FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: JVYG9

Calculation Name: 2LE3-A-Other547

Preferred Name: Carnitine O-palmitoyltransferase 1, liver isoform

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

PDB ID: 2LE3

Chain ID: A

ChEMBL ID: CHEMBL1293194

UniProt ID: P50416

Base Structure: SolutionNMR

Registration Date: 2025-10-05

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 42
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -156861.551774
FMO2-HF: Nuclear repulsion 140235.268335
FMO2-HF: Total energy -16626.283439
FMO2-MP2: Total energy -16675.151033


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.
-54.231-50.4670.039-1.983-1.82-0.014
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 : 1 / q_Mulliken : 0.840 / q_NPA : 0.896
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].
3A3GLU-1-0.918-0.9593.109-75.834-72.0700.039-1.983-1.820-0.014
4A4ALA00.006-0.0085.5554.9054.9050.0000.0000.0000.000
5A5HIS00.0350.0129.1112.6072.6070.0000.0000.0000.000
6A6GLN00.0100.0065.039-3.072-3.0720.0000.0000.0000.000
7A7ALA0-0.043-0.0149.2652.0932.0930.0000.0000.0000.000
8A8VAL0-0.037-0.01411.0022.5312.5310.0000.0000.0000.000
9A9ALA00.0440.03213.843-0.093-0.0930.0000.0000.0000.000
10A10PHE0-0.042-0.03515.2471.0831.0830.0000.0000.0000.000
11A11GLN0-0.004-0.00217.079-0.995-0.9950.0000.0000.0000.000
12A12PHE0-0.004-0.00320.5220.4590.4590.0000.0000.0000.000
13A13THR0-0.0050.00424.207-0.365-0.3650.0000.0000.0000.000
14A14VAL0-0.0030.00626.1300.2720.2720.0000.0000.0000.000
15A15THR0-0.030-0.03328.977-0.230-0.2300.0000.0000.0000.000
16A16PRO00.002-0.01431.6520.1510.1510.0000.0000.0000.000
17A17ASP-1-0.896-0.93334.163-8.864-8.8640.0000.0000.0000.000
18A18GLY0-0.017-0.00334.1720.1290.1290.0000.0000.0000.000
19A19ILE0-0.067-0.02729.930-0.190-0.1900.0000.0000.0000.000
20A20ASP-1-0.854-0.92524.937-12.756-12.7560.0000.0000.0000.000
21A21LEU0-0.012-0.01924.609-0.212-0.2120.0000.0000.0000.000
22A22ARG10.9100.97118.99715.44315.4430.0000.0000.0000.000
23A23LEU00.0270.00419.159-0.347-0.3470.0000.0000.0000.000
24A24SER00.0540.03514.2120.5480.5480.0000.0000.0000.000
25A25HIS00.045-0.00516.6480.6460.6460.0000.0000.0000.000
26A26GLU-1-0.970-0.97710.988-26.868-26.8680.0000.0000.0000.000
27A27ALA00.0560.02915.5350.5430.5430.0000.0000.0000.000
28A28LEU00.0020.00617.9260.8070.8070.0000.0000.0000.000
29A29ARG10.9500.97716.63717.89717.8970.0000.0000.0000.000
30A30GLN00.0160.00314.4261.2291.2290.0000.0000.0000.000
31A31ILE00.0280.02719.5220.7110.7110.0000.0000.0000.000
32A32TYR00.0060.00822.8610.6680.6680.0000.0000.0000.000
33A33LEU0-0.017-0.01419.9490.5100.5100.0000.0000.0000.000
34A34SER0-0.004-0.01322.1350.3390.3390.0000.0000.0000.000
35A35GLY00.0170.02424.5380.5120.5120.0000.0000.0000.000
36A36LEU0-0.042-0.02126.5360.4670.4670.0000.0000.0000.000
37A37HIS0-0.022-0.03123.8590.7890.7890.0000.0000.0000.000
38A38SER0-0.064-0.03528.1230.2600.2600.0000.0000.0000.000
39A39TRP0-0.023-0.00830.3840.4610.4610.0000.0000.0000.000
40A40LYS10.8930.96930.23010.63610.6360.0000.0000.0000.000
41A41LYS10.9440.96732.9977.9437.9430.0000.0000.0000.000
42A42LYS00.0790.04730.0220.9560.9560.0000.0000.0000.000