You were close. That should do it:
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;

[download]
It prints: 
C    3
H   19
Mo   1
N    1
O    1
P    4

[download]

-- stefp

In reply to Re: Re: Re: Regexps for Parsing Brackets in Chemical Formulae by stefp
in thread Regexps for Parsing Brackets in Chemical Formulae by Elgon

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