# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 04:24:25 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 5-(3,3-dimethylbut-1-yn-1-yl)-3-{2,2-dimethyl-1-[(trans-4-methylcyclohexyl)carbonyl]hydrazinyl}thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1CC[C@@H](CC1)C(=O)N(N(C)C)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
 0S3  0S3  '5-(3,3-dimethylbut-1-yn-1-yl)-3-{2,2-dimethyl-1-[(trans-4-methylcyclohexyl)carbonyl]hydrazinyl}thiophene-2-carboxylic acid'  ligand  56  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_0S3
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
 0S3  C01  C  C1     0  -0.181  -0.7550  -0.6038  -0.9208
 0S3  C02  C  C      0   0.314   0.4826  -0.7313  -0.2363
 0S3  C03  C  C      0  -0.341   0.3433  -1.1128   1.0743
 0S3  S04  S  S2     0   0.314  -1.3121  -1.3079   1.4702
 0S3  C05  C  C      0  -0.532  -1.8286  -0.8933  -0.1207
 0S3  C06  C  CSP    0   0.169  -3.2041  -0.8143  -0.4176
 0S3  C07  C  CSP    0   0.160  -4.3870  -0.7403  -0.6309
 0S3  C08  C  CT     0  -0.257  -5.8274  -0.6606  -0.8673
 0S3  C09  C  CH3    0  -0.648  -6.5283  -0.3334   0.4562
 0S3  C10  C  CH3    0  -0.637  -6.1225   0.4397  -1.8951
 0S3  C11  C  CH3    0  -0.633  -6.3290  -2.0135  -1.3850
 0S3  N12  N  NT     0  -0.364   1.7102  -0.4945  -0.8905
 0S3  C13  C  C      0   0.511   2.5984   0.4660  -0.5083
 0S3  N14  N  NT     0  -0.338   2.0187  -1.4521  -1.8559
 0S3  C15  C  CH1    0  -0.419   2.0456   1.6354   0.2815
 0S3  O16  O  O      0  -0.448   3.7517   0.4590  -0.9052
 0S3  C17  C  CH2    0  -0.419   3.0719   2.2249   1.2410
 0S3  C18  C  CH2    0  -0.437   2.5054   3.4509   1.9502
 0S3  C19  C  CH1    0  -0.252   2.0278   4.5208   0.9696
 0S3  C20  C  CH2    0  -0.428   1.0275   3.9248  -0.0170
 0S3  C21  C  CH2    0  -0.413   1.5810   2.6970  -0.7288
 0S3  C22  C  CH3    0  -0.653   1.4377   5.7197   1.6998
 0S3  C23  C  CH3    0  -0.521   2.3122  -0.9104  -3.1674
 0S3  C24  C  CH3    0  -0.539   2.9311  -2.4895  -1.4147
 0S3  C25  C  C      0   0.472   1.3370  -1.3551   2.1608
 0S3  O26  O  O      0  -0.648   2.5388  -1.1402   1.9152
 0S3  O27  O  OC    -1  -0.573   0.8493  -1.7686   3.2373
 0S3  H1   H  H      0   0.246  -0.8500  -0.2888  -1.9512
 0S3  H2   H  HCH3   0   0.234  -7.6066  -0.2765   0.2967
 0S3  H3   H  HCH3   0   0.236  -6.3407  -1.1004   1.2078
 0S3  H4   H  HCH3   0   0.245  -6.1964   0.6242   0.8600
 0S3  H5   H  HCH3   0   0.236  -5.7424   1.4046  -1.5601
 0S3  H6   H  HCH3   0   0.252  -5.6675   0.2113  -2.8598
 0S3  H7   H  HCH3   0   0.206  -7.2007   0.5286  -2.0380
 0S3  H8   H  HCH3   0   0.254  -5.8283  -2.3003  -2.3100
 0S3  H9   H  HCH3   0   0.221  -6.1576  -2.7996  -0.6483
 0S3  H10  H  HCH3   0   0.241  -7.4015  -1.9582  -1.5802
 0S3  H11  H  HCH1   0   0.218   1.1689   1.3314   0.8565
 0S3  H12  H  HCH2   0   0.255   3.3697   1.4714   1.9733
 0S3  H13  H  HCH2   0   0.208   3.9732   2.5103   0.6903
 0S3  H14  H  HCH2   0   0.239   1.6648   3.1512   2.5877
 0S3  H15  H  HCH2   0   0.182   3.2616   3.8734   2.6181
