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: P534Z
Calculation Name: 1L2Y-A-MD4-33700ps
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 | -55024.495538 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47585.484843 |
| FMO2-HF: Total energy | -7439.010695 |
| FMO2-MP2: Total energy | -7461.3481 |
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. |
| 21.885 | 26.779 | 7.689 | -4.187 | -8.397 | 0.027 |
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 | 0.111 | 0.062 | 2.351 | 2.405 | 5.539 | 2.651 | -2.064 | -3.721 | 0.011 | |
| 4 | 4 | ILE | 0 | 0.017 | 0.005 | 2.084 | -5.426 | -4.459 | 5.027 | -1.853 | -4.141 | 0.015 | |
| 5 | 5 | GLN | 0 | -0.079 | -0.041 | 3.962 | -1.592 | -0.799 | 0.011 | -0.270 | -0.535 | 0.001 | |
| 6 | 6 | TRP | 0 | 0.059 | 0.026 | 6.324 | 2.520 | 2.520 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 7 | 7 | LEU | 0 | 0.030 | -0.003 | 6.190 | 1.739 | 1.739 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 8 | 8 | LYS | 1 | 0.884 | 0.970 | 5.994 | 41.748 | 41.748 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 9 | 9 | ASP | -1 | -0.832 | -0.908 | 9.936 | -24.566 | -24.566 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 10 | 10 | GLY | 0 | -0.003 | -0.001 | 11.393 | 1.796 | 1.796 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 11 | 11 | GLY | 0 | 0.003 | 0.000 | 10.678 | 0.588 | 0.588 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 12 | 12 | PRO | 0 | -0.077 | -0.037 | 11.544 | 0.291 | 0.291 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 13 | 13 | SER | 0 | -0.010 | 0.005 | 14.831 | 0.389 | 0.389 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 14 | 14 | SER | 0 | -0.017 | -0.006 | 13.333 | 0.559 | 0.559 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 15 | 15 | GLY | 0 | 0.074 | 0.042 | 15.731 | 0.500 | 0.500 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 16 | 16 | ARG | 1 | 0.786 | 0.888 | 9.200 | 26.061 | 26.061 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 17 | 17 | PRO | 0 | 0.019 | 0.013 | 13.996 | -0.276 | -0.276 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 18 | 18 | PRO | 0 | -0.014 | -0.013 | 9.255 | -1.062 | -1.062 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 19 | 19 | PRO | 0 | -0.102 | -0.052 | 6.153 | 0.546 | 0.546 | 0.000 | 0.000 | 0.000 | 0.000 | |
| 20 | 20 | SER | -1 | -0.891 | -0.937 | 8.970 | -24.335 | -24.335 | 0.000 | 0.000 | 0.000 | 0.000 |