Just write straight to the files:

#!/usr/bin/perl

# http://perlmonks.org/?node_id=1167222

use strict;
use warnings;

my %files;

while(<DATA>)
  {
  /(.*\S)\s+(\S+)/ or next;
  $files{abs $2} or open $files{abs $2}, '>', "output_@{[abs $2]}.txt"
+ or die;
  printf {$files{abs $2}} "%3d  %3d  %s\n", $2, $., $1;
  }
close $_ for values %files;

system 'more output_*.txt | cat';  # for debugging

__DATA__
-59.077    89.301   115.664       7
-61.251    77.435   117.760      -6
-60.950    71.712   116.061      -7
-56.247    83.685   114.576       1
-59.263    76.107   112.555      -2
-59.895    65.296   111.185       3
-60.141    63.694   111.257      -3
-61.667    63.707   116.937       2
-58.722    60.429   111.307      -1
-57.511    42.922   112.108       6
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