CONFLEX Tutorials

Crystal structure optimization

[Definition of energy]

Crystal structure can be built by periodically arranging a unit cell through translational symmetry (Figure 1). The unit cell is defined by an asymmetric unit, lattice constants, and space group symmetry. Therefore, in simulations, the crystal structure is constructed by using the asymmetric unit, the lattice constants, the space group symmetry, and the translational symmetry, and an energy of the crystal is defined by the equation 1 as the energy per the asymmetric unit.

Crystal Equations

Here, the Eintra is the sum of intramolecular interaction energies in the asymmetric unit, and the Elattice is defined by the equation 2. In the equation 2, the EAUinter is the sum of intermolecular interaction energies in the asymmetric unit. When the number of molecules in the asymmetric unit is one, the the EAUinter is zero. The second term in the equation 2 is the sum of intermolecular interaction energies between the molecule(s) in the asymmetric unit and molecules replicated by symmetry operations within a cut-off radius Rcrystal in the crystal. The Ewald method is applied to the calculation of electrostatic interactions.

The Ewald method calculates coulombic potential by using four terms of real space term, Φreal, reciprocal space term, Φrecip, self energy term, Φself, surface term, Φsurf. In the default setting, the Φsurf term is omitted. You can activate this term through a keyword. Please refer to the manual.

EWald Equations

Here, the q is atomic charge, the α is Ewald convergence parameter, the |ri;S,J| is interatomic distance, the V is volume of the unit cell, the n is reciprocal lattice vector, and the r is position vector of atom in the unit cell. The Z is the number of the smallest building blocks (the asymmetric unit and replicated units created by applying symmetry operations to the asymmetric unit) in the unit cell. The parameter α and the cutoff distance in the reciprocal lattice space are automatically determined so that the interatomic interaction energy is smaller than 10-8 based on the cutoff distance in the real space. The values of these parameters can be specified by keywords. Please refer to the manual.

Crystal Model
Figure 1. Crystal model

[Types of crystal structure optimization]

The program can perform three types of crystal structure optimization shown blow. These optimizations are performed under a specified space group symmetry.

Molecular geometry optimization under crystal environment (MOL)
The geometry, orientation, and translation of molecules in the crystal are relaxed. In the calculation, the lattice constants do not change.
Optimization of crystal structure assuming rigid molecules (RIGID)
The orientation and translation of molecules in the crystal and the lattice constants are relaxed. In the calculation, the molecular geometry does not change.
Full crystal structure optimization (ALL)
The all degree of freedoms for expressing the crystal structure, that is, the geometry, orientation and translation of molecules in the crystal and the lattice constants are relaxed.

[Execution of crystal structure optimization]

This section explains how to execute the crystal structure optimization. For the execution, as input data, atomic coordinates of asymmetric unit, lattice constants, and space group are necessary. Here, we use a crystal of hydroxy malonic acid which is one of malonic acid derivatives (Roelofsen, G.; Kanters, J.A.; Kroon, J.; Doesburg, H.M.; Koops, T. Acta Cryst.1978, B34, 2565.).

Hydroxy Tartronic Acid
Molecular structure of hydroxy malonic acid

In case of using CMF file

We prepare tartronicacid.cmf shown below as input file. The tartronicacid.cmf has the crystal structure data of hydroxy malonic acid in CIFMIF (Combined CIF and MIF file, CIF:Crystallographic Information File, MIF: Molecular Information File) file format. You can find the tartronicacid.cmf in Sample_Files folder in the folder installed CONFLEX (Sample_Files\CONFLEX\crystal\optimization\cmf_file\tartronicacid.cmf).

tartronicacid.cmf file

data_Tartronicacid
_symmetry_cell_setting ORTHORHOMBIC
_symmetry_space_group_name_H-M 'P212121 '
_ccdc_symmetry_space_group_name P212121 
_symmetry_Int_Tables_number 19
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z 
2 1/2+x,1/2-y,-z 
3 -x,1/2+y,1/2-z 
4 1/2-x,-y,1/2+z 
_cell_length_a 4.49400
_cell_length_b 8.81900
_cell_length_c 10.88200
_cell_angle_alpha 90.00000
_cell_angle_beta 90.00000
_cell_angle_gamma 90.00000
_cell_formula_units_Z 4
_cell_volume 431.28180
_exptl_crystal_density_diffrn 1.84821
loop_
_ccdc_atom_site_atom_id_number
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_ccdc_atom_site_symmetry
_ccdc_atom_site_base
1 O1 O 1.12990 -0.13910 0.36040 1_555 1
2 O2 O 0.97510 0.09280 0.30700 1_555 2
3 O3 O 1.01480 0.11550 0.66290 1_555 3
4 O4 O 1.13030 -0.12820 0.62810 1_555 4
5 O5 O 0.57240 0.09790 0.48970 1_555 5
6 C1 C 0.97750 -0.01540 0.37600 1_555 6
7 C2 C 0.78810 -0.01520 0.49230 1_555 7
8 C3 C 0.99010 -0.00160 0.60420 1_555 8
9 H1 H 0.66800 -0.11200 0.49600 1_555 9
10 H2 H 0.60500 0.14900 0.45600 1_555 10
11 H3 H 1.23700 -0.13800 0.31000 1_555 11
12 H4 H 1.27100 -0.12000 0.68000 1_555 12
loop_
_atom_id
_atom_type
_atom_attach_nh
_atom_attach_h
_atom_charge
1 O 1 1 0
2 O 1 0 0
3 O 1 0 0
4 O 1 1 0
5 O 1 1 0
6 C 3 0 0
7 C 3 1 0
8 C 3 0 0
loop_
_bond_id_1
_bond_id_2
_bond_type_ccdc
_bond_environment
1 6 S chain
1 11 S chain
2 6 D chain
3 8 D chain
4 8 S chain
4 12 S chain
5 7 S chain
5 10 S chain
6 7 S chain
7 8 S chain
7 9 S chain

