# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:06:43 2020
#   Inital geometry file: a 43 line input string
#   Ligand name: 2,6-dichloropyridine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(Cl)nc(Cl)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
 JKP  JKP  '2,6-dichloropyridine-4-carboxylic acid'  ligand  13  11  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JKP
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
 JKP  O01   O   OC    -1  -0.574  -3.3638  -0.9280   0.0323
 JKP  C02   C   C      0   0.424  -2.7569   0.1545   0.0207
 JKP  O03   O   O      0  -0.574  -3.2272   1.3031   0.0186
 JKP  C04   C   CR6    0   0.005  -1.2264   0.0596   0.0081
 JKP  C05   C   CR16   0  -0.301  -0.5928  -1.1770   0.0078
 JKP  C06   C   CR6    0   0.167   0.7897  -1.1901  -0.0039
 JKP  CL07  CL  CL     0  -0.100   1.6223  -2.7105  -0.0055
 JKP  N08   N   N      0  -0.384   1.5481  -0.1164  -0.0142
 JKP  C09   C   CR6    0   0.167   0.9310   1.0439  -0.0126
 JKP  CL10  CL  CL     0  -0.100   1.9487   2.4474  -0.0251
 JKP  C11   C   CR16   0  -0.301  -0.4424   1.2061  -0.0024
 JKP  H051  H   HCR6   0   0.286  -1.1650  -2.0931   0.0155
 JKP  H111  H   HCR6   0   0.285  -0.8907   2.1888  -0.0016

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
 JKP  CL07  C06   single    1.733  0.020  1.733
 JKP  O03   C02   deloc     1.241  0.020  1.241
 JKP  C05   C06   aromatic  1.383  0.020  1.383
 JKP  C05   C04   aromatic  1.389  0.020  1.389
 JKP  C06   N08   aromatic  1.315  0.020  1.315
 JKP  C02   C04   single    1.533  0.020  1.533
 JKP  C02   O01   deloc     1.241  0.020  1.241
 JKP  C04   C11   aromatic  1.389  0.020  1.389
 JKP  N08   C09   aromatic  1.314  0.020  1.314
 JKP  C11   C09   aromatic  1.383  0.020  1.383
 JKP  C09   CL10  single    1.734  0.020  1.734
 JKP  C05   H051  single    0.930  0.020  1.080
 JKP  C11   H111  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
 JKP  C04   C02  O03   115.81  3.000
 JKP  C04   C02  O01   115.73  3.000
 JKP  O03   C02  O01   128.46  3.000
 JKP  C11   C04  C05   118.50  3.000
 JKP  C11   C04  C02   120.82  3.000
 JKP  C05   C04  C02   120.68  3.000
 JKP  H051  C05  C06   121.44  3.000
 JKP  H051  C05  C04   120.88  3.000
 JKP  C06   C05  C04   117.68  3.000
 JKP  N08   C06  CL07  116.05  3.000
 JKP  N08   C06  C05   124.69  3.000
 JKP  CL07  C06  C05   119.25  3.000
 JKP  C09   N08  C06   116.75  3.000
 JKP  C11   C09  CL10  119.21  3.000
 JKP  CL10  C09  N08   116.04  3.000
 JKP  C11   C09  N08   124.75  3.000
 JKP  H111  C11  C09   121.26  3.000
 JKP  H111  C11  C04   121.11  3.000
 JKP  C09   C11  C04   117.63  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
 JKP  CONST_01  N08   C06  C05  C04     0.00   0.0  0
 JKP  CONST_02  N08   C09  C11  C04     0.00   0.0  0
 JKP  CONST_03  C09   N08  C06  C05     0.00   0.0  0
 JKP  CONST_04  C09   C11  C04  C05     0.00   0.0  0
 JKP  CONST_05  C11   C04  C05  C06     0.00   0.0  0
 JKP  CONST_06  C11   C09  N08  C06     0.00   0.0  0
 JKP  CONST_07  C06   C05  C04  C02   180.00   0.0  0
 JKP  CONST_08  C09   C11  C04  C02   180.00   0.0  0
 JKP  CONST_09  CL07  C06  C05  C04   180.00   0.0  0
 JKP  CONST_10  CL10  C09  C11  C04   180.00   0.0  0
 JKP  CONST_11  CL10  C09  N08  C06   180.00   0.0  0
 JKP  CONST_12  C09   N08  C06  CL07  180.00   0.0  0
 JKP  CONST_13  H111  C11  C04  C05   180.00   0.0  0
 JKP  CONST_14  H051  C05  C06  N08   180.00   0.0  0
 JKP  Var_01    C05   C04  C02  O01     0.10  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
 JKP  plan-1  C02   0.020
 JKP  plan-1  C04   0.020
 JKP  plan-1  C05   0.020
 JKP  plan-1  C06   0.020
 JKP  plan-1  CL07  0.020
 JKP  plan-1  N08   0.020
 JKP  plan-1  C09   0.020
 JKP  plan-1  CL10  0.020
 JKP  plan-1  C11   0.020
 JKP  plan-1  H051  0.020
 JKP  plan-1  H111  0.020
 JKP  plan-2  O01   0.020
 JKP  plan-2  C02   0.020
 JKP  plan-2  O03   0.020
 JKP  plan-2  C04   0.020

