Here is some example code. Your file has blank lines, i.e. things other than ATOM lines.
That is fine.
What we want is a regex that only modifies ATOM lines with a new column #2 (index 1)
In Perl it is possible for the second part of a substitution regex to be executable code.
I think this does what you want?
Note that /$1.$num++.$3, the "." is not regex "dot" it is concatenation "operator".
Perl regex is extremely powerful! 
#/usr/bin/perl/

use strict;
use warnings;

my $num=1;
while (my $line = <DATA>) 
{
    $line =~ s/^(ATOM\s+)(\d+)(.*)/$1.$num++.$3/e;  #e flag means exec
+ute
    print $line;
}

=Prints
ATOM 1 H5T THY C 1 107.274 35.359 -9.821 0.00 0.00 N1 H

ATOM 2 O5' THY C 1 107.686 36.230 -9.553 1.00 0.00 N1 O

ATOM 3 C5' THY C 1 108.813 35.973 -8.710 1.00 0.00 N1 C

ATOM 4 H5' THY C 1 109.513 35.493 -9.239 0.00 0.00 N1 H

ATOM 5 H5'' THY C 1 108.495 35.550 -7.861 0.00 0.00 N1 H

ATOM 6 N1 THY C 1 107.956 38.157 -5.232 1.00 0.00 N1 N

ATOM 7 C6 THY C 1 107.862 39.006 -4.149 1.00 0.00 N1 C

ATOM 8 H6 THY C 1 108.479 39.755 -3.910 0.00 0.00 N1 H

ATOM 9 C2 THY C 1 107.024 37.166 -5.449 1.00 0.00 N1 C

ATOM 10 O2 THY C 1 107.071 36.398 -6.397 1.00 0.00 N1 O

ATOM 11 N3 THY C 1 106.027 37.104 -4.506 1.00 0.00 N1 N
=cut


__DATA__
ATOM 9 H5T THY C 1 107.274 35.359 -9.821 0.00 0.00 N1 H

ATOM 10 O5' THY C 1 107.686 36.230 -9.553 1.00 0.00 N1 O

ATOM 11 C5' THY C 1 108.813 35.973 -8.710 1.00 0.00 N1 C

ATOM 12 H5' THY C 1 109.513 35.493 -9.239 0.00 0.00 N1 H

ATOM 13 H5'' THY C 1 108.495 35.550 -7.861 0.00 0.00 N1 H

ATOM 14 N1 THY C 1 107.956 38.157 -5.232 1.00 0.00 N1 N

ATOM 15 C6 THY C 1 107.862 39.006 -4.149 1.00 0.00 N1 C

ATOM 16 H6 THY C 1 108.479 39.755 -3.910 0.00 0.00 N1 H

ATOM 17 C2 THY C 1 107.024 37.166 -5.449 1.00 0.00 N1 C

ATOM 18 O2 THY C 1 107.071 36.398 -6.397 1.00 0.00 N1 O

ATOM 19 N3 THY C 1 106.027 37.104 -4.506 1.00 0.00 N1 N

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In reply to Re: renumber entries in column? by Marshall
in thread renumber entries in column? by aria

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