In general ownerships and permissions can be restored.
For example if you modified only PP installation directory, you may run these commands in order to bring everything back to order:
Permissions and ownerships reset to their default settings:
for p in $(rpm -qa | grep plesk); do rpm --setugids $p; done
for p in $(rpm -qa | grep psa); do rpm --setugids $p; done
for p in $(rpm -qa | grep plesk); do rpm --setperms $p; done
for p in $(rpm -qa | grep psa); do rpm --setperms $p; done
The order in which you execute the commands is important.
You can also verify the correctness of the ownerships you have reset by comparing them with those on a working server. If all those actions fail then you can always re-install or update Plesk to the last version (11.5: supports Nginx) the user rights will be updated.
When ready add your nginx user to the root group using usermod
command.