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: 9YKL2
Calculation Name: 1L2Y-A-MD58-93600ps
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 | -24864.91252 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20262.758681 |
| FMO2-HF: Total energy | -4602.153839 |
| FMO2-MP2: Total energy | -4615.606809 |
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. |
| -52.078 | -44.828 | 12.388 | -8.513 | -11.129 | -0.087 |
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 | 0.102 | 0.059 | 1.828 | -22.982 | -21.824 | 9.509 | -5.682 | -4.986 | -0.070 | |
| 4 | 4 | GLN | 0 | 0.083 | 0.034 | 4.646 | -2.824 | -2.753 | -0.001 | -0.013 | -0.057 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.001 | -0.015 | 6.635 | -0.736 | -0.736 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.006 | 0.012 | 2.789 | 0.674 | 2.347 | 0.696 | -0.672 | -1.698 | 0.003 | |
| 7 | 7 | GLN | 0 | -0.022 | -0.035 | 2.588 | -2.576 | -0.098 | 1.068 | -1.437 | -2.110 | -0.016 | |
| 8 | 8 | GLN | 0 | -0.068 | -0.015 | 3.521 | 3.111 | 3.210 | 0.023 | 0.065 | -0.188 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.032 | -0.020 | 4.057 | 5.106 | 5.339 | -0.001 | -0.036 | -0.196 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.952 | -0.948 | 2.213 | -31.851 | -30.313 | 1.094 | -0.738 | -1.894 | -0.004 |