Because it is a Roth IRA (not traditional), you never pay penalties for withdrawing any amount up to your total contributions amount. This is because you are funding it with after tax money.
But it sounds like your Roth had $11K in it and you zeroed it out? If you were less than 59.5 years old at the time you made the withdrawal, then if you did not return anything to the account, then you would pay tax on the 6K as income this year at your normal tax rate, plus an additional 10% penalty on that 6K ($600). The 5K in contributions is not taxable. Now, since it's been more than 60 days since you withdrew the money, you cannot put the 6K in earnings back in without paying the penalty, however, you can still contribute $5500 per year (or $6500 if you're over 50). So, you can put back $5500 and then you would only have to pay tax + 10% on the $500 difference.
Update: I would recommend talking to an accountant. The fact that you intended to buy a house might provide a mechanism for getting the money back in if you wish. If this was your first house or you have not owned a home in the last 2 years, then you would be considered a "first-time homebuyer" and there is a special exception allowing you to remove 10K without penalty. If you end up not purchasing the home, you have 120 days to contribute those funds back in (treated as a rollover- thank you littleadv for the link to this). As for the final 1K overage, I believe you can count that towards your $5500/yr contribution when you put the entire amount back.
Lastly, after digging into this, you have hit so many edge cases with your scenario (6K in earnings being between 5500 for under 50 and 6500 for over 50, it's been 70 days which is between the 60 day normal cutoff and the 120 day extended cutoff for home purchase falling through, and 11K total being just over the 10K cutoff for the same), that I'm starting to wonder if this is some sort of contrived case for an accounting exam!?