CONFLEX Tutorials

Crystal structure search

Polymorphism phenomenon is often observed for organic molecules. CONFLEX can search possible crystal structures of an organic molecule including not only packing polymorphs but also conformational polymorphs using the original algorithm [Ishii, H., Obata, S., Niitsu, N. et al. Sci. Rep. 10, 2524 (2020).].

[Crystal structure search from a structural formula]

Cambridge Crystallographic Data Center (CCDC) carries out blind tests of crystal structure prediction (CSP) on a regular basis [P.M. Lommerse, et al, Acta Cryst. B56, 697-714, 2000]. Here, for explaining the prediction of crystal structures by CONFLEX program, we employ 5-Cyano-3-hydroxythiophene (II) (refer to the below figure) which was used in CSP blind test.

Cyano Hydroxythiophene
Structural formula of 5-Cyano-3-hydroxythiophene (II)

First, we create a molecular file for II by using PerkinElmer ChemDraw software. Please see a manual of ChemDraw for getting how to use that.

ChemDraw Cyano Hydroxythiophene
Creation of molecular file of II by ChemDraw software

The molecular file of II is saved as “II.mol” using MDL-MOL file format.

II.mol file

II.mol
ChemDraw08301910352D

  8  8  0  0  0  0  0  0  0  0999 V2000
    0.2633    0.3011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0883    0.3011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0083   -0.4836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6758   -0.9685    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    1.3432   -0.4836    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5732    0.9685    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7763   -0.7385    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5732   -0.9520    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0      
  1  3  2  0      
  3  4  1  0      
  4  5  1  0      
  5  2  2  0      
  2  6  1  0      
  3  7  1  0      
  7  8  3  0      
M  END

Next, we optimize the single molecular structure of II.

[Execution by Interface]

Open the II.mol file by CONFLEX Interface.

Interface Cyano Hydroxythiophene

Select [CONFLEX] in Calculation menu, and click Submit in the calculation setting dialog displayed. The structure optimization of II will start.

Basic Dialog

[Execution by command line]

Store the II.mol in a folder, and execute below command. The structure optimization of II will start. When you do not prepare an ini file, CONFLEX performs the optimization of input structure in default setting.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   IIenter

The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].

Next, we perform a conformation search of II.

[Execution by Interface]

Open the II-F.mol file by CONFLEX Interface.

Interface II-F

Select [CONFLEX] in Calculation menu, and select [Conformation Search] in the pull-down menu of [Calculation Type:] on the calculation setting dialog displayed.
Edit value of [Search Limit:] to 10.0. This parameter is used as a criteria for selecting initial structure in the conformation search. When the calculation settings are complete, click Submit. The calculation will start.

Basic Interface

[Execution by command line]

The calculation settings are defined by describing keywords in the II-F.ini file.

II-F.ini file

CONFLEX SEL=10.0

[CONFLEX] means to execute a conformation search.
[SEL=10.0] means that a search limit, which is used as a criteria for selecting initial structure in the conformation search, sets to 10.0 kcal/mol.

Store the two files of II-F.mol and II-F.ini in an one folder, and execute below command. The calculation will start.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   II-Fenter

The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].

After the conformation search, we can get two conformers of II. Here, we employ the second most stable conformer for a calculation of crystal structure search.
We extract structure data of the selected conformer from “II-F.sdf” file and save as “II-c2.mol”. The II-F.sdf file is in the folder contained the II-F.mol file. When you executed the conformation search by using Interface, the file name may be II-F_conv.sdf.

II-c2.mol file

II.mol                                                                          
CONFLEX 19083010373D 1   1.00000     4.54816     1                            
CS  ,E =       4.548, G = 0.974E-10, P =  48.3970, M( 0), IFN =00000002-00000001
 11 11  0     0               999 V2000
    1.1214   -0.0104    0.0000 C   0  0  0  0  0     
    0.7822   -1.3858    0.0000 C   0  0  0  0  0     
   -0.0000    0.7946   -0.0000 C   0  0  0  0  0     
   -1.4433   -0.1296   -0.0000 S   0  0  0  0  0     
   -0.5732   -1.6069    0.0000 C   0  0  0  0  0     
    1.6924   -2.3749    0.0000 O   0  0  0  0  0     
    0.0137    2.2245   -0.0000 C   0  0  0  0  0     
    0.0454    3.3854   -0.0000 N   0  0  0  0  0     
    2.1374    0.3665    0.0000 H   0  0  0  0  0     
   -1.1076   -2.5464    0.0000 H   0  0  0  0  0     
    1.2623   -3.2477    0.0000 H   0  0  0  0  0     
  1  2  1  0     0
  1  3  2  0     0
  3  4  1  0     0
  4  5  1  0     0
  5  2  2  0     0
  2  6  1  0     0
  3  7  1  0     0
  7  8  3  0     0
  1  9  1  0     0
  5 10  1  0     0
  6 11  1  0     0
M  END

Next, we perform a crystal structure search of II.

[Execution by Interface]

Open the II-c2.mol file by CONFLEX Interface.

Interface II_c2

Select [CONFLEX] in Calculation menu, and click Detail Settings in the calculation setting dialog displayed. A detail setting dialog will be displayed.

Basic Settings

In order to perform the crystal structure search, in [General Settings] dialog on the detail setting dialog, select [Crystal Search] in the pull-down menu of [Calculation Type:].

General Settings

Method of crystal structure optimization is [ALL] in default setting. You can change the type of crystal structure optimization by the pull-down menu of [Crystal optimization:] in [Crystal Calculation] dialog.
In this dialog, we can also change settings for calculating intermolecular interactions such as cutoff distance, calculation method of coulombic interactions, and so on.

Crystal Opt

Next, we set parameters for the crystal structure search by [Crystal Search] dialog.
First, to select space groups using in the search, click Select of [Search Space Group:].

Interface Crystal Search

The dialog displayed is showing top 10 space groups in the space group frequency ranking which is provided by CCDC. Check the check boxes of all space groups, and click OK.

Interface SPGP

[Rotation Method:] and [Position Prediction Method:] set methods to determine initial molecular orientation and position, respectively. Here, both the methods set to [Random]. If you want to search in detail, each method should set to [Grid] and [Full], respectively.
[Trial Structures:] sets the number of trial structures that are created for the search. Here, the number of trial structures sets to 10000. If you use more large number, you can perform more accuracy search but a computational cost becomes high.

Crystal Search Set

When the calculation settings are complete, click Submit. The calculation will start.

[Execution by command line]

The calculation settings are defined by describing keywords in the II-c2.ini file.

II-c2.ini file

CRYSTAL_SEARCH
CSP_SPGP=(P21/C,P-1,C2/C,P212121,P21,PBCA,PNA21,PNMA,CC,P1)  
CSP_ROT_MODE=RANDOM 
CSP_AUS_MODE=RANDOM 
CSP_MAX_CRYSTAL=10000  
CRYSTAL_OPTIMIZATION=ALL  

[CRYSTAL_SEARCH] means to execute a crystal structure search.
Space groups using in the search are defined by [CSP_SPGP=] keyword. Here, we use P21/c, P-1, C2/c, P212121, P21, Pbca, Pna21, Pnma, Cc, and P1 that are top 10 space groups in the space group frequency ranking which is provided by CCDC.
[CSP_ROT_MODE=] and [CSP_AUS_MODE=] set methods to determine initial molecular orientation and position, respectively. Here, both the methods set to [Random]. If you want to search in detail, each method should set to [Grid] and [Full], respectively.
[CSP_MAX_CRYSTAL=] sets the number of trial structures that are created for the search. Here, the number of trial structures sets to 10000. If you use more large number, you can perform more accuracy search but a computational cost becomes high.
Method of crystal structure optimization is defined by [CRYSTAL_OPTIMIZATION=] keyword and sets to “ALL”. The “ALL” optimization relaxes molecular geometry, position, and orientation and cell dimensions of the crystal.

