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: LLVM9
Calculation Name: 1L2Y-A-MD57-61700ps
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 | -24923.227152 |
|---|---|
| FMO2-HF: Nuclear repulsion | 20320.948052 |
| FMO2-HF: Total energy | -4602.279101 |
| FMO2-MP2: Total energy | -4615.723042 |
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. |
| -115.488 | -110.16 | 25.248 | -12.823 | -17.755 | -0.137 |
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 | 0.052 | 0.026 | 1.845 | -16.994 | -19.117 | 9.610 | -3.713 | -3.775 | -0.037 | |
| 4 | 4 | GLN | 0 | -0.015 | -0.013 | 3.918 | 6.651 | 6.886 | -0.001 | -0.003 | -0.231 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.025 | -0.021 | 5.612 | -4.774 | -4.774 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.029 | 0.012 | 1.975 | -9.468 | -10.535 | 6.023 | -1.908 | -3.048 | -0.015 | |
| 7 | 7 | GLN | 0 | 0.014 | 0.033 | 3.280 | 0.679 | 2.623 | 0.268 | -0.719 | -1.494 | -0.006 | |
| 8 | 8 | GLN | 0 | 0.062 | 0.012 | 2.137 | -25.188 | -20.175 | 7.230 | -5.516 | -6.727 | -0.044 | |
| 9 | 9 | GLN | 0 | -0.080 | -0.064 | 2.388 | -19.230 | -17.961 | 2.119 | -0.949 | -2.439 | -0.035 | |
| 10 | 10 | GLN | -1 | -0.861 | -0.920 | 4.534 | -47.164 | -47.107 | -0.001 | -0.015 | -0.041 | 0.000 |