# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 22:13:35 2020
#   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  57  27  .  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_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  -0.652   1.1531   3.2884   2.4300
 0S2  C11  C  CH1    0  -0.097   1.6725   2.9315   1.0420
 0S2  C14  C  C      0   0.572   2.2601   0.5325   1.2709
 0S2  C13  C  CH3    0  -0.673   3.0956   3.4235   0.8111
 0S2  C15  C  CH1    0  -0.395   2.0780  -0.8832   0.7535
 0S2  C17  C  CH2    0  -0.411   2.2981  -1.9311   1.8411
 0S2  C18  C  CH2    0  -0.419   2.1529  -3.3356   1.2648
 0S2  C19  C  CH1    0  -0.224   3.1039  -3.5829   0.0946
 0S2  C20  C  CH2    0  -0.414   2.9124  -2.5104  -0.9762
 0S2  C21  C  CH2    0  -0.428   3.0535  -1.1025  -0.4118
 0S2  C02  C  CR15   0  -0.221  -0.8755   0.7378   0.6639
 0S2  C03  C  CR5    0  -0.477  -1.9113   0.5146  -0.2035
 0S2  S04  S  S2     0   0.233  -1.4396   0.8764  -1.8252
 0S2  C05  C  CR5    0  -0.381   0.1489   1.3135  -1.3465
 0S2  C06  C  CR5    0   0.343   0.3042   1.1835   0.0101
 0S2  N07  N  NT     0  -0.547   1.4741   1.5009   0.7365
 0S2  O09  O  O      0  -0.554   2.2420   2.0397  -2.1555
 0S2  O10  O  OC    -1  -0.594   0.5433   1.7564  -3.5833
 0S2  O16  O  O      0  -0.497   3.1370   0.7885   2.0849
 0S2  C22  C  CH3    0  -0.655   2.9248  -4.9818  -0.4791
 0S2  C23  C  CSP    0   0.250  -4.3323  -0.3215   0.3379
 0S2  C24  C  CT     0  -0.304  -5.6916  -0.7823   0.6321
 0S2  C25  C  CH3    0  -0.634  -6.5235   0.3979   1.1513
 0S2  C26  C  CH3    0  -0.635  -6.3167  -1.3400  -0.6528
 0S2  C27  C  CH3    0  -0.634  -5.6306  -1.8823   1.6996
 0S2  H1   H  HCH3   0   0.227   1.2270   4.3654   2.5883
 0S2  H2   H  HCH3   0   0.229   0.1041   3.0114   2.5460
 0S2  H3   H  HCH3   0   0.229   1.7285   2.7929   3.2107
 0S2  H4   H  HCH1   0   0.244   1.0466   3.4448   0.3110
 0S2  H5   H  HCH3   0   0.226   3.7737   3.1433   1.6129
 0S2  H6   H  HCH3   0   0.245   3.4799   3.0436  -0.1333
 0S2  H7   H  HCH3   0   0.220   3.0801   4.5129   0.7519
 0S2  H8   H  HCH1   0   0.252   1.0687  -1.0231   0.3584
 0S2  H9   H  HCH2   0   0.216   3.2964  -1.8151   2.2716
 0S2  H10  H  HCH2   0   0.230   1.5827  -1.7868   2.6553
 0S2  H11  H  HCH2   0   0.225   2.3298  -4.0776   2.0489
 0S2  H12  H  HCH2   0   0.205   1.1213  -3.4900   0.9241
 0S2  H13  H  HCH1   0   0.208   4.1302  -3.4944   0.4754
 0S2  H14  H  HCH2   0   0.226   3.6321  -2.6585  -1.7862
 0S2  H15  H  HCH2   0   0.206   1.9155  -2.6218  -1.4202
 0S2  H16  H  HCH2   0   0.252   2.8736  -0.3564  -1.1885
 0S2  H17  H  HCH2   0   0.216   4.0783  -0.9467  -0.0572
 0S2  H18  H  HCR5   0   0.267  -0.9467   0.5810   1.7318
 0S2  H20  H  HCH3   0   0.212   1.9110  -5.1170  -0.8645
 0S2  H21  H  HCH3   0   0.223   3.6192  -5.1703  -1.3001
 0S2  H22  H  HCH3   0   0.223   3.0939  -5.7481   0.2801
 0S2  H23  H  HCH3   0   0.235  -7.5395   0.0654   1.3714
 0S2  H24  H  HCH3   0   0.235  -6.0962   0.8082   2.0669
 0S2  H25  H  HCH3   0   0.236  -6.5817   1.1981   0.4131
 0S2  H26  H  HCH3   0   0.236  -6.3533  -0.5839  -1.4375
 0S2  H27  H  HCH3   0   0.236  -5.7502  -2.1934  -1.0259
