which doesn't contain any kind of malware and virus.
How can we have the same to appear in safe to browse category ?
In general, you should to avoid these troubles in future too. Otherwise, domain can be blacklisted or rated as harmful/malicious then.
Good to maintain all infrastructure with carefulness. Since, from time to time, websites can be rated as harmful due the fact that website is hacked or malicious payload is added to website by some way (not by owners).