Hello,
LM_STRUCTURE belongs to SUM functionality which has been added in SPS3. If your system was first setup without this components you can install them afterwards using the script attached to note:
1793303 - Install and configure SUM for SAP HANA (non-distributed systems)
Doing it this way the hostagent, LM_STRUCTURE and SUM are installed and configured automatically if missing. Of course you can do a fresh installation of SPS5 using the Unified Installer, but I'm sure the note provided will help in this case.
Regarding AFL installation, the AFL revision needs to be identical to the HANA revision (at the moment). SMP only holds the latest main HANA SP0x software components installation files (of rev. 45 and 53). However, this should not be a problem as the revision of your appliance should be updated frequently.
Best regards,
Michael