# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:55:16 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 3-(pyridin-2-yl)-1H-pyrazole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1[nH]nc(c1)c2ccccn2
#
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
 ODK  ODK  '3-(pyridin-2-yl)-1H-pyrazole-5-carboxylic acid'  ligand  20  14  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ODK
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
 ODK  C12  C  CR16   0  -0.312   2.5531   1.1672   0.0183
 ODK  C14  C  CR16   0  -0.158   3.9120   0.9082   0.0121
 ODK  C13  C  CR16   0  -0.324   4.3479  -0.4095  -0.0064
 ODK  C11  C  CR16   0  -0.080   3.3881  -1.4098  -0.0178
 ODK  N8   N  N      0  -0.432   2.0830  -1.1734  -0.0120
 ODK  C7   C  CR6    0   0.184   1.6645   0.0910   0.0058
 ODK  C4   C  CR5    0   0.236   0.2145   0.2935   0.0117
 ODK  C2   C  CR15   0  -0.514  -0.7941  -0.6875   0.0061
 ODK  C1   C  CR5    0   0.228  -1.9748   0.0217   0.0146
 ODK  C6   C  C      0   0.372  -3.4177  -0.4059   0.0138
 ODK  O10  O  O      0  -0.582  -3.6211  -1.6306   0.0061
 ODK  O9   O  OC    -1  -0.600  -4.2518   0.5191   0.0204
 ODK  N5   N  NR15   0  -0.453  -1.6160   1.3207   0.0246
 ODK  N3   N  N      0  -0.293  -0.3123   1.5134   0.0230
 ODK  H12  H  HCR6   0   0.265   2.1810   2.1824   0.0333
 ODK  H14  H  HCR6   0   0.272   4.6227   1.7241   0.0217
 ODK  H13  H  HCR6   0   0.269   5.4003  -0.6570  -0.0118
 ODK  H11  H  HCR6   0   0.260   3.6867  -2.4522  -0.0324
 ODK  H2   H  HCR5   0   0.255  -0.6719  -1.7568  -0.0027
 ODK  HN5  H  HNR5   0   0.408  -2.2497   2.1053   0.0321

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
 ODK  C12  C7   aromatic  1.396  0.020  1.396
 ODK  C12  C14  aromatic  1.383  0.020  1.383
 ODK  C12  H12  single    0.930  0.020  1.080
 ODK  C14  C13  aromatic  1.388  0.020  1.388
 ODK  C14  H14  single    0.930  0.020  1.080
 ODK  C13  C11  aromatic  1.386  0.020  1.386
 ODK  C13  H13  single    0.930  0.020  1.080
 ODK  N8   C11  aromatic  1.326  0.020  1.326
 ODK  C11  H11  single    0.930  0.020  1.080
 ODK  C7   N8   aromatic  1.332  0.020  1.332
 ODK  C4   C7   single    1.464  0.020  1.464
 ODK  N3   C4   aromatic  1.329  0.020  1.329
 ODK  C4   C2   aromatic  1.407  0.020  1.407
 ODK  C1   C2   aromatic  1.377  0.020  1.377
 ODK  C2   H2   single    0.930  0.020  1.080
 ODK  N5   C1   aromatic  1.348  0.020  1.348
 ODK  C6   C1   single    1.505  0.020  1.505
 ODK  O10  C6   deloc     1.241  0.020  1.241
 ODK  C6   O9   deloc     1.246  0.020  1.246
 ODK  N5   N3   aromatic  1.318  0.020  1.318
 ODK  N5   HN5  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
 ODK  H12  C12  C7   120.33  3.000
 ODK  H12  C12  C14  120.92  3.000
 ODK  C7   C12  C14  118.75  3.000
 ODK  H14  C14  C13  120.64  3.000
 ODK  H14  C14  C12  120.26  3.000
 ODK  C13  C14  C12  119.10  3.000
 ODK  H13  C13  C11  120.58  3.000
 ODK  H13  C13  C14  121.54  3.000
 ODK  C11  C13  C14  117.88  3.000