Store the two files of II-c2.mol and II-c2.ini in an one folder, and execute below command. The calculation will start.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   II-c2enter

The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].

Calculation results

After the calculation of crystal structure search, you can get II-C2.csp file that describes results of the search calculation in detail.
In the part of [*** PREDICTED CRYSTAL STRUCTURES:] of the II-c2.csp file, computationally suggested polymorphs of II are shown in order of crystal energy.
Structure data of the polymorphs are stored in II-c2-PCS.cif file.

 *** PREDICTED CRYSTAL STRUCTURES:

    IDX    CID    E_RNK     CRYST      INTRA      INTER        VOL      DES        A         B         C       ALPHA     BETA      GAMMA     SPGP      NCALMOL   NCALATM    DMAX    NNEV 
      1    571      1     -15.7921     4.6942   -20.4864    607.6657   1.3663    9.5996    8.3419   10.7545   90.0000  135.1221   90.0000   P21/C          365      4015    20.00     0    
     39   5295      2     -15.6634     4.7074   -20.3708    306.9963   1.3522   11.0245    7.0951    4.3469   90.0000  115.4610   90.0000   P21            371      4081    20.00     0    
     89    150      3     -15.6476     4.6816   -20.3292    606.6216   1.3686    7.2689    8.3106   10.7652   90.0000  111.1225   90.0000   P21/C          375      4125    20.00     0    
    170   3622      4     -15.6125     4.7219   -20.3344    614.2783   1.3515    4.3718   19.8181    7.0899   90.0000   90.0000   90.0000   P212121        373      4103    20.00     0    
    183   3677      5     -15.6089     4.6925   -20.3014    612.8164   1.3548    7.6268    9.6305    8.3433   90.0000   90.0000   90.0000   P212121        355      3905    20.00     0    
    204    404      6     -15.5986     4.7162   -20.3147    614.9313   1.3501    4.3234    7.1069   20.0163   90.0000   89.0064   90.0000   P21/C          371      4081    20.00     0    
    221     51      7     -15.4618     4.7170   -20.1789    618.7977   1.3417    4.3746    7.0720   20.4156   90.0000   78.4425   90.0000   P21/C          374      4114    20.00     0    
    229   2134      8     -15.3029     4.7145   -20.0173   1222.4436   1.3583   14.5999    8.3633   10.4384   90.0000   73.5604   90.0000   C2/C           357      3927    20.00     0    
    236    215      9     -15.2948     4.7210   -20.0158    612.9536   1.3545    4.0230    8.3785   18.2131   90.0000   86.8178   90.0000   P21/C          358      3938    20.00     0    
    263     28     10     -15.2940     4.7263   -20.0203    612.5302   1.3554    8.3759   18.2972    8.8552   90.0000   26.8303   90.0000   P21/C          365      4015    20.00     0    

Here, comparing the experimental structure (left figure) and the 1st structure (right figure), you can see that both the structures match well.

Crystal Search CSP II

[Crystal structure search for a multi component system]

This section explains a crystal structure search of an asymmetric unit with multi component.
Here, we employ a co-crystal of 2-amino-4-methylpyrimidine and 2-methylbenzoic acid which was used in CSP blind test.
First, molecular files of 2-amino-4-methylpyrimidine and 2-methylbenzoic acid are made by using PerkinElmer ChemDraw software. Please see a manual of ChemDraw for getting how to use that.

The molecular file of 2-amino-4-methylpyrimidine is saved as “AMP.mol” using MDL-MOL file format.

ChemDraw AMP

AMP.mol file

AMP.mol
ChemDraw09022015212D

  8  8  0  0  0  0  0  0  0  0999 V2000
   -0.7145    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    0.4125    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0      
  2  3  1  0      
  3  4  2  0      
  4  5  1  0      
  5  6  2  0      
  6  1  1  0      
  2  7  1  0      
  4  8  1  0      
M  END

The molecular file of 2-methylbenzoic acid is saved as “MBA.mol” using MDL-MOL file format.

ChemDraw MBA

MBA.mol file

MBA.mol
ChemDraw09022015232D

 10 10  0  0  0  0  0  0  0  0999 V2000
   -1.0717   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572   -1.4438    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    1.4438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572    1.4438    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  8  9  2  0      
  8 10  1  0      
  6  8  1  0      
  1  2  2  0      
  2  3  1  0      
  3  4  2  0      
  4  5  1  0      
  5  6  2  0      
  6  1  1  0      
  5  7  1  0      
M  STY  1   1 SUP
M  SLB  1   1   1
M  SAL   1  3   8   9  10
M  SBL   1  1   3
M  SMT   1 COOH
M  SBV   1   3    0.0000   -0.8250
M  END

Next, structure optimizations of 2-amino-4-methylpyrimidine and 2-methylbenzoic acid are performed.

[Execution by Interface]

Open the AMP.mol file by CONFLEX Interface.

Interface AMP

Select [CONFLEX] in Calculation menu, and click Submit in the calculation setting dialog displayed. The structure optimization of 2-amino-4-methylpyrimidine will start.

Basic Settings

Next, open the MBA.mol file by CONFLEX Interface.

Interface MBA

Select [CONFLEX] in Calculation menu, and click Submit in the calculation setting dialog displayed. The structure optimization of 2-methylbenzoic acid will start.

Basic Settings

[Execution by command line]

Store the AMP.mol and MBA.mol in a folder, and execute below commands. The structure optimizations will start.
When you do not prepare ini files, CONFLEX performs the optimizations of input structures in default setting.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   AMP
enter
C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   MBA
enter

The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].

The 2-methylbenzoic acid molecule has some conformations. Therefore, we should perform a conformation search of 2-methylbenzoic acid.

[Execution by Interface]

Open the MBA-F.mol file by CONFLEX Interface.

Interface MBA-F

Select [CONFLEX] in Calculation menu, and select [Conformation Search] in the pull-down menu of [Calculation Type:] on the calculation setting dialog displayed.
Edit value of [Search Limit:] to 10.0. This parameter is used as a criteria for selecting initial structure in the conformation search.
When the calculation settings are complete, click Submit. The calculation will start.

Interface MBA cs

[Execution by command line]

The calculation settings are defined by describing keywords in the MBA-F.ini file.

MBA-F.ini file

CONFLEX SEL=10.0

[CONFLEX] means to execute a conformation search.
[SEL=10.0] means that a search limit, which is used as a criteria for selecting initial structure in the conformation search, set to 10.0 kcal/mol.

Store the two files of MBA-F.mol and MBA-F.ini in an one folder, and execute below command. The calculation will start.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   MBA-Fenter

The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].

After the conformation search, we can get seven conformers of 2-methylbenzoic acid.
Here, we employ the most stable conformer for a next calculation. Structure data of the selected conformer is extracted from “MBA-F.sdf” file and saved as “MBA-c1.mol”. The MBA-F.sdf file is in the folder contained the MBA-F.mol file.

