# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 21:14:40 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-[(S)-(2-chlorophenyl){2-[(2S)-1-methylpyrrolidin-2-yl]ethoxy}methyl]thieno[3,2-b]pyridine-7-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCC[C@H]1CCO[C@H](c2sc3c(c2)nccc3C(O)=O)c4ccccc4Cl
#
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
 H6T  H6T  '2-[(S)-(2-chlorophenyl){2-[(2S)-1-methylpyrrolidin-2-yl]ethoxy}methyl]thieno[3,2-b]pyridine-7-carboxylic acid'  ligand  52  29  .  2021-08-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_H6T
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
 H6T  C02  C   CR6   0  -0.120   0.4522   3.2351   0.0704
 H6T  C03  C   CR16  0  -0.196   0.5102   4.2931  -0.8264
 H6T  C04  C   CR16  0  -0.273   0.5916   4.0304  -2.1840
 H6T  C05  C   CR16  0  -0.229   0.6139   2.7172  -2.6343
 H6T  C06  C   CR16  0  -0.302   0.5564   1.6748  -1.7247
 H6T  C07  C   CR6   0   0.177   0.4767   1.9117  -0.3537
 H6T  C08  C   CH1   0  -0.059   0.3908   0.7317   0.6036
 H6T  C11  C   CH2   0  -0.447   3.2101  -1.3853  -0.4054
 H6T  C12  C   CH1   0  -0.062   4.7293  -1.2837  -0.3554
 H6T  C15  C   CH2   0  -0.293   6.1940  -2.4461   1.1044
 H6T  C16  C   CH2   0  -0.457   6.6944  -2.6677  -0.3183
 H6T  C17  C   CH2   0  -0.465   5.4167  -2.4319  -1.1122
 H6T  C18  C   CR5   0  -0.158  -1.0357   0.2831   0.7134
 H6T  C20  C   CR15  0  -0.219  -2.0069   0.7690   1.5152
 H6T  C21  C   CR56  0   0.283  -3.2642   0.1219   1.2863
 H6T  C22  C   CR56  0  -0.224  -3.1780  -0.8635   0.2812
 H6T  C23  C   CR6   0   0.035  -4.3148  -1.5967  -0.0497
 H6T  C24  C   C     0   0.542  -4.2200  -2.6382  -1.1005
 H6T  C27  C   CR16  0  -0.361  -5.4821  -1.3010   0.6351
 H6T  C28  C   CR16  0  -0.083  -5.4675  -0.3035   1.6119
 H6T  N13  N   NT    0  -0.426   5.2512  -1.3298   1.0220
 H6T  N29  N   N     0  -0.420  -4.3947   0.3935   1.9374
 H6T  O09  O   O2    0  -0.490   1.1265  -0.3633   0.1416
 H6T  O25  O   O     0  -0.424  -3.1872  -2.8648  -1.6837
 H6T  O26  O   OH1   0  -0.583  -5.3558  -3.2704  -1.3178
 H6T  S19  S   S2    0   0.258  -1.5790  -0.9848  -0.3527
 H6T  CL   CL  CL    0  -0.126   0.3454   3.6176   1.7635
 H6T  H1   H   HCR6  0   0.281   0.4933   5.3125  -0.4648
 H6T  H2   H   HCR6  0   0.271   0.6378   4.8525  -2.8853
 H6T  H3   H   HCR6  0   0.265   0.6772   2.5056  -3.6932
 H6T  H4   H   HCR6  0   0.268   0.5852   0.6535  -2.0829
 H6T  H5   H   HCH1  0   0.267   0.7324   1.0395   1.6000
 H6T  H8   H   HCH2  0   0.224   2.8991  -2.3190   0.0733
 H6T  H9   H   HCH2  0   0.226   2.8933  -1.4360  -1.4523
