# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 03:59:55 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: (3~{S})-1-[4-chloranyl-3-(trifluoromethyl)phenyl]pyrrolidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1CCN(C1)c2ccc(Cl)c(c2)C(F)(F)F
#
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
 PJK  PJK  '(3~{S})-1-[4-chloranyl-3-(trifluoromethyl)phenyl]pyrrolidine-3-carboxylic acid'  ligand  29  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PJK
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
 PJK  C10  C   CR16   0  -0.366  -1.7937  4.4566  4.4760
 PJK  C13  C   CR6    0  -0.099  -0.4189  6.5000  5.7629
 PJK  C15  C   CT     0   1.065   0.2983  7.6295  6.4447
 PJK  C02  C   C      0   0.426  -7.0677  3.3192  5.3272
 PJK  C04  C   CH1    0  -0.416  -6.0027  4.4037  5.5489
 PJK  C05  C   CH2    0  -0.466  -5.7541  4.8271  6.9931
 PJK  C06  C   CH2    0  -0.277  -4.4267  5.5734  6.9197
 PJK  C08  C   CH2    0  -0.249  -4.6054  4.0320  5.0668
 PJK  C09  C   CR6    0   0.452  -2.4606  5.1996  5.4671
 PJK  C11  C   CR16   0  -0.182  -0.4805  4.7279  4.1488
 PJK  C12  C   CR6    0  -0.125   0.2179  5.7428  4.7829
 PJK  C14  C   CR16   0  -0.439  -1.7332  6.2228  6.1045
 PJK  F16  F   F      0  -0.312   1.3633  7.2082  7.1381
 PJK  F17  F   F      0  -0.299  -0.4881  8.2805  7.3056
 PJK  F18  F   F      0  -0.312   0.7410  8.5390  5.5665
 PJK  N07  N   NT     0  -0.534  -3.7486  4.9521  5.7934
 PJK  CL1  CL  CL     0  -0.132   1.8703  6.0214  4.3336
 PJK  H1   H   HCR6   0   0.279  -2.2947  3.6470  3.9635
 PJK  H2   H   HCH1   0   0.244  -6.3226  5.2924  4.9872
 PJK  H3   H   HCH2   0   0.240  -6.5486  5.4472  7.4048
 PJK  H4   H   HCH2   0   0.228  -5.6576  3.9463  7.6330
 PJK  H5   H   HCH2   0   0.237  -3.8428  5.4733  7.8397
 PJK  H6   H   HCH2   0   0.226  -4.5796  6.6459  6.7488
 PJK  H7   H   HCH2   0   0.217  -4.3665  2.9883  5.3063
 PJK  H8   H   HCH2   0   0.234  -4.4900  4.1544  3.9879
 PJK  H9   H   HCR6   0   0.280   0.0087  4.1344  3.3879
 PJK  H10  H   HCR6   0   0.286  -2.2151  6.8147  6.8686
 PJK  O01  O   OC    -1  -0.601  -8.0150  3.2943  6.1359
 PJK  O03  O   O      0  -0.604  -6.9021  2.5795  4.3359

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
 PJK  C11  C10  aromatic  1.380  0.020  1.380
 PJK  C11  C12  aromatic  1.386  0.020  1.386
 PJK  CL1  C12  single    1.735  0.020  1.735
 PJK  C10  C09  aromatic  1.407  0.020  1.407
 PJK  C12  C13  aromatic  1.393  0.020  1.393
 PJK  C08  C04  single    1.524  0.020  1.524
 PJK  C08  N07  single    1.452  0.020  1.452
 PJK  O03  C02  deloc     1.248  0.020  1.248
 PJK  C02  C04  single    1.536  0.020  1.536
 PJK  C02  O01  deloc     1.246  0.020  1.246
 PJK  C09  N07  single    1.351  0.020  1.351
 PJK  C09  C14  aromatic  1.408  0.020  1.408
 PJK  C04  C05  single    1.525  0.020  1.525
 PJK  F18  C15  single    1.340  0.020  1.340
 PJK  C13  C14  aromatic  1.386  0.020  1.386
 PJK  C13  C15  single    1.502  0.020  1.502
 PJK  N07  C06  single    1.454  0.020  1.454
 PJK  C15  F16  single    1.339  0.020  1.339
 PJK  C15  F17  single    1.335  0.020  1.335
 PJK  C06  C05  single    1.525  0.020  1.525
 PJK  C10  H1   single    0.930  0.020  1.080
 PJK  C04  H2   single    0.970  0.020  1.090
 PJK  C05  H3   single    0.970  0.020  1.090
 PJK  C05  H4   single    0.970  0.020  1.090
 PJK  C06  H5   single    0.970  0.020  1.090
 PJK  C06  H6   single    0.970  0.020  1.090
 PJK  C08  H7   single    0.970  0.020  1.090
 PJK  C08  H8   single    0.970  0.020  1.090
 PJK  C11  H9   single    0.930  0.020  1.080
 PJK  C14  H10  single    0.930  0.020  1.080

