FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: PK3V3
Calculation Name: 1L2Y-A-MD4-25900ps
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
PDB ID: 1L2Y
Chain ID: A
Base Structure: MD
Registration Date: 2018-03-06
Reference:
Apendix: None
Modeling method
| Optimization | BaseStructure_original |
|---|---|
| Restraint | BaseStructure_original |
| Protonation | BaseStructure_original |
| Complement | BaseStructure_original |
| Water | No |
| Procedure | Auto-FMO protocol ver. 1.20171117 |
| Remarks |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 20 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -55821.684913 |
|---|---|
| FMO2-HF: Nuclear repulsion | 48382.657214 |
| FMO2-HF: Total energy | -7439.027699 |
| FMO2-MP2: Total energy | -7461.37317 |
3D Structure
Ligand structure
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/A | N/A | N/A | N/A | N/A | N/A |
Interactive mode: IFIE and PIEDA for fragment #1(:1:ASN)
Summations of interaction energy for
fragment #1(:1:ASN)
| 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. |
| 11.404 | 14.143 | 11.564 | -5.777 | -8.526 | 0.038 |
Interaction energy analysis for fragmet #1(:1:ASN)
| 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]. |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3 | 3 | TYR | 0 | 0.115 | 0.065 | 2.417 | 2.068 | 4.706 | 2.017 | -1.631 | -3.024 | 0.011 | |
| 4 | 4 | ILE | 0 | -0.030 | -0.055 | 1.931 | -10.506 | -11.081 | 9.528 | -3.857 | -5.096 | 0.026 | |
| 5 | 5 | GLN | 0 | 0.031 | 0.035 | 3.981 | -2.699 | -2.023 | 0.019 | -0.289 | -0.406 | 0.001 | |
| 6 | 6 | TRP | 0 | 0.027 | -0.009 | 5.642 | 3.402 | 3.402 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | LEU | 0 | -0.012 | 0.008 | 6.486 | 2.275 | 2.275 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.879 | 0.927 | 6.073 | 41.690 | 41.690 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.904 | -0.932 | 9.406 | -21.030 | -21.030 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.080 | 0.046 | 11.770 | 1.629 | 1.629 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | 0.008 | 0.003 | 10.455 | 0.951 | 0.951 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.063 | -0.036 | 11.435 | 0.296 | 0.296 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.042 | -0.010 | 14.895 | 0.633 | 0.633 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.004 | 0.025 | 12.187 | 0.522 | 0.522 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.014 | -0.008 | 14.411 | 0.729 | 0.729 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.803 | 0.893 | 9.544 | 26.569 | 26.569 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.059 | 0.020 | 13.408 | -0.049 | -0.049 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.007 | -0.012 | 9.436 | -1.202 | -1.202 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.068 | -0.021 | 6.745 | 0.160 | 0.160 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.935 | -0.954 | 5.921 | -34.034 | -34.034 | 0.000 | 0.000 | 0.000 | 0.000 |