# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:01:55 2021
#   Inital geometry file: a 149 line input string
#   Ligand name: 6-{4-[3-(dimethylamino)propoxy]phenyl}-2-(methylsulfonyl)-N-[3-(1H-pyrazol-1-yl)propyl]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)CCCOc1ccc(cc1)c2cc(NCCCn3cccn3)nc(n2)[S](C)(=O)=O
#
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
 WCS  WCS  6-{4-[3-(dimethylamino)propoxy]phenyl}-2-(methylsulfonyl)-N-[3-(1H-pyrazol-1-yl)propyl]pyrimidin-4-amine  ligand  62  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WCS
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
 WCS  C10  C  CR6   0   0.033  16.9101   9.6743  127.7599
 WCS  C11  C  CR6   0   0.301  18.0581  10.1937  128.5158
 WCS  C13  C  CR6   0   0.158  19.4068  10.0217  130.2976
 WCS  C15  C  CH3   0  -0.797  19.8603   7.4414  131.3240
 WCS  O16  O  OS    0  -0.674  18.6157   9.3118  132.7107
 WCS  O17  O  OS    0  -0.666  21.0841   9.5650  132.3113
 WCS  C19  C  CR6   0   0.554  19.8653  11.7159  128.9093
 WCS  C01  C  CH3   0  -0.516  13.8635   5.3543  122.2703
 WCS  C03  C  CH2   0  -0.269  12.3112   6.5720  123.6127
 WCS  C04  C  CH2   0  -0.500  11.8806   7.9279  124.1578
 WCS  C05  C  CH2   0  -0.185  13.0206   8.7852  124.6616
 WCS  C07  C  CR6   0   0.400  14.7033   8.6578  126.3447
 WCS  C08  C  CR16  0  -0.336  15.3147   7.9020  127.3507
 WCS  C09  C  CR16  0  -0.261  16.3926   8.4061  128.0455
 WCS  C21  C  CH2   0  -0.306  20.4187  13.6426  127.4821
 WCS  C22  C  CH2   0  -0.467  21.0420  13.0839  126.2059
 WCS  C23  C  CH2   0  -0.296  20.7071  13.9216  124.9834
 WCS  C25  C  CR15  0   0.043  18.5327  15.1045  124.5938
 WCS  C26  C  CR15  0  -0.510  17.2415  14.6901  124.3567
 WCS  C27  C  CR15  0  -0.048  17.3233  13.2903  124.3836
 WCS  C29  C  CR16  0  -0.442  18.7986  11.2829  128.0972
 WCS  C30  C  CR16  0  -0.305  16.2931  10.4155  126.7548
 WCS  C31  C  CR16  0  -0.371  15.2061   9.9256  126.0496
 WCS  C32  C  CH3   0  -0.525  12.7855   7.2697  121.3606
 WCS  N02  N  NT    0  -0.402  13.3087   6.6581  122.5632
 WCS  N12  N  N     0  -0.448  18.3732   9.5473  129.6555
 WCS  N18  N  N     0  -0.444  20.1768  11.0393  130.0324
 WCS  N20  N  NH1   0  -0.645  20.6092  12.7881  128.6297
 WCS  N24  N  NR5   0  -0.264  19.2785  13.9949  124.7407
 WCS  N28  N  N     0  -0.288  18.5601  12.8832  124.6172
 WCS  O06  O  O2    0  -0.463  13.6522   8.0992  125.7359
 WCS  S14  S  S     0   1.202  19.7733   9.1403  131.8359
 WCS  H1   H  HCH3  0   0.314  20.1034   6.8571  132.2109
 WCS  H2   H  HCH3  0   0.298  18.9001   7.1319  130.9221
 WCS  H3   H  HCH3  0   0.297  20.6437   7.3279  130.5780
 WCS  H4   H  HCH3  0   0.231  14.2979   4.9184  123.1710
 WCS  H5   H  HCH3  0   0.188  13.1186   4.6425  121.8794
 WCS  H6   H  HCH3  0   0.230  14.6572   5.4425  121.5270
 WCS  H7   H  HCH2  0   0.201  11.4118   6.0292  123.2722
 WCS  H8   H  HCH2  0   0.231  12.7314   5.9799  124.4293
 WCS  H9   H  HCH2  0   0.243  11.3503   8.5054  123.3967
