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: PK353
Calculation Name: 1L2Y-A-MD4-37900ps
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 | -54530.265941 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47091.312475 |
| FMO2-HF: Total energy | -7438.953466 |
| FMO2-MP2: Total energy | -7461.296229 |
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. |
| -24.596 | -15.312 | 7.449 | -6.693 | -10.04 | -0.031 |
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 | 0.070 | 0.061 | 2.797 | 1.118 | 4.018 | 0.691 | -1.321 | -2.271 | 0.008 | |
| 4 | 4 | ILE | 0 | 0.070 | 0.018 | 2.236 | -5.799 | -3.487 | 3.561 | -1.784 | -4.088 | 0.018 | |
| 5 | 5 | GLN | 0 | -0.044 | -0.015 | 2.173 | -27.772 | -23.865 | 3.198 | -3.577 | -3.529 | -0.057 | |
| 6 | 6 | TRP | 0 | 0.064 | -0.010 | 5.257 | 3.801 | 3.966 | -0.001 | -0.011 | -0.152 | 0.000 | |
| 7 | 7 | LEU | 0 | -0.012 | -0.013 | 6.701 | 2.957 | 2.957 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.879 | 0.946 | 8.160 | 27.944 | 27.944 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.918 | -0.956 | 9.501 | -26.368 | -26.368 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | 0.015 | 0.010 | 11.403 | 2.031 | 2.031 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | -0.026 | -0.011 | 10.861 | 1.253 | 1.253 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.048 | -0.016 | 11.901 | 0.309 | 0.309 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | 0.034 | 0.049 | 14.514 | 0.885 | 0.885 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.063 | -0.041 | 13.200 | 0.534 | 0.534 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.011 | -0.001 | 15.706 | 0.538 | 0.538 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.923 | 0.960 | 12.500 | 20.381 | 20.381 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.046 | 0.022 | 13.507 | -0.339 | -0.339 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | 0.004 | 0.007 | 9.236 | -1.076 | -1.076 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.087 | -0.044 | 6.499 | 0.247 | 0.247 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.929 | -0.948 | 7.628 | -25.240 | -25.240 | 0.000 | 0.000 | 0.000 | 0.000 |