# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 18:35:13 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 2-[4-[(2-oxidanylidene-3~{H}-pyridin-4-yl)oxy]phenyl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1ccc(OC2=CC=NC(=O)C2)cc1
#
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
 HGK  HGK  '2-[4-[(2-oxidanylidene-3~{H}-pyridin-4-yl)oxy]phenyl]ethanoic acid'  ligand  28  18  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HGK
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
 HGK  C4   C  CR16   0  -0.316  -1.7788  -1.0639  -0.4414
 HGK  C5   C  CR16   0  -0.280  -0.5798  -0.6450  -1.0046
 HGK  C6   C  CR6    0   0.270  -0.0330   0.5551  -0.5920
 HGK  C11  C  C      0  -0.727   2.4060  -0.2136   0.5310
 HGK  C7   C  CR6    0   0.490   2.3230   0.6513  -0.6735
 HGK  C8   C  CR16   0  -0.431   3.4536   1.0779  -1.2760
 HGK  C9   C  CR16   0  -0.020   4.7024   0.6804  -0.7159
 HGK  C10  C  CR6    0   0.469   3.8119  -0.4887   1.0417
 HGK  C12  C  CR16   0  -0.284  -0.6596   1.3389   0.3632
 HGK  C13  C  CR16   0  -0.299  -1.8579   0.9052   0.9076
 HGK  N1   N  N      0  -0.453   4.9104  -0.0369   0.3436
 HGK  C3   C  CR6    0   0.177  -2.4369  -0.3028   0.5206
 HGK  O1   O  OC    -1  -0.619  -6.0729  -0.5748   0.7624
 HGK  C1   C  C      0   0.423  -4.9825  -0.0053   0.5636
 HGK  O2   O  O      0  -0.595  -4.7983   1.0945   0.0149
 HGK  C2   C  CH2    0  -0.688  -3.7360  -0.7549   1.1051
 HGK  O3   O  O2     0  -0.472   1.1440   1.0060  -1.1730
 HGK  O4   O  O      0  -0.435   3.9517  -1.1238   2.0660
 HGK  H1   H  HCR6   0   0.255  -2.2059  -2.0067  -0.7615
 HGK  H2   H  HCR6   0   0.277  -0.0837  -1.2478  -1.7553
 HGK  H3   H  H      0   0.333   1.8203   0.2112   1.3526
 HGK  H4   H  H      0   0.337   1.9379  -1.1827   0.3215
 HGK  H5   H  HCR6   0   0.286   3.4381   1.6980  -2.1608
 HGK  H6   H  HCR6   0   0.284   5.5931   1.0201  -1.2376
 HGK  H7   H  HCR6   0   0.275  -0.2196   2.2788   0.6729
 HGK  H8   H  HCR6   0   0.252  -2.3429   1.5159   1.6586
 HGK  H10  H  HCH2   0   0.240  -3.8654  -1.8287   0.9532
 HGK  H11  H  HCH2   0   0.253  -3.7240  -0.6047   2.1904

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
 HGK  O4   C10  double    1.213  0.020  1.213
 HGK  C10  N1   single    1.378  0.020  1.378
 HGK  C10  C11  single    1.521  0.020  1.521
 HGK  N1   C9   double    1.296  0.020  1.296
 HGK  C11  C7   single    1.485  0.020  1.485
 HGK  C9   C8   single    1.425  0.020  1.425
 HGK  C7   C8   double    1.350  0.020  1.350
 HGK  C7   O3   single    1.329  0.020  1.329
 HGK  O3   C6   single    1.388  0.020  1.388
 HGK  C12  C6   aromatic  1.385  0.020  1.385
 HGK  C12  C13  aromatic  1.386  0.020  1.386
 HGK  C6   C5   aromatic  1.382  0.020  1.382
 HGK  C13  C3   aromatic  1.394  0.020  1.394
 HGK  C5   C4   aromatic  1.389  0.020  1.389
 HGK  C3   C4   aromatic  1.392  0.020  1.392
 HGK  C3   C2   single    1.495  0.020  1.495
 HGK  C2   C1   single    1.552  0.020  1.552
 HGK  O2   C1   deloc     1.243  0.020  1.243
 HGK  C1   O1   deloc     1.246  0.020  1.246
 HGK  C4   H1   single    0.930  0.020  1.080
 HGK  C5   H2   single    0.930  0.020  1.080
 HGK  C11  H3   single    0.970  0.020  1.090
 HGK  C11  H4   single    0.970  0.020  1.090
 HGK  C8   H5   single    0.930  0.020  1.080
 HGK  C9   H6   single    0.930  0.020  1.080
 HGK  C12  H7   single    0.930  0.020  1.080
 HGK  C13  H8   single    0.930  0.020  1.080
 HGK  C2   H10  single    0.970  0.020  1.090
 HGK  C2   H11  single    0.970  0.020  1.090

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
 HGK  H1   C4   C3   119.58  3.000
 HGK  H1   C4   C5   118.86  3.000
 HGK  C3   C4   C5   121.56  3.000
 HGK  H2   C5   C6   120.60  3.000
 HGK  H2   C5   C4   120.57  3.000
 HGK  C6   C5   C4   118.83  3.000
 HGK  O3   C6   C12  119.23  3.000
 HGK  C12  C6   C5   121.21  3.000
 HGK  O3   C6   C5   119.52  3.000
 HGK  H4   C11  H3   104.94  3.000
 HGK  H4   C11  C10  107.39  3.000
 HGK  H3   C11  C10  108.23  3.000
 HGK  H4   C11  C7   109.63  3.000
 HGK  H3   C11  C7   110.66  3.000
 HGK  C10  C11  C7   115.43  3.000
 HGK  O3   C7   C8   119.40  3.000
 HGK  O3   C7   C11  120.66  3.000
 HGK  C8   C7   C11  119.94  3.000
 HGK  H5   C8   C9   119.63  3.000
 HGK  H5   C8   C7   122.32  3.000
 HGK  C9   C8   C7   118.05  3.000
 HGK  H6   C9   N1   115.71  3.000
 HGK  H6   C9   C8   116.25  3.000
 HGK  N1   C9   C8   128.04  3.000
 HGK  O4   C10  N1   120.50  3.000
 HGK  N1   C10  C11  120.50  3.000
 HGK  O4   C10  C11  118.99  3.000
 HGK  H7   C12  C13  120.70  3.000
 HGK  H7   C12  C6   120.30  3.000
 HGK  C13  C12  C6   119.00  3.000
 HGK  H8   C13  C3   119.69  3.000
 HGK  H8   C13  C12  118.90  3.000
 HGK  C3   C13  C12  121.41  3.000
 HGK  C10  N1   C9   117.88  3.000
 HGK  C2   C3   C13  120.96  3.000
 HGK  C2   C3   C4   121.05  3.000
 HGK  C13  C3   C4   117.98  3.000
 HGK  C2   C1   O2   117.54  3.000
 HGK  O2   C1   O1   127.20  3.000
 HGK  C2   C1   O1   115.24  3.000
 HGK  H11  C2   H10  105.89  3.000
 HGK  H11  C2   C1   106.75  3.000
 HGK  H10  C2   C1   109.34  3.000
 HGK  H11  C2   C3   109.65  3.000
 HGK  H10  C2   C3   110.25  3.000
 HGK  C1   C2   C3   114.55  3.000
 HGK  C7   O3   C6   120.56  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
 HGK  CONST_01  C12  C6   C5   C4      0.00   0.0  0
 HGK  CONST_02  C12  C13  C3   C4      0.00   0.0  0
 HGK  CONST_03  C13  C12  C6   C5      0.00   0.0  0
 HGK  CONST_04  C13  C3   C4   C5      0.00   0.0  0
 HGK  CONST_05  C3   C13  C12  C6      0.00   0.0  0
 HGK  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 HGK  CONST_07  O3   C6   C5   C4    180.00   0.0  0
 HGK  CONST_08  C2   C3   C4   C5    180.00   0.0  0
 HGK  CONST_09  C2   C3   C13  C12   180.00   0.0  0
 HGK  CONST_10  O3   C6   C12  C13   180.00   0.0  0
 HGK  CONST_11  H8   C13  C3   C4    180.00   0.0  0
 HGK  CONST_12  H7   C12  C6   C5    180.00   0.0  0
 HGK  CONST_13  H1   C4   C5   C6    180.00   0.0  0
 HGK  CONST_14  H2   C5   C6   C12   180.00   0.0  0
 HGK  Var_01    C9   C8   C7   C11    -0.40  30.0  1
 HGK  Var_02    N1   C10  C11  C7     -4.93  30.0  1
 HGK  Var_03    N1   C9   C8   C7     -1.55  30.0  1
 HGK  Var_04    C10  C11  C7   C8      3.34  30.0  1
 HGK  Var_05    C11  C7   O3   C6     -1.15  30.0  2
 HGK  Var_06    C12  C6   O3   C7     93.43  30.0  2
 HGK  Var_07    C1   C2   C3   C4   -103.98  30.0  2
 HGK  Var_08    O2   C1   C2   C3    -19.26  30.0  3

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
 HGK  plan-1  C4   0.020
 HGK  plan-1  C5   0.020
 HGK  plan-1  C6   0.020
 HGK  plan-1  C12  0.020
 HGK  plan-1  C13  0.020
 HGK  plan-1  C3   0.020
 HGK  plan-1  C2   0.020
 HGK  plan-1  O3   0.020
 HGK  plan-1  H1   0.020
 HGK  plan-1  H2   0.020
 HGK  plan-1  H7   0.020
 HGK  plan-1  H8   0.020
 HGK  plan-2  O1   0.020
 HGK  plan-2  C1   0.020
 HGK  plan-2  O2   0.020
 HGK  plan-2  C2   0.020
 HGK  plan-3  C11  0.020
 HGK  plan-3  C10  0.020
 HGK  plan-3  N1   0.020
 HGK  plan-3  O4   0.020

