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: XM39Z
Calculation Name: 1L2Y-A-MD4-20500ps
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 | -55657.337693 |
|---|---|
| FMO2-HF: Nuclear repulsion | 48218.356687 |
| FMO2-HF: Total energy | -7438.981006 |
| FMO2-MP2: Total energy | -7461.331725 |
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. |
| 15.423 | 19.584 | 9.681 | -4.753 | -9.088 | 0.025 |
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 | 0.123 | 0.071 | 2.490 | 1.366 | 3.916 | 2.384 | -1.808 | -3.125 | 0.011 | |
| 4 | 4 | ILE | 0 | -0.019 | -0.021 | 2.089 | -9.247 | -8.193 | 7.281 | -2.763 | -5.573 | 0.013 | |
| 5 | 5 | GLN | 0 | 0.039 | -0.012 | 3.997 | 2.539 | 3.096 | 0.016 | -0.182 | -0.390 | 0.001 | |
| 6 | 6 | TRP | 0 | -0.003 | 0.031 | 6.139 | 2.497 | 2.497 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | LEU | 0 | 0.057 | 0.025 | 6.151 | 1.963 | 1.963 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.809 | 0.925 | 6.439 | 35.686 | 35.686 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.813 | -0.890 | 9.456 | -23.954 | -23.954 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | -0.008 | -0.006 | 11.710 | 1.632 | 1.632 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | -0.005 | -0.034 | 10.896 | 1.016 | 1.016 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.003 | -0.005 | 11.776 | 0.266 | 0.266 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.024 | 0.005 | 15.253 | 1.107 | 1.107 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.026 | -0.008 | 13.776 | 0.489 | 0.489 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.031 | 0.015 | 15.707 | 0.492 | 0.492 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.810 | 0.896 | 8.866 | 26.079 | 26.079 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.070 | 0.049 | 12.978 | -0.168 | -0.168 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.026 | -0.015 | 8.822 | -1.499 | -1.499 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.079 | -0.051 | 5.743 | -0.069 | -0.069 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.944 | -0.950 | 7.861 | -24.772 | -24.772 | 0.000 | 0.000 | 0.000 | 0.000 |