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: PLL29
Calculation Name: 1L2Y-A-MD4-6500ps
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 | -55482.929638 |
|---|---|
| FMO2-HF: Nuclear repulsion | 48043.867395 |
| FMO2-HF: Total energy | -7439.062243 |
| FMO2-MP2: Total energy | -7461.39175 |
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. |
| 10.688 | 10.087 | 16.971 | -5.77 | -10.6 | 0.047 |
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 | 0.116 | 0.074 | 2.021 | 1.464 | -0.072 | 8.880 | -2.909 | -4.435 | 0.027 | |
| 4 | 4 | ILE | 0 | 0.005 | -0.023 | 2.084 | -8.063 | -8.778 | 8.079 | -2.118 | -5.246 | 0.020 | |
| 5 | 5 | GLN | 0 | -0.022 | -0.012 | 3.318 | 2.894 | 4.308 | 0.013 | -0.725 | -0.702 | 0.000 | |
| 6 | 6 | TRP | 0 | 0.046 | 0.033 | 4.883 | 4.461 | 4.697 | -0.001 | -0.018 | -0.217 | 0.000 | |
| 7 | 7 | LEU | 0 | -0.008 | -0.008 | 6.421 | 2.796 | 2.796 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.904 | 0.943 | 7.671 | 30.890 | 30.890 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.926 | -0.952 | 8.874 | -23.019 | -23.019 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.038 | 0.022 | 10.784 | 1.997 | 1.997 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | 0.007 | 0.012 | 10.417 | 1.283 | 1.283 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.006 | -0.004 | 11.341 | 0.783 | 0.783 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.015 | 0.019 | 14.349 | 1.138 | 1.138 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.089 | -0.063 | 13.054 | 0.282 | 0.282 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.039 | 0.011 | 15.364 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.803 | 0.907 | 9.062 | 27.963 | 27.963 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.068 | 0.027 | 13.033 | -0.428 | -0.428 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.028 | -0.007 | 8.294 | -1.129 | -1.129 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.054 | -0.041 | 6.698 | 0.919 | 0.919 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.937 | -0.957 | 6.132 | -33.544 | -33.544 | 0.000 | 0.000 | 0.000 | 0.000 |