FMODB ID: 82LKY
Calculation Name: 1G3J-D-Xray372
Preferred Name: Catenin beta-1
Target Type: SINGLE PROTEIN
Ligand Name:
ligand 3-letter code:
PDB ID: 1G3J
Chain ID: D
ChEMBL ID: CHEMBL5866
UniProt ID: P35222
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.
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 | 34 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -83091.708384 |
---|---|
FMO2-HF: Nuclear repulsion | 70397.329041 |
FMO2-HF: Total energy | -12694.379343 |
FMO2-MP2: Total energy | -12731.678495 |
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(D:2:PRO)
Summations of interaction energy for
fragment #1(D:2:PRO)
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. |
0.014 | 2.464 | -0.034 | -1.327 | -1.09 | 0.001 |
Interaction energy analysis for fragmet #1(D:2:PRO)
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 | D | 4 | LEU | 0 | -0.001 | 0.006 | 3.795 | 0.245 | 2.695 | -0.034 | -1.327 | -1.090 | 0.001 |
4 | D | 5 | ASN | 0 | -0.057 | -0.026 | 6.462 | -0.139 | -0.139 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | D | 6 | SER | 0 | -0.006 | -0.004 | 8.878 | -0.141 | -0.141 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | D | 7 | GLY | 0 | 0.009 | 0.009 | 11.269 | 0.046 | 0.046 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | D | 8 | GLY | 0 | -0.017 | -0.014 | 12.147 | -0.008 | -0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | D | 9 | GLY | 0 | 0.003 | -0.006 | 12.874 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | D | 10 | ASP | -1 | -0.859 | -0.915 | 14.249 | -0.086 | -0.086 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | D | 11 | GLU | -1 | -0.956 | -0.978 | 16.745 | -0.095 | -0.095 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | D | 12 | LEU | 0 | -0.104 | -0.050 | 19.861 | 0.008 | 0.008 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | D | 13 | GLY | 0 | -0.037 | -0.013 | 20.223 | 0.011 | 0.011 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | D | 14 | ALA | 0 | -0.054 | -0.033 | 17.832 | -0.004 | -0.004 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | D | 15 | ASN | 0 | -0.011 | -0.013 | 13.789 | -0.031 | -0.031 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | D | 16 | ASP | -1 | -0.912 | -0.940 | 17.888 | 0.068 | 0.068 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | D | 17 | GLU | -1 | -0.886 | -0.961 | 15.775 | 0.267 | 0.267 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | D | 18 | LEU | 0 | -0.062 | -0.028 | 19.872 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | D | 19 | ILE | 0 | 0.035 | 0.024 | 21.038 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | D | 20 | ARG | 1 | 0.900 | 0.931 | 18.773 | -0.172 | -0.172 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | D | 21 | PHE | 0 | 0.036 | 0.021 | 24.098 | 0.005 | 0.005 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | D | 22 | LYS | 1 | 0.904 | 0.936 | 24.001 | -0.124 | -0.124 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | D | 23 | ASP | -1 | -0.943 | -0.957 | 29.031 | 0.070 | 0.070 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | D | 24 | GLU | -1 | -0.959 | -0.963 | 32.409 | 0.059 | 0.059 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | D | 40 | ASP | -1 | -0.929 | -0.975 | 52.611 | 0.028 | 0.028 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | D | 41 | LEU | 0 | 0.056 | 0.021 | 51.583 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | D | 42 | ALA | 0 | -0.070 | -0.042 | 56.011 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | D | 43 | ASP | -1 | -0.857 | -0.929 | 59.403 | 0.019 | 0.019 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | D | 44 | VAL | 0 | 0.004 | 0.011 | 56.117 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
29 | D | 45 | LYS | 1 | 0.948 | 0.961 | 56.244 | -0.024 | -0.024 | 0.000 | 0.000 | 0.000 | 0.000 |
30 | D | 46 | SER | 0 | -0.002 | 0.004 | 60.103 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
31 | D | 47 | SER | 0 | 0.013 | -0.008 | 62.808 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
32 | D | 48 | LEU | 0 | -0.063 | -0.009 | 58.846 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
33 | D | 49 | VAL | 0 | -0.048 | -0.012 | 62.803 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
34 | D | 50 | ASN | 0 | -0.051 | -0.021 | 65.335 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |