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: XR1Z8
Calculation Name: 1L2Y-A-MD4-1800ps
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1L2Y
Chain ID: A
Base Structure: MD
Registration Date: 2018-03-06
Reference:
Apendix: None
Modeling method
| Optimization | BaseStructure_original |
|---|---|
| Restraint | BaseStructure_original |
| Protonation | BaseStructure_original |
| Complement | BaseStructure_original |
| Water | No |
| Procedure | Auto-FMO protocol ver. 1.20171117 |
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 | -55336.59435 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47897.554139 |
| FMO2-HF: Total energy | -7439.04021 |
| FMO2-MP2: Total energy | -7461.386204 |
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(:1:ASN)
Summations of interaction energy for
fragment #1(: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. |
| 10.52 | 8.482 | 17.845 | -6.71 | -9.095 | 0.03 |
Interaction energy analysis for fragmet #1(: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 | 3 | TYR | 0 | 0.104 | 0.044 | 2.476 | 4.407 | 7.620 | 1.882 | -1.854 | -3.241 | 0.008 | |
| 4 | 4 | ILE | 0 | -0.014 | -0.016 | 1.762 | -4.500 | -10.371 | 15.904 | -4.677 | -5.355 | 0.020 | |
| 5 | 5 | GLN | 0 | -0.010 | -0.019 | 3.762 | 1.694 | 2.225 | 0.060 | -0.177 | -0.414 | 0.002 | |
| 6 | 6 | TRP | 0 | 0.048 | 0.044 | 5.918 | 1.017 | 1.017 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | LEU | 0 | -0.034 | -0.041 | 4.657 | 1.358 | 1.447 | -0.001 | -0.002 | -0.085 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.891 | 0.952 | 7.786 | 28.977 | 28.977 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.799 | -0.866 | 9.920 | -20.380 | -20.380 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.010 | 0.011 | 11.443 | 1.211 | 1.211 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | 0.003 | -0.008 | 10.496 | 0.831 | 0.831 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | 0.000 | -0.003 | 11.484 | 0.203 | 0.203 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.041 | -0.017 | 14.563 | 0.715 | 0.715 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.023 | 0.002 | 12.719 | 0.746 | 0.746 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | -0.009 | -0.004 | 14.875 | 0.188 | 0.188 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.854 | 0.904 | 8.984 | 23.543 | 23.543 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.006 | -0.010 | 13.584 | -0.537 | -0.537 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.035 | 0.001 | 8.647 | -0.695 | -0.695 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.099 | -0.048 | 5.810 | 0.362 | 0.362 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.896 | -0.939 | 8.720 | -28.620 | -28.620 | 0.000 | 0.000 | 0.000 | 0.000 |