MBA-c1.mol file

MBA.mol                                                                         
CONFLEX 20090215293D 1   1.00000    16.90241     3                            
CS  ,E =      16.902, G = 0.213E-06, P =  89.7913, M( 0), IFN =00000001-00000003
 18 18  0     0               999 V2000
   -1.3006    0.8083    0.0000 C   0  0  0  0  0     
   -2.4209   -0.0240    0.0000 C   0  0  0  0  0     
   -2.2574   -1.4041    0.0000 C   0  0  0  0  0     
   -0.9754   -1.9534   -0.0000 C   0  0  0  0  0     
    0.1671   -1.1315   -0.0000 C   0  0  0  0  0     
   -0.0000    0.2708    0.0000 C   0  0  0  0  0     
    1.5196   -1.7909   -0.0000 C   0  0  0  0  0     
    1.1760    1.1942    0.0000 C   0  0  0  0  0     
    2.3544    0.8930    0.0000 O   0  0  0  0  0     
    0.8165    2.4930   -0.0000 O   0  0  0  0  0     
   -1.4568    1.8849    0.0000 H   0  0  0  0  0     
   -3.4187    0.4075    0.0000 H   0  0  0  0  0     
   -3.1277   -2.0558    0.0000 H   0  0  0  0  0     
   -0.8717   -3.0372   -0.0000 H   0  0  0  0  0     
    2.0811   -1.5139    0.8977 H   0  0  0  0  0     
    1.4333   -2.8831   -0.0000 H   0  0  0  0  0     
    2.0811   -1.5139   -0.8977 H   0  0  0  0  0     
    1.6744    2.9669   -0.0000 H   0  0  0  0  0     
  8  9  2  0     0
  8 10  1  0     0
  6  8  1  0     0
  1  2  2  0     0
  2  3  1  0     0
  3  4  2  0     0
  4  5  1  0     0
  5  6  2  0     0
  6  1  1  0     0
  5  7  1  0     0
  1 11  1  0     0
  2 12  1  0     0
  3 13  1  0     0
  4 14  1  0     0
  7 15  1  0     0
  7 16  1  0     0
  7 17  1  0     0
 10 18  1  0     0
M  END

Next, by using the AMP-F.mol and MBA-c1.mol files, a structure file for a molecular complex of 2-amino-4-methylpyrimidine and 2-methylbenzoic acid is made, and it saves as “XV.mol”.
The XV.mol file makes by adding data of atomic coordinates and bond information in the MBA-c1.mol to the AMP-F.mol file. The 4th line in the XV.mol, “33 33”, shows the number of atoms and bonds in the complex, respectively.

The bond information, “  1  2  2  0     0”, means that the atoms 1 and 2 are bonded by a double bond. Therefore, when you add the bond information of 2-methylbenzoic acid to the AMP-F.mol file, you should change the original serial number of atoms in the bond information. For an example, change from “  8  9  2  0     0” to “ 23 24  2  0     0”.

XV.mol file

XV.mol                                                                         


 33 33  0     0               999 V2000
    1.2096   -1.0822   -0.0000 C   0  0  0  0  0     
    1.1638    0.2958    0.0000 C   0  0  0  0  0     
   -0.0000    0.9788    0.0000 N   0  0  0  0  0     
   -1.1295    0.2628    0.0000 C   0  0  0  0  0     
   -1.1861   -1.0719    0.0000 N   0  0  0  0  0     
   -0.0075   -1.7194   -0.0000 C   0  0  0  0  0     
    2.4311    1.0955   -0.0000 C   0  0  0  0  0     
   -2.3091    0.9449   -0.0000 N   0  0  0  0  0     
    2.1397   -1.6334   -0.0000 H   0  0  0  0  0     
   -0.0748   -2.8030   -0.0000 H   0  0  0  0  0     
    2.2152    2.1688    0.0000 H   0  0  0  0  0     
    3.0226    0.8673    0.8921 H   0  0  0  0  0     
    3.0226    0.8673   -0.8921 H   0  0  0  0  0     
   -3.1598    0.4121   -0.0000 H   0  0  0  0  0     
   -2.2706    1.9481   -0.0000 H   0  0  0  0  0     
   -1.3006    0.8083    0.0000 C   0  0  0  0  0     
   -2.4209   -0.0240    0.0000 C   0  0  0  0  0     
   -2.2574   -1.4041    0.0000 C   0  0  0  0  0     
   -0.9754   -1.9534   -0.0000 C   0  0  0  0  0     
    0.1671   -1.1315   -0.0000 C   0  0  0  0  0     
   -0.0000    0.2708    0.0000 C   0  0  0  0  0     
    1.5196   -1.7909   -0.0000 C   0  0  0  0  0     
    1.1760    1.1942    0.0000 C   0  0  0  0  0     
    2.3544    0.8930    0.0000 O   0  0  0  0  0     
    0.8165    2.4930   -0.0000 O   0  0  0  0  0     
   -1.4568    1.8849    0.0000 H   0  0  0  0  0     
   -3.4187    0.4075    0.0000 H   0  0  0  0  0     
   -3.1277   -2.0558    0.0000 H   0  0  0  0  0     
   -0.8717   -3.0372   -0.0000 H   0  0  0  0  0     
    2.0811   -1.5139    0.8977 H   0  0  0  0  0     
    1.4333   -2.8831   -0.0000 H   0  0  0  0  0     
    2.0811   -1.5139   -0.8977 H   0  0  0  0  0     
    1.6744    2.9669   -0.0000 H   0  0  0  0  0     
  1  2  2  0     0
  2  3  1  0     0
  3  4  2  0     0
  4  5  1  0     0
  5  6  2  0     0
  6  1  1  0     0
  2  7  1  0     0
  4  8  1  0     0
  1  9  1  0     0
  6 10  1  0     0
  7 11  1  0     0
  7 12  1  0     0
  7 13  1  0     0
  8 14  1  0     0
  8 15  1  0     0
 23 24  2  0     0
 23 25  1  0     0
 21 23  1  0     0
 16 17  2  0     0
 17 18  1  0     0
 18 19  2  0     0
 19 20  1  0     0
 20 21  2  0     0
 21 16  1  0     0
 20 22  1  0     0
 16 26  1  0     0
 17 27  1  0     0
 18 28  1  0     0
 19 29  1  0     0
 22 30  1  0     0
 22 31  1  0     0
 22 32  1  0     0
 25 33  1  0     0
M  END

Next, in order to determine possible molecular positions of 2-amino-4-methylpyrimidine and 2-methylbenzoic acid in the molecular complex, a host-ligand configuration search is performed.

[Execution by Interface]

Open the XV.mol file by CONFLEX Interface. Both the molecules are clashed at the moment, but the molecular positions change according to a search algorithm.

Interface XV

Select [CONFLEX] in Calculation menu, and click Detail Settings in the calculation setting dialog displayed. A detail setting dialog will be displayed.

Basic Settings

In order to perform the host-ligand configuration search, in [General Settings] dialog on the detail setting dialog, select [Host Ligand Search] in the pull-down menu of [Calculation Type:].

General Settings HL

Settings of the host-ligand configuration search calculation are made in [Host Ligand Search] dialog.

