Will I be penalized for the not knowing how much to pay for the sale of my rental property?

In 2021 we sold our rental property.  We were under the assumption that we wouldn't have to pay capital gains taxes since we make jointly under $80,800.   Now that we know that we will have to pay taxes on the allowed depreciation of the property, if it is over $1,000, do we have to pay a penalty.   If you have a tax payment due over $1000, are we penalized by the IRS (because we somehow should have known) and paid the tax bill during the quarterly tax payment dates?