[Execution by Interface]

Open the tartronicacid.cmf file by CONFLEX Interface.

Interface CMF

Select [CONFLEX] in Calculation menu, and click Detail Settings in the calculation setting dialog displayed.
Next, in [General Settings] dialog on the detail setting dialog, select [Molecular Crystal] in the pull-down menu of [Calculation Type:].

General Settings

Settings of the crystal calculation are made in [Crystal calculation] dialog.

Crystal Calculation

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

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 tartronicacid.ini file.

tartronicacid.ini file

CRYSTAL MMFF94S

[CRYSTAL] means to execute a crystal calculation, and in the default, CONFLEX executes full crystal structure optimization (ALL) of the input structure. If you change the type of crystal structure optimization, add [CRYSTAL_OPTIMIZATION=] keyword, for example, [CRYSTAL_OPTIMIZATION=MOL].
[MMFF94s] means to use MMFF94s force field.

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

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

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

In the case of using CIF file

In CIF file, bond information (bond order) are not included, although information which are necessary for the crystal calculation, that is, atomic coordinates of molecule in the asymmetric unit, lattice constants, and space group are described.
Here, we prepare input data, tartronicacid.cif, of crystal structure of hydroxy malonic acid based on CIF file format. The tartronicacid.cif is in Sample_Files folder in the folder installed CONFLEX (Sample_Files\CONFLEX\crystal\optimization\cif_file\tartronicacid.cif).

tartronicacid.cif file

data_Tartronicacid
_symmetry_cell_setting ORTHORHOMBIC
_symmetry_space_group_name_H-M 'P212121 '
_symmetry_Int_Tables_number 19
loop_
_symmetry_equiv_pos_as_xyz
x,y,z 
-x+1/2,-y,z+1/2 
-x,y+1/2,-z+1/2 
x+1/2,-y+1/2,-z 
_cell_length_a 4.49400
_cell_length_b 8.81900
_cell_length_c 10.88200
_cell_angle_alpha 90.00000
_cell_angle_beta 90.00000
_cell_angle_gamma 90.00000
_cell_formula_units_Z 4
_cell_volume 431.28180
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
O1 O 1.12990 -0.13910 0.36040
O2 O 0.97510 0.09280 0.30700
O3 O 1.01480 0.11550 0.66290
O4 O 1.13030 -0.12820 0.62810
O5 O 0.57240 0.09790 0.48970
C1 C 0.97750 -0.01540 0.37600
C2 C 0.78810 -0.01520 0.49230
C3 C 0.99010 -0.00160 0.60420
H1 H 0.66800 -0.11200 0.49600
H2 H 0.60500 0.14900 0.45600
H3 H 1.23700 -0.13800 0.31000
H4 H 1.27100 -0.12000 0.68000

[Execution by Interface]

Open tartronicacid.cif file by CONFLEX Interface

Interface CIF

Select [CONFLEX] in Calculation menu, click Detail Settings in the calculation setting dialog displayed.
Next, in [General Settings] dialog on the detail setting dialog, select [Molecular Crystal] in the pull-down menu of [Calculation Type:].

General Settings

Settings of the crystal calculation are made in [Crystal calculation] dialog.

Crystal Calculation

We can change the type of crystal structure optimization by the pull-down menu of [Crystal optimization:]. The default setting is "ALL". In this dialog, we can also change settings for calculating intermolecular interactions such as cutoff distance, calculation method of coulombic interactions, and so on. When the calculation settings are complete, click Edit & Submit.

A dialog with the keywords for the calculation settings is displayed.

Edit and Submit

Here, we will modify bond order.
CONFLEX Interface automatically creates [CIF_BOND=] keyword with 1 bond order for all atomic pairs that are considered to be bonded from the interatomic distance.
The bond order between atom 2 and atom 6 and between atom 3 and atom 8 in the hydroxy malonic acid molecule is 2 (refer to the below figure). Therefore, we have to change CIF_BOND=(2,6,1) and CIF_BOND=(3,8,1) to CIF_BOND=(2,6,2) and CIF_BOND=(3,8,2), respectively.
When you want to set a bond with n bond order to an atomic pair of atom i and atom j, CIF_BOND=(i,j,n) keyword should be described. The serial number of each atom are shown in the below figure.

Atom Numbers
* By using View menu, you can change viewing style of molecule and show the serial number of atoms.

