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: 2K8RR
Calculation Name: 1L2Y-A-MD58-95300ps
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 | -24571.980869 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19969.820775 |
| FMO2-HF: Total energy | -4602.160094 |
| FMO2-MP2: Total energy | -4615.626689 |
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. |
| -70.063 | -62.414 | 8.132 | -7.131 | -8.648 | -0.064 |
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 | 0.091 | 0.048 | 1.962 | -18.815 | -16.154 | 6.292 | -4.492 | -4.461 | -0.050 | |
| 4 | 4 | GLN | 0 | 0.030 | 0.011 | 5.079 | -0.234 | -0.144 | -0.001 | -0.008 | -0.080 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.005 | -0.004 | 7.766 | -0.710 | -0.710 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.019 | 0.000 | 2.785 | -13.277 | -9.617 | 1.841 | -2.354 | -3.146 | -0.013 | |
| 7 | 7 | GLN | 0 | -0.033 | -0.002 | 3.918 | -4.352 | -3.895 | 0.001 | -0.096 | -0.362 | 0.000 | |
| 8 | 8 | GLN | 0 | -0.050 | -0.027 | 4.996 | 3.911 | 4.030 | -0.001 | -0.002 | -0.115 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.058 | -0.024 | 4.482 | 3.676 | 3.786 | -0.001 | -0.002 | -0.107 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.914 | -0.942 | 3.773 | -40.262 | -39.710 | 0.001 | -0.177 | -0.377 | -0.001 |