Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Rafal Dolot]

Dear CCP4 Users,

Thank you very much for all suggestions. Special thanks to Oliver for 
the ready-to-use files. Great job :) Hopefully it will solve my 
problems...


Best wishes,

Rafal
--
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Division of Bioorganic Chemistry  |
|Macromolecular Crystallography Laboratory |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803325 |
|Cell:  +48 502897781  |
|--|



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Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Oliver Smart]

Dear Rafal,

Apologies my email client rather scrambled the text from my previous message, 
so I will send again here

Please find attached (in the previous message!) a restraint CIF file and a 
corresponding PDB file for your FESAN ligand.

Details:

Your ligand FESAN is a difficult test case for all restraint generation and 
refinement programs. It combines two carborane groups with a charged iron atom. 
Carborane groups have unusual chemistry that does not conform to normal valence 
models (they have carbon atoms bonded to six other atoms). Combining these 
groups with an iron atom that is bonded to 12 other atoms makes things even 
more complicated. Starting from a SMILES string is not wise for such a molecule.

Fortunately, such chemistry can be handled by the Grade2 restraint generator, 
that is supplied with BUSTER:

https://gphl.gitlab.io/grade2_docs/ 
Starting from the PDB file you supplied I converted to MOL2 format using CSD 
Mercury. Grade2 can read the MOL2 file and produce restraints (despite RDKit 
not being able to handle carboranes). All bond restraints are based on Mogul 
searches of CSD small molecule structures.

I manually edited the restraint CIF because there were too many bond angles to 
be useful. In the carborane cluster, each non-hydrogen atom is bonded to 5 
others to form an icosahedral shell, so that the bond length restraints alone 
are sufficient to fully define the geometry since all angles are implied. 
Additional bond angle restraints both within the cluster and for the 
12-coordinated FE atom are unnecessary and likely to be counter-productive.

It appears from CSD entries that FESAN is a cation carrying an overall charge 
of +1. But I did not correct this.

Please note that the atom names are slightly different from your PDB file as 
the FE atom has an uppercase atom name.

Unfortunately, the current CCP4 distribution of Coot 0.8.9.2-pre EL (revision 
count 7766) cannot cope this molecule as 'Send in the bond angels! Ahem I mean 
"Regularize Zone (Click two atoms)' produces a lock-up using all the CPU that 
has to be terminated by a kill. But you should be able to do a manual fit in 
Coot. BUSTER has no difficulty refining a structure with such restraints, as 
shown in this test using PDB entry 3I8W with FESAN replacing the CB5 ligand:

(Picture attached to previous message)
I hope that the restraint dictionary works for you.

All the best,

Oliver Smart, Andrew Sharff for BUSTER Developers.


> On 7 Jun 2022, at 08:35, Rafal Dolot  wrote:
> 
> Dear all,
> 
> Thank you very much for all your messages. Unfortunately, I'm still on the 
> same place, as yesterday...
> 
> First of all, I prepared a pdb/cif file of the ligand based on CCDC entry 
> 1176355 containing FESAN molecule. Also, I prepared SMILES file based on 
> SMILES of CB5 ligand (COSAN) available on PDB, where I simply switched Co 
> into Fe atom.
> 
> -> When I tried use acedrg with SMILES, I received an error info:
> 
> Input file: FSM.smi
> Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.cif
> Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.pdb
> workMode :  12
> Can not generate a molecule from the input SMILES string!
> Check your SMILES or report the bug
> Can not get the element symbols of atoms. Check input file format
> Error : The job stops because of errors
> 
> -> When I tried use acedrg with *pdb/*cif files I received no output files:
> 
> Input file: fsm.cif
> Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.cif
> Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.pdb
> workMode :  11
> Number of atoms in the cif file  0
> 
> -> When I tried use acedrg with *.mol file I received no output files:
> 
> Input file: fsm.mol
> Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.cif
> Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.pdb
> workMode :  13
> The system contains atoms of the following elements
> C B   Fe  H
> The input ligands/molecules contains metal or other heavier atoms
> Acedrg currently deals with ligands/molecules with following elements only
> C, N, O, S, P, B, F, Cl, Br, I, H
> The job finishes succesfully
> 
> 
> -> When I tried use prodrg, the program has been crashed:
> 
> The program run with command: cprodrg XYZIN 
> "C:/data_cryst/hsa_fesan_04/fsm.pdb" LIBOUT 
> "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.cif" XYZOUT 
> "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.pdb" MOLOUT 
> "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.mol"
> has failed with error message
> forrtl: severe (157): Program Exception - access violation
> Image  PCRoutineLineSource
> cprodrg.exe7FF623CB058F  Unknown   Unknown  Unknown
> cprodrg.exe7FF623CB05E0  Unknown   Unknown  Unknown
> cprodrg.exe7FF623CAFB4F  Unknown   Unknown  Unknown
> 

