# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 16:14:39 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: ~{N}-[4-(5-cyano-2-methoxy-phenyl)thiophen-2-yl]-2-(4-ethylsulfonylphenyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[S](=O)(=O)c1ccc(CC(=O)Nc2scc(c2)c3cc(ccc3OC)C#N)cc1
#
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
 8Y8  8Y8  ~{N}-[4-(5-cyano-2-methoxy-phenyl)thiophen-2-yl]-2-(4-ethylsulfonylphenyl)ethanamide  ligand  50  30  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8Y8
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
 8Y8  C1   C  CSP   0   0.043  -7.4711  -2.7488  -0.6699
 8Y8  C2   C  CR16  0  -0.234  -8.0636  -0.4250  -0.2119
 8Y8  C3   C  CR16  0  -0.288   3.9275   0.1824   1.6070
 8Y8  C4   C  CR16  0  -0.277   3.6186  -1.3822  -0.1868
 8Y8  C5   C  CR16  0  -0.377  -7.6830   0.8787   0.0413
 8Y8  C6   C  CR16  0  -0.218   5.1965   0.4815   1.1390
 8Y8  C7   C  CR16  0  -0.218   4.8842  -1.0942  -0.6702
 8Y8  C8   C  CR16  0  -0.302  -5.7416  -1.0566  -0.3505
 8Y8  C9   C  CR15  0  -0.335  -2.9545  -0.3799   0.5065
 8Y8  C10  C  CR15  0  -0.572  -3.2828   1.6707  -0.5071
 8Y8  C11  C  CR6   0   0.001  -7.0922  -1.4018  -0.4071
 8Y8  C12  C  CR6   0  -0.010  -5.3364   0.2452  -0.1013
 8Y8  C13  C  CR5   0   0.218  -3.8973   0.5470  -0.0354
 8Y8  C14  C  CR6   0   0.159   3.1294  -0.7509   0.9532
 8Y8  C15  C  CR6   0   0.378  -6.3322   1.2255   0.1012
 8Y8  C16  C  CR6   0  -0.190   5.6637  -0.1629   0.0017
 8Y8  C17  C  CR5   0   0.118  -1.6699   0.0659   0.4266
 8Y8  C18  C  C     0   0.570   0.7135  -0.1507   0.8182
 8Y8  C19  C  CH3   0  -0.672   9.7882  -0.8078  -0.1108
 8Y8  C20  C  CH3   0  -0.444  -6.8540   3.4885   0.6064
 8Y8  C21  C  CH2   0  -0.704   1.7494  -1.0579   1.4495
 8Y8  C22  C  CH2   0  -0.589   8.3308  -0.9897   0.2764
 8Y8  N23  N  NS    0  -0.260  -7.7816  -3.8392  -0.8808
 8Y8  N24  N  NH1   0  -0.709  -0.5564  -0.6136   0.8857
 8Y8  O25  O  O     0  -0.451   0.9793   0.9231   0.3111
 8Y8  O26  O  OS    0  -0.672   7.3482  -0.1131  -2.0190
 8Y8  O27  O  OS    0  -0.672   7.6685   1.5359  -0.1507
 8Y8  O28  O  O2    0  -0.450  -5.9082   2.4620   0.3586
 8Y8  S29  S  S2    0   0.256  -1.5778   1.6231  -0.3138
 8Y8  S30  S  S     0   1.208   7.2967   0.1905  -0.5888
 8Y8  H1   H  HCR6  0   0.285  -9.1140  -0.6779  -0.2579
 8Y8  H2   H  HCR6  0   0.269   3.5598   0.6805   2.4951
 8Y8  H3   H  HCR6  0   0.270   3.0045  -2.1079  -0.7049
 8Y8  H4   H  HCR6  0   0.298  -8.4539   1.6208   0.1919
 8Y8  H5   H  HCR6  0   0.284   5.8068   1.2090   1.6569
