[MySQL Query] How to make a mysql query with MODx

$query = $xpdo->newQuery('Box');
$query->select($xpdo->getSelectColumns('Box','Box','',array('id','name')));
$boxes = $xpdo->getCollection('Box',$query);

// Box is a table?
$c = $xpdo->newQuery('Box');
// BowOwner is the second table to join?
$c->innerJoin('BoxOwner','Owner');
$c->where(array(
   'width' => 5,
   'Owner.user' => 2,
));
$c->sortby('name','ASC');
$c->limit(5);
// What's Box here
$boxes = $xpdo->getCollection('Box',$c);

// Extartait id de l'user
		$user = $modx->getObject('modUser', array('username'=>$logUser));	
  		$user->get('id');
	  	
	  	// Extrait les documents protégés mais dont il est autorisé 	  
	  	$sql = "SELECT mg.user_group, mg.member, dg.document_group, dg.document FROM modx_member_groups mg, modx_document_groups dg WHERE mg.user_group = dg.document_group AND mg.member = {$user->get('id')}";
  		
	  	if ($stmt = $modx->prepare($sql) AND $stmt->execute() AND $result = $stmt->fetchAll(PDO::FETCH_ASSOC)){
		
		  	foreach($result as $key => $val){
			
			  	array_push($docProtectedShow,$val['document']);
			  	// $docProtected = id Document protégé et autorisé pour l'user
	  		
			}
	 	
		}

// Stock dans $obj les infos sur le document enfant
			$obj = $modx->getObject('modDocument', array('id'=>$id));
		  
		  	// Si le document est publié, le menu pas caché, pas effacé, retient le et continue 
		  	if($obj->get('published') == 1 AND $obj->get('hidemenu') == 0 AND $obj->get('delete') == 0){