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Fei Long]

Dear Rafal,

Acedrg could not handle with ligands containing metal elements at the
moment. When your input file was a mol file, acedrg gave that information.
For other kind of input format, acedrg should give the same information.
We are checking why it produced those confusing info.

The developments are under way to make acedrg capable of handling with
ligands containing atoms of metal elements.

Sorry about your situations.

Best wishes,

Fei


Dear all,

Thank you very much for all your messages. Unfortunately, I'm still on
the same place, as yesterday...

First of all, I prepared a pdb/cif file of the ligand based on CCDC
entry 1176355 containing FESAN molecule. Also, I prepared SMILES file
based on SMILES of CB5 ligand (COSAN) available on PDB, where I simply
switched Co into Fe atom.

-> When I tried use acedrg with SMILES, I received an error info:

Input file: FSM.smi
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.pdb
workMode :  12
Can not generate a molecule from the input SMILES string!
Check your SMILES or report the bug
Can not get the element symbols of atoms. Check input file format
Error : The job stops because of errors

-> When I tried use acedrg with *pdb/*cif files I received no output
files:

Input file: fsm.cif
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.pdb
workMode :  11
Number of atoms in the cif file  0

-> When I tried use acedrg with *.mol file I received no output files:

Input file: fsm.mol
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.pdb
workMode :  13
The system contains atoms of the following elements
C   B   Fe  H
The input ligands/molecules contains metal or other heavier atoms
Acedrg currently deals with ligands/molecules with following elements
only
C, N, O, S, P, B, F, Cl, Br, I, H
The job finishes succesfully


-> When I tried use prodrg, the program has been crashed:

The program run with command: cprodrg XYZIN
"C:/data_cryst/hsa_fesan_04/fsm.pdb" LIBOUT
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.cif" XYZOUT
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.pdb" MOLOUT
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.mol"
has failed with error message
forrtl: severe (157): Program Exception - access violation
Image  PCRoutineLine
Source
cprodrg.exe7FF623CB058F  Unknown   Unknown
Unknown
cprodrg.exe7FF623CB05E0  Unknown   Unknown
Unknown
cprodrg.exe7FF623CAFB4F  Unknown   Unknown
Unknown
cprodrg.exe7FF623CB008E  Unknown   Unknown
Unknown
cprodrg.exe7FF623C5BDA8  Unknown   Unknown
Unknown
cprodrg.exe7FF623C3204E  Unknown   Unknown
Unknown
cprodrg.exe7FF623CAA81E  Unknown   Unknown
Unknown
cprodrg.exe7FF623CB3144  Unknown   Unknown
Unknown
KERNEL32.DLL   7FFEB3447034  Unknown   Unknown
Unknown
ntdll.dll  7FFEB4A22651  Unknown   Unknown
Unknown
***

-> I am still waiting for tokens from the prodrg web page ;) To be sure,
I used two emails, but with no response...

-> Ok, then I back to way I used years ago... JLigand was a good
solution, but... actually it is not working at all. I'm working under
Windows 10 / CCP4i, and I remember, there was the same issue in previous
version of CCP4.

-> Ok, then I back to the oldest solution -> using Sketcher. The program
is reading my PDB/CIF, but gave a warning when preparing a library, and
of course, no output _mon_lib.cif:

   WARNING : monomer:FSM  - has a minimal description.
   WARNING: there is no metal chirality for:Fe1
   WARNING: coords are not good enough to create Chirality
   WARNING :  /subroutine CALC_VOBSN/

I attached the PDB file containing the ligand of interest. From my
knowledge, it looks correct, but maybe I'm wrong. Have you any idea,
where is a problem?

Best,

Rafal

---
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Division of Bioorganic Chemistry  |
|Macromolecular Crystallography Laboratory |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803325 |
|Cell:  +48 502897781  |
|--|



W dniu 2022-06-06 14:52, Paul Emsley napisał(a):
> Although it may not be apparent, there has been a lot of work going on
> in 

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Rafal Dolot]

Dear all,

Thank you very much for all your messages. Unfortunately, I'm still on 
the same place, as yesterday...


