To send a SITE command and get the result, you can try this:
<?php
function ftpsite($conn, $cmd) {
    return ftp_raw($conn, "SITE $cmd");
}
?>(PHP 4, PHP 5, PHP 7, PHP 8)
ftp_site — Sendet ein SITE-Kommando zum Server
   ftp_site() sendet das angegebene
   SITE-Kommando zum FTP-Server.
  
   SITE-Kommandos sind nicht standardisiert und
   unterscheiden sich von Server zu Server. Sie sind nützlich, um Dinge
   wie Datei-Zugriffsrechte und Gruppen-Mitgliedschaften zu handhaben.
  
ftpEine FTP\Connection-Instanz.
commandDas SITE-Kommando. Zu beachten ist, dass dieser Parameter nicht maskiert ist und dass deswegen Probleme bei Dateinamen mit Leerzeichen oder anderen Zeichen auftreten können.
| Version | Beschreibung | 
|---|---|
| 8.1.0 | Der Parameter ftperwartet nun eine
  FTP\Connection-Instanz; vorher wurde eine Ressource
  erwartet. | 
Beispiel #1 Ein SITE-Kommando an einen FTP-Server senden
<?php
// Verbindung aufbauen
$ftp = ftp_connect('ftp.example.com');
if (!$ftp) die('Verbindung zu ftp.example.com konnte nicht aufgebaut werden');
// Login mit Benutzername und Passwort
if (!ftp_login($ftp, 'user', 'pass')) die('Fehler beim Login zu ftp.example.com');
// Kommando "SITE CHMOD 0600 /home/user/privatefile" an den Server senden */
if (ftp_site($ftp, 'CHMOD 0600 /home/user/privatefile')) {
   echo "Kommando erfolgreich ausgeführt.\n";
} else {
   die('Kommando fehlgeschlagen.');
}
?>To send a SITE command and get the result, you can try this:
<?php
function ftpsite($conn, $cmd) {
    return ftp_raw($conn, "SITE $cmd");
}
?>Hya, 
  Recently I had to work with FTP over PHP, since I didn't found any help about this topic I decided to post this here. If you need to chmod one file, I tested this on the ftp server using a ftp client and after I knew that the ftp server supported chmod I used the following commands:
$upload = ftp_put($conn_id, "/home/to/public_html/index.php", $source_file, FTP_ASCII);
$ch=@ftp_site($conn_id,"chmod 755 /home/to/public_html/index.php");
Hope this help!
Tósite commands are extra-functionality provided by some ftp servers, and depend on the server : 
e.g. trying "ftp> site help" (with an interactive ftp client) on a proftp server would give :
 
214-The following SITE extensions are recognized:
 RATIO -- show all ratios in effect
 The following SITE commands are recognized (* =>'s unimplemented).
 HELP    CHMOD
214 Direct comments to admin@ftp.blahblah.fr
while with wu-ftpd on can typically get :
214-The following SITE commands are recognized (* =>'s unimplemented).
   UMASK           GROUP           INDEX           GROUPS
   IDLE            GPASS           EXEC            CHECKMETHOD
   CHMOD           NEWER           ALIAS           CHECKSUM
   HELP            MINFO           CDPATH                   
214 blabla
Unfortunately, ftp_site only returns true or false. It would be nice to have a way to get the server's reply in full : ftp_site('help') return 1, which pretty much useless.
Hope that helps,
IvanUse ftp_raw() (PHP 5+) instead of ftp_site() if you need the results of the remote command.I'd like to follow up with Ivan's observation there. Unless I am missing the obvious, which is entirely possible of course, this command is quite useless unless it returns the data from the SITE <foo> request.
Besides the obvious SITE HELP command, another one that would require catching the feedback would be the SITE LOCATE | SITE SEARCH commands. I completely recognize that SITE <foo> commands are indeed insanely proprietary, but the fact still remains that changing this to return the results, or at least having the option to do so (such as exec() and the like) would be vastly preferred to the current method of returning true/false values.
Thanks.I wrote some functions for an ftp server for windows called GuildFTPd.
Here they are, they are pretty much so self explanitory:
<?
function guildftpd_adduser($ftp_stream,$group,$username,$password){
    ftp_site($ftp_stream,"SITE ADDUSER $group $username $password");
}
function guildftpd_addgroup($ftp_stream,$groupname){
    ftp_site($ftp_stream,"SITE ADDGROUP $groupname");
}
function guildftpd_deluser($ftp_stream,$username){
    ftp_site($ftp_stream,"SITE DELUSER $username");
}
function guildftpd_addpath($ftp_stream,$username,$path,$vpath){
    ftp_site($ftp_stream,"SITE ADDPATH $username $path $vpath");
}
function guildftpd_delpath($ftp_stream,$username,$path,$vpath){
    ftp_site($ftp_stream,"SITE DELPATH $username $path $vpath");
}
function guildftpd_anon($ftp_stream){
    ftp_site($ftp_stream,"SITE ANON ALLOW");
}
function guildftpd_anond($ftp_stream){
    ftp_site($ftp_stream,"SITE ANON DENY");
}
function guildftpd_chpass($ftp_stream,$user,$pass){
    ftp_site($ftp_stream,"SITE CHPASS $user $pass");
}
function guildftpd_disable($ftp_stream,$user){
    ftp_site($ftp_stream,"SITE DISABLE $user");
}
function guildftpd_enable($ftp_stream,$user){
    ftp_site($ftp_stream,"SITE ENABLE $user");
}
function guildftpd_who($ftp_stream){
    $who = ftp_site($ftp_stream,"SITE WHO");
}
function guildftpd_kick($ftp_stream,$user);
    ftp_site($ftp_stream,"SITE KICK $user");
}
function guildftpd_msg($ftp_stream,$text);
    ftp_site($ftp_stream,"SITE MSG $text");
}
?>