 8Y8  H6   H  HCR6  0   0.284   5.2485  -1.5910  -1.5592
 8Y8  H7   H  HCR6  0   0.280  -4.9945  -1.8215  -0.5169
 8Y8  H8   H  HCR5  0   0.276  -3.2222  -1.3252   0.9587
 8Y8  H9   H  HCR5  0   0.289  -3.7285   2.5259  -0.9880
 8Y8  H10  H  HCH3  0   0.250   9.9447  -0.9735  -1.1750
 8Y8  H11  H  HCH3  0   0.250  10.1540   0.1840   0.1496
 8Y8  H12  H  HCH3  0   0.267  10.3882  -1.5374   0.4302
 8Y8  H13  H  HCH3  0   0.238  -7.4946   3.6652  -0.2601
 8Y8  H14  H  HCH3  0   0.238  -7.4780   3.2620   1.4738
 8Y8  H15  H  HCH3  0   0.268  -6.2788   4.3877   0.8086
 8Y8  H16  H  HCH2  0   0.301   1.4961  -2.1038   1.2630
 8Y8  H17  H  HCH2  0   0.318   1.6907  -0.9149   2.5327
 8Y8  H18  H  HCH2  0   0.299   7.9609  -1.9822   0.0161
 8Y8  H19  H  HCH2  0   0.299   8.1680  -0.8299   1.3431
 8Y8  H20  H  HNH1  0   0.431  -0.7275  -1.5158   1.3052

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
 8Y8  N23  C1   triple    1.153  0.020  1.153
 8Y8  C1   C11  single    1.424  0.020  1.424
 8Y8  C2   C11  aromatic  1.391  0.020  1.391
 8Y8  C2   C5   aromatic  1.382  0.020  1.382
 8Y8  C11  C8   aromatic  1.395  0.020  1.395
 8Y8  C5   C15  aromatic  1.396  0.020  1.396
 8Y8  C8   C12  aromatic  1.386  0.020  1.386
 8Y8  O26  S30  double    1.463  0.020  1.463
 8Y8  C19  C22  single    1.519  0.020  1.519
 8Y8  C15  C12  aromatic  1.412  0.020  1.412
 8Y8  C15  O28  single    1.332  0.020  1.332
 8Y8  C12  C13  single    1.472  0.020  1.472
 8Y8  C22  S30  single    1.792  0.020  1.792
 8Y8  S30  O27  double    1.463  0.020  1.463
 8Y8  S30  C16  single    1.772  0.020  1.772
 8Y8  C20  O28  single    1.418  0.020  1.418
 8Y8  C6   C16  aromatic  1.388  0.020  1.388
 8Y8  C6   C3   aromatic  1.385  0.020  1.385
 8Y8  C13  C9   aromatic  1.429  0.020  1.429
 8Y8  C13  C10  aromatic  1.365  0.020  1.365
 8Y8  C9   C17  aromatic  1.362  0.020  1.362
 8Y8  C16  C7   aromatic  1.388  0.020  1.388
 8Y8  C10  S29  aromatic  1.717  0.020  1.717
 8Y8  C3   C14  aromatic  1.391  0.020  1.391
 8Y8  C17  S29  aromatic  1.727  0.020  1.727
 8Y8  C17  N24  single    1.383  0.020  1.383
 8Y8  C7   C4   aromatic  1.385  0.020  1.385
 8Y8  N24  C18  single    1.353  0.020  1.353
 8Y8  C14  C4   aromatic  1.392  0.020  1.392
 8Y8  C14  C21  single    1.498  0.020  1.498
 8Y8  C18  C21  single    1.515  0.020  1.515
 8Y8  C18  O25  double    1.217  0.020  1.217
 8Y8  C2   H1   single    0.930  0.020  1.080
 8Y8  C3   H2   single    0.930  0.020  1.080
 8Y8  C4   H3   single    0.930  0.020  1.080
 8Y8  C5   H4   single    0.930  0.020  1.080
 8Y8  C6   H5   single    0.930  0.020  1.080
 8Y8  C7   H6   single    0.930  0.020  1.080
 8Y8  C8   H7   single    0.930  0.020  1.080
 8Y8  C9   H8   single    0.930  0.020  1.080
 8Y8  C10  H9   single    0.930  0.020  1.080
 8Y8  C19  H10  single    0.970  0.020  1.090
 8Y8  C19  H11  single    0.970  0.020  1.090
 8Y8  C19  H12  single    0.970  0.020  1.090
 8Y8  C20  H13  single    0.970  0.020  1.090
 8Y8  C20  H14  single    0.970  0.020  1.090
 8Y8  C20  H15  single    0.970  0.020  1.090
 8Y8  C21  H16  single    0.970  0.020  1.090
 8Y8  C21  H17  single    0.970  0.020  1.090
 8Y8  C22  H18  single    0.970  0.020  1.090
 8Y8  C22  H19  single    0.970  0.020  1.090
 8Y8  N24  H20  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
 8Y8  N23  C1   C11  180.00  3.000
 8Y8  H1   C2   C11  120.53  3.000
 8Y8  H1   C2   C5   119.74  3.000
 8Y8  C11  C2   C5   119.73  3.000
 8Y8  H2   C3   C14  119.96  3.000
 8Y8  H2   C3   C6   119.27  3.000
 8Y8  C14  C3   C6   120.77  3.000
 8Y8  H3   C4   C14  119.77  3.000
 8Y8  H3   C4   C7   119.38  3.000
 8Y8  C14  C4   C7   120.85  3.000
 8Y8  H4   C5   C15  120.92  3.000
 8Y8  H4   C5   C2   118.49  3.000
 8Y8  C15  C5   C2   120.59  3.000
 8Y8  H5   C6   C16  120.97  3.000
 8Y8  H5   C6   C3   120.02  3.000
 8Y8  C16  C6   C3   119.00  3.000
 8Y8  H6   C7   C16  121.12  3.000
 8Y8  H6   C7   C4   119.95  3.000
 8Y8  C16  C7   C4   118.93  3.000
 8Y8  H7   C8   C12  119.32  3.000
 8Y8  H7   C8   C11  119.16  3.000
 8Y8  C12  C8   C11  121.52  3.000
 8Y8  H8   C9   C17  122.96  3.000
 8Y8  H8   C9   C13  124.21  3.000
 8Y8  C17  C9   C13  112.81  3.000
 8Y8  H9   C10  S29  118.89  3.000
 8Y8  H9   C10  C13  128.42  3.000
 8Y8  S29  C10  C13  112.67  3.000
 8Y8  C8   C11  C2   119.77  3.000
 8Y8  C8   C11  C1   119.95  3.000
 8Y8  C2   C11  C1   120.29  3.000
 8Y8  C15  C12  C13  122.74  3.000
 8Y8  C13  C12  C8   119.11  3.000
 8Y8  C15  C12  C8   118.15  3.000
 8Y8  C12  C13  C10  126.41  3.000
 8Y8  C10  C13  C9   111.60  3.000
 8Y8  C12  C13  C9   121.94  3.000
 8Y8  C21  C14  C4   120.14  3.000
 8Y8  C21  C14  C3   120.68  3.000
 8Y8  C4   C14  C3   119.18  3.000
 8Y8  O28  C15  C12  116.59  3.000
 8Y8  O28  C15  C5   123.15  3.000
 8Y8  C12  C15  C5   120.25  3.000
 8Y8  S30  C16  C7   119.35  3.000
 8Y8  C7   C16  C6   121.27  3.000
 8Y8  S30  C16  C6   119.38  3.000
 8Y8  S29  C17  N24  122.86  3.000
 8Y8  N24  C17  C9   125.38  3.000
 8Y8  S29  C17  C9   111.75  3.000
 8Y8  O25  C18  N24  121.84  3.000
 8Y8  O25  C18  C21  123.56  3.000
 8Y8  N24  C18  C21  114.58  3.000
 8Y8  H12  C19  H11  107.85  3.000
 8Y8  H12  C19  H10  107.73  3.000
 8Y8  H11  C19  H10  108.92  3.000
 8Y8  H12  C19  C22  108.78  3.000
 8Y8  H11  C19  C22  111.75  3.000
 8Y8  H10  C19  C22  111.66  3.000
 8Y8  H15  C20  H14  109.04  3.000
 8Y8  H15  C20  H13  108.93  3.000
 8Y8  H14  C20  H13  109.19  3.000
 8Y8  H15  C20  O28  106.18  3.000
 8Y8  H14  C20  O28  111.70  3.000
 8Y8  H13  C20  O28  111.70  3.000
 8Y8  H17  C21  H16  106.37  3.000
 8Y8  H17  C21  C18  107.32  3.000
 8Y8  H16  C21  C18  110.11  3.000
 8Y8  H17  C21  C14  110.51  3.000
 8Y8  H16  C21  C14  110.69  3.000
 8Y8  C18  C21  C14  111.66  3.000
 8Y8  H19  C22  H18  108.42  3.000
 8Y8  H19  C22  S30  106.83  3.000
 8Y8  H18  C22  S30  106.76  3.000
 8Y8  H19  C22  C19  112.02  3.000
 8Y8  H18  C22  C19  111.93  3.000
 8Y8  S30  C22  C19  110.60  3.000
 8Y8  H20  N24  C18  119.04  3.000
 8Y8  H20  N24  C17  116.14  3.000
 8Y8  C18  N24  C17  124.81  3.000
 8Y8  C20  O28  C15  119.57  3.000
 8Y8  C17  S29  C10   91.16  3.000
 8Y8  O27  S30  O26  118.34  3.000
 8Y8  O27  S30  C22  108.32  3.000
 8Y8  O26  S30  C22  108.36  3.000
 8Y8  O27  S30  C16  108.53  3.000
 8Y8  C22  S30  C16  103.86  3.000
 8Y8  O26  S30  C16  108.47  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
 8Y8  CONST_01  C12  C8   C11  C2      0.00   0.0  0
 8Y8  CONST_02  C12  C15  C5   C2      0.00   0.0  0
 8Y8  CONST_03  C7   C16  C6   C3      0.00   0.0  0
 8Y8  CONST_04  C7   C4   C14  C3      0.00   0.0  0
 8Y8  CONST_05  C6   C16  C7   C4      0.00   0.0  0
 8Y8  CONST_06  C6   C3   C14  C4      0.00   0.0  0
 8Y8  CONST_07  C8   C11  C2   C5      0.00   0.0  0
 8Y8  CONST_08  C8   C12  C15  C5      0.00   0.0  0
 8Y8  CONST_09  C13  C12  C15  C5    180.00   0.0  0
 8Y8  CONST_13  S29  C10  C13  C9      0.00   0.0  0
 8Y8  CONST_14  C10  S29  C17  C9      0.00   0.0  0
 8Y8  CONST_16  C17  C9   C13  C10     0.00   0.0  0
 8Y8  CONST_17  C15  C5   C2   C11     0.00   0.0  0
 8Y8  CONST_18  C15  C12  C8   C11     0.00   0.0  0
 8Y8  CONST_19  C13  C12  C8   C11   180.00   0.0  0
 8Y8  CONST_20  C17  C9   C13  C12   180.00   0.0  0
 8Y8  CONST_21  S29  C10  C13  C12   180.00   0.0  0
 8Y8  CONST_22  S29  C17  C9   C13     0.00   0.0  0
 8Y8  CONST_23  C17  S29  C10  C13     0.00   0.0  0
 8Y8  CONST_24  C16  C6   C3   C14     0.00   0.0  0
 8Y8  CONST_25  C16  C7   C4   C14     0.00   0.0  0
 8Y8  CONST_26  C5   C2   C11  C1    180.00   0.0  0
 8Y8  CONST_27  C12  C8   C11  C1    180.00   0.0  0
