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selected data collection: 1,2,3

CompChem-Database


CompChem-DataBase (CCDB) belongs to CompChem Laboratory, Minia University, Egypt.

All listed database were prepared as following:
  • All multimolecules comounds were splitted and indeicated with _m.
  • All molecules were then subjected to conformational analysis using Omega software and the most stable conform was seleted.
  • Protonation state and tautomerization for each molecule was examined. If molecule has protontation state differnt from the one listed in the original database, they are termed as _p0 and _p7, respectively. _t0 and _t1 refer to different tatuomers.
  • If the Omega software could not predict the 3D structure due to strick stereo configuration, the molecule is named as s0 and the 3D structure will be prepared by --gen3d option in babel.
  • If sum of the gast partial atomic charges is different from the sum of MOPAC partial charges, the molecule is named as c0 to highlight this issue
  • All molecules were then subjected to molecular minmization at MMFF94S level using SZY and atomic charges were assigned according to Gast. method
  • If the charge of the pdbqt file equals the charge of the mol2 file, but the charge of the pdbqt file does NOT equal the charge of the QM file, so the molecule is named with _c0
  • If the charge of the pdbqt file does NOT equal the charge of the mol2 file, but the charge of the pdbqt file equals the charge of the QM file, so the molecule is named with _c1
  • If the charge of the pdbqt file does NOT equal the charge of the mol2 file, but the charge of the pdbqt file does NOT equal the charge of the QM file, so the molecule is named with _c2

    • Available data collections:

    [S] = structures, [R] = reactions

    Current selection:

    DrugBank DatabaseThis data collection was imported from an SDF file.
    ChEBI DatabaseThis data collection was imported from an SDF file.
    ChEMBL DatabaseThis data collection was imported from an SDF file.

     

    MolDB6 2014