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: 4NYZN
Calculation Name: 1L2Y-A-MD57-88700ps
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 | -23835.903995 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19233.659039 |
| FMO2-HF: Total energy | -4602.244955 |
| FMO2-MP2: Total energy | -4615.67424 |
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. |
| -101.885 | -101.996 | 28.803 | -14.183 | -14.51 | -0.151 |
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 | 0.022 | 3.085 | -0.365 | 2.694 | 0.214 | -1.194 | -2.079 | -0.005 | |
| 4 | 4 | GLN | 0 | -0.023 | -0.006 | 4.111 | 2.709 | 2.940 | -0.001 | -0.004 | -0.226 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.017 | -0.015 | 6.413 | -1.460 | -1.460 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.015 | 0.016 | 1.740 | -22.656 | -27.328 | 14.264 | -4.883 | -4.709 | -0.050 | |
| 7 | 7 | GLN | 0 | 0.029 | 0.048 | 3.412 | -1.846 | -0.459 | 0.165 | -0.353 | -1.199 | -0.006 | |
| 8 | 8 | GLN | 0 | 0.028 | -0.003 | 2.847 | -16.666 | -13.901 | 0.939 | -1.878 | -1.827 | -0.019 | |
| 9 | 9 | GLN | 0 | -0.035 | 0.003 | 1.756 | -30.055 | -33.037 | 13.221 | -5.851 | -4.388 | -0.071 | |
| 10 | 10 | GLN | -1 | -0.891 | -0.948 | 4.170 | -31.546 | -31.445 | 0.001 | -0.020 | -0.082 | 0.000 |