 0S3  H16  H  HCH1   0   0.199   2.9012   4.8661   0.4008
 0S3  H17  H  HCH2   0   0.248   0.1127   3.6485   0.5205
 0S3  H18  H  HCH2   0   0.203   0.7363   4.6747  -0.7577
 0S3  H19  H  HCH2   0   0.249   2.4264   2.9867  -1.3603
 0S3  H20  H  HCH2   0   0.253   0.8195   2.2776  -1.3903
 0S3  H21  H  HCH3   0   0.272   2.1700   6.1792   2.3672
 0S3  H22  H  HCH3   0   0.190   1.1038   6.4876   0.9990
 0S3  H23  H  HCH3   0   0.208   0.5734   5.4224   2.2991
 0S3  H24  H  HCH3   0   0.214   3.3117  -0.4723  -3.2607
 0S3  H25  H  HCH3   0   0.260   2.2280  -1.7161  -3.8988
 0S3  H26  H  HCH3   0   0.251   1.5717  -0.1529  -3.4248
 0S3  H27  H  HCH3   0   0.252   2.6133  -2.8637  -0.4430
 0S3  H28  H  HCH3   0   0.265   2.8826  -3.3140  -2.1282
 0S3  H29  H  HCH3   0   0.204   3.9716  -2.1612  -1.3449

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
 0S3  C11  C08  single    1.533  0.020  1.533
 0S3  C08  C10  single    1.534  0.020  1.534
 0S3  C08  C09  single    1.533  0.020  1.533
 0S3  C08  C07  single    1.462  0.020  1.462
 0S3  C07  C06  triple    1.204  0.020  1.204
 0S3  S04  C05  aromatic  1.723  0.020  1.723
 0S3  S04  C03  aromatic  1.713  0.020  1.713
 0S3  C22  C19  single    1.523  0.020  1.523
 0S3  C06  C05  single    1.409  0.020  1.409
 0S3  O26  C25  deloc     1.245  0.020  1.245
 0S3  C05  C01  aromatic  1.370  0.020  1.370
 0S3  C18  C19  single    1.528  0.020  1.528
 0S3  C18  C17  single    1.525  0.020  1.525
 0S3  C25  C03  single    1.492  0.020  1.492
 0S3  C25  O27  deloc     1.252  0.020  1.252
 0S3  C19  C20  single    1.526  0.020  1.526
 0S3  C03  C02  aromatic  1.372  0.020  1.372
 0S3  C20  C21  single    1.523  0.020  1.523
 0S3  C01  C02  aromatic  1.420  0.020  1.420
 0S3  C17  C15  single    1.524  0.020  1.524
 0S3  C02  N12  single    1.411  0.020  1.411
 0S3  C15  C21  single    1.537  0.020  1.537
 0S3  C15  C13  single    1.516  0.020  1.516
 0S3  N12  C13  single    1.363  0.020  1.363
 0S3  N12  N14  single    1.394  0.020  1.394
 0S3  C13  O16  double    1.220  0.020  1.220
 0S3  C23  N14  single    1.449  0.020  1.449
 0S3  N14  C24  single    1.450  0.020  1.450
 0S3  C01  H1   single    0.930  0.020  1.080
 0S3  C09  H2   single    0.970  0.020  1.090
 0S3  C09  H3   single    0.970  0.020  1.090
 0S3  C09  H4   single    0.970  0.020  1.090
 0S3  C10  H5   single    0.970  0.020  1.090
 0S3  C10  H6   single    0.970  0.020  1.090
 0S3  C10  H7   single    0.970  0.020  1.090
 0S3  C11  H8   single    0.970  0.020  1.090
 0S3  C11  H9   single    0.970  0.020  1.090
 0S3  C11  H10  single    0.970  0.020  1.090
 0S3  C15  H11  single    0.970  0.020  1.090
 0S3  C17  H12  single    0.970  0.020  1.090
 0S3  C17  H13  single    0.970  0.020  1.090
 0S3  C18  H14  single    0.970  0.020  1.090
 0S3  C18  H15  single    0.970  0.020  1.090
 0S3  C19  H16  single    0.970  0.020  1.090
 0S3  C20  H17  single    0.970  0.020  1.090
 0S3  C20  H18  single    0.970  0.020  1.090
 0S3  C21  H19  single    0.970  0.020  1.090
