You'll enter that as an "estimated payment" by clicking on the Federal Taxes tab, then Deductions & Credits, then scroll down to Estimates & Other Taxes Paid and select Estimates.
This will take you to the Estimated Tax Payments page where you'll see categories for federal, state, and local estimates. Select Federal Estimated Taxes for 2016 and answer the question "yes" for did you pay federal estimated payments?
Then you'll see an input box for each quarter of the year. If you made the payment in the final quarter (or in January 2017) then enter the amount paid in the 4th Quarter box, and adjust the date to reflect your actual date paid.
This payment will appear on line 65 of the 1040.
