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: 437LN
Calculation Name: 3OUW-B-Xray372
Preferred Name: Catenin beta-1
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 3OUW
Chain ID: B
ChEMBL ID: CHEMBL4105846
UniProt ID: Q02248
Base Structure: X-ray
Registration Date: 2023-06-20
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 | 28 |
| LigandResidueName | |
| LigandFragmentNumber | 0 |
| LigandCharge | |
| Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
| FMO2-HF: Electronic energy | -64348.084331 |
|---|---|
| FMO2-HF: Nuclear repulsion | 53115.02793 |
| FMO2-HF: Total energy | -11233.056401 |
| FMO2-MP2: Total energy | -11264.103475 |
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(B:11:GLY)
Summations of interaction energy for
fragment #1(B:11:GLY)
| 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. |
| -1.097 | 0.752 | -0.008 | -0.942 | -0.897 | 0.004 |
Interaction energy analysis for fragmet #1(B:11:GLY)
| 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 | B | 13 | PRO | 0 | -0.029 | -0.034 | 3.785 | -0.641 | 0.973 | -0.020 | -0.882 | -0.711 | 0.004 |
| 4 | B | 14 | GLU | -1 | -0.953 | -0.970 | 6.390 | -0.962 | -0.962 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | B | 15 | LEU | 0 | 0.018 | 0.017 | 3.399 | 0.347 | 0.582 | 0.012 | -0.060 | -0.186 | 0.000 |
| 6 | B | 16 | CYS | 0 | -0.090 | -0.041 | 7.414 | 0.393 | 0.393 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 17 | ALA | 0 | 0.004 | 0.015 | 10.342 | 0.131 | 0.131 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 18 | THR | 0 | -0.019 | -0.018 | 12.207 | 0.087 | 0.087 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 19 | ASP | -1 | -0.904 | -0.937 | 13.759 | -0.354 | -0.354 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 20 | GLU | -1 | -0.983 | -0.996 | 16.033 | -0.254 | -0.254 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 21 | MET | 0 | -0.050 | -0.026 | 19.630 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 22 | ILE | 0 | 0.019 | 0.007 | 22.348 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 23 | PRO | 0 | -0.039 | -0.003 | 25.435 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 24 | PHE | 0 | 0.028 | 0.002 | 26.555 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 25 | LYS | 1 | 0.946 | 0.973 | 31.386 | 0.082 | 0.082 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 48 | LEU | 0 | 0.013 | 0.000 | 52.776 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 49 | ALA | 0 | -0.014 | -0.027 | 56.780 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 50 | ASP | -1 | -0.867 | -0.941 | 57.219 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 51 | ILE | 0 | 0.036 | 0.008 | 54.543 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 52 | LYS | 1 | 0.905 | 0.962 | 58.660 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 53 | SER | 0 | 0.028 | 0.001 | 60.762 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 54 | SER | 0 | 0.000 | 0.009 | 60.879 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 55 | LEU | 0 | 0.003 | 0.013 | 58.597 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 56 | VAL | 0 | -0.034 | -0.017 | 62.264 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 57 | ASN | 0 | 0.054 | 0.036 | 65.497 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 58 | GLU | -1 | -1.011 | -0.987 | 60.963 | 0.014 | 0.014 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 59 | SER | 0 | -0.086 | -0.053 | 64.581 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 60 | GLU | -1 | -1.027 | -1.005 | 66.934 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |