# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 22:29:12 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: 1-[(3S)-1-{[3-(3-chlorophenoxy)-4-hydroxyphenyl]sulfonyl}piperidin-3-yl]-5-methylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@H]2CCCN(C2)[S](=O)(=O)c3ccc(O)c(Oc4cccc(Cl)c4)c3)C(=O)NC1=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
 16T  16T  1-[(3S)-1-{[3-(3-chlorophenoxy)-4-hydroxyphenyl]sulfonyl}piperidin-3-yl]-5-methylpyrimidine-2,4(1H,3H)-dione  ligand  55  33  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_16T
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
 16T  C1   C   CH3   0  -0.707   7.8603   0.6994   0.6400
 16T  C2   C   CR6   0  -0.179   6.5772   0.3694  -0.0489
 16T  C3   C   CR16  0   0.057   5.3832   0.8295   0.3633
 16T  N4   N   NR6   0  -0.551   4.1862   0.5494  -0.2458
 16T  C5   C   CR6   0   0.741   4.1424  -0.2515  -1.3623
 16T  O6   O   O     0  -0.484   3.1177  -0.5371  -1.9495
 16T  N7   N   NR16  0  -0.732   5.3627  -0.7200  -1.7765
 16T  C8   C   CR6   0   0.557   6.6053  -0.4844  -1.2176
 16T  O9   O   O     0  -0.456   7.6080  -0.9757  -1.7038
 16T  C10  C   CH1   0  -0.085   2.9619   1.1407   0.3076
 16T  C11  C   CH2   0  -0.444   2.2769   2.1333  -0.6226
 16T  C12  C   CH2   0  -0.444   1.0890   2.7464   0.1087
 16T  C13  C   CH2   0  -0.314   0.1506   1.6787   0.6485
 16T  N14  N   N     0  -0.569   0.9067   0.7671   1.5154
 16T  C15  C   CH2   0  -0.303   1.9862   0.0751   0.8093
 16T  S16  S   S     0   1.376   0.0209  -0.1505   2.5767
 16T  O17  O   OS    0  -0.648   0.9666  -0.9218   3.3653
 16T  O18  O   OS    0  -0.648  -0.9001   0.7541   3.2440
 16T  C19  C   CR6   0  -0.220  -0.9229  -1.2730   1.5969
 16T  C20  C   CR16  0  -0.229  -0.3863  -2.5059   1.2410
 16T  C21  C   CR16  0  -0.340  -1.1097  -3.3582   0.4299
 16T  C22  C   CR6   0   0.328  -2.3657  -2.9856  -0.0453
 16T  C23  C   CR6   0   0.224  -2.8864  -1.7421   0.3259
 16T  C24  C   CR16  0  -0.284  -2.1798  -0.8892   1.1495
 16T  O25  O   O2    0  -0.518  -4.1421  -1.4290  -0.1195
 16T  C26  C   CR6   0   0.362  -4.3076  -0.3508  -0.9446
 16T  C27  C   CR16  0  -0.319  -3.2814   0.1908  -1.7089
 16T  C28  C   CR16  0  -0.251  -3.5612   1.2672  -2.5387
 16T  C29  C   CR16  0  -0.227  -4.8361   1.8057  -2.6189
 16T  C30  C   CR6   0  -0.029  -5.8381   1.2396  -1.8455
 16T  C31  C   CR16  0  -0.285  -5.5938   0.1696  -1.0022
 16T  CL1  CL  CL    0  -0.119  -7.4411   1.8902  -1.9222
 16T  O33  O   OH1   0  -0.602  -3.0316  -3.8318  -0.8325
 16T  H1   H   HCH3  0   0.248   8.3579  -0.1991   1.0072
 16T  H2   H   HCH3  0   0.247   8.5555   1.2014  -0.0342
 16T  H3   H   HCH3  0   0.247   7.6863   1.3572   1.4897
 16T  H4   H   HCR6  0   0.314   5.3105   1.4726   1.2297
 16T  H5   H   HNR6  0   0.425   5.3374  -1.3140  -2.5966
 16T  H6   H   HCH1  0   0.278   3.2923   1.6900   1.1910
 16T  H7   H   HCH2  0   0.258   2.9818   2.9121  -0.9189
 16T  H8   H   HCH2  0   0.248   1.9336   1.6323  -1.5283
 16T  H9   H   HCH2  0   0.241   1.4368   3.3667   0.9382
 16T  H10  H   HCH2  0   0.259   0.5268   3.3941  -0.5654
 16T  H11  H   HCH2  0   0.281  -0.6456   2.1498   1.2201
 16T  H12  H   HCH2  0   0.231  -0.3053   1.1261  -0.1849
 16T  H13  H   HCH2  0   0.255   1.5913  -0.5127  -0.0247
 16T  H14  H   HCH2  0   0.288   2.5095  -0.5898   1.4938
 16T  H15  H   HCR6  0   0.291   0.5858  -2.8141   1.6001
 16T  H16  H   HCR6  0   0.290  -0.7039  -4.3226   0.1535
 16T  H17  H   HCR6  0   0.312  -2.6161   0.0590   1.4381
 16T  H18  H   HCR6  0   0.285  -2.2782  -0.2128  -1.6758
 16T  H19  H   HCR6  0   0.279  -2.7679   1.6905  -3.1398
 16T  H20  H   HCR6  0   0.282  -5.0417   2.6446  -3.2686
 16T  H21  H   HCR6  0   0.297  -6.3828  -0.2598  -0.3994
 16T  H22  H   HOH1  0   0.483  -3.9042  -3.4849  -1.0589

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
 16T  O9   C8   double    1.218  0.020  1.218
 16T  N7   C8   single    1.383  0.020  1.383
 16T  N7   C5   single    1.371  0.020  1.371
 16T  C8   C2   single    1.448  0.020  1.448
 16T  O6   C5   double    1.215  0.020  1.215
 16T  C5   N4   single    1.375  0.020  1.375
 16T  C2   C1   single    1.493  0.020  1.493
 16T  C2   C3   double    1.344  0.020  1.344
 16T  CL1  C30  single    1.732  0.020  1.732
 16T  N4   C3   single    1.372  0.020  1.372
 16T  N4   C10  single    1.468  0.020  1.468
 16T  C30  C29  aromatic  1.387  0.020  1.387
 16T  C30  C31  aromatic  1.384  0.020  1.384
 16T  C29  C28  aromatic  1.386  0.020  1.386
 16T  C10  C15  single    1.529  0.020  1.529
 16T  C10  C11  single    1.523  0.020  1.523
 16T  C31  C26  aromatic  1.389  0.020  1.389
 16T  C28  C27  aromatic  1.388  0.020  1.388
 16T  C15  N14  single    1.464  0.020  1.464
 16T  C11  C12  single    1.524  0.020  1.524
 16T  O18  S16  double    1.453  0.020  1.453
 16T  C26  C27  aromatic  1.389  0.020  1.389
 16T  C26  O25  single    1.368  0.020  1.368
 16T  N14  S16  single    1.659  0.020  1.659
 16T  N14  C13  single    1.468  0.020  1.468
 16T  C12  C13  single    1.521  0.020  1.521
 16T  O25  C23  single    1.369  0.020  1.369
 16T  S16  C19  single    1.764  0.020  1.764
 16T  S16  O17  double    1.453  0.020  1.453
 16T  C24  C23  aromatic  1.380  0.020  1.380
 16T  C24  C19  aromatic  1.388  0.020  1.388
 16T  C23  C22  aromatic  1.398  0.020  1.398
 16T  C19  C20  aromatic  1.391  0.020  1.391
 16T  C22  O33  single    1.334  0.020  1.334
 16T  C22  C21  aromatic  1.394  0.020  1.394
 16T  C20  C21  aromatic  1.381  0.020  1.381
 16T  C1   H1   single    0.970  0.020  1.090
 16T  C1   H2   single    0.970  0.020  1.090
 16T  C1   H3   single    0.970  0.020  1.090
 16T  C3   H4   single    0.930  0.020  1.080
 16T  N7   H5   single    0.860  0.020  1.020
 16T  C10  H6   single    0.970  0.020  1.090
 16T  C11  H7   single    0.970  0.020  1.090
 16T  C11  H8   single    0.970  0.020  1.090
 16T  C12  H9   single    0.970  0.020  1.090
 16T  C12  H10  single    0.970  0.020  1.090
 16T  C13  H11  single    0.970  0.020  1.090
 16T  C13  H12  single    0.970  0.020  1.090
 16T  C15  H13  single    0.970  0.020  1.090
 16T  C15  H14  single    0.970  0.020  1.090
 16T  C20  H15  single    0.930  0.020  1.080
 16T  C21  H16  single    0.930  0.020  1.080
 16T  C24  H17  single    0.930  0.020  1.080
 16T  C27  H18  single    0.930  0.020  1.080
 16T  C28  H19  single    0.930  0.020  1.080
 16T  C29  H20  single    0.930  0.020  1.080
 16T  C31  H21  single    0.930  0.020  1.080
 16T  O33  H22  single    0.850  0.020  0.980

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
 16T  H3   C1   H2   107.83  3.000
 16T  H3   C1   H1   107.93  3.000
 16T  H2   C1   H1   107.25  3.000
 16T  H3   C1   C2   110.87  3.000
 16T  H2   C1   C2   111.36  3.000
 16T  H1   C1   C2   111.42  3.000
 16T  C8   C2   C3   117.82  3.000
 16T  C3   C2   C1   123.10  3.000
 16T  C8   C2   C1   119.08  3.000
 16T  H4   C3   N4   114.74  3.000
 16T  H4   C3   C2   120.59  3.000
 16T  N4   C3   C2   124.67  3.000
 16T  C10  N4   C5   120.95  3.000
 16T  C10  N4   C3   118.56  3.000
 16T  C5   N4   C3   120.49  3.000
 16T  N7   C5   O6   121.62  3.000
 16T  O6   C5   N4   123.80  3.000
 16T  N7   C5   N4   114.58  3.000
 16T  H5   N7   C8   116.72  3.000
 16T  H5   N7   C5   115.00  3.000
 16T  C8   N7   C5   128.28  3.000
 16T  O9   C8   N7   120.65  3.000
 16T  N7   C8   C2   114.17  3.000
 16T  O9   C8   C2   125.19  3.000
 16T  H6   C10  C15  106.16  3.000
 16T  H6   C10  C11  107.60  3.000
 16T  C15  C10  C11  111.56  3.000
 16T  H6   C10  N4   104.79  3.000
 16T  C11  C10  N4   114.04  3.000
 16T  C15  C10  N4   112.03  3.000
 16T  H8   C11  H7   107.80  3.000
 16T  H8   C11  C12  109.76  3.000
 16T  H7   C11  C12  110.29  3.000
 16T  H8   C11  C10  110.45  3.000
 16T  H7   C11  C10  109.90  3.000
 16T  C12  C11  C10  108.64  3.000
 16T  H10  C12  H9   107.22  3.000
 16T  H10  C12  C13  108.55  3.000
 16T  H9   C12  C13  109.00  3.000
 16T  H10  C12  C11  110.13  3.000
 16T  H9   C12  C11  110.16  3.000
 16T  C13  C12  C11  111.65  3.000
 16T  H12  C13  H11  108.22  3.000
 16T  H12  C13  N14  110.45  3.000
 16T  H11  C13  N14  109.62  3.000
 16T  H12  C13  C12  109.87  3.000
 16T  H11  C13  C12  109.53  3.000
 16T  N14  C13  C12  109.14  3.000
 16T  S16  N14  C15  116.16  3.000
 16T  S16  N14  C13  116.50  3.000
 16T  C15  N14  C13  112.87  3.000
 16T  H14  C15  H13  108.96  3.000
 16T  H14  C15  N14  109.88  3.000
 16T  H13  C15  N14  110.82  3.000
 16T  H14  C15  C10  108.98  3.000
 16T  H13  C15  C10  110.76  3.000
 16T  N14  C15  C10  107.42  3.000
 16T  C19  S16  O18  108.18  3.000
 16T  C19  S16  O17  108.18  3.000
 16T  O18  S16  O17  119.58  3.000
 16T  O17  S16  N14  107.05  3.000
 16T  C19  S16  N14  106.40  3.000
 16T  O18  S16  N14  106.73  3.000
 16T  C24  C19  C20  120.79  3.000
 16T  C20  C19  S16  119.99  3.000
 16T  C24  C19  S16  119.18  3.000
 16T  H15  C20  C21  119.35  3.000
 16T  H15  C20  C19  120.97  3.000
 16T  C21  C20  C19  119.68  3.000
 16T  H16  C21  C22  119.29  3.000
 16T  H16  C21  C20  120.23  3.000
 16T  C22  C21  C20  120.48  3.000
 16T  O33  C22  C23  122.34  3.000
 16T  O33  C22  C21  118.78  3.000
 16T  C23  C22  C21  118.87  3.000
 16T  O25  C23  C24  121.51  3.000
 16T  C24  C23  C22  121.15  3.000
 16T  O25  C23  C22  117.30  3.000
 16T  H17  C24  C23  119.59  3.000
 16T  H17  C24  C19  121.39  3.000
 16T  C23  C24  C19  119.01  3.000
 16T  C26  O25  C23  119.19  3.000
 16T  C31  C26  C27  121.01  3.000
 16T  C27  C26  O25  123.35  3.000
 16T  C31  C26  O25  115.63  3.000
 16T  H18  C27  C28  119.65  3.000
 16T  H18  C27  C26  121.51  3.000
 16T  C28  C27  C26  118.84  3.000
 16T  H19  C28  C29  119.36  3.000
 16T  H19  C28  C27  119.21  3.000
 16T  C29  C28  C27  121.43  3.000
 16T  H20  C29  C30  120.98  3.000
 16T  H20  C29  C28  120.74  3.000
 16T  C30  C29  C28  118.27  3.000
 16T  CL1  C30  C31  118.74  3.000
 16T  C31  C30  C29  121.87  3.000
 16T  CL1  C30  C29  119.40  3.000
 16T  H21  C31  C30  121.17  3.000
 16T  H21  C31  C26  120.24  3.000
 16T  C30  C31  C26  118.58  3.000
 16T  H22  O33  C22  111.19  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
 16T  CONST_01  C22  C23  C24  C19     0.00   0.0  0
 16T  CONST_02  C22  C21  C20  C19     0.00   0.0  0
 16T  CONST_03  C23  C24  C19  C20     0.00   0.0  0
 16T  CONST_04  C23  C22  C21  C20     0.00   0.0  0
 16T  CONST_05  C24  C23  C22  C21     0.00   0.0  0
 16T  CONST_06  C24  C19  C20  C21     0.00   0.0  0
 16T  CONST_07  C29  C30  C31  C26     0.00   0.0  0
 16T  CONST_08  C29  C28  C27  C26     0.00   0.0  0
 16T  CONST_09  C30  C29  C28  C27     0.00   0.0  0
 16T  CONST_10  C30  C31  C26  C27     0.00   0.0  0
 16T  CONST_11  C31  C30  C29  C28     0.00   0.0  0
 16T  CONST_12  C31  C26  C27  C28     0.00   0.0  0
 16T  CONST_13  C5   N7   C8   C2      0.00   0.0  0
 16T  CONST_14  N7   C5   N4   C3      0.00   0.0  0
 16T  CONST_15  C8   N7   C5   N4      0.00   0.0  0
 16T  CONST_16  C10  N4   C5   N7    180.00   0.0  0
 16T  CONST_17  C23  C24  C19  S16   180.00   0.0  0
 16T  CONST_18  C21  C20  C19  S16   180.00   0.0  0
 16T  CONST_19  O25  C23  C24  C19   180.00   0.0  0
 16T  CONST_20  O33  C22  C21  C20   180.00   0.0  0
 16T  CONST_21  O25  C23  C22  C21   180.00   0.0  0
 16T  CONST_22  O33  C22  C23  C24   180.00   0.0  0
 16T  CONST_23  C30  C31  C26  O25   180.00   0.0  0
 16T  CONST_24  C28  C27  C26  O25   180.00   0.0  0
 16T  CONST_25  CL1  C30  C31  C26   180.00   0.0  0
 16T  CONST_26  CL1  C30  C29  C28   180.00   0.0  0
 16T  CONST_27  O6   C5   N4   C3    180.00   0.0  0
 16T  CONST_28  O9   C8   N7   C5    180.00   0.0  0
 16T  CONST_29  C8   N7   C5   O6    180.00   0.0  0
 16T  CONST_30  C10  N4   C5   O6      0.00   0.0  0
 16T  CONST_31  H16  C21  C20  C19   180.00   0.0  0
 16T  CONST_32  H17  C24  C19  C20   180.00   0.0  0
 16T  CONST_33  H15  C20  C21  C22   180.00   0.0  0
 16T  CONST_34  H19  C28  C27  C26   180.00   0.0  0
 16T  CONST_35  H20  C29  C28  C27   180.00   0.0  0
 16T  CONST_36  H21  C31  C26  C27   180.00   0.0  0
 16T  CONST_37  H18  C27  C28  C29   180.00   0.0  0
 16T  CONST_38  H5   N7   C8   C2    180.00   0.0  0
 16T  Var_01    C13  N14  C15  C10    61.89  30.0  1
 16T  Var_02    C13  C12  C11  C10   -54.22  30.0  1
 16T  Var_03    N14  C13  C12  C11    56.15  30.0  1
 16T  Var_04    C15  N14  C13  C12   -61.01  30.0  1
 16T  Var_05    C19  S16  N14  C13    67.07  30.0  3
 16T  Var_06    C24  C19  S16  N14   -89.09  30.0  2
 16T  Var_07    C31  C26  O25  C23  -159.66  30.0  3
 16T  Var_08    H1   C1   C2   C3    119.53  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 16T  chir_01  C10  N4  C15  C11  positiv

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
 16T  plan-1  C1   0.020
 16T  plan-1  C2   0.020
 16T  plan-1  C3   0.020
 16T  plan-1  N4   0.020
 16T  plan-1  C5   0.020
 16T  plan-1  O6   0.020
 16T  plan-1  N7   0.020
 16T  plan-1  C8   0.020
 16T  plan-1  O9   0.020
 16T  plan-1  C10  0.020
 16T  plan-1  H4   0.020
 16T  plan-1  H5   0.020
 16T  plan-2  S16  0.020
 16T  plan-2  C19  0.020
 16T  plan-2  C20  0.020
 16T  plan-2  C21  0.020
 16T  plan-2  C22  0.020
 16T  plan-2  C23  0.020
 16T  plan-2  C24  0.020
 16T  plan-2  O25  0.020
 16T  plan-2  O33  0.020
 16T  plan-2  H15  0.020
 16T  plan-2  H16  0.020
 16T  plan-2  H17  0.020
 16T  plan-3  O25  0.020
 16T  plan-3  C26  0.020
 16T  plan-3  C27  0.020
 16T  plan-3  C28  0.020
 16T  plan-3  C29  0.020
 16T  plan-3  C30  0.020
 16T  plan-3  C31  0.020
 16T  plan-3  CL1  0.020
 16T  plan-3  H18  0.020
 16T  plan-3  H19  0.020
 16T  plan-3  H20  0.020
 16T  plan-3  H21  0.020

