SSL with specific port on Nginx server

Server
5

I do not specifically have an index.html. In my home directory /home/ronny there's a folder called domain.nl. This folder contains a node app which's index is located at /dist/server/index.js. With the npm package pm2 I'm running this process on port 6000.
I will try to set it up during your suggestions and the generator from Mozilla.

EDIT:
I've tried adding the certificate, but when running:
sudo letsencrypt certonly --webroot -w /home/ronny -d domain.nl -d domain.nl

I get the following errors:

Failed authorization procedure. domain.nl (http-01): urn:acme:error:unauthorized :: The client lacks sufficient authorization :: Invalid response from http://domain.nl/.well-known/acme-challenge/frU8k1SdHc8a-XT9w2aBkB1cuot2iIgqIWsT9cIWOGc [95.85.21.130]: 404

IMPORTANT NOTES:
 - The following errors were reported by the server:

   Domain: domain.nl
   Type:   unauthorized
   Detail: Invalid response from http://domain.nl/.well-known/acme-
   challenge/frU8k1SdHc8a-XT9w2aBkB1cuot2iIgqIWsT9cIWOGc
   [95.85.21.130]: 404

   To fix these errors, please make sure that your domain name was
   entered correctly and the DNS A record(s) for that domain
   contain(s) the right IP address.

Does anyone know how to fix this?
My website is up and running on the domain so it's accessible.