When you wish to send an S/MIME based encrypted email using iOS Mail, your iPhone or iPad needs to be aware of the S/MIME certificate of the recipients, and you must have a valid S/MIME certificate installed in iOS.
You can either manually install an S/MIME certificate on your iOS device, or have it installed by an MDM solution such as Intune or Mobile Iron.
To manually configure your installed S/MIME certificate for iOS Mail, go to: Settings -> Mail -> Accounts -> <Select your account> -> select the account again -> Advanced Settings -> Sign -> <select the available certificate> -> back -> Account -> Done
