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: XV2Y1
Calculation Name: 1L2Y-A-NMR5-Model7
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1L2Y
Chain ID: A
Base Structure: NMR
Registration Date: 2018-02-27
Reference:
Apendix: None
Modeling method
| Optimization | BaseStructure_original |
|---|---|
| Restraint | BaseStructure_original |
| Protonation | BaseStructure_original |
| Complement | BaseStructure_original |
| Water | No |
| Procedure | Auto-FMO protocol ver. 1.20180117 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 20 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | MIZUHO/ABINIT-MP 3.0 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -54660.688976 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47221.286278 |
| FMO2-HF: Total energy | -7439.402699 |
| FMO2-MP2: Total energy | -7461.686428 |
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(A:1:ASN)
Summations of interaction energy for
fragment #1(A: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. |
| 13.683 | 20.588 | 0.884 | -3.084 | -4.706 | 0.004 |
Interaction energy analysis for fragmet #1(A: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 | A | 3 | TYR | 0 | 0.048 | 0.038 | 2.670 | -1.993 | 3.004 | 0.560 | -2.393 | -3.164 | 0.009 |
| 4 | A | 4 | ILE | 0 | 0.011 | 0.006 | 2.611 | 1.581 | 2.746 | 0.302 | -0.512 | -0.955 | -0.006 |
| 5 | A | 5 | GLN | 0 | -0.021 | -0.019 | 5.967 | 5.904 | 5.904 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | A | 6 | TRP | 0 | -0.005 | -0.008 | 7.077 | 2.456 | 2.456 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | LEU | 0 | 0.006 | -0.018 | 7.892 | 2.338 | 2.338 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.842 | 0.923 | 9.931 | 25.828 | 25.828 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.926 | -0.941 | 12.123 | -17.053 | -17.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLY | 0 | 0.091 | 0.042 | 13.640 | 1.245 | 1.245 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLY | 0 | -0.005 | 0.006 | 11.896 | 0.672 | 0.672 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | PRO | 0 | -0.003 | 0.012 | 12.962 | 0.280 | 0.280 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | SER | 0 | -0.049 | -0.016 | 15.001 | 0.612 | 0.612 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | SER | 0 | 0.014 | -0.015 | 13.797 | 0.403 | 0.403 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | GLY | 0 | -0.028 | 0.001 | 16.001 | 0.212 | 0.212 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ARG | 1 | 0.939 | 0.964 | 9.278 | 21.439 | 21.439 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | PRO | 0 | 0.024 | 0.024 | 11.616 | -0.602 | -0.602 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | PRO | 0 | 0.009 | 0.004 | 7.488 | -0.700 | -0.700 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | PRO | 0 | -0.084 | -0.047 | 3.544 | 0.058 | 0.537 | 0.021 | -0.128 | -0.372 | 0.001 |
| 20 | A | 20 | SER | -1 | -0.918 | -0.948 | 3.843 | -28.997 | -28.733 | 0.001 | -0.051 | -0.215 | 0.000 |