PHP许可证生成器保护与paypal IPN冲突？

I'm going to integrate a license key generator in my web site, in the way that It can automatically generate license keys when occurs a paypal notification (IPN)... but my question is: what is the best way to protect the php file (that contains the method used to generate the key) and the private (a .pem file)?I'm going to integrate a license key generator