Interface HL

Here, in order to rotate the 2-methylbenzoic acid molecule assigned as a ligand by a step of 45 degrees, each value of “Rotational number x, y, z” sets to 8, respectively.
When you complete the settings, click Submit. The calculation will start.

[Execution by command line]

The calculation settings are defined by describing keywords in the XV.ini file.

XV.ini file

HLSEARCH  
HLSEARCH_LIGAND_ROT=(8,8,8) 

[HLSEARCH] means to execute a host-ligand configuration search calculation.
[HLSEARCH_LIGAND_ROT=(8,8,8)] is for rotating the 2-methylbenzoic acid molecule assigned as a ligand by a step of 45 degrees around x, y, and z axes.

Store the two files of XV.mol and XV.ini in an one folder, and execute below command. The calculation will start.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   XVenter

The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].

After the calculation, we can get 47 structures of the complex. Here, we employ the most stable structure for a crystal structure search. Structure data of the selected structure is extracted from “XV.sdf” file and saved as “XV-c1.mol”. The XV.sdf file is in the folder contained the XV.mol file.

XV-c1.mol file

XV.mol                                                                          
CONFLEX 20090215503D 1   1.00000   -86.91814    17                            
NONE,E =     -86.918, G = 0.249E-06, P =  20.9930, M( 0), IFN =00000001-00000017
 33 33  0     0               999 V2000
   -4.6389    1.0672    0.0877 C   0  0  0  0  0     
   -3.2840    1.2059    0.3058 C   0  0  0  0  0     
   -2.4142    0.1779    0.1589 N   0  0  0  0  0     
   -2.9370   -1.0122   -0.1834 C   0  0  0  0  0     
   -4.2342   -1.2388   -0.4067 N   0  0  0  0  0     
   -5.0617   -0.1892   -0.2687 C   0  0  0  0  0     
   -2.7235    2.5426    0.6933 C   0  0  0  0  0     
   -2.0889   -2.0671   -0.3182 N   0  0  0  0  0     
   -5.3328    1.8902    0.1921 H   0  0  0  0  0     
   -6.1102   -0.3980   -0.4587 H   0  0  0  0  0     
   -1.6892    2.4500    1.0374 H   0  0  0  0  0     
   -2.7441    3.2203   -0.1656 H   0  0  0  0  0     
   -3.3069    2.9800    1.5099 H   0  0  0  0  0     
   -2.4812   -2.9552   -0.5738 H   0  0  0  0  0     
   -1.0952   -1.9477   -0.1563 H   0  0  0  0  0     
    2.8428    1.4208   -0.4637 C   0  0  0  0  0     
    4.1800    1.8122   -0.5390 C   0  0  0  0  0     
    5.1849    0.9050   -0.2233 C   0  0  0  0  0     
    4.8550   -0.3923    0.1698 C   0  0  0  0  0     
    3.5126   -0.8046    0.2572 C   0  0  0  0  0     
    2.4937    0.1165   -0.0682 C   0  0  0  0  0     
    3.2239   -2.2160    0.6905 C   0  0  0  0  0     
    1.0518   -0.2696   -0.0173 C   0  0  0  0  0     
    0.6010   -1.3998    0.0329 O   0  0  0  0  0     
    0.2426    0.8063   -0.0191 O   0  0  0  0  0     
    2.0730    2.1442   -0.7236 H   0  0  0  0  0     
    4.4339    2.8231   -0.8471 H   0  0  0  0  0     
    6.2281    1.2054   -0.2833 H   0  0  0  0  0     
    5.6587   -1.0857    0.4113 H   0  0  0  0  0     
    2.7876   -2.7870   -0.1349 H   0  0  0  0  0     
    4.1382   -2.7349    0.9990 H   0  0  0  0  0     
    2.5491   -2.2242    1.5524 H   0  0  0  0  0     
   -0.6842    0.4546    0.0376 H   0  0  0  0  0     
  1  2  2  0     0
  2  3  1  0     0
  3  4  2  0     0
  4  5  1  0     0
  5  6  2  0     0
  6  1  1  0     0
  2  7  1  0     0
  4  8  1  0     0
  1  9  1  0     0
  6 10  1  0     0
  7 11  1  0     0
  7 12  1  0     0
  7 13  1  0     0
  8 14  1  0     0
  8 15  1  0     0
 23 24  2  0     0
 23 25  1  0     0
 21 23  1  0     0
 16 17  2  0     0
 17 18  1  0     0
 18 19  2  0     0
 19 20  1  0     0
 20 21  2  0     0
 21 16  1  0     0
 20 22  1  0     0
 16 26  1  0     0
 17 27  1  0     0
 18 28  1  0     0
 19 29  1  0     0
 22 30  1  0     0
 22 31  1  0     0
 22 32  1  0     0
 25 33  1  0     0
M  END

Finally, we perform the crystal structure search.

[Execution by Interface]

Open the XV-c1.mol file by CONFLEX Interface.

Interface XV c1

Select [CONFLEX] in Calculation menu, and click Detail Settings in the calculation setting dialog displayed. A detail setting dialog will be displayed.

Basic Settings

In order to perform the crystal structure search, in [General Settings] dialog on the detail setting dialog, select [Crystal Search] in the pull-down menu of [Calculation Type:].

General Settings

Method of crystal structure optimization is [ALL] in default setting. You can change the type of crystal structure optimization by the pull-down menu of [Crystal optimization:] in [Crystal Calculation] dialog.
In this dialog, we can also change settings for calculating intermolecular interactions such as cutoff distance, calculation method of coulombic interactions, and so on.

Crystal Opt

Next, we make settings for the crystal structure search by [Crystal Search] dialog.

Crystal Search XV

In order to use space group of P21/c, edit the [Search Space Group:] from “P21/C,P212121” to “P21/C”.
When the calculation settings are complete, click Submit. The calculation will start.

[Execution by command line]

The calculation settings are defined by describing keywords in the XV-c1.ini file.

XV-c1.ini file

CRYSTAL_SEARCH 
CSP_SPGP=(P21/C)

[CRYSTAL_SEARCH] means to execute a crystal structure search.
Space groups using in the crystal structure search are defined by “CSP_SPGP=” keyword. Here, “CSP_SPGP=(P21/C)” sets, that is, the P21/c is applied to the search.

Store the two files of XV-c1.mol and XV-c1.ini in an one folder, and execute below command. The calculation will start.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   XV-c1enter

The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].

Calculation results

After the calculation, you can get XV-c1.csp file that describes results of the search calculation in detail.
In the part of [*** PREDICTED CRYSTAL STRUCTURES:] of the XV-c1.csp file, computationally suggested polymorphs of 2-amino-4-methylpyrimidine and 2-methylbenzoic acid co-crystal are shown in order of crystal energy.
Structure data of the polymorphs are stored in XV-c1-PCS.cif file.

