# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 23:04:04 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 1-(4-chlorophenyl)-~{N}-[2-(4-methoxyphenyl)-5,5-bis(oxidanylidene)-4,6-dihydrothieno[3,4-c]pyrazol-3-yl]cyclopentane-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)n2nc3C[S](=O)(=O)Cc3c2NC(=O)C4(CCCC4)c5ccc(Cl)cc5
#
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
 DYX  DYX  1-(4-chlorophenyl)-~{N}-[2-(4-methoxyphenyl)-5,5-bis(oxidanylidene)-4,6-dihydrothieno[3,4-c]pyrazol-3-yl]cyclopentane-1-carboxamide  ligand  57  33  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DYX
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
 DYX  C10  C   CR16  0  -0.241  -0.3406  -3.3421   1.1411
 DYX  C13  C   CR16  0  -0.380   0.9922  -3.8336  -1.2531
 DYX  C17  C   CH2   0  -0.650  -4.9089  -0.3451   0.7106
 DYX  C22  C   CR5   0  -0.331   1.5119   1.5329  -1.6171
 DYX  C24  C   CH2   0  -0.435   1.3884   2.1127  -4.0011
 DYX  C26  C   CH2   0  -0.450   2.0708   0.3650  -2.4528
 DYX  C28  C   CR16  0  -0.297   1.8707   2.9140   0.4490
 DYX  C04  C   CR5   0   0.603  -1.4411  -0.2656  -0.1659
 DYX  C05  C   CR55  0  -0.133  -2.6582   0.3404   0.0189
 DYX  C06  C   CR55  0   0.262  -3.5088  -0.7147   0.3836
 DYX  C09  C   CR6   0   0.248  -0.6549  -2.6074   0.0024
 DYX  C11  C   CR16  0  -0.343   0.6283  -4.3224   1.0811
 DYX  C12  C   CR6   0   0.397   1.3121  -4.5702  -0.1138
 DYX  C14  C   CR16  0  -0.263   0.0013  -2.8635  -1.1905
 DYX  C19  C   CH2   0  -0.642  -3.2474   1.6998   0.0416
 DYX  C23  C   CH2   0  -0.411   1.6575   2.7032  -2.6049
 DYX  C25  C   CH2   0  -0.457   1.4560   0.5812  -3.8331
 DYX  C27  C   CR6   0   0.166   2.2101   1.7839  -0.2969
 DYX  C29  C   CR16  0  -0.196   2.4717   3.1823   1.6666
 DYX  C30  C   CR6   0  -0.055   3.4285   2.3036   2.1544
 DYX  C31  C   CR16  0  -0.186   3.7821   1.1722   1.4416
 DYX  C32  C   CR16  0  -0.340   3.1692   0.9197   0.2206
 DYX  N03  N   NH1   0  -0.742  -0.1898   0.2163  -0.4863
 DYX  N07  N   N     0  -0.291  -2.8980  -1.8725   0.4326
 DYX  N08  N   NR5   0  -0.451  -1.6372  -1.5907   0.0667
 DYX  O02  O   O     0  -0.423  -0.8836   1.8817  -1.8381
 DYX  O15  O   O2    0  -0.465   2.2501  -5.5274  -0.0711
 DYX  S18  S   S     0   1.198  -4.6946   1.4194   1.1224
 DYX  CL1  CL  CL    0  -0.127   4.1882   2.6294   3.6772
 DYX  H1   H   HCR6  0   0.277  -0.8533  -3.1449   2.0735
 DYX  H2   H   HCR6  0   0.291   1.4882  -4.0054  -2.1981
 DYX  H3   H   HCH2  0   0.328  -5.5822  -0.4132  -0.1454
 DYX  H4   H   HCH2  0   0.331  -5.3410  -0.8579   1.5692
 DYX  H5   H   HCH2  0   0.236   0.4164   2.4211  -4.3836
 DYX  H6   H   HCH2  0   0.235   2.1349   2.4657  -4.7128
 DYX  H7   H   HCH2  0   0.259   3.1574   0.4693  -2.5061
 DYX  H8   H   HCH2  0   0.239   1.8641  -0.6266  -2.0440
 DYX  H9   H   HCR6  0   0.266   1.1233   3.6047   0.0779
