RMD Taken One Year Late

I have a question regarding taking an RMD late.  I turned 70 1/2 in 2016, and had a small deferred compensation account that I established just before I retired in 2004.  It was a small account, and I didn;’t keep track of it as well as I should have, and consequently didn’t see the notice from the account administrator regarding taking the RMD until after I filed my 2016 tax return in April 2017.   I filed the paperwork to start receiving 5 distributions to be taken annually over the following 5 years.   My first distribution was made in October of 2017, leaving me with no distribution or 1099R in 2016.  I will likely have to pay a penalty, but need to advise IRS of this late distribution, and I’m not sure how to handle it. I have the 2016 year-end statement showing the account value at the end of 2016, so I can estimate how much the 2016 distribution should have been (1/5 of the 2016 account value).  I have reviewed similar questions/answers regarding this topic that have been asked by others, but most of the ones I saw didn’t match my situation, and I am not sure how I should proceed.  It appears I need to file a Form 5329 for 2016 to explain and calculate the penalty.  I have downloaded a blank Form 5329 but the following questions come to mind:
 
Does it need to be filed with my 2017 return?
Independently by itself?
Or do I need to file an amended 2016 return and include Form 5329 with that?
 
Thank you for any guidance you can provide,  creswela.