I have got a replica content problem where there are 2 cases of my website indexed in the search engines:

the very first is the particular domain: http://domain.com

the seconds is my WHM/CPanel preview from the account: http://123.456.78.9/~/domain

Can there be in whatever way to redirect the IP version towards the real domain?

Do this

RewriteEngine on  
RewriteBase /
RewriteCond %{HTTP_HOST} ^123.456.78.9$ [NC] 
RewriteRule (.*) http://domain.com/$1 [R=301,L]