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: P4NKN
Calculation Name: 1L2Y-A-NMR6-Model29
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 | MOE:Amber10:EHT |
|---|---|
| Restraint | OptH |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| 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 | -54163.77003 |
|---|---|
| FMO2-HF: Nuclear repulsion | 46724.426656 |
| FMO2-HF: Total energy | -7439.343374 |
| FMO2-MP2: Total energy | -7461.63224 |
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. |
| 25.361 | 28.633 | 1.776 | -1.921 | -3.126 | -0.011 |
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 | 0.112 | 0.040 | 3.187 | 5.981 | 8.962 | 0.013 | -1.378 | -1.616 | -0.004 |
| 4 | A | 4 | ILE | 0 | 0.000 | 0.000 | 2.366 | 2.775 | 3.066 | 1.763 | -0.543 | -1.510 | -0.007 |
| 5 | A | 5 | GLN | 0 | -0.030 | -0.015 | 5.640 | 8.030 | 8.030 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | TRP | 0 | 0.001 | -0.013 | 7.244 | 2.751 | 2.751 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | LEU | 0 | -0.001 | -0.020 | 7.419 | 2.769 | 2.769 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.878 | 0.944 | 9.702 | 28.342 | 28.342 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.935 | -0.950 | 11.714 | -18.359 | -18.359 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLY | 0 | 0.094 | 0.047 | 13.456 | 1.444 | 1.444 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLY | 0 | -0.009 | 0.003 | 12.000 | 0.877 | 0.877 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | PRO | 0 | -0.012 | -0.002 | 13.039 | 0.142 | 0.142 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | SER | 0 | -0.058 | -0.019 | 15.690 | 0.941 | 0.941 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | SER | 0 | 0.040 | 0.005 | 14.330 | 0.513 | 0.513 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | GLY | 0 | -0.036 | -0.004 | 16.798 | 0.085 | 0.085 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ARG | 1 | 0.936 | 0.972 | 11.930 | 23.764 | 23.764 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | PRO | 0 | 0.031 | 0.019 | 14.136 | -0.635 | -0.635 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | PRO | 0 | 0.004 | 0.001 | 9.374 | -1.118 | -1.118 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | PRO | 0 | -0.093 | -0.047 | 5.980 | 0.665 | 0.665 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | SER | -1 | -0.925 | -0.955 | 6.824 | -33.606 | -33.606 | 0.000 | 0.000 | 0.000 | 0.000 |