 0S2  H28  H  HCH3   0   0.236  -7.3374  -1.6716  -0.4547
 0S2  H29  H  HCH3   0   0.235  -5.0559  -2.7408   1.3505
 0S2  H30  H  HCH3   0   0.236  -5.1732  -1.5170   2.6196
 0S2  H31  H  HCH3   0   0.235  -6.6395  -2.2241   1.9360
 0S2  C01  C  CSP    0   0.126  -3.2140   0.0629   0.0948
 0S2  C08  C  C      0   0.423   1.0750   1.7464  -2.4553

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    1.534  0.020  1.534
 0S2  C24  C26  single    1.534  0.020  1.534
 0S2  C24  C25  single    1.534  0.020  1.534
 0S2  C24  C23  single    1.465  0.020  1.465
 0S2  C23  C01  triple    1.207  0.020  1.207
 0S2  S04  C03  aromatic  1.727  0.020  1.727
 0S2  S04  C05  aromatic  1.716  0.020  1.716
 0S2  C22  C19  single    1.523  0.020  1.523
 0S2  C01  C03  single    1.411  0.020  1.411
 0S2  O09  C08  deloc     1.240  0.020  1.240
 0S2  C03  C02  aromatic  1.369  0.020  1.369
 0S2  C20  C19  single    1.528  0.020  1.528
 0S2  C20  C21  single    1.523  0.020  1.523
 0S2  C08  C05  single    1.508  0.020  1.508
 0S2  C08  O10  deloc     1.247  0.020  1.247
 0S2  C19  C18  single    1.528  0.020  1.528
 0S2  C05  C06  aromatic  1.372  0.020  1.372
 0S2  C18  C17  single    1.525  0.020  1.525
 0S2  C02  C06  aromatic  1.421  0.020  1.421
 0S2  C21  C15  single    1.535  0.020  1.535
 0S2  C06  N07  single    1.413  0.020  1.413
 0S2  C15  C17  single    1.526  0.020  1.526
 0S2  C15  C14  single    1.518  0.020  1.518
 0S2  N07  C14  single    1.357  0.020  1.357
 0S2  N07  C11  single    1.476  0.020  1.476
 0S2  C14  O16  double    1.223  0.020  1.223
 0S2  C12  C11  single    1.524  0.020  1.524
 0S2  C11  C13  single    1.523  0.020  1.523
 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  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   108.44  3.000
 0S2  H3   C12  H1   108.02  3.000
 0S2  H2   C12  H1   107.47  3.000
 0S2  H3   C12  C11  111.48  3.000
 0S2  H2   C12  C11  111.41  3.000
 0S2  H1   C12  C11  109.88  3.000
 0S2  H4   C11  N07  103.90  3.000
 0S2  H4   C11  C13  106.41  3.000
 0S2  N07  C11  C13  114.03  3.000
 0S2  H4   C11  C12  107.72  3.000
 0S2  C13  C11  C12  112.38  3.000
 0S2  N07  C11  C12  111.69  3.000
 0S2  O16  C14  N07  121.86  3.000
 0S2  O16  C14  C15  120.52  3.000
 0S2  N07  C14  C15  117.50  3.000
 0S2  H7   C13  H6   107.85  3.000
 0S2  H7   C13  H5   107.84  3.000
 0S2  H6   C13  H5   109.27  3.000
 0S2  H7   C13  C11  108.50  3.000
 0S2  H6   C13  C11  110.41  3.000
 0S2  H5   C13  C11  112.81  3.000
 0S2  H8   C15  C21  107.10  3.000
 0S2  H8   C15  C17  107.64  3.000
 0S2  C21  C15  C17  110.56  3.000
 0S2  H8   C15  C14  110.69  3.000
 0S2  C17  C15  C14  112.34  3.000
 0S2  C21  C15  C14  108.40  3.000
 0S2  H10  C17  H9   106.87  3.000
 0S2  H10  C17  C18  109.92  3.000
 0S2  H9   C17  C18  109.48  3.000
 0S2  H10  C17  C15  110.22  3.000
 0S2  H9   C17  C15  109.84  3.000
 0S2  C18  C17  C15  110.44  3.000
 0S2  H12  C18  H11  106.21  3.000
 0S2  H12  C18  C19  108.93  3.000
 0S2  H11  C18  C19  109.79  3.000
 0S2  H12  C18  C17  109.66  3.000
 0S2  H11  C18  C17  109.78  3.000
 0S2  C19  C18  C17  112.28  3.000
 0S2  H13  C19  C22  108.34  3.000
