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: 53MNZ
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 | OptAll |
| 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 | -64648.852862 |
|---|---|
| FMO2-HF: Nuclear repulsion | 53415.566191 |
| FMO2-HF: Total energy | -11233.286671 |
| FMO2-MP2: Total energy | -11264.349689 |
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. |
| -0.841 | 0.83 | 0.055 | -0.869 | -0.857 | 0.002 |
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 | -0.031 | -0.040 | 3.843 | -0.821 | 0.488 | -0.001 | -0.749 | -0.559 | 0.003 |
| 4 | B | 14 | GLU | -1 | -0.933 | -0.952 | 6.491 | -0.735 | -0.735 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | B | 15 | LEU | 0 | -0.021 | -0.011 | 3.031 | 0.377 | 0.739 | 0.056 | -0.120 | -0.298 | -0.001 |
| 6 | B | 16 | CYS | 0 | -0.072 | -0.033 | 7.075 | 0.383 | 0.383 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 17 | ALA | 0 | 0.002 | 0.013 | 10.319 | 0.100 | 0.100 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 18 | THR | 0 | -0.043 | -0.036 | 12.239 | 0.103 | 0.103 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 19 | ASP | -1 | -0.914 | -0.942 | 14.112 | -0.186 | -0.186 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 20 | GLU | -1 | -0.968 | -0.978 | 16.215 | -0.203 | -0.203 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 21 | MET | 0 | -0.035 | -0.025 | 19.814 | 0.034 | 0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 22 | ILE | 0 | 0.019 | 0.009 | 22.476 | -0.003 | -0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 23 | PRO | 0 | 0.013 | 0.020 | 25.712 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 24 | PHE | 0 | 0.032 | 0.000 | 26.611 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 25 | LYS | 1 | 0.875 | 0.946 | 31.183 | 0.053 | 0.053 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 48 | LEU | 0 | 0.046 | 0.007 | 52.862 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 49 | ALA | 0 | -0.049 | -0.033 | 56.910 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 50 | ASP | -1 | -0.802 | -0.887 | 57.227 | 0.018 | 0.018 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 51 | ILE | 0 | 0.034 | 0.002 | 54.446 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 52 | LYS | 1 | 0.898 | 0.960 | 58.573 | -0.011 | -0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 53 | SER | 0 | -0.002 | -0.014 | 60.670 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 54 | SER | 0 | -0.083 | -0.054 | 60.737 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 55 | LEU | 0 | 0.041 | 0.018 | 58.673 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 56 | VAL | 0 | -0.008 | 0.004 | 62.036 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 57 | ASN | 0 | 0.007 | 0.003 | 65.567 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 58 | GLU | -1 | -0.960 | -0.958 | 60.746 | 0.024 | 0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 59 | SER | 0 | -0.087 | -0.047 | 64.410 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 60 | GLU | -1 | -1.035 | -1.002 | 66.657 | 0.013 | 0.013 | 0.000 | 0.000 | 0.000 | 0.000 |