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Alignment Troubles

Having troubles with assigning the rotate to a program I'm working on. The part in question is roughly a vertical rectangle. The mating face is my z level and origin. In the top center of mating face is a dowel pin hole that is x and y origin and there is a second dowel hole on the bottom right of mating face. I'm trying to get the y axis to be vertically up the centerline of part but have no idea how to since the two holes are not in line with each other and there is no angle callout between them. Thanks in advance.