Any penalty amount you paid with Forms 5329 is independent of any tax calculated on your 2016 tax return. You do not get "credit" for the penalty amounts on your 2016 tax return.
On your Forms 5329 you probably should have requested a waiver and not paid the penalty; the IRS would have billed you for the penalty if they denied the waiver (which is rare). If you did request a waiver of the penalty but (contrary to IRS instructions) paid the penalty anyway, the IRS will refund the penalty to you if they grant the waiver.