First of all, I prepared a pdb/cif file of the ligand based on CCDC 
entry 1176355 containing FESAN molecule. Also, I prepared SMILES file 
based on SMILES of CB5 ligand (COSAN) available on PDB, where I simply 
switched Co into Fe atom.


-> When I tried use acedrg with SMILES, I received an error info:

Input file: FSM.smi
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.pdb
workMode :  12
Can not generate a molecule from the input SMILES string!
Check your SMILES or report the bug
Can not get the element symbols of atoms. Check input file format
Error : The job stops because of errors

-> When I tried use acedrg with *pdb/*cif files I received no output 
files:


Input file: fsm.cif
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.pdb
workMode :  11
Number of atoms in the cif file  0

-> When I tried use acedrg with *.mol file I received no output files:

Input file: fsm.mol
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.pdb
workMode :  13
The system contains atoms of the following elements
C   B   Fe  H
The input ligands/molecules contains metal or other heavier atoms
Acedrg currently deals with ligands/molecules with following elements 
only

C, N, O, S, P, B, F, Cl, Br, I, H
The job finishes succesfully


-> When I tried use prodrg, the program has been crashed:

The program run with command: cprodrg XYZIN 
"C:/data_cryst/hsa_fesan_04/fsm.pdb" LIBOUT 
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.cif" XYZOUT 
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.pdb" MOLOUT 
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.mol"

has failed with error message
forrtl: severe (157): Program Exception - access violation
Image  PCRoutineLine
Source
cprodrg.exe7FF623CB058F  Unknown   Unknown  
Unknown
cprodrg.exe7FF623CB05E0  Unknown   Unknown  
Unknown
cprodrg.exe7FF623CAFB4F  Unknown   Unknown  
Unknown
cprodrg.exe7FF623CB008E  Unknown   Unknown  
Unknown
cprodrg.exe7FF623C5BDA8  Unknown   Unknown  
Unknown
cprodrg.exe7FF623C3204E  Unknown   Unknown  
Unknown
cprodrg.exe7FF623CAA81E  Unknown   Unknown  
Unknown
cprodrg.exe7FF623CB3144  Unknown   Unknown  
Unknown
KERNEL32.DLL   7FFEB3447034  Unknown   Unknown  
Unknown
ntdll.dll  7FFEB4A22651  Unknown   Unknown  
Unknown

***

-> I am still waiting for tokens from the prodrg web page ;) To be sure, 
I used two emails, but with no response...


-> Ok, then I back to way I used years ago... JLigand was a good 
solution, but... actually it is not working at all. I'm working under 
Windows 10 / CCP4i, and I remember, there was the same issue in previous 
version of CCP4.


-> Ok, then I back to the oldest solution -> using Sketcher. The program 
is reading my PDB/CIF, but gave a warning when preparing a library, and 
of course, no output _mon_lib.cif:


  WARNING : monomer:FSM  - has a minimal description.
  WARNING: there is no metal chirality for:Fe1
  WARNING: coords are not good enough to create Chirality
  WARNING :  /subroutine CALC_VOBSN/

I attached the PDB file containing the ligand of interest. From my 
knowledge, it looks correct, but maybe I'm wrong. Have you any idea, 
where is a problem?


Best,

Rafal

---
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Division of Bioorganic Chemistry  |
|Macromolecular Crystallography Laboratory |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803325 |
|Cell:  +48 502897781  |
|--|



W dniu 2022-06-06 14:52, Paul Emsley napisał(a):

Although it may not be apparent, there has been a lot of work going on
in Acedrg development regarding Boron.

One cannot say the same for Coot though and I can reproduce the
behaviour reported by Rafa Dolot. If/when I can fix it, it will be
available in 0.9.8.4.

Paul.

On 06/06/2022 13:24, Boaz Shaanan wrote:


Hi,
In case you don't have a cif file for the ligand, I would load the
SMILES expression into acedrg (or use any other input option) to
create a cif file which 

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Lucrezia Catapano - MRC LMB]

Hi,

as previously suggested you can use AceDRG to generate a cif file for your
ligand by input different type of files (SMILES, mmCIF, SDF/MOL, and SYBYL
MOL2 files).

You can use the AceDRG command line:
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/acedrg/acedrg.html

or via ccp4i2, 'Ligands' menu, 'make ligand-AceDRG'.


