FMODB ID: R5Z78
Calculation Name: 2GL7-E-Xray372
Preferred Name: beta-catenin-B-cell lymphoma 9 protein complex
Target Type: PROTEIN COMPLEX
Ligand Name:
ligand 3-letter code:
PDB ID: 2GL7
Chain ID: E
ChEMBL ID: CHEMBL3885525
UniProt ID: O00512
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 | 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 |
LigandCharge | |
Software | ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP) |
Total energy (hartree)
FMO2-HF: Electronic energy | -63350.970321 |
---|---|
FMO2-HF: Nuclear repulsion | 52658.129567 |
FMO2-HF: Total energy | -10692.840754 |
FMO2-MP2: Total energy | -10724.160141 |
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(E:12:LEU)
Summations of interaction energy for
fragment #1(E:12:LEU)
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. |
-0.38 | 1.353 | -0.025 | -0.9 | -0.807 | 0.001 |
Interaction energy analysis for fragmet #1(E:12:LEU)
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 | E | 14 | ALA | 0 | -0.042 | -0.016 | 3.816 | 0.737 | 2.470 | -0.025 | -0.900 | -0.807 | 0.001 |
4 | E | 15 | ASN | 0 | 0.002 | 0.000 | 6.632 | -0.283 | -0.283 | 0.000 | 0.000 | 0.000 | 0.000 |
5 | E | 16 | ASP | -1 | -0.896 | -0.934 | 8.003 | -0.908 | -0.908 | 0.000 | 0.000 | 0.000 | 0.000 |
6 | E | 17 | GLU | -1 | -0.970 | -0.994 | 10.671 | 0.199 | 0.199 | 0.000 | 0.000 | 0.000 | 0.000 |
7 | E | 18 | LEU | 0 | -0.059 | -0.026 | 14.031 | -0.038 | -0.038 | 0.000 | 0.000 | 0.000 | 0.000 |
8 | E | 19 | ILE | 0 | 0.016 | 0.009 | 17.622 | 0.032 | 0.032 | 0.000 | 0.000 | 0.000 | 0.000 |
9 | E | 20 | SER | 0 | -0.065 | -0.030 | 20.799 | -0.012 | -0.012 | 0.000 | 0.000 | 0.000 | 0.000 |
10 | E | 21 | PHE | 0 | 0.039 | 0.005 | 22.975 | 0.006 | 0.006 | 0.000 | 0.000 | 0.000 | 0.000 |
11 | E | 22 | LYS | 1 | 0.891 | 0.930 | 26.884 | 0.030 | 0.030 | 0.000 | 0.000 | 0.000 | 0.000 |
12 | E | 23 | ASP | -1 | -0.902 | -0.940 | 30.289 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
13 | E | 24 | GLU | -1 | -0.970 | -0.981 | 33.200 | -0.035 | -0.035 | 0.000 | 0.000 | 0.000 | 0.000 |
14 | E | 25 | GLY | 0 | -0.025 | -0.003 | 36.326 | -0.002 | -0.002 | 0.000 | 0.000 | 0.000 | 0.000 |
15 | E | 26 | GLU | -1 | -0.978 | -1.010 | 38.746 | -0.017 | -0.017 | 0.000 | 0.000 | 0.000 | 0.000 |
16 | E | 27 | GLN | 0 | -0.079 | -0.022 | 42.432 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
17 | E | 28 | GLU | -1 | -0.941 | -0.961 | 45.180 | -0.020 | -0.020 | 0.000 | 0.000 | 0.000 | 0.000 |
18 | E | 40 | ASP | -1 | -0.893 | -0.953 | 50.594 | -0.034 | -0.034 | 0.000 | 0.000 | 0.000 | 0.000 |
19 | E | 41 | LEU | 0 | 0.019 | -0.002 | 50.432 | -0.001 | -0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
20 | E | 42 | ALA | 0 | -0.034 | -0.012 | 54.462 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |
21 | E | 43 | ASP | -1 | -0.850 | -0.926 | 57.870 | -0.027 | -0.027 | 0.000 | 0.000 | 0.000 | 0.000 |
22 | E | 44 | VAL | 0 | -0.002 | 0.001 | 53.612 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
23 | E | 45 | LYS | 1 | 0.928 | 0.954 | 56.227 | 0.026 | 0.026 | 0.000 | 0.000 | 0.000 | 0.000 |
24 | E | 46 | SER | 0 | -0.001 | -0.017 | 58.707 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
25 | E | 47 | SER | 0 | -0.060 | -0.028 | 59.270 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
26 | E | 48 | LEU | 0 | -0.012 | 0.004 | 56.969 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
27 | E | 49 | VAL | 0 | -0.054 | -0.022 | 60.469 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
28 | E | 50 | ASN | 0 | -0.042 | 0.000 | 63.448 | 0.001 | 0.001 | 0.000 | 0.000 | 0.000 | 0.000 |