FMODB: The database of quantum mechanical data based on the FMO method
Last updated: 2024-07-23
All entries: 37478
Number of unique PDB entries: 7783
FMODB ID: G5NJ1
Calculation Name: 1W5L-A-Xray372
Preferred Name:
Target Type:
Ligand Name:
ligand 3-letter code:
PDB ID: 1W5L
Chain ID: A
UniProt ID: P03069
Base Structure: X-ray
Registration Date: 2023-09-21
Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.
Apendix: None
Modeling method
| Optimization | MOE:Amber10:EHT |
|---|---|
| Restraint | OptHSide |
| Protonation | MOE:Protonate 3D |
| Complement | MOE:Structure Preparation |
| Water | No |
| Procedure | Auto-FMO protocol ver. 2.20220422 |
FMO calculation
| FMO method | FMO2-MP2/6-31G(d) |
|---|---|
| Fragmentation | Auto |
| Number of fragment | 32 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -114768.95405 |
|---|---|
| FMO2-HF: Nuclear repulsion | 101255.750139 |
| FMO2-HF: Total energy | -13513.203911 |
| FMO2-MP2: Total energy | -13551.641504 |
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:ARG)
Summations of interaction energy for
fragment #1(A:1:ARG)
| 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. |
| -24.435 | -18.23 | 6.301 | -4.969 | -7.537 | -0.034 |
Interaction energy analysis for fragmet #1(A:1:ARG)
| 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 | LYS | 1 | 0.879 | 0.928 | 3.045 | 23.819 | 26.783 | 0.152 | -1.384 | -1.732 | 0.005 |
| 4 | A | 4 | GLN | 0 | 0.030 | 0.023 | 2.053 | -26.483 | -24.558 | 6.033 | -3.247 | -4.711 | -0.037 |
| 5 | A | 5 | ILE | 0 | -0.024 | -0.016 | 2.922 | 0.671 | 1.987 | 0.116 | -0.338 | -1.094 | -0.002 |
| 6 | A | 6 | GLU | -1 | -0.838 | -0.910 | 5.565 | -20.918 | -20.918 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | A | 7 | ASP | -1 | -0.805 | -0.891 | 7.270 | -27.455 | -27.455 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | A | 8 | LYS | 1 | 0.772 | 0.852 | 6.381 | 30.898 | 30.898 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | A | 9 | LEU | 0 | -0.013 | 0.004 | 8.610 | 2.731 | 2.731 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | A | 10 | GLU | -1 | -0.904 | -0.944 | 11.097 | -18.907 | -18.907 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | A | 11 | GLU | -1 | -0.863 | -0.907 | 11.312 | -23.248 | -23.248 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | A | 12 | ILE | 0 | -0.019 | -0.027 | 10.798 | 1.536 | 1.536 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | A | 13 | LEU | 0 | -0.004 | -0.001 | 14.287 | 1.469 | 1.469 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | A | 14 | SER | 0 | -0.004 | 0.012 | 16.503 | 1.535 | 1.535 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | A | 15 | LYS | 1 | 0.927 | 0.957 | 17.170 | 15.595 | 15.595 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | A | 16 | GLY | 0 | 0.047 | 0.037 | 18.904 | 0.751 | 0.751 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | A | 17 | TYR | 0 | 0.041 | 0.013 | 20.597 | 0.993 | 0.993 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | A | 18 | HIS | 0 | -0.100 | -0.053 | 22.034 | 0.318 | 0.318 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | A | 19 | ILE | 0 | 0.038 | 0.012 | 21.382 | 0.555 | 0.555 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | A | 20 | CYS | 0 | -0.023 | -0.013 | 24.570 | 0.580 | 0.580 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | A | 21 | ASN | 0 | 0.002 | -0.002 | 26.447 | 0.789 | 0.789 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | A | 22 | GLU | -1 | -0.910 | -0.957 | 26.219 | -11.136 | -11.136 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | A | 23 | LEU | 0 | 0.036 | 0.012 | 27.915 | 0.400 | 0.400 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | A | 24 | ALA | 0 | -0.019 | -0.002 | 30.932 | 0.373 | 0.373 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | A | 25 | ARG | 1 | 0.890 | 0.944 | 28.727 | 10.456 | 10.456 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | A | 26 | ILE | 0 | 0.013 | 0.001 | 31.281 | 0.277 | 0.277 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | A | 27 | LYS | 1 | 0.987 | 0.999 | 33.920 | 9.075 | 9.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | A | 28 | LYS | 1 | 0.936 | 0.965 | 36.462 | 8.620 | 8.620 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | A | 29 | LEU | 0 | -0.035 | -0.008 | 36.848 | 0.200 | 0.200 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | A | 30 | LEU | 0 | -0.003 | 0.009 | 37.446 | 0.182 | 0.182 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | A | 31 | GLY | 0 | -0.018 | 0.011 | 41.014 | 0.143 | 0.143 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | A | 32 | GLU | -1 | -1.024 | -1.016 | 38.177 | -8.254 | -8.254 | 0.000 | 0.000 | 0.000 | 0.000 |