 *** PREDICTED CRYSTAL STRUCTURES:

    IDX    CID    E_RNK     CRYST      INTRA      INTER        VOL      DES        A         B         C       ALPHA     BETA      GAMMA     SPGP      NCALMOL   NCALATM    DMAX    NNEV 
     10    166      1    -112.2561   -73.1657   -39.0905   1384.6750   1.1758    6.3597   14.7215   17.2181   90.0000  120.8001   90.0000   P21/C          426      7035    20.00     0    
     15   2275      2    -112.2287   -73.4042   -38.8245   1407.5982   1.1567   14.6059   11.7504    9.5465   90.0000   59.2174   90.0000   P21/C          412      6810    20.00     0    
     16    207      3    -112.1190   -73.0217   -39.0973   1373.5185   1.1854   12.8837   14.8932   13.7315   90.0000  148.5805   90.0000   P21/C          421      6951    20.00     0    
     17   1026      4    -112.0257   -72.0386   -39.9871   1368.6700   1.1895    8.9646    9.9375   15.9967   90.0000  106.1736   90.0000   P21/C          431      7128    20.00     0    
     24     93      5    -111.9827   -73.1843   -38.7984   1399.2561   1.1635    6.4118   15.4366   15.2107   90.0000  111.6533   90.0000   P21/C          424      6996    20.00     0    
     25   2294      6    -111.8335   -73.1270   -38.7065   1409.7873   1.1549   13.5655   12.0776    8.6539   90.0000   96.1068   90.0000   P21/C          421      6948    20.00     0    
     27    488      7    -111.7751   -73.3963   -38.3788   1415.1006   1.1505   13.0894   10.0679   11.9525   90.0000  116.0510   90.0000   P21/C          430      7092    20.00     0    
     29    156      8    -111.7587   -73.2931   -38.4656   1403.7919   1.1598   15.1088   11.1575    8.6903   90.0000  106.6192   90.0000   P21/C          420      6936    20.00     0    
     32    308      9    -111.7046   -72.2275   -39.4771   1399.2931   1.1635    7.1345   12.0828   17.0823   90.0000   71.8502   90.0000   P21/C          426      7035    20.00     0    
     33   2528     10    -111.5790   -72.6694   -38.9096   1366.5010   1.1914    7.8968   23.9564    8.1596   90.0000  117.7171   90.0000   P21/C          431      7125    20.00     0    

Here, comparing the experimental structure (left figure) and the 3rd structure (right figure), you can see that both the structures match well.

Crystal Search CSP XV

[Crystal structure search using PXRD data]

We explain how to apply CONFLEX to a crystal structure determination from powder X-ray diffraction (PXRD) data. Here, we use the crystal structure of pamonic acid that was reported by Haynes et al [D. A. Haynes et al., Acta Cryst. 2006, E62, o1170.].
First, we create a molecular file for pamonic acid by using PerkinElmer ChemDraw software. Please see a manual of ChemDraw for getting how to use that.

The molecular file of pamonic acid is saved as “pamonic-acid.mol” using MDL-MOL file format.

ChemDraw Pamo

pamonic-acid.mol file

pamoic-acid.mol
ChemDraw10031813162D

 29 32  0  0  0  0  0  0  0  0999 V2000
   -2.1471   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4326   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4326    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1471    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8616    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8616   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5761   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5761   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8616   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1471   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4294   -1.0931    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7182   -0.4538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4326   -0.8662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1471   -0.4538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1471    0.3712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4326    0.7837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7182    0.3712    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4326    1.6087    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7182    2.0212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0037    1.6087    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0037    0.7837    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4326   -1.6912    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8616   -0.8663    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5761   -0.4538    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8616   -1.6913    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1471    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8616    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4326    2.0625    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7182    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0      
  2  3  1  0      
  3  4  2  0      
  4  5  1  0      
  5  6  2  0      
  6  1  1  0      
  6  7  1  0      
  7  8  2  0      
  8  9  1  0      
  9 10  2  0      
 10  1  1  0      
  2 11  1  0      
 11 12  1  0      
 12 13  1  0      
 13 14  2  0      
 14 15  1  0      
 15 16  2  0      
 16 17  1  0      
 17 12  2  0      
 16 18  1  0      
 18 19  2  0      
 19 20  1  0      
 20 21  2  0      
 21 17  1  0      
 13 22  1  0      
 14 23  1  0      
 23 24  2  0      
 23 25  1  0      
  4 26  1  0      
 26 27  2  0      
 26 28  1  0      
  3 29  1  0     
M  END

Next, we optimize the single molecular structure of pamonic acid.

[Execution by Interface]

Open the pamonic-acid.mol file by CONFLEX Interface.

Interface Pamo

Select [CONFLEX] in Calculation menu, and click Submit in the calculation setting dialog displayed. The structure optimization of II will start.

Basic Settings

[Execution by command line]

Store the pamonic-acid.mol in a folder, and execute below command. The structure optimization of pamonic acid will start. When you do not prepare an ini file, CONFLEX performs the optimization of input structure in default setting.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   pamonic-acidenter

The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].

Next, we perform a conformation search of pamonic acid.

[Execution by Interface]

Open the pamonic-acid-F.mol file by CONFLEX Interface.

Interface Opt Pamo

Select [CONFLEX] in Calculation menu, and select [Conformation Search] in the pull-down menu of [Calculation Type:] on the calculation setting dialog displayed.
Edit value of [Search Limit:] to 30.0. This parameter is used as a criteria for selecting initial structure in the conformation search.
When the calculation settings are complete, click Submit. The calculation will start.

Basic Settings Pamo

[Execution by command line]

The calculation settings are defined by describing keywords in the pamonic-acid-F.ini file.

pamonic-acid-F.ini file

CONFLEX SEL=30.0

[CONFLEX] means to execute a conformation search.
[SEL=30.0] means that a search limit, which is used as a criteria for selecting initial structure in the conformation search, sets to 30.0 kcal/mol.

Store the two files of pamonic-acid-F.mol and pamonic-acid-F.ini in an one folder, and execute below command. The calculation will start.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   pamonic-acid-Fenter

The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].

After the conformation search, we can get 118 conformers of pamonic acid. Here, we employ the 3rd most stable conformer for a calculation of crystal structure search. Structure data of the selected conformer is extracted from “pamonic-acid-F.sdf” file and saved as “pamonic-acid-c3.mol”. The pamonic-acid-F.sdf file is in the folder contained pamonic-acid-F.mol file.

