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: 2KMYR
Calculation Name: 1L2Y-A-MD57-93300ps
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 | -23635.731902 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19033.638851 |
| FMO2-HF: Total energy | -4602.09305 |
| FMO2-MP2: Total energy | -4615.550693 |
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. |
| -77.897 | -66.249 | 11.947 | -9.553 | -14.043 | -0.092 |
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 | -0.008 | -0.015 | 3.188 | -0.751 | 1.180 | 0.054 | -0.884 | -1.101 | -0.004 | |
| 4 | 4 | GLN | 0 | 0.086 | 0.073 | 5.959 | 4.057 | 4.057 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.048 | -0.051 | 5.607 | -3.950 | -3.950 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.008 | 0.000 | 2.624 | -1.601 | 0.100 | 1.487 | -0.799 | -2.389 | 0.004 | |
| 7 | 7 | GLN | 0 | 0.052 | 0.040 | 2.625 | -13.716 | -11.614 | 1.670 | -1.200 | -2.573 | -0.021 | |
| 8 | 8 | GLN | 0 | 0.008 | -0.004 | 2.346 | -44.730 | -39.024 | 8.734 | -6.615 | -7.825 | -0.071 | |
| 9 | 9 | GLN | 0 | -0.044 | -0.032 | 3.767 | 9.419 | 9.627 | 0.002 | -0.055 | -0.155 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.898 | -0.928 | 6.479 | -26.625 | -26.625 | 0.000 | 0.000 | 0.000 | 0.000 |