# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 18:14:04 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 3-[(2R)-2-cyclohexyl-5-oxopyrrolidin-1-yl]-5-phenylthiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1sc(cc1N2[C@H](CCC2=O)C3CCCCC3)c4ccccc4
#
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
 33J  33J  '3-[(2R)-2-cyclohexyl-5-oxopyrrolidin-1-yl]-5-phenylthiophene-2-carboxylic acid'  ligand  48  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_33J
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
 33J  C1   C  C      0   0.416   0.7940   3.1455   0.4230
 33J  C2   C  CR5    0  -0.386  -0.0426   1.9524   0.0435
 33J  C3   C  CR5    0  -0.212  -1.9930   0.4237  -0.2200
 33J  O1   O  OC    -1  -0.593   0.1657   4.0573   0.9943
 33J  O2   O  O      0  -0.565   2.0040   3.1084   0.1409
 33J  C11  C  CH2    0  -0.438   1.8102  -2.5708  -0.5759
 33J  C12  C  CH2    0  -0.425   1.2221  -3.8284   0.0555
 33J  C13  C  CH2    0  -0.430   2.1269  -4.3520   1.1665
 33J  C14  C  CH2    0  -0.430   2.4020  -3.2741   2.2109
 33J  C15  C  CH2    0  -0.420   2.9594  -2.0038   1.5735
 33J  C16  C  CR6    0   0.150  -3.3131  -0.2033  -0.1737
 33J  C17  C  CR16   0  -0.325  -4.2712   0.1889   0.7649
 33J  C18  C  CR16   0  -0.236  -5.5161  -0.4202   0.8068
 33J  C19  C  CR16   0  -0.269  -5.8277  -1.4405  -0.0815
 33J  C20  C  CR16   0  -0.233  -4.8823  -1.8414  -1.0175
 33J  C21  C  CR16   0  -0.329  -3.6412  -1.2273  -1.0673
 33J  S1   S  S2     0   0.225  -1.7071   1.9877   0.4526
 33J  C4   C  CR15   0  -0.261  -0.8385  -0.0840  -0.7520
 33J  C5   C  CR5    0   0.412   0.2727   0.7827  -0.5972
 33J  N1   N  NR5    0  -0.586   1.5744   0.4537  -1.0174
 33J  C6   C  CR5    0   0.526   2.1774   1.1373  -2.0249
 33J  C7   C  CH2    0  -0.583   3.6667   0.9359  -1.8974
 33J  C8   C  CH2    0  -0.489   3.8142  -0.1985  -0.8916
 33J  C9   C  CR15   0  -0.026   2.5193  -0.1494  -0.0735
 33J  C10  C  CH1    0  -0.248   2.0269  -1.4858   0.4785
 33J  H4   H  HCH2   0   0.208   0.2305  -3.6030   0.4637
 33J  H5   H  HCH2   0   0.226   1.0768  -4.5976  -0.7071
 33J  H6   H  HCH2   0   0.226   1.6825  -5.2320   1.6380
 33J  H7   H  HCH2   0   0.208   3.0762  -4.6786   0.7277
 33J  H8   H  HCH2   0   0.210   1.4691  -3.0305   2.7313
 33J  H9   H  HCH2   0   0.226   3.0922  -3.6495   2.9704
 33J  H10  H  HCH2   0   0.226   3.1035  -1.2341   2.3376
 33J  H11  H  HCH2   0   0.216   3.9480  -2.2119   1.1478
 33J  H12  H  HCR6   0   0.253  -4.0451   0.9669   1.4845
 33J  H13  H  HCR6   0   0.260  -6.2417  -0.0994   1.5428
 33J  H14  H  HCR6   0   0.259  -6.7981  -1.9179  -0.0464
 33J  H15  H  HCR6   0   0.260  -5.1134  -2.6323  -1.7192
 33J  H16  H  HCR6   0   0.255  -2.9269  -1.5414  -1.8176
 33J  H17  H  HCR5   0   0.261  -0.7677  -1.0558  -1.2207
 33J  H18  H  HCH2   0   0.266   4.1334   0.7413  -2.8625
 33J  H19  H  HCH2   0   0.271   4.0779   1.8732  -1.5131
 33J  H20  H  HCH2   0   0.245   3.8983  -1.1501  -1.4166