pamonic-acid-c3.mol file

pamoic-acid.mol                                                                 
CONFLEX 18102311013D 1   1.00000    57.28062    16                            
C2  ,E =      57.281, G = 0.144E-07, P =   4.5793, M( 0), IFN =00000003-00000016
 45 48  0     0               999 V2000
   -1.3167    2.0796   -0.8640 C   0  0  0  0  0     
   -0.1166    1.2932   -0.8876 C   0  0  0  0  0     
    1.0079    1.7433   -0.1606 C   0  0  0  0  0     
    0.9563    2.9081    0.6175 C   0  0  0  0  0     
   -0.2214    3.6554    0.6552 C   0  0  0  0  0     
   -1.3466    3.2641   -0.0791 C   0  0  0  0  0     
   -2.5025    4.0623   -0.0282 C   0  0  0  0  0     
   -3.6457    3.7218   -0.7444 C   0  0  0  0  0     
   -3.6457    2.5743   -1.5200 C   0  0  0  0  0     
   -2.5025    1.7708   -1.5777 C   0  0  0  0  0     
   -0.0000    0.0000   -1.6979 C   0  0  0  0  0     
    0.1166   -1.2932   -0.8876 C   0  0  0  0  0     
   -1.0079   -1.7433   -0.1606 C   0  0  0  0  0     
   -0.9563   -2.9081    0.6175 C   0  0  0  0  0     
    0.2214   -3.6554    0.6552 C   0  0  0  0  0     
    1.3466   -3.2641   -0.0791 C   0  0  0  0  0     
    1.3167   -2.0796   -0.8640 C   0  0  0  0  0     
    2.5025   -4.0623   -0.0282 C   0  0  0  0  0     
    3.6457   -3.7218   -0.7444 C   0  0  0  0  0     
    3.6457   -2.5743   -1.5200 C   0  0  0  0  0     
    2.5025   -1.7708   -1.5777 C   0  0  0  0  0     
   -2.1663   -1.0131   -0.2688 O   0  0  0  0  0     
   -2.1487   -3.3401    1.3832 C   0  0  0  0  0     
   -3.2090   -2.7368    1.4055 O   0  0  0  0  0     
   -1.9746   -4.4795    2.0733 O   0  0  0  0  0     
    2.1487    3.3401    1.3832 C   0  0  0  0  0     
    3.2090    2.7368    1.4055 O   0  0  0  0  0     
    1.9746    4.4795    2.0733 O   0  0  0  0  0     
    2.1663    1.0131   -0.2688 O   0  0  0  0  0     
   -0.2634    4.5620    1.2557 H   0  0  0  0  0     
   -2.5220    4.9676    0.5759 H   0  0  0  0  0     
   -4.5311    4.3490   -0.6932 H   0  0  0  0  0     
   -4.5334    2.2918   -2.0797 H   0  0  0  0  0     
   -2.5709    0.8759   -2.1893 H   0  0  0  0  0     
   -0.8381   -0.1310   -2.3887 H   0  0  0  0  0     
    0.8381    0.1310   -2.3887 H   0  0  0  0  0     
    0.2634   -4.5620    1.2557 H   0  0  0  0  0     
    2.5220   -4.9676    0.5759 H   0  0  0  0  0     
    4.5311   -4.3490   -0.6932 H   0  0  0  0  0     
    4.5334   -2.2918   -2.0797 H   0  0  0  0  0     
    2.5709   -0.8759   -2.1893 H   0  0  0  0  0     
   -2.8489   -1.3798    0.3330 H   0  0  0  0  0     
   -2.8335   -4.6307    2.5208 H   0  0  0  0  0     
    2.8335    4.6307    2.5208 H   0  0  0  0  0     
    2.8489    1.3798    0.3330 H   0  0  0  0  0      
  1  2  2  0     0
  2  3  1  0     0
  3  4  2  0     0
  4  5  1  0     0
  5  6  2  0     0
  6  1  1  0     0
  6  7  1  0     0
  7  8  2  0     0
  8  9  1  0     0
  9 10  2  0     0
 10  1  1  0     0
  2 11  1  0     0
 11 12  1  0     0
 12 13  1  0     0
 13 14  2  0     0
 14 15  1  0     0
 15 16  2  0     0
 16 17  1  0     0
 17 12  2  0     0
 16 18  1  0     0
 18 19  2  0     0
 19 20  1  0     0
 20 21  2  0     0
 21 17  1  0     0
 13 22  1  0     0
 14 23  1  0     0
 23 24  2  0     0
 23 25  1  0     0
  4 26  1  0     0
 26 27  2  0     0
 26 28  1  0     0
  3 29  1  0     0
  5 30  1  0     0
  7 31  1  0     0
  8 32  1  0     0
  9 33  1  0     0
 10 34  1  0     0
 11 35  1  0     0
 11 36  1  0     0
 15 37  1  0     0
 18 38  1  0     0
 19 39  1  0     0
 20 40  1  0     0
 21 41  1  0     0
 22 42  1  0     0
 25 43  1  0     0
 28 44  1  0     0
 29 45  1  0     0
M  END

Next, we ready a diffraction data file for CONFLEX program from a raw data obtained by PXRD experiment. Haynes et al. provide the raw data of pamonic acid crystal. Here, we use “cv6632Isup2.rtv” for making a reference diffraction data, pamonic-acid-c3.xrd, shown below.

pamonic-acid-c3.xrd file

Co
8.010 79.990 0.01 7199
8.010    0.000000
8.020    0.000000
8.030    0.000000
8.040    91.252560
8.050    9.827270
8.060    0.000000
(中略)
79.970    43.877350
79.980    17.738100
79.990    42.620530

First row means a type of X-ray source, and second row shows a range and step of 2 theta and total the number of diffraction data. At the first row you can also set wave length of X-ray source, not characters of atomic name.
The diffraction data is shown on the third and subsequent rows. The intensity data at each 2-theta point are generated by subtracting “_pd_proc_intensity_bkg_calc” value from “_pd_meas_counts_total” value. If the intensity has negative value due to the subtraction, we set to “zero” as the intensity at the point.
You can find the pamonic-acid-c3.xrd in Sample_Files folder in the folder installed CONFLEX (Sample_Files\CONFLEX\crystal\powder\pamonic-acid-c3.xrd).

Do not include blank lines in the xrd file, and remove back ground from the raw data for using in CONFLEX.

Finally, we perform a crystal structure search of pamonic acid

[Execution by Interface]

Open the pamonic-acid-c3.mol file by CONFLEX Interface.

Interface Pamo c3

Select [CONFLEX] in Calculation menu, and click Detail Settings in the calculation setting dialog displayed. A detail setting dialog will be displayed.

Basic Settings c3

In order to perform the crystal structure search, in [General Settings] dialog on the detail setting dialog, select [Crystal Search] in the pull-down menu of [Calculation Type:].

General Settings

Method of crystal structure optimization is [ALL] in default setting. You can change the type of crystal structure optimization by the pull-down menu of [Crystal optimization:] in [Crystal Calculation] dialog.
In this dialog, we can also change settings for calculating intermolecular interactions such as cutoff distance, calculation method of coulombic interactions, and so on.

Next, we set parameters for the crystal structure search by [Crystal Search] dialog.

Crystal Search Pamo

In order to use space group of P21/c, edit the [Search Space Group:] from “P21/C,P212121” to “P21/C”.
[Rotation Method:] and [Position Prediction Method:] set methods to determine initial molecular orientation and position, respectively. Here, both the methods set to [Random].
[Trial Structures:] sets the number of trial structures that are created for the search. Here, the number of trial structures sets to 1000.

Next, we change the pull-down menu of “Crystal Search by:” from [Energy] to [Powder Pattern]. In this setting, the found crystal structures from the crystal structure search are estimated according to similarity of PXRD patterns between the found structures and experimental structure.
Finally, click Select of [PXRD File:], and select “pamonic-acid-c3.xrd” prepared above.

When the calculation settings are complete, click Submit. The calculation will start.

[Execution by command line]

The calculation settings are defined by describing keywords in the pamonic-acid-c3.ini.

pamonic-acid-c3.ini file

CRYSTAL_SEARCH
CSP_SEARCH=POWDER_PATTERN
CSP_SPGP=(P21/C)
CSP_AUS_MODE=RANDOM
CSP_ROT_MODE=RANDOM
CSP_MAX_CRYSTAL=1000
CRYSTAL_OPTIMIZATION=ALL

[CRYSTAL_SEARCH] means to execute a crystal structure search.
[CSP_SEARCH=POWDER_PATTERN] means that the found crystal structures from the crystal structure search are estimated according to similarity of PXRD patterns between the found structures and experimental structure.
[CSP_SPGP=P21/C] means to use space group of P21/c in the search.
[CSP_ROT_MODE=RANDOM] and [CSP_AUS_MODE=RANDOM] means to randomly determine initial molecular orientation and position.
[CSP_MAX_CRYSTAL=1000] means to set 1000 of the number of trial crystal structures.
[CRYSTAL_OPTIMIZATION=ALL] means to set “ALL” as a crystal structure optimization.

