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: XMM5Z
Calculation Name: 1L2Y-A-MD4-2300ps
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 | -54792.939627 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47353.90024 |
| FMO2-HF: Total energy | -7439.039386 |
| FMO2-MP2: Total energy | -7461.386481 |
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. |
| 30.763 | 35.941 | 0.854 | -2.024 | -4.009 | -0.002 |
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 | 0.090 | 2.643 | 1.951 | 5.976 | 0.847 | -1.690 | -3.182 | -0.002 | |
| 4 | 4 | ILE | 0 | -0.029 | -0.046 | 3.547 | 5.382 | 6.302 | 0.008 | -0.322 | -0.607 | 0.000 | |
| 5 | 5 | GLN | 0 | 0.028 | 0.001 | 5.387 | 7.911 | 8.144 | -0.001 | -0.012 | -0.220 | 0.000 | |
| 6 | 6 | TRP | 0 | 0.005 | 0.027 | 8.017 | 2.328 | 2.328 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | LEU | 0 | -0.025 | -0.020 | 6.735 | 2.000 | 2.000 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.899 | 0.966 | 9.138 | 32.913 | 32.913 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.832 | -0.910 | 11.182 | -20.908 | -20.908 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.014 | -0.014 | 13.584 | 1.331 | 1.331 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | 0.013 | 0.020 | 11.847 | 0.975 | 0.975 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.030 | -0.016 | 12.844 | 0.317 | 0.317 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.047 | -0.034 | 15.890 | 0.923 | 0.923 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | 0.005 | 0.006 | 14.227 | 0.958 | 0.958 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | -0.004 | 0.022 | 16.729 | 0.551 | 0.551 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.830 | 0.918 | 11.518 | 23.408 | 23.408 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.045 | 0.026 | 12.512 | -0.359 | -0.359 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.012 | -0.022 | 8.107 | -0.527 | -0.527 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.101 | -0.053 | 6.020 | 1.149 | 1.149 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.906 | -0.934 | 6.676 | -29.540 | -29.540 | 0.000 | 0.000 | 0.000 | 0.000 |