If you are having problem to connect MySQL from Remote System, please check the following things on the Webserver Control Panel or Cpanel before connecting it.
1. Is there any local firewall running on the server, do you have the connecting servers listed in
WHM -> SQL Services »Additional MySQL Access Hosts _and_ cPanel -> Remote MySQL?
2. If so, you've to also add a rule to CSF to allow MySQL connections. For that, go to
WHM -> Plugins -> Configserver CSF Firewall -> Firewall Allow IPs.
And, after that, you'll see that there is a line:
tcp|in|d=3306|s=88.xxx.xxx.xx (your connecting computer's IP address)
which only allows incoming MySQL connections from your IP Address.