To resequence the atoms in a data set, to put them into the standard PDB order, use RESEQ.
By default, when hydrogen atoms are added or removed, when keywords ADD-H or SITE are used, or if the input data set is a pure PDB file, the atom sequence will be changed to that of the standard PDB format, i.e., all atoms in a given residue will be together in the new data-set. If this is not wanted, use NORESEQ.
Be aware that the PDB convention cannot, and does not, uniquely define the order of atoms in a residue. This is because there are sometimes two exactly equivalent ways of labeling an atom. This situation occurs in valine, leucine, arginine, phenylalanine, and tyrosine, and when two or more hydrogen atoms are attached to the same atom. This is not very important however, because operations in MOPAC that depend on atom sequences can correct most simple errors of this type, unless NOSWAP is present, and if the second sequence is different to the first sequence then the second sequence will be changed during the run to conform with the first sequence.