"There is no pen."
Translation:لَيْسَ هُناك قَلَم.
yes, the order is a bit weird this way. The trick with the negative article ليس is the following:
Imagine you have a regular sentence with subject and predicative, and then just add ليس to its beginning.
So, for the example above, the original sentence is there is a pen which in Arabic is هناك قلم - as you can see, the word هناك comes first just like the English (there). Then we add ليس to make negative: ليس هناك قلم.
We can of course say قلم هناك (qalamun hunák), but the typical translation for this in English would be a pen is there (pointing to the place of the pen, and not the fact that a pen exists). Adding ليس here would make the sentence القلم ليس هناك (which is quite different because we are forced here to add "al" to the "pen" and make it definite).