If you have taxes owed that were not paid as of April 18, 2017 on the 2016 tax return, there will be a failure to pay penalty and interest on the amount of the taxes owed and not paid. Since you filed an extension request, there will not be a failure to file penalty if you file the return on or before October 16, 2017. The IRS will send you a bill in the mail for the penalties owed after they receive your tax payment.
See this IRS website for penalties - https://www.irs.gov/businesses/small-businesses-self-employed/understanding-penalties-and-interest
