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: 9YRG2
Calculation Name: 1L2Y-A-MD57-65600ps
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 | -24693.903776 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20091.674096 |
| FMO2-HF: Total energy | -4602.22968 |
| FMO2-MP2: Total energy | -4615.692781 |
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. |
| -82.67 | -72.605 | 14.672 | -10.282 | -14.457 | -0.1 |
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 | 0.081 | 0.027 | 3.432 | -0.012 | 2.019 | 0.007 | -0.917 | -1.122 | -0.002 | |
| 4 | 4 | GLN | 0 | 0.012 | 0.026 | 5.484 | 2.882 | 2.882 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.004 | -0.008 | 6.131 | -1.415 | -1.415 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.038 | -0.015 | 1.942 | -4.535 | -4.035 | 1.743 | -0.727 | -1.516 | -0.001 | |
| 7 | 7 | GLN | 0 | 0.035 | 0.027 | 2.134 | -12.908 | -10.835 | 4.771 | -3.010 | -3.834 | -0.043 | |
| 8 | 8 | GLN | 0 | 0.005 | -0.038 | 2.369 | -32.392 | -27.225 | 8.086 | -5.830 | -7.423 | -0.051 | |
| 9 | 9 | GLN | 0 | -0.080 | -0.035 | 3.268 | -4.004 | -3.710 | 0.065 | 0.202 | -0.562 | -0.003 | |
| 10 | 10 | GLN | -1 | -0.893 | -0.928 | 5.450 | -30.286 | -30.286 | 0.000 | 0.000 | 0.000 | 0.000 |