# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 04:42:26 2021
#   Inital geometry file: a 70 line input string
#   Ligand name: (3~{R})-1-(2-chlorophenyl)pyrrolidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCN(C1)c2ccccc2Cl
#
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
 PQT  PQT  '(3~{R})-1-(2-chlorophenyl)pyrrolidine-3-carboxylic acid'  ligand  27  15  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PQT
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
 PQT  C1   C   CR16  0  -0.361   1.3309  -4.2812  4.3416
 PQT  C2   C   CR6   0   0.448   1.5937  -5.2483  5.3283
 PQT  C3   C   CR6   0  -0.129   0.5083  -6.0745  5.6758
 PQT  C4   C   CR16  0  -0.213  -0.7176  -5.9907  5.0342
 PQT  C5   C   CR16  0  -0.293  -0.9327  -5.0459  4.0441
 PQT  C6   C   CH2   0  -0.256   3.8068  -4.2813  5.7154
 PQT  C8   C   CH2   0  -0.463   4.9827  -6.3119  6.0284
 PQT  C9   C   CH2   0  -0.278   3.4999  -6.6170  6.2025
 PQT  C10  C   C     0   0.560   6.3292  -4.1533  5.9582
 PQT  O1   O   OH1   0  -0.592   6.2444  -2.8340  6.0846
 PQT  N    N   NT    0  -0.536   2.8310  -5.3367  5.9286
 PQT  C    C   CR16  0  -0.237   0.0991  -4.1788  3.7186
 PQT  C7   C   CH1   0  -0.420   5.0612  -4.8364  6.3870
 PQT  CL   CL  CL    0  -0.122   0.6171  -7.1859  7.0099
 PQT  H1   H   HCR6  0   0.272   2.1108  -3.5962  4.0417
 PQT  H2   H   HCR6  0   0.273  -1.5160  -6.6571  5.3333
 PQT  H3   H   HCR6  0   0.258  -1.8949  -4.9809  3.5550
 PQT  H4   H   HCH2  0   0.229   4.0110  -4.1065  4.6503
 PQT  H5   H   HCH2  0   0.261   3.4679  -3.3389  6.1487
 PQT  H6   H   HCH2  0   0.246   5.2887  -6.4614  4.9912
 PQT  H7   H   HCH2  0   0.262   5.6047  -6.9453  6.6587
 PQT  H8   H   HCH2  0   0.244   3.1647  -7.3989  5.5186
 PQT  H9   H   HCH2  0   0.234   3.3036  -6.9579  7.2198
 PQT  H10  H   HOH1  0   0.483   7.0725  -2.4180  5.8008
 PQT  H11  H   HCR6  0   0.259  -0.0430  -3.4186  2.9616
 PQT  H12  H   HCH1  0   0.306   4.9701  -4.7102  7.4726
 PQT  O    O   O     0  -0.435   7.3156  -4.7178  5.5576

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
 PQT  C    C5   aromatic  1.387  0.020  1.387
 PQT  C    C1   aromatic  1.384  0.020  1.384
 PQT  C5   C4   aromatic  1.385  0.020  1.385
 PQT  C1   C2   aromatic  1.406  0.020  1.406
 PQT  C4   C3   aromatic  1.386  0.020  1.386
 PQT  O    C10  double    1.205  0.020  1.205
 PQT  O1   C10  single    1.328  0.020  1.328
 PQT  C2   C3   aromatic  1.408  0.020  1.408
 PQT  C2   N    single    1.378  0.020  1.378
 PQT  C10  C7   single    1.503  0.020  1.503
 PQT  C3   CL   single    1.740  0.020  1.740
 PQT  C8   C7   single    1.520  0.020  1.520
 PQT  C8   C9   single    1.524  0.020  1.524
 PQT  N    C6   single    1.453  0.020  1.453
 PQT  N    C9   single    1.470  0.020  1.470
 PQT  C6   C7   single    1.527  0.020  1.527
 PQT  C1   H1   single    0.930  0.020  1.080
 PQT  C4   H2   single    0.930  0.020  1.080
 PQT  C5   H3   single    0.930  0.020  1.080
 PQT  C6   H4   single    0.970  0.020  1.090
 PQT  C6   H5   single    0.970  0.020  1.090
 PQT  C8   H6   single    0.970  0.020  1.090
 PQT  C8   H7   single    0.970  0.020  1.090
 PQT  C9   H8   single    0.970  0.020  1.090
 PQT  C9   H9   single    0.970  0.020  1.090
 PQT  O1   H10  single    0.850  0.020  0.980
 PQT  C    H11  single    0.930  0.020  1.080
 PQT  C7   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
