The IRS requires you to pay your tax as you earn it. If you paid the 110% mostly at the end of the year, the IRS deemed your earlier quarters "underpaid". If you paid the 110% in four equal, timely installments and still have a penalty, ensure that "110%" was calculated based on your total tax liability from the previous year, not just the amount you owed at filing.
Review Form 2210 to see how your penalty was calculated by quarter.
Here's more detailed info on Form 2210.
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