Add a META.yml to the distribution. Your buildtool should be able to autogenerate it.
Add a section called "LICENSE" to the documentation, or add a file named LICENSE to the distribution.
Add =head1 LICENSE and the text of the license to the main module in your code.
List all used modules in META.yml requires
Add a META.json to the distribution. Your buildtool should be able to autogenerate it.
Move your *.pm files in a directory named 'lib'. The directory structure should look like 'lib/Your/Module.pm' for a module named 'Your::Module'. If you need to provide additional files, e.g. for testing, that should not be considered for Kwalitee, then you should look at the 'provides' map in META.yml to limit the files scanned; or use the 'no_index' map to exclude parts of the distribution.
Error: MDLMol.pm, SDF.pm
Define the license if you are using in Build.PL. If you are using MakeMaker (Makefile.PL) you should upgrade to ExtUtils::MakeMaker version 6.31.
Add =head1 LICENSE and/or the proper text of the well-known license to the main module in your code.
Add 'use warnings' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.
Error: Chemistry::File::MDLMol, Chemistry::File::SDF
This is not a critical issue. Currently mainly informative for the CPANTS authors. It might be removed later.