Apple has been ordered to pay $208.5 million for violating a patent, despite holding a patent on the same technology.

The patent, on the Cover Flow system for browsing albums visually, is one of three patents held by Mirror Worlds that Apple was found to have infringed. The others were for the Time Machine backup file and the Spotlight search system.

The court awarded the same penalty for each offense, totaling $625.5 million, one of the largest ever awards in a patent suit. The large amount is partly because Apple was held to have willfully infringed the patent, rather than it being unintentional.

Mirror Worlds was formed by David Gelernter, a professor of computer science at Yale. He was among the people injured by letter bombs from Theodore Kacynski, better known as the Unabomber.

What makes the case particularly complicated is that Apple was itself granted a patent on the Cover Flow system earlier this year. The two patents aren’t necessarily incompatible (they may deal with different aspects of the same technology), but it’s clearly far from an open and shut case. Legal records show the Mirror Worlds vs LLC case has been a particularly complex legal process running for three and a half years.

Apple has now filed an emergency motion seeking a stay of the ruling: that would mean the company wouldn’t have to pay up until any appeal has been heard and ruled upon.

Though Apple hasn’t detailed any appeal, it says there are “outstanding issues” with two of the patents. It’s also taking issue with the decision to apply the damages figure to each of the three claims rather than as a single penalty.