When you complete the modifications, click Submit. The calculation will start.

[Execution by command line]

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

tartronicacid.ini file

CRYSTAL MMFF94S
CIF_BOND=(1,6,1) 
CIF_BOND=(1,11,1) 
CIF_BOND=(2,6,2) 
CIF_BOND=(3,8,2) 
CIF_BOND=(4,8,1) 
CIF_BOND=(4,12,1) 
CIF_BOND=(5,7,1) 
CIF_BOND=(5,10,1) 
CIF_BOND=(6,7,1) 
CIF_BOND=(7,8,1) 
CIF_BOND=(7,9,1) 

[CRYSTAL] means to execute a crystal calculation, and in the default, CONFLEX executes full crystal structure optimization (ALL) of the input structure. If you change the type of crystal structure optimization, add [CRYSTAL_OPTIMIZATION=] keyword, for example, [CRYSTAL_OPTIMIZATION=MOL].
[MMFF94s] means to use MMFF94s force field.
[CIF_BOND=] sets bond information of hydroxy malonic acid molecule. When you want to set a bond with n bond order to an atomic pair of atom i and atom j, CIF_BOND=(i,j,n) keyword should be described.

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

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

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

In case of using MOL file

The molecule in MDL-MOL file is used as the asymmetric unit. Therefore, when you use MDL-MOL file for the crystal calculation, you should care orientation and spatial position of the molecule. Depending on the orientation and spatial position of the molecule, the molecules in the crystal possible to be sterically clashed due to symmetry operations.
Here, we prepare input data, tartronicacid.mol, of hydroxy malonic acid molecule based on MDL-MOL file format. The tartronicacid.mol is in Sample_Files folder in the folder installed CONFLEX (Sample_Files\CONFLEX\crystal\optimization\mol_file\tartronicacid.mol).

tartronicacid.mol file

Tartronicacid.mol


 12 11  0  0  0  0  0  0  0  0  1 V2000
    5.0778   -1.2267    3.9219 O   0  0  0  0  0
    4.3821    0.8184    3.3408 O   0  0  0  0  0
    4.5605    1.0186    7.2137 O   0  0  0  0  0
    5.0796   -1.1306    6.8350 O   0  0  0  0  0
    2.5724    0.8634    5.3289 O   0  0  0  0  0
    4.3929   -0.1358    4.0916 C   0  0  0  0  0
    3.5417   -0.1340    5.3572 C   0  0  0  0  0
    4.4495   -0.0141    6.5749 C   0  0  0  0  0
    3.0020   -0.9877    5.3975 H   0  0  0  0  0
    2.7189    1.3140    4.9622 H   0  0  0  0  0
    5.5591   -1.2170    3.3734 H   0  0  0  0  0
    5.7119   -1.0583    7.3998 H   0  0  0  0  0
  1  6  1  0  0
  1 11  1  0  0
  2  6  2  0  0
  3  8  2  0  0
  4  8  1  0  0
  4 12  1  0  0
  5  7  1  0  0
  5 10  1  0  0
  6  7  1  0  0
  7  8  1  0  0
  7  9  1  0  0
M  END

[Execution by Interface]

Open the tartronicacid.mol file by CONFLEX Interface.

Interface MOL

Select [CONFLEX] in Calculation menu, click Detail Settings in the calculation setting dialog displayed.
Next, in [General Settings] dialog on the detail setting dialog, select [Molecular Crystal] in the pull-down menu of [Calculation Type:].

General Settings

Settings of the crystal calculation are made in [Crystal calculation] dialog.

Crystal Opt

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

The data of space group and lattice constants are not included in the tartronicacid.mol file. Therefore, these parameters should set in this dialog.
First, to set space group, select P212121 from the pull-down menu of [Space group:]. Next, to set lattice constants, check the check box of [Lattice Constants], and input values of lattice constants. The lattice constants of crystal structure of hydroxy malonic acid are a=4.494 Å,b=8.819 Å,c=10.882 Å,α=90.0 °,β=90.0 °,γ=90.0 °.

Crystal Opt Settings

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 tartronicacid.ini file.

tartronicacid.ini file

CRYSTAL MMFF94S
SPACE_GROUP=P212121
LATTICE_CONSTANT=(4.494,8.819,10.882,90.0,90.0,90.0) 

[CRYSTAL] means to execute a crystal calculation, and in the default, CONFLEX executes full crystal structure optimization (ALL) of the input structure. If you change the type of crystal structure optimization, add [CRYSTAL_OPTIMIZATION=] keyword, for example, [CRYSTAL_OPTIMIZATION=MOL].
[MMFF94s] means to use MMFF94s force field.
The data of space group and lattice constants are not included in MDL-MOL file. The [SPACE_GROUP=] and [LATTICE_CONSTANT=] keywords are for setting space group and lattice constants, respectively. The space group of crystal structure of hydroxy malonic acid is P212121, and the lattice constants are a=4.494 Å,b=8.819 Å,c=10.882 Å,α=90.0 °,β=90.0 °,γ=90.0 °.

