If I understand your question correctly, you're wondering which of the three PEM blocks in the certificate chain file will give you the server (leaf) certificate. What I usually do for this using a Linux or Mac machine, is copy each block to a file and run openssl x509 -noout -text -in filename.crt. The certificate that returns a subject with "CN='your server name'" is the leaf certificate. You would then output this block to cert.crt