 PQT  H1   C1   C    118.07  3.000
 PQT  H1   C1   C2   119.72  3.000
 PQT  C    C1   C2   122.21  3.000
 PQT  N    C2   C3   123.17  3.000
 PQT  N    C2   C1   121.17  3.000
 PQT  C3   C2   C1   115.64  3.000
 PQT  CL   C3   C4   116.67  3.000
 PQT  CL   C3   C2   121.07  3.000
 PQT  C4   C3   C2   122.15  3.000
 PQT  H2   C4   C5   120.19  3.000
 PQT  H2   C4   C3   119.16  3.000
 PQT  C5   C4   C3   120.63  3.000
 PQT  H3   C5   C    121.23  3.000
 PQT  H3   C5   C4   120.16  3.000
 PQT  C    C5   C4   118.60  3.000
 PQT  H5   C6   H4   107.78  3.000
 PQT  H5   C6   C7   113.22  3.000
 PQT  H4   C6   C7   109.36  3.000
 PQT  H5   C6   N    111.13  3.000
 PQT  H4   C6   N    112.50  3.000
 PQT  C7   C6   N    102.89  3.000
 PQT  H7   C8   H6   108.07  3.000
 PQT  H7   C8   C7   113.49  3.000
 PQT  H6   C8   C7   110.03  3.000
 PQT  H7   C8   C9   111.92  3.000
 PQT  H6   C8   C9   110.73  3.000
 PQT  C7   C8   C9   102.57  3.000
 PQT  H9   C9   H8   107.77  3.000
 PQT  H9   C9   N    111.35  3.000
 PQT  H8   C9   N    111.55  3.000
 PQT  H9   C9   C8   110.14  3.000
 PQT  H8   C9   C8   111.76  3.000
 PQT  N    C9   C8   104.30  3.000
 PQT  C7   C10  O    124.93  3.000
 PQT  C7   C10  O1   111.75  3.000
 PQT  O    C10  O1   123.32  3.000
 PQT  H10  O1   C10  110.12  3.000
 PQT  C9   N    C6   110.75  3.000
 PQT  C9   N    C2   123.06  3.000
 PQT  C6   N    C2   119.50  3.000
 PQT  H11  C    C5   120.38  3.000
 PQT  H11  C    C1   118.93  3.000
 PQT  C5   C    C1   120.68  3.000
 PQT  H12  C7   C10  107.47  3.000
 PQT  H12  C7   C8   109.93  3.000
 PQT  C10  C7   C8   114.67  3.000
 PQT  H12  C7   C6   108.98  3.000
 PQT  C8   C7   C6   101.92  3.000
 PQT  C10  C7   C6   113.72  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
 PQT  CONST_01  C4   C5  C    C1     0.00   0.0  0
 PQT  CONST_02  C4   C3  C2   C1     0.00   0.0  0
 PQT  CONST_03  C5   C   C1   C2     0.00   0.0  0
 PQT  CONST_04  C5   C4  C3   C2     0.00   0.0  0
 PQT  CONST_05  C    C5  C4   C3     0.00   0.0  0
 PQT  CONST_06  C    C1  C2   C3     0.00   0.0  0
 PQT  CONST_07  N    C2  C3   C4   180.00   0.0  0
 PQT  CONST_08  C    C1  C2   N    180.00   0.0  0
 PQT  CONST_09  CL   C3  C2   C1   180.00   0.0  0
 PQT  CONST_10  CL   C3  C4   C5   180.00   0.0  0
 PQT  CONST_11  CL   C3  C2   N      0.00   0.0  0
 PQT  CONST_12  H3   C5  C    C1   180.00   0.0  0
 PQT  CONST_13  H11  C   C1   C2   180.00   0.0  0
 PQT  CONST_14  H2   C4  C3   C2   180.00   0.0  0
 PQT  CONST_15  H1   C1  C2   C3   180.00   0.0  0
 PQT  CONST_16  H10  O1  C10  C7   180.00   0.0  0
 PQT  Var_01    C6   N   C2   C1    10.73  30.0  2
 PQT  Var_02    C7   C6  N    C2  -173.19  30.0  1
 PQT  Var_03    C8   C9  N    C2   146.38  30.0  1
 PQT  Var_04    C7   C8  C9   N     28.47  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
 PQT  chir_01  C7  C10  C8  C6  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
 PQT  plan-1  C1   0.020
 PQT  plan-1  C2   0.020
 PQT  plan-1  C3   0.020
 PQT  plan-1  C4   0.020
 PQT  plan-1  C5   0.020
 PQT  plan-1  N    0.020
 PQT  plan-1  C    0.020
 PQT  plan-1  CL   0.020
 PQT  plan-1  H1   0.020
 PQT  plan-1  H2   0.020
 PQT  plan-1  H3   0.020
 PQT  plan-1  H11  0.020
 PQT  plan-2  C10  0.020
 PQT  plan-2  O1   0.020
 PQT  plan-2  C7   0.020
 PQT  plan-2  H10  0.020
 PQT  plan-2  O    0.020

