Almost all the custom changes that can be made in Plesk but not through the GUI, must be set in vhost.conf file for each domain.
The location of this file is under $DOMAIN$/conf/
$DOMAIN$ should be replaced with a real path to domain home. For example it could be/var/www/vhosts/domain.com/ (on Fedora with Plesk) or/usr/local/psa/home/vhosts/domain.com (on FreeBSD with Plesk). As you can see this location may vary depending on Plesk version and OS. To find where the vhosts home is look into /etc/psa/psa.conf for HTTPD_VHOSTS_D variable set.
Inside $DOMAIN$/conf/vhost.conf you can change the options with the appropriate apache format. Here is an example about how to set open_basedir with 'none' option:
<Directory /var/www/vhosts/somedomain.com/httpdocs>
php_admin_flag engine on
php_admin_value open_basedir none
</Directory>
In case you want to do the same for SSL, just create a file 'vhost_ssl.conf'
Then put the settings inside to be for the secured document root folder :
<Directory $DOMAIN$/httpdocs>
php_admin_value open_basedir "$DOMAIN$/httpdocs:/tmp:/ADD_PATH"
</Directory>
There is one thing you have to do for appropriate using of $DOMAIN$/conf/vhost.conf . You must include this file into $DOMAIN$/conf/httpd.include like in the example bellow.
Just run the command below to make this happen:
/usr/local/psa/admin/sbin/websrvmng -v -a
