As you mention the path in
/opt, it looks like you installed some third party package that does not come from Ubuntu repositiories and is not a native part of Ubuntu.
I would suggest uninstalling this and install native Apache, PHP and MySQL packages from Ubuntu repositories. From what you write, apparently they got already installed, so all you have to do is to uninstall the software you installed.
As for the question "how can I run my php project with the apache that is not from lampp?" I don't understand it, as I don't see any difference in running a PHP enabled website in Apache regardless of how you did install the software. In any case you need to put your PHP scripts in the appropriate directory that is served by Apache (you have to check in the Apache configuration file what directory it is, usually with default Apache configuration it should be
/var/www - you can of course add other directories if you like, or enable the "userdir" Apache module and use
/home/<user>/public_html) and then access the script via web browser.