[phenixbb] Creating cif file of ligands by Elbow/ReadySet

Nigel Moriarty nwmoriarty at lbl.gov
Thu Apr 21 14:40:02 PDT 2011


You can very easily access the files in the chemical components that
are installed with PHENIX using

phenix.elbow --chemical_components=CR2

or to view the ligand

phenix.reel --chemical-components cr2

(case is unimportant)

You can also get the Mogul values (if you have Mogul installed and in
you $PATH and a recent PHENIX version)

phenix.elbow --chem=cr2 --mogul

Using the chemical components input in the latest eLBOW release, I
tabulated the bond lengths for C3-CA3 in CR2

eLBOW : 1.492
AM1 : 1.567
Mogul GUI: 1.528 with a range up to 1.56
Mogul command-line : 1.511

I'm sure you will agree that not every C-C bond should be 1.51A. There
is a range so any attempt to construct a ligand with exactly 1.51A for
all C-C bonds is wrong. The range in Mogul is about 0.02 Angstrom.
There are of course limits to the accuracy of any method used to
determine a bond length but I believe that eLBOW and AM1 gets within
the acceptable range for most ligands.

Some of the other problems you are seeing may be due to using a PDB
file as input. Its always better to use the --chemical-components or
some other chemically rich format.


On Wed, Apr 20, 2011 at 3:23 AM, Ngan Nguyen Bich
<ngan.nguyenbich at student.kuleuven.be> wrote:
> Dear Phenix developers,
> I'm quite new in crystallography and use PhenixGUI for refinement my
> protein.
> I got a problem when I had to create cif file of the new ligand to feed
> in phenix_refine by Elbow/ReadySet
> I saw that program creates some bonds shorter or longer compared to the
> statistic value from the CSD for example.
> Here are some examples when I play with Elbow (same problem with ReadySet)
> 1. when I feed program the chemical string, (template PDB file is the
> mylidand_idea.pdb)
> CR2 C3 CA3 single 1.569 0.038
>  and if I choose AM1 optimization
> CR2   C3      CA3   single        1.602 0.040
> 2. when I feed program the .pdb file, choose Use geometry for Initial
> geometry.
> GYC   N       CA1   single        1.409 0.020      *
> GYC   N      HN1    single        0.902 0.020
> GYC   N      HN2    single        0.901 0.020
> GYC   SG1     CB1   single        1.797 0.020
> GYC   SG1    HG1    single        1.204 0.020
> GYC   CB1     CA1   single        1.500 0.020
> GYC   CB1    HB11   single        1.006 0.020
> GYC   CB1    HB12   single        0.972 0.020
> GYC   CA1     C1    single        1.528 0.020
> GYC   CA1    HA1    single        1.010 0.020
> GYC   C1      N2    aromatic      1.412 0.020
> GYC   C1      N3    aromatic      1.304 0.020
> GYC   N2      CA2   aromatic      1.505 0.020   **
> GYC   N3      C2    aromatic      1.349 0.020
> GYC   N3      CA3   single        1.423 0.020
> GYC   C2      O2    double        1.370 0.020
> GYC   C2      CA2   aromatic      1.509 0.020
> GYC   CA2     CB2   single        1.532 0.020
> GYC   CA3     C     single        1.496 0.020
> It's strange to me when comparing * and **
> and if I run AM1
> GYC   CB1     CA1   single        1.533 0.035
> GYC   CA3     C     single        1.564 0.035
> as I know, the C-C single bond should be about 1.51.
> Does anyone get a problem like me?
> I wonder if I didn't do properly or some thing else, or any suggestion for
> my case.
> One more questions is that afterward I found cif file (seemly mmcif file) of
> my ligand in phenix-1.7-650/chem_data/chemical_components
> And I'm wondering that How the program use these cif file, or I can use them
> in which way?
> Thank you in advance.
> Best regards,
> Ngan Nguyen Bich
> KULeuven
> Belgium
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb

Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

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