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: K3N23
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 | OptH |
| 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 | -64366.516353 |
|---|---|
| FMO2-HF: Nuclear repulsion | 53133.61742 |
| FMO2-HF: Total energy | -11232.898933 |
| FMO2-MP2: Total energy | -11263.955438 |
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. |
| 1.923 | 3.11 | -0.011 | -0.491 | -0.685 | 0 |
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 | -0.032 | -0.036 | 3.785 | 1.748 | 2.733 | -0.018 | -0.439 | -0.528 | 0.000 |
| 4 | B | 14 | GLU | -1 | -0.957 | -0.978 | 6.750 | 0.303 | 0.303 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | B | 15 | LEU | 0 | 0.016 | 0.022 | 3.525 | -0.069 | 0.133 | 0.007 | -0.052 | -0.157 | 0.000 |
| 6 | B | 16 | CYS | 0 | -0.086 | -0.042 | 7.415 | 0.043 | 0.043 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 17 | ALA | 0 | 0.005 | 0.017 | 10.344 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 18 | THR | 0 | -0.016 | -0.016 | 12.208 | 0.040 | 0.040 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 19 | ASP | -1 | -0.915 | -0.945 | 13.392 | -0.089 | -0.089 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 20 | GLU | -1 | -0.987 | -0.996 | 16.034 | -0.075 | -0.075 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 21 | MET | 0 | -0.035 | -0.020 | 19.631 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 22 | ILE | 0 | -0.001 | 0.002 | 22.349 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 23 | PRO | 0 | -0.016 | 0.003 | 25.436 | 0.009 | 0.009 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 24 | PHE | 0 | 0.015 | -0.002 | 26.829 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 25 | LYS | 1 | 0.951 | 0.976 | 31.387 | 0.015 | 0.015 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 48 | LEU | 0 | 0.014 | 0.003 | 52.931 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 49 | ALA | 0 | -0.006 | -0.024 | 56.781 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 50 | ASP | -1 | -0.858 | -0.934 | 57.244 | 0.007 | 0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 51 | ILE | 0 | 0.024 | -0.001 | 54.733 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 52 | LYS | 1 | 0.904 | 0.959 | 58.739 | -0.006 | -0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 53 | SER | 0 | 0.029 | 0.001 | 60.763 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 54 | SER | 0 | 0.001 | 0.012 | 60.891 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 55 | LEU | 0 | -0.017 | 0.001 | 58.872 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 56 | VAL | 0 | -0.045 | -0.040 | 62.265 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 57 | ASN | 0 | 0.084 | 0.045 | 65.503 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 58 | GLU | -1 | -1.023 | -0.988 | 60.905 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 59 | SER | 0 | -0.066 | -0.025 | 64.568 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 60 | GLU | -1 | -1.039 | -1.009 | 66.935 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |