# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 08:33:18 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 1-[4-(piperidin-1-ylsulfonyl)phenyl]-3-(pyridin-3-ylmethyl)thiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=[S](=O)(N1CCCCC1)c2ccc(NC(=S)NCc3cccnc3)cc2
#
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
 1LS  1LS  1-[4-(piperidin-1-ylsulfonyl)phenyl]-3-(pyridin-3-ylmethyl)thiourea  ligand  48  26  .  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_1LS
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
 1LS  C4   C  CR16  0  -0.086  -6.7299  -1.3028   1.0067
 1LS  C6   C  CR16  0  -0.064  -8.4645   0.1596   0.8644
 1LS  C7   C  CH2   0  -0.309  -4.7094  -1.2143  -0.4906
 1LS  C13  C  CR16  0  -0.265   0.4607   0.6165  -1.2167
 1LS  C15  C  CR6   0  -0.212   2.5077   1.2895  -0.1501
 1LS  C17  C  CR16  0  -0.324   0.4911   1.1631   1.1296
 1LS  C22  C  C     0  -0.310   4.7968  -0.9361  -0.9942
 1LS  C24  C  C     0  -0.446   5.7266  -2.6506   0.5836
 1LS  C26  C  C     0  -0.309   4.7866  -0.4715   1.4098
 1LS  C1   C  CR16  0  -0.319  -7.8727   0.8378  -0.1924
 1LS  C2   C  CR16  0  -0.163  -6.6431   0.3982  -0.6520
 1LS  C3   C  CR6   0  -0.043  -6.0470  -0.7015  -0.0435
 1LS  N5   N  N     0  -0.400  -7.9097  -0.8910   1.4551
 1LS  N8   N  NH1   0  -0.613  -3.6682  -0.3029  -0.0569
 1LS  C9   C  C     0   0.412  -2.3915  -0.3908  -0.4408
 1LS  S10  S  S1    0  -0.382  -1.8725  -1.5571  -1.5234
 1LS  N11  N  NH1   0  -0.743  -1.5806   0.5289   0.1521
 1LS  C12  C  CR6   0   0.390  -0.2112   0.7371   0.0004
 1LS  C14  C  CR16  0  -0.233   1.8166   0.8843  -1.2857
 1LS  C16  C  CR16  0  -0.226   1.8423   1.4410   1.0600
 1LS  O19  O  OS    0  -0.655   4.5996   1.9285  -1.5874
 1LS  O20  O  OS    0  -0.655   4.6303   2.4211   0.8714
 1LS  N21  N  NR6   0  -0.560   4.9544   0.0748   0.0580
 1LS  C23  C  C     0  -0.432   5.8317  -2.0339  -0.8039
 1LS  C25  C  C     0  -0.433   5.8154  -1.5664   1.6478
 1LS  H1   H  HCR6  0   0.264  -6.2976  -2.1645   1.5065
 1LS  H2   H  HCR6  0   0.268  -9.4278   0.4789   1.2459
 1LS  H3   H  HCH2  0   0.264  -4.5315  -2.2158  -0.0903
 1LS  H4   H  HCH2  0   0.270  -4.6774  -1.2982  -1.5780
 1LS  H5   H  HCR6  0   0.282  -0.0681   0.3300  -2.1113
 1LS  H6   H  HCR6  0   0.286  -0.0265   1.2762   2.0742
 1LS  H8   H  H     0   0.272   4.9271  -0.4712  -1.9689
 1LS  H9   H  H     0   0.220   4.7719  -3.1792   0.6747
 1LS  H10  H  H     0   0.242   6.5123  -3.3938   0.7310
 1LS  H11  H  H     0   0.272   4.9196   0.3225   2.1418
 1LS  H12  H  H     0   0.231   3.7740  -0.8790   1.5375
 1LS  H13  H  HCR6  0   0.275  -8.3696   1.6857  -0.6431
 1LS  H14  H  HCR6  0   0.276  -6.1532   0.9006  -1.4776
 1LS  H15  H  HNH1  0   0.411  -3.9227   0.3758   0.6468
 1LS  H16  H  HNH1  0   0.417  -1.9848   1.0388   0.9261
 1LS  H17  H  HCR6  0   0.286   2.3192   0.7962  -2.2397
 1LS  H18  H  HCR6  0   0.287   2.3603   1.7751   1.9482
 1LS  H19  H  H     0   0.246   5.6778  -2.7881  -1.5779
 1LS  H20  H  H     0   0.230   6.8308  -1.6167  -0.9561
 1LS  H21  H  H     0   0.246   5.6499  -1.9821   2.6433
 1LS  H22  H  H     0   0.230   6.8141  -1.1215   1.6460
 1LS  S18  S  S     0   1.373   4.2537   1.5461  -0.2275
 1LS  H7   H  H     0   0.231   3.7876  -1.3695  -0.9592

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
 1LS  C23  C24  single    1.522  0.020  1.522
 1LS  C23  C22  single    1.521  0.020  1.521
 1LS  C24  C25  single    1.522  0.020  1.522
 1LS  C22  N21  single    1.468  0.020  1.468
 1LS  C25  C26  single    1.521  0.020  1.521
 1LS  N21  C26  single    1.468  0.020  1.468
 1LS  N21  S18  single    1.655  0.020  1.655
 1LS  O20  S18  double    1.454  0.020  1.454
 1LS  S18  O19  double    1.454  0.020  1.454
 1LS  S18  C15  single    1.766  0.020  1.766
 1LS  C14  C15  aromatic  1.390  0.020  1.390
 1LS  C14  C13  aromatic  1.384  0.020  1.384
 1LS  C15  C16  aromatic  1.389  0.020  1.389
 1LS  C13  C12  aromatic  1.395  0.020  1.395
 1LS  C16  C17  aromatic  1.381  0.020  1.381
 1LS  C12  C17  aromatic  1.396  0.020  1.396
 1LS  C12  N11  single    1.393  0.020  1.393
 1LS  N11  C9   single    1.362  0.020  1.362
 1LS  S10  C9   double    1.674  0.020  1.674
 1LS  C9   N8   single    1.336  0.020  1.336
 1LS  N8   C7   single    1.450  0.020  1.450
 1LS  C7   C3   single    1.501  0.020  1.501
 1LS  C3   C2   aromatic  1.391  0.020  1.391
 1LS  C3   C4   aromatic  1.390  0.020  1.390
 1LS  C2   C1   aromatic  1.384  0.020  1.384
 1LS  C4   N5   aromatic  1.328  0.020  1.328
 1LS  C1   C6   aromatic  1.388  0.020  1.388
 1LS  N5   C6   aromatic  1.327  0.020  1.327
 1LS  C4   H1   single    0.930  0.020  1.080
 1LS  C6   H2   single    0.930  0.020  1.080
 1LS  C7   H3   single    0.970  0.020  1.090
 1LS  C7   H4   single    0.970  0.020  1.090
 1LS  C13  H5   single    0.930  0.020  1.080
 1LS  C17  H6   single    0.930  0.020  1.080
 1LS  C22  H7   single    0.970  0.020  1.090
 1LS  C22  H8   single    0.970  0.020  1.090
 1LS  C24  H9   single    0.970  0.020  1.090
 1LS  C24  H10  single    0.970  0.020  1.090
 1LS  C26  H11  single    0.970  0.020  1.090
 1LS  C26  H12  single    0.970  0.020  1.090
 1LS  C1   H13  single    0.930  0.020  1.080
 1LS  C2   H14  single    0.930  0.020  1.080
 1LS  N8   H15  single    0.860  0.020  1.020
 1LS  N11  H16  single    0.860  0.020  1.020
 1LS  C14  H17  single    0.930  0.020  1.080
 1LS  C16  H18  single    0.930  0.020  1.080
 1LS  C23  H19  single    0.970  0.020  1.090
 1LS  C23  H20  single    0.970  0.020  1.090
 1LS  C25  H21  single    0.970  0.020  1.090
 1LS  C25  H22  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
 1LS  H1   C4   N5   116.39  3.000
 1LS  H1   C4   C3   119.71  3.000
 1LS  N5   C4   C3   123.90  3.000
 1LS  H2   C6   N5   116.62  3.000
 1LS  H2   C6   C1   120.19  3.000
 1LS  N5   C6   C1   123.19  3.000
 1LS  H4   C7   H3   106.85  3.000
 1LS  H4   C7   N8   108.99  3.000
 1LS  H3   C7   N8   110.45  3.000
 1LS  H4   C7   C3   110.44  3.000
 1LS  H3   C7   C3   110.43  3.000
 1LS  N8   C7   C3   109.64  3.000
 1LS  H5   C13  C14  119.39  3.000
 1LS  H5   C13  C12  120.70  3.000
 1LS  C14  C13  C12  119.90  3.000
 1LS  S18  C15  C16  119.72  3.000
 1LS  C16  C15  C14  120.35  3.000
 1LS  S18  C15  C14  119.87  3.000
 1LS  H6   C17  C16  119.37  3.000
 1LS  H6   C17  C12  119.79  3.000
 1LS  C16  C17  C12  120.84  3.000
 1LS  H8   C22  H7   107.89  3.000
 1LS  H8   C22  C23  109.83  3.000
 1LS  H7   C22  C23  109.65  3.000
 1LS  H8   C22  N21  109.58  3.000
 1LS  H7   C22  N21  110.33  3.000
 1LS  C23  C22  N21  109.54  3.000
 1LS  H10  C24  H9   106.72  3.000
 1LS  H10  C24  C25  110.41  3.000
 1LS  H9   C24  C25  109.67  3.000
 1LS  H10  C24  C23  110.45  3.000
 1LS  H9   C24  C23  109.36  3.000
 1LS  C25  C24  C23  110.17  3.000
 1LS  H12  C26  H11  107.76  3.000
 1LS  H12  C26  C25  109.76  3.000
 1LS  H11  C26  C25  109.72  3.000
 1LS  H12  C26  N21  110.51  3.000
 1LS  H11  C26  N21  109.52  3.000
 1LS  C25  C26  N21  109.56  3.000
 1LS  H13  C1   C2   121.26  3.000
 1LS  H13  C1   C6   120.30  3.000
 1LS  C2   C1   C6   118.44  3.000
 1LS  H14  C2   C3   120.41  3.000
 1LS  H14  C2   C1   120.48  3.000
 1LS  C3   C2   C1   119.11  3.000
 1LS  C2   C3   C7   121.45  3.000
 1LS  C2   C3   C4   117.53  3.000
 1LS  C7   C3   C4   121.02  3.000
 1LS  C6   N5   C4   117.83  3.000
 1LS  H15  N8   C9   119.02  3.000
 1LS  H15  N8   C7   116.73  3.000
 1LS  C9   N8   C7   123.97  3.000
 1LS  N11  C9   S10  124.58  3.000
 1LS  S10  C9   N8   121.87  3.000
 1LS  N11  C9   N8   113.54  3.000
 1LS  H16  N11  C12  113.63  3.000
 1LS  H16  N11  C9   115.84  3.000
 1LS  C12  N11  C9   129.69  3.000
 1LS  N11  C12  C17  116.86  3.000
 1LS  N11  C12  C13  123.73  3.000
 1LS  C17  C12  C13  119.31  3.000
 1LS  H17  C14  C15  120.88  3.000
 1LS  H17  C14  C13  118.91  3.000
 1LS  C15  C14  C13  120.19  3.000
 1LS  H18  C16  C17  119.31  3.000
 1LS  H18  C16  C15  121.31  3.000
 1LS  C17  C16  C15  119.38  3.000
 1LS  S18  N21  C26  116.20  3.000
 1LS  S18  N21  C22  116.32  3.000
 1LS  C26  N21  C22  113.06  3.000
 1LS  H20  C23  H19  107.08  3.000
 1LS  H20  C23  C24  110.16  3.000
 1LS  H19  C23  C24  110.90  3.000
 1LS  H20  C23  C22  109.21  3.000
 1LS  H19  C23  C22  108.31  3.000
 1LS  C24  C23  C22  111.08  3.000
 1LS  H22  C25  H21  107.16  3.000
 1LS  H22  C25  C26  108.94  3.000
 1LS  H21  C25  C26  108.32  3.000
 1LS  H22  C25  C24  110.00  3.000
 1LS  H21  C25  C24  110.95  3.000
 1LS  C26  C25  C24  111.34  3.000
 1LS  N21  S18  O20  107.15  3.000
 1LS  O20  S18  O19  119.13  3.000
 1LS  N21  S18  O19  107.12  3.000
 1LS  O19  S18  C15  108.32  3.000
 1LS  O20  S18  C15  108.07  3.000
 1LS  N21  S18  C15  106.37  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
 1LS  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 1LS  CONST_02  C1   C6   N5   C4      0.00   0.0  0
 1LS  CONST_03  C3   C2   C1   C6      0.00   0.0  0
 1LS  CONST_04  C3   C4   N5   C6      0.00   0.0  0
 1LS  CONST_05  C16  C15  C14  C13     0.00   0.0  0
 1LS  CONST_06  C16  C17  C12  C13     0.00   0.0  0
 1LS  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 1LS  CONST_08  C12  C17  C16  C15     0.00   0.0  0
 1LS  CONST_09  C14  C15  C16  C17     0.00   0.0  0
 1LS  CONST_10  C14  C13  C12  C17     0.00   0.0  0
 1LS  CONST_11  N5   C4   C3   C2      0.00   0.0  0
 1LS  CONST_12  N5   C6   C1   C2      0.00   0.0  0
 1LS  CONST_13  C1   C2   C3   C7    180.00   0.0  0
 1LS  CONST_14  N5   C4   C3   C7    180.00   0.0  0
 1LS  CONST_15  S18  C15  C14  C13   180.00   0.0  0
 1LS  CONST_16  S18  C15  C16  C17   180.00   0.0  0
 1LS  CONST_17  C14  C13  C12  N11   180.00   0.0  0
 1LS  CONST_18  C16  C17  C12  N11   180.00   0.0  0
 1LS  CONST_19  H14  C2   C3   C4    180.00   0.0  0
 1LS  CONST_20  H2   C6   N5   C4    180.00   0.0  0
 1LS  CONST_21  H1   C4   N5   C6    180.00   0.0  0
 1LS  CONST_22  H6   C17  C12  C13   180.00   0.0  0
 1LS  CONST_23  H5   C13  C14  C15   180.00   0.0  0
 1LS  CONST_24  H13  C1   C2   C3    180.00   0.0  0
 1LS  CONST_25  H17  C14  C13  C12   180.00   0.0  0
 1LS  CONST_26  H18  C16  C17  C12   180.00   0.0  0
 1LS  CONST_30  C12  N11  C9   N8    180.00   0.0  0
 1LS  CONST_31  C12  N11  C9   S10     0.00   0.0  0
 1LS  CONST_32  N11  C9   N8   C7    180.00   0.0  0
 1LS  CONST_33  S10  C9   N8   C7      0.00   0.0  0
 1LS  CONST_34  H15  N8   C9   S10   180.00   0.0  0
 1LS  Var_01    C25  C24  C23  C22   -54.30  30.0  1
 1LS  Var_02    C25  C26  N21  C22    59.34  30.0  1
 1LS  Var_03    N21  C22  C23  C24    56.34  30.0  1
 1LS  Var_04    N21  C26  C25  C24   -55.74  30.0  1
 1LS  Var_05    C23  C24  C25  C26    54.06  30.0  1
 1LS  Var_06    C23  C22  N21  C26   -59.72  30.0  1
 1LS  Var_07    C22  N21  S18  C15    69.60  30.0  2
 1LS  Var_08    N21  S18  C15  C14   -86.68  30.0  2
 1LS  Var_09    N8   C7   C3   C4   -106.23  30.0  2
 1LS  Var_10    C9   N8   C7   C3   -171.26  30.0  1

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
 1LS  plan-1  C4   0.020
 1LS  plan-1  C6   0.020
 1LS  plan-1  C7   0.020
 1LS  plan-1  C1   0.020
 1LS  plan-1  C2   0.020
 1LS  plan-1  C3   0.020
 1LS  plan-1  N5   0.020
 1LS  plan-1  H1   0.020
 1LS  plan-1  H2   0.020
 1LS  plan-1  H13  0.020
 1LS  plan-1  H14  0.020
 1LS  plan-2  C13  0.020
 1LS  plan-2  C15  0.020
 1LS  plan-2  C17  0.020
 1LS  plan-2  N11  0.020
 1LS  plan-2  C12  0.020
 1LS  plan-2  C14  0.020
 1LS  plan-2  C16  0.020
 1LS  plan-2  H5   0.020
 1LS  plan-2  H6   0.020
 1LS  plan-2  H17  0.020
 1LS  plan-2  H18  0.020
 1LS  plan-2  S18  0.020
 1LS  plan-3  C7   0.020
 1LS  plan-3  N8   0.020
 1LS  plan-3  C9   0.020
 1LS  plan-3  S10  0.020
 1LS  plan-3  N11  0.020
 1LS  plan-3  C12  0.020
 1LS  plan-3  H15  0.020
 1LS  plan-3  H16  0.020

