FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: R1LY8
Calculation Name: 1L2Y-A-MD57-71000ps
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2OTU
Chain ID: A
UniProt ID: A2NN81
Base Structure: MD
Registration Date: 2019-08-13
Reference:
Apendix: None
Modeling method
| Optimization | BaseStructure_original |
|---|---|
| Restraint | BaseStructure_original |
| Protonation | BaseStructure_original |
| Complement | No |
| Water | No |
| Procedure | Manual calculation |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 10 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -24819.875415 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20217.654207 |
| FMO2-HF: Total energy | -4602.221208 |
| FMO2-MP2: Total energy | -4615.67041 |
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:GLN )
Summations of interaction energy for
fragment #1(:1:GLN )
| 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. |
| -97.484 | -87.696 | 15.397 | -11.297 | -13.89 | -0.125 |
Interaction energy analysis for fragmet #1(:1:GLN )
| 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 | GLN | 0 | 0.064 | 0.043 | 3.159 | 2.044 | 4.367 | 0.282 | -0.896 | -1.710 | -0.005 | |
| 4 | 4 | GLN | 0 | 0.014 | 0.002 | 4.611 | 4.997 | 5.146 | -0.001 | -0.005 | -0.143 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.021 | 0.004 | 6.330 | -2.591 | -2.591 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.006 | -0.002 | 1.994 | -16.462 | -16.834 | 4.859 | -1.737 | -2.751 | -0.023 | |
| 7 | 7 | GLN | 0 | 0.047 | 0.038 | 2.076 | -7.593 | -7.842 | 5.266 | -2.025 | -2.991 | -0.030 | |
| 8 | 8 | GLN | 0 | -0.010 | -0.019 | 2.162 | -15.526 | -10.802 | 3.095 | -4.038 | -3.781 | -0.025 | |
| 9 | 9 | GLN | 0 | -0.057 | -0.052 | 2.369 | -34.913 | -31.814 | 1.897 | -2.591 | -2.405 | -0.042 | |
| 10 | 10 | GLN | -1 | -0.873 | -0.917 | 5.129 | -27.440 | -27.326 | -0.001 | -0.005 | -0.109 | 0.000 |