# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 11:16:23 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 4-(3-piperidin-1-ylpropyl)-6-[3-(trifluoromethyl)phenyl]pyrimidine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(c1)c2cc(CCCN3CCCCC3)nc(n2)C#N
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 KWZ  KWZ  4-(3-piperidin-1-ylpropyl)-6-[3-(trifluoromethyl)phenyl]pyrimidine-2-carbonitrile  ligand  48  27  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KWZ
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 KWZ  N1    N  N     0  -0.437  -1.3211   1.3200   0.6579
 KWZ  C2    C  CR6   0   0.335  -1.2244  -0.0098   0.6244
 KWZ  C3    C  CR16  0  -0.377  -0.0282  -0.6259   0.9792
 KWZ  C4    C  CR6   0   0.312   1.0450   0.1714   1.3564
 KWZ  N5    N  N     0  -0.406   0.9298   1.4997   1.3809
 KWZ  C6    C  CR6   0   0.360  -0.2467   1.9800   1.0320
 KWZ  C7    C  CR6   0   0.074  -2.4288  -0.7553   0.2093
 KWZ  C8    C  CH2   0  -0.505   2.3757  -0.4068   1.7112
 KWZ  C9    C  CH2   0  -0.453   3.3657  -0.2611   0.5520
 KWZ  C10   C  CH2   0  -0.253   4.7453  -0.7715   0.9473
 KWZ  N11   N  NT    0  -0.421   5.7045  -0.7502  -0.1400
 KWZ  C12   C  CR16  0  -0.317  -3.6304  -0.0683   0.0299
 KWZ  C13   C  CR6   0  -0.169  -4.7728  -0.7488  -0.3541
 KWZ  C14   C  CR16  0  -0.268  -4.7349  -2.1230  -0.5730
 KWZ  C15   C  CR16  0  -0.220  -3.5439  -2.8067  -0.4001
 KWZ  C16   C  CR16  0  -0.318  -2.3982  -2.1305  -0.0111
 KWZ  C17   C  CT    0   1.058  -6.0616  -0.0191  -0.5773
 KWZ  F18   F  F     0  -0.314  -6.3539   0.0680  -1.8834
 KWZ  F19   F  F     0  -0.311  -7.0929  -0.6455   0.0031
 KWZ  F20   F  F     0  -0.301  -6.0390   1.2274  -0.0995
 KWZ  C21   C  CH2   0  -0.276   6.8686  -1.5619   0.1808
 KWZ  C22   C  CH2   0  -0.439   7.8366  -1.6431  -0.9889
 KWZ  C23   C  CH2   0  -0.439   8.2695  -0.2516  -1.4291
 KWZ  C24   C  CH2   0  -0.436   7.0405   0.6046  -1.7009
 KWZ  C25   C  CH2   0  -0.284   6.0970   0.6012  -0.5069
 KWZ  C26   C  CSP   0   0.042  -0.3756   3.4212   1.0682
 KWZ  N27   N  NS    0  -0.219  -0.4737   4.5662   1.0980
 KWZ  H3    H  HCR6  0   0.290   0.0864  -1.6995   0.9778
 KWZ  H8    H  HCH2  0   0.265   2.7615   0.1166   2.5896
 KWZ  H8A   H  HCH2  0   0.259   2.2637  -1.4591   1.9785
 KWZ  H9    H  HCH2  0   0.237   3.0089  -0.8216  -0.3160
 KWZ  H9A   H  HCH2  0   0.243   3.4088   0.7898   0.2585
 KWZ  H10   H  HCH2  0   0.189   5.1061  -0.2019   1.8227
 KWZ  H10A  H  HCH2  0   0.229   4.6430  -1.8085   1.2805
 KWZ  H12   H  HCR6  0   0.278  -3.6527   0.9989   0.1998
 KWZ  H14   H  HCR6  0   0.285  -5.6217  -2.6649  -0.8749
 KWZ  H15   H  HCR6  0   0.280  -3.5055  -3.8738  -0.5688
 KWZ  H16   H  HCR6  0   0.272  -1.4844  -2.6962   0.1092
 KWZ  H21   H  HCH2  0   0.181   7.4017  -1.1658   1.0646
 KWZ  H21A  H  HCH2  0   0.231   6.5262  -2.5649   0.4472
 KWZ  H22   H  HCH2  0   0.229   8.6991  -2.2484  -0.7001
 KWZ  H22A  H  HCH2  0   0.214   7.3493  -2.1581  -1.8225
