# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:43:29 2021
#   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  25  13  .  2022-03-29  2022-11-18
;
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  -0.433   0.8160  15.3446  -3.2522
 W2G  C5   C  CR15  0  -0.339  -0.3889  14.3999  -3.3505
 W2G  C6   C  CR5   0   0.232  -1.4054  14.5250  -2.2564
 W2G  C7   C  CR15  0  -0.552  -2.7512  14.5318  -2.4811
 W2G  C8   C  CR15  0  -0.467  -2.2254  14.7164  -0.0860
 W2G  O    O  OH1   0  -0.587   1.6813  12.8549  -1.6781
 W2G  O1   O  O     0  -0.447  -0.0138  11.4138  -1.7443
 W2G  C1   C  CR15  0  -0.361   0.2274  12.9891  -3.5410
 W2G  C9   C  CR15  0  -0.222  -1.1114  14.6345  -0.8613
 W2G  C2   C  CH2   0  -0.452   1.4224  13.2803  -4.4585
 W2G  C3   C  CH2   0  -0.442   1.9288  14.6887  -4.0901
 W2G  S    S  S2    0   0.207  -3.6537  14.6641  -1.0305
 W2G  H1   H  HCH2  0   0.234   1.1342  15.4623  -2.2162
 W2G  H2   H  HCH2  0   0.245   0.5515  16.3398  -3.6108
 W2G  H3   H  HCR5  0   0.269  -0.8958  14.6054  -4.2979
 W2G  H4   H  HCR5  0   0.289  -3.2564  14.4663  -3.4334
 W2G  H5   H  HCR5  0   0.293  -2.2806  14.8073   0.9877
 W2G  H6   H  HOH1  0   0.479   1.8742  12.4007  -0.8437
 W2G  H7   H  HCR5  0   0.280  -0.4995  12.3343  -4.0229
 W2G  H8   H  HCR5  0   0.259  -0.1120  14.6585  -0.4495
 W2G  H9   H  HCH2  0   0.249   1.0556  13.2716  -5.4863
 W2G  H10  H  HCH2  0   0.248   2.2015  12.5197  -4.4001
 W2G  H11  H  HCH2  0   0.234   2.8586  14.6395  -3.5242
 W2G  H12  H  HCH2  0   0.234   2.1431  15.2625  -4.9923
 W2G  C    C  C     0   0.549   0.5984  12.3274  -2.2420

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    1.541  0.020  1.541
 W2G  C2  C1   single    1.535  0.020  1.535
 W2G  C3  C4   single    1.540  0.020  1.540
 W2G  C1  C5   single    1.551  0.020  1.551
 W2G  C1  C    single    1.504  0.020  1.504
 W2G  C5  C4   single    1.534  0.020  1.534
 W2G  C5  C6   single    1.499  0.020  1.499
 W2G  C   O1   double    1.207  0.020  1.207
 W2G  C   O    single    1.330  0.020  1.330
 W2G  C7  C6   aromatic  1.364  0.020  1.364
 W2G  C7  S    aromatic  1.714  0.020  1.714
 W2G  C6  C9   aromatic  1.430  0.020  1.430
 W2G  S   C8   aromatic  1.713  0.020  1.713
 W2G  C9  C8   aromatic  1.360  0.020  1.360
 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  O   H6   single    0.850  0.020  0.980
 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   106.55  3.000
 W2G  H2   C4  C3   112.65  3.000
 W2G  H1   C4  C3   110.62  3.000
 W2G  H2   C4  C5   110.51  3.000
 W2G  H1   C4  C5   110.89  3.000
 W2G  C3   C4  C5   105.69  3.000
 W2G  H3   C5  C1   104.39  3.000
 W2G  H3   C5  C6   107.59  3.000
 W2G  C1   C5  C6   115.79  3.000
 W2G  H3   C5  C4   107.69  3.000
 W2G  C6   C5  C4   115.75  3.000
 W2G  C1   C5  C4   104.83  3.000
 W2G  C9   C6  C7   111.29  3.000
 W2G  C9   C6  C5   125.39  3.000
 W2G  C7   C6  C5   123.31  3.000
 W2G  H4   C7  S    120.31  3.000
 W2G  H4   C7  C6   127.32  3.000
 W2G  S    C7  C6   112.36  3.000
 W2G  H5   C8  S    120.56  3.000
 W2G  H5   C8  C9   127.91  3.000
 W2G  S    C8  C9   111.52  3.000
 W2G  H6   O   C    109.95  3.000
 W2G  H7   C1  C2   111.64  3.000
 W2G  H7   C1  C    106.37  3.000
 W2G  C2   C1  C    114.06  3.000
 W2G  H7   C1  C5   109.60  3.000
 W2G  C    C1  C5   113.08  3.000
 W2G  C2   C1  C5   102.13  3.000
 W2G  H8   C9  C8   122.60  3.000
 W2G  H8   C9  C6   124.29  3.000
 W2G  C8   C9  C6   113.10  3.000
 W2G  H10  C2  H9   106.56  3.000
 W2G  H10  C2  C3   112.95  3.000
 W2G  H9   C2  C3   110.05  3.000
 W2G  H10  C2  C1   113.08  3.000
 W2G  H9   C2  C1   107.44  3.000
 W2G  C3   C2  C1   106.64  3.000
 W2G  H12  C3  H11  106.60  3.000
 W2G  H12  C3  C2   110.35  3.000
 W2G  H11  C3  C2   111.30  3.000
 W2G  H12  C3  C4   111.60  3.000
 W2G  H11  C3  C4   110.69  3.000
 W2G  C2   C3  C4   106.37  3.000
 W2G  C8   S   C7    91.72  3.000
 W2G  C1   C   O1   124.33  3.000
 W2G  O1   C   O    122.56  3.000
 W2G  C1   C   O    113.11  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  CONST_11  H6  O   C   C1  180.00   0.0  0
 W2G  Var_01    C1  C2  C3  C4  -14.95  30.0  1
 W2G  Var_02    C2  C3  C4  C5   -9.06  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  H6  0.020
 W2G  plan-2  C   0.020