 0S2  H13  C19  C20  107.67  3.000
 0S2  C22  C19  C20  111.48  3.000
 0S2  H13  C19  C18  107.64  3.000
 0S2  C20  C19  C18  110.19  3.000
 0S2  C22  C19  C18  111.35  3.000
 0S2  H15  C20  H14  106.53  3.000
 0S2  H15  C20  C21  109.15  3.000
 0S2  H14  C20  C21  109.79  3.000
 0S2  H15  C20  C19  109.05  3.000
 0S2  H14  C20  C19  109.97  3.000
 0S2  C21  C20  C19  112.19  3.000
 0S2  H17  C21  H16  106.69  3.000
 0S2  H17  C21  C20  109.76  3.000
 0S2  H16  C21  C20  110.66  3.000
 0S2  H17  C21  C15  109.16  3.000
 0S2  H16  C21  C15  109.73  3.000
 0S2  C20  C21  C15  110.75  3.000
 0S2  H18  C02  C06  123.67  3.000
 0S2  H18  C02  C03  123.50  3.000
 0S2  C06  C02  C03  112.82  3.000
 0S2  S04  C03  C02  110.73  3.000
 0S2  C02  C03  C01  128.08  3.000
 0S2  S04  C03  C01  121.19  3.000
 0S2  C05  S04  C03   92.54  3.000
 0S2  C08  C05  C06  133.22  3.000
 0S2  C06  C05  S04  110.90  3.000
 0S2  C08  C05  S04  115.88  3.000
 0S2  N07  C06  C05  125.51  3.000
 0S2  N07  C06  C02  121.43  3.000
 0S2  C05  C06  C02  113.01  3.000
 0S2  C06  N07  C14  121.44  3.000
 0S2  C14  N07  C11  122.16  3.000
 0S2  C06  N07  C11  115.80  3.000
 0S2  H22  C22  H21  107.65  3.000
 0S2  H22  C22  H20  107.59  3.000
 0S2  H21  C22  H20  107.66  3.000
 0S2  H22  C22  C19  111.38  3.000
 0S2  H21  C22  C19  111.54  3.000
 0S2  H20  C22  C19  110.83  3.000
 0S2  C24  C23  C01  180.00  3.000
 0S2  C27  C24  C26  109.78  3.000
 0S2  C26  C24  C25  110.01  3.000
 0S2  C27  C24  C25  109.73  3.000
 0S2  C25  C24  C23  109.21  3.000
 0S2  C26  C24  C23  108.92  3.000
 0S2  C27  C24  C23  109.17  3.000
 0S2  H25  C25  H24  108.25  3.000
 0S2  H25  C25  H23  108.09  3.000
 0S2  H24  C25  H23  108.06  3.000
 0S2  H25  C25  C24  111.37  3.000
 0S2  H24  C25  C24  111.16  3.000
 0S2  H23  C25  C24  109.79  3.000
 0S2  H28  C26  H27  108.07  3.000
 0S2  H28  C26  H26  108.06  3.000
 0S2  H27  C26  H26  108.30  3.000
 0S2  H28  C26  C24  109.86  3.000
 0S2  H27  C26  C24  111.07  3.000
 0S2  H26  C26  C24  111.37  3.000
 0S2  H31  C27  H30  108.06  3.000
 0S2  H31  C27  H29  108.06  3.000
 0S2  H30  C27  H29  108.22  3.000
 0S2  H31  C27  C24  109.80  3.000
 0S2  H30  C27  C24  111.32  3.000
 0S2  H29  C27  C24  111.27  3.000
 0S2  C23  C01  C03  180.00  3.000
 0S2  O10  C08  O09  128.17  3.000
 0S2  O10  C08  C05  113.92  3.000
 0S2  O09  C08  C05  117.91  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_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  O16  C14  N07  C11     0.00   0.0  0
 0S2  Var_01    C19  C20  C21  C15   -55.87  30.0  1
 0S2  Var_02    C19  C18  C17  C15    56.60  30.0  1
 0S2  Var_03    O09  C08  C05  S04  -178.29  30.0  2
 0S2  Var_04    C06  N07  C11  C12    95.32  30.0  2
 0S2  Var_05    C27  C24  C23  C01  -144.67  30.0  2
 0S2  Var_06    H5   C13  C11  C12    50.13  30.0  3
 0S2  Var_07    H1   C12  C11  C13    55.73  30.0  3
 0S2  Var_08    H29  C27  C24  C23   -61.15  30.0  3
 0S2  Var_09    H26  C26  C24  C23   -59.30  30.0  3
 0S2  Var_10    H23  C25  C24  C23   179.87  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  C01  0.020
 0S2  plan-1  C08  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  C08  0.020