 DYX  H10  H   HCR6  0   0.275   0.8743  -4.8978   1.9644
 DYX  H11  H   HCR6  0   0.285  -0.2630  -2.3156  -2.0863
 DYX  H12  H   HCH3  0   0.233   2.3622  -6.1679  -2.0533
 DYX  H13  H   HCH3  0   0.233   3.5449  -4.9223  -1.5892
 DYX  H14  H   HCH3  0   0.264   3.7101  -6.5776  -0.9770
 DYX  H15  H   HCH2  0   0.319  -2.6351   2.4741   0.5029
 DYX  H16  H   HCH2  0   0.318  -3.6089   2.0422  -0.9286
 DYX  H17  H   HCH2  0   0.249   1.0090   3.5446  -2.3635
 DYX  H18  H   HCH2  0   0.247   2.6856   3.0642  -2.5384
 DYX  H19  H   HCH2  0   0.234   0.4554   0.1445  -3.8742
 DYX  H20  H   HCH2  0   0.247   2.0393   0.0949  -4.6146
 DYX  H21  H   HCR6  0   0.283   2.1949   4.0645   2.2276
 DYX  H22  H   HCR6  0   0.283   4.5270   0.4885   1.8254
 DYX  H23  H   HCR6  0   0.273   3.4648   0.0303  -0.3206
 DYX  H24  H   HNH1  0   0.414   0.6059  -0.2450  -0.0685
 DYX  O20  O   OS    0  -0.674  -4.2470   1.5014   2.5098
 DYX  C16  C   CH3   0  -0.440   2.9966  -5.8017  -1.2422
 DYX  O21  O   OS    0  -0.666  -5.8436   2.2162   0.7114
 DYX  C01  C   C     0   0.598   0.0296   1.2603  -1.3402

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
 DYX  O21  S18  double    1.457  0.020  1.457
 DYX  O20  S18  double    1.460  0.020  1.460
 DYX  S18  C19  single    1.828  0.020  1.828
 DYX  S18  C17  single    1.825  0.020  1.825
 DYX  C19  C05  single    1.482  0.020  1.482
 DYX  C17  C06  single    1.484  0.020  1.484
 DYX  C05  C06  aromatic  1.403  0.020  1.403
 DYX  C05  C04  aromatic  1.372  0.020  1.372
 DYX  C26  C25  single    1.526  0.020  1.526
 DYX  C26  C22  single    1.541  0.020  1.541
 DYX  C06  N07  aromatic  1.310  0.020  1.310
 DYX  C04  N03  single    1.379  0.020  1.379
 DYX  C04  N08  aromatic  1.360  0.020  1.360
 DYX  N07  N08  aromatic  1.343  0.020  1.343
 DYX  C25  C24  single    1.542  0.020  1.542
 DYX  N03  C01  single    1.366  0.020  1.366
 DYX  C10  C11  aromatic  1.380  0.020  1.380
 DYX  C10  C09  aromatic  1.391  0.020  1.391
 DYX  N08  C09  single    1.415  0.020  1.415
 DYX  C01  O02  double    1.212  0.020  1.212
 DYX  C01  C22  single    1.532  0.020  1.532
 DYX  C11  C12  aromatic  1.399  0.020  1.399
 DYX  C09  C14  aromatic  1.385  0.020  1.385
 DYX  C22  C23  single    1.538  0.020  1.538
 DYX  C22  C27  single    1.514  0.020  1.514
 DYX  C24  C23  single    1.540  0.020  1.540
 DYX  C32  C27  aromatic  1.391  0.020  1.391
 DYX  C32  C31  aromatic  1.389  0.020  1.389
 DYX  C12  O15  single    1.341  0.020  1.341
 DYX  C12  C13  aromatic  1.394  0.020  1.394
 DYX  C14  C13  aromatic  1.388  0.020  1.388
 DYX  C27  C28  aromatic  1.396  0.020  1.396
 DYX  O15  C16  single    1.416  0.020  1.416
 DYX  C31  C30  aromatic  1.383  0.020  1.383
 DYX  C28  C29  aromatic  1.384  0.020  1.384
 DYX  C30  C29  aromatic  1.388  0.020  1.388
 DYX  C30  CL1  single    1.733  0.020  1.733
 DYX  C10  H1   single    0.930  0.020  1.080
