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: PK5R3
Calculation Name: 1L2Y-A-MD52-2800ps
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2OTU
Chain ID: A
UniProt ID: A2NN81
Base Structure: MD
Registration Date: 2019-08-09
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 | -21541.391185 |
|---|---|
| FMO2-HF: Nuclear repulsion | 16939.222795 |
| FMO2-HF: Total energy | -4602.16839 |
| FMO2-MP2: Total energy | -4615.586037 |
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. |
| -15.369 | -11.723 | 1.066 | -1.985 | -2.727 | -0.024 |
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 | 0.043 | 0.033 | 2.512 | -4.369 | -0.820 | 1.067 | -1.979 | -2.637 | -0.024 | |
| 4 | 4 | GLN | 0 | 0.022 | 0.021 | 5.166 | 4.074 | 4.171 | -0.001 | -0.006 | -0.090 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.033 | -0.026 | 7.565 | -0.288 | -0.288 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.037 | -0.029 | 9.620 | 1.237 | 1.237 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | GLN | 0 | 0.020 | 0.035 | 13.395 | 0.074 | 0.074 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | GLN | 0 | -0.028 | -0.039 | 14.902 | -1.317 | -1.317 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | GLN | 0 | 0.031 | 0.025 | 15.383 | 0.914 | 0.914 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.952 | -0.963 | 16.800 | -15.694 | -15.694 | 0.000 | 0.000 | 0.000 | 0.000 |