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: XQ1JY
Calculation Name: 1L2Y-A-MD4-32000ps
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 | -55627.627524 |
|---|---|
| FMO2-HF: Nuclear repulsion | 48188.635113 |
| FMO2-HF: Total energy | -7438.992411 |
| FMO2-MP2: Total energy | -7461.356376 |
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. |
| -44.721 | -39.861 | 17.773 | -11.139 | -11.497 | -0.048 |
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 | 0.079 | 0.055 | 1.906 | -7.404 | -5.036 | 7.548 | -4.350 | -5.566 | 0.034 | |
| 4 | 4 | ILE | 0 | 0.026 | 0.007 | 3.710 | 3.061 | 3.822 | 0.033 | -0.369 | -0.425 | 0.002 | |
| 5 | 5 | GLN | 0 | 0.022 | -0.021 | 4.815 | -1.739 | -1.721 | -0.001 | -0.025 | 0.007 | 0.000 | |
| 6 | 6 | TRP | 0 | 0.043 | 0.042 | 6.619 | 2.437 | 2.437 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | LEU | 0 | -0.007 | -0.007 | 7.410 | 2.114 | 2.114 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.838 | 0.931 | 8.476 | 29.681 | 29.681 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.914 | -0.953 | 11.669 | -20.417 | -20.417 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.055 | 0.032 | 13.158 | 1.206 | 1.206 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | -0.006 | -0.018 | 10.840 | 0.609 | 0.609 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.043 | -0.034 | 11.919 | 0.474 | 0.474 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.088 | -0.024 | 14.443 | 0.872 | 0.872 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | 0.012 | 0.021 | 12.847 | 0.627 | 0.627 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.025 | 0.019 | 14.696 | -0.046 | -0.046 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.914 | 0.957 | 7.772 | 25.046 | 25.046 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.069 | 0.034 | 11.694 | -0.199 | -0.199 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.046 | -0.043 | 7.434 | -0.905 | -0.905 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.091 | -0.035 | 3.118 | -0.570 | 0.166 | 0.091 | -0.283 | -0.545 | 0.003 | |
| 20 | 20 | SER | -1 | -0.843 | -0.899 | 1.808 | -79.568 | -78.591 | 10.102 | -6.112 | -4.968 | -0.087 |