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: 4NYKN
Calculation Name: 1L2Y-A-MD57-80700ps
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 | -24139.45089 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19537.201765 |
| FMO2-HF: Total energy | -4602.249125 |
| FMO2-MP2: Total energy | -4615.696055 |
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. |
| -116.78 | -108.389 | 19.843 | -12.56 | -15.674 | -0.119 |
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 | 0.064 | 0.028 | 2.644 | -6.478 | -3.765 | 0.748 | -1.316 | -2.144 | -0.010 | |
| 4 | 4 | GLN | 0 | 0.022 | 0.019 | 4.864 | 2.956 | 3.101 | -0.001 | -0.004 | -0.140 | 0.000 | |
| 5 | 5 | GLN | 0 | -0.035 | -0.043 | 6.120 | -4.669 | -4.669 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.004 | 0.023 | 2.431 | -6.133 | -4.409 | 1.196 | -0.924 | -1.996 | 0.002 | |
| 7 | 7 | GLN | 0 | 0.063 | 0.053 | 1.821 | -22.065 | -24.338 | 11.025 | -4.776 | -3.976 | -0.061 | |
| 8 | 8 | GLN | 0 | 0.023 | -0.016 | 1.949 | -43.458 | -36.867 | 6.817 | -6.366 | -7.043 | -0.050 | |
| 9 | 9 | GLN | 0 | -0.068 | -0.021 | 3.078 | 2.817 | 2.308 | 0.058 | 0.826 | -0.375 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.918 | -0.957 | 5.138 | -39.750 | -39.750 | 0.000 | 0.000 | 0.000 | 0.000 |