I think that I need to create config file like “/etc/letsencrypt/configs/fundebug.com.conf” to apply certification, what should I do since /etc/letsencrypt is almost empty?
You're not forced to using nginx, you can use Apache too or any other webserver or service which uses TLS for that matter.
Although @_az is correct you could use the standalone or manual plugins too, I think it's easier to install the webserver you would like to use, configure the website first and then use certbot to configure HTTPS with the webserver plugin (nginx or apache).
If you aren't going to use Apache or nginx, but another webserver, I would recommend the webroot plugin. Otherwise, you could use manual or standalone, but I would use any of the other authentication plugins first.