# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:08:05 2021
#   Inital geometry file: a 139 line input string
#   Ligand name: 5-(3,3-dimethylbut-1-yn-1-yl)-3-{[(trans-4-methylcyclohexyl)carbonyl](propan-2-yl)amino}thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)N(C(=O)[C@@H]1CC[C@@H](C)CC1)c2cc(sc2C(O)=O)C#CC(C)(C)C
#
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
 0S2  0S2  '5-(3,3-dimethylbut-1-yn-1-yl)-3-{[(trans-4-methylcyclohexyl)carbonyl](propan-2-yl)amino}thiophene-2-carboxylic acid'  ligand  58  27  .  2021-08-03  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0S2
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
 0S2  C12  C  CH3   0  -0.679   6.6449  31.6950  76.1791
 0S2  C11  C  CH1   0  -0.121   7.2082  33.0366  76.6226
 0S2  C14  C  C     0   0.583   7.3458  35.2849  75.6456
 0S2  C13  C  CH3   0  -0.652   8.4645  32.8626  77.4670
 0S2  C15  C  CH1   0  -0.410   7.7703  36.1849  74.5028
 0S2  C17  C  CH2   0  -0.414   9.2134  36.6484  74.7540
 0S2  C18  C  CH2   0  -0.415   9.6852  37.5810  73.6444
 0S2  C19  C  CH1   0  -0.227   8.7547  38.7782  73.4559
 0S2  C20  C  CH2   0  -0.419   7.3227  38.2972  73.2285
 0S2  C21  C  CH2   0  -0.412   6.8393  37.3860  74.3507
 0S2  C02  C  CR15  0  -0.218   9.1471  32.8675  74.0159
 0S2  C03  C  CR5   0  -0.464   9.2834  32.3137  72.7671
 0S2  S04  S  S2    0   0.302   7.8142  32.3965  71.8774
 0S2  C05  C  CR5   0  -0.369   7.0051  33.1620  73.1805
 0S2  C06  C  CR5   0   0.396   7.8449  33.3580  74.2555
 0S2  N07  N  NT    0  -0.567   7.4596  33.9353  75.4771
 0S2  O09  O  O     0  -0.440   5.0269  33.2365  71.9332
 0S2  O10  O  OH1   0  -0.581   5.0435  34.1430  73.9796
 0S2  O16  O  O     0  -0.485   6.9787  35.7561  76.7101
 0S2  C22  C  CH3   0  -0.655   9.2279  39.6747  72.3200
 0S2  C23  C  CSP   0   0.282  11.4052  31.2382  71.6815
 0S2  C24  C  CT    0  -0.312  12.5814  30.6316  71.0569
 0S2  C25  C  CH3   0  -0.635  13.8501  31.2093  71.6965
 0S2  C26  C  CH3   0  -0.633  12.5345  29.1123  71.2714
 0S2  C27  C  CH3   0  -0.633  12.5646  30.9489  69.5556
 0S2  H1   H  HCH3  0   0.250   6.3790  31.1180  77.0652
 0S2  H2   H  HCH3  0   0.241   5.7415  31.8101  75.5805
 0S2  H3   H  HCH3  0   0.230   7.3653  31.1068  75.6086
 0S2  H4   H  HCH1  0   0.259   6.4494  33.5332  77.2261
 0S2  H5   H  HCH3  0   0.236   8.2343  32.2826  78.3615
 0S2  H6   H  HCH3  0   0.222   9.2427  32.3278  76.9201
 0S2  H7   H  HCH3  0   0.239   8.8671  33.8234  77.7864
 0S2  H8   H  HCH1  0   0.252   7.7663  35.6393  73.5562
 0S2  H9   H  HCH2  0   0.237   9.8818  35.7849  74.8189
 0S2  H10  H  HCH2  0   0.226   9.2635  37.1632  75.7184
 0S2  H11  H  HCH2  0   0.209   9.7428  37.0229  72.7021
 0S2  H12  H  HCH2  0   0.230  10.6997  37.9258  73.8627
 0S2  H13  H  HCH1  0   0.210   8.7668  39.3639  74.3846
 0S2  H14  H  HCH2  0   0.228   6.6509  39.1550  73.1381
 0S2  H15  H  HCH2  0   0.206   7.2740  37.7609  72.2728
 0S2  H16  H  HCH2  0   0.220   6.8047  37.9475  75.2879
 0S2  H17  H  HCH2  0   0.234   5.8216  37.0448  74.1458
 0S2  H18  H  HCR5  0   0.284   9.9538  32.9273  74.7317
 0S2  H19  H  HOH1  0   0.492   4.1193  34.3506  73.7724
 0S2  H20  H  HCH3  0   0.224  10.2310  40.0621  72.5080
 0S2  H21  H  HCH3  0   0.212   9.2574  39.1245  71.3762
 0S2  H22  H  HCH3  0   0.224   8.5630  40.5297  72.1849
 0S2  H23  H  HCH3  0   0.238  13.8843  31.0063  72.7672
 0S2  H24  H  HCH3  0   0.238  14.7279  30.7532  71.2360
 0S2  H25  H  HCH3  0   0.238  13.9122  32.2880  71.5510
 0S2  H26  H  HCH3  0   0.237  12.5387  28.8619  72.3327
 0S2  H27  H  HCH3  0   0.237  11.6425  28.6759  70.8211
 0S2  H28  H  HCH3  0   0.238  13.4094  28.6500  70.8108
 0S2  H29  H  HCH3  0   0.238  12.5951  32.0244  69.3798
 0S2  H30  H  HCH3  0   0.238  13.4377  30.5024  69.0765
 0S2  H31  H  HCH3  0   0.237  11.6707  30.5497  69.0753
 0S2  C08  C  C     0   0.534   5.6006  33.5095  72.9623
 0S2  C01  C  CSP   0   0.140  10.4323  31.7373  72.1918

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
 0S2  C27  C24  single    1.535  0.020  1.535
 0S2  C24  C26  single    1.535  0.020  1.535
 0S2  C24  C25  single    1.534  0.020  1.534
 0S2  C24  C23  single    1.463  0.020  1.463
 0S2  C23  C01  triple    1.207  0.020  1.207
 0S2  S04  C03  aromatic  1.720  0.020  1.720
 0S2  S04  C05  aromatic  1.714  0.020  1.714
 0S2  C22  C19  single    1.522  0.020  1.522
 0S2  C01  C03  single    1.408  0.020  1.408
 0S2  O09  C08  double    1.209  0.020  1.209
 0S2  C03  C02  aromatic  1.373  0.020  1.373
 0S2  C20  C19  single    1.528  0.020  1.528
 0S2  C20  C21  single    1.524  0.020  1.524
 0S2  C08  C05  single    1.463  0.020  1.463
 0S2  C08  O10  single    1.322  0.020  1.322
 0S2  C19  C18  single    1.528  0.020  1.528
 0S2  C05  C06  aromatic  1.378  0.020  1.378
 0S2  C18  C17  single    1.524  0.020  1.524
 0S2  C02  C06  aromatic  1.412  0.020  1.412
 0S2  C21  C15  single    1.527  0.020  1.527
 0S2  C06  N07  single    1.405  0.020  1.405
 0S2  C15  C17  single    1.536  0.020  1.536
 0S2  C15  C14  single    1.515  0.020  1.515
 0S2  N07  C14  single    1.365  0.020  1.365
 0S2  N07  C11  single    1.477  0.020  1.477
 0S2  C14  O16  double    1.221  0.020  1.221
 0S2  C12  C11  single    1.521  0.020  1.521
 0S2  C11  C13  single    1.524  0.020  1.524
 0S2  C12  H1   single    0.970  0.020  1.090
 0S2  C12  H2   single    0.970  0.020  1.090
 0S2  C12  H3   single    0.970  0.020  1.090
 0S2  C11  H4   single    0.970  0.020  1.090
 0S2  C13  H5   single    0.970  0.020  1.090
 0S2  C13  H6   single    0.970  0.020  1.090
 0S2  C13  H7   single    0.970  0.020  1.090
 0S2  C15  H8   single    0.970  0.020  1.090
 0S2  C17  H9   single    0.970  0.020  1.090
 0S2  C17  H10  single    0.970  0.020  1.090
 0S2  C18  H11  single    0.970  0.020  1.090
 0S2  C18  H12  single    0.970  0.020  1.090
 0S2  C19  H13  single    0.970  0.020  1.090
 0S2  C20  H14  single    0.970  0.020  1.090
 0S2  C20  H15  single    0.970  0.020  1.090
 0S2  C21  H16  single    0.970  0.020  1.090
 0S2  C21  H17  single    0.970  0.020  1.090
 0S2  C02  H18  single    0.930  0.020  1.080
 0S2  O10  H19  single    0.850  0.020  0.980
 0S2  C22  H20  single    0.970  0.020  1.090
 0S2  C22  H21  single    0.970  0.020  1.090
 0S2  C22  H22  single    0.970  0.020  1.090
 0S2  C25  H23  single    0.970  0.020  1.090
 0S2  C25  H24  single    0.970  0.020  1.090
 0S2  C25  H25  single    0.970  0.020  1.090
 0S2  C26  H26  single    0.970  0.020  1.090
 0S2  C26  H27  single    0.970  0.020  1.090
 0S2  C26  H28  single    0.970  0.020  1.090
 0S2  C27  H29  single    0.970  0.020  1.090
 0S2  C27  H30  single    0.970  0.020  1.090
 0S2  C27  H31  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
 0S2  H3   C12  H2   108.49  3.000
 0S2  H3   C12  H1   107.49  3.000
 0S2  H2   C12  H1   107.47  3.000
 0S2  H3   C12  C11  112.54  3.000
 0S2  H2   C12  C11  111.96  3.000
 0S2  H1   C12  C11  108.67  3.000
 0S2  H4   C11  N07  105.71  3.000
 0S2  H4   C11  C13  108.62  3.000
 0S2  N07  C11  C13  111.03  3.000
 0S2  H4   C11  C12  107.79  3.000
 0S2  C13  C11  C12  111.48  3.000
 0S2  N07  C11  C12  111.93  3.000
 0S2  O16  C14  N07  120.96  3.000
 0S2  O16  C14  C15  120.84  3.000
 0S2  N07  C14  C15  118.09  3.000
 0S2  H7   C13  H6   108.39  3.000
 0S2  H7   C13  H5   107.84  3.000
 0S2  H6   C13  H5   107.52  3.000
 0S2  H7   C13  C11  111.49  3.000
 0S2  H6   C13  C11  111.48  3.000
 0S2  H5   C13  C11  109.96  3.000
 0S2  H8   C15  C21  107.71  3.000
 0S2  H8   C15  C17  107.20  3.000
 0S2  C21  C15  C17  110.59  3.000
 0S2  H8   C15  C14  110.84  3.000
 0S2  C17  C15  C14  108.61  3.000
 0S2  C21  C15  C14  111.80  3.000
 0S2  H10  C17  H9   106.92  3.000
 0S2  H10  C17  C18  109.85  3.000
 0S2  H9   C17  C18  109.70  3.000
 0S2  H10  C17  C15  109.20  3.000
 0S2  H9   C17  C15  110.21  3.000
 0S2  C18  C17  C15  110.87  3.000
 0S2  H12  C18  H11  106.46  3.000
 0S2  H12  C18  C19  110.03  3.000
 0S2  H11  C18  C19  108.95  3.000
 0S2  H12  C18  C17  109.56  3.000
 0S2  H11  C18  C17  109.29  3.000
 0S2  C19  C18  C17  112.38  3.000
 0S2  H13  C19  C22  108.27  3.000
 0S2  H13  C19  C20  107.71  3.000
 0S2  C22  C19  C20  111.45  3.000
 0S2  H13  C19  C18  107.87  3.000
 0S2  C20  C19  C18  110.03  3.000
 0S2  C22  C19  C18  111.35  3.000
 0S2  H15  C20  H14  106.52  3.000
 0S2  H15  C20  C21  109.58  3.000
 0S2  H14  C20  C21  109.58  3.000
 0S2  H15  C20  C19  108.98  3.000
 0S2  H14  C20  C19  109.95  3.000
 0S2  C21  C20  C19  112.08  3.000
 0S2  H17  C21  H16  106.96  3.000
 0S2  H17  C21  C20  110.12  3.000
 0S2  H16  C21  C20  109.52  3.000
 0S2  H17  C21  C15  109.93  3.000
 0S2  H16  C21  C15  109.75  3.000
 0S2  C20  C21  C15  110.50  3.000
 0S2  H18  C02  C06  123.85  3.000
 0S2  H18  C02  C03  123.43  3.000
 0S2  C06  C02  C03  112.71  3.000
 0S2  S04  C03  C02  111.49  3.000
 0S2  C02  C03  C01  128.15  3.000
 0S2  S04  C03  C01  120.36  3.000
 0S2  C05  S04  C03   91.81  3.000
 0S2  C08  C05  C06  131.87  3.000
 0S2  C06  C05  S04  111.64  3.000
 0S2  C08  C05  S04  116.47  3.000
 0S2  N07  C06  C05  124.72  3.000
 0S2  N07  C06  C02  122.90  3.000
 0S2  C05  C06  C02  112.35  3.000
 0S2  C06  N07  C14  122.44  3.000
 0S2  C14  N07  C11  119.45  3.000
 0S2  C06  N07  C11  118.09  3.000
 0S2  H19  O10  C08  109.87  3.000
 0S2  H22  C22  H21  107.69  3.000
 0S2  H22  C22  H20  107.64  3.000
 0S2  H21  C22  H20  107.61  3.000
 0S2  H22  C22  C19  111.36  3.000
 0S2  H21  C22  C19  110.88  3.000
 0S2  H20  C22  C19  111.48  3.000
