A PDB file can be generated from a normal MOPAC Z-matrix by using PDBOUT. Any comments in the MOPAC data set (lines starting with an asterisk, '*') that look like PDB lines are put at the start of the pdb file.
Normally, the labeling of the atoms in the PDB file will be the same as that of the data set, whether it is a MOPAC-style data set or a PDB file data set. If there is no labeling, or if RESIDUES or RESIDUES0 is present, then the atom labels will be constructed from the topology of the system. If a residue is not one of the standard 20 residues, it will be labeled "UNK", for unknown. If it is a modified standard residue, for example the retinal group in rhodopsin is a modified lysine residue, then keyword XENO can be used to give it a standard name.
Data-set:
*HEADER WORKED EXAMPLE *TITLE A TRI-PEPTIDE *REMARK 3 DATA USED IN REFINEMENT. *CRYST1 60.850 60.850 108.400 90.00 90.00 120.00 P 63 6 * * This line, the previous line, and the following comments will NOT be in the PDB file! * START_RES and CHAINS are optional * The defaults are START_RES=(1) CHAINS=(A) 0scf pdbout RESIDUES start_res=(10) chains=(E) N 0.00000000 +1 0.0000000 +1 0.0000000 +1 C 1.45099200 +1 0.0000000 +1 0.0000000 +1 C 2.07379016 +1 1.3847514 +1 0.0000000 +1 O 3.16479845 +1 1.5510512 +1 0.5346009 +1 C 1.98010532 +1 -0.7816083 +1 -1.2061384 +1 S 2.91021593 +1 -2.2138976 +1 -0.5916694 +1 H 1.78639414 +1 -0.4791530 +1 0.9215042 +1 H 2.66987764 +1 -0.1661407 +1 -1.7918980 +1 H 1.16732537 +1 -1.1139738 +1 -1.8582339 +1 H 3.33442776 +1 -2.8105177 +1 -1.7526284 +1 H -0.45944146 +1 -0.5439661 +1 -0.7191795 +1 H -0.45944146 +1 -0.5439661 +1 0.7191795 +1 N 1.41779186 +1 2.3818640 +1 -0.5930817 +1 C 1.96005201 +1 3.7395708 +1 -0.5873182 +1 C 0.87144992 +1 4.6925379 +1 -0.0859199 +1 O -0.30894710 +1 4.3852105 +1 -0.2277412 +1 C 2.58984680 +1 4.0757744 +1 -1.9613244 +1 C 3.95504011 +1 3.4174209 +1 -2.2109945 +1 C 5.13263384 +1 4.0760823 +1 -1.8023387 +1 C 6.39390379 +1 3.5338821 +1 -2.0746443 +1 C 6.51251534 +1 2.3040175 +1 -2.7409980 +1 C 5.35236761 +1 1.6339502 +1 -3.1585724 +1 C 4.08327785 +1 2.1864831 +1 -2.9055825 +1 H 2.75184646 +1 3.8479695 +1 0.1426395 +1 H 2.74129210 +1 5.1566073 +1 -1.9998683 +1 H 1.90797747 +1 3.8313152 +1 -2.7790034 +1 H 5.07815939 +1 5.0182815 +1 -1.2765870 +1 H 7.28256125 +1 4.0711027 +1 -1.8000485 +1 H 3.20599873 +1 1.6658896 +1 -3.2578962 +1 H 5.45626342 +1 0.6951745 +1 -3.6940611 +1 H 7.49097179 +1 1.8927662 +1 -2.9377954 +1 H 0.46717507 +1 2.2471723 +1 -0.9238687 +1 N 1.23320241 +1 5.8266104 +1 0.5208984 +1 C 0.26492485 +1 6.8517935 +1 0.8919516 +1 C 0.31272594 +1 7.9119232 +1 -0.2244470 +1 O 1.39993820 +1 8.1980713 +1 -0.7103118 +1 C 0.56056668 +1 7.4759401 +1 2.2689288 +1 C 1.27996141 +1 6.5571211 +1 3.2666683 +1 C 1.60234572 +1 7.3416902 +1 4.5312735 +1 O 2.41760942 +1 8.2681242 +1 4.3634539 +1 O 1.02819708 +1 7.0347336 +1 5.6046982 +1 H -0.71623918 +1 6.4059436 +1 1.0059751 +1 H -0.39373680 +1 7.7519156 +1 2.7226369 +1 H 1.15143293 +1 8.3863594 +1 2.1332694 +1 H 2.23164513 +1 6.2323719 +1 2.8483475 +1 H 0.67739509 +1 5.6796776 +1 3.4974943 +1 H 2.66377974 +1 8.7825627 +1 5.0596961 +1 H 2.20037691 +1 6.1233889 +1 0.4986194 +1 H -0.81037727 +1 8.4883333 +1 -0.6911228 +1