Retirement tax questions

I think you mean that you owe a penalty from owing taxes as a result of taking a distribution from your IRA.  You mention that there is a capital gain involved, but that would not affect the taxability of your traditional IRA withdrawal. Accept in rare cases when you take a complete withdrawal of all your IRA funds during the year, you simply pay ordinary income tax on all the money you withdraw from your IRA (from deducted contributions), regardless of whether there are capital gains or losses involved. This is so since you deducted your contributions to your traditional IRA, so any monies withdrawn will be taxed since they were deducted when you put them into the plan, or represent earnings on the monies contributed. 

You may be able to reduce the penalty for late payment of tax by using the underpayment penalties routine in the Other Tax Situations tab in TurboTax. You will see it under Additional Tax Payments: