How am i to explain to my kid later in life that his dad didnt want him?

I would not say his father did not want him. His father doesn't even know him, and won't if he never comes around. I would when the time seems right - when he asks and is old enough to understand a little - tell him his father did not want the responsibility and did not want to take the time to get to know and love him. It is not rejection of your son, but a failure to be a grownup himself.