You can and should need to amend you r 2016 tax return and file Form 5329 to calculate the excise tax.
Follow the instructions in How to Amend (Change or Correct) a Return You Already Filed.
If you missed the deadline due to a reasonable cause, you may ask the IRS to waive the 50% excise tax. The request for waiver may be included in a letter of explanation, which you attach to your tax return (Form 1040X) along with your Form 5329. When requesting a waiver, do not pay the excess accumulation penalty up front. Instead, follow the instructions for requesting a waiver in the Instructions for Form 5329. If the IRS does not honor your waiver request, you will be notified.
The amended tax return and the attached waiver request must be filed by mail.
Instructions for Form 5329: https://www.irs.gov/pub/irs-pdf/i5329.pdf