Appearance > Menus > Left Sidebar > Add Toggle

You custom box can be added with adding meta box on nav menu page. So –

function Register_My_Nav_Menu_Metaboxes(){
    add_meta_box( $id, $title, $callback, 'nav-menus', 'side' );
}
add_action('load-nav-menu.php', 'Register_My_Nav_Menu_Metaboxes');

I hope you know how to add the metabox $id, $title, $callback and utilize it.