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: 4NY2N
Calculation Name: 1L2Y-A-MD57-92700ps
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 | -24317.428828 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19715.200549 |
| FMO2-HF: Total energy | -4602.228279 |
| FMO2-MP2: Total energy | -4615.670578 |
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. |
| -109.272 | -96.831 | 13.113 | -11.335 | -14.215 | -0.115 |
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 | 0.077 | 0.029 | 2.982 | -2.463 | -0.057 | 0.143 | -1.135 | -1.414 | -0.005 | |
| 4 | 4 | GLN | 0 | 0.057 | 0.022 | 5.459 | 0.758 | 0.758 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.017 | 0.001 | 5.806 | -5.249 | -5.249 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | -0.075 | -0.041 | 2.403 | -3.473 | -2.473 | 1.323 | -0.682 | -1.640 | 0.003 | |
| 7 | 7 | GLN | 0 | 0.006 | 0.020 | 2.077 | -18.997 | -16.786 | 4.660 | -3.194 | -3.676 | -0.046 | |
| 8 | 8 | GLN | 0 | 0.008 | 0.002 | 2.238 | -28.566 | -24.883 | 4.775 | -3.948 | -4.509 | -0.035 | |
| 9 | 9 | GLN | 0 | 0.003 | -0.025 | 2.291 | -26.004 | -22.847 | 2.213 | -2.368 | -3.001 | -0.032 | |
| 10 | 10 | GLN | -1 | -0.904 | -0.924 | 4.956 | -25.278 | -25.294 | -0.001 | -0.008 | 0.025 | 0.000 |