 8Y8  CONST_28  O28  C15  C5   C2    180.00   0.0  0
 8Y8  CONST_29  S30  C16  C6   C3    180.00   0.0  0
 8Y8  CONST_30  S30  C16  C7   C4    180.00   0.0  0
 8Y8  CONST_31  C21  C14  C3   C6    180.00   0.0  0
 8Y8  CONST_32  C21  C14  C4   C7    180.00   0.0  0
 8Y8  CONST_33  O28  C15  C12  C8    180.00   0.0  0
 8Y8  CONST_34  N24  C17  S29  C10   180.00   0.0  0
 8Y8  CONST_35  O28  C15  C12  C13     0.00   0.0  0
 8Y8  CONST_36  N24  C17  C9   C13   180.00   0.0  0
 8Y8  CONST_37  H7   C8   C11  C2    180.00   0.0  0
 8Y8  CONST_38  H3   C4   C14  C3    180.00   0.0  0
 8Y8  CONST_39  H2   C3   C14  C4    180.00   0.0  0
 8Y8  CONST_40  H6   C7   C16  C6    180.00   0.0  0
 8Y8  CONST_41  H5   C6   C16  C7    180.00   0.0  0
 8Y8  CONST_42  H1   C2   C11  C8    180.00   0.0  0
 8Y8  CONST_43  H9   C10  C13  C9    180.00   0.0  0
 8Y8  CONST_44  H8   C9   C13  C10   180.00   0.0  0
 8Y8  CONST_45  H4   C5   C2   C11   180.00   0.0  0
 8Y8  CONST_46  C18  N24  C17  C9    180.00   0.0  0
 8Y8  CONST_47  S29  C17  N24  C18     0.00   0.0  0
 8Y8  CONST_48  H20  N24  C17  C9      0.00   0.0  0
 8Y8  CONST_49  C21  C18  N24  C17   180.00   0.0  0
 8Y8  CONST_50  O25  C18  N24  C17     0.00   0.0  0
 8Y8  Var_01    C18  C21  C14  C3     89.87  30.0  2
 8Y8  Var_02    O26  S30  C16  C6   -155.77  30.0  2
 8Y8  Var_03    N24  C18  C21  C14   160.64  30.0  1
 8Y8  Var_04    C19  C22  S30  C16  -179.34  30.0  1
 8Y8  Var_05    H13  C20  O28  C15   -62.56  30.0  3
 8Y8  Var_06    H10  C19  C22  S30   -61.23  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
 8Y8  plan-1  C9   0.020
 8Y8  plan-1  C10  0.020
 8Y8  plan-1  C12  0.020
 8Y8  plan-1  C13  0.020
 8Y8  plan-1  C17  0.020
 8Y8  plan-1  N24  0.020
 8Y8  plan-1  S29  0.020
 8Y8  plan-1  H8   0.020
 8Y8  plan-1  H9   0.020
 8Y8  plan-2  C1   0.020
 8Y8  plan-2  C2   0.020
 8Y8  plan-2  C5   0.020
 8Y8  plan-2  C8   0.020
 8Y8  plan-2  C11  0.020
 8Y8  plan-2  C12  0.020
 8Y8  plan-2  C13  0.020
 8Y8  plan-2  C15  0.020
 8Y8  plan-2  N23  0.020
 8Y8  plan-2  O28  0.020
 8Y8  plan-2  H1   0.020
 8Y8  plan-2  H4   0.020
 8Y8  plan-2  H7   0.020
 8Y8  plan-3  C3   0.020
 8Y8  plan-3  C4   0.020
 8Y8  plan-3  C6   0.020
 8Y8  plan-3  C7   0.020
 8Y8  plan-3  C14  0.020
 8Y8  plan-3  C16  0.020
 8Y8  plan-3  C21  0.020
 8Y8  plan-3  S30  0.020
 8Y8  plan-3  H2   0.020
 8Y8  plan-3  H3   0.020
 8Y8  plan-3  H5   0.020
 8Y8  plan-3  H6   0.020
 8Y8  plan-4  C17  0.020
 8Y8  plan-4  C18  0.020
 8Y8  plan-4  C21  0.020
 8Y8  plan-4  N24  0.020
 8Y8  plan-4  O25  0.020
 8Y8  plan-4  H20  0.020