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

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

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

[Optimization while fixing structure and position of a specified molecule]

CONFLEX can perform the crystal structure optimization while fixing structure and position of a specified molecule, when there is more than one molecule in the asymmetric unit. Here, for explaining this function, we employ co-crystal butylparaben-isonicotinamide.
From supporting information of Bhardwaj’s paper [R. M. Bhardwaj, H. Yang and A. J. Florence, Acta Cryst. (2016). E72, 53-55], we can get “cv5494sup1.cif” which is for structure of the co-crystal. The “cv5494sup1.cif” is modified for treating by CONFLEX program, and the modified data is saved as “BPN-ISN.cif”. The BPN-ISN.cif is in Sample_Files folder in the folder installed CONFLEX (Sample_Files\CONFLEX\crystal\molecular.fixing\BPN-ISN.cif).

BPN-ISN.cif file

data_I
_symmetry_cell_setting     triclinic
_symmetry_Int_Tables_number 2
_symmetry_space_group_name_H-M     'P-1'
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
-x,-y,-z
_cell_length_a     5.6257(6)
_cell_length_b     9.8661(11)
_cell_length_c     14.3979(15)
_cell_angle_alpha     90.834(7)
_cell_angle_beta     91.431(7)
_cell_angle_gamma     91.645(7)
_cell_volume     798.47(15)
_cell_formula_units_Z     2
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
_atom_site_adp_type
_atom_site_calc_flag
_atom_site_occupancy
_atom_site_disorder_assembly
_atom_site_disorder_group
H H1N -0.623(3) 1.480(2) 1.4226(13) 0.019(5) Uiso d 1 . .
H H2N -0.626(4) 1.399(2) 1.3256(16) 0.035(6) Uiso d 1 . .
H H3O 0.140(5) 0.939(3) 1.1807(17) 0.054(7) Uiso d 1 . .
O O4 0.1197(2) 0.47988(13) 0.82145(8) 0.0227(3) Uani d 1 . .
O O1 -0.2641(2) 1.38157(14) 1.49057(9) 0.0275(3) Uani d 1 . .
N N1 -0.5594(3) 1.41555(17) 1.38514(11) 0.0238(4) Uani d 1 . .
O O2 0.2637(2) 0.88155(15) 1.16227(9) 0.0308(4) Uani d 1 . .
N N2 -0.0392(3) 1.05682(16) 1.24155(10) 0.0234(4) Uani d 1 . .
O O3 -0.2134(2) 0.59634(14) 0.80166(9) 0.0297(3) Uani d 1 . .
C C13 -0.0315(3) 0.57543(19) 0.84578(12) 0.0207(4) Uani d 1 . .
C C7 0.2633(3) 0.63083(19) 0.97609(12) 0.0220(4) Uani d 1 . .
H H8 0.3619 0.5641 0.9542 0.026 Uiso calc 1 . .
C C6 -0.3631(3) 1.35566(18) 1.41440(12) 0.0194(4) Uani d 1 . .
C C12 0.0462(3) 0.65243(18) 0.93023(12) 0.0190(4) Uani d 1 . .
C C14 0.0586(3) 0.40447(19) 0.73615(12) 0.0223(4) Uani d 1 . .
H H15A 0.0438 0.4660 0.6845 0.027 Uiso calc 1 . .
H H15B -0.0918 0.3552 0.7423 0.027 Uiso calc 1 . .
C C8 0.3330(3) 0.7076(2) 1.05364(13) 0.0239(4) Uani d 1 . .
H H9 0.4775 0.6920 1.0839 0.029 Uiso calc 1 . .
C C2 -0.0520(3) 1.18936(19) 1.38204(13) 0.0234(4) Uani d 1 . .
H H2 0.0162 1.2121 1.4399 0.028 Uiso calc 1 . .
C C10 -0.0302(3) 0.83018(19) 1.04128(12) 0.0229(4) Uani d 1 . .
H H11 -0.1290 0.8969 1.0631 0.027 Uiso calc 1 . .
C C16 0.2264(3) 0.2420(2) 0.62252(13) 0.0242(4) Uani d 1 . .
H H17A 0.0722 0.1955 0.6171 0.029 Uiso calc 1 . .
H H17B 0.2306 0.3126 0.5764 0.029 Uiso calc 1 . .
C C5 -0.3533(3) 1.21153(19) 1.26476(12) 0.0213(4) Uani d 1 . .
H H6 -0.4918 1.2498 1.2420 0.026 Uiso calc 1 . .
C C15 0.2548(3) 0.30708(19) 0.71924(12) 0.0220(4) Uani d 1 . .
H H16A 0.2511 0.2370 0.7658 0.026 Uiso calc 1 . .
H H16B 0.4075 0.3551 0.7248 0.026 Uiso calc 1 . .
C C1 -0.2580(3) 1.25031(18) 1.35125(12) 0.0185(4) Uani d 1 . .
C C9 0.1866(3) 0.80852(19) 1.08652(12) 0.0221(4) Uani d 1 . .
C C11 -0.0986(3) 0.75279(19) 0.96404(12) 0.0223(4) Uani d 1 . .
H H12 -0.2437 0.7680 0.9342 0.027 Uiso calc 1 . .
C C3 0.0504(3) 1.0945(2) 1.32551(13) 0.0251(4) Uani d 1 . .
H H3 0.1888 1.0544 1.3467 0.030 Uiso calc 1 . .
C C4 -0.2387(3) 1.11486(19) 1.21283(13) 0.0240(4) Uani d 1 . .
H H5 -0.3042 1.0892 1.1551 0.029 Uiso calc 1 . .
C C17 0.4194(4) 0.1414(2) 0.60224(14) 0.0314(5) Uani d 1 . .
H H18A 0.5725 0.1869 0.6068 0.047 Uiso calc 1 . .
H H18B 0.3946 0.1042 0.5407 0.047 Uiso calc 1 . .
H H18C 0.4130 0.0696 0.6465 0.047 Uiso calc 1 . .

