What do you consider a "loop". If you are considering the outer while() to be a loop, then I would expect it to take a little while. You are iterating scalar(@list)*301*201 or over 500K times for each while.

The logic baffles me, however. Your inner loop is iterating over all of the items in @list1, and even going well beyond the end of the list, but it looks to me like you only want to loop over them with a step value of 3. Perhaps a loop like:

$indx = 0;
while ($indx < $count1) {
  $var1 = $num1 + $list1[$indx++];
  $var2 = $num2 + $list1[$indx++];
  $var3 = $list1[$indx++];

  # further code...
}
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Please note the difference between $list1[$indx...] and @list1[$indx...]. The first (my code) accesses a list element. The second (yours), if you use strict and warnings, should complain to you, and tell you to use the $list[...] form (that is, after you declare your variables with my).

Update: I just did some testing, and your code, 100 times, executes in 41.6 seconds. Mine (yes, it is doing something different, although I suspect, correct) executes in 8.3 seconds. I would also concur with the above poster that the Further code will make a huge difference.