# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 06:48:35 2022
#   Inital geometry file: a 43 line input string
#   Ligand name: 5-bromopyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cncc(Br)c1
#
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
 Y31  Y31  '5-bromopyridine-3-carboxylic acid'  ligand  13  10  .  2022-03-29  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Y31
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
 Y31  C4  C   CR6    0  -0.174  -20.3913  12.8047  26.4442
 Y31  C5  C   CR16   0  -0.150  -21.4643  13.1501  27.2464
 Y31  BR  BR  BR     0  -0.038  -18.6285  13.2257  26.9639
 Y31  C3  C   CR16   0  -0.050  -20.6127  12.1456  25.2430
 Y31  N   N   N      0  -0.393  -21.8330  11.8329  24.8322
 Y31  C2  C   CR16   0  -0.079  -22.8647  12.1646  25.6003
 Y31  C1  C   CR6    0  -0.188  -22.7451  12.8249  26.8186
 Y31  C   C   C      0   0.411  -23.9700  13.1896  27.6574
 Y31  O   O   O      0  -0.578  -25.0687  12.8265  27.2031
 Y31  O1  O   OC    -1  -0.577  -23.7428  13.8145  28.7076
 Y31  H1  H   HCR6   0   0.279  -21.3250  13.6627  28.1892
 Y31  H2  H   HCR6   0   0.276  -19.7872  11.8653  24.5978
 Y31  H3  H   HCR6   0   0.261  -23.8469  11.8948  25.2313

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
 Y31  N   C3  aromatic  1.325  0.020  1.325
 Y31  N   C2  aromatic  1.328  0.020  1.328
 Y31  C3  C4  aromatic  1.388  0.020  1.388
 Y31  C2  C1  aromatic  1.391  0.020  1.391
 Y31  C4  BR  single    1.885  0.020  1.885
 Y31  C4  C5  aromatic  1.384  0.020  1.384
 Y31  C1  C5  aromatic  1.389  0.020  1.389
 Y31  C1  C   single    1.529  0.020  1.529
 Y31  O   C   deloc     1.243  0.020  1.243
 Y31  C   O1  deloc     1.243  0.020  1.243
 Y31  C5  H1  single    0.930  0.020  1.080
 Y31  C3  H2  single    0.930  0.020  1.080
 Y31  C2  H3  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
 Y31  C3  C4  BR  119.59  3.000
 Y31  BR  C4  C5  120.63  3.000
 Y31  C3  C4  C5  119.78  3.000
 Y31  H1  C5  C1  119.86  3.000
 Y31  H1  C5  C4  121.58  3.000
 Y31  C1  C5  C4  118.56  3.000
 Y31  H2  C3  N   117.10  3.000
 Y31  H2  C3  C4  121.07  3.000
 Y31  N   C3  C4  121.82  3.000
 Y31  C2  N   C3  118.50  3.000
 Y31  H3  C2  C1  119.64  3.000
 Y31  H3  C2  N   116.42  3.000
 Y31  C1  C2  N   123.94  3.000
 Y31  C   C1  C2  121.67  3.000
 Y31  C   C1  C5  120.94  3.000
 Y31  C2  C1  C5  117.40  3.000
 Y31  O1  C   O   128.11  3.000
 Y31  O1  C   C1  115.91  3.000
 Y31  O   C   C1  115.98  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
 Y31  CONST_01  C2  N   C3  C4     0.00   0.0  0
 Y31  CONST_02  C2  C1  C5  C4     0.00   0.0  0
 Y31  CONST_03  N   C3  C4  C5     0.00   0.0  0
 Y31  CONST_04  N   C2  C1  C5     0.00   0.0  0
 Y31  CONST_05  C1  C2  N   C3     0.00   0.0  0
 Y31  CONST_06  C1  C5  C4  C3     0.00   0.0  0
 Y31  CONST_07  C   C1  C5  C4   180.00   0.0  0
 Y31  CONST_08  N   C3  C4  BR   180.00   0.0  0
 Y31  CONST_09  C1  C5  C4  BR   180.00   0.0  0
 Y31  CONST_10  C   C1  C2  N    180.00   0.0  0
 Y31  CONST_11  H2  C3  C4  C5   180.00   0.0  0
 Y31  CONST_12  H3  C2  C1  C5   180.00   0.0  0
 Y31  CONST_13  H1  C5  C4  C3   180.00   0.0  0
 Y31  Var_01    O   C   C1  C5  -178.34  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
 Y31  plan-1  C4  0.020
 Y31  plan-1  C5  0.020
 Y31  plan-1  BR  0.020
 Y31  plan-1  C3  0.020
 Y31  plan-1  N   0.020
 Y31  plan-1  C2  0.020
 Y31  plan-1  C1  0.020
 Y31  plan-1  C   0.020
 Y31  plan-1  H1  0.020
 Y31  plan-1  H2  0.020
 Y31  plan-1  H3  0.020
 Y31  plan-2  C1  0.020
 Y31  plan-2  C   0.020
 Y31  plan-2  O   0.020
 Y31  plan-2  O1  0.020

