The most simple definition of an atom is to use either its chemical symbol or its atomic number, thus:
Mg 1.23 1 1.23 1 1.23 1 or
12 1.23 1 1.23 1 1.23 1
If isotopes are used, then the atomic number option cannot be used.
In addition to the symbol or atomic number, a label can be added to an atom. The format of the label is: "(text)" (without the quotation marks), that is, "open curved bracket, text, closed curved bracket" The label should be immediately after the chemical symbol or after the isotopic mass, if present.
text can be up to38 characters long, but much shorter descriptions should normally be used, otherwise the layout of the output becomes very messy. text can be any description that does not involve any of the symbols ")", or "+", or "-" if MOZYME is used.
Examples of atom labels:
Mg(At center of porphyrin ring) 1.23 1 1.23 1 1.23 1
C( 17 PHE* 2) 1.19 1 4.59 1 -0.18 1
C14.0( 17 PHE* 2) 1.19 1 4.59 1 -0.18 1
If RESIDUES is present, the resulting ARC file will include labels on each atom.
Charges on individual charges for use in MOZYME can be specified by the symbols "+" and "-" in the atom labels. When the symbol "+" is present, the atom is given a unit positive charge, when "-" is present, the atom is given a unit negative charge. Avoid using these keywords unless necessary. Thus if the ethyl group, C2H5, is run with CHARGE=1, then the CH2 carbon will automatically be given a positive charge, if CHARGE=-1 is present, the it will be given a negative charge.
See also SETPI to explicitly assign p bonds, also CVB to explicitly make or break bonds.