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: 4NY9N
Calculation Name: 1L2Y-A-MD57-66700ps
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 | -24803.422342 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20201.243755 |
| FMO2-HF: Total energy | -4602.178586 |
| FMO2-MP2: Total energy | -4615.637259 |
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. |
| -92.631 | -82.85 | 13.775 | -10.445 | -13.109 | -0.118 |
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 | 0.097 | 0.032 | 2.725 | -2.848 | 0.561 | 1.402 | -1.708 | -3.103 | -0.012 | |
| 4 | 4 | GLN | 0 | 0.008 | 0.018 | 3.947 | 2.985 | 3.219 | 0.000 | -0.011 | -0.222 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.041 | 0.018 | 5.640 | -3.899 | -3.899 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.023 | -0.015 | 1.868 | -23.080 | -23.887 | 7.705 | -3.242 | -3.655 | -0.043 | |
| 7 | 7 | GLN | 0 | 0.003 | 0.022 | 3.080 | -3.009 | -0.614 | 0.551 | -1.134 | -1.811 | -0.013 | |
| 8 | 8 | GLN | 0 | -0.018 | -0.051 | 2.437 | -30.633 | -27.680 | 3.959 | -3.392 | -3.521 | -0.039 | |
| 9 | 9 | GLN | 0 | -0.060 | -0.035 | 2.999 | -8.830 | -7.294 | 0.159 | -0.953 | -0.742 | -0.011 | |
| 10 | 10 | GLN | -1 | -0.912 | -0.941 | 5.163 | -23.317 | -23.256 | -0.001 | -0.005 | -0.055 | 0.000 |