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: KRV53
Calculation Name: 1L2Y-A-MD57-88800ps
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 | -24145.656321 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19543.408333 |
| FMO2-HF: Total energy | -4602.247988 |
| FMO2-MP2: Total energy | -4615.701464 |
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. |
| -95.953 | -87.826 | 19.555 | -12.539 | -15.142 | -0.12 |
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 | 0.062 | 0.016 | 2.576 | -9.159 | -5.100 | 2.126 | -2.446 | -3.738 | -0.006 | |
| 4 | 4 | GLN | 0 | 0.000 | -0.008 | 4.248 | 1.896 | 2.117 | -0.001 | -0.008 | -0.212 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.064 | 0.019 | 6.250 | -2.684 | -2.684 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.027 | 0.003 | 1.755 | -24.964 | -28.482 | 14.126 | -5.326 | -5.282 | -0.057 | |
| 7 | 7 | GLN | 0 | 0.052 | 0.049 | 2.635 | -11.200 | -8.283 | 1.295 | -1.658 | -2.553 | -0.024 | |
| 8 | 8 | GLN | 0 | -0.045 | -0.039 | 2.706 | -18.659 | -15.857 | 1.465 | -2.101 | -2.166 | -0.023 | |
| 9 | 9 | GLN | 0 | -0.021 | -0.014 | 2.731 | -4.498 | -2.852 | 0.544 | -1.000 | -1.191 | -0.010 | |
| 10 | 10 | GLN | -1 | -0.923 | -0.950 | 5.534 | -26.685 | -26.685 | 0.000 | 0.000 | 0.000 | 0.000 |