$node = entity_create('node', array('type' => 'MY-CONTENT-TYPE'));
$entity = entity_metadata_wrapper('node',  $node);

$data = array('column_1'=>'value 1', 'column_2'=>'value 2', 'column_3'=>'value 3');

$entity->field_custom_compound_field = $data;

$entity->save();

/**
* Implements hook_field_info().
*
* Provides the description of the field.
*/
function field_example_field_info() {
  return array(
  // We name our field as the associative name of the array.
    'field_example_rgb' => array(
      'label' => t('Example Color RGB'),
      'description' => t('Demonstrates a field composed of an RGB color.'),
      'default_widget' => 'field_example_3text',
      'default_formatter' => 'field_example_simple_text',
      'property_type' => 'field_example_rgb', // we add the propert type here
      'property_callbacks' => array('field_example_rgb_property_info_callback'), // we add the callback
    ),
  );
}

function field_example_rgb_property_info_callback(&$info, $entity_type, $field, $instance, $field_type) {
  $property = &$info[$entity_type]['bundles'][$instance['bundle']]['properties'][$field['field_name']];

  $property['getter callback'] = 'entity_metadata_field_verbatim_get';
  $property['setter callback'] = 'entity_metadata_field_verbatim_set';
  unset($property['query callback']);

  $property['property info']['rgb'] = array(
    'type' => 'text',
    'label' => t('RGB'),
    'setter callback' => 'entity_property_verbatim_set',
  );
  $property['property info']['someothervalue'] = array(
    'type' => 'text',
    'label' => t('Some other value'),
    'setter callback' => 'entity_property_verbatim_set',
  );
}

$node = entity_create('node', array('type' => 'MY-CONTENT-TYPE'));
$entity = entity_metadata_wrapper('node',  $node);

$data = array('column_1'=>'value 1', 'column_2'=>'value 2', 'column_3'=>'value 3');

$entity->field_custom_compound_field = $data;

$entity->save();