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
 PJK  H1   C10  C11  118.40  3.000
 PJK  H1   C10  C09  120.64  3.000
 PJK  C11  C10  C09  120.95  3.000
 PJK  C14  C13  C12  119.89  3.000
 PJK  C14  C13  C15  119.43  3.000
 PJK  C12  C13  C15  120.67  3.000
 PJK  F18  C15  F17  106.64  3.000
 PJK  F17  C15  F16  106.73  3.000
 PJK  F18  C15  F16  106.88  3.000
 PJK  F17  C15  C13  112.22  3.000
 PJK  F16  C15  C13  112.23  3.000
 PJK  F18  C15  C13  111.77  3.000
 PJK  O03  C02  O01  127.21  3.000
 PJK  O01  C02  C04  116.59  3.000
 PJK  O03  C02  C04  116.18  3.000
 PJK  H2   C04  C08  107.60  3.000
 PJK  H2   C04  C05  107.87  3.000
 PJK  C08  C04  C05  102.58  3.000
 PJK  H2   C04  C02  107.18  3.000
 PJK  C05  C04  C02  116.46  3.000
 PJK  C08  C04  C02  114.69  3.000
 PJK  H4   C05  H3   107.58  3.000
 PJK  H4   C05  C06  110.23  3.000
 PJK  H3   C05  C06  112.01  3.000
 PJK  H4   C05  C04  110.18  3.000
 PJK  H3   C05  C04  113.40  3.000
 PJK  C06  C05  C04  103.43  3.000
 PJK  H6   C06  H5   107.15  3.000
 PJK  H6   C06  N07  111.23  3.000
 PJK  H5   C06  N07  111.30  3.000
 PJK  H6   C06  C05  111.39  3.000
 PJK  H5   C06  C05  112.29  3.000
 PJK  N07  C06  C05  103.54  3.000
 PJK  H8   C08  H7   107.42  3.000
 PJK  H8   C08  N07  111.16  3.000
 PJK  H7   C08  N07  111.41  3.000
 PJK  H8   C08  C04  112.46  3.000
 PJK  H7   C08  C04  111.26  3.000
 PJK  N07  C08  C04  103.18  3.000
 PJK  N07  C09  C14  121.07  3.000
 PJK  C14  C09  C10  117.25  3.000
 PJK  N07  C09  C10  121.68  3.000
 PJK  H9   C11  C12  119.72  3.000
 PJK  H9   C11  C10  119.28  3.000
 PJK  C12  C11  C10  121.00  3.000
 PJK  CL1  C12  C11  118.63  3.000
 PJK  CL1  C12  C13  122.04  3.000
 PJK  C11  C12  C13  119.33  3.000
 PJK  H10  C14  C09  119.21  3.000
 PJK  H10  C14  C13  119.20  3.000
 PJK  C09  C14  C13  121.58  3.000
 PJK  C09  N07  C08  123.88  3.000
 PJK  C09  N07  C06  123.59  3.000
 PJK  C08  N07  C06  112.53  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
 PJK  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 PJK  CONST_02  C13  C14  C09  C10     0.00   0.0  0
 PJK  CONST_03  C12  C11  C10  C09     0.00   0.0  0
 PJK  CONST_04  C12  C13  C14  C09     0.00   0.0  0
 PJK  CONST_05  C14  C09  C10  C11     0.00   0.0  0
 PJK  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 PJK  CONST_07  N07  C09  C14  C13   180.00   0.0  0
 PJK  CONST_08  N07  C09  C10  C11   180.00   0.0  0
 PJK  CONST_09  CL1  C12  C11  C10   180.00   0.0  0
 PJK  CONST_10  C11  C12  C13  C15   180.00   0.0  0
 PJK  CONST_11  C09  C14  C13  C15   180.00   0.0  0
 PJK  CONST_12  CL1  C12  C13  C14   180.00   0.0  0
 PJK  CONST_13  H10  C14  C09  C10   180.00   0.0  0
 PJK  CONST_14  H9   C11  C12  C13   180.00   0.0  0
 PJK  CONST_15  H1   C10  C11  C12   180.00   0.0  0
 PJK  Var_01    C08  N07  C09  C10    -7.62  30.0  2
 PJK  Var_02    C09  N07  C08  C04  -164.32  30.0  1
 PJK  Var_03    N07  C06  C05  C04   -28.59  30.0  1
 PJK  Var_04    F18  C15  C13  C12    57.21  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
 PJK  chir_01  C04  C08  C02  C05  negativ

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
 PJK  plan-1  C10  0.020
 PJK  plan-1  C13  0.020
 PJK  plan-1  C15  0.020
 PJK  plan-1  C09  0.020
 PJK  plan-1  C11  0.020
 PJK  plan-1  C12  0.020
 PJK  plan-1  C14  0.020
 PJK  plan-1  N07  0.020
 PJK  plan-1  CL1  0.020
 PJK  plan-1  H1   0.020
 PJK  plan-1  H9   0.020
 PJK  plan-1  H10  0.020
 PJK  plan-2  C02  0.020
 PJK  plan-2  C04  0.020
 PJK  plan-2  O01  0.020
 PJK  plan-2  O03  0.020

