FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37450
Number of unique PDB entries: 7783
FMODB ID: PG641
Calculation Name: 1L2Y-A-MD4-71400ps
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:
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 |
| LigandCharge | |
| Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -54939.961143 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47500.929396 |
| FMO2-HF: Total energy | -7439.031747 |
| FMO2-MP2: Total energy | -7461.37116 |
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. |
| -20.345 | -17.815 | 18.594 | -8.863 | -12.258 | -0.025 |
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 | 0.085 | 0.057 | 2.662 | 2.023 | 5.652 | 0.934 | -1.905 | -2.658 | 0.004 | |
| 4 | 4 | ILE | 0 | 0.050 | 0.015 | 1.916 | -5.905 | -7.707 | 10.960 | -3.327 | -5.830 | 0.012 | |
| 5 | 5 | GLN | 0 | -0.019 | -0.031 | 2.078 | -28.451 | -27.927 | 6.701 | -3.623 | -3.601 | -0.041 | |
| 6 | 6 | TRP | 0 | 0.095 | 0.054 | 5.348 | 4.041 | 4.220 | -0.001 | -0.008 | -0.169 | 0.000 | |
| 7 | 7 | LEU | 0 | 0.006 | 0.021 | 6.428 | 2.368 | 2.368 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.864 | 0.948 | 7.613 | 31.128 | 31.128 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.941 | -0.977 | 9.294 | -27.351 | -27.351 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.009 | 0.001 | 11.564 | 1.755 | 1.755 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | 0.002 | -0.012 | 10.727 | 1.224 | 1.224 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | 0.028 | 0.015 | 11.724 | -0.209 | -0.209 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.004 | -0.004 | 15.099 | 0.489 | 0.489 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.031 | -0.020 | 12.381 | 0.394 | 0.394 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.001 | 0.004 | 14.449 | 0.044 | 0.044 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.866 | 0.939 | 10.778 | 24.404 | 24.404 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.029 | 0.005 | 13.728 | -0.752 | -0.752 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.025 | 0.006 | 9.846 | -0.940 | -0.940 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.111 | -0.067 | 6.224 | 0.270 | 0.270 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.882 | -0.919 | 9.219 | -24.877 | -24.877 | 0.000 | 0.000 | 0.000 | 0.000 |