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: PZ2GN
Calculation Name: 1L2Y-A-NMR6-Model32
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 | -54774.629948 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47335.170597 |
| FMO2-HF: Total energy | -7439.45935 |
| FMO2-MP2: Total energy | -7461.759245 |
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. |
| 1.732 | 5.236 | 0.014 | -1.37 | -2.148 | -0.004 |
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 | 0.084 | 0.042 | 3.033 | 8.443 | 11.235 | 0.005 | -1.256 | -1.542 | -0.004 |
| 4 | A | 4 | ILE | 0 | 0.030 | 0.022 | 3.390 | 8.354 | 8.947 | 0.010 | -0.105 | -0.497 | 0.000 |
| 5 | A | 5 | GLN | 0 | -0.021 | -0.019 | 5.130 | 1.105 | 1.105 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | TRP | 0 | 0.014 | 0.008 | 7.491 | 2.222 | 2.222 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | LEU | 0 | 0.001 | -0.015 | 8.235 | 3.110 | 3.110 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.893 | 0.960 | 10.468 | 24.618 | 24.618 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.932 | -0.971 | 12.423 | -22.099 | -22.099 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLY | 0 | 0.032 | 0.022 | 13.865 | 1.586 | 1.586 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLY | 0 | -0.001 | 0.006 | 12.044 | 0.595 | 0.595 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | PRO | 0 | -0.012 | 0.002 | 13.051 | 0.460 | 0.460 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | SER | 0 | -0.042 | -0.009 | 15.558 | 0.712 | 0.712 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | SER | 0 | 0.015 | -0.015 | 14.940 | 0.840 | 0.840 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | GLY | 0 | -0.037 | -0.014 | 17.413 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ARG | 1 | 0.926 | 0.967 | 13.270 | 20.311 | 20.311 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | PRO | 0 | 0.041 | 0.031 | 13.050 | -0.412 | -0.412 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | PRO | 0 | 0.007 | 0.004 | 8.695 | -0.778 | -0.778 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | PRO | 0 | -0.078 | -0.035 | 5.203 | 0.717 | 0.717 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | SER | -1 | -0.930 | -0.962 | 4.559 | -48.084 | -47.965 | -0.001 | -0.009 | -0.109 | 0.000 |