You are looking for a GP tool Create SQLite Database
available since 10.4 (previously, in 10.3, you had to use an arcpy
function CreateSQLiteDatabase()
.
Choose as spatial_type
parameter GEOPACKAGE
which will create an OGC GeoPackage dataset. This is essentially an SQLite database with ST_Geometry storage plus some extra OGC features.
You can use this workspace very much like any SQLite geodatabase, that is load/export feature classes and tables and create views. You can read more about support for SQLite in ArcGIS in this help topic SQLite and ArcGIS. To see an example of data load, look at this blog post Load Esri geodatabase tables into SQLite