 0S3  C21  H20  single    0.970  0.020  1.090
 0S3  C22  H21  single    0.970  0.020  1.090
 0S3  C22  H22  single    0.970  0.020  1.090
 0S3  C22  H23  single    0.970  0.020  1.090
 0S3  C23  H24  single    0.970  0.020  1.090
 0S3  C23  H25  single    0.970  0.020  1.090
 0S3  C23  H26  single    0.970  0.020  1.090
 0S3  C24  H27  single    0.970  0.020  1.090
 0S3  C24  H28  single    0.970  0.020  1.090
 0S3  C24  H29  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
 0S3  H1   C01  C05  123.31  3.000
 0S3  H1   C01  C02  124.18  3.000
 0S3  C05  C01  C02  112.49  3.000
 0S3  N12  C02  C03  125.30  3.000
 0S3  N12  C02  C01  121.31  3.000
 0S3  C03  C02  C01  113.38  3.000
 0S3  C25  C03  S04  117.18  3.000
 0S3  C25  C03  C02  132.30  3.000
 0S3  S04  C03  C02  110.52  3.000
 0S3  C05  S04  C03   92.81  3.000
 0S3  C06  C05  S04  120.03  3.000
 0S3  C06  C05  C01  129.05  3.000
 0S3  S04  C05  C01  110.80  3.000
 0S3  C07  C06  C05  180.00  3.000
 0S3  C08  C07  C06  180.00  3.000
 0S3  C11  C08  C10  110.11  3.000
 0S3  C10  C08  C09  109.72  3.000
 0S3  C11  C08  C09  109.29  3.000
 0S3  C09  C08  C07  108.81  3.000
 0S3  C10  C08  C07  109.69  3.000
 0S3  C11  C08  C07  109.20  3.000
 0S3  H4   C09  H3   108.06  3.000
 0S3  H4   C09  H2   107.99  3.000
 0S3  H3   C09  H2   107.90  3.000
 0S3  H4   C09  C08  111.59  3.000
 0S3  H3   C09  C08  111.50  3.000
 0S3  H2   C09  C08  109.67  3.000
 0S3  H7   C10  H6   108.27  3.000
 0S3  H7   C10  H5   108.23  3.000
 0S3  H6   C10  H5   108.17  3.000
 0S3  H7   C10  C08  109.64  3.000
 0S3  H6   C10  C08  111.22  3.000
 0S3  H5   C10  C08  111.22  3.000
 0S3  H10  C11  H9   108.16  3.000
 0S3  H10  C11  H8   108.24  3.000
 0S3  H9   C11  H8   108.13  3.000
 0S3  H10  C11  C08  109.70  3.000
 0S3  H9   C11  C08  110.89  3.000
 0S3  H8   C11  C08  111.62  3.000
 0S3  N14  N12  C13  122.27  3.000
 0S3  N14  N12  C02  113.47  3.000
 0S3  C13  N12  C02  123.73  3.000
 0S3  O16  C13  C15  121.26  3.000
 0S3  O16  C13  N12  121.39  3.000
 0S3  C15  C13  N12  116.88  3.000
 0S3  C24  N14  C23  114.54  3.000
 0S3  C24  N14  N12  114.83  3.000
 0S3  C23  N14  N12  114.50  3.000
 0S3  H11  C15  C21  107.20  3.000
 0S3  H11  C15  C17  108.48  3.000
 0S3  C21  C15  C17  110.50  3.000
 0S3  H11  C15  C13  110.65  3.000
 0S3  C21  C15  C13  107.49  3.000
 0S3  C17  C15  C13  112.40  3.000
 0S3  H13  C17  H12  107.03  3.000
 0S3  H13  C17  C18  109.29  3.000
 0S3  H12  C17  C18  110.12  3.000
 0S3  H13  C17  C15  109.81  3.000
 0S3  H12  C17  C15  109.81  3.000
 0S3  C18  C17  C15  110.71  3.000
 0S3  H15  C18  H14  106.29  3.000
 0S3  H15  C18  C19  109.72  3.000
 0S3  H14  C18  C19  108.95  3.000
 0S3  H15  C18  C17  109.73  3.000
 0S3  H14  C18  C17  109.59  3.000
 0S3  C19  C18  C17  112.36  3.000
 0S3  H16  C19  C22  108.00  3.000
 0S3  H16  C19  C20  108.01  3.000
 0S3  C22  C19  C20  111.31  3.000
 0S3  H16  C19  C18  107.71  3.000
 0S3  C20  C19  C18  110.27  3.000
 0S3  C22  C19  C18  111.39  3.000
 0S3  H18  C20  H17  106.43  3.000
 0S3  H18  C20  C21  109.45  3.000
