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: PLJ49
Calculation Name: 1L2Y-A-MD4-38800ps
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 | -54691.491058 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47252.551124 |
| FMO2-HF: Total energy | -7438.939933 |
| FMO2-MP2: Total energy | -7461.25953 |
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. |
| -0.055999999999994 | 2.621 | 9.869 | -3.818 | -8.728 | 0.027 |
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 | 0.138 | 0.066 | 2.361 | 1.883 | 3.246 | 3.032 | -1.307 | -3.088 | 0.011 | |
| 4 | 4 | ILE | 0 | -0.013 | -0.033 | 1.985 | -7.834 | -7.840 | 6.827 | -1.977 | -4.844 | 0.016 | |
| 5 | 5 | GLN | 0 | -0.045 | -0.002 | 3.458 | -3.789 | -2.726 | 0.012 | -0.516 | -0.559 | 0.000 | |
| 6 | 6 | TRP | 0 | 0.027 | 0.038 | 4.775 | 5.055 | 5.258 | -0.001 | -0.016 | -0.185 | 0.000 | |
| 7 | 7 | LEU | 0 | 0.000 | -0.012 | 6.558 | 2.962 | 2.962 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.870 | 0.939 | 7.407 | 28.654 | 28.654 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.867 | -0.937 | 9.013 | -28.726 | -28.726 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.010 | -0.014 | 11.103 | 2.242 | 2.242 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | -0.031 | -0.031 | 10.204 | 1.154 | 1.154 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.016 | 0.013 | 11.083 | 0.602 | 0.602 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.016 | -0.001 | 14.030 | 0.914 | 0.914 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.088 | -0.027 | 12.681 | 0.373 | 0.373 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.032 | 0.012 | 15.217 | 0.439 | 0.439 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.929 | 0.964 | 12.495 | 22.256 | 22.256 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.082 | 0.041 | 13.098 | -0.406 | -0.406 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.044 | -0.007 | 8.788 | -1.296 | -1.296 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.084 | -0.062 | 5.113 | 0.114 | 0.168 | -0.001 | -0.002 | -0.052 | 0.000 | |
| 20 | 20 | SER | -1 | -0.910 | -0.942 | 8.026 | -24.653 | -24.653 | 0.000 | 0.000 | 0.000 | 0.000 |