# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 07:12:05 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: (3~{R})-1-phenylpyrrolidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CCN(C1)c2ccccc2
#
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
 PUE  PUE  '(3~{R})-1-phenylpyrrolidine-3-carboxylic acid'  ligand  26  14  .  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_PUE
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
 PUE  C2   C  CH2    0  -0.460   5.0920  -5.9402  6.4109
 PUE  C3   C  CH2    0  -0.270   3.6377  -6.3802  6.5228
 PUE  C4   C  CH2    0  -0.243   3.8133  -4.5748  4.9298
 PUE  C5   C  CR6    0   0.401   1.6986  -5.8577  5.0740
 PUE  C6   C  CR16   0  -0.366   1.1362  -5.1654  3.9828
 PUE  C10  C  CR16   0  -0.368   0.8847  -6.8000  5.7336
 PUE  N    N  NT     0  -0.529   2.9750  -5.6242  5.4767
 PUE  C    C  C      0   0.422   6.2602  -3.8801  5.3118
 PUE  O    O  O      0  -0.609   6.0828  -2.8911  4.5706
 PUE  C1   C  CH1    0  -0.414   4.9878  -4.5065  5.9047
 PUE  C7   C  CR16   0  -0.238  -0.1680  -5.4079  3.5843
 PUE  C8   C  CR16   0  -0.305  -0.9631  -6.3391  4.2418
 PUE  C9   C  CR16   0  -0.238  -0.4168  -7.0284  5.3176
 PUE  O1   O  OC    -1  -0.598   7.3520  -4.3836  5.6400
 PUE  H1   H  HCH2   0   0.223   5.6178  -6.5631  5.6832
 PUE  H2   H  HCH2   0   0.235   5.6201  -6.0256  7.3597
 PUE  H3   H  HCH2   0   0.215   3.2237  -6.1442  7.5119
 PUE  H4   H  HCH2   0   0.229   3.5188  -7.4577  6.3752
 PUE  H5   H  HCH2   0   0.210   4.1503  -4.8190  3.9137
 PUE  H6   H  HCH2   0   0.225   3.2729  -3.6270  4.8700
 PUE  H7   H  HCR6   0   0.257   1.7254  -4.4402  3.4375
 PUE  H8   H  HCR6   0   0.256   1.2668  -7.3500  6.5832
 PUE  H9   H  HCH1   0   0.240   4.6789  -3.8734  6.7476
 PUE  H10  H  HCR6   0   0.243  -0.5656  -4.8583  2.7395
 PUE  H11  H  HCR6   0   0.237  -1.9812  -6.5219  3.9245
 PUE  H12  H  HCR6   0   0.243  -1.0145  -7.7576  5.8511

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
 PUE  C7   C6   aromatic  1.385  0.020  1.385
 PUE  C7   C8   aromatic  1.390  0.020  1.390
 PUE  C6   C5   aromatic  1.409  0.020  1.409
 PUE  C8   C9   aromatic  1.390  0.020  1.390
 PUE  O    C    deloc     1.249  0.020  1.249
 PUE  C4   N    single    1.450  0.020  1.450
 PUE  C4   C1   single    1.528  0.020  1.528
 PUE  O1   C    deloc     1.246  0.020  1.246
 PUE  C5   N    single    1.359  0.020  1.359
 PUE  C5   C10  aromatic  1.409  0.020  1.409
 PUE  C9   C10  aromatic  1.385  0.020  1.385
 PUE  C    C1   single    1.537  0.020  1.537
 PUE  N    C3   single    1.451  0.020  1.451
 PUE  C1   C2   single    1.524  0.020  1.524
 PUE  C2   C3   single    1.524  0.020  1.524
 PUE  C2   H1   single    0.970  0.020  1.090
 PUE  C2   H2   single    0.970  0.020  1.090
 PUE  C3   H3   single    0.970  0.020  1.090
 PUE  C3   H4   single    0.970  0.020  1.090
 PUE  C4   H5   single    0.970  0.020  1.090
 PUE  C4   H6   single    0.970  0.020  1.090
 PUE  C6   H7   single    0.930  0.020  1.080
 PUE  C10  H8   single    0.930  0.020  1.080
 PUE  C1   H9   single    0.970  0.020  1.090
 PUE  C7   H10  single    0.930  0.020  1.080
 PUE  C8   H11  single    0.930  0.020  1.080
