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: XV241
Calculation Name: 1L2Y-A-MD4-9200ps
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 | -55633.446547 |
|---|---|
| FMO2-HF: Nuclear repulsion | 48194.50083 |
| FMO2-HF: Total energy | -7438.945716 |
| FMO2-MP2: Total energy | -7461.307921 |
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. |
| 18.093 | 15.999 | 18.878 | -5.247 | -11.537 | 0.041 |
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 | 0.117 | 0.078 | 1.981 | 3.758 | 1.223 | 11.215 | -3.352 | -5.327 | 0.022 | |
| 4 | 4 | ILE | 0 | 0.000 | -0.026 | 2.099 | -7.602 | -8.355 | 7.659 | -1.533 | -5.374 | 0.019 | |
| 5 | 5 | GLN | 0 | -0.123 | -0.076 | 3.747 | -6.472 | -5.585 | 0.006 | -0.351 | -0.542 | 0.000 | |
| 6 | 6 | TRP | 0 | 0.089 | 0.069 | 5.383 | 1.699 | 1.935 | -0.001 | -0.010 | -0.225 | 0.000 | |
| 7 | 7 | LEU | 0 | -0.001 | -0.002 | 6.638 | 2.589 | 2.589 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.892 | 0.925 | 4.613 | 49.123 | 49.194 | -0.001 | -0.001 | -0.069 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.845 | -0.901 | 9.455 | -25.271 | -25.271 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | -0.001 | 0.004 | 12.188 | 1.745 | 1.745 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | 0.004 | 0.000 | 10.324 | 0.916 | 0.916 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | 0.000 | -0.004 | 11.250 | 0.439 | 0.439 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.040 | 0.001 | 14.297 | 0.668 | 0.668 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.043 | -0.016 | 12.784 | 0.317 | 0.317 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.037 | -0.001 | 15.299 | 0.504 | 0.504 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.828 | 0.917 | 8.908 | 27.857 | 27.857 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.040 | 0.026 | 12.941 | -0.402 | -0.402 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | 0.009 | 0.008 | 8.850 | -1.285 | -1.285 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.100 | -0.061 | 5.448 | 0.285 | 0.285 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.912 | -0.941 | 6.441 | -30.775 | -30.775 | 0.000 | 0.000 | 0.000 | 0.000 |