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: V2NG1
Calculation Name: 1L2Y-A-MD57-48400ps
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 | -24105.307425 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19503.121159 |
| FMO2-HF: Total energy | -4602.186266 |
| FMO2-MP2: Total energy | -4615.616997 |
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. |
| -62.256 | -53.045 | 6.065 | -5.676 | -9.598 | -0.05 |
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 | 0.036 | 0.032 | 2.794 | -5.766 | -3.102 | 0.411 | -1.311 | -1.765 | -0.008 | |
| 4 | 4 | GLN | 0 | 0.039 | 0.030 | 5.329 | -0.233 | -0.165 | -0.001 | -0.006 | -0.060 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.016 | -0.017 | 6.925 | -0.974 | -0.974 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.012 | -0.025 | 7.754 | -0.871 | -0.871 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | GLN | 0 | -0.042 | 0.007 | 2.602 | -5.347 | -3.685 | 0.657 | -0.823 | -1.496 | -0.003 | |
| 8 | 8 | GLN | 0 | 0.071 | 0.038 | 3.777 | -0.225 | 0.134 | 0.002 | -0.100 | -0.260 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.069 | -0.044 | 2.125 | -21.409 | -18.694 | 3.884 | -2.860 | -3.739 | -0.035 | |
| 10 | 10 | GLN | -1 | -0.935 | -0.957 | 2.401 | -27.431 | -25.688 | 1.112 | -0.576 | -2.278 | -0.004 |