add TRP-MAN link and modifications

[louholland]

Added a link description for the TRP-MAN link and corresponding modifications to the TRM and MAN residues, including a conformational change for MAN.

Link created using Acedrg 277with instruction:
LINK: RES-NAME-1 TRP ATOM-NAME-1 CD1 RES-NAME-2 MAN ATOM-NAME-2 C1 BOND-TYPE SINGLE DELETE ATOM O1 2

The TRPm1 modification was not changed. The MANm1 modification was edited to include torsion angles to specify the correct 1C4 conformation for the mannose.

Some high resolution examples from the PDB:

PDB	resolution	source	residues
6plh	1.6 A	X-ray	MAN-301/C_TRP-16/C
7r84	1.34 A	X-ray	MAN-201/A_TRP-7/A ; MAN-202/A_TRP-10/A
8ckk	1.56 A	X-ray	MAN-801/A_TRP-656/A ; MAN-811/A_TRP-659/A

[keitaroyam]

Thanks for your contribution! Overall, this looks good. I plan to remove some unnecessary modifications (for example, _chem_mod_tor for TRPm1). More importantly, has this been tested in Coot?

The MANm1 modification was edited to include torsion angles to specify the correct 1C4 conformation for the mannose.

For future reference, how were these torsion angles generated?

[louholland]

Apologies, I did not test in Coot. I tested by using the revised monomer library to refine with refmac (including the torsion restraints) on the high resolution structures (checking that they remained correct) and on 5m5e (resolution 2.3 A) which previously had the mannose in the wrong conformation (3h2) and with a slightly distorted link (checking that the MAN-309/B_TRP-194/B link and residues were improved after). I'm happy to complete further testing if this is required.

The torsion angles for MANm1 were generated by flipping the signs on the existing MAN torsion angles in the monomer library. If it is preferable, I could instead use those provided by privateer (similar, but slightly different, as they are just generic torsion angles for any 1C4 conformation).

[glycojones]

I should add that these torsion angles are consistent with the only high resolution structure of the this modification. Sadly, not a lot to go on!

…

On Fri, 6 Feb 2026 at 10:23, louholland ***@***.***> wrote: *louholland* left a comment (MonomerLibrary/monomers#67) <#67 (comment)> Apologies, I did not test in Coot. I tested by using the revised monomer library to refine with refmac (including the torsion restraints) on the high resolution structures (checking that they remained correct) and on 5m5e (resolution 2.3 A) which previously had the mannose in the wrong conformation (3h2) and with a slightly distorted link (checking that the MAN-309/B_TRP-194/B link and residues were improved after). I'm happy to complete further testing if this is required. The torsion angles for MANm1 were generated by flipping the signs on the existing MAN torsion angles in the monomer library. If it is preferable, I could instead use those provided by privateer (similar, but slightly different, as they are just generic torsion angles for any 1C4 conformation). — Reply to this email directly, view it on GitHub <#67 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEIHCVFKSDGQCI75P33MEXT4KRTQJAVCNFSM6AAAAACTNUMH5OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTQNJZGQZDANJVGQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[keitaroyam]

No worries, I just tested this in Coot, and it appeared to work properly. I also tested a few cases in servalcat enabling torsion angles (using --keywords "rest tors incl link TRP-MAN name *" "rest tors incl resi MAN name *") and those looked fine.