@Entity
public class Entity1 {
    @Id
    private long id;
    @ManyToMany
    private List<Entity2> entity2s;
    @ManyToMany
    private List<Entity2> otherEntity2s;
    ... // getter and setter.
}

@Entity
public class Entity2 {
    @Id
    private long id;
    @ManyToMany(mappedBy = "entity2s")
    private List<Entity1> entity1s;
    @ManyToMany(mappedBy = "otherEntity2s")
    private List<Entity1> otherEntity1s;
    ... // getter and setter.
}

create table Entity1_Entity2 (
    otherEntity1s_id bigint not null,
    otherEntity2s_id bigint not null,
    entity1s_id bigint not null,
    entity2s_id bigint not null
)