 0S3  H17  C20  C21  109.22  3.000
 0S3  H18  C20  C19  110.16  3.000
 0S3  H17  C20  C19  109.17  3.000
 0S3  C21  C20  C19  112.25  3.000
 0S3  H20  C21  H19  106.90  3.000
 0S3  H20  C21  C20  109.82  3.000
 0S3  H19  C21  C20  109.70  3.000
 0S3  H20  C21  C15  110.09  3.000
 0S3  H19  C21  C15  109.18  3.000
 0S3  C20  C21  C15  111.06  3.000
 0S3  H23  C22  H22  107.54  3.000
 0S3  H23  C22  H21  108.04  3.000
 0S3  H22  C22  H21  107.54  3.000
 0S3  H23  C22  C19  110.80  3.000
 0S3  H22  C22  C19  111.37  3.000
 0S3  H21  C22  C19  111.37  3.000
 0S3  H26  C23  H25  107.60  3.000
 0S3  H26  C23  H24  108.77  3.000
 0S3  H25  C23  H24  107.98  3.000
 0S3  H26  C23  N14  109.63  3.000
 0S3  H25  C23  N14  108.36  3.000
 0S3  H24  C23  N14  114.30  3.000
 0S3  H29  C24  H28  108.11  3.000
 0S3  H29  C24  H27  108.91  3.000
 0S3  H28  C24  H27  108.12  3.000
 0S3  H29  C24  N14  113.78  3.000
 0S3  H28  C24  N14  108.27  3.000
 0S3  H27  C24  N14  109.50  3.000
 0S3  O27  C25  O26  127.04  3.000
 0S3  O27  C25  C03  114.85  3.000
 0S3  O26  C25  C03  118.10  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
 0S3  CONST_01  C03  S04  C05  C01     0.00   0.0  0
 0S3  CONST_02  S04  C03  C02  C01     0.00   0.0  0
 0S3  CONST_03  C05  S04  C03  C02     0.00   0.0  0
 0S3  CONST_04  S04  C05  C01  C02     0.00   0.0  0
 0S3  CONST_05  C05  C01  C02  C03     0.00   0.0  0
 0S3  CONST_06  C25  C03  C02  C01   180.00   0.0  0
 0S3  CONST_07  C06  C05  C01  C02   180.00   0.0  0
 0S3  CONST_08  C06  C05  S04  C03   180.00   0.0  0
 0S3  CONST_09  N12  C02  C03  S04   180.00   0.0  0
 0S3  CONST_10  C25  C03  S04  C05   180.00   0.0  0
 0S3  CONST_11  N12  C02  C01  C05   180.00   0.0  0
 0S3  CONST_12  H1   C01  C02  C03   180.00   0.0  0
 0S3  CONST_19  C15  C13  N12  N14   180.00   0.0  0
 0S3  CONST_22  O16  C13  N12  N14     0.00   0.0  0
 0S3  Var_01    C19  C18  C17  C15   -56.43  30.0  1
 0S3  Var_02    C19  C20  C21  C15    55.50  30.0  1
 0S3  Var_03    O26  C25  C03  C02     3.26  30.0  2
 0S3  Var_04    C11  C08  C07  C06   -83.52  30.0  1
 0S3  Var_05    H8   C11  C08  C07   -59.10  30.0  3
 0S3  Var_06    H5   C10  C08  C07   -57.85  30.0  3
 0S3  Var_07    H2   C09  C08  C07  -179.65  30.0  3
 0S3  Var_08    H24  C23  N14  N12    77.15  30.0  3
 0S3  Var_09    H27  C24  N14  N12    46.71  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
 0S3  chir_01  C15  C17  C21  C13  negativ
 0S3  chir_02  C19  C22  C18  C20  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
 0S3  plan-1  C01  0.020
 0S3  plan-1  C02  0.020
 0S3  plan-1  C03  0.020
 0S3  plan-1  S04  0.020
 0S3  plan-1  C05  0.020
 0S3  plan-1  C06  0.020
 0S3  plan-1  C07  0.020
 0S3  plan-1  N12  0.020
 0S3  plan-1  C25  0.020
 0S3  plan-1  H1   0.020
 0S3  plan-2  C02  0.020
 0S3  plan-2  N12  0.020
 0S3  plan-2  C13  0.020
 0S3  plan-2  N14  0.020
 0S3  plan-2  C15  0.020
 0S3  plan-2  O16  0.020
 0S3  plan-3  C03  0.020
 0S3  plan-3  C25  0.020
 0S3  plan-3  O26  0.020
 0S3  plan-3  O27  0.020