 KWZ  H23   H  HCH2  0   0.209   8.8682   0.2118  -0.6374
 KWZ  H23A  H  HCH2  0   0.230   8.9076  -0.3042  -2.3141
 KWZ  H24   H  HCH2  0   0.229   7.3251   1.6341  -1.9292
 KWZ  H24A  H  HCH2  0   0.214   6.5100   0.2188  -2.5768
 KWZ  H25   H  HCH2  0   0.236   5.2079   1.1830  -0.7572
 KWZ  H25A  H  HCH2  0   0.181   6.5826   1.1164   0.3427

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 KWZ  N1   C2    aromatic  1.334  0.020  1.334
 KWZ  N1   C6    aromatic  1.315  0.020  1.315
 KWZ  C2   C3    aromatic  1.392  0.020  1.392
 KWZ  C2   C7    single    1.476  0.020  1.476
 KWZ  C3   C4    aromatic  1.389  0.020  1.389
 KWZ  C4   N5    aromatic  1.333  0.020  1.333
 KWZ  C4   C8    single    1.494  0.020  1.494
 KWZ  N5   C6    aromatic  1.318  0.020  1.318
 KWZ  C6   C26   single    1.447  0.020  1.447
 KWZ  C7   C12   aromatic  1.396  0.020  1.396
 KWZ  C7   C16   aromatic  1.393  0.020  1.393
 KWZ  C8   C9    single    1.531  0.020  1.531
 KWZ  C9   C10   single    1.523  0.020  1.523
 KWZ  C10  N11   single    1.450  0.020  1.450
 KWZ  N11  C21   single    1.455  0.020  1.455
 KWZ  N11  C25   single    1.454  0.020  1.454
 KWZ  C12  C13   aromatic  1.384  0.020  1.384
 KWZ  C13  C14   aromatic  1.392  0.020  1.392
 KWZ  C13  C17   single    1.498  0.020  1.498
 KWZ  C14  C15   aromatic  1.384  0.020  1.384
 KWZ  C15  C16   aromatic  1.386  0.020  1.386
 KWZ  C17  F18   single    1.341  0.020  1.341
 KWZ  C17  F19   single    1.339  0.020  1.339
 KWZ  C17  F20   single    1.335  0.020  1.335
 KWZ  C21  C22   single    1.520  0.020  1.520
 KWZ  C22  C23   single    1.522  0.020  1.522
 KWZ  C23  C24   single    1.522  0.020  1.522
 KWZ  C24  C25   single    1.522  0.020  1.522
 KWZ  C26  N27   triple    1.150  0.020  1.150
 KWZ  C3   H3    single    0.930  0.020  1.080
 KWZ  C8   H8    single    0.970  0.020  1.090
 KWZ  C8   H8A   single    0.970  0.020  1.090
 KWZ  C9   H9    single    0.970  0.020  1.090
 KWZ  C9   H9A   single    0.970  0.020  1.090
 KWZ  C10  H10   single    0.970  0.020  1.090
 KWZ  C10  H10A  single    0.970  0.020  1.090
 KWZ  C12  H12   single    0.930  0.020  1.080
 KWZ  C14  H14   single    0.930  0.020  1.080
 KWZ  C15  H15   single    0.930  0.020  1.080
 KWZ  C16  H16   single    0.930  0.020  1.080
 KWZ  C21  H21   single    0.970  0.020  1.090
 KWZ  C21  H21A  single    0.970  0.020  1.090
 KWZ  C22  H22   single    0.970  0.020  1.090
 KWZ  C22  H22A  single    0.970  0.020  1.090
 KWZ  C23  H23   single    0.970  0.020  1.090
 KWZ  C23  H23A  single    0.970  0.020  1.090
 KWZ  C24  H24   single    0.970  0.020  1.090
 KWZ  C24  H24A  single    0.970  0.020  1.090
 KWZ  C25  H25   single    0.970  0.020  1.090
 KWZ  C25  H25A  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 KWZ  C6    N1   C2   116.64  3.000
 KWZ  C7    C2   C3   123.33  3.000
 KWZ  C7    C2   N1   116.84  3.000
 KWZ  C3    C2   N1   119.83  3.000
 KWZ  H3    C3   C4   119.28  3.000
 KWZ  H3    C3   C2   122.09  3.000