 ODK  H11  C11  N8   116.26  3.000
 ODK  H11  C11  C13  120.20  3.000
 ODK  N8   C11  C13  123.55  3.000
 ODK  C7   N8   C11  118.58  3.000
 ODK  C4   C7   N8   116.27  3.000
 ODK  C4   C7   C12  121.59  3.000
 ODK  N8   C7   C12  122.14  3.000
 ODK  N3   C4   C2   110.85  3.000
 ODK  C2   C4   C7   127.84  3.000
 ODK  N3   C4   C7   121.31  3.000
 ODK  H2   C2   C1   127.51  3.000
 ODK  H2   C2   C4   127.69  3.000
 ODK  C1   C2   C4   104.80  3.000
 ODK  N5   C1   C6   121.95  3.000
 ODK  C6   C1   C2   132.50  3.000
 ODK  N5   C1   C2   105.55  3.000
 ODK  O9   C6   O10  128.53  3.000
 ODK  O9   C6   C1   115.53  3.000
 ODK  O10  C6   C1   115.94  3.000
 ODK  HN5  N5   N3   120.51  3.000
 ODK  HN5  N5   C1   125.64  3.000
 ODK  N3   N5   C1   113.85  3.000
 ODK  N5   N3   C4   104.95  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
 ODK  CONST_01  C11  N8   C7   C12    0.00   0.0  0
 ODK  CONST_02  N3   C4   C7   C12    0.00   0.0  0
 ODK  CONST_03  C2   C4   C7   C12  180.00   0.0  0
 ODK  CONST_04  C11  C13  C14  C12    0.00   0.0  0
 ODK  CONST_05  N8   C7   C12  C14    0.00   0.0  0
 ODK  CONST_06  C4   C7   C12  C14  180.00   0.0  0
 ODK  CONST_07  N8   C11  C13  C14    0.00   0.0  0
 ODK  CONST_08  C7   C12  C14  C13    0.00   0.0  0
 ODK  CONST_09  C7   N8   C11  C13    0.00   0.0  0
 ODK  CONST_10  C4   C7   N8   C11  180.00   0.0  0
 ODK  CONST_11  N3   C4   C7   N8   180.00   0.0  0
 ODK  CONST_12  C2   C4   C7   N8     0.00   0.0  0
 ODK  CONST_13  N5   N3   C4   C7   180.00   0.0  0
 ODK  CONST_14  C1   C2   C4   C7   180.00   0.0  0
 ODK  CONST_15  C1   N5   N3   C4     0.00   0.0  0
 ODK  CONST_16  N5   C1   C2   C4     0.00   0.0  0
 ODK  CONST_17  N5   N3   C4   C2     0.00   0.0  0
 ODK  CONST_18  N3   N5   C1   C2     0.00   0.0  0
 ODK  CONST_19  N3   C4   C2   C1     0.00   0.0  0
 ODK  CONST_20  C6   C1   C2   C4   180.00   0.0  0
 ODK  CONST_21  N3   N5   C1   C6   180.00   0.0  0
 ODK  CONST_22  H13  C13  C14  C12  180.00   0.0  0
 ODK  CONST_23  H11  C11  C13  C14  180.00   0.0  0
 ODK  CONST_24  H12  C12  C14  C13  180.00   0.0  0
 ODK  CONST_25  H14  C14  C13  C11  180.00   0.0  0
 ODK  CONST_26  H2   C2   C4   C7     0.00   0.0  0
 ODK  CONST_27  HN5  N5   N3   C4   180.00   0.0  0
 ODK  Var_01    O10  C6   C1   C2     0.13  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
 ODK  plan-1  C7   0.020
 ODK  plan-1  C4   0.020
 ODK  plan-1  C2   0.020
 ODK  plan-1  C1   0.020
 ODK  plan-1  C6   0.020
 ODK  plan-1  N5   0.020
 ODK  plan-1  N3   0.020
 ODK  plan-1  H2   0.020
 ODK  plan-1  HN5  0.020
 ODK  plan-2  C12  0.020
 ODK  plan-2  C14  0.020
 ODK  plan-2  C13  0.020
 ODK  plan-2  C11  0.020
 ODK  plan-2  N8   0.020
 ODK  plan-2  C7   0.020
 ODK  plan-2  C4   0.020
 ODK  plan-2  H12  0.020
 ODK  plan-2  H14  0.020
 ODK  plan-2  H13  0.020
 ODK  plan-2  H11  0.020
 ODK  plan-3  C1   0.020
 ODK  plan-3  C6   0.020
 ODK  plan-3  O10  0.020
 ODK  plan-3  O9   0.020

