Well, you certainly are an attractive lady- no doubt about that! But chemistry, IMO, is that interestingly, unexplainable feeling that people just can't know how it will manifest itself, until a couple has had a chance to be with each other more than once or twice! As you say:
At least he was nice about it and didn't try to get in my pants just because I had a vagina.
If that's the case, maybe he's still worth continuing to pursue, if both of you are still interested in at least being friends and seeing each other. You never know how things might work out!
Just my 2¢ worth and then, I may have change coming back!