 KWZ  C4    C3   C2   118.63  3.000
 KWZ  C8    C4   N5   117.27  3.000
 KWZ  C8    C4   C3   122.04  3.000
 KWZ  N5    C4   C3   120.66  3.000
 KWZ  C6    N5   C4   115.81  3.000
 KWZ  C26   C6   N5   115.84  3.000
 KWZ  C26   C6   N1   115.73  3.000
 KWZ  N5    C6   N1   128.43  3.000
 KWZ  C16   C7   C12  118.98  3.000
 KWZ  C16   C7   C2   121.68  3.000
 KWZ  C12   C7   C2   119.34  3.000
 KWZ  H8A   C8   H8   107.52  3.000
 KWZ  H8A   C8   C9   110.09  3.000
 KWZ  H8    C8   C9   109.54  3.000
 KWZ  H8A   C8   C4   109.88  3.000
 KWZ  H8    C8   C4   108.67  3.000
 KWZ  C9    C8   C4   111.06  3.000
 KWZ  H9A   C9   H9   107.03  3.000
 KWZ  H9A   C9   C10  110.89  3.000
 KWZ  H9    C9   C10  109.26  3.000
 KWZ  H9A   C9   C8   108.70  3.000
 KWZ  H9    C9   C8   109.95  3.000
 KWZ  C10   C9   C8   110.93  3.000
 KWZ  H10A  C10  H10  106.13  3.000
 KWZ  H10A  C10  N11  107.70  3.000
 KWZ  H10   C10  N11  111.75  3.000
 KWZ  H10A  C10  C9   108.18  3.000
 KWZ  H10   C10  C9   109.18  3.000
 KWZ  N11   C10  C9   113.55  3.000
 KWZ  C25   N11  C21  110.98  3.000
 KWZ  C25   N11  C10  112.42  3.000
 KWZ  C21   N11  C10  110.84  3.000
 KWZ  H12   C12  C13  120.80  3.000
 KWZ  H12   C12  C7   118.92  3.000
 KWZ  C13   C12  C7   120.28  3.000
 KWZ  C17   C13  C14  118.75  3.000
 KWZ  C17   C13  C12  120.80  3.000
 KWZ  C14   C13  C12  120.43  3.000
 KWZ  H14   C14  C15  119.51  3.000
 KWZ  H14   C14  C13  121.05  3.000
 KWZ  C15   C14  C13  119.43  3.000
 KWZ  H15   C15  C16  119.74  3.000
 KWZ  H15   C15  C14  119.91  3.000
 KWZ  C16   C15  C14  120.36  3.000
 KWZ  H16   C16  C15  118.33  3.000
 KWZ  H16   C16  C7   121.15  3.000
 KWZ  C15   C16  C7   120.52  3.000
 KWZ  F20   C17  F19  107.14  3.000
 KWZ  F20   C17  F18  106.95  3.000
 KWZ  F19   C17  F18  106.54  3.000
 KWZ  F20   C17  C13  112.77  3.000
 KWZ  F19   C17  C13  111.73  3.000
 KWZ  F18   C17  C13  111.36  3.000
 KWZ  H21A  C21  H21  106.56  3.000
 KWZ  H21A  C21  C22  109.75  3.000
 KWZ  H21   C21  C22  109.10  3.000
 KWZ  H21A  C21  N11  108.36  3.000
 KWZ  H21   C21  N11  111.23  3.000
 KWZ  C22   C21  N11  111.69  3.000
 KWZ  H22A  C22  H22  106.99  3.000
 KWZ  H22A  C22  C23  109.66  3.000
 KWZ  H22   C22  C23  111.00  3.000
 KWZ  H22A  C22  C21  109.13  3.000
 KWZ  H22   C22  C21  109.20  3.000
 KWZ  C23   C22  C21  110.77  3.000
 KWZ  H23A  C23  H23  106.66  3.000
 KWZ  H23A  C23  C24  110.74  3.000
 KWZ  H23   C23  C24  109.42  3.000
 KWZ  H23A  C23  C22  110.87  3.000
 KWZ  H23   C23  C22  109.45  3.000
 KWZ  C24   C23  C22  109.65  3.000
 KWZ  H24A  C24  H24  106.93  3.000
 KWZ  H24A  C24  C25  109.07  3.000
 KWZ  H24   C24  C25  109.13  3.000
 KWZ  H24A  C24  C23  109.63  3.000
 KWZ  H24   C24  C23  110.92  3.000
 KWZ  C25   C24  C23  111.05  3.000
 KWZ  H25A  C25  H25  106.59  3.000
 KWZ  H25A  C25  C24  109.23  3.000
 KWZ  H25   C25  C24  108.90  3.000
 KWZ  H25A  C25  N11  110.96  3.000
 KWZ  H25   C25  N11  109.47  3.000
