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: P4NGN
Calculation Name: 1L2Y-A-NMR6-Model10
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 | -54664.845556 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47225.261748 |
| FMO2-HF: Total energy | -7439.583808 |
| FMO2-MP2: Total energy | -7461.889877 |
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. |
| 16.66 | 20.485 | 0.003 | -1.66 | -2.168 | -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 | 0.073 | 0.036 | 2.943 | 7.583 | 10.986 | -0.003 | -1.569 | -1.831 | -0.005 |
| 4 | A | 4 | ILE | 0 | 0.044 | 0.030 | 3.672 | 6.450 | 6.872 | 0.006 | -0.091 | -0.337 | 0.000 |
| 5 | A | 5 | GLN | 0 | 0.012 | -0.010 | 6.613 | 7.224 | 7.224 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | TRP | 0 | -0.012 | -0.006 | 7.821 | 1.996 | 1.996 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | LEU | 0 | 0.023 | -0.006 | 8.359 | 2.757 | 2.757 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.824 | 0.914 | 10.625 | 25.986 | 25.986 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.825 | -0.885 | 12.665 | -20.042 | -20.042 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLY | 0 | 0.035 | 0.032 | 14.124 | 1.446 | 1.446 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLY | 0 | 0.005 | 0.008 | 12.332 | 0.628 | 0.628 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | PRO | 0 | -0.011 | 0.004 | 13.315 | 0.397 | 0.397 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | SER | 0 | -0.028 | -0.008 | 15.921 | 0.666 | 0.666 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | SER | 0 | 0.001 | -0.016 | 14.951 | 0.679 | 0.679 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | GLY | 0 | -0.030 | -0.009 | 17.404 | 0.256 | 0.256 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ARG | 1 | 0.836 | 0.894 | 13.299 | 19.948 | 19.948 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | PRO | 0 | 0.046 | 0.041 | 13.107 | -0.387 | -0.387 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | PRO | 0 | -0.007 | -0.004 | 8.764 | -0.992 | -0.992 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | PRO | 0 | -0.080 | -0.041 | 5.143 | 0.558 | 0.558 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | SER | -1 | -0.925 | -0.952 | 5.707 | -38.493 | -38.493 | 0.000 | 0.000 | 0.000 | 0.000 |