# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 14:40:13 2021
#   Inital geometry file: a 69 line input string
#   Ligand name: (2R)-2-(4-cyanophenoxy)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Oc1ccc(cc1)C#N)C(N)=O
#
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
 WKD  WKD  (2R)-2-(4-cyanophenoxy)propanamide  ligand  24  14  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WKD
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
 WKD  C10  C  CR16  0  -0.227  -33.4952  22.7333  -1.7477
 WKD  C01  C  CH3   0  -0.672  -33.1601  20.1130   3.2704
 WKD  C02  C  CH1   0  -0.115  -33.0779  21.1098   2.1279
 WKD  C04  C  CR6   0   0.409  -34.3440  21.5153   0.1411
 WKD  C05  C  CR16  0  -0.336  -35.5436  21.2977  -0.5435
 WKD  C06  C  CR16  0  -0.223  -35.7155  21.7909  -1.8173
 WKD  C07  C  CR6   0  -0.021  -34.6875  22.5123  -2.4319
 WKD  C08  C  CSP   0   0.052  -34.8594  23.0179  -3.7518
 WKD  C11  C  CR16  0  -0.355  -33.3192  22.2411  -0.4662
 WKD  C12  C  C     0   0.483  -32.8761  22.5208   2.6825
 WKD  N09  N  NS    0  -0.259  -34.9985  23.4218  -4.8228
 WKD  N14  N  NH2   0  -0.787  -33.9866  23.2284   2.9037
 WKD  O03  O  O2    0  -0.476  -34.2735  20.9848   1.3736
 WKD  H1   H  HCR6  0   0.288  -32.6969  23.2940  -2.2141
 WKD  H2   H  HCH3  0   0.253  -32.2572  20.1725   3.8759
 WKD  H3   H  HCH3  0   0.246  -34.0184  20.3089   3.9131
 WKD  H4   H  HCH3  0   0.259  -33.2368  19.0988   2.8807
 WKD  H5   H  HCH1  0   0.276  -32.2074  20.8693   1.5095
 WKD  H6   H  HCR6  0   0.284  -36.3361  20.7379  -0.0645
 WKD  H7   H  HCR6  0   0.284  -36.6466  21.6172  -2.3395
 WKD  H8   H  HCR6  0   0.296  -32.3791  22.4367   0.0305
 WKD  H9   H  HNH2  0   0.410  -33.9285  24.1433   3.3217
 WKD  H10  H  HNH2  0   0.413  -34.9061  22.8604   2.7291
 WKD  O13  O  O     0  -0.482  -31.7475  22.9115   2.9381

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
 WKD  N09  C08  triple    1.153  0.020  1.153
 WKD  C08  C07  single    1.424  0.020  1.424
 WKD  C07  C06  aromatic  1.398  0.020  1.398
 WKD  C07  C10  aromatic  1.392  0.020  1.392
 WKD  C06  C05  aromatic  1.377  0.020  1.377
 WKD  C10  C11  aromatic  1.384  0.020  1.384
 WKD  C05  C04  aromatic  1.398  0.020  1.398
 WKD  C11  C04  aromatic  1.395  0.020  1.395
 WKD  C04  O03  single    1.344  0.020  1.344
 WKD  O03  C02  single    1.419  0.020  1.419
 WKD  C02  C12  single    1.529  0.020  1.529
 WKD  C02  C01  single    1.518  0.020  1.518
 WKD  O13  C12  double    1.221  0.020  1.221
 WKD  C12  N14  single    1.335  0.020  1.335
 WKD  C10  H1   single    0.930  0.020  1.080
 WKD  C01  H2   single    0.970  0.020  1.090
 WKD  C01  H3   single    0.970  0.020  1.090
 WKD  C01  H4   single    0.970  0.020  1.090
 WKD  C02  H5   single    0.970  0.020  1.090
 WKD  C05  H6   single    0.930  0.020  1.080
 WKD  C06  H7   single    0.930  0.020  1.080
 WKD  C11  H8   single    0.930  0.020  1.080
 WKD  N14  H9   single    0.860  0.020  1.020
 WKD  N14  H10  single    0.860  0.020  1.020