 33J  H21  H  HCH2   0   0.254   4.6921  -0.0980  -0.2561
 33J  H22  H  HCR5   0   0.240   2.6412   0.5438   0.7680
 33J  H23  H  HCH1   0   0.225   1.0565  -1.2902   0.9554
 33J  H2   H  HCH2   0   0.215   2.7657  -2.8343  -1.0427
 33J  O3   O  O      0  -0.487   1.6000   1.7955  -2.8690
 33J  H3   H  HCH2   0   0.232   1.1668  -2.2109  -1.3825

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
 33J  C13  C12  single    1.526  0.020  1.526
 33J  C13  C14  single    1.526  0.020  1.526
 33J  C8   C7   single    1.523  0.020  1.523
 33J  C8   C9   single    1.532  0.020  1.532
 33J  C11  C12  single    1.525  0.020  1.525
 33J  C11  C10  single    1.528  0.020  1.528
 33J  C7   C6   single    1.508  0.020  1.508
 33J  C14  C15  single    1.527  0.020  1.527
 33J  C9   C10  single    1.527  0.020  1.527
 33J  C9   N1   single    1.465  0.020  1.465
 33J  C15  C10  single    1.529  0.020  1.529
 33J  C6   O3   double    1.216  0.020  1.216
 33J  C6   N1   single    1.359  0.020  1.359
 33J  N1   C5   single    1.407  0.020  1.407
 33J  O2   C1   deloc     1.243  0.020  1.243
 33J  C5   C2   aromatic  1.370  0.020  1.370
 33J  C5   C4   aromatic  1.418  0.020  1.418
 33J  C1   C2   single    1.506  0.020  1.506
 33J  C1   O1   deloc     1.246  0.020  1.246
 33J  C2   S1   aromatic  1.714  0.020  1.714
 33J  C4   C3   aromatic  1.369  0.020  1.369
 33J  C3   S1   aromatic  1.726  0.020  1.726
 33J  C3   C16  single    1.462  0.020  1.462
 33J  C21  C16  aromatic  1.398  0.020  1.398
 33J  C21  C20  aromatic  1.386  0.020  1.386
 33J  C16  C17  aromatic  1.397  0.020  1.397
 33J  C20  C19  aromatic  1.389  0.020  1.389
 33J  C17  C18  aromatic  1.387  0.020  1.387
 33J  C19  C18  aromatic  1.388  0.020  1.388
 33J  C11  H2   single    0.970  0.020  1.090
 33J  C11  H3   single    0.970  0.020  1.090
 33J  C12  H4   single    0.970  0.020  1.090
 33J  C12  H5   single    0.970  0.020  1.090
 33J  C13  H6   single    0.970  0.020  1.090
 33J  C13  H7   single    0.970  0.020  1.090
 33J  C14  H8   single    0.970  0.020  1.090
 33J  C14  H9   single    0.970  0.020  1.090
 33J  C15  H10  single    0.970  0.020  1.090
 33J  C15  H11  single    0.970  0.020  1.090
 33J  C17  H12  single    0.930  0.020  1.080
 33J  C18  H13  single    0.930  0.020  1.080
 33J  C19  H14  single    0.930  0.020  1.080
 33J  C20  H15  single    0.930  0.020  1.080
 33J  C21  H16  single    0.930  0.020  1.080
 33J  C4   H17  single    0.930  0.020  1.080
 33J  C7   H18  single    0.970  0.020  1.090
 33J  C7   H19  single    0.970  0.020  1.090
 33J  C8   H20  single    0.970  0.020  1.090
 33J  C8   H21  single    0.970  0.020  1.090
 33J  C9   H22  single    0.970  0.020  1.090
 33J  C10  H23  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
 33J  O2   C1   O1   128.08  3.000
 33J  O1   C1   C2   114.54  3.000
 33J  O2   C1   C2   117.39  3.000
 33J  C5   C2   S1   110.64  3.000
 33J  S1   C2   C1   117.58  3.000
 33J  C5   C2   C1   131.78  3.000
