# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun  4 14:51:55 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: (~{S})-phenyl-[(2~{S})-pyrrolidin-2-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]([C@@H]1CCCN1)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
 M5E  M5E  (~{S})-phenyl-[(2~{S})-pyrrolidin-2-yl]methanol  ligand  28  13  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M5E
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
 M5E  C10  C  CR16  0  -0.239  -2.9550  -1.0788  -0.8028
 M5E  C13  C  CR16  0  -0.303  -1.7985   0.7205   0.9465
 M5E  C02  C  CH1   0  -0.053   0.2220   1.0243  -0.5039
 M5E  C03  C  CH1   0  -0.124   1.3065   0.3531   0.3435
 M5E  C04  C  CH2   0  -0.447   2.7112   0.9679   0.2182
 M5E  C05  C  CH2   0  -0.469   3.6526  -0.1849   0.6151
 M5E  C06  C  CH2   0  -0.324   2.7111  -1.4006   0.7745
 M5E  C08  C  CR6   0   0.143  -1.1310   0.3980  -0.2333
 M5E  C09  C  CR16  0  -0.337  -1.7269  -0.5040  -1.1079
 M5E  C11  C  CR16  0  -0.273  -3.6084  -0.7566   0.3784
 M5E  C12  C  CR16  0  -0.241  -3.0248   0.1500   1.2544
 M5E  N07  N  NH1   0  -0.578   1.4658  -1.0749   0.0865
 M5E  O01  O  OH1   0  -0.656   0.5388   1.0932  -1.8736
 M5E  H1   H  HCR6  0   0.254  -3.4044  -1.7790  -1.4954
 M5E  H2   H  HCR6  0   0.247  -1.3556   1.4337   1.6331
 M5E  H3   H  HCH1  0   0.253   0.1758   2.0666  -0.1734
 M5E  H4   H  HCH1  0   0.242   0.9842   0.4506   1.3872
 M5E  H5   H  HCH2  0   0.229   2.8944   1.2776  -0.8118
 M5E  H6   H  HCH2  0   0.234   2.8267   1.8492   0.8500
 M5E  H7   H  HCH2  0   0.231   4.3992  -0.3636  -0.1595
 M5E  H8   H  HCH2  0   0.232   4.1937   0.0197   1.5395
 M5E  H9   H  HCH2  0   0.238   3.1317  -2.3293   0.3897
 M5E  H10  H  HCH2  0   0.225   2.4915  -1.5581   1.8342
 M5E  H11  H  HCR6  0   0.236  -1.2524  -0.7690  -2.0445
 M5E  H12  H  HCR6  0   0.254  -4.5673  -1.2010   0.6112
 M5E  H13  H  HCR6  0   0.254  -3.5271   0.4193   2.1749
 M5E  H14  H  HNH1  0   0.327   1.6247  -1.2226  -0.9056
 M5E  H16  H  HOH1  0   0.447   0.7144   0.2150  -2.2242

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
 M5E  O01  C02  single    1.408  0.020  1.408
 M5E  N07  C06  single    1.460  0.020  1.460
 M5E  N07  C03  single    1.460  0.020  1.460
 M5E  C06  C05  single    1.546  0.020  1.546
 M5E  C02  C03  single    1.531  0.020  1.531
 M5E  C02  C08  single    1.515  0.020  1.515
 M5E  C03  C04  single    1.538  0.020  1.538
 M5E  C13  C08  aromatic  1.393  0.020  1.393
 M5E  C13  C12  aromatic  1.387  0.020  1.387
 M5E  C08  C09  aromatic  1.391  0.020  1.391
 M5E  C12  C11  aromatic  1.389  0.020  1.389
 M5E  C05  C04  single    1.540  0.020  1.540
 M5E  C09  C10  aromatic  1.390  0.020  1.390
 M5E  C11  C10  aromatic  1.388  0.020  1.388
 M5E  C10  H1   single    0.930  0.020  1.080
 M5E  C13  H2   single    0.930  0.020  1.080
 M5E  C02  H3   single    0.970  0.020  1.090
 M5E  C03  H4   single    0.970  0.020  1.090
 M5E  C04  H5   single    0.970  0.020  1.090
 M5E  C04  H6   single    0.970  0.020  1.090
 M5E  C05  H7   single    0.970  0.020  1.090
 M5E  C05  H8   single    0.970  0.020  1.090
 M5E  C06  H9   single    0.970  0.020  1.090
 M5E  C06  H10  single    0.970  0.020  1.090
 M5E  C09  H11  single    0.930  0.020  1.080
 M5E  C11  H12  single    0.930  0.020  1.080
 M5E  C12  H13  single    0.930  0.020  1.080
 M5E  N07  H14  single    0.890  0.020  1.040
 M5E  O01  H16  single    0.850  0.020  0.980

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
 M5E  H1   C10  C11  119.95  3.000
 M5E  H1   C10  C09  119.60  3.000
 M5E  C11  C10  C09  120.45  3.000
 M5E  H2   C13  C12  119.40  3.000
 M5E  H2   C13  C08  119.52  3.000
 M5E  C12  C13  C08  121.08  3.000
 M5E  H3   C02  O01  104.87  3.000
 M5E  H3   C02  C08  107.58  3.000
 M5E  O01  C02  C08  113.26  3.000
 M5E  H3   C02  C03  106.28  3.000
 M5E  C08  C02  C03  110.64  3.000
 M5E  O01  C02  C03  113.61  3.000
 M5E  H4   C03  N07  106.65  3.000
 M5E  H4   C03  C04  108.07  3.000
 M5E  N07  C03  C04  106.08  3.000
 M5E  H4   C03  C02  106.23  3.000
 M5E  C04  C03  C02  115.25  3.000
 M5E  N07  C03  C02  114.12  3.000
 M5E  H6   C04  H5   107.44  3.000
 M5E  H6   C04  C05  113.01  3.000
 M5E  H5   C04  C05  110.68  3.000
 M5E  H6   C04  C03  111.87  3.000
 M5E  H5   C04  C03  110.09  3.000
 M5E  C05  C04  C03  103.77  3.000
 M5E  H8   C05  H7   107.04  3.000
 M5E  H8   C05  C06  111.25  3.000
 M5E  H7   C05  C06  111.18  3.000
 M5E  H8   C05  C04  112.41  3.000
 M5E  H7   C05  C04  110.98  3.000
 M5E  C06  C05  C04  104.06  3.000
 M5E  H10  C06  H9   107.27  3.000
 M5E  H10  C06  N07  108.51  3.000
 M5E  H9   C06  N07  110.68  3.000
 M5E  H10  C06  C05  109.60  3.000
 M5E  H9   C06  C05  113.50  3.000
 M5E  N07  C06  C05  107.19  3.000
 M5E  C09  C08  C02  122.58  3.000
 M5E  C09  C08  C13  118.52  3.000
 M5E  C02  C08  C13  118.90  3.000
 M5E  H11  C09  C08  120.99  3.000
 M5E  H11  C09  C10  118.41  3.000
 M5E  C08  C09  C10  120.59  3.000
 M5E  H12  C11  C12  120.30  3.000
 M5E  H12  C11  C10  120.33  3.000
 M5E  C12  C11  C10  119.37  3.000
 M5E  H13  C12  C11  120.24  3.000
 M5E  H13  C12  C13  119.77  3.000
 M5E  C11  C12  C13  119.99  3.000
 M5E  H14  N07  C06  107.13  3.000
 M5E  H14  N07  C03  109.35  3.000
 M5E  C06  N07  C03  103.21  3.000
 M5E  H16  O01  C02  110.56  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
 M5E  CONST_01  C13  C08  C09  C10    0.00   0.0  0
 M5E  CONST_02  C13  C12  C11  C10    0.00   0.0  0
 M5E  CONST_03  C11  C12  C13  C08    0.00   0.0  0
 M5E  CONST_04  C11  C10  C09  C08    0.00   0.0  0
 M5E  CONST_05  C12  C13  C08  C09    0.00   0.0  0
 M5E  CONST_06  C12  C11  C10  C09    0.00   0.0  0
 M5E  CONST_07  C02  C08  C09  C10  180.00   0.0  0
 M5E  CONST_08  C12  C13  C08  C02  180.00   0.0  0
 M5E  CONST_09  H13  C12  C11  C10  180.00   0.0  0
 M5E  CONST_10  H11  C09  C08  C13  180.00   0.0  0
 M5E  CONST_11  H12  C11  C12  C13  180.00   0.0  0
 M5E  CONST_12  H1   C10  C09  C08  180.00   0.0  0
 M5E  CONST_13  H2   C13  C08  C09  180.00   0.0  0
 M5E  Var_01    C05  C06  N07  C03  -36.01  30.0  1
 M5E  Var_02    C06  C05  C04  C03    6.27  30.0  1
 M5E  Var_03    N07  C06  C05  C04   17.93  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
 M5E  chir_01  C02  O01  C03  C08  positiv
 M5E  chir_02  C03  N07  C04  C02  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
 M5E  plan-1  C10  0.020
 M5E  plan-1  C13  0.020
 M5E  plan-1  C02  0.020
 M5E  plan-1  C08  0.020
 M5E  plan-1  C09  0.020
 M5E  plan-1  C11  0.020
 M5E  plan-1  C12  0.020
 M5E  plan-1  H1   0.020
 M5E  plan-1  H2   0.020
 M5E  plan-1  H11  0.020
 M5E  plan-1  H12  0.020
 M5E  plan-1  H13  0.020

