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Methods, Problems and Solutions

Powder Diffraction Structure Solution Pathways

Solving an Organic Structure (Cimetidine - C 10 H 16 N6 S) from Powder Diffraction Data

Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3

The CCP14 Homepage is at http://www.ccp14.ac.uk
[Back to: Problems and Solutions] | [Back to: Tutorials]
[Back to: Powder Diffraction Structure Solution Pathways Index]
[Back to: Solving an Organic Structure (Cimetidine) from Powder Diffraction Data]
[Back to: Initial Connectivity Searching of the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD]
[Back to: Peak Profiling of Cimetidine using XFIT]
[Back to: Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs]
[Back to: CELL Searching the Cambridge database via Platon and Quest]
[Back to: Le Bail fitting and generating an EXPO starting file using LHPM-Rietica]
[Back to: Solve the structure of Cimetidine using the Sireware EXPO direct methods software]
[Back to: Finding possibly missing Symmetry in cimetidine using the Platon ADDSYM option]
[Back to: Searching the Cambridge database via Platon and Quest for related strutures]
[Back to: Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3]
[Back to: Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software]
[Back to: Solve the structure of Cimetidine using Dirdif fragment searching]
[Back to: Solve the structure of Cimetidine using ESPOIR with no restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with bond restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies freely moving atoms]
[To: Xfit-Koalariet Peak Profiling Software] | [To: Crysfire Powder Indexing Suite] | [To: Chekcell Powder Indexing Helper Tool] | [To: Platon/System S Crystallographic Toolset] | [To: LHPM-Rietica Rietveld for Win95/NT] | [To: EXPO Directory Methods Structure Solution from Powder Data] | [To: Sir97 Single Crystal Structure Solution Software] | [To: WinGX Single Crystal Suite] | [To: Espoir Monte Carlo Structure Solution Software]

This example uses example Cimetidine data from the EXPO software

If EXPO gives problems, another option is to use fragment searching via single crystal (or Monte Carlo) methods.

However, the major problem you might initially encounter is how to generate the fragment. There are a number of programs that can take a 2D structure and try and convert it into a 3D structure.

Refer: Starting Links to 2D to 3D Model Builders and Molecular Modelling Software

In this tutorial, we will use the Web-based CORINA software (with Java building applet) to give us a 3D fragment.

Go to the CORINA page at http://www2.ccc.uni-erlangen.de/software/corina/free_struct.html and scroll down until you see the data entry for the SMILES string.

Corina web interface

Select the Create Molecule button to bring up the JME Molecular Editor and enter the fragment in 2D format. You may like to play with just entering a part of the structure - or the entire structure - and see what the optimisation algoirthm does. Here we have entered the entire molecule.

JME Molecular Editor

Now Submit the fragment to be minimized into a 3D conformation; and viewed with the JAVA applet (smile string it uses being CNC(=NC#N)NCCSCc1nc[NH]c1C).

JME Molecular Editor

Save the now 3D fragment into PDB file ready to import into various crystallographic software for possible structure solution. Following is the PDB file. (Platon can directly import the PDB file as well)

For instance, Ortep-3 by Louis Farrugia can import a PDB file and save it as a Shelx file in a ready to edit format.

Use File, Open File and the list box to the PDB format to import the PDB file.

Import the PDB file into Ortep-3

Import the PDB file into Ortep-3

Use File, Write SHELX File to output the file into Shelx format. (Though XYZ format is also possible)

