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

Ngan Nguyen Bich ngan.nguyenbich at student.kuleuven.be
Wed Apr 20 03:23:34 PDT 2011

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
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