 H6T  H10  H   HCH1  0   0.217   5.0307  -0.3338  -0.8194
 H6T  H11  H   HCH3  0   0.197   6.6860   0.2587   0.8644
 H6T  H12  H   HCH3  0   0.229   5.0673   0.7205   1.3970
 H6T  H13  H   HCH3  0   0.231   6.1294  -0.1359   2.4984
 H6T  H14  H   HCH2  0   0.219   5.6820  -3.3480   1.4578
 H6T  H15  H   HCH2  0   0.231   6.9893  -2.2319   1.8203
 H6T  H16  H   HCH2  0   0.224   7.4542  -1.9255  -0.5782
 H6T  H17  H   HCH2  0   0.233   7.1255  -3.6574  -0.4744
 H6T  H18  H   HCH2  0   0.223   4.7906  -3.3294  -1.0887
 H6T  H19  H   HCH2  0   0.242   5.5875  -2.1815  -2.1594
 H6T  H20  H   HCR5  0   0.269  -1.8698   1.5535   2.2454
 H6T  H21  H   HCR6  0   0.285  -6.4042  -1.8261   0.4316
 H6T  H22  H   HCR6  0   0.274  -6.3794  -0.0722   2.1493
 H6T  H23  H   HOH1  0   0.496  -5.2441  -3.9398  -2.0102
 H6T  C10  C   CH2   0  -0.142   2.5311  -0.2090   0.2607
 H6T  C14  C   CH3   0  -0.535   5.8174  -0.0695   1.4553
 H6T  H6   H   HCH2  0   0.219   2.8051  -0.1540   1.3213
 H6T  H7   H   HCH2  0   0.206   2.8590   0.7262  -0.2125

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
 H6T  C15  N13  single    1.463  0.020  1.463
 H6T  C15  C16  single    1.524  0.020  1.524
 H6T  C14  N13  single    1.448  0.020  1.448
 H6T  N13  C12  single    1.474  0.020  1.474
 H6T  C16  C17  single    1.523  0.020  1.523
 H6T  C12  C17  single    1.537  0.020  1.537
 H6T  C12  C11  single    1.523  0.020  1.523
 H6T  C11  C10  single    1.513  0.020  1.513
 H6T  C10  O09  single    1.418  0.020  1.418
 H6T  O09  C08  single    1.398  0.020  1.398
 H6T  CL   C02  single    1.739  0.020  1.739
 H6T  C20  C21  aromatic  1.432  0.020  1.432
 H6T  C20  C18  aromatic  1.350  0.020  1.350
 H6T  N29  C21  aromatic  1.332  0.020  1.332
 H6T  N29  C28  aromatic  1.320  0.020  1.320
 H6T  C08  C18  single    1.499  0.020  1.499
 H6T  C08  C07  single    1.522  0.020  1.522
 H6T  C02  C07  aromatic  1.390  0.020  1.390
 H6T  C02  C03  aromatic  1.388  0.020  1.388
 H6T  C21  C22  aromatic  1.410  0.020  1.410
 H6T  C18  S19  aromatic  1.743  0.020  1.743
 H6T  C28  C27  aromatic  1.396  0.020  1.396
 H6T  C07  C06  aromatic  1.394  0.020  1.394
 H6T  C03  C04  aromatic  1.385  0.020  1.385
 H6T  C06  C05  aromatic  1.385  0.020  1.385
 H6T  C22  S19  aromatic  1.724  0.020  1.724
 H6T  C22  C23  aromatic  1.393  0.020  1.393
 H6T  C27  C23  aromatic  1.385  0.020  1.385
 H6T  C04  C05  aromatic  1.388  0.020  1.388
 H6T  C23  C24  single    1.482  0.020  1.482
 H6T  C24  O25  double    1.207  0.020  1.207
 H6T  C24  O26  single    1.318  0.020  1.318
 H6T  C03  H1   single    0.930  0.020  1.080
 H6T  C04  H2   single    0.930  0.020  1.080