 KWZ  C24   C25  N11  111.55  3.000
 KWZ  N27   C26  C6   180.00  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 KWZ  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 KWZ  CONST_02  C12  C7   C2   N1      0.00   0.0  0
 KWZ  CONST_03  C16  C7   C2   N1    180.00   0.0  0
 KWZ  CONST_04  C4   N5   C6   N1      0.00   0.0  0
 KWZ  CONST_05  N5   C6   N1   C2      0.00   0.0  0
 KWZ  CONST_06  N5   C4   C3   C2      0.00   0.0  0
 KWZ  CONST_07  C13  C12  C7   C2    180.00   0.0  0
 KWZ  CONST_08  C15  C16  C7   C2    180.00   0.0  0
 KWZ  CONST_09  C6   N1   C2   C3      0.00   0.0  0
 KWZ  CONST_10  C12  C7   C2   C3    180.00   0.0  0
 KWZ  CONST_11  C16  C7   C2   C3      0.00   0.0  0
 KWZ  CONST_12  C6   N5   C4   C3      0.00   0.0  0
 KWZ  CONST_13  C7   C2   C3   C4    180.00   0.0  0
 KWZ  CONST_14  C7   C2   N1   C6    180.00   0.0  0
 KWZ  CONST_15  C14  C13  C12  C7      0.00   0.0  0
 KWZ  CONST_16  C14  C15  C16  C7      0.00   0.0  0
 KWZ  CONST_17  C15  C16  C7   C12     0.00   0.0  0
 KWZ  CONST_18  C15  C14  C13  C12     0.00   0.0  0
 KWZ  CONST_19  C16  C7   C12  C13     0.00   0.0  0
 KWZ  CONST_20  C16  C15  C14  C13     0.00   0.0  0
 KWZ  CONST_21  C26  C6   N1   C2    180.00   0.0  0
 KWZ  CONST_22  C8   C4   C3   C2    180.00   0.0  0
 KWZ  CONST_23  C26  C6   N5   C4    180.00   0.0  0
 KWZ  CONST_24  C8   C4   N5   C6    180.00   0.0  0
 KWZ  CONST_25  C17  C13  C12  C7    180.00   0.0  0
 KWZ  CONST_26  C17  C13  C14  C15   180.00   0.0  0
 KWZ  CONST_27  H3   C3   C2   N1    180.00   0.0  0
 KWZ  CONST_28  H12  C12  C7   C2      0.00   0.0  0
 KWZ  CONST_29  H16  C16  C7   C2      0.00   0.0  0
 KWZ  CONST_30  H15  C15  C16  C7    180.00   0.0  0
 KWZ  CONST_31  H14  C14  C13  C12   180.00   0.0  0
 KWZ  Var_01    C23  C22  C21  N11    56.68  30.0  1
 KWZ  Var_02    C23  C24  C25  N11   -56.29  30.0  1
 KWZ  Var_03    C24  C25  N11  C21    58.53  30.0  1
 KWZ  Var_04    C24  C23  C22  C21   -53.33  30.0  1
 KWZ  Var_05    C25  N11  C21  C22   -58.87  30.0  1
 KWZ  Var_06    C25  C24  C23  C22    53.24  30.0  1
 KWZ  Var_07    C9   C8   C4   C3    101.52  30.0  2
 KWZ  Var_08    C21  N11  C10  C9   -164.79  30.0  3
 KWZ  Var_09    F18  C17  C13  C12   106.83  30.0  2
 KWZ  Var_10    C10  C9   C8   C4    176.42  30.0  3
 KWZ  Var_11    N11  C10  C9   C8    175.77  30.0  3

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 KWZ  plan-1  N1   0.020
 KWZ  plan-1  C2   0.020
 KWZ  plan-1  C3   0.020
 KWZ  plan-1  C4   0.020
 KWZ  plan-1  N5   0.020
 KWZ  plan-1  C6   0.020
 KWZ  plan-1  C7   0.020
 KWZ  plan-1  C8   0.020
 KWZ  plan-1  C26  0.020
 KWZ  plan-1  N27  0.020
 KWZ  plan-1  H3   0.020
 KWZ  plan-2  C2   0.020
 KWZ  plan-2  C7   0.020
 KWZ  plan-2  C12  0.020
 KWZ  plan-2  C13  0.020
 KWZ  plan-2  C14  0.020
 KWZ  plan-2  C15  0.020
 KWZ  plan-2  C16  0.020
 KWZ  plan-2  C17  0.020
 KWZ  plan-2  H12  0.020
 KWZ  plan-2  H14  0.020
 KWZ  plan-2  H15  0.020
 KWZ  plan-2  H16  0.020