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
 WKD  H1   C10  C11  119.34  3.000
 WKD  H1   C10  C07  120.17  3.000
 WKD  C11  C10  C07  120.50  3.000
 WKD  H4   C01  H3   108.83  3.000
 WKD  H4   C01  H2   107.96  3.000
 WKD  H3   C01  H2   108.38  3.000
 WKD  H4   C01  C02  110.23  3.000
 WKD  H3   C01  C02  111.61  3.000
 WKD  H2   C01  C02  109.74  3.000
 WKD  H5   C02  O03  110.51  3.000
 WKD  H5   C02  C12  107.62  3.000
 WKD  O03  C02  C12  112.66  3.000
 WKD  H5   C02  C01  108.90  3.000
 WKD  C12  C02  C01  109.87  3.000
 WKD  O03  C02  C01  107.25  3.000
 WKD  O03  C04  C11  124.49  3.000
 WKD  O03  C04  C05  115.63  3.000
 WKD  C11  C04  C05  119.88  3.000
 WKD  H6   C05  C06  120.23  3.000
 WKD  H6   C05  C04  119.48  3.000
 WKD  C06  C05  C04  120.29  3.000
 WKD  H7   C06  C07  120.24  3.000
 WKD  H7   C06  C05  119.78  3.000
 WKD  C07  C06  C05  119.98  3.000
 WKD  C08  C07  C06  120.12  3.000
 WKD  C06  C07  C10  119.71  3.000
 WKD  C08  C07  C10  120.17  3.000
 WKD  N09  C08  C07  180.00  3.000
 WKD  H8   C11  C04  122.20  3.000
 WKD  H8   C11  C10  118.14  3.000
 WKD  C04  C11  C10  119.65  3.000
 WKD  O13  C12  N14  124.35  3.000
 WKD  N14  C12  C02  116.06  3.000
 WKD  O13  C12  C02  119.53  3.000
 WKD  H10  N14  H9   117.20  3.000
 WKD  H10  N14  C12  122.53  3.000
 WKD  H9   N14  C12  120.13  3.000
 WKD  C04  O03  C02  119.80  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
 WKD  CONST_01  C05  C06  C07  C10    0.00   0.0  0
 WKD  CONST_02  C05  C04  C11  C10    0.00   0.0  0
 WKD  CONST_03  C07  C06  C05  C04    0.00   0.0  0
 WKD  CONST_04  C07  C10  C11  C04    0.00   0.0  0
 WKD  CONST_05  C11  C10  C07  C06    0.00   0.0  0
 WKD  CONST_06  C11  C04  C05  C06    0.00   0.0  0
 WKD  CONST_07  O03  C04  C11  C10  180.00   0.0  0
 WKD  CONST_08  C08  C07  C06  C05  180.00   0.0  0
 WKD  CONST_09  O03  C04  C05  C06  180.00   0.0  0
 WKD  CONST_10  C11  C10  C07  C08  180.00   0.0  0
 WKD  CONST_11  H7   C06  C07  C10  180.00   0.0  0
 WKD  CONST_12  H1   C10  C11  C04  180.00   0.0  0
 WKD  CONST_13  H8   C11  C04  C05  180.00   0.0  0
 WKD  CONST_14  H6   C05  C06  C07  180.00   0.0  0
 WKD  CONST_15  H9   N14  C12  C02  180.00   0.0  0
 WKD  CONST_16  H10  N14  C12  C02    0.00   0.0  0
 WKD  Var_01    C05  C04  O03  C02  177.68  30.0  3

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
 WKD  chir_01  C02  O03  C12  C01  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
 WKD  plan-1  C10  0.020
 WKD  plan-1  C04  0.020
 WKD  plan-1  C05  0.020
 WKD  plan-1  C06  0.020
 WKD  plan-1  C07  0.020
 WKD  plan-1  C08  0.020
 WKD  plan-1  C11  0.020
 WKD  plan-1  N09  0.020
 WKD  plan-1  O03  0.020
 WKD  plan-1  H1   0.020
 WKD  plan-1  H6   0.020
 WKD  plan-1  H7   0.020
 WKD  plan-1  H8   0.020
 WKD  plan-2  C02  0.020
 WKD  plan-2  C12  0.020
 WKD  plan-2  N14  0.020
 WKD  plan-2  H9   0.020
 WKD  plan-2  H10  0.020
 WKD  plan-2  O13  0.020