 H6T  C05  H3   single    0.930  0.020  1.080
 H6T  C06  H4   single    0.930  0.020  1.080
 H6T  C08  H5   single    0.970  0.020  1.090
 H6T  C10  H6   single    0.970  0.020  1.090
 H6T  C10  H7   single    0.970  0.020  1.090
 H6T  C11  H8   single    0.970  0.020  1.090
 H6T  C11  H9   single    0.970  0.020  1.090
 H6T  C12  H10  single    0.970  0.020  1.090
 H6T  C14  H11  single    0.970  0.020  1.090
 H6T  C14  H12  single    0.970  0.020  1.090
 H6T  C14  H13  single    0.970  0.020  1.090
 H6T  C15  H14  single    0.970  0.020  1.090
 H6T  C15  H15  single    0.970  0.020  1.090
 H6T  C16  H16  single    0.970  0.020  1.090
 H6T  C16  H17  single    0.970  0.020  1.090
 H6T  C17  H18  single    0.970  0.020  1.090
 H6T  C17  H19  single    0.970  0.020  1.090
 H6T  C20  H20  single    0.930  0.020  1.080
 H6T  C27  H21  single    0.930  0.020  1.080
 H6T  C28  H22  single    0.930  0.020  1.080
 H6T  O26  H23  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
 H6T  CL   C02  C07  120.50  3.000
 H6T  C07  C02  C03  121.86  3.000
 H6T  CL   C02  C03  117.64  3.000
 H6T  H1   C03  C04  120.48  3.000
 H6T  H1   C03  C02  120.11  3.000
 H6T  C04  C03  C02  119.41  3.000
 H6T  H2   C04  C05  120.52  3.000
 H6T  H2   C04  C03  119.59  3.000
 H6T  C05  C04  C03  119.88  3.000
 H6T  H3   C05  C06  119.88  3.000
 H6T  H3   C05  C04  120.23  3.000
 H6T  C06  C05  C04  119.89  3.000
 H6T  H4   C06  C07  119.17  3.000
 H6T  H4   C06  C05  119.45  3.000
 H6T  C07  C06  C05  121.37  3.000
 H6T  C08  C07  C06  119.35  3.000
 H6T  C06  C07  C02  117.59  3.000
 H6T  C08  C07  C02  123.05  3.000
 H6T  H5   C08  O09  110.86  3.000
 H6T  H5   C08  C18  108.27  3.000
 H6T  O09  C08  C18  106.89  3.000
 H6T  H5   C08  C07  109.64  3.000
 H6T  C18  C08  C07  109.37  3.000
 H6T  O09  C08  C07  111.71  3.000
 H6T  H9   C11  H8   107.24  3.000
 H6T  H9   C11  C12  108.85  3.000
 H6T  H8   C11  C12  109.02  3.000
 H6T  H9   C11  C10  109.10  3.000
 H6T  H8   C11  C10  110.07  3.000
 H6T  C12  C11  C10  112.42  3.000
 H6T  H10  C12  N13  108.93  3.000
 H6T  H10  C12  C17  108.36  3.000
 H6T  N13  C12  C17  106.16  3.000
 H6T  H10  C12  C11  108.50  3.000
 H6T  C17  C12  C11  112.33  3.000
 H6T  N13  C12  C11  112.45  3.000
 H6T  H15  C15  H14  106.89  3.000
 H6T  H15  C15  N13  110.90  3.000
 H6T  H14  C15  N13  110.18  3.000
 H6T  H15  C15  C16  113.68  3.000
 H6T  H14  C15  C16  109.56  3.000
 H6T  N13  C15  C16  105.65  3.000
 H6T  H17  C16  H16  107.89  3.000
 H6T  H17  C16  C17  113.43  3.000
 H6T  H16  C16  C17  110.74  3.000
 H6T  H17  C16  C15  113.28  3.000
 H6T  H16  C16  C15  110.56  3.000
 H6T  C17  C16  C15  100.88  3.000
 H6T  H19  C17  H18  107.37  3.000
 H6T  H19  C17  C16  113.88  3.000
 H6T  H18  C17  C16  109.99  3.000
 H6T  H19  C17  C12  111.80  3.000
 H6T  H18  C17  C12  110.25  3.000
 H6T  C16  C17  C12  103.55  3.000
 H6T  S19  C18  C20  113.63  3.000
 H6T  S19  C18  C08  117.99  3.000
 H6T  C20  C18  C08  128.34  3.000
 H6T  H20  C20  C21  123.19  3.000
 H6T  H20  C20  C18  124.85  3.000
 H6T  C21  C20  C18  111.96  3.000
 H6T  N29  C21  C22  122.85  3.000
 H6T  C22  C21  C20  112.08  3.000
 H6T  N29  C21  C20  125.06  3.000
 H6T  S19  C22  C23  129.24  3.000
 H6T  C23  C22  C21  119.17  3.000
 H6T  S19  C22  C21  111.59  3.000
 H6T  C27  C23  C24  123.66  3.000
 H6T  C24  C23  C22  119.08  3.000
 H6T  C27  C23  C22  117.26  3.000
 H6T  O26  C24  O25  124.57  3.000
 H6T  O26  C24  C23  113.50  3.000
 H6T  O25  C24  C23  121.93  3.000
 H6T  H21  C27  C28  119.21  3.000
 H6T  H21  C27  C23  121.49  3.000
 H6T  C28  C27  C23  119.31  3.000
 H6T  H22  C28  N29  116.68  3.000
 H6T  H22  C28  C27  119.39  3.000
 H6T  N29  C28  C27  123.94  3.000
 H6T  C15  N13  C14  113.27  3.000
 H6T  C14  N13  C12  113.01  3.000
 H6T  C15  N13  C12  107.74  3.000
 H6T  C28  N29  C21  117.48  3.000
 H6T  C10  O09  C08  114.10  3.000
 H6T  H23  O26  C24  110.46  3.000
 H6T  C22  S19  C18   90.74  3.000
 H6T  H7   C10  H6   107.42  3.000
 H6T  H7   C10  O09  110.62  3.000
 H6T  H6   C10  O09  109.52  3.000
 H6T  H7   C10  C11  109.78  3.000
 H6T  H6   C10  C11  110.65  3.000
 H6T  O09  C10  C11  108.85  3.000
 H6T  H13  C14  H12  106.97  3.000
 H6T  H13  C14  H11  107.81  3.000
 H6T  H12  C14  H11  107.34  3.000
 H6T  H13  C14  N13  110.18  3.000
 H6T  H12  C14  N13  110.21  3.000
 H6T  H11  C14  N13  114.04  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
 H6T  CONST_01  C05  C06  C07  C02     0.00   0.0  0
 H6T  CONST_02  C05  C04  C03  C02     0.00   0.0  0
 H6T  CONST_03  C06  C07  C02  C03     0.00   0.0  0
 H6T  CONST_04  C06  C05  C04  C03     0.00   0.0  0
 H6T  CONST_05  C07  C02  C03  C04     0.00   0.0  0
 H6T  CONST_06  C07  C06  C05  C04     0.00   0.0  0
 H6T  CONST_07  N29  C21  C20  C18   180.00   0.0  0
 H6T  CONST_08  C22  C21  C20  C18     0.00   0.0  0
 H6T  CONST_09  C21  C22  S19  C18     0.00   0.0  0
 H6T  CONST_10  C23  C22  S19  C18   180.00   0.0  0
 H6T  CONST_11  C28  N29  C21  C20   180.00   0.0  0
 H6T  CONST_12  S19  C22  C21  C20     0.00   0.0  0
 H6T  CONST_13  C23  C22  C21  C20   180.00   0.0  0
 H6T  CONST_14  C22  S19  C18  C20     0.00   0.0  0
 H6T  CONST_15  S19  C18  C20  C21     0.00   0.0  0
 H6T  CONST_16  C27  C28  N29  C21     0.00   0.0  0
