So the will-known will be under your webroot (where your web page files are located)
I was just curious. I have quite a few friends and colleagues around the middle east. My Arabic isn't much, but I do say as-salamu alaykum a few times a week. 
I did created once a folder earlier while grinding with the error so I am not sure if this was created just now but this is what it looks like:
Is /html/ where your web site starts?
haha, that's awesome. I love languages even something as small as as-salama alaykum, all of a sudden a person feels more familiar. Good for you, let me know if you need some translations 
yes, its Magento. It's how it works I guess. I am not tech savvy. 
We may need to have you remove that folder. Let's see on a minute.
I did a little checking and it looks like you've never had a Let's Encrypt certificate issued for emiratespass.net or its subdomains. Is this correct?
You are right, we never had any certificate issued for this domain. It’s basically a staging domain, we will later move the website to the “currently live” domain. Once everything is tested and all. To configure and test services we need SSL.
Got it. Give me a minute to see a few things.
Absolutely, please take your time. Thanks a million in advance.
What command did you use to install Let’s Encrypt the first time?
I believe it was certbot certonly --nginx
For magento, I found something that might be able to help us:
I’m working from this to deal with magento’s oddities.
Let’s try this:
sudo apt install letsencrypt -y
root@ip-172-31-17-82:/home/ubuntu# sudo apt install letsencrypt -y
Reading package lists... Done
Building dependency tree
Reading state information... Done
The following packages were automatically installed and are no longer required:
linux-aws-5.3-headers-5.3.0-1017 linux-aws-5.3-headers-5.3.0-1019 linux-aws-5.3-headers-5.3.0-1023 linux-aws-5.3-headers-5.3.0-1028
Use 'sudo apt autoremove' to remove them.
The following NEW packages will be installed:
letsencrypt
0 upgraded, 1 newly installed, 0 to remove and 54 not upgraded.
Need to get 5504 B of archives.
After this operation, 13.3 kB of additional disk space will be used.
Get:1 Index of /certbot/certbot/ubuntu bionic/main amd64 letsencrypt all 0.31.0-1+ubuntu18.04.1+certbot+1 [5504 B]
Fetched 5504 B in 0s (17.9 kB/s)
Selecting previously unselected package letsencrypt.
(Reading database ... 198624 files and directories currently installed.)
Preparing to unpack .../letsencrypt_0.31.0-1+ubuntu18.04.1+certbot+1_all.deb ...
Unpacking letsencrypt (0.31.0-1+ubuntu18.04.1+certbot+1) ...
Setting up letsencrypt (0.31.0-1+ubuntu18.04.1+certbot+1) ...
root@ip-172-31-17-82:/home/ubuntu#
Looking good. Let’s stop nginx to generate a cert.
sudo systemctl stop nginx
Done, where do we go from here 
root@ip-172-31-17-82:/home/ubuntu# sudo certbot certonly --standalone -d emiratespass.net,www.emiratespass.net
Saving debug log to /var/log/letsencrypt/letsencrypt.log
Plugins selected: Authenticator standalone, Installer None
Obtaining a new certificate
Performing the following challenges:
http-01 challenge for emiratespass.net
http-01 challenge for www.emiratespass.net
Cleaning up challenges
Problem binding to port 80: Could not bind to IPv4 or IPv6.
Try this then:
sudo certbot certonly --nginx -d emiratespass.net,www.emiratespass.net
I forgot to have you kill the other session. Hopefully it won’t interfere.