Store the three files of pamonic-acid-c3.mol, pamonic-acid-c3.ini, and pamonic-acid-c3.xrd in an one folder, and execute below command. The calculation will start.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   pamonic-acid-c3enter

The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].

Calculation results

After the calculation, you can get pamonic-acid-c3.csp file that describes results of the search calculation in detail.
In the search using the reference diffraction data, in the part of [*** PREDICTED CRYSTAL STRUCTURES:] of the pamonic-acid.csp file, the found crystal structures from the search are arranged according to similarity of PXRD patterns between the found structures and experimental structure. The 1st structure shows the most similar diffraction pattern to the reference one. Structure data of the found crystals are stored in pamonic-acid-c3-PCS.cif file.
Gelder's method (R. de Gelder et al, J Comput Chem 22: 273–289, 2001.) is employed for the PXRD similarity calculation.

 *** PREDICTED CRYSTAL STRUCTURES:

    IDX     CID    E_RNK   R_RNK  PXRD_SIM      CRYST      INTRA     INTER        VOL       DES        A         B         C       ALPHA     BETA      GAMMA     SPGP      NCALMOL   NCALATM    DMAX    NNEV 
      1    882       1       1     0.9056      12.3774    59.3730   -46.9957   1829.5937   1.4089   20.3676    4.9453   19.2844   90.0000  109.6233   90.0000   P21/C          225     10125    20.00     0    
      2    662     260       2     0.8349      26.0620    65.8365   -39.7745   1834.4689   1.4052   13.7876    7.0968   28.9328   90.0000  139.6100   90.0000   P21/C          210      9450    20.00     0    
      4    232      76       3     0.8235      21.4836    61.1121   -39.6285   1929.2047   1.3362   12.0076   12.5142   16.0878   90.0000   52.9432   90.0000   P21/C          205      9225    20.00     0    
      8      6       3       4     0.8219      14.2830    58.8049   -44.5220   1897.8000   1.3583   10.1471    4.8134   39.0029   90.0000   85.0212   90.0000   P21/C          202      9090    20.00     0    
      9     60     383       5     0.8177      28.4589    58.0370   -29.5781   1981.9578   1.3006    4.7838   11.1176   37.2683   90.0000   90.6615   90.0000   P21/C          202      9090    20.00     0    
     10     38     175       6     0.8137      24.3246    58.3375   -34.0128   1917.4130   1.3444    4.9060   15.6069   25.2169   90.0000   83.2541   90.0000   P21/C          202      9090    20.00     0    
     19      5      45       7     0.8122      20.3188    58.3402   -38.0214   1945.9817   1.3247    4.8345   10.1697   39.5911   90.0000   88.6467   90.0000   P21/C          204      9180    20.00     0    
     21     56      72       8     0.8115      21.4423    59.5779   -38.1356   1926.0086   1.3384    8.7084   12.1206   18.2473   90.0000   90.2492   90.0000   P21/C          206      9270    20.00     0    
     22    422     404       9     0.8061      28.9872    58.8269   -29.8397   2013.9816   1.2799    8.1416   13.0775   19.6888   90.0000   73.8900   90.0000   P21/C          197      8865    20.00     0    
     24    541     460      10     0.8050      30.6621    59.6480   -28.9860   1940.5521   1.3284    7.5235    9.2889   27.9119   90.0000   84.1753   90.0000   P21/C          200      9000    20.00     0   

Here, comparing the diffraction patterns of the 1st structure (red) and the experimental one (white), you can see that both the patterns match well. Therefore, by using the 1st structure, it is expected that a structure refinement by Rietveld analysis will be easily completed, compared with a case of that without supports of CONFLEX.

Spectra Analyzer Pamo

The experimental structure (left figure) and the 1st structure (right figure) are shown below. You can see that both the structures match well.

Interface Pamo PRD

[Output files]

After the calculation of crystal structure search, below files are outputted.

File type Explanation
(Input file name).csp Detail information on the crystal structure search calculation is described to this file.
(Input file name).cpt Information for restarting the calculation is described to this file.
(Input file name).ical Powder X-ray diffraction data of crystal structures found by the search are described to this file. The crystal structure data corresponding to the PXRD data are described in the -PCS.cif file.
(Input file name)-PCS.cif Crystal structures found by the search are described to this file in order of crystal energy (or similarity of PXRD pattern).
(Input file name)-FCS.cif When optimization of a trial finished in the search process, the optimized structure is outputted to this file. You can see the optimized structure before the search calculation doesn't finish.

In the part of [*** PREDICTED CRYSTAL STRUCTURES:] of csp file, computationally suggested polymorphs are shown in order of crystal energy.

 *** PREDICTED CRYSTAL STRUCTURES:

    IDX    CID    E_RNK     CRYST      INTRA      INTER        VOL      DES        A         B         C       ALPHA     BETA      GAMMA     SPGP      NCALMOL   NCALATM    DMAX    NNEV 
      1    571      1     -15.7921     4.6942   -20.4864    607.6657   1.3663    9.5996    8.3419   10.7545   90.0000  135.1221   90.0000   P21/C          365      4015    20.00     0    
     39   5295      2     -15.6634     4.7074   -20.3708    306.9963   1.3522   11.0245    7.0951    4.3469   90.0000  115.4610   90.0000   P21            371      4081    20.00     0    
     89    150      3     -15.6476     4.6816   -20.3292    606.6216   1.3686    7.2689    8.3106   10.7652   90.0000  111.1225   90.0000   P21/C          375      4125    20.00     0    
    170   3622      4     -15.6125     4.7219   -20.3344    614.2783   1.3515    4.3718   19.8181    7.0899   90.0000   90.0000   90.0000   P212121        373      4103    20.00     0    
    183   3677      5     -15.6089     4.6925   -20.3014    612.8164   1.3548    7.6268    9.6305    8.3433   90.0000   90.0000   90.0000   P212121        355      3905    20.00     0    
    204    404      6     -15.5986     4.7162   -20.3147    614.9313   1.3501    4.3234    7.1069   20.0163   90.0000   89.0064   90.0000   P21/C          371      4081    20.00     0    
    221     51      7     -15.4618     4.7170   -20.1789    618.7977   1.3417    4.3746    7.0720   20.4156   90.0000   78.4425   90.0000   P21/C          374      4114    20.00     0    
    229   2134      8     -15.3029     4.7145   -20.0173   1222.4436   1.3583   14.5999    8.3633   10.4384   90.0000   73.5604   90.0000   C2/C           357      3927    20.00     0    
    236    215      9     -15.2948     4.7210   -20.0158    612.9536   1.3545    4.0230    8.3785   18.2131   90.0000   86.8178   90.0000   P21/C          358      3938    20.00     0    
    263     28     10     -15.2940     4.7263   -20.0203    612.5302   1.3554    8.3759   18.2972    8.8552   90.0000   26.8303   90.0000   P21/C          365      4015    20.00     0    

On the other hand, when you performed the crystal structure search using a reference diffraction data, they are shown in order of PXRD pattern similarity.