[Execution by Interface]

Open the BPN-ISN.cif file by CONFLEX Interface.

Interface BPN-ISN

Select [CONFLEX] in Calculation menu, and click Detail Settings in the calculation setting dialog displayed.
Next, in [General Settings] dialog on the detail setting dialog, select [Molecular Crystal] in the pull-down menu of [Calculation Type:].

General Settings

Settings of the crystal calculation are made in [Crystal calculation] dialog.

Crystal Opt

Select [Molecule] of the pull-down menu of [Crystal optimization:] on this dialog. We can not use other methods in the case of the optimization with the restrictions. Next, click Edit & Submit in the detail setting dialog.

A dialog with the keywords for the calculation settings is displayed.

Edit and Submit BPN-ISN

The molecule to be frozen in the crystal structure optimization is defined by [CRYSTAL_FIXED_MOL=] keyword.
Molecular ID of each molecule in the input file are automatically determined according to atom serial number. In case of “BPN-ISN.cif”, the molecular ID of isonicotinamide is 1, and that of butylparaben is 2. Here, to freeze structure and position of buthlparaben, we add [CRYSTAL_FIXED_MOL=2] keyword to this dialog. If you want to optimize hydrogen atom positions of buthylparaben, you should also add [CRYSTAL_FIXED_MOL=EXCLUDE_HYDROGEN] keyword to this dialog.

Next, we will modify bond order.
CONFLEX Interface automatically creates [CIF_BOND=] keyword with 1 bond order for all atomic pairs that are considered to be bonded from the interatomic distance. Here, you should modify bond order of atomic pairs with double bond. When you want to set a bond with n bond order to an atomic pair of atom i and atom j, CIF_BOND=(i,j,n) keyword should be described. The serial number of each atom are shown in the below figure.

CIF_BOND=(5,13,1) → CIF_BOND=(5,13,2)
CIF_BOND=(8,38,1) → CIF_BOND=(8,38,2)
CIF_BOND=(9,10,1) → CIF_BOND=(9,10,2)
CIF_BOND=(11,14,1) → CIF_BOND=(11,14,2)
CIF_BOND=(18,33,1) → CIF_BOND=(18,33,2)
CIF_BOND=(20,36,1) → CIF_BOND=(20,36,2)
CIF_BOND=(22,34,1) → CIF_BOND=(22,34,2)
CIF_BOND=(27,32,1) → CIF_BOND=(27,32,2)
BPN-ISN Numbers
* By using View menu, you can change viewing style of molecule and show the serial number of atoms.

The dialog modified is shown below.

Edit Submit Modified

When you complete the modifications, click Submit. The calculation will start. The structure and position of buthlparaben in the crystal after and before the optimization are equivalent.

[Execution by command line]

The calculation settings are defined by describing keywords in the BPN-ISN.ini file.

BPN-ISN.ini file

CRYSTAL MMFF94S
CRYSTAL_OPTIMIZATION=MOL 
CRYSTAL_FIXED_MOL=2 
CIF_BOND=(1,6,1)
CIF_BOND=(2,6,1)
CIF_BOND=(3,7,1)
CIF_BOND=(4,10,1)
CIF_BOND=(4,15,1)
CIF_BOND=(5,13,2)
CIF_BOND=(6,13,1)
CIF_BOND=(7,33,1)
CIF_BOND=(8,38,2)
CIF_BOND=(8,36,1)
CIF_BOND=(9,10,2)
CIF_BOND=(10,14,1)
CIF_BOND=(11,12,1)
CIF_BOND=(11,18,1)
CIF_BOND=(11,14,2)
CIF_BOND=(13,32,1)
CIF_BOND=(14,34,1)
CIF_BOND=(15,17,1)
CIF_BOND=(15,16,1)
CIF_BOND=(15,29,1)
CIF_BOND=(18,19,1)
CIF_BOND=(18,33,2)
CIF_BOND=(20,21,1)
CIF_BOND=(20,36,2)
CIF_BOND=(20,32,1)
CIF_BOND=(22,23,1)
CIF_BOND=(22,34,2)
CIF_BOND=(22,33,1)
CIF_BOND=(24,26,1)
CIF_BOND=(24,25,1)
CIF_BOND=(24,40,1)
CIF_BOND=(24,29,1)
CIF_BOND=(27,28,1)
CIF_BOND=(27,38,1)
CIF_BOND=(27,32,2)
CIF_BOND=(29,31,1)
CIF_BOND=(29,30,1)
CIF_BOND=(34,35,1)
CIF_BOND=(36,37,1)
CIF_BOND=(38,39,1)
CIF_BOND=(40,42,1)
CIF_BOND=(40,41,1)
CIF_BOND=(40,43,1)

