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: 2KMKR
Calculation Name: 1L2Y-A-MD57-63300ps
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:
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 | -24894.622843 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20292.31068 |
| FMO2-HF: Total energy | -4602.312163 |
| FMO2-MP2: Total energy | -4615.75746 |
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. |
| -129.082 | -117.701 | 12.924 | -11.024 | -13.281 | -0.109 |
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 | 0.073 | 0.040 | 3.214 | 1.259 | 3.387 | 0.038 | -0.899 | -1.268 | -0.005 | |
| 4 | 4 | GLN | 0 | 0.009 | 0.004 | 5.570 | 5.282 | 5.282 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.007 | -0.012 | 6.390 | -2.872 | -2.872 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.039 | -0.007 | 2.467 | -3.679 | -2.409 | 0.546 | -0.543 | -1.272 | 0.002 | |
| 7 | 7 | GLN | 0 | -0.019 | -0.010 | 1.893 | -15.758 | -16.939 | 7.879 | -3.414 | -3.284 | -0.045 | |
| 8 | 8 | GLN | 0 | -0.025 | -0.026 | 2.701 | -25.491 | -21.107 | 1.062 | -2.073 | -3.373 | -0.014 | |
| 9 | 9 | GLN | 0 | -0.017 | 0.001 | 2.480 | 9.377 | 10.300 | 0.215 | -0.398 | -0.741 | -0.002 | |
| 10 | 10 | GLN | -1 | -0.827 | -0.891 | 2.480 | -97.200 | -93.343 | 3.184 | -3.697 | -3.343 | -0.045 |