Output the structure into Shelx INS format

PDF File

HEADER    NONAME 16-Apr-00                                              NONE   1
TITLE                                                                   NONE   2
AUTHOR    SVR4 nobody uid                                               NONE   3
REVDAT   1  16-Apr-00     0                                             NONE   4
ATOM      1  C           0      -5.282  -1.101   1.291  0.00  0.00           C+0
ATOM      2  N           0      -3.941  -0.740   0.825  0.00  0.00           N+0
ATOM      3  C           0      -3.792   0.071  -0.264  0.00  0.00           C+0
ATOM      4  N           0      -4.852   0.625  -0.826  0.00  0.00           N+0
ATOM      5  C           0      -6.069   0.503  -0.243  0.00  0.00           C+0
ATOM      6  N           0      -7.089   0.401   0.247  0.00  0.00           N+0
ATOM      7  N           0      -2.547   0.310  -0.773  0.00  0.00           N+0
ATOM      8  C           0      -1.362  -0.212  -0.086  0.00  0.00           C+0
ATOM      9  C           0      -0.101   0.297  -0.786  0.00  0.00           C+0
ATOM     10  S           0       1.365  -0.349   0.065  0.00  0.00           S+0
ATOM     11  C           0       2.672   0.395  -0.951  0.00  0.00           C+0
ATOM     12  C           0       4.019  -0.016  -0.416  0.00  0.00           C+0
ATOM     13  N           0       4.716  -1.101  -0.784  0.00  0.00           N+0
ATOM     14  C           0       5.836  -1.140  -0.115  0.00  0.00           C+0
ATOM     15  N           0       5.887  -0.071   0.707  0.00  0.00           N+0
ATOM     16  H           0       6.607   0.151   1.319  0.00  0.00           H+0
ATOM     17  C           0       4.737   0.645   0.512  0.00  0.00           C+0
ATOM     18  C           0       4.345   1.923   1.208  0.00  0.00           C+0
ATOM     19  H           0      -5.849  -1.532   0.467  0.00  0.00           H+0
ATOM     20  H           0      -5.202  -1.830   2.098  0.00  0.00           H+0
ATOM     21  H           0      -5.792  -0.210   1.656  0.00  0.00           H+0
ATOM     22  H           0      -3.159  -1.076   1.290  0.00  0.00           H+0
ATOM     23  H           0      -2.446   0.825  -1.588  0.00  0.00           H+0
ATOM     24  H           0      -1.365   0.127   0.950  0.00  0.00           H+0
ATOM     25  H           0      -1.378  -1.301  -0.112  0.00  0.00           H+0
ATOM     26  H           0      -0.099  -0.041  -1.822  0.00  0.00           H+0
ATOM     27  H           0      -0.086   1.387  -0.760  0.00  0.00           H+0
ATOM     28  H           0       2.570   0.053  -1.981  0.00  0.00           H+0
ATOM     29  H           0       2.583   1.481  -0.918  0.00  0.00           H+0
ATOM     30  H           0       6.596  -1.902  -0.205  0.00  0.00           H+0
ATOM     31  H           0       4.715   2.776   0.639  0.00  0.00           H+0
ATOM     32  H           0       3.259   1.979   1.282  0.00  0.00           H+0
ATOM     33  H           0       4.778   1.939   2.209  0.00  0.00           H+0
CONECT    1    2   19   20   21                                         NONE  38
CONECT    2    1    3   22    0                                         NONE  39
CONECT    3    2    4    7    0                                         NONE  40
CONECT    4    3    5    0    0                                         NONE  41
CONECT    5    4    6    0    0                                         NONE  42
CONECT    6    5    0    0    0                                         NONE  43
CONECT    7    3    8   23    0                                         NONE  44
CONECT    8    7    9   24   25                                         NONE  45
CONECT    9    8   10   26   27                                         NONE  46
CONECT   10    9   11    0    0                                         NONE  47
CONECT   11   10   12   28   29                                         NONE  48
CONECT   12   11   13   17    0                                         NONE  49
CONECT   13   12   14    0    0                                         NONE  50
CONECT   14   13   15   30    0                                         NONE  51
CONECT   15   14   16   17    0                                         NONE  52
CONECT   17   15   12   18    0                                         NONE  53
CONECT   18   17   31   32   33                                         NONE  54
END                                                                     NONE  55