 33J  C4   C3   S1   110.35  3.000
 33J  S1   C3   C16  121.71  3.000
 33J  C4   C3   C16  127.93  3.000
 33J  H3   C11  H2   106.15  3.000
 33J  H3   C11  C10  111.03  3.000
 33J  H2   C11  C10  109.94  3.000
 33J  H3   C11  C12  110.50  3.000
 33J  H2   C11  C12  108.32  3.000
 33J  C10  C11  C12  110.76  3.000
 33J  H5   C12  H4   106.53  3.000
 33J  H5   C12  C13  110.21  3.000
 33J  H4   C12  C13  109.63  3.000
 33J  H5   C12  C11  110.05  3.000
 33J  H4   C12  C11  109.49  3.000
 33J  C13  C12  C11  110.84  3.000
 33J  H7   C13  H6   106.56  3.000
 33J  H7   C13  C14  109.18  3.000
 33J  H6   C13  C14  110.30  3.000
 33J  H7   C13  C12  108.94  3.000
 33J  H6   C13  C12  110.45  3.000
 33J  C14  C13  C12  111.28  3.000
 33J  H9   C14  H8   106.51  3.000
 33J  H9   C14  C15  110.21  3.000
 33J  H8   C14  C15  108.92  3.000
 33J  H9   C14  C13  110.29  3.000
 33J  H8   C14  C13  109.19  3.000
 33J  C15  C14  C13  111.58  3.000
 33J  H11  C15  H10  106.61  3.000
 33J  H11  C15  C10  109.65  3.000
 33J  H10  C15  C10  110.01  3.000
 33J  H11  C15  C14  109.48  3.000
 33J  H10  C15  C14  109.99  3.000
 33J  C10  C15  C14  111.00  3.000
 33J  C21  C16  C17  118.29  3.000
 33J  C17  C16  C3   121.33  3.000
 33J  C21  C16  C3   120.38  3.000
 33J  H12  C17  C18  118.86  3.000
 33J  H12  C17  C16  120.30  3.000
 33J  C18  C17  C16  120.84  3.000
 33J  H13  C18  C19  120.17  3.000
 33J  H13  C18  C17  119.49  3.000
 33J  C19  C18  C17  120.34  3.000
 33J  H14  C19  C20  120.32  3.000
 33J  H14  C19  C18  120.32  3.000
 33J  C20  C19  C18  119.36  3.000
 33J  H15  C20  C21  119.46  3.000
 33J  H15  C20  C19  120.15  3.000
 33J  C21  C20  C19  120.39  3.000
 33J  H16  C21  C20  119.17  3.000
 33J  H16  C21  C16  120.04  3.000
 33J  C20  C21  C16  120.79  3.000
 33J  C3   S1   C2    92.82  3.000
 33J  H17  C4   C5   123.05  3.000
 33J  H17  C4   C3   123.86  3.000
 33J  C5   C4   C3   113.07  3.000
 33J  N1   C5   C4   123.34  3.000
 33J  C4   C5   C2   113.11  3.000
 33J  N1   C5   C2   123.51  3.000
 33J  C9   N1   C6   113.49  3.000
 33J  C6   N1   C5   120.96  3.000
 33J  C9   N1   C5   120.03  3.000
 33J  C7   C6   N1   107.96  3.000
 33J  N1   C6   O3   125.19  3.000
 33J  C7   C6   O3   126.85  3.000
 33J  H19  C7   H18  107.66  3.000
 33J  H19  C7   C8   111.71  3.000
 33J  H18  C7   C8   114.23  3.000
 33J  H19  C7   C6   106.65  3.000
 33J  H18  C7   C6   111.84  3.000
 33J  C8   C7   C6   104.53  3.000
 33J  H21  C8   H20  107.44  3.000
 33J  H21  C8   C9   111.53  3.000
 33J  H20  C8   C9   110.50  3.000
 33J  H21  C8   C7   113.25  3.000
 33J  H20  C8   C7   109.85  3.000
 33J  C9   C8   C7   104.29  3.000
 33J  H22  C9   C10  108.15  3.000
 33J  H22  C9   C8   109.63  3.000
 33J  C10  C9   C8   115.93  3.000
 33J  H22  C9   N1   107.80  3.000
 33J  C10  C9   N1   112.64  3.000
 33J  C8   C9   N1   102.37  3.000
 33J  H23  C10  C9   106.60  3.000
 33J  H23  C10  C15  106.74  3.000
 33J  C9   C10  C15  111.02  3.000
 33J  H23  C10  C11  107.50  3.000
 33J  C15  C10  C11  109.88  3.000
 33J  C9   C10  C11  114.68  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
 33J  CONST_01  C3   C4   C5   C2     0.00   0.0  0
 33J  CONST_02  C4   C3   S1   C2     0.00   0.0  0
 33J  CONST_03  C16  C3   S1   C2   180.00   0.0  0
 33J  CONST_04  C5   C2   S1   C3     0.00   0.0  0
 33J  CONST_05  C20  C21  C16  C3   180.00   0.0  0
 33J  CONST_06  C18  C17  C16  C3   180.00   0.0  0
 33J  CONST_07  C5   C4   C3   C16  180.00   0.0  0
 33J  CONST_08  C19  C20  C21  C16    0.00   0.0  0
 33J  CONST_09  C19  C18  C17  C16    0.00   0.0  0
 33J  CONST_12  C20  C21  C16  C17    0.00   0.0  0
 33J  CONST_13  C20  C19  C18  C17    0.00   0.0  0
 33J  CONST_14  C21  C16  C17  C18    0.00   0.0  0
 33J  CONST_15  C21  C20  C19  C18    0.00   0.0  0
 33J  CONST_18  C4   C5   C2   S1     0.00   0.0  0
 33J  CONST_19  C5   C4   C3   S1     0.00   0.0  0
 33J  CONST_20  N1   C5   C4   C3   180.00   0.0  0
 33J  CONST_21  N1   C5   C2   S1   180.00   0.0  0
 33J  CONST_23  C9   N1   C6   C7     0.00   0.0  0
 33J  CONST_24  N1   C5   C2   C1     0.00   0.0  0
 33J  CONST_25  C4   C5   C2   C1   180.00   0.0  0
 33J  CONST_26  C3   S1   C2   C1   180.00   0.0  0
 33J  CONST_27  C9   N1   C6   O3   180.00   0.0  0
 33J  CONST_29  H17  C4   C5   C2   180.00   0.0  0
 33J  CONST_30  H16  C21  C16  C3     0.00   0.0  0
 33J  CONST_31  H12  C17  C16  C3     0.00   0.0  0
 33J  CONST_32  H15  C20  C21  C16  180.00   0.0  0
 33J  CONST_33  H13  C18  C17  C16  180.00   0.0  0
 33J  CONST_34  H14  C19  C18  C17  180.00   0.0  0
 33J  Var_01    C9   N1   C5   C2    83.81  30.0  3
 33J  Var_02    C14  C13  C12  C11   55.14  30.0  1
 33J  Var_03    C15  C14  C13  C12  -54.22  30.0  1
 33J  Var_04    C10  C11  C12  C13  -57.54  30.0  1
 33J  Var_05    C10  C15  C14  C13   55.43  30.0  1
 33J  Var_06    C8   C7   C6   N1    12.58  30.0  1
 33J  Var_07    C9   C8   C7   C6   -24.23  30.0  1
 33J  Var_08    C5   C2   C1   O1   179.17  30.0  2

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
 33J  chir_01  C9   C8   C10  N1   positiv
 33J  chir_02  C10  C11  C9   C15  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
 33J  plan-1  C1   0.020
 33J  plan-1  C2   0.020
 33J  plan-1  C3   0.020
 33J  plan-1  C16  0.020
 33J  plan-1  S1   0.020
 33J  plan-1  C4   0.020
 33J  plan-1  C5   0.020
 33J  plan-1  N1   0.020
 33J  plan-1  H17  0.020
 33J  plan-2  C5   0.020
 33J  plan-2  N1   0.020
 33J  plan-2  C6   0.020
 33J  plan-2  C7   0.020
 33J  plan-2  C9   0.020
 33J  plan-2  O3   0.020
 33J  plan-3  C3   0.020
 33J  plan-3  C16  0.020
 33J  plan-3  C17  0.020
 33J  plan-3  C18  0.020
 33J  plan-3  C19  0.020
 33J  plan-3  C20  0.020
 33J  plan-3  C21  0.020
 33J  plan-3  H12  0.020
 33J  plan-3  H13  0.020
 33J  plan-3  H14  0.020
 33J  plan-3  H15  0.020
 33J  plan-3  H16  0.020
 33J  plan-4  C1   0.020
 33J  plan-4  C2   0.020
 33J  plan-4  O1   0.020
 33J  plan-4  O2   0.020

