# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 09:28:51 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: (1R,2S)-2-(thiophen-3-yl)cyclopentane-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCC[C@@H]1c2cscc2
#
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
 W2G  W2G  '(1R,2S)-2-(thiophen-3-yl)cyclopentane-1-carboxylic acid'  ligand  24  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_W2G
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
 W2G  C4   C  CH2    0  -0.414   0.7552  15.3508  -3.2744
 W2G  C5   C  CR15   0  -0.330  -0.4123  14.3642  -3.3620
 W2G  C6   C  CR5    0   0.241  -1.4300  14.5006  -2.2707
 W2G  C7   C  CR15   0  -0.562  -2.7690  14.6242  -2.5005
 W2G  C8   C  CR15   0  -0.472  -2.2489  14.7036  -0.0984
 W2G  O    O  OC    -1  -0.604   1.7376  12.8846  -1.6352
 W2G  O1   O  O      0  -0.611   0.0438  11.4398  -1.7219
 W2G  C1   C  CR15   0  -0.336   0.2707  12.9831  -3.5160
 W2G  C9   C  CR15   0  -0.211  -1.1411  14.5485  -0.8702
 W2G  C2   C  CH2    0  -0.436   1.4341  13.3080  -4.4666
 W2G  C3   C  CH2    0  -0.437   1.8043  14.7917  -4.2443
 W2G  S    S  S2     0   0.188  -3.6721  14.7961  -1.0514
 W2G  H1   H  HCH2   0   0.223   1.1523  15.3711  -2.2602
 W2G  H2   H  HCH2   0   0.221   0.4440  16.3672  -3.5234
 W2G  H3   H  HCR5   0   0.233  -0.9302  14.5521  -4.3100
 W2G  H4   H  HCR5   0   0.281  -3.2691  14.6304  -3.4578
 W2G  H5   H  HCR5   0   0.285  -2.3044  14.7670   0.9775
 W2G  H7   H  HCR5   0   0.208  -0.4317  12.2881  -3.9831
 W2G  H8   H  HCR5   0   0.251  -0.1447  14.4641  -0.4617
 W2G  H9   H  HCH2   0   0.216   1.1064  13.1604  -5.4984
 W2G  H10  H  HCH2   0   0.220   2.2854  12.6435  -4.3155
 W2G  H11  H  HCH2   0   0.218   2.8111  14.9043  -3.8413
 W2G  H12  H  HCH2   0   0.214   1.7866  15.3358  -5.1904
 W2G  C    C  C      0   0.415   0.7265  12.3813  -2.1737

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
 W2G  C2  C3   single    1.545  0.020  1.545
 W2G  C2  C1   single    1.537  0.020  1.537
 W2G  C3  C4   single    1.534  0.020  1.534
 W2G  C1  C5   single    1.548  0.020  1.548
 W2G  C1  C    single    1.540  0.020  1.540
 W2G  C5  C4   single    1.531  0.020  1.531
 W2G  C5  C6   single    1.498  0.020  1.498
 W2G  C   O1   deloc     1.248  0.020  1.248
 W2G  C   O    deloc     1.251  0.020  1.251
 W2G  C7  C6   aromatic  1.364  0.020  1.364
 W2G  C7  S    aromatic  1.716  0.020  1.716
 W2G  C6  C9   aromatic  1.431  0.020  1.431
 W2G  S   C8   aromatic  1.715  0.020  1.715
 W2G  C9  C8   aromatic  1.359  0.020  1.359
 W2G  C4  H1   single    0.970  0.020  1.090
 W2G  C4  H2   single    0.970  0.020  1.090
 W2G  C5  H3   single    0.970  0.020  1.090
 W2G  C7  H4   single    0.930  0.020  1.080
 W2G  C8  H5   single    0.930  0.020  1.080
 W2G  C1  H7   single    0.970  0.020  1.090
 W2G  C9  H8   single    0.930  0.020  1.080
