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 to 38 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
A special type of atom label is used in protein work. These labels are
exactly 26 characters long, and correspond to the first 26 characters of a PDB
file. Labels for atoms in proteins can be generated in two ways:
(A) When a PDB file is read in, the resulting MOPAC data set has the atoms labeled automatically. See also atom numbering.
(B) When a MOPAC data set is read in, and there is enough information in the atom labels to allow the PDB atom labels to be written.
If RESIDUES is present, the resulting ARC file will include labels on each atom. If RESIDUES is used, all existing labels, including labels defining individual charges, will be replaced.
Charges on individual atoms for use in MOZYME can be specified by the symbols "+", "0", and "-" in the atom labels. When the symbol "+" is present, the atom is given a unit positive charge, when "0" is present, the atom will be given a zero charge, and when "-" is present, the atom is given a unit negative charge. The zero charge option is useful when metal ions in enzymes are being modeled, thus the MoO2 moiety should have MoIV, but by default, Mo is MoVI, i.e., [MoO2 ]2+. To specify that MoIV should be used, after Mo add a "0" to give Mo0. 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 π bonds, also CVB to explicitly make or break bonds.