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: R5NR8
Calculation Name: 3OUW-B-Xray320
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: 2021-09-07
Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.
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. 1.20200129 |
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. 15 / 20190524 |
Total energy (hartree)
| FMO2-HF: Electronic energy | -67640.503995 |
|---|---|
| FMO2-HF: Nuclear repulsion | 56065.645289 |
| FMO2-HF: Total energy | -11574.858706 |
| FMO2-MP2: Total energy | -11607.011694 |
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:10:ACE )
Summations of interaction energy for
fragment #1(B:10:ACE )
| 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. |
| -1.1 | 0.034 | -0.007 | -0.512 | -0.615 | -0.002 |
Interaction energy analysis for fragmet #1(B:10:ACE )
| 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 | 12 | ASP | -1 | -0.902 | -0.938 | 3.806 | -0.743 | 0.391 | -0.007 | -0.512 | -0.615 | -0.002 |
| 4 | B | 13 | PRO | 0 | -0.040 | -0.039 | 6.076 | 0.045 | 0.045 | 0.000 | 0.000 | 0.000 | 0.000 |
| 5 | B | 14 | GLU | -1 | -0.956 | -0.977 | 7.990 | -0.158 | -0.158 | 0.000 | 0.000 | 0.000 | 0.000 |
| 6 | B | 15 | LEU | 0 | 0.017 | 0.023 | 5.194 | 0.016 | 0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 7 | B | 16 | CYS | 0 | -0.086 | -0.042 | 9.638 | 0.073 | 0.073 | 0.000 | 0.000 | 0.000 | 0.000 |
| 8 | B | 17 | ALA | 0 | 0.004 | 0.017 | 12.841 | 0.060 | 0.060 | 0.000 | 0.000 | 0.000 | 0.000 |
| 9 | B | 18 | THR | 0 | -0.014 | -0.016 | 14.885 | -0.007 | -0.007 | 0.000 | 0.000 | 0.000 | 0.000 |
| 10 | B | 19 | ASP | -1 | -0.915 | -0.945 | 17.198 | -0.328 | -0.328 | 0.000 | 0.000 | 0.000 | 0.000 |
| 11 | B | 20 | GLU | -1 | -0.988 | -0.996 | 19.638 | -0.112 | -0.112 | 0.000 | 0.000 | 0.000 | 0.000 |
| 12 | B | 21 | MET | 0 | -0.035 | -0.020 | 23.253 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 13 | B | 22 | ILE | 0 | -0.001 | 0.002 | 26.039 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
| 14 | B | 23 | PRO | 0 | -0.015 | 0.003 | 29.292 | 0.003 | 0.003 | 0.000 | 0.000 | 0.000 | 0.000 |
| 15 | B | 24 | PHE | 0 | 0.011 | -0.006 | 30.812 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
| 16 | B | 25 | LYS | 1 | 0.938 | 0.938 | 35.242 | 0.069 | 0.069 | 0.000 | 0.000 | 0.000 | 0.000 |
| 17 | B | 26 | NME | 0 | 0.013 | 0.040 | 39.000 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 18 | B | 47 | ACE | 0 | -0.005 | -0.013 | 58.920 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 19 | B | 48 | LEU | 0 | 0.023 | 0.004 | 56.420 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 20 | B | 49 | ALA | 0 | -0.017 | -0.015 | 60.334 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 21 | B | 50 | ASP | -1 | -0.850 | -0.930 | 60.644 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
| 22 | B | 51 | ILE | 0 | 0.029 | 0.001 | 58.034 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 23 | B | 52 | LYS | 1 | 0.902 | 0.958 | 62.076 | 0.025 | 0.025 | 0.000 | 0.000 | 0.000 | 0.000 |
| 24 | B | 53 | SER | 0 | 0.027 | 0.000 | 64.069 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 25 | B | 54 | SER | 0 | 0.003 | 0.014 | 64.031 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 26 | B | 55 | LEU | 0 | -0.017 | 0.002 | 61.937 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 27 | B | 56 | VAL | 0 | -0.042 | -0.039 | 65.284 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 28 | B | 57 | ASN | 0 | 0.095 | 0.049 | 68.499 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
| 29 | B | 58 | GLU | -1 | -1.007 | -0.985 | 63.665 | -0.022 | -0.022 | 0.000 | 0.000 | 0.000 | 0.000 |
| 30 | B | 59 | SER | 0 | -0.057 | -0.030 | 67.424 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| 31 | B | 60 | GLU | -1 | -1.023 | -1.003 | 69.729 | -0.016 | -0.016 | 0.000 | 0.000 | 0.000 | 0.000 |
| 32 | B | 61 | NME | 0 | -0.061 | -0.013 | 72.004 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |