# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 23:41:22 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 4-[(pyridin-2-yl)oxy]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(Oc2ccccn2)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
 DN7  DN7  '4-[(pyridin-2-yl)oxy]benzoic acid'  ligand  24  16  .  2021-08-08  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DN7
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
 DN7  C12  C  CR16   0  -0.292   1.8333   0.4544   1.1006
 DN7  C8   C  CR16   0  -0.148  -4.7538  -0.0081   0.0430
 DN7  C7   C  CR16   0  -0.389  -3.7097  -0.7995   0.4734
 DN7  C3   C  CR16   0  -0.291   1.9515  -0.9697  -0.8161
 DN7  C2   C  CR6    0  -0.101   2.5804  -0.0846   0.0553
 DN7  C1   C  C      0   0.397   4.0484   0.2809  -0.1235
 DN7  C4   C  CR16   0  -0.305   0.6150  -1.3079  -0.6567
 DN7  C5   C  CR6    0   0.354  -0.1023  -0.7592   0.3930
 DN7  C6   C  CR6    0   0.515  -2.4146  -0.3712   0.1735
 DN7  O1   O  OC    -1  -0.593   4.5259   1.0855   0.6993
 DN7  O2   O  O      0  -0.594   4.6445  -0.2556  -1.0771
 DN7  O3   O  O2     0  -0.521  -1.4042  -1.1607   0.5968
 DN7  C9   C  CR16   0  -0.347  -4.4826   1.1657  -0.6578
 DN7  C10  C  CR16   0  -0.060  -3.1601   1.4822  -0.8949
 DN7  N1   N  N      0  -0.440  -2.1390   0.7269  -0.4883
 DN7  C11  C  CR16   0  -0.296   0.4980   0.1253   1.2754
 DN7  H1   H  HCR6   0   0.249   2.3058   1.1407   1.7905
 DN7  H4   H  HCR6   0   0.248   2.5144  -1.4013  -1.6327
 DN7  H5   H  HCR6   0   0.261   0.1353  -1.9998  -1.3380
 DN7  H7   H  HCR6   0   0.269  -5.2751   1.8122  -1.0068
 DN7  H8   H  HCR6   0   0.266  -2.8985   2.3832  -1.4377
 DN7  H9   H  HCR6   0   0.261  -0.0698   0.5461   2.0959
 DN7  H2   H  HCR6   0   0.278  -5.7741  -0.3009   0.2519
 DN7  H3   H  HCR6   0   0.279  -3.8784  -1.7161   1.0220

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
 DN7  C8   C7   aromatic  1.379  0.020  1.379
 DN7  C8   C9   aromatic  1.394  0.020  1.394
 DN7  C7   C6   aromatic  1.397  0.020  1.397
 DN7  O2   C1   deloc     1.246  0.020  1.246
 DN7  C9   C10  aromatic  1.380  0.020  1.380
 DN7  C3   C4   aromatic  1.388  0.020  1.388
 DN7  C3   C2   aromatic  1.392  0.020  1.392
 DN7  C4   C5   aromatic  1.385  0.020  1.385
 DN7  C6   O3   single    1.350  0.020  1.350
 DN7  C6   N1   aromatic  1.311  0.020  1.311
 DN7  C1   C2   single    1.523  0.020  1.523
 DN7  C1   O1   deloc     1.246  0.020  1.246
 DN7  C2   C12  aromatic  1.393  0.020  1.393
 DN7  C5   O3   single    1.378  0.020  1.378
 DN7  C5   C11  aromatic  1.386  0.020  1.386
 DN7  C10  N1   aromatic  1.334  0.020  1.334
 DN7  C12  C11  aromatic  1.386  0.020  1.386
 DN7  C12  H1   single    0.930  0.020  1.080
 DN7  C8   H2   single    0.930  0.020  1.080
 DN7  C7   H3   single    0.930  0.020  1.080
 DN7  C3   H4   single    0.930  0.020  1.080
 DN7  C4   H5   single    0.930  0.020  1.080
 DN7  C9   H7   single    0.930  0.020  1.080
 DN7  C10  H8   single    0.930  0.020  1.080
 DN7  C11  H9   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
 DN7  H1   C12  C11  119.40  3.000
 DN7  H1   C12  C2   119.32  3.000
 DN7  C11  C12  C2   121.28  3.000
 DN7  H2   C8   C9   120.57  3.000
 DN7  H2   C8   C7   119.90  3.000
 DN7  C9   C8   C7   119.53  3.000
 DN7  H3   C7   C6   120.89  3.000
 DN7  H3   C7   C8   121.78  3.000
 DN7  C6   C7   C8   117.33  3.000
 DN7  H4   C3   C4   119.38  3.000
 DN7  H4   C3   C2   119.42  3.000
 DN7  C4   C3   C2   121.20  3.000
 DN7  C1   C2   C3   120.95  3.000
 DN7  C1   C2   C12  120.79  3.000
 DN7  C3   C2   C12  118.25  3.000
 DN7  O2   C1   O1   126.89  3.000
 DN7  O1   C1   C2   116.53  3.000
 DN7  O2   C1   C2   116.58  3.000
 DN7  H5   C4   C5   120.04  3.000
 DN7  H5   C4   C3   120.66  3.000
 DN7  C5   C4   C3   119.30  3.000
 DN7  C11  C5   O3   120.07  3.000
 DN7  C11  C5   C4   120.73  3.000
 DN7  O3   C5   C4   119.10  3.000
 DN7  N1   C6   O3   119.37  3.000
 DN7  N1   C6   C7   124.06  3.000
 DN7  O3   C6   C7   116.57  3.000
 DN7  C6   O3   C5   119.37  3.000
 DN7  H7   C9   C10  120.66  3.000
 DN7  H7   C9   C8   121.56  3.000
 DN7  C10  C9   C8   117.77  3.000
 DN7  H8   C10  N1   116.02  3.000
 DN7  H8   C10  C9   120.52  3.000
 DN7  N1   C10  C9   123.46  3.000
 DN7  C10  N1   C6   117.85  3.000
 DN7  H9   C11  C5   120.21  3.000
 DN7  H9   C11  C12  120.55  3.000
 DN7  C5   C11  C12  119.23  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
 DN7  CONST_01  C4   C3   C2   C12    0.00   0.0  0
 DN7  CONST_02  C4   C5   C11  C12    0.00   0.0  0
 DN7  CONST_03  N1   C6   C7   C8     0.00   0.0  0
 DN7  CONST_04  N1   C10  C9   C8     0.00   0.0  0
 DN7  CONST_05  C10  C9   C8   C7     0.00   0.0  0
 DN7  CONST_06  C10  N1   C6   C7     0.00   0.0  0
 DN7  CONST_07  C11  C5   C4   C3     0.00   0.0  0
 DN7  CONST_08  C11  C12  C2   C3     0.00   0.0  0
 DN7  CONST_09  C5   C4   C3   C2     0.00   0.0  0
 DN7  CONST_10  C5   C11  C12  C2     0.00   0.0  0
 DN7  CONST_11  C9   C8   C7   C6     0.00   0.0  0
 DN7  CONST_12  C9   C10  N1   C6     0.00   0.0  0
 DN7  CONST_13  O3   C5   C11  C12  180.00   0.0  0
 DN7  CONST_14  O3   C6   C7   C8   180.00   0.0  0
 DN7  CONST_15  O3   C5   C4   C3   180.00   0.0  0
 DN7  CONST_16  C4   C3   C2   C1   180.00   0.0  0
 DN7  CONST_17  C11  C12  C2   C1   180.00   0.0  0
 DN7  CONST_18  C10  N1   C6   O3   180.00   0.0  0
 DN7  CONST_19  H4   C3   C2   C12  180.00   0.0  0
 DN7  CONST_20  H8   C10  C9   C8   180.00   0.0  0
 DN7  CONST_21  H7   C9   C8   C7   180.00   0.0  0
 DN7  CONST_22  H1   C12  C2   C3   180.00   0.0  0
 DN7  CONST_23  H5   C4   C3   C2   180.00   0.0  0
 DN7  CONST_24  H9   C11  C12  C2   180.00   0.0  0
 DN7  CONST_25  H2   C8   C7   C6   180.00   0.0  0
 DN7  CONST_26  H3   C7   C8   C9   180.00   0.0  0
 DN7  Var_01    N1   C6   O3   C5     3.71  30.0  1
 DN7  Var_02    C11  C5   O3   C6    82.75  30.0  2
 DN7  Var_03    O2   C1   C2   C12  179.38  30.0  2

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
 DN7  plan-1  C8   0.020
 DN7  plan-1  C7   0.020
 DN7  plan-1  C6   0.020
 DN7  plan-1  O3   0.020
 DN7  plan-1  C9   0.020
 DN7  plan-1  C10  0.020
 DN7  plan-1  N1   0.020
 DN7  plan-1  H7   0.020
 DN7  plan-1  H8   0.020
 DN7  plan-1  H2   0.020
 DN7  plan-1  H3   0.020
 DN7  plan-2  C12  0.020
 DN7  plan-2  C3   0.020
 DN7  plan-2  C2   0.020
 DN7  plan-2  C1   0.020
 DN7  plan-2  C4   0.020
 DN7  plan-2  C5   0.020
 DN7  plan-2  O3   0.020
 DN7  plan-2  C11  0.020
 DN7  plan-2  H1   0.020
 DN7  plan-2  H4   0.020
 DN7  plan-2  H5   0.020
 DN7  plan-2  H9   0.020
 DN7  plan-3  C2   0.020
 DN7  plan-3  C1   0.020
 DN7  plan-3  O1   0.020
 DN7  plan-3  O2   0.020

