create table Parent_elements (Parent_id bigint not null, enabled bit not null, child_id bigint not null, primary key (Parent_id, enabled))

import org.hibernate.annotations.AccessType;
import org.hibernate.annotations.CollectionOfElements;
import org.hibernate.cfg.AnnotationConfiguration;
import org.hibernate.tool.hbm2ddl.SchemaExport;

import javax.persistence.Embeddable;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.ManyToOne;
import javax.persistence.Table;
import java.util.Set;

public class TestPrimaryKeyForCollectionOfElements {

    @Entity
    @AccessType("field")
    @Table(name = "Child")
    static class Child {
        @Id
        Long id;

        String name;
    }


    @Entity
    @AccessType("field")
    @Table(name = "Parent")
    static class Parent {

        @Id
        Long id;

        @CollectionOfElements(targetElement = Element.class)
        Set<Element> elements;

    }

    @Embeddable
    static class Element {
        boolean enabled = true;

        @ManyToOne(optional = false)
        Child child;
    }


    public static void main(String[] pArgs) throws Exception {
        AnnotationConfiguration tConfiguration = new AnnotationConfiguration();
        tConfiguration.addAnnotatedClass(Child.class);
        tConfiguration.addAnnotatedClass(Element.class);
        tConfiguration.addAnnotatedClass(Parent.class);
        tConfiguration.setProperty("hibernate.dialect", "org.hibernate.dialect.MySQLDialect");

        SchemaExport tSchemaExport = new SchemaExport(tConfiguration);

        tSchemaExport.create(true, false);
    }
}