There are some penalties that are pretty straight forward and then there is the IRS Failure to File (FTF) penalty 6651(a)(1). The FTF is a 5% per month penalty to a maximum of 5 months or 25% from the due date or the extension date, whichever is later. If the FTF and the Failure to Pay (FTP) penalty run simultaneously, you only pay 4.5% for the FTF penalty and it caps out at 22.5% as the IRS is limiting the combination of the two penalties to 5% overall. That is the good news.
Did you know the Estimated Tax Penalty is actually an interest calculation? You calculate interest from each deposit due date with the net amount due and then you calculate the interest till the tax due date. The IRS uses the Federal interest rates for the calculations but they use a simple interest methodology versus daily compounding of interest.