FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2025-04-23
All entries: 37539
Number of unique PDB entries: 7791
FMODB ID: N2ZNQ
Calculation Name: 1L2Y-A-Other510
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1L2Y
Chain ID: A
Base Structure: SolutionNMR
Registration Date: 2024-05-02
Reference:
Apendix: Link
Modeling method
| Optimization | ABINIT-MP:FMO/FDD/HF/6-31G |
|---|---|
| Restraint | Partial optimization |
| Protonation | BaseStructure_original |
| Complement | No |
| Water | No |
| Procedure | Manual calculation |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 20 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230322 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -54719.209554 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47279.649951 |
| FMO2-HF: Total energy | -7439.559603 |
| FMO2-MP2: Total energy | -7461.855883 |
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:ASN)
Summations of interaction energy for
fragment #1(:1:ASN)
| 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. |
| 26 | 29.467 | 1.599 | -1.8 | -3.266 | -0.008 |
Interaction energy analysis for fragmet #1(:1:ASN)
| 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 | TYR | 0 | 0.115 | 0.051 | 3.543 | 4.530 | 6.218 | -0.005 | -0.669 | -1.015 | -0.001 | |
| 4 | 4 | ILE | 0 | -0.014 | -0.004 | 2.448 | 2.835 | 4.275 | 1.605 | -1.044 | -2.000 | -0.007 | |
| 5 | 5 | GLN | 0 | 0.009 | -0.005 | 4.160 | 10.448 | 10.787 | -0.001 | -0.087 | -0.251 | 0.000 | |
| 6 | 6 | TRP | 0 | 0.015 | 0.014 | 6.056 | 3.815 | 3.815 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | LEU | 0 | 0.014 | -0.006 | 7.573 | 3.404 | 3.404 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.858 | 0.947 | 7.930 | 31.672 | 31.672 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.900 | -0.950 | 9.963 | -22.590 | -22.590 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.011 | 0.025 | 12.376 | 1.911 | 1.911 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | 0.007 | -0.001 | 12.287 | 1.022 | 1.022 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.024 | -0.022 | 13.199 | 0.451 | 0.451 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.052 | -0.015 | 16.433 | 0.871 | 0.871 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | 0.013 | -0.017 | 14.985 | 0.586 | 0.586 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | -0.029 | 0.000 | 17.062 | -0.111 | -0.111 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.913 | 0.958 | 12.686 | 20.964 | 20.964 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.047 | 0.032 | 15.048 | -0.429 | -0.429 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.013 | -0.009 | 11.108 | -1.192 | -1.192 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.085 | -0.038 | 7.284 | 0.708 | 0.708 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.907 | -0.950 | 9.000 | -32.895 | -32.895 | 0.000 | 0.000 | 0.000 | 0.000 |