 DYX  C13  H2   single    0.930  0.020  1.080
 DYX  C17  H3   single    0.970  0.020  1.090
 DYX  C17  H4   single    0.970  0.020  1.090
 DYX  C24  H5   single    0.970  0.020  1.090
 DYX  C24  H6   single    0.970  0.020  1.090
 DYX  C26  H7   single    0.970  0.020  1.090
 DYX  C26  H8   single    0.970  0.020  1.090
 DYX  C28  H9   single    0.930  0.020  1.080
 DYX  C11  H10  single    0.930  0.020  1.080
 DYX  C14  H11  single    0.930  0.020  1.080
 DYX  C16  H12  single    0.970  0.020  1.090
 DYX  C16  H13  single    0.970  0.020  1.090
 DYX  C16  H14  single    0.970  0.020  1.090
 DYX  C19  H15  single    0.970  0.020  1.090
 DYX  C19  H16  single    0.970  0.020  1.090
 DYX  C23  H17  single    0.970  0.020  1.090
 DYX  C23  H18  single    0.970  0.020  1.090
 DYX  C25  H19  single    0.970  0.020  1.090
 DYX  C25  H20  single    0.970  0.020  1.090
 DYX  C29  H21  single    0.930  0.020  1.080
 DYX  C31  H22  single    0.930  0.020  1.080
 DYX  C32  H23  single    0.930  0.020  1.080
 DYX  N03  H24  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
 DYX  H1   C10  C11  119.98  3.000
 DYX  H1   C10  C09  120.14  3.000
 DYX  C11  C10  C09  119.89  3.000
 DYX  H2   C13  C14  118.56  3.000
 DYX  H2   C13  C12  121.69  3.000
 DYX  C14  C13  C12  119.75  3.000
 DYX  H4   C17  H3   110.13  3.000
 DYX  H4   C17  S18  108.90  3.000
 DYX  H3   C17  S18  108.06  3.000
 DYX  H4   C17  C06  115.49  3.000
 DYX  H3   C17  C06  113.18  3.000
 DYX  S18  C17  C06  100.35  3.000
 DYX  C27  C22  C23  112.96  3.000
 DYX  C27  C22  C01  108.54  3.000
 DYX  C23  C22  C01  110.06  3.000
 DYX  C27  C22  C26  115.54  3.000
 DYX  C23  C22  C26  101.19  3.000
 DYX  C01  C22  C26  108.30  3.000
 DYX  H6   C24  H5   106.87  3.000
 DYX  H6   C24  C25  111.27  3.000
 DYX  H5   C24  C25  111.01  3.000
 DYX  H6   C24  C23  110.38  3.000
 DYX  H5   C24  C23  111.46  3.000
 DYX  C25  C24  C23  105.93  3.000
 DYX  H8   C26  H7   107.04  3.000
 DYX  H8   C26  C25  113.00  3.000
 DYX  H7   C26  C25  110.04  3.000
 DYX  H8   C26  C22  114.61  3.000
 DYX  H7   C26  C22  108.34  3.000
 DYX  C25  C26  C22  103.71  3.000
 DYX  H9   C28  C29  118.51  3.000
 DYX  H9   C28  C27  120.06  3.000
 DYX  C29  C28  C27  121.43  3.000
 DYX  N08  C04  N03  120.76  3.000
 DYX  N08  C04  C05  106.23  3.000
 DYX  N03  C04  C05  133.00  3.000
 DYX  C19  C05  C06  116.40  3.000
 DYX  C06  C05  C04  103.92  3.000
 DYX  C19  C05  C04  139.46  3.000
 DYX  N07  C06  C05  113.05  3.000
 DYX  N07  C06  C17  130.66  3.000
 DYX  C05  C06  C17  116.21  3.000
 DYX  N08  C09  C14  120.05  3.000
 DYX  C14  C09  C10  120.01  3.000
 DYX  N08  C09  C10  119.93  3.000
 DYX  H10  C11  C12  119.46  3.000
 DYX  H10  C11  C10  120.12  3.000
 DYX  C12  C11  C10  120.42  3.000
 DYX  O15  C12  C11  116.19  3.000
 DYX  O15  C12  C13  124.32  3.000
 DYX  C11  C12  C13  119.50  3.000
 DYX  H11  C14  C09  120.21  3.000
