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: PJL19
Calculation Name: 1L2Y-A-MD4-83300ps
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 | -54835.88102 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47396.905948 |
| FMO2-HF: Total energy | -7438.975072 |
| FMO2-MP2: Total energy | -7461.338918 |
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. |
| 18.586 | 24.559 | 0.319 | -2.435 | -3.856 | -0.006 |
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 | 0.143 | 0.089 | 3.688 | 6.302 | 9.078 | 0.003 | -1.386 | -1.393 | -0.008 | |
| 4 | 4 | ILE | 0 | -0.016 | -0.009 | 3.220 | 5.857 | 6.613 | 0.040 | -0.192 | -0.604 | -0.001 | |
| 5 | 5 | GLN | 0 | -0.019 | -0.035 | 3.031 | 2.337 | 4.720 | 0.277 | -0.854 | -1.805 | 0.003 | |
| 6 | 6 | TRP | 0 | 0.050 | 0.042 | 5.675 | 2.629 | 2.687 | -0.001 | -0.003 | -0.054 | 0.000 | |
| 7 | 7 | LEU | 0 | 0.013 | 0.002 | 7.800 | 2.962 | 2.962 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.866 | 0.917 | 6.776 | 29.028 | 29.028 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.824 | -0.894 | 9.361 | -21.964 | -21.964 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | -0.013 | -0.004 | 12.188 | 1.726 | 1.726 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | -0.018 | 0.001 | 12.458 | 0.782 | 0.782 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.014 | -0.007 | 13.371 | 0.064 | 0.064 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.052 | -0.023 | 16.556 | 0.520 | 0.520 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | 0.022 | 0.001 | 13.922 | 0.373 | 0.373 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | -0.002 | 0.009 | 15.895 | 0.048 | 0.048 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.872 | 0.937 | 10.359 | 24.027 | 24.027 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.000 | 0.000 | 15.408 | -0.277 | -0.277 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | 0.011 | 0.016 | 11.051 | -1.220 | -1.220 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.102 | -0.043 | 7.439 | 0.758 | 0.758 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.919 | -0.966 | 7.416 | -35.366 | -35.366 | 0.000 | 0.000 | 0.000 | 0.000 |