Here is a solution in Perl.

Working, tested code:

use strict;
use warnings;

my @field_names = qw(
  PdbId   MetalAtm MetalName MetalNumber MetalChn
  AtmName ResName  ResNumber ResChn      Distance
);
# Trick for concise sample data.
sub aref_to_href {
  my @field_values = @_;
  die unless @field_names == @field_values;

  my %h;
  @h{@field_names} = @field_values;

  \%h;
}

my @records_AoH = map { aref_to_href( @{$_} ) } (
  [ qw( 1nc7 MG MG 1501 - CL CL 1401 - 3.065 ) ],
  [ qw( 1nc7 MG MG 1501 - CL CL 1402 - 2.660 ) ],
  [ qw( 1pex CA CA  503 - CL CL  501 - 2.895 ) ],
  [ qw( 1qhu NA NA    3 - CL CL    1 - 3.096 ) ],
  [ qw( 1qjs NA NA  513 A CL CL  511 A 3.096 ) ],
  [ qw( 1rtg CA CA    2 - CL CL    1 - 3.079 ) ],
  [ qw( 1xj6 NA NA 5002 - CL CL 5001 - 2.628 ) ],
  [ qw( 2caj NI NI 1151 B CL CL 1150 B 3.551 ) ],
  [ qw( 2oa9 CD CD  911 - CL CL  800 - 2.291 ) ],
  [ qw( 2oa9 CD CD  913 - CL CL  801 - 2.403 ) ],
# Added for testing different ResName columns
  [ qw( 99zz CD CD  911 - CL YY  800 - 2.291 ) ],
  [ qw( 99zz CD CD  913 - CL YY  801 - 2.403 ) ],
);

my %count;
$count{ $_->{PdbId} }{ $_->{ResName} }++ foreach @records_AoH;

# Uncomment the second `grep` line if needed.
# (See the SQL discussion in the previous node).
my @filtered_AoH = grep { $count{$_->{PdbId}}{$_->{ResName}} >= 2 }
#                  grep { $_->{ResName} eq 'CL' }
                   @records_AoH;

my $template = '%5s %8s %9s %11s %8s %7s %7s %9s %6s %8s';
printf "$template\n", @field_names;
foreach (@filtered_AoH) {
  printf "$template\n", @{ $_ }{@field_names};
}
[download]

Output:

PdbId MetalAtm MetalName MetalNumber MetalChn AtmName ResName ResNumbe
+r ResChn Distance
 1nc7       MG        MG        1501        -      CL      CL      140
+1      -    3.065
 1nc7       MG        MG        1501        -      CL      CL      140
+2      -    2.660
 2oa9       CD        CD         911        -      CL      CL       80
+0      -    2.291
 2oa9       CD        CD         913        -      CL      CL       80
+1      -    2.403
 99zz       CD        CD         911        -      CL      YY       80
+0      -    2.291
 99zz       CD        CD         913        -      CL      YY       80
+1      -    2.403
[download]

Output with the second `grep` uncommented:

PdbId MetalAtm MetalName MetalNumber MetalChn AtmName ResName ResNumbe
+r ResChn Distance
 1nc7       MG        MG        1501        -      CL      CL      140
+1      -    3.065
 1nc7       MG        MG        1501        -      CL      CL      140
+2      -    2.660
 2oa9       CD        CD         911        -      CL      CL       80
+0      -    2.291
 2oa9       CD        CD         913        -      CL      CL       80
+1      -    2.403
[download]