<p.It looks like your data is column oriented. If it is, the substr() would be a better choice.

#!/usr/bin/perl

use strict;
use warnings;

use Data::Dumper;

# Make Data::Dumper pretty
$Data::Dumper::Sortkeys = 1;
$Data::Dumper::Indent   = 1;

# Set maximum depth for Data::Dumper, zero means unlimited
local $Data::Dumper::Maxdepth = 0;

my @data;
while( <DATA> ){
  print;
  chomp;
  @data = ();

  $data[0] = substr( $_, 0, 7 );
  $data[1] = substr( $_, 9, 35 );
  $data[2] = substr( $_, 45, 8 );
  $data[3] = substr( $_, 54, 1 );
  $data[4] = substr( $_, 56, 1 );
  $data[5] = substr( $_, 58, 1 );
  print '@data ', Dumper \@data;
}

__DATA__
1xny_01  PROPIONYL-COA CARBOXYLASE COMPLEX B -0.8192  A A A
1xqd_00  CYTOCHROME P450 55A1                -46.5601 A B A
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