My father's will allowed my step-mother to live in the house if she paid the mortgage & HOA dues. She made no payments. My company owns the property. How do I take loss.

It depends. The property was used for personal reasons and any expenses during that time would not be deductible unless there was a rental agreement, which seems unlikely from your comments. 

If you owned (not your company) the property while she lived it it, you could take mortgage interest paid by you as your second home, and property taxes, if applicable. And only if you itemize your deductions. If you use the standard deduction there would be nothing to deduct.

• Can I deduct mortgage interest on a second home?

If you rent the property, from the time it is available for rent then your company can deduct expenses paid for operating the home, such as the HOA fees, mortgage interest, taxes, utilities, insurance, etc.