The files have to be bundled into a keystore (keystore.pfx) for use in tomcat. For this you can use:
openssl pkcs12 -export -in cert1.pem -inkey privkey1.pem -out keystore.pfx -name tomcat -CAfile chain1.pem -caname root -chain
"keystore.pfx" must be renamed to "keystore" and keystore password used when creating keystore.pfx have to be specified in server.xml.
More information at: https://hardwarehacks.org/blog/setting_up_tomcat_with_a_lets_encrypt_certificate/