A25GLY00.033-0.00336.917-0.002-0.0020.0000.0000.0000.000
27A26ASP-1-0.860-0.92137.178-0.032-0.0320.0000.0000.0000.000
28A27GLU-1-0.727-0.84236.655-0.028-0.0280.0000.0000.0000.000
29A28GLY0-0.025-0.00236.3640.0000.0000.0000.0000.0000.000
30A29PHE00.006-0.01032.722-0.001-0.0010.0000.0000.0000.000
31A30MET00.0390.03032.048-0.004-0.0040.0000.0000.0000.000
32A31ARG10.7130.82331.8620.0260.0260.0000.0000.0000.000
33A32ASN0-0.024-0.01530.3250.0030.0030.0000.0000.0000.000
34A33ILE00.0110.01227.102-0.003-0.0030.0000.0000.0000.000
35A34GLU-1-0.788-0.89126.917-0.035-0.0350.0000.0000.0000.000
36A35ALA0-0.040-0.01027.4700.0030.0030.0000.0000.0000.000
37A36TYR00.010-0.00123.6600.0020.0020.0000.0000.0000.000
38A37ILE00.0180.01322.894-0.005-0.0050.0000.0000.0000.000
39A38SER0-0.013-0.00922.7570.0050.0050.0000.0000.0000.000
40A39ASP-1-0.914-0.95922.920-0.019-0.0190.0000.0000.0000.000
41A40SER0-0.090-0.05418.1460.0070.0070.0000.0000.0000.000
42A41ARG10.8060.88018.6000.0340.0340.0000.0000.0000.000
43A42TYR0-0.014-0.00119.5980.0180.0180.0000.0000.0000.000
44A43PHE0-0.021-0.03517.5130.0180.0180.0000.0000.0000.000
45A44LEU0-0.013-0.00712.9040.0290.0290.0000.0000.0000.000
46A45GLU-1-0.933-0.94915.2240.0880.0880.0000.0000.0000.000
47A46LYS10.7300.86017.294-0.056-0.0560.0000.0000.0000.000
48A47GLY00.010-0.00213.2960.0110.0110.0000.0000.0000.000
49A48ASP-1-0.873-0.92212.6510.1060.1060.0000.0000.0000.000
50A49LEU0-0.011-0.0148.239-0.031-0.0310.0000.0000.0000.000
51A50VAL00.0060.00412.100-0.081-0.0810.0000.0000.0000.000
52A51ARG10.8230.89613.8240.0440.0440.0000.0000.0000.000
53A52ALA00.0570.02914.621-0.015-0.0150.0000.0000.0000.000
54A53PHE00.0280.02213.118-0.033-0.0330.0000.0000.0000.000
55A54GLU-1-0.816-0.88315.275-0.116-0.1160.0000.0000.0000.000
56A55CYS0-0.051-0.01818.1400.0090.0090.0000.0000.0000.000
57A56VAL00.0430.02616.5520.0040.0040.0000.0000.0000.000
58A57VAL0-0.024-0.00817.0120.0020.0020.0000.0000.0000.000
59A58TRP0-0.045-0.01819.8730.0110.0110.0000.0000.0000.000
60A59ALA00.0080.00922.9220.0090.0090.0000.0000.0000.000
61A60TRP0-0.022-0.03320.2350.0070.0070.0000.0000.0000.000
62A61ALA0-0.041-0.00523.6880.0060.0060.0000.0000.0000.000
63A62TRP0-0.022-0.02825.3270.0100.0100.0000.0000.0000.000
64A63LEU00.0060.01126.5380.0060.0060.0000.0000.0000.000
65A64GLU-1-0.787-0.91625.255-0.073-0.0730.0000.0000.0000.000
66A65ILE0-0.026-0.01127.0610.0040.0040.0000.0000.0000.000
67A66GLY00.007-0.00630.1000.0050.0050.0000.0000.0000.000
68A67LEU0-0.022-0.00129.8690.0050.0050.0000.0000.0000.000
69A68GLU-1-0.939-0.95231.405-0.055-0.0550.0000.0000.0000.000
70A69VAL0-0.115-0.06533.4230.0040.0040.0000.0000.0000.000
71A70GLY0-0.0010.00936.1140.0030.0030.0000.0000.0000.000
72A71LYS10.7850.88735.7420.0380.0380.0000.0000.0000.000
73A72LEU0-0.081-0.02932.0110.0020.0020.0000.0000.0000.000
74A73HIS0-0.009-0.00835.865-0.001-0.0010.0000.0000.0000.000
75A74GLU-1-0.820-0.89931.687-0.049-0.0490.0000.0000.0000.000
76A75THR0-0.123-0.07335.7630.0020.0020.0000.0000.0000.000