Regards
Lucrezia
> Dear CCP4 Users,
>
> I am working with data containing a possible complex of protein with
> FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this
> ligand is not available in PDB. The closest molecule is COSAN (cobalt
> bis(1,2-dicarbollide)), which is labelled as CB5 and is available in two
> PDB entries. I can load this molecule into Coot, but attempts at ligand
> search or refinement of the manually matched molecule result in freezing
> of the Coot window. FESAN is not present in CCDC as a single molecule,
> but only in some complexes. Could you give me some advice on how to
> prepare a new ligand like this one, for incorporation into the protein
> and further refinement?
>
> Best regards,
>
> Rafal Dolot
>
> --
> |--|
> |Rafal Dolot, Ph.D.|
> |  |
> |Polish Academy of Sciences|
> |Centre of Molecular and Macromolecular Studies|
> |Division of Bioorganic Chemistry  |
> |Macromolecular Crystallography Laboratory |
> |Sienkiewicza 112  |
> |90-363 Lodz, Poland   |
> |Phone: +48(42)6803325 |
> |Cell:  +48 502897781  |
> |--|
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at
> https://www.jiscmail.ac.uk/policyandsecurity/
>


Lucrezia Catapano
PhD student
Murshudov Group
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge CB2 0QH
United Kingdom



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Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Paul Emsley]

Although it may not be apparent, there has been a lot of work going on 
in Acedrg development regarding Boron.


One cannot say the same for Coot though and I can reproduce the 
behaviour reported by Rafa Dolot. If/when I can fix it, it will be 
available in 0.9.8.4.


Paul.


On 06/06/2022 13:24, Boaz Shaanan wrote:

Hi,
In case you don't have a cif file for the ligand, I would load the 
SMILES expression into acedrg (or use any other input option) to 
create a cif file which you can then read into Coot.

Cheers,
Boaz
On Jun 6, 2022 15:06, Rafal Dolot  wrote:
Dear CCP4 Users,

I am working with data containing a possible complex of protein with
FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this
ligand is not available in PDB. The closest molecule is COSAN (cobalt
bis(1,2-dicarbollide)), which is labelled as CB5 and is available in two
PDB entries. I can load this molecule into Coot, but attempts at ligand
search or refinement of the manually matched molecule result in freezing
of the Coot window. FESAN is not present in CCDC as a single molecule,
but only in some complexes. Could you give me some advice on how to
prepare a new ligand like this one, for incorporation into the protein
and further refinement?




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Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Boaz Shaanan]

Hi,
In case you don't have a cif file for the ligand, I would load the SMILES 
expression into acedrg (or use any other input option) to create a cif file 
which you can then read into Coot.
Cheers,
Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion University
Beer Sheva, Israel

On Jun 6, 2022 15:06, Rafal Dolot  wrote:
Dear CCP4 Users,

I am working with data containing a possible complex of protein with
FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this
ligand is not available in PDB. The closest molecule is COSAN (cobalt
bis(1,2-dicarbollide)), which is labelled as CB5 and is available in two
PDB entries. I can load this molecule into Coot, but attempts at ligand
search or refinement of the manually matched molecule result in freezing
of the Coot window. FESAN is not present in CCDC as a single molecule,
but only in some complexes. Could you give me some advice on how to
prepare a new ligand like this one, for incorporation into the protein
and further refinement?

Best regards,

Rafal Dolot

--
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Division of Bioorganic Chemistry  |
|Macromolecular Crystallography Laboratory |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803325 |
|Cell:  +48 502897781  |
|--|



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of 
www.jiscmail.ac.uk/CCP4BB, a mailing list 
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[ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Rafal Dolot]

Dear CCP4 Users,

I am working with data containing a possible complex of protein with 
FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this 
ligand is not available in PDB. The closest molecule is COSAN (cobalt 
bis(1,2-dicarbollide)), which is labelled as CB5 and is available in two 
PDB entries. I can load this molecule into Coot, but attempts at ligand 
search or refinement of the manually matched molecule result in freezing 
of the Coot window. FESAN is not present in CCDC as a single molecule, 
but only in some complexes. Could you give me some advice on how to 
prepare a new ligand like this one, for incorporation into the protein 
and further refinement?


Best regards,

Rafal Dolot

--
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Division of Bioorganic Chemistry  |
|Macromolecular Crystallography Laboratory |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803325 |
|Cell:  +48 502897781  |
|--|



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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