The molecule to be frozen in the crystal structure optimization is defined by [CRYSTAL_FIXED_MOL=] keyword.
Molecular ID of each molecule in the input file are automatically determined according to atom serial number. In case of “BPN-ISN.cif”, the molecular ID of isonicotinamide is 1, and that of butylparaben is 2. Here, to freeze structure and position of buthlparaben, we add [CRYSTAL_FIXED_MOL=2] keyword to the BPN-ISN.ini file. If you want to optimize hydrogen atom positions of buthylparaben, you should also add [CRYSTAL_FIXED_MOL=EXCLUDE_HYDROGEN] keyword to the BPN-ISN.ini file.
We can select only the crystal structure optimization of [CRYSTAL_OPTIMIZATION=MOL] in the case of the optimization with the restrictions.

[CRYSTAL] means to execute a crystal calculation. [MMFF94s] means to use MMFF94s force field. The bond information for isonicotinamide and butylparaben molecules are set by [CIF_BOND=] keywords. When you want to set a bond with n bond order to an atomic pair of atom i and atom j, CIF_BOND=(i,j,n) keyword should be described.

Store the two files of BPN-ISN.cif and BPN-ISN.ini in an one folder, and execute below command. The calculation will start. The structure and position of buthlparaben in the crystal after and before the optimization are equivalent.

C:\CONFLEX\bin\flex9a_win_x64.exe   -par   C:\CONFLEX\par   BPN-ISNenter

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

[Output files]

After the calculation, you can get output files below.

File type Explanation
(Input file name).bso Detail information on the crystal calculation is described to this file.
(Input file name).ical Powder X-ray diffraction data of initial and optimized structures are described to this file.
(Input file name)-F.cmf Crystal structure data after the optimization is described to this file in CIFMIF file format (In case of using cmf/mol file as input).
(Input file name)-F.cif Crystal structure data after the optimization is described to this file in CIF file format (In case of using cif file as input).

[CRYSTAL STRUCTURE INFORMATION] part in the bso file shows information of crystal structure model built and each energy value. In the bso file, these data of both initial and optimized structures are shown.
A part of "tartronicacid.bso" is shown below.

 --------------------------  CRYSTAL STRUCTURE INFORMATION  --------------------------

                          CRYSTAL SYSTEM:   ORTHORHOMBIC   
                        SPACE GROUP NAME:   P212121 
                                  NUMBER:      19

         SYMMETRY EQUIVALENT POSITION  1:   x,y,z                    
                                       2:   1/2+x,1/2-y,-z           
                                       3:   -x,1/2+y,1/2-z           
                                       4:   1/2-x,-y,1/2+z           

                       CELL LENGTHS    a:        4.4940 ANGSTROM
                                       b:        8.8190
                                       c:       10.8820
                       CELL ANGLES alpha:       90.0000 DEGREE
                                    beta:       90.0000
                                   gamma:       90.0000

                            CELL  VOLUME:      431.2818 ANGSTROM**3
                            CELL DENSITY:        1.8482 MG/M**3

                                 Z      :        4 (ZCFX:      4)

                    CRYSTAL RADIUS (VDW):       20.00 ANGSTROM
              CRYSTAL RADIUS (COULOMBIC):       20.00 ANGSTROM
                      CRYSTAL PACKING GA:         15 (PGA:         8  NGA:        -7)
                                      GB:         11 (PGB:         6  NGB:        -5)
                                      GC:          9 (PGC:         5  NGC:        -4)

        NUM. OF ATOMS IN ASYMMETRIC UNIT:         12
        NUM. OF MOLS  IN ASYMMETRIC UNIT:          1
              NUM. OF ATOMS IN UNIT CELL:         48
           NUM. OF CALCULATED UNIT CELLS:        195
      NUM. OF CALCULATED MOLECULES (VDW):        513
          NUM. OF CALCULATED ATOMS (VDW):       6156
  NUM. OF CALCULATED MOLECULES (COULOM.):        513
      NUM. OF CALCULATED ATOMS (COULOM.):       6156

                   INTRAMOLECULAR ENERGY:      258.8731 KCAL/MOL
                          LATTICE ENERGY:      -22.4774 KCAL/MOL
                          CRYSTAL ENERGY:      236.3957 KCAL/MOL
Item Explanation
CRYSTAL RADIUS(VDW): Cutoff distance of vdW interaction
CRYSTAL RADIUS(COULOMBIC): Cutoff distance of coulombic interaction on a real space
CRYSTAL PACKING GA GB GC: Packing area of unit cell along a, b, and c axes
NUM. OF ATOMS IN ASYMMETRIC UNIT: Total the number of atoms in the asymmetric unit
NUM. OF MOLS IN ASYMMETRIC UNIT: Total the number of molecules in the asymmetric unit
NUM. OF ATOMS IN UNIT CELL: Total the number of atoms in the unit cell
NUM. OF CALCULATED UNIT CELLS: Total the number of unit cells in the crystal model
NUM. OF CALCULATED MOLECULES (VDW): Total the number of molecules including in the calculation of vdW interactions
NUM. OF CALCULATED ATOMS (VDW): Total the number of atoms including in the calculation of vdW interactions
NUM. OF CALCULATED MOLECULES (COULOM.) Total the number of molecules including in the calculation of coulombic interactions (real space)
NUM. OF CALCULATED ATOMS (COULOM.): Total the number of atoms including in the calculation of coulombic interactions (real space)
INTRAMOLECULAR ENERGY: Eintra
LATTICE ENERGY: Elattice
CRYSTAL ENERGY: Ecrystal

