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: P3N4L
Calculation Name: 1L2Y-A-NMR6-Model3
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 | -54873.740816 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47434.174932 |
| FMO2-HF: Total energy | -7439.565884 |
| FMO2-MP2: Total energy | -7461.865959 |
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. |
| 17.654 | 21.132 | -0.015 | -1.475 | -1.987 | -0.005 |
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 | 0.054 | 0.041 | 3.418 | 7.638 | 10.733 | -0.012 | -1.450 | -1.632 | -0.005 |
| 4 | A | 4 | ILE | 0 | 0.048 | 0.026 | 4.152 | 5.622 | 5.840 | -0.001 | -0.017 | -0.200 | 0.000 |
| 5 | A | 5 | GLN | 0 | -0.023 | -0.021 | 6.545 | 5.878 | 5.878 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | TRP | 0 | 0.036 | 0.022 | 7.838 | 1.751 | 1.751 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | LEU | 0 | 0.011 | -0.009 | 9.056 | 2.645 | 2.645 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.873 | 0.942 | 10.141 | 29.049 | 29.049 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.898 | -0.930 | 12.670 | -22.478 | -22.478 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLY | 0 | 0.028 | 0.043 | 14.382 | 1.469 | 1.469 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLY | 0 | 0.005 | -0.002 | 12.862 | 0.657 | 0.657 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | PRO | 0 | -0.016 | -0.022 | 13.868 | 0.491 | 0.491 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | SER | 0 | -0.075 | -0.022 | 16.429 | 0.826 | 0.826 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | SER | 0 | 0.039 | -0.018 | 15.887 | 0.915 | 0.915 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | GLY | 0 | -0.051 | -0.004 | 17.805 | 0.183 | 0.183 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ARG | 1 | 0.900 | 0.950 | 12.763 | 21.274 | 21.274 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | PRO | 0 | 0.034 | 0.023 | 12.649 | -0.545 | -0.545 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | PRO | 0 | 0.005 | 0.003 | 8.524 | -0.945 | -0.945 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | PRO | 0 | -0.079 | -0.049 | 4.694 | -0.286 | -0.221 | -0.001 | -0.005 | -0.059 | 0.000 |
| 20 | A | 20 | SER | -1 | -0.907 | -0.945 | 4.672 | -36.490 | -36.390 | -0.001 | -0.003 | -0.096 | 0.000 |