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: X663Z
Calculation Name: 1L2Y-A-MD4-12100ps
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1L2Y
Chain ID: A
Base Structure: MD
Registration Date: 2018-03-06
Reference:
Apendix: None
Modeling method
| Optimization | BaseStructure_original |
|---|---|
| Restraint | BaseStructure_original |
| Protonation | BaseStructure_original |
| Complement | BaseStructure_original |
| Water | No |
| Procedure | Auto-FMO protocol ver. 1.20171117 |
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 | -55211.112081 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47772.081467 |
| FMO2-HF: Total energy | -7439.030615 |
| FMO2-MP2: Total energy | -7461.372581 |
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. |
| 31.676 | 36.047 | 2.603 | -1.854 | -5.12 | -0.011 |
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 | 0.091 | 0.040 | 3.300 | 4.222 | 5.735 | -0.001 | -0.380 | -1.133 | -0.001 | |
| 4 | 4 | ILE | 0 | 0.030 | 0.002 | 2.291 | 0.584 | 2.293 | 2.590 | -1.128 | -3.171 | -0.009 | |
| 5 | 5 | GLN | 0 | -0.047 | -0.035 | 3.118 | 0.477 | 1.485 | 0.015 | -0.339 | -0.685 | -0.001 | |
| 6 | 6 | TRP | 0 | -0.013 | 0.021 | 5.257 | 4.713 | 4.854 | -0.001 | -0.007 | -0.131 | 0.000 | |
| 7 | 7 | LEU | 0 | 0.051 | 0.026 | 6.415 | 3.170 | 3.170 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.858 | 0.930 | 6.016 | 40.947 | 40.947 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.855 | -0.916 | 9.334 | -23.268 | -23.268 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.086 | 0.054 | 11.409 | 2.187 | 2.187 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | -0.056 | -0.032 | 11.522 | 1.307 | 1.307 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | 0.000 | -0.020 | 12.450 | 0.509 | 0.509 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.002 | 0.015 | 15.875 | 0.966 | 0.966 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.066 | -0.017 | 14.296 | 0.753 | 0.753 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.019 | 0.009 | 16.542 | 0.593 | 0.593 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.846 | 0.902 | 9.322 | 28.695 | 28.695 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.028 | 0.026 | 14.468 | -0.268 | -0.268 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.016 | -0.020 | 9.992 | -1.138 | -1.138 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.102 | -0.048 | 6.593 | 0.400 | 0.400 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.899 | -0.941 | 7.731 | -33.173 | -33.173 | 0.000 | 0.000 | 0.000 | 0.000 |