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: X1JYZ
Calculation Name: 1L2Y-A-NMR5-Model23
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1L2Y
Chain ID: A
Base Structure: NMR
Registration Date: 2018-02-27
Reference:
Apendix: None
Modeling method
| Optimization | BaseStructure_original |
|---|---|
| Restraint | BaseStructure_original |
| Protonation | BaseStructure_original |
| Complement | BaseStructure_original |
| Water | No |
| Procedure | Auto-FMO protocol ver. 1.20180117 |
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 | -54855.346246 |
|---|---|
| FMO2-HF: Nuclear repulsion | 47415.943406 |
| FMO2-HF: Total energy | -7439.40284 |
| FMO2-MP2: Total energy | -7461.717995 |
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(A:1:ASN)
Summations of interaction energy for
fragment #1(A: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. |
| 30.62 | 34.801 | 1.689 | -2.127 | -3.744 | -0.008 |
Interaction energy analysis for fragmet #1(A: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 | A | 3 | TYR | 0 | 0.109 | 0.039 | 3.347 | 6.711 | 9.869 | 0.008 | -1.506 | -1.661 | -0.005 |
| 4 | A | 4 | ILE | 0 | 0.016 | 0.007 | 2.400 | 4.632 | 5.506 | 1.682 | -0.607 | -1.949 | -0.003 |
| 5 | A | 5 | GLN | 0 | -0.013 | -0.010 | 4.678 | 5.964 | 6.113 | -0.001 | -0.014 | -0.134 | 0.000 |
| 6 | A | 6 | TRP | 0 | -0.032 | -0.023 | 6.667 | 2.821 | 2.821 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | LEU | 0 | 0.033 | 0.005 | 7.245 | 3.073 | 3.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.865 | 0.930 | 8.452 | 27.140 | 27.140 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | ASP | -1 | -0.869 | -0.885 | 10.709 | -19.488 | -19.488 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLY | 0 | 0.070 | 0.047 | 12.589 | 1.534 | 1.534 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLY | 0 | -0.020 | -0.015 | 11.844 | 0.867 | 0.867 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | PRO | 0 | -0.011 | -0.022 | 12.721 | 0.486 | 0.486 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | SER | 0 | -0.033 | 0.005 | 15.975 | 1.126 | 1.126 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | SER | 0 | -0.035 | -0.056 | 15.700 | 1.166 | 1.166 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | GLY | 0 | -0.030 | -0.003 | 17.745 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | ARG | 1 | 0.902 | 0.947 | 10.627 | 25.541 | 25.541 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | PRO | 0 | 0.057 | 0.041 | 14.229 | -0.623 | -0.623 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | PRO | 0 | -0.024 | -0.012 | 9.233 | -1.244 | -1.244 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | PRO | 0 | -0.073 | -0.047 | 6.067 | 0.141 | 0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | SER | -1 | -0.910 | -0.943 | 6.374 | -29.358 | -29.358 | 0.000 | 0.000 | 0.000 | 0.000 |