FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: YVGK2

Calculation Name: 3C8P-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3C8P

Chain ID: A

ChEMBL ID:

UniProt ID: P83554

Base Structure: X-ray

Registration Date: 2023-09-23

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 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 43
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -201297.706142
FMO2-HF: Nuclear repulsion 182677.782208
FMO2-HF: Total energy -18619.923934
FMO2-MP2: Total energy -18669.049067


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:LYS)


Summations of interaction energy for fragment #1(A:1:LYS)
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.
55.22967.3415.516-11.971-15.656-0.106
Interaction energy analysis for fragmet #1(A:1:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.941 / q_NPA : 0.979
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].
3A3CYS0-0.044-0.0032.816-15.736-10.5562.042-2.149-5.073-0.012
4A4CYS0-0.114-0.0474.6053.6373.729-0.002-0.012-0.0780.000
5A5PRO00.0860.0468.174-1.479-1.4790.0000.0000.0000.000
6A6SER00.0320.01311.4920.6300.6300.0000.0000.0000.000
7A7THR00.0390.00211.940-1.826-1.8260.0000.0000.0000.000
8A8THR00.0580.03513.222-0.302-0.3020.0000.0000.0000.000
9A9GLY00.0600.04012.3620.3020.3020.0000.0000.0000.000
10A10ARG10.8220.8854.79037.15837.229-0.001-0.001-0.0690.000
11A11ASN00.023-0.00210.737-0.964-0.9640.0000.0000.0000.000
12A12ILE00.0290.02713.9840.4840.4840.0000.0000.0000.000
13A13TYR0-0.024-0.0186.0630.2190.2190.0000.0000.0000.000
14A14ASN00.013-0.0239.494-1.043-1.0430.0000.0000.0000.000
15A15THR00.0490.03411.7750.8430.8430.0000.0000.0000.000
16A16CYS00.0050.00810.6611.0861.0860.0000.0000.0000.000
17A17ARG10.8670.9268.53520.77220.7720.0000.0000.0000.000
18A18LEU0-0.0100.00412.4840.1780.1780.0000.0000.0000.000
19A19THR0-0.036-0.02115.5880.7490.7490.0000.0000.0000.000
20A20GLY00.0320.03515.6870.5880.5880.0000.0000.0000.000
21A21SER0-0.0070.00114.9350.2820.2820.0000.0000.0000.000
22A22SER00.0290.00712.048-1.182-1.1820.0000.0000.0000.000
23A23ARG10.9960.9735.10623.37223.3720.0000.0000.0000.000
24A24GLU-1-0.882-0.9349.121-17.013-17.0130.0000.0000.0000.000
25A25THR00.0090.00310.8020.3200.3200.0000.0000.0000.000
26A27ALA0-0.043-0.0198.730-0.414-0.4140.0000.0000.0000.000
27A28LYS10.9500.97610.80014.54314.5430.0000.0000.0000.000
28A29LEU00.0240.02114.1540.2120.2120.0000.0000.0000.000
29A30SER0-0.048-0.03211.403-0.415-0.4150.0000.0000.0000.000
30A31GLY00.0260.02313.038-0.373-0.3730.0000.0000.0000.000
31A33LYS10.9570.9837.35523.34123.3410.0000.0000.0000.000
32A34ILE0-0.016-0.0163.336-4.879-4.2660.041-0.253-0.4010.001
33A35ILE00.016-0.0032.6493.2874.6720.089-0.499-0.9760.000
34A36SER00.0420.0321.899-14.537-16.5669.319-4.203-3.087-0.044
35A37ALA00.0170.0093.2444.6635.2080.020-0.161-0.4050.001
36A38SER00.0480.0242.785-10.860-8.2890.785-1.350-2.006-0.012
37A39THR0-0.051-0.0402.111-30.612-27.0783.223-3.317-3.439-0.040
38A41PRO00.0720.0394.2832.6222.7710.000-0.026-0.1220.000
39A42SER00.0470.0057.992-0.772-0.7720.0000.0000.0000.000
40A43ASN00.0400.02410.633-0.898-0.8980.0000.0000.0000.000
41A44TYR0-0.080-0.0467.7172.1452.1450.0000.0000.0000.000
42A45PRO00.0560.0366.907-5.102-5.1020.0000.0000.0000.000
43A46LYS10.9631.0006.14422.20322.2030.0000.0000.0000.000