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: 9YGN2
Calculation Name: 1L2Y-A-MD55-21600ps
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 | -22607.601877 |
|---|---|
| FMO2-HF: Nuclear repulsion | 18005.349422 |
| FMO2-HF: Total energy | -4602.252455 |
| FMO2-MP2: Total energy | -4615.68514 |
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. |
| -111.242 | -106.948 | 32.119 | -17.715 | -18.698 | -0.145 |
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 | 0.008 | 0.002 | 3.163 | -1.798 | 0.379 | 0.209 | -0.907 | -1.479 | -0.002 | |
| 4 | 4 | GLN | 0 | 0.013 | 0.008 | 5.727 | 4.522 | 4.522 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.035 | 0.015 | 6.262 | -3.982 | -3.982 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 6 | 6 | GLN | 0 | 0.005 | -0.005 | 2.309 | -28.486 | -23.966 | 3.710 | -3.869 | -4.362 | -0.036 | |
| 7 | 7 | GLN | 0 | 0.038 | 0.060 | 1.822 | -15.768 | -17.908 | 12.579 | -5.932 | -4.507 | -0.035 | |
| 8 | 8 | GLN | 0 | 0.031 | 0.026 | 1.744 | -38.866 | -39.248 | 15.610 | -6.987 | -8.240 | -0.072 | |
| 9 | 9 | GLN | 0 | -0.020 | -0.030 | 3.955 | -1.882 | -1.763 | 0.011 | -0.020 | -0.110 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.920 | -0.938 | 7.602 | -24.982 | -24.982 | 0.000 | 0.000 | 0.000 | 0.000 |