use strict;
use Data::Dumper;
use Sort::Key qw(nkeysort_inplace);

my @data;

while (<DATA>) {
	chomp;
	my @line = grep { defined $_ and length $_ } split /[()\t+\s+]/;
	push @data, \@line;
}
nkeysort_inplace { $_->[0] } @data;

print Dumper \@data;

__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