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
FMODB ID: P43KN
Calculation Name: 1L2Y-A-MD4-29800ps
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
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 |
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 | -54887.58657 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47448.641312 |
| FMO2-HF: Total energy | -7438.945258 |
| FMO2-MP2: Total energy | -7461.321431 |
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. |
| 18.962 | 24.944 | 5.793 | -4.074 | -7.699 | 0.021 |
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 | 0.096 | 0.056 | 2.567 | 3.711 | 6.435 | 1.196 | -1.440 | -2.480 | 0.009 | |
| 4 | 4 | ILE | 0 | 0.017 | 0.005 | 2.200 | -3.872 | -1.464 | 4.589 | -2.346 | -4.650 | 0.012 | |
| 5 | 5 | GLN | 0 | -0.065 | -0.039 | 3.635 | -4.245 | -3.583 | 0.009 | -0.276 | -0.395 | 0.000 | |
| 6 | 6 | TRP | 0 | 0.018 | 0.005 | 5.244 | 4.568 | 4.756 | -0.001 | -0.012 | -0.174 | 0.000 | |
| 7 | 7 | LEU | 0 | 0.004 | -0.014 | 5.918 | 2.403 | 2.403 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.904 | 0.963 | 7.619 | 30.311 | 30.311 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.741 | -0.821 | 9.364 | -21.653 | -21.653 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.025 | 0.038 | 11.620 | 1.834 | 1.834 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | -0.059 | -0.064 | 10.826 | 1.264 | 1.264 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | 0.016 | 0.008 | 11.265 | 0.723 | 0.723 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.065 | -0.016 | 14.188 | 1.000 | 1.000 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.062 | -0.038 | 13.797 | 1.156 | 1.156 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.050 | 0.019 | 15.796 | 0.659 | 0.659 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.747 | 0.849 | 11.189 | 24.999 | 24.999 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.049 | 0.028 | 13.737 | -0.165 | -0.165 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.002 | -0.006 | 9.610 | -1.524 | -1.524 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.085 | -0.051 | 5.745 | -0.108 | -0.108 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.913 | -0.933 | 8.837 | -22.099 | -22.099 | 0.000 | 0.000 | 0.000 | 0.000 |