FRAG

• What is FRAG?
• BiSSCat Structure Search option
• Click here to see all contents in the help page.

What is FRAG?

A FRAG is one of the pre-calculated SUBSTRUCTURE types, and is defined as a fragment obtained when all rotatable bonds are cut. A rotatable bond is defined in the following way: only a single bond (saturated bond) that is not included in any ring substructure can be rotated. Amide bonds are not rotatable as they are known to have an energy barrier that prevents rotation. Two cases that have not yet been considered are where steric hindrance prevents rotation, and where an enzymic reaction helps rotation (such as occurs with cis-trans-isomerases). A bond consisting of one hydrogen atom and one non-hydrogen atom is also excluded. FRAG entries can be searched using Substructure Search option.

• S0000006 C-methyl
• S0002697 Amide bond
• S0042613 Guanine
• S0553422 Fravin
• S0591047 Naphthoquinone

BiSSCat Structure Search option

The BiSSCat Structure Search option can be used to look up compounds, functional groups, and substructures based on structural information or physicochemical properties.

• Elements: This option is used to specify the elements comprising functional groups or substructures (e.g. CO2 for carboxylate, C6O6 for sugars, etc). The number of hydrogen atoms is not taken into account unless specified explicitly.
• The database is divided into a number of subsections based on the type of data, as follows:
  • compound
  • fgroup: an index of functional groups and substructures
  • substructure: a collection of pre-calculated substructures
    • atom: an atom with physicochemical/electrochemical properties
    • vici: a central non-hydrogen atom and the atoms attached to it
    • bond: a chemical bond consisting of two non-hydrogen atoms
    • ring: a cyclic substructure
    • frag: a fragment obtained when all rotatable bonds are cut
    • skel: a carbon skeleton/backbone
    • conj: conjugated double bonds
• Properties: physicochemical and electrochemical properties