 *** PREDICTED CRYSTAL STRUCTURES:

    IDX     CID    E_RNK   R_RNK  PXRD_SIM      CRYST      INTRA     INTER        VOL       DES        A         B         C       ALPHA     BETA      GAMMA     SPGP      NCALMOL   NCALATM    DMAX    NNEV 
      1    882       1       1     0.9056      12.3774    59.3730   -46.9957   1829.5937   1.4089   20.3676    4.9453   19.2844   90.0000  109.6233   90.0000   P21/C          225     10125    20.00     0    
      2    662     260       2     0.8349      26.0620    65.8365   -39.7745   1834.4689   1.4052   13.7876    7.0968   28.9328   90.0000  139.6100   90.0000   P21/C          210      9450    20.00     0    
      4    232      76       3     0.8235      21.4836    61.1121   -39.6285   1929.2047   1.3362   12.0076   12.5142   16.0878   90.0000   52.9432   90.0000   P21/C          205      9225    20.00     0    
      8      6       3       4     0.8219      14.2830    58.8049   -44.5220   1897.8000   1.3583   10.1471    4.8134   39.0029   90.0000   85.0212   90.0000   P21/C          202      9090    20.00     0    
      9     60     383       5     0.8177      28.4589    58.0370   -29.5781   1981.9578   1.3006    4.7838   11.1176   37.2683   90.0000   90.6615   90.0000   P21/C          202      9090    20.00     0    
     10     38     175       6     0.8137      24.3246    58.3375   -34.0128   1917.4130   1.3444    4.9060   15.6069   25.2169   90.0000   83.2541   90.0000   P21/C          202      9090    20.00     0    
     19      5      45       7     0.8122      20.3188    58.3402   -38.0214   1945.9817   1.3247    4.8345   10.1697   39.5911   90.0000   88.6467   90.0000   P21/C          204      9180    20.00     0    
     21     56      72       8     0.8115      21.4423    59.5779   -38.1356   1926.0086   1.3384    8.7084   12.1206   18.2473   90.0000   90.2492   90.0000   P21/C          206      9270    20.00     0    
     22    422     404       9     0.8061      28.9872    58.8269   -29.8397   2013.9816   1.2799    8.1416   13.0775   19.6888   90.0000   73.8900   90.0000   P21/C          197      8865    20.00     0    
     24    541     460      10     0.8050      30.6621    59.6480   -28.9860   1940.5521   1.3284    7.5235    9.2889   27.9119   90.0000   84.1753   90.0000   P21/C          200      9000    20.00     0   

Meaning of the items in the part of [*** PREDICTED CRYSTAL STRUCTURES:] are shown below.

Item Explanation
E_RNK Crystal energy rank
R_RNK PXRD pattern similarity rank
CRYST Ecrystal
INTRA Eintra
INTER Elattice
VOL Volume of unit cell
DES Density of unit cell
A,B,C,ALPHA,BETA,GAMMA Lattice constants
SPGP Space group
NCALMOL Total the number of molecules including in the calculation
NCALATM Total the number of atoms including in the calculation
DMAX Cut-off distance
NNEV The number of negative eigenvalues

* On the values of “NCALMOL, NCALATM, DMAX”, when you used different cut-off distance in the calculations for vdW and coulombic interactions, these values show about the calculation of vdW interactions.

The ical file has powder X-ray diffraction data of crystal structures found by the search. The -PCS.cif file has the crystal structure data corresponding to the PXRD data. The “data_” in the -PCS.cif file and “NAME:” in the ical file match in the same structure.

 ------------ SIMULATED POWDER PATTERNS ------------
      CID:   882
     NAME: R000001E000001C000882         
    X-RAY: CO (KA1)
     WAVE: 1.78899600
  2*THETA:   8.010 -  79.990 ,   0.010 STEP

   H   K   L  2*THETA       INTENSITY         d
              (DEGREE)                   (ANGSTROME)
   0   0   0    8.010           1.167      0.00000
   0   0   0    8.020           1.174      0.00000
   0   0   0    8.030           1.182      0.00000
   0   0   0    8.040           1.190      0.00000
   0   0   0    8.050           1.197      0.00000
   0   0   0    8.060           1.205      0.00000
   0   0   0    8.070           1.213      0.00000
   0   0   0    8.080           1.221      0.00000
   0   0   0    8.090           1.229      0.00000
   0   0   0    8.100           1.237      0.00000
   0   0   0    8.110           1.246      0.00000
   0   0   0    8.120           1.254      0.00000
   0   0   0    8.130           1.263      0.00000
   0   0   0    8.140           1.271      0.00000
* snip *

[Visualization of search results]

The polymorphs found by the search are outputted to the -PCS.cif file. Open the -PCS.cif file by CONFLEX Interface, you can see them.

Interface PCS

Select [Spectra_Analyzer] in the menu of [Applications] with the -PCS file open, you can also see PXRD pattern of each structure.

[Restart of crystal structure search]

[Execution by Interface]

Store molecular structure, ini, and cpt files that were used in the search calculation to an one folder. If you used a reference diffraction data, the xrd file is also needed.

Open the molecular structure file by CONFLEX Interface.

Interface Pamo c3

Select [CONFLEX] in Calculation menu, and click Detail Settings in the calculation setting dialog displayed. A detail setting dialog will be displayed.

In order to restart the search calculation, check the check box of [Restart calculation] at the bottom of [Crystal Search] dialog in the detail setting dialog.

Interface Restart

The other settings are automatically set from the ini file. When the setting for the restart is complete, click Submit.
If you executed the search calculation by Edit & Submit and manually added keywords, you should click Edit & Submit and add same keywords on the restart. If the settings for the search calculation do not match, you may not be able to restart the calculation correctly.

[Execution by command line]

Store molecular structure, ini, and cpt files that were used in the search calculation to an one folder. If you used a reference diffraction data, the xrd file is also needed.
Next, change suffix of the cpt file to “rst”, and add “CSP_RESTART” keyword to the ini file. It is note that the you do not change the settings for the search calculation in the ini file. If the settings do not match, you may not be able to restart the calculation correctly.

When you are ready to restart, execute below command. The calculation will start.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   (Input file name)enter

The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].

[Unavailable space groups]

The following space group can not be used in crystal structure search.
P4MM, P4BM, P42CM, P42NM, I4MM, I4CM, P-42M, P-421M, I-42M, P4/MMM, P4/NBM, P4/MBM, P4/NMM, P42/MCM, P42/NNM, P42/MNM, P42/NCM, I4MMM, I4/MCM, P3, P31, P32, R3, P-3, R-3, P312, P321, P3112, P3121, P3212, P3221, R32, P3M1, P31M, P3C1, P31C, R3M, R3C, P-31M, P-31C, P-3M1, P-3C1, R-3M, R-3C, P6, P61, P65, P62, P64, P63, P-6, P6/M, P63/M, P622, P6122, P6522, P6222, P6422, P6322, P6MM, P6CC, P63CM, P63MC, P-6M2, P-6C2, P-62M, P-62C, P6/MMM, P6/MCC, P63/MCM, P63/MMC, P23, F23, I23, P213, I213, PM-3, PN-3, FM-3, FD-3, IM-3, PA-3, IA-3, P432, P4232, F432, F4132, I432, P4332, P4132, I4132, P-43M, F-43M, I-43M, P-43N, F-43C, I-43D, PM-3M, PN-3N, PM-3N, PN-3M, FM-3M, FM-3C, FD-3M, FD-3C, IM-3M, IA-3D