 WCS  H10  H  HCH2  0   0.249  11.1578   7.7660  124.9617
 WCS  H11  H  HCH2  0   0.228  13.7454   8.9735  123.8632
 WCS  H12  H  HCH2  0   0.235  12.6349   9.7513  125.0040
 WCS  H13  H  HCR6  0   0.267  14.9324   6.9151  127.5786
 WCS  H14  H  HCR6  0   0.263  16.8487   7.8043  128.8197
 WCS  H15  H  HCH2  0   0.280  20.8606  14.6098  127.7203
 WCS  H16  H  HCH2  0   0.248  19.3488  13.8202  127.3463
 WCS  H17  H  HCH2  0   0.252  20.7165  12.0550  126.0411
 WCS  H18  H  HCH2  0   0.260  22.1281  13.0566  126.3106
 WCS  H19  H  HCH2  0   0.276  21.1989  13.5102  124.1010
 WCS  H20  H  HCH2  0   0.261  21.0602  14.9455  125.1058
 WCS  H21  H  HCR5  0   0.292  18.9632  16.0901  124.6672
 WCS  H22  H  HCR5  0   0.263  16.3738  15.3062  124.1917
 WCS  H23  H  HCR5  0   0.260  16.5327  12.5698  124.2345
 WCS  H24  H  HCR6  0   0.276  18.5806  11.7723  127.1593
 WCS  H25  H  HCR6  0   0.253  16.6386  11.4133  126.5184
 WCS  H26  H  HCR6  0   0.281  14.7574  10.5484  125.2882
 WCS  H27  H  HCH3  0   0.235  12.4675   8.2957  121.5466
 WCS  H28  H  HCH3  0   0.233  13.5608   7.3074  120.5944
 WCS  H29  H  HCH3  0   0.191  11.9250   6.7230  120.9425
 WCS  H31  H  HNH1  0   0.403  21.3744  12.9821  129.2560

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
 WCS  C32  N02  single    1.447  0.020  1.447
 WCS  C01  N02  single    1.447  0.020  1.447
 WCS  N02  C03  single    1.450  0.020  1.450
 WCS  C03  C04  single    1.523  0.020  1.523
 WCS  C04  C05  single    1.513  0.020  1.513
 WCS  N28  C27  aromatic  1.323  0.020  1.323
 WCS  N28  N24  aromatic  1.329  0.020  1.329
 WCS  C27  C26  aromatic  1.402  0.020  1.402
 WCS  C05  O06  single    1.423  0.020  1.423
 WCS  N24  C23  single    1.451  0.020  1.451
 WCS  N24  C25  aromatic  1.345  0.020  1.345
 WCS  C23  C22  single    1.519  0.020  1.519
 WCS  C26  C25  aromatic  1.377  0.020  1.377
 WCS  O06  C07  single    1.337  0.020  1.337
 WCS  C31  C07  aromatic  1.395  0.020  1.395
 WCS  C31  C30  aromatic  1.385  0.020  1.385
 WCS  C22  C21  single    1.526  0.020  1.526
 WCS  C07  C08  aromatic  1.399  0.020  1.399
 WCS  C30  C10  aromatic  1.393  0.020  1.393
 WCS  C21  N20  single    1.443  0.020  1.443
 WCS  C08  C09  aromatic  1.378  0.020  1.378
 WCS  C10  C09  aromatic  1.399  0.020  1.399
 WCS  C10  C11  single    1.469  0.020  1.469
 WCS  C29  C11  aromatic  1.382  0.020  1.382
 WCS  C29  C19  aromatic  1.409  0.020  1.409
 WCS  C11  N12  aromatic  1.348  0.020  1.348
 WCS  N20  C19  single    1.335  0.020  1.335
 WCS  C19  N18  aromatic  1.348  0.020  1.348
 WCS  N12  C13  aromatic  1.306  0.020  1.306
 WCS  N18  C13  aromatic  1.303  0.020  1.303
 WCS  C13  S14  single    1.810  0.020  1.810
 WCS  C15  S14  single    1.776  0.020  1.776
 WCS  S14  O17  double    1.458  0.020  1.458
 WCS  S14  O16  double    1.461  0.020  1.461
 WCS  C15  H1   single    0.970  0.020  1.090
 WCS  C15  H2   single    0.970  0.020  1.090
 WCS  C15  H3   single    0.970  0.020  1.090
 WCS  C01  H4   single    0.970  0.020  1.090
