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: PLLG9
Calculation Name: 1L2Y-A-NMR5-Model18
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1L2Y
Chain ID: A
Base Structure: NMR
Registration Date: 2018-02-27
Reference:
Apendix: None
Modeling method
| Optimization | BaseStructure_original |
|---|---|
| Restraint | BaseStructure_original |
| Protonation | BaseStructure_original |
| Complement | BaseStructure_original |
| Water | No |
| Procedure | Auto-FMO protocol ver. 1.20180117 |
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 | -54556.395808 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47116.920344 |
| FMO2-HF: Total energy | -7439.475463 |
| FMO2-MP2: Total energy | -7461.759163 |
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(A:1:ASN)
Summations of interaction energy for
fragment #1(A: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. |
| -19.106 | -14.689 | 0.047 | -1.898 | -2.565 | -0.003 |
Interaction energy analysis for fragmet #1(A: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 | A | 3 | TYR | 0 | 0.064 | 0.028 | 3.288 | 7.953 | 11.085 | 0.047 | -1.514 | -1.665 | 0.000 |
| 4 | A | 4 | ILE | 0 | 0.036 | 0.020 | 5.010 | 5.537 | 5.747 | -0.001 | -0.011 | -0.197 | 0.000 |
| 5 | A | 5 | GLN | 0 | -0.020 | -0.013 | 4.608 | 3.287 | 3.383 | -0.001 | -0.003 | -0.092 | 0.000 |
| 6 | A | 6 | TRP | 0 | -0.011 | 0.001 | 7.883 | 0.738 | 0.738 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | LEU | 0 | 0.024 | -0.003 | 9.067 | 2.253 | 2.253 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.905 | 0.964 | 11.206 | 20.938 | 20.938 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.920 | -0.962 | 13.096 | -17.362 | -17.362 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLY | 0 | 0.041 | 0.046 | 14.662 | 1.045 | 1.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLY | 0 | 0.016 | 0.005 | 12.037 | 0.488 | 0.488 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | PRO | 0 | -0.035 | -0.033 | 13.013 | 0.175 | 0.175 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | SER | 0 | -0.051 | -0.027 | 15.269 | 1.059 | 1.059 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | SER | 0 | -0.016 | -0.007 | 14.328 | 0.403 | 0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | GLY | 0 | -0.022 | -0.001 | 16.453 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ARG | 1 | 0.943 | 0.966 | 11.518 | 24.409 | 24.409 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | PRO | 0 | 0.030 | 0.024 | 11.421 | -0.373 | -0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | PRO | 0 | 0.022 | 0.010 | 7.226 | -0.527 | -0.527 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | PRO | 0 | -0.060 | -0.019 | 4.331 | 0.806 | 1.009 | -0.001 | -0.029 | -0.173 | 0.000 |
| 20 | A | 20 | SER | -1 | -0.972 | -0.988 | 3.740 | -69.919 | -69.143 | 0.003 | -0.341 | -0.438 | -0.003 |