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: P9G62
Calculation Name: 1L2Y-A-MD4-46700ps
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 | -55314.766356 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47875.768842 |
| FMO2-HF: Total energy | -7438.997514 |
| FMO2-MP2: Total energy | -7461.337769 |
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. |
| -22.719 | -17.8 | 13.528 | -7.738 | -10.709 | -0.011 |
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 | 0.115 | 0.080 | 2.386 | 2.757 | 4.670 | 3.075 | -1.601 | -3.387 | 0.010 | |
| 4 | 4 | ILE | 0 | -0.011 | -0.027 | 1.997 | -5.891 | -6.426 | 7.058 | -2.455 | -4.068 | 0.021 | |
| 5 | 5 | GLN | 0 | -0.030 | -0.034 | 2.086 | -33.889 | -30.560 | 3.396 | -3.671 | -3.054 | -0.042 | |
| 6 | 6 | TRP | 0 | 0.085 | 0.036 | 5.270 | 3.503 | 3.715 | -0.001 | -0.011 | -0.200 | 0.000 | |
| 7 | 7 | LEU | 0 | 0.000 | -0.004 | 6.022 | 2.471 | 2.471 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.849 | 0.925 | 5.913 | 36.768 | 36.768 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.914 | -0.945 | 9.552 | -28.101 | -28.101 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | -0.004 | -0.010 | 11.451 | 1.990 | 1.990 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | 0.040 | 0.019 | 10.421 | 1.031 | 1.031 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.060 | -0.028 | 11.508 | 0.375 | 0.375 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | 0.025 | 0.016 | 14.273 | 0.955 | 0.955 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.056 | 0.002 | 13.271 | 0.061 | 0.061 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | -0.038 | -0.029 | 15.452 | 0.529 | 0.529 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.949 | 0.967 | 9.830 | 26.482 | 26.482 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.057 | 0.052 | 13.513 | -0.044 | -0.044 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.003 | -0.021 | 9.604 | -1.307 | -1.307 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.086 | -0.038 | 6.257 | 0.500 | 0.500 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.931 | -0.949 | 7.489 | -30.909 | -30.909 | 0.000 | 0.000 | 0.000 | 0.000 |