The powder X-ray diffraction data of initial (NAME: INITIAL STRUCTURE) and optimized (NAME: FINAL STRUCTURE) structures are outputted to the ical file.
A part of "tartronicacid.ical" is shown below.

 ------------ SIMULATED POWDER PATTERNS ------------
    CID:     1
   NAME: INITIAL STRUCTURE             
  X-RAY: Cu (KA1)
   WAVE: 1.54059290
2*THETA:   0.000 -  50.000 ,   0.020 STEP

 H   K   L  2*THETA       INTENSITY         d
            (DEGREE)                   (ANGSTROME)
 0   0   0    0.000           0.000      0.00000
 0   0   0    0.020           0.000      0.00000
 0   0   0    0.040           0.000      0.00000
 0   0   0    0.060           0.000      0.00000
 0   0   0    0.080           0.000      0.00000
 0   0   0    0.100           0.000      0.00000
 
* snip *

------------ SIMULATED POWDER PATTERNS ------------
    CID:     2
   NAME: FINAL STRUCTURE               
  X-RAY: Cu (KA1)
   WAVE: 1.54059290
2*THETA:   0.000 -  50.000 ,   0.020 STEP

 H   K   L  2*THETA       INTENSITY         d
            (DEGREE)                   (ANGSTROME)
 0   0   0    0.000           0.000      0.00000
 0   0   0    0.020           0.000      0.00000
 0   0   0    0.040           0.000      0.00000
 0   0   0    0.060           0.000      0.00000
 0   0   0    0.080           0.000      0.00000
 0   0   0    0.100           0.000      0.00000

 * snip *

[Visualization of calculation results]

[If you executed the calculation by using Interface]

After the submission, the Job Manager will appear at the bottom of CONFLEX Interface window. The Job Manager shows a state of the calculation job executed. When the state of the job changed to "Finished", double-click the row of job finished (the red frame part). The output file (-F.cmf or -F.cif file) will open and the structure optimized will be displayed.

Interface Job Manager

After the open of output file (-F.cmf or -F.cif file), you can show the powder X-ray diffraction pattern by selecting [Spectra_Analyzer] in [Application] menu.

Crystal PXRD

[If you executed the calculation by using command line]

The all output files will be stored in the folder contained input files. If you open the -F.cmf or -F.cif file, you can visualize the optimized crystal structure.

Interface Opt Struct

After the open of output file (-F.cmf or -F.cif file), you can show the powder X-ray diffraction pattern by selecting [Spectra_Analyzer] in [Application] menu.

Crystal PXRD

[Available space groups]

