[phenixbb] how to modify C-D bond length restraints in phenix?

[Maxime Cuypers]

Hi,

i am refining a perdeuterated neutron structure and have noticed a lot of
positive density aside the D atoms on aliphatic and aromatic side chains.
just in the alignment of C-D bonds (C-D then +), suggesting that
phenix.refine constraints these bond lengths too short in my case. i tried
automatic weights for geometry refinement and unrestrained specific C-D
refinement but it is not satisfactory.

then i found the following funny distances (angströms) in the pdb database
neutron structures:

3KYX:
program: Phenix.refine
D-prot
Distances:
C-D aromatics = 0.93-0.94
C-D aliph. =  0.98

1CQ2
Program : xplor3.1
D-protein (despite the atoms being labelled as H according to abstract)
Distances:
C-D aromatics = 1.06-1.08
C-D aliph. = 1.08

4FC1
H-protein
Distances:
program: Phenix.refine
C-H aromatics = 0.93
C-H aliph. = 0.97

1VCX
H-protein
program: CNS
Distances:
C-H aromatics = 1.06-1.10
C-H aliph. = 1.09

those neutron C-D/C-H bond lengths in pdb seem pretty much inconsistentto
me.

So it seems that phenix.refine uses  C-D/ C-H bonds restrains that are
different to other programs to below 1.0 Ang. ( ca. 0.10 A differences)
how can i change the restraints to make it all longer bond lengths for C-D
only? with a .cif file?
i saw that phenix uses the CCP4 monomer library but the one in :
/usr/local/phenix-.../chem_data/mon_lib/list
only seem to be applying modifications.

any clue on how to specifically modify the restraints parameters on C-D
bonds would be very appreciated.

Thanks,

Maxime
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