You will mail in the 2016 Form 5329 separately (without amending your 2016 tax return). If you provide a reasonable explanation, and any documentation to support your RMD omission, the penalty may be waived.
Remember, you need to take the missed RMD as soon as possible if you haven't done so already.
Keep in mind, if you have other retirement plans, the combined RMD amount can be taken from one account. To do this, you would total all account values and then determine the RMD amount using this combined total. The combined total value is based on "the account balances" at the end of the prior calendar year. For your 2016 RMD, you will use the December 31, 2015 balances to determine your RMD amount.
I'm sharing this because you may have taken an RMD for another account. Perhaps there was excess that could apply towards your deferred compensation account RMD. Fingers crossed. Also, you will not mail the 2016 Form 5329 with your 2017 return.