 H6T  CONST_17  C27  C23  C22  C21     0.00   0.0  0
 H6T  CONST_18  C28  N29  C21  C22     0.00   0.0  0
 H6T  CONST_19  C28  C27  C23  C22     0.00   0.0  0
 H6T  CONST_20  N29  C21  C22  C23     0.00   0.0  0
 H6T  CONST_21  N29  C28  C27  C23     0.00   0.0  0
 H6T  CONST_22  S19  C22  C23  C27   180.00   0.0  0
 H6T  CONST_23  S19  C22  C21  N29   180.00   0.0  0
 H6T  CONST_24  C08  C07  C02  C03   180.00   0.0  0
 H6T  CONST_25  CL   C02  C03  C04   180.00   0.0  0
 H6T  CONST_26  C08  C07  C06  C05   180.00   0.0  0
 H6T  CONST_27  CL   C02  C07  C06   180.00   0.0  0
 H6T  CONST_28  C21  C20  C18  C08   180.00   0.0  0
 H6T  CONST_29  C22  S19  C18  C08   180.00   0.0  0
 H6T  CONST_30  C24  C23  C22  C21   180.00   0.0  0
 H6T  CONST_31  S19  C22  C23  C24     0.00   0.0  0
 H6T  CONST_32  C28  C27  C23  C24   180.00   0.0  0
 H6T  CONST_33  H4   C06  C07  C02   180.00   0.0  0
 H6T  CONST_34  H2   C04  C03  C02   180.00   0.0  0
 H6T  CONST_35  H3   C05  C04  C03   180.00   0.0  0
 H6T  CONST_36  H1   C03  C04  C05   180.00   0.0  0
 H6T  CONST_37  H22  C28  N29  C21   180.00   0.0  0
 H6T  CONST_38  H20  C20  C21  C22   180.00   0.0  0
 H6T  CONST_39  H21  C27  C23  C22   180.00   0.0  0
 H6T  CONST_40  H23  O26  C24  C23   180.00   0.0  0
 H6T  Var_01    C16  C15  N13  C12    24.62  30.0  1
 H6T  Var_02    C15  C16  C17  C12    37.35  30.0  1
 H6T  Var_03    N13  C15  C16  C17   -38.60  30.0  1
 H6T  Var_04    O25  C24  C23  C22    -0.42  30.0  2
 H6T  Var_05    H11  C14  N13  C12   -62.28  30.0  3
 H6T  Var_06    O09  C10  C11  C12   178.56  30.0  3
 H6T  Var_07    C11  C10  O09  C08  -173.93  30.0  1

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
 H6T  chir_01  C08  O09  C18  C07  positiv
 H6T  chir_02  C12  N13  C17  C11  negativ

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
 H6T  plan-1  C02  0.020
 H6T  plan-1  C03  0.020
 H6T  plan-1  C04  0.020
 H6T  plan-1  C05  0.020
 H6T  plan-1  C06  0.020
 H6T  plan-1  C07  0.020
 H6T  plan-1  C08  0.020
 H6T  plan-1  CL   0.020
 H6T  plan-1  H1   0.020
 H6T  plan-1  H2   0.020
 H6T  plan-1  H3   0.020
 H6T  plan-1  H4   0.020
 H6T  plan-2  C08  0.020
 H6T  plan-2  C18  0.020
 H6T  plan-2  C20  0.020
 H6T  plan-2  C21  0.020
 H6T  plan-2  C22  0.020
 H6T  plan-2  C23  0.020
 H6T  plan-2  C24  0.020
 H6T  plan-2  C27  0.020
 H6T  plan-2  C28  0.020
 H6T  plan-2  N29  0.020
 H6T  plan-2  S19  0.020
 H6T  plan-2  H20  0.020
 H6T  plan-2  H21  0.020
 H6T  plan-2  H22  0.020
 H6T  plan-3  C23  0.020
 H6T  plan-3  C24  0.020
 H6T  plan-3  O25  0.020
 H6T  plan-3  O26  0.020
 H6T  plan-3  H23  0.020

