FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-10-17
All entries: 77277
Number of unique PDB entries: 32023
FMODB ID: 2KKKR
Calculation Name: 1L2Y-A-MD54-83300ps
Preferred Name:
Target Type:
Ligand Name:
Ligand 3-letter code:
Ligand of Interest (LOI):
Structure Source: PDB
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 |
| Remarks |
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 | -24388.051947 |
|---|---|
| FMO2-HF: Nuclear repulsion | 19785.90274 |
| FMO2-HF: Total energy | -4602.149207 |
| FMO2-MP2: Total energy | -4615.609029 |
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. |
| -27.638 | -24.272 | 11.246 | -6.173 | -8.44 | -0.017 |
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 | 0.081 | 0.055 | 1.820 | -15.947 | -15.563 | 11.102 | -5.164 | -6.322 | -0.020 | |
| 4 | 4 | GLN | 0 | 0.011 | 0.003 | 2.999 | 1.723 | 3.916 | 0.141 | -0.766 | -1.568 | 0.004 | |
| 5 | 5 | GLN | 0 | -0.062 | -0.020 | 3.288 | -4.397 | -3.782 | 0.004 | -0.229 | -0.391 | -0.001 | |
| 6 | 6 | GLN | 0 | 0.061 | 0.017 | 4.940 | 6.381 | 6.555 | -0.001 | -0.014 | -0.159 | 0.000 | |
| 7 | 7 | GLN | 0 | -0.054 | -0.023 | 8.247 | 2.899 | 2.899 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | GLN | 0 | -0.048 | -0.021 | 6.843 | 1.192 | 1.192 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | GLN | 0 | -0.027 | -0.012 | 8.328 | -0.585 | -0.585 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLN | -1 | -0.942 | -0.947 | 10.684 | -18.904 | -18.904 | 0.000 | 0.000 | 0.000 | 0.000 |