 DYX  H11  C14  C13  119.37  3.000
 DYX  C09  C14  C13  120.41  3.000
 DYX  H16  C19  H15  109.86  3.000
 DYX  H16  C19  S18  108.17  3.000
 DYX  H15  C19  S18  107.67  3.000
 DYX  H16  C19  C05  113.97  3.000
 DYX  H15  C19  C05  115.78  3.000
 DYX  S18  C19  C05  100.55  3.000
 DYX  H18  C23  H17  106.95  3.000
 DYX  H18  C23  C24  110.28  3.000
 DYX  H17  C23  C24  113.15  3.000
 DYX  H18  C23  C22  107.55  3.000
 DYX  H17  C23  C22  112.89  3.000
 DYX  C24  C23  C22  105.90  3.000
 DYX  H20  C25  H19  106.55  3.000
 DYX  H20  C25  C26  111.70  3.000
 DYX  H19  C25  C26  110.26  3.000
 DYX  H20  C25  C24  112.86  3.000
 DYX  H19  C25  C24  110.65  3.000
 DYX  C26  C25  C24  104.88  3.000
 DYX  C32  C27  C28  118.16  3.000
 DYX  C28  C27  C22  119.20  3.000
 DYX  C32  C27  C22  122.63  3.000
 DYX  H21  C29  C30  120.71  3.000
 DYX  H21  C29  C28  120.22  3.000
 DYX  C30  C29  C28  119.07  3.000
 DYX  CL1  C30  C31  119.65  3.000
 DYX  CL1  C30  C29  119.49  3.000
 DYX  C31  C30  C29  120.87  3.000
 DYX  H22  C31  C32  120.05  3.000
 DYX  H22  C31  C30  120.68  3.000
 DYX  C32  C31  C30  119.26  3.000
 DYX  H23  C32  C31  117.93  3.000
 DYX  H23  C32  C27  120.86  3.000
 DYX  C31  C32  C27  121.21  3.000
 DYX  H24  N03  C04  117.33  3.000
 DYX  H24  N03  C01  118.74  3.000
 DYX  C04  N03  C01  123.92  3.000
 DYX  N08  N07  C06  104.01  3.000
 DYX  N07  N08  C09  120.89  3.000
 DYX  C09  N08  C04  126.32  3.000
 DYX  N07  N08  C04  112.75  3.000
 DYX  C16  O15  C12  118.74  3.000
 DYX  O21  S18  O20  118.61  3.000
 DYX  O20  S18  C19  108.09  3.000
 DYX  O21  S18  C19  111.94  3.000
 DYX  C19  S18  C17   96.19  3.000
 DYX  O20  S18  C17  107.75  3.000
 DYX  O21  S18  C17  111.87  3.000
 DYX  H14  C16  H13  108.81  3.000
 DYX  H14  C16  H12  108.84  3.000
 DYX  H13  C16  H12  108.98  3.000
 DYX  H14  C16  O15  106.42  3.000
 DYX  H13  C16  O15  111.79  3.000
 DYX  H12  C16  O15  111.89  3.000
 DYX  O02  C01  N03  121.84  3.000
 DYX  O02  C01  C22  124.30  3.000
 DYX  N03  C01  C22  113.84  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
 DYX  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 DYX  CONST_04  C13  C14  C09  C10     0.00   0.0  0
 DYX  CONST_05  N08  C09  C14  C13   180.00   0.0  0
 DYX  CONST_06  C31  C32  C27  C28     0.00   0.0  0
 DYX  CONST_07  C31  C30  C29  C28     0.00   0.0  0
 DYX  CONST_08  N07  C06  C05  C04     0.00   0.0  0
 DYX  CONST_09  C06  N07  N08  C04     0.00   0.0  0
 DYX  CONST_11  N08  N07  C06  C05     0.00   0.0  0
 DYX  CONST_12  N07  N08  C04  C05     0.00   0.0  0
 DYX  CONST_13  C09  N08  C04  C05   180.00   0.0  0
 DYX  CONST_14  N08  C04  C05  C06     0.00   0.0  0
 DYX  CONST_15  C09  N08  N07  C06   180.00   0.0  0
 DYX  CONST_16  C12  C11  C10  C09     0.00   0.0  0
 DYX  CONST_17  C12  C13  C14  C09     0.00   0.0  0
 DYX  CONST_18  N08  C09  C10  C11   180.00   0.0  0
