use strict;
my %count;

# added gratuitous parentheses for embedded formula testing sake.
$_='Mo(P(H)3)4(CO)(NH2C2(H)5)';


# at each iteration do subformula with rigtmost left parenthesis. 
# quit when no more parenthesis
s/(.*)\((.*?)\)(\d*)/$1 . $2 x ($3 ? $3 : 1) /e while m/\(/;

s/([A-Z](?:[a-z])?)(\d*)/  $count{$1} += $2 ? $2  : 1 ;''/eg;

printf "%-2s %3d\n", $_, $count{$_} for sort keys %count;