It's very hard to tell what it is over the internet, it's probably impossible. To be on the safe side I'd advise you to not run until you can do so without pain. Without seeing you and getting to know exactly where on the inside of the knee the pain is I can't say if it is just a tendon, a muscle or ligaments of the knee. You probably just overdid it on the exercises and need to take it easy for a while.
how is the mobility in the knee? can you move it through full range of motion without pain or the knee "locking up" (like a point you have to "click" it through)?