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: XR5V8
Calculation Name: 1L2Y-A-MD4-32100ps
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 | -55356.723953 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47917.816175 |
| FMO2-HF: Total energy | -7438.907778 |
| FMO2-MP2: Total energy | -7461.283422 |
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. |
| 34.325 | 38.361 | 9.581 | -4.117 | -9.499 | 0.017 |
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 | 0.053 | 0.033 | 2.026 | 2.222 | 1.780 | 7.568 | -2.610 | -4.516 | 0.014 | |
| 4 | 4 | ILE | 0 | 0.055 | 0.049 | 2.548 | -4.997 | -2.833 | 1.720 | -0.507 | -3.376 | 0.013 | |
| 5 | 5 | GLN | 0 | -0.064 | -0.057 | 3.028 | 2.125 | 4.349 | 0.294 | -0.999 | -1.519 | -0.010 | |
| 6 | 6 | TRP | 0 | 0.070 | 0.043 | 5.616 | 3.208 | 3.208 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | LEU | 0 | 0.016 | -0.004 | 6.861 | 2.360 | 2.360 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.834 | 0.917 | 5.277 | 45.974 | 45.974 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.801 | -0.877 | 9.732 | -27.009 | -27.009 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.023 | 0.028 | 11.970 | 1.941 | 1.941 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | -0.029 | -0.028 | 10.617 | 1.246 | 1.246 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.006 | -0.027 | 11.649 | 0.530 | 0.530 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.032 | 0.016 | 14.378 | 1.145 | 1.145 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.041 | -0.012 | 13.565 | 0.686 | 0.686 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.026 | 0.012 | 15.452 | 0.717 | 0.717 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.798 | 0.877 | 8.721 | 28.011 | 28.011 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.061 | 0.036 | 13.425 | -0.330 | -0.330 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | 0.001 | 0.001 | 9.331 | -1.182 | -1.182 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.102 | -0.066 | 5.033 | -0.027 | 0.063 | -0.001 | -0.001 | -0.088 | 0.000 | |
| 20 | 20 | SER | -1 | -0.922 | -0.937 | 8.270 | -22.295 | -22.295 | 0.000 | 0.000 | 0.000 | 0.000 |