Do I have to wait till I have it 3 years or 5 years to apply to become a US citizen if I have a green card with a IB6 category?

Generally, a foreign national must be a Permanent Resident for five years before becoming eligible to apply to become a naturalized U.S. citizen. An exception allowing a wait of only three years generally is available to someone who is married and living in a bona fide marriage with a U.S. citizen. (Note also that an application may be filed as early as 90 days before the end of the 5-year or 3-year period.) Since you no longer are living together in a bona fide marriage to a U.S. citizen, the three-year period will not apply to you. It would be wise for you to consult with an immigration attorney who, after learning all of the relevant information, could advise about eligibilities, options and strategies to attain your goals, and who then could offer legal representation in the often complex application process.