 PUE  C9   H12  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
 PUE  H2   C2   H1   107.59  3.000
 PUE  H2   C2   C1   113.34  3.000
 PUE  H1   C2   C1   110.37  3.000
 PUE  H2   C2   C3   112.10  3.000
 PUE  H1   C2   C3   110.10  3.000
 PUE  C1   C2   C3   103.34  3.000
 PUE  H4   C3   H3   107.00  3.000
 PUE  H4   C3   N    111.49  3.000
 PUE  H3   C3   N    111.43  3.000
 PUE  H4   C3   C2   112.22  3.000
 PUE  H3   C3   C2   111.34  3.000
 PUE  N    C3   C2   103.45  3.000
 PUE  H6   C4   H5   107.11  3.000
 PUE  H6   C4   C1   112.11  3.000
 PUE  H5   C4   C1   111.37  3.000
 PUE  H6   C4   N    111.25  3.000
 PUE  H5   C4   N    111.43  3.000
 PUE  C1   C4   N    103.65  3.000
 PUE  N    C5   C10  121.26  3.000
 PUE  C10  C5   C6   117.42  3.000
 PUE  N    C5   C6   121.33  3.000
 PUE  H7   C6   C7   119.02  3.000
 PUE  H7   C6   C5   120.15  3.000
 PUE  C7   C6   C5   120.83  3.000
 PUE  H8   C10  C9   118.93  3.000
 PUE  H8   C10  C5   120.24  3.000
 PUE  C9   C10  C5   120.82  3.000
 PUE  C5   N    C4   123.75  3.000
 PUE  C5   N    C3   123.59  3.000
 PUE  C4   N    C3   112.64  3.000
 PUE  O1   C    C1   117.32  3.000
 PUE  C1   C    O    115.73  3.000
 PUE  O1   C    O    126.93  3.000
 PUE  H9   C1   C    107.09  3.000
 PUE  H9   C1   C4   107.41  3.000
 PUE  C    C1   C4   114.10  3.000
 PUE  H9   C1   C2   107.86  3.000
 PUE  C    C1   C2   117.05  3.000
 PUE  C4   C1   C2   102.85  3.000
 PUE  H10  C7   C8   119.92  3.000
 PUE  H10  C7   C6   118.75  3.000
 PUE  C8   C7   C6   121.32  3.000
 PUE  H11  C8   C9   120.88  3.000
 PUE  H11  C8   C7   120.85  3.000
 PUE  C9   C8   C7   118.27  3.000
 PUE  H12  C9   C8   119.88  3.000
 PUE  H12  C9   C10  118.78  3.000
 PUE  C8   C9   C10  121.34  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
 PUE  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 PUE  CONST_02  C8   C9   C10  C5      0.00   0.0  0
 PUE  CONST_03  C9   C8   C7   C6      0.00   0.0  0
 PUE  CONST_04  C9   C10  C5   C6      0.00   0.0  0
 PUE  CONST_05  C7   C6   C5   C10     0.00   0.0  0
 PUE  CONST_06  C7   C8   C9   C10     0.00   0.0  0
 PUE  CONST_07  C7   C6   C5   N     180.00   0.0  0
 PUE  CONST_08  C9   C10  C5   N     180.00   0.0  0
 PUE  CONST_09  H10  C7   C6   C5    180.00   0.0  0
 PUE  CONST_10  H12  C9   C10  C5    180.00   0.0  0
 PUE  CONST_11  H11  C8   C7   C6    180.00   0.0  0
 PUE  CONST_12  H8   C10  C5   C6    180.00   0.0  0
 PUE  CONST_13  H7   C6   C5   C10   180.00   0.0  0
 PUE  Var_01    C4   N    C3   C2    -12.01  30.0  1
 PUE  Var_02    C1   C4   N    C3    -11.54  30.0  1
 PUE  Var_03    C6   C5   N    C3   -174.97  30.0  3
 PUE  Var_04    C1   C2   C3   N      30.60  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
 PUE  chir_01  C1  C4  C  C2  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
 PUE  plan-1  C5   0.020
 PUE  plan-1  C6   0.020
 PUE  plan-1  C10  0.020
 PUE  plan-1  N    0.020
 PUE  plan-1  C7   0.020
 PUE  plan-1  C8   0.020
 PUE  plan-1  C9   0.020
 PUE  plan-1  H7   0.020
 PUE  plan-1  H8   0.020
 PUE  plan-1  H10  0.020
 PUE  plan-1  H11  0.020
 PUE  plan-1  H12  0.020
 PUE  plan-2  C    0.020
 PUE  plan-2  O    0.020
 PUE  plan-2  C1   0.020
 PUE  plan-2  O1   0.020

