You probably should file an amended return since it should be reported on line 59 on the 1040 form but the IRS will probably accept a stand alone 5329. If they send a letter you can just explain that it would have no effect on anything else on the return.
Be sure that you have removed the excess before the filing date with a normal distribution or the penalty will repeat every year that it remains in the Roth. Since you will pay the 2016 penalty, it is not necessary to remove any earnings, only the excess contribution.
2916 5329 form: https://www.irs.gov/pub/irs-prior/f5329--2016.pdf
2016 5329 instructions: https://www.irs.gov/pub/irs-prior/i5329--2016.pdf
Where to file: https://www.irs.gov/filing/where-to-file-addresses-for-taxpayers-and-tax-professionals-filing-form-1...
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**