 WCS  C01  H5   single    0.970  0.020  1.090
 WCS  C01  H6   single    0.970  0.020  1.090
 WCS  C03  H7   single    0.970  0.020  1.090
 WCS  C03  H8   single    0.970  0.020  1.090
 WCS  C04  H9   single    0.970  0.020  1.090
 WCS  C04  H10  single    0.970  0.020  1.090
 WCS  C05  H11  single    0.970  0.020  1.090
 WCS  C05  H12  single    0.970  0.020  1.090
 WCS  C08  H13  single    0.930  0.020  1.080
 WCS  C09  H14  single    0.930  0.020  1.080
 WCS  C21  H15  single    0.970  0.020  1.090
 WCS  C21  H16  single    0.970  0.020  1.090
 WCS  C22  H17  single    0.970  0.020  1.090
 WCS  C22  H18  single    0.970  0.020  1.090
 WCS  C23  H19  single    0.970  0.020  1.090
 WCS  C23  H20  single    0.970  0.020  1.090
 WCS  C25  H21  single    0.930  0.020  1.080
 WCS  C26  H22  single    0.930  0.020  1.080
 WCS  C27  H23  single    0.930  0.020  1.080
 WCS  C29  H24  single    0.930  0.020  1.080
 WCS  C30  H25  single    0.930  0.020  1.080
 WCS  C31  H26  single    0.930  0.020  1.080
 WCS  C32  H27  single    0.970  0.020  1.090
 WCS  C32  H28  single    0.970  0.020  1.090
 WCS  C32  H29  single    0.970  0.020  1.090
 WCS  N20  H31  single    0.860  0.020  1.020

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
 WCS  C30  C10  C09  117.76  3.000
 WCS  C09  C10  C11  120.29  3.000
 WCS  C30  C10  C11  121.95  3.000
 WCS  N12  C11  C29  120.59  3.000
 WCS  N12  C11  C10  116.63  3.000
 WCS  C29  C11  C10  122.78  3.000
 WCS  S14  C13  N18  115.68  3.000
 WCS  S14  C13  N12  113.65  3.000
 WCS  N18  C13  N12  130.63  3.000
 WCS  H3   C15  H2   110.69  3.000
 WCS  H3   C15  H1   109.98  3.000
 WCS  H2   C15  H1   110.23  3.000
 WCS  H3   C15  S14  109.43  3.000
 WCS  H2   C15  S14  109.63  3.000
 WCS  H1   C15  S14  106.81  3.000
 WCS  N20  C19  N18  116.69  3.000
 WCS  N18  C19  C29  120.07  3.000
 WCS  N20  C19  C29  123.24  3.000
 WCS  H6   C01  H5   107.60  3.000
 WCS  H6   C01  H4   107.76  3.000
 WCS  H5   C01  H4   107.70  3.000
 WCS  H6   C01  N02  110.12  3.000
 WCS  H5   C01  N02  113.25  3.000
 WCS  H4   C01  N02  110.22  3.000
 WCS  H8   C03  H7   106.09  3.000
 WCS  H8   C03  N02  107.97  3.000
 WCS  H7   C03  N02  111.48  3.000
 WCS  H8   C03  C04  108.88  3.000
 WCS  H7   C03  C04  108.52  3.000
 WCS  N02  C03  C04  113.61  3.000
 WCS  H10  C04  H9   105.64  3.000
 WCS  H10  C04  C05  109.72  3.000
 WCS  H9   C04  C05  107.34  3.000
 WCS  H10  C04  C03  108.56  3.000
 WCS  H9   C04  C03  111.00  3.000
 WCS  C05  C04  C03  114.24  3.000
 WCS  H12  C05  H11  108.03  3.000
 WCS  H12  C05  O06  110.22  3.000
 WCS  H11  C05  O06  109.87  3.000
 WCS  H12  C05  C04  109.80  3.000
 WCS  H11  C05  C04  110.71  3.000
 WCS  O06  C05  C04  108.22  3.000
 WCS  O06  C07  C31  124.51  3.000
 WCS  C31  C07  C08  119.04  3.000
 WCS  O06  C07  C08  116.44  3.000
 WCS  H13  C08  C09  120.23  3.000
 WCS  H13  C08  C07  119.31  3.000
 WCS  C09  C08  C07  120.45  3.000
 WCS  H14  C09  C08  119.16  3.000
 WCS  H14  C09  C10  119.64  3.000
 WCS  C08  C09  C10  121.20  3.000