International Table Number Space group name
1 P1
2 P-1
3 P2 unique axis b
3 P2 unique axis c
4 P21 unique axis b
4 P21 unique axis c
5 C2 unique axis b
5 C2 unique axis c
6 PM unique axis b
6 PM unique axis c
7 PC unique axis b
7 PC unique axis c
8 CM unique axis b
8 CM unique axis c
9 CC unique axis b
9 CC unique axis c
10 P2/M unique axis b
10 P2/M unique axis c
11 P21/M unique axis b
11 P21/M unique axis c
12 C2/M unique axis b
12 C2/M unique axis c
13 P2/C unique axis b
13 P2/C unique axis c
14 P21/C unique axis b
14 P21/C unique axis c
15 C2/C unique axis b
15 C2/C unique axis c
16 P222
17 P2221
18 P21212
19 P212121
20 C2221
21 C222
22 F222
23 I222
24 I212121
25 PMM2
26 PMC21
27 PCC2
28 PMA2
29 PCA21
30 PNC2
31 PMN21
32 PBA2
33 PNA21
34 PNN2
35 CMM2
36 CMC21
37 CCC2
38 AMM2
39 ABM2
40 AMA2
41 ABA2
42 FMM2
43 FDD2
44 IMM2
45 IBA2
46 IMA2
47 PMMM
48 PNNN origin choice 1
48 PNNN origin choice 2
49 PCCM
50 PBAN origin choice 1
50 PBAN origin choice 2
51 PMMA
52 PNNA
53 PMNA
54 PCCA
55 PBAM
56 PCCN
57 PBCM
58 PNNM
59 PMMN origin choice 1
59 PMMN origin choice 2
60 PBCN
61 PBCA
62 PNMA
63 CMCM
64 CMCA
65 CMMM
66 CCCM
67 CMMA
68 CCCA origin choice 1
68 CCCA origin choice 2
69 FMMM
70 FDDD origin choice 1
70 FDDD origin choice 2
71 IMMM
72 IBAM
73 IBCA
74 IMMA
75 P4
76 P41
77 P42
78 P43
79 I4
80 I41
81 P-4
82 I-4
83 P4/M
84 P42/M
85 P4/N origin choice 1
85 P4/N origin choice 2
86 P42/N origin choice 1
86 P42/N origin choice 2
87 I4/M
88 I41/A origin choice 1
88 I41/A origin choice 2
89 P422
90 P4212
91 P4122
92 P41212
93 P4222
94 P42212
95 P4322
96 P43212
97 I422
98 I4122
99 P4MM
100 P4BM
101 P42CM
102 P42NM
103 P4CC
104 P4NC
105 P42MC
106 P42BC
107 I4MM
108 I4CM
109 I41MD
110 I41CD
111 P-42M
112 P-42C
113 P-421M
114 P-421C
115 P-4M2
116 P-4C2
117 P-4B2
118 P-4N2
119 I-4M2
120 I-4C2
121 I-42M
122 I-42D
123 P4/MMM
124 P4/MCC
125 P4/NBM origin choice 1
125 P4/NBM origin choice 2
126 P4/NNC origin choice 1
126 P4/NNC origin choice 2
127 P4/MBM
128 P4/MNC
129 P4/NMM origin choice 1
129 P4/NMM origin choice 2
130 P4/NCC origin choice 1
130 P4/NCC origin choice 2
131 P42/MMC
132 P42/MCM
133 P42/NBC origin choice 1
133 P42/NBC origin choice 2
134 P42/NNM origin choice 1
134 P42/NNM origin choice 2
135 P42/MBC
136 P42/MNM
137 P42/NMC origin choice 1
137 P42/NMC origin choice 2
138 P42/NCM origin choice 1
138 P42/NCM origin choice 2
139 I4/MMM
140 I4/MCM
141 I41/AMD origin choice 1
141 I41/AMD origin choice 2
142 I41/ACD origin choice 1
142 I41/ACD origin choice 2
143 P3
144 P31
145 P32
146 R3 hexagonal axes
146 R3 rhombohedral axes
147 P-3
148 R-3 hexagonal axes
148 R-3 rhombohedral axes
149 P312
150 P321
151 P3112
152 P3121
153 P3212
154 P3221
155 R32 hexagonal axes
155 R32 rhombohedral axes
156 P3M1
157 P31M
158 P3C1
159 P31C
160 R3M hexagonal axes
160 R3M rhombohedral axes
161 R3C hexagonal axes
161 R3C rhombohedral axes
162 P-31M
163 P-31C
164 P-3M1
165 P-3C1
166 R-3M hexagonal axes
166 R-3M rhombohedral axes
167 R-3C hexagonal axes
167 R-3C rhombohedral axes
168 P6
169 P61
170 P65
171 P62
172 P64
173 P63
174 P-6
175 P6/M
176 P63/M
177 P622
178 P6122
179 P6522
180 P6222
181 P6422
182 P6322
183 P6MM
184 P6CC
185 P63CM
186 P63MC
187 P-6M2
188 P-6C2
189 P-62M
190 P-62C
191 P6/MMM
192 P6/MCC
193 P63/MCM
194 P63/MMC
195 P23
196 F23
197 I23
198 P213
199 I213
200 PM-3
201 PN-3 origin choice 1
201 PN-3 origin choice 2
202 FM-3
203 FD-3 origin choice 1
203 FD-3 origin choice 2
204 IM-3
205 PA-3
206 IA-3
207 P432
208 P4232
209 F432
210 F4132
211 I432
212 P4332
213 P4132
214 I4132
215 P-43M
216 F-43M
217 I-43M
218 P-43N
219 F-43C
220 I-43D
221 PM-3M
222 PN-3N origin choice 1
222 PN-3N origin choice 2
223 PM-3N
224 PN-3M origin choice 1
224 PN-3M origin choice 2
225 FM-3M
226 FM-3C
227 FD-3M origin choice 1
227 FD-3M origin choice 2
228 FD-3C origin choice 1
228 FD-3C origin choice 2
229 IM-3M
230 IA-3D

[Available X-ray sources]

Kα1 wavelength (Ang.)
Mg 9.889554
Al 8.339514
Si 7.125588
S 5.3722
Cl 4.727818
Ar 4.191938
K 3.7412838
Cr 2.289726
Mn 2.101854
Fe 1.936041
Co 1.788996
Ni 1.65793
Cu 1.5405929
Ga 1.340127
As 1.175956
Se 1.10478
Br 1.039756
Kr 0.980267
Zr 0.7859579
Mo 0.70931715
Ru 0.6430994
Rh 0.6132937
Pd 0.5854639
Ag 0.55942178
Cd 0.5350147
In 0.5121251
Sn 0.4906115
Sb 0.47037
Xe 0.4163508
Ba 0.38512464
Nd 0.33185689
Pm 0.3201648
Sm 0.30904506
Ho 0.2607608
Er 0.25237359
Tm 0.24434486
W 0.20901314
Au 0.1801978
Pb 0.16537816
Bi 0.1607903