# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:21:39 2021
#   Inital geometry file: a 69 line input string
#   Ligand name: (2S)-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
 VW1  VW1  (2S)-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_VW1
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
 VW1  N1   N  NS    0  -0.259  -38.1067  38.7886  -14.6188
 VW1  C4   C  CR16  0  -0.354  -38.5371  41.2291  -10.4896
 VW1  C5   C  CR16  0  -0.226  -38.5748  40.2828  -11.4989
 VW1  C6   C  CR6   0  -0.021  -38.0298  40.5607  -12.7496
 VW1  C7   C  CSP   0   0.052  -38.0732  39.5815  -13.7824
 VW1  C8   C  CR16  0  -0.223  -37.4410  41.8064  -12.9868
 VW1  C10  C  C     0   0.482  -39.8617  43.2685   -8.4249
 VW1  C1   C  CH3   0  -0.673  -37.7639  44.3658   -7.6398
 VW1  C2   C  CH1   0  -0.114  -38.3342  43.2531   -8.5019
 VW1  C3   C  CR6   0   0.409  -37.9464  42.4701  -10.7289
 VW1  C9   C  CR16  0  -0.336  -37.4003  42.7502  -11.9851
 VW1  N2   N  NH2   0  -0.787  -40.4898  43.9847   -9.3608
 VW1  H5   H  HCR6  0   0.296  -38.9714  40.9724   -9.5337
 VW1  H6   H  HCR6  0   0.287  -39.0334  39.3224  -11.3064
 VW1  H7   H  HCR6  0   0.284  -37.0154  42.0320  -13.9551
 VW1  H1   H  HCH3  0   0.253  -38.0826  44.2321   -6.6075
 VW1  H2   H  HCH3  0   0.259  -36.6752  44.3383   -7.6615
 VW1  H3   H  HCH3  0   0.246  -38.0987  45.3460   -7.9788
 VW1  H4   H  HCH1  0   0.277  -37.9917  42.2888   -8.1137
 VW1  H8   H  HCR6  0   0.284  -36.9451  43.7153  -12.1654
 VW1  H9   H  HNH2  0   0.409  -41.4928  44.0763   -9.3374
 VW1  H10  H  HNH2  0   0.413  -39.9990  44.4961  -10.0742
 VW1  O1   O  O2    0  -0.477  -37.8529  43.4566   -9.8218
 VW1  O2   O  O     0  -0.482  -40.4251  42.6839   -7.5124

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
 VW1  C1   C2   single    1.519  0.020  1.519
 VW1  C2   O1   single    1.420  0.020  1.420
 VW1  O1   C3   single    1.343  0.020  1.343
 VW1  C3   C4   aromatic  1.395  0.020  1.395
 VW1  C4   C5   aromatic  1.384  0.020  1.384
 VW1  C5   C6   aromatic  1.392  0.020  1.392
 VW1  C6   C7   single    1.424  0.020  1.424
 VW1  C7   N1   triple    1.153  0.020  1.153
 VW1  C6   C8   aromatic  1.398  0.020  1.398
 VW1  C8   C9   aromatic  1.377  0.020  1.377
 VW1  C2   C10  single    1.529  0.020  1.529
 VW1  C10  O2   double    1.221  0.020  1.221
 VW1  C10  N2   single    1.335  0.020  1.335
 VW1  C3   C9   aromatic  1.398  0.020  1.398
 VW1  C4   H5   single    0.930  0.020  1.080
 VW1  C5   H6   single    0.930  0.020  1.080
 VW1  C8   H7   single    0.930  0.020  1.080
 VW1  C1   H1   single    0.970  0.020  1.090
 VW1  C1   H2   single    0.970  0.020  1.090
 VW1  C1   H3   single    0.970  0.020  1.090
 VW1  C2   H4   single    0.970  0.020  1.090
 VW1  C9   H8   single    0.930  0.020  1.080
 VW1  N2   H9   single    0.860  0.020  1.020
 VW1  N2   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
