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: 9Y882
Calculation Name: 1L2Y-A-MD56-9600ps
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 | -23665.822922 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19063.599136 |
| FMO2-HF: Total energy | -4602.223786 |
| FMO2-MP2: Total energy | -4615.653581 |
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. |
| -92.372 | -89.838 | 29.918 | -13.134 | -19.316 | -0.077 |
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 | 0.097 | 0.032 | 3.074 | -8.302 | -6.560 | 0.104 | -0.935 | -0.911 | -0.004 | |
| 4 | 4 | GLN | 0 | -0.061 | -0.038 | 5.733 | 0.107 | 0.107 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.027 | 0.028 | 2.542 | -10.603 | -8.162 | 1.421 | -1.216 | -2.646 | -0.010 | |
| 6 | 6 | GLN | 0 | 0.017 | -0.003 | 4.128 | -1.052 | -0.800 | 0.001 | -0.046 | -0.207 | 0.000 | |
| 7 | 7 | GLN | 0 | -0.033 | -0.008 | 4.155 | 1.957 | 2.325 | 0.000 | -0.150 | -0.217 | 0.000 | |
| 8 | 8 | GLN | 0 | 0.057 | 0.025 | 1.960 | -24.030 | -28.315 | 17.841 | -7.189 | -6.366 | -0.048 | |
| 9 | 9 | GLN | 0 | -0.035 | -0.022 | 2.426 | -13.505 | -10.654 | 4.369 | -1.041 | -6.178 | -0.040 | |
| 10 | 10 | GLN | -1 | -0.912 | -0.954 | 1.941 | -36.944 | -37.779 | 6.182 | -2.557 | -2.791 | 0.025 |