 0S2  C24  C23  C01  180.00  3.000
 0S2  C27  C24  C26  109.94  3.000
 0S2  C26  C24  C25  109.86  3.000
 0S2  C27  C24  C25  109.83  3.000
 0S2  C25  C24  C23  109.31  3.000
 0S2  C26  C24  C23  109.03  3.000
 0S2  C27  C24  C23  108.85  3.000
 0S2  H25  C25  H24  108.14  3.000
 0S2  H25  C25  H23  108.27  3.000
 0S2  H24  C25  H23  108.15  3.000
 0S2  H25  C25  C24  111.35  3.000
 0S2  H24  C25  C24  109.39  3.000
 0S2  H23  C25  C24  111.43  3.000
 0S2  H28  C26  H27  108.18  3.000
 0S2  H28  C26  H26  108.08  3.000
 0S2  H27  C26  H26  108.26  3.000
 0S2  H28  C26  C24  109.61  3.000
 0S2  H27  C26  C24  111.31  3.000
 0S2  H26  C26  C24  111.29  3.000
 0S2  H31  C27  H30  108.22  3.000
 0S2  H31  C27  H29  108.25  3.000
 0S2  H30  C27  H29  108.08  3.000
 0S2  H31  C27  C24  111.36  3.000
 0S2  H30  C27  C24  109.64  3.000
 0S2  H29  C27  C24  111.19  3.000
 0S2  O10  C08  O09  124.28  3.000
 0S2  O10  C08  C05  113.81  3.000
 0S2  O09  C08  C05  121.91  3.000
 0S2  C23  C01  C03  180.00  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
 0S2  CONST_01  C05  S04  C03  C02    0.00   0.0  0
 0S2  CONST_02  S04  C05  C06  C02    0.00   0.0  0
 0S2  CONST_03  C06  C05  S04  C03    0.00   0.0  0
 0S2  CONST_04  C05  C06  C02  C03    0.00   0.0  0
 0S2  CONST_05  C06  C02  C03  S04    0.00   0.0  0
 0S2  CONST_06  C05  S04  C03  C01  180.00   0.0  0
 0S2  CONST_07  C06  C02  C03  C01  180.00   0.0  0
 0S2  CONST_08  C08  C05  C06  C02  180.00   0.0  0
 0S2  CONST_09  C08  C05  S04  C03  180.00   0.0  0
 0S2  CONST_10  N07  C06  C02  C03  180.00   0.0  0
 0S2  CONST_11  N07  C06  C05  S04  180.00   0.0  0
 0S2  CONST_12  H18  C02  C03  S04  180.00   0.0  0
 0S2  CONST_13  C06  N07  C14  C15    0.00   0.0  0
 0S2  CONST_18  C15  C14  N07  C11  180.00   0.0  0
 0S2  CONST_19  O16  C14  N07  C06  180.00   0.0  0
 0S2  CONST_20  H19  O10  C08  C05  180.00   0.0  0
 0S2  CONST_21  O16  C14  N07  C11    0.00   0.0  0
 0S2  Var_01    C19  C20  C21  C15  -57.20  30.0  1
 0S2  Var_02    C19  C18  C17  C15   55.33  30.0  1
 0S2  Var_03    O09  C08  C05  S04    2.15  30.0  1
 0S2  Var_04    C06  N07  C11  C12  -32.52  30.0  2
 0S2  Var_05    C27  C24  C23  C01   35.36  30.0  2
 0S2  Var_06    H5   C13  C11  C12  -60.33  30.0  3
 0S2  Var_07    H1   C12  C11  C13   61.02  30.0  3
 0S2  Var_08    H29  C27  C24  C23   60.51  30.0  3
 0S2  Var_09    H26  C26  C24  C23  -60.36  30.0  3
 0S2  Var_10    H23  C25  C24  C23   60.13  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
 0S2  chir_01  C15  C21  C17  C14  negativ
 0S2  chir_02  C19  C22  C20  C18  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
 0S2  plan-1  C02  0.020
 0S2  plan-1  C03  0.020
 0S2  plan-1  S04  0.020
 0S2  plan-1  C05  0.020
 0S2  plan-1  C06  0.020
 0S2  plan-1  N07  0.020
 0S2  plan-1  C23  0.020
 0S2  plan-1  H18  0.020
 0S2  plan-1  C08  0.020
 0S2  plan-1  C01  0.020
 0S2  plan-2  C11  0.020
 0S2  plan-2  C14  0.020
 0S2  plan-2  C15  0.020
 0S2  plan-2  C06  0.020
 0S2  plan-2  N07  0.020
 0S2  plan-2  O16  0.020
 0S2  plan-3  C05  0.020
 0S2  plan-3  O09  0.020
 0S2  plan-3  O10  0.020
 0S2  plan-3  H19  0.020
 0S2  plan-3  C08  0.020

