Or without the  while loop (the file  chem.data holds the data specified in the OP):

>perl -wMstrict -ne
"print qq{$_\t}, join(qq{\t}, /([A-Z][a-z]?(\d*))(?=.*(\n?))/g);
"
chem.data
CH4N2O
        C
        H4      4
        N2      2
        O
C9H12N2O6
        C9      9
        H12     12
        N2      2
        O6      6
C5H11NO2
        C5      5
        H11     11
        N
        O2      2
C5H4N4O2
        C5      5
        H4      4
        N4      4
        O2      2
C10H11N4O9P
        C10     10
        H11     11
        N4      4
        O9      9
        P
C10H12N4O6
        C10     10
        H12     12
        N4      4
        O6      6
C5H10O5
        C5      5
        H10     10
        O5      5
C5H12O5
        C5      5
        H12     12
        O5      5
C5H10O5
        C5      5
        H10     10
        O5      5
C27H44O
        C27     27
        H44     44
        O
C1694H2993O101
        C1694   1694
        H2993   2993
        O101    101
[download]

Note, however, that this approach:

• produces a superfluous tab immediately before the newline in each 'individual chemical component' output line;
• produces oddball output for the last record (i.e., the last line) in the data file if it is not newline-terminated.