 WCS  H16  C21  H15  106.25  3.000
 WCS  H16  C21  N20  108.91  3.000
 WCS  H15  C21  N20  107.35  3.000
 WCS  H16  C21  C22  110.82  3.000
 WCS  H15  C21  C22  110.00  3.000
 WCS  N20  C21  C22  113.21  3.000
 WCS  H18  C22  H17  106.71  3.000
 WCS  H18  C22  C23  108.08  3.000
 WCS  H17  C22  C23  109.42  3.000
 WCS  H18  C22  C21  109.59  3.000
 WCS  H17  C22  C21  110.46  3.000
 WCS  C23  C22  C21  112.39  3.000
 WCS  H20  C23  H19  107.40  3.000
 WCS  H20  C23  N24  106.88  3.000
 WCS  H19  C23  N24  109.12  3.000
 WCS  H20  C23  C22  110.87  3.000
 WCS  H19  C23  C22  110.10  3.000
 WCS  N24  C23  C22  112.30  3.000
 WCS  H21  C25  N24  121.69  3.000
 WCS  H21  C25  C26  131.42  3.000
 WCS  N24  C25  C26  106.89  3.000
 WCS  H22  C26  C27  128.39  3.000
 WCS  H22  C26  C25  127.58  3.000
 WCS  C27  C26  C25  104.03  3.000
 WCS  H23  C27  N28  120.23  3.000
 WCS  H23  C27  C26  128.36  3.000
 WCS  N28  C27  C26  111.42  3.000
 WCS  H24  C29  C19  120.94  3.000
 WCS  H24  C29  C11  120.79  3.000
 WCS  C19  C29  C11  118.25  3.000
 WCS  H25  C30  C31  117.74  3.000
 WCS  H25  C30  C10  120.45  3.000
 WCS  C31  C30  C10  121.78  3.000
 WCS  H26  C31  C30  118.71  3.000
 WCS  H26  C31  C07  121.52  3.000
 WCS  C30  C31  C07  119.76  3.000
 WCS  H29  C32  H28  107.80  3.000
 WCS  H29  C32  H27  107.69  3.000
 WCS  H28  C32  H27  107.14  3.000
 WCS  H29  C32  N02  112.83  3.000
 WCS  H28  C32  N02  109.96  3.000
 WCS  H27  C32  N02  111.18  3.000
 WCS  C32  N02  C03  112.20  3.000
 WCS  C03  N02  C01  110.89  3.000
 WCS  C32  N02  C01  110.56  3.000
 WCS  C13  N12  C11  115.25  3.000
 WCS  C19  N18  C13  115.15  3.000
 WCS  H31  N20  C21  118.71  3.000
 WCS  H31  N20  C19  116.60  3.000
 WCS  C21  N20  C19  124.65  3.000
 WCS  N28  N24  C25  112.34  3.000
 WCS  C25  N24  C23  127.29  3.000
 WCS  N28  N24  C23  120.36  3.000
 WCS  N24  N28  C27  105.32  3.000
 WCS  C07  O06  C05  119.44  3.000
 WCS  O17  S14  O16  118.88  3.000
 WCS  O16  S14  C15  108.88  3.000
 WCS  O17  S14  C15  109.18  3.000
 WCS  O16  S14  C13  106.93  3.000
 WCS  O17  S14  C13  108.50  3.000
 WCS  C15  S14  C13  103.34  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
 WCS  CONST_01  C07  C31  C30  C10     0.00   0.0  0
 WCS  CONST_02  C07  C08  C09  C10     0.00   0.0  0
 WCS  CONST_03  C19  C29  C11  C10   180.00   0.0  0
 WCS  CONST_04  C13  N12  C11  C10   180.00   0.0  0
 WCS  CONST_05  C31  C30  C10  C11   180.00   0.0  0
 WCS  CONST_06  C08  C09  C10  C11   180.00   0.0  0
 WCS  CONST_07  N18  C19  C29  C11     0.00   0.0  0
 WCS  CONST_08  N18  C13  N12  C11     0.00   0.0  0
 WCS  CONST_09  C29  C11  N12  C13     0.00   0.0  0
 WCS  CONST_10  C29  C19  N18  C13     0.00   0.0  0
 WCS  CONST_11  N12  C11  C29  C19     0.00   0.0  0
 WCS  CONST_12  N12  C13  N18  C19     0.00   0.0  0
 WCS  CONST_13  C30  C31  C07  C08     0.00   0.0  0
 WCS  CONST_14  C30  C10  C09  C08     0.00   0.0  0
 WCS  CONST_15  C31  C07  C08  C09     0.00   0.0  0
 WCS  CONST_16  C31  C30  C10  C09     0.00   0.0  0