Shelx File

TITL
CELL    0.71073   10.0000   10.0000   10.0000   90.0000   90.0000   90.0000
ZERR      1    0.0010    0.0010    0.0010    0.0100    0.0100    0.0100
LATT   1
SFAC   C   N   S   H
UNIT     10   6   1  16
FVAR   1.0
H        4  -0.52020  -0.18300   0.20980    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4   0.47780   0.19390   0.22090    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4  -0.57920  -0.02100   0.16560    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4   0.66070   0.01510   0.13190    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
C        1  -0.52820  -0.11010   0.12910    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4  -0.31590  -0.10760   0.12900    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
C        1   0.43450   0.19230   0.12080    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4   0.32590   0.19790   0.12820    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
N        2   0.58870  -0.00710   0.07070    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
N        2  -0.39410  -0.07400   0.08250    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4  -0.58490  -0.15320   0.04670    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4  -0.13650   0.01270   0.09500    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
N        2  -0.70890   0.04010   0.02470    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
C        1   0.47370   0.06450   0.05120    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4   0.47150   0.27760   0.06390    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4   0.65960  -0.19020  -0.02050    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
C        1   0.58360  -0.11400  -0.01150    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
S        3   0.13650  -0.03490   0.00650    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
C        1  -0.60690   0.05030  -0.02430    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4  -0.13780  -0.13010  -0.01120    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
C        1  -0.13620  -0.02120  -0.00860    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
C        1  -0.37920   0.00710  -0.02640    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
C        1   0.40190  -0.00160  -0.04160    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
N        2   0.47160  -0.11010  -0.07840    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
N        2  -0.48520   0.06250  -0.08260    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
N        2  -0.25470   0.03100  -0.07730    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
C        1  -0.01010   0.02970  -0.07860    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
C        1   0.26720   0.03950  -0.09510    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4  -0.00860   0.13870  -0.07600    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4   0.25830   0.14810  -0.09180    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4  -0.24460   0.08250  -0.15880    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4  -0.00990  -0.00410  -0.18220    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
H        4   0.25700   0.00530  -0.19810    11.00000     0.03000   0.03000 =
         0.03000   0.00000   0.00000   0.00000
HKLF     4
END

[Back to: Problems and Solutions] | [Back to: Tutorials]
[Back to: Powder Diffraction Structure Solution Pathways Index]
[Back to: Solving an Organic Structure (Cimetidine) from Powder Diffraction Data]
[Back to: Initial Connectivity Searching of the Cambridge database for Cimetidine like molecules using CORINA, Platon and Quest/CSD]
[Back to: Peak Profiling of Cimetidine using XFIT]
[Back to: Powder Indexing and Spacegroup Assignment of Cimetidine using the Crysfire and Chekcell combination of programs]
[Back to: CELL Searching the Cambridge database via Platon and Quest]
[Back to: Le Bail fitting and generating an EXPO starting file using LHPM-Rietica]
[Back to: Solve the structure of Cimetidine using the Sireware EXPO direct methods software]
[Back to: Finding possibly missing Symmetry in cimetidine using the Platon ADDSYM option]
[Back to: Searching the Cambridge database via Platon and Quest for related strutures]
[Back to: Generating a 2D to 3D fragement for fragment searching using the web based CORINA; then getting into a Shelx format using Ortep-3]
[Back to: Solve the structure of Cimetidine using Sir97 Single Crystal Direct Methods Software]
[Back to: Solve the structure of Cimetidine using Dirdif fragment searching]
[Back to: Solve the structure of Cimetidine using ESPOIR with no restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with bond restraints]
[Back to: Solve the structure of Cimetidine using ESPOIR with a combination of rigid bodies freely moving atoms]
[To: Xfit-Koalariet Peak Profiling Software] | [To: Crysfire Powder Indexing Suite] | [To: Chekcell Powder Indexing Helper Tool] | [To: Platon/System S Crystallographic Toolset] | [To: LHPM-Rietica Rietveld for Win95/NT] | [To: EXPO Directory Methods Structure Solution from Powder Data] | [To: Sir97 Single Crystal Structure Solution Software] | [To: WinGX Single Crystal Suite] | [To: Espoir Monte Carlo Structure Solution Software]
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