 VW1  H5   C4   C3   122.21  3.000
 VW1  H5   C4   C5   118.14  3.000
 VW1  C3   C4   C5   119.65  3.000
 VW1  H6   C5   C6   120.21  3.000
 VW1  H6   C5   C4   119.26  3.000
 VW1  C6   C5   C4   120.53  3.000
 VW1  C8   C6   C7   120.16  3.000
 VW1  C8   C6   C5   119.68  3.000
 VW1  C7   C6   C5   120.16  3.000
 VW1  C6   C7   N1   180.00  3.000
 VW1  H7   C8   C9   119.79  3.000
 VW1  H7   C8   C6   120.23  3.000
 VW1  C9   C8   C6   119.98  3.000
 VW1  N2   C10  O2   124.29  3.000
 VW1  N2   C10  C2   116.09  3.000
 VW1  O2   C10  C2   119.57  3.000
 VW1  H3   C1   H2   108.87  3.000
 VW1  H3   C1   H1   108.39  3.000
 VW1  H2   C1   H1   107.97  3.000
 VW1  H3   C1   C2   111.53  3.000
 VW1  H2   C1   C2   110.22  3.000
 VW1  H1   C1   C2   109.78  3.000
 VW1  H4   C2   O1   110.48  3.000
 VW1  H4   C2   C1   109.06  3.000
 VW1  O1   C2   C1   107.19  3.000
 VW1  H4   C2   C10  107.67  3.000
 VW1  O1   C2   C10  112.58  3.000
 VW1  C1   C2   C10  109.82  3.000
 VW1  C9   C3   O1   115.62  3.000
 VW1  C9   C3   C4   119.84  3.000
 VW1  O1   C3   C4   124.53  3.000
 VW1  H8   C9   C3   119.51  3.000
 VW1  H8   C9   C8   120.17  3.000
 VW1  C3   C9   C8   120.32  3.000
 VW1  H10  N2   H9   117.14  3.000
 VW1  H10  N2   C10  122.71  3.000
 VW1  H9   N2   C10  120.05  3.000
 VW1  C3   O1   C2   119.93  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
 VW1  CONST_01  C8   C9  C3   C4     0.00   0.0  0
 VW1  CONST_02  C8   C6  C5   C4     0.00   0.0  0
 VW1  CONST_03  C9   C3  C4   C5     0.00   0.0  0
 VW1  CONST_04  C9   C8  C6   C5     0.00   0.0  0
 VW1  CONST_05  C3   C4  C5   C6     0.00   0.0  0
 VW1  CONST_06  C3   C9  C8   C6     0.00   0.0  0
 VW1  CONST_07  C7   C6  C5   C4   180.00   0.0  0
 VW1  CONST_08  O1   C3  C4   C5   180.00   0.0  0
 VW1  CONST_09  C9   C8  C6   C7   180.00   0.0  0
 VW1  CONST_10  O1   C3  C9   C8   180.00   0.0  0
 VW1  CONST_11  H8   C9  C3   C4   180.00   0.0  0
 VW1  CONST_12  H7   C8  C6   C5   180.00   0.0  0
 VW1  CONST_13  H5   C4  C5   C6   180.00   0.0  0
 VW1  CONST_14  H6   C5  C6   C8   180.00   0.0  0
 VW1  CONST_15  H9   N2  C10  C2   180.00   0.0  0
 VW1  CONST_16  H10  N2  C10  C2     0.00   0.0  0
 VW1  Var_01    C9   C3  O1   C2  -177.73  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
 VW1  chir_01  C2  C1  O1  C10  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
 VW1  plan-1  N1   0.020
 VW1  plan-1  C4   0.020
 VW1  plan-1  C5   0.020
 VW1  plan-1  C6   0.020
 VW1  plan-1  C7   0.020
 VW1  plan-1  C8   0.020
 VW1  plan-1  C3   0.020
 VW1  plan-1  C9   0.020
 VW1  plan-1  H5   0.020
 VW1  plan-1  H6   0.020
 VW1  plan-1  H7   0.020
 VW1  plan-1  H8   0.020
 VW1  plan-1  O1   0.020
 VW1  plan-2  C10  0.020
 VW1  plan-2  C2   0.020
 VW1  plan-2  N2   0.020
 VW1  plan-2  H9   0.020
 VW1  plan-2  H10  0.020
 VW1  plan-2  O2   0.020