 WCS  CONST_17  C29  C11  C10  C09   180.00   0.0  0
 WCS  CONST_18  N12  C11  C10  C09     0.00   0.0  0
 WCS  CONST_19  C27  N28  N24  C25     0.00   0.0  0
 WCS  CONST_20  N28  C27  C26  C25     0.00   0.0  0
 WCS  CONST_21  N24  N28  C27  C26     0.00   0.0  0
 WCS  CONST_22  N28  N24  C25  C26     0.00   0.0  0
 WCS  CONST_23  N24  C25  C26  C27     0.00   0.0  0
 WCS  CONST_26  N20  C19  C29  C11   180.00   0.0  0
 WCS  CONST_27  S14  C13  N12  C11   180.00   0.0  0
 WCS  CONST_28  N20  C19  N18  C13   180.00   0.0  0
 WCS  CONST_29  S14  C13  N18  C19   180.00   0.0  0
 WCS  CONST_30  O06  C07  C08  C09   180.00   0.0  0
 WCS  CONST_31  C27  N28  N24  C23   180.00   0.0  0
 WCS  CONST_32  C26  C25  N24  C23   180.00   0.0  0
 WCS  CONST_33  O06  C07  C31  C30   180.00   0.0  0
 WCS  CONST_34  H26  C31  C30  C10   180.00   0.0  0
 WCS  CONST_35  H13  C08  C09  C10   180.00   0.0  0
 WCS  CONST_36  H24  C29  C11  C10     0.00   0.0  0
 WCS  CONST_37  H25  C30  C10  C11     0.00   0.0  0
 WCS  CONST_38  H14  C09  C10  C11     0.00   0.0  0
 WCS  CONST_39  H23  C27  C26  C25   180.00   0.0  0
 WCS  CONST_40  H21  C25  C26  C27   180.00   0.0  0
 WCS  CONST_41  H22  C26  C25  N24   180.00   0.0  0
 WCS  CONST_42  C29  C19  N20  C21     0.00   0.0  0
 WCS  CONST_43  N18  C19  N20  C21   180.00   0.0  0
 WCS  CONST_44  H31  N20  C19  C29   180.00   0.0  0
 WCS  Var_01    N12  C13  S14  C15    52.48  30.0  2
 WCS  Var_02    C31  C07  O06  C05     3.48  30.0  2
 WCS  Var_03    N28  N24  C23  C22   -54.90  30.0  2
 WCS  Var_04    C22  C21  N20  C19   -81.22  30.0  1
 WCS  Var_05    N24  C23  C22  C21   -60.19  30.0  1
 WCS  Var_06    H1   C15  S14  C13   178.72  30.0  3
 WCS  Var_07    H11  C05  O06  C07    58.55  30.0  2
 WCS  Var_08    C04  C03  N02  C01   168.87  30.0  3
 WCS  Var_09    O06  C05  C04  C03   -61.53  30.0  3
 WCS  Var_10    N02  C03  C04  C05   -55.33  30.0  1
 WCS  Var_11    N20  C21  C22  C23   173.99  30.0  3
 WCS  Var_12    H27  C32  N02  C01  -173.60  30.0  3
 WCS  Var_13    H4   C01  N02  C03   -57.54  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
 WCS  plan-1  C23  0.020
 WCS  plan-1  C25  0.020
 WCS  plan-1  C26  0.020
 WCS  plan-1  C27  0.020
 WCS  plan-1  N24  0.020
 WCS  plan-1  N28  0.020
 WCS  plan-1  H21  0.020
 WCS  plan-1  H22  0.020
 WCS  plan-1  H23  0.020
 WCS  plan-2  C10  0.020
 WCS  plan-2  C11  0.020
 WCS  plan-2  C13  0.020
 WCS  plan-2  C19  0.020
 WCS  plan-2  C29  0.020
 WCS  plan-2  N12  0.020
 WCS  plan-2  N18  0.020
 WCS  plan-2  N20  0.020
 WCS  plan-2  S14  0.020
 WCS  plan-2  H24  0.020
 WCS  plan-3  C10  0.020
 WCS  plan-3  C11  0.020
 WCS  plan-3  C07  0.020
 WCS  plan-3  C08  0.020
 WCS  plan-3  C09  0.020
 WCS  plan-3  C30  0.020
 WCS  plan-3  C31  0.020
 WCS  plan-3  O06  0.020
 WCS  plan-3  H13  0.020
 WCS  plan-3  H14  0.020
 WCS  plan-3  H25  0.020
 WCS  plan-3  H26  0.020
 WCS  plan-4  C19  0.020
 WCS  plan-4  C21  0.020
 WCS  plan-4  N20  0.020
 WCS  plan-4  H31  0.020

