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: 9YLR2
Calculation Name: 1L2Y-A-MD56-97600ps
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 | -23670.595591 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19068.353888 |
| FMO2-HF: Total energy | -4602.241704 |
| FMO2-MP2: Total energy | -4615.64935 |
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. |
| -49.366 | -41.422 | 1.888 | -3.307 | -6.524 | -0.008 |
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 | 0.094 | 0.042 | 3.131 | -8.921 | -6.622 | 0.076 | -1.132 | -1.242 | -0.006 | |
| 4 | 4 | GLN | 0 | 0.002 | 0.008 | 5.872 | 0.420 | 0.420 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.040 | 0.011 | 4.762 | 1.967 | 2.179 | -0.001 | -0.016 | -0.196 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.040 | -0.016 | 2.624 | -14.184 | -10.675 | 1.459 | -1.312 | -3.656 | 0.005 | |
| 7 | 7 | GLN | 0 | 0.007 | 0.004 | 3.342 | -9.776 | -9.009 | 0.188 | -0.372 | -0.583 | -0.002 | |
| 8 | 8 | GLN | 0 | -0.057 | -0.029 | 2.944 | 3.540 | 4.629 | 0.167 | -0.474 | -0.782 | -0.005 | |
| 9 | 9 | GLN | 0 | 0.003 | 0.006 | 4.702 | 1.091 | 1.159 | -0.001 | -0.001 | -0.065 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.927 | -0.952 | 8.539 | -23.503 | -23.503 | 0.000 | 0.000 | 0.000 | 0.000 |