 DYX  CONST_19  C14  C09  C10  C11     0.00   0.0  0
 DYX  CONST_20  C14  C13  C12  C11     0.00   0.0  0
 DYX  CONST_22  C30  C31  C32  C27     0.00   0.0  0
 DYX  CONST_23  C30  C29  C28  C27     0.00   0.0  0
 DYX  CONST_24  C32  C27  C28  C29     0.00   0.0  0
 DYX  CONST_25  C32  C31  C30  C29     0.00   0.0  0
 DYX  CONST_26  C31  C32  C27  C22   180.00   0.0  0
 DYX  CONST_27  C29  C28  C27  C22   180.00   0.0  0
 DYX  CONST_28  O15  C12  C11  C10   180.00   0.0  0
 DYX  CONST_29  CL1  C30  C29  C28   180.00   0.0  0
 DYX  CONST_30  N03  C04  C05  C06   180.00   0.0  0
 DYX  CONST_31  N03  C04  N08  C09     0.00   0.0  0
 DYX  CONST_32  O15  C12  C13  C14   180.00   0.0  0
 DYX  CONST_33  N03  C04  C05  C19     0.00   0.0  0
 DYX  CONST_34  CL1  C30  C31  C32   180.00   0.0  0
 DYX  CONST_35  N07  N08  C04  N03   180.00   0.0  0
 DYX  CONST_36  H11  C14  C09  C10   180.00   0.0  0
 DYX  CONST_37  H10  C11  C12  C13   180.00   0.0  0
 DYX  CONST_38  H23  C32  C27  C22     0.00   0.0  0
 DYX  CONST_39  H9   C28  C27  C22     0.00   0.0  0
 DYX  CONST_40  H2   C13  C14  C09   180.00   0.0  0
 DYX  CONST_41  H1   C10  C11  C12   180.00   0.0  0
 DYX  CONST_42  H22  C31  C32  C27   180.00   0.0  0
 DYX  CONST_43  H21  C29  C28  C27   180.00   0.0  0
 DYX  CONST_44  C04  N03  C01  C22   180.00   0.0  0
 DYX  CONST_48  O02  C01  N03  C04     0.00   0.0  0
 DYX  Var_01    C05  C19  S18  C17   -27.90  30.0  1
 DYX  Var_02    C24  C25  C26  C22    34.87  30.0  1
 DYX  Var_03    C25  C24  C23  C22   -14.22  30.0  1
 DYX  Var_04    C23  C24  C25  C26   -12.71  30.0  1
 DYX  Var_05    S18  C19  C05  C04  -154.13  30.0  1
 DYX  Var_06    S18  C17  C06  C05   -21.89  30.0  1
 DYX  Var_07    C19  S18  C17  C06    28.66  30.0  1
 DYX  Var_08    H12  C16  O15  C12   -62.97  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
 DYX  chir_01  C22  C26  C23  C27  positiv

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
 DYX  plan-1  C10  0.020
 DYX  plan-1  C13  0.020
 DYX  plan-1  C09  0.020
 DYX  plan-1  C11  0.020
 DYX  plan-1  C12  0.020
 DYX  plan-1  C14  0.020
 DYX  plan-1  N08  0.020
 DYX  plan-1  O15  0.020
 DYX  plan-1  H1   0.020
 DYX  plan-1  H2   0.020
 DYX  plan-1  H10  0.020
 DYX  plan-1  H11  0.020
 DYX  plan-2  C22  0.020
 DYX  plan-2  C28  0.020
 DYX  plan-2  C27  0.020
 DYX  plan-2  C29  0.020
 DYX  plan-2  C30  0.020
 DYX  plan-2  C31  0.020
 DYX  plan-2  C32  0.020
 DYX  plan-2  CL1  0.020
 DYX  plan-2  H9   0.020
 DYX  plan-2  H21  0.020
 DYX  plan-2  H22  0.020
 DYX  plan-2  H23  0.020
 DYX  plan-3  C22  0.020
 DYX  plan-3  C04  0.020
 DYX  plan-3  N03  0.020
 DYX  plan-3  O02  0.020
 DYX  plan-3  H24  0.020
 DYX  plan-3  C01  0.020
 DYX  plan-4  C17  0.020
 DYX  plan-4  C04  0.020
 DYX  plan-4  C05  0.020
 DYX  plan-4  C06  0.020
 DYX  plan-4  C09  0.020
 DYX  plan-4  C19  0.020
 DYX  plan-4  N03  0.020
 DYX  plan-4  N07  0.020
 DYX  plan-4  N08  0.020

