Because the leading digits are '0' padded, you can take advantage of that fact. They can be sorted by a simple lexical sort. Just another approach, but a simpler one.  :-)

map creates an anonymous array reference filled with the fields that have been split and assigned to the array reference. Because you sort the file lines, @sorted collects array references in sorted order;

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my @sorted = map [ split /[()\s]+/ ], sort <DATA>;    

print Dumper \@sorted;

__DATA__
00000(IDR) 86480 22 41.435 40.696 40.728167 0 FRM 3 
00015( B ) 9312 24 45.460 43.808 42.001 409 208 FRM 0
00002( P ) 35248 24 38.568 39.327 40.641 253 53 FRM 2
[download]

Output was:

$VAR1 = [
          [
            '00000',
            'IDR',
            '86480',
            '22',
            '41.435',
            '40.696',
            '40.728167',
            '0',
            'FRM',
            '3'
          ],
          [
            '00002',
            'P',
            '35248',
            '24',
            '38.568',
            '39.327',
            '40.641',
            '253',
            '53',
            'FRM',
            '2'
          ],
          [
            '00015',
            'B',
            '9312',
            '24',
            '45.460',
            '43.808',
            '42.001',
            '409',
            '208',
            'FRM',
            '0'
          ]
        ];
[download]

Update: Since the you have tabs, perhaps you are dealing with tab separated data, so perhaps a simple split /\t/ would do. If you wanted to get the values in the parentheses, you could easily extract them later. Just a thought. The change would be:
my @sorted = map{chomp; [ split /\t/ ]} sort <DATA>;