Simple points to consider:
It is a better practice to store your website files inside the users folder like below example:
/home/user/www OR /home/user/public_html
You may want to use the same concept for other files that you would need to access like access logs or error logs, for example:
/home/user/logs
Here is a sample Apache VirtualHost configuration for HTTPS:
<VirtualHost *:443>
DocumentRoot /home/user/www
ServerName domain.com
ServerAlias www.domain.com
SSLEngine on
SSLProtocol all -SSLv2 -SSLv3 -TLSv1
SSLCipherSuite ALL:!ADH:!EXPORT:!SSLv2:!SSLv3:!TLSv1:RC4+RSA:+HIGH:+MEDIUM:+LOW
SSLCertificateFile /home/user/certificates/domain.com.cer
SSLCACertificateFile /home/user/certificates/domain.chain.cer
SSLCertificateKeyFile /home/user/certificates/domain.com.key
ErrorLog /home/user/logs/error.log
CustomLog /home/user/logs/access.log combined
<Directory "/home/user/www">
AllowOverride All
Options -Indexes -MultiViews +SymLinksIfOwnerMatch
Require all granted
</Directory>
</VirtualHost>
<VirtualHost *:80 <
DocumentRoot /home/user/www
ServerName domain.com
ServerAlias www.domain.com
ErrorLog /home/user/logs/error.log
CustomLog /home/user/logs/access.log combined
<Directory "/home/user/www">
AllowOverride All
Options -Indexes -MultiViews +SymLinksIfOwnerMatch
Require all granted
</Directory>
</VirtualHost>