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: X13KZ
Calculation Name: 1L2Y-A-MD50-70300ps
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 2OTU
Chain ID: A
UniProt ID: A2NN81
Base Structure: MD
Registration Date: 2019-08-09
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 | -23122.56001 |
|---|---|
| FMO2-HF: Nuclear repulsion | 18520.428813 |
| FMO2-HF: Total energy | -4602.131197 |
| FMO2-MP2: Total energy | -4615.588103 |
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. |
| -96.128 | -84.019 | 15.928 | -12.081 | -15.956 | -0.079 |
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 | -0.002 | -0.005 | 2.023 | -3.635 | -1.123 | 5.123 | -3.390 | -4.245 | 0.025 | |
| 4 | 4 | GLN | 0 | 0.036 | 0.017 | 2.491 | -13.399 | -11.464 | 0.924 | -1.118 | -1.741 | -0.015 | |
| 5 | 5 | GLN | 0 | -0.036 | -0.024 | 2.582 | 2.786 | 4.278 | 1.476 | -0.757 | -2.212 | 0.004 | |
| 6 | 6 | GLN | 0 | 0.049 | 0.030 | 2.417 | -19.849 | -17.272 | 1.697 | -1.923 | -2.351 | -0.027 | |
| 7 | 7 | GLN | 0 | 0.091 | 0.047 | 1.937 | -43.750 | -40.314 | 6.700 | -4.884 | -5.251 | -0.066 | |
| 8 | 8 | GLN | 0 | -0.038 | -0.022 | 4.000 | 7.622 | 7.779 | 0.008 | -0.009 | -0.156 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.108 | -0.088 | 6.561 | -0.979 | -0.979 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.896 | -0.912 | 7.253 | -24.924 | -24.924 | 0.000 | 0.000 | 0.000 | 0.000 |