 W2G  C2  H9   single    0.970  0.020  1.090
 W2G  C2  H10  single    0.970  0.020  1.090
 W2G  C3  H11  single    0.970  0.020  1.090
 W2G  C3  H12  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
 W2G  H2   C4  H1   107.39  3.000
 W2G  H2   C4  C3   112.96  3.000
 W2G  H1   C4  C3   110.24  3.000
 W2G  H2   C4  C5   111.69  3.000
 W2G  H1   C4  C5   110.07  3.000
 W2G  C3   C4  C5   104.50  3.000
 W2G  H3   C5  C1   105.97  3.000
 W2G  H3   C5  C6   107.06  3.000
 W2G  C1   C5  C6   116.95  3.000
 W2G  H3   C5  C4   107.41  3.000
 W2G  C6   C5  C4   114.68  3.000
 W2G  C1   C5  C4   104.13  3.000
 W2G  C9   C6  C7   111.10  3.000
 W2G  C9   C6  C5   125.37  3.000
 W2G  C7   C6  C5   123.52  3.000
 W2G  H4   C7  S    120.28  3.000
 W2G  H4   C7  C6   127.18  3.000
 W2G  S    C7  C6   112.54  3.000
 W2G  H5   C8  S    120.54  3.000
 W2G  H5   C8  C9   127.93  3.000
 W2G  S    C8  C9   111.53  3.000
 W2G  H7   C1  C2   110.88  3.000
 W2G  H7   C1  C    108.31  3.000
 W2G  C2   C1  C    113.43  3.000
 W2G  H7   C1  C5   109.04  3.000
 W2G  C    C1  C5   113.11  3.000
 W2G  C2   C1  C5   101.94  3.000
 W2G  H8   C9  C8   123.10  3.000
 W2G  H8   C9  C6   123.63  3.000
 W2G  C8   C9  C6   113.27  3.000
 W2G  H10  C2  H9   106.42  3.000
 W2G  H10  C2  C3   112.22  3.000
 W2G  H9   C2  C3   109.72  3.000
 W2G  H10  C2  C1   112.11  3.000
 W2G  H9   C2  C1   109.17  3.000
 W2G  C3   C2  C1   107.17  3.000
 W2G  H12  C3  H11  106.50  3.000
 W2G  H12  C3  C2   110.49  3.000
 W2G  H11  C3  C2   111.94  3.000
 W2G  H12  C3  C4   110.80  3.000
 W2G  H11  C3  C4   111.11  3.000
 W2G  C2   C3  C4   106.08  3.000
 W2G  C8   S   C7    91.55  3.000
 W2G  C1   C   O1   116.65  3.000
 W2G  O1   C   O    126.14  3.000
 W2G  C1   C   O    117.20  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
 W2G  CONST_01  C8  S   C7  C6    0.00   0.0  0
 W2G  CONST_02  S   C8  C9  C6    0.00   0.0  0
 W2G  CONST_03  C8  C9  C6  C7    0.00   0.0  0
 W2G  CONST_04  C9  C8  S   C7    0.00   0.0  0
 W2G  CONST_05  S   C7  C6  C9    0.00   0.0  0
 W2G  CONST_06  S   C7  C6  C5  180.00   0.0  0
 W2G  CONST_07  C8  C9  C6  C5  180.00   0.0  0
 W2G  CONST_08  H4  C7  C6  C5    0.00   0.0  0
 W2G  CONST_09  H8  C9  C6  C5    0.00   0.0  0
 W2G  CONST_10  H5  C8  C9  C6  180.00   0.0  0
 W2G  Var_01    C1  C2  C3  C4   -5.82  30.0  1
 W2G  Var_02    C2  C3  C4  C5  -19.10  30.0  1

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
 W2G  chir_01  C5  C1  C4  C6  positiv
 W2G  chir_02  C1  C2  C5  C   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
 W2G  plan-1  C5  0.020
 W2G  plan-1  C6  0.020
 W2G  plan-1  C7  0.020
 W2G  plan-1  C8  0.020
 W2G  plan-1  C9  0.020
 W2G  plan-1  S   0.020
 W2G  plan-1  H4  0.020
 W2G  plan-1  H5  0.020
 W2G  plan-1  H8  0.020
 W2G  plan-2  O   0.020
 W2G  plan-2  O1  0.020
 W2G  plan-2  C1  0.020
 W2G  plan-2  C   0.020

