# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 05:42:58 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (3~{S})-3-(4-chlorophenyl)-3-(2-oxidanylidene-1~{H}-pyridin-4-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@H](c1ccc(Cl)cc1)C2=CC(=O)NC=C2
#
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
 J6H  J6H  '(3~{S})-3-(4-chlorophenyl)-3-(2-oxidanylidene-1~{H}-pyridin-4-yl)propanoic acid'  ligand  31  19  .  2021-08-12  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J6H
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
 J6H  C2   C   C     0   0.560   0.2708   3.2571   0.1078
 J6H  C5   C   CH1   0  -0.431  -0.6579   0.9560  -0.3698
 J6H  C6   C   CR6   0   0.186   0.6559   0.2177  -0.2258
 J6H  C7   C   CR16  0  -0.334   1.4028   0.2256   0.9470
 J6H  C8   C   CR16  0  -0.191   2.5808  -0.5015   1.0539
 J6H  C11  C   CR16  0  -0.195   2.2910  -1.2759  -1.2102
 J6H  C12  C   CR16  0  -0.300   1.1183  -0.5433  -1.2964
 J6H  C13  C   CR6   0   0.321  -1.8057   0.0258  -0.0438
 J6H  C14  C   CR16  0  -0.433  -1.9216  -0.5322   1.2586
 J6H  C15  C   CR16  0   0.067  -2.9685  -1.3520   1.5165
 J6H  C19  C   CR16  0  -0.552  -2.7360  -0.2762  -0.9925
 J6H  O1   O   O     0  -0.432   0.9285   3.2458  -0.9011
 J6H  O3   O   OH1   0  -0.593   0.3510   4.2131   1.0253
 J6H  C4   C   CH2   0  -0.592  -0.7635   2.2252   0.4724
 J6H  C9   C   CR6   0  -0.058   3.0153  -1.2475  -0.0283
 J6H  CL1  CL  CL    0  -0.131   4.4868  -2.1564   0.0948
 J6H  N16  N   NR16  0  -0.663  -3.8812  -1.6389   0.5621
 J6H  C17  C   CR6   0   0.549  -3.8491  -1.1503  -0.7296
 J6H  O18  O   O     0  -0.514  -4.7177  -1.4652  -1.5396
 J6H  H20  H   HCH1  0   0.289  -0.7609   1.2455  -1.4181
 J6H  H24  H   HCR6  0   0.263   1.0838   0.8017   1.8069
 J6H  H25  H   HCR6  0   0.281   3.1491  -0.4828   1.9738
 J6H  H26  H   HCR6  0   0.280   2.6344  -1.8584  -2.0544
 J6H  H27  H   HCR6  0   0.263   0.5552  -0.5649  -2.2218
 J6H  H28  H   HCR6  0   0.272  -1.2028  -0.3255   2.0380
 J6H  H29  H   HCR6  0   0.312  -3.1302  -1.8158   2.4784
 J6H  H30  H   HCR6  0   0.268  -2.6640   0.1397  -1.9893
 J6H  H1   H   HOH1  0   0.482   0.9871   4.8899   0.7485
 J6H  H22  H   HCH2  0   0.284  -0.7214   2.0208   1.5442
 J6H  H23  H   HCH2  0   0.320  -1.7453   2.6795   0.3052
 J6H  H21  H   HNR6  0   0.422  -4.6489  -2.2530   0.7986

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
 J6H  O1   C2   double    1.204  0.020  1.204
 J6H  O3   C2   single    1.327  0.020  1.327
 J6H  C2   C4   single    1.506  0.020  1.506
 J6H  C15  N16  single    1.351  0.020  1.351
 J6H  C15  C14  double    1.354  0.020  1.354
 J6H  N16  C17  single    1.381  0.020  1.381
 J6H  C14  C13  single    1.422  0.020  1.422
 J6H  C17  O18  double    1.229  0.020  1.229
 J6H  C17  C19  single    1.440  0.020  1.440
 J6H  C4   C5   single    1.527  0.020  1.527
 J6H  C13  C19  double    1.363  0.020  1.363
 J6H  C13  C5   single    1.513  0.020  1.513
 J6H  C5   C6   single    1.514  0.020  1.514
 J6H  C6   C12  aromatic  1.393  0.020  1.393
 J6H  C6   C7   aromatic  1.390  0.020  1.390
 J6H  C12  C11  aromatic  1.385  0.020  1.385
 J6H  C7   C8   aromatic  1.388  0.020  1.388
 J6H  C11  C9   aromatic  1.387  0.020  1.387
 J6H  C8   C9   aromatic  1.384  0.020  1.384
 J6H  C9   CL1  single    1.734  0.020  1.734
 J6H  C5   H20  single    0.970  0.020  1.090
 J6H  C7   H24  single    0.930  0.020  1.080
 J6H  C8   H25  single    0.930  0.020  1.080
 J6H  C11  H26  single    0.930  0.020  1.080
 J6H  C12  H27  single    0.930  0.020  1.080
 J6H  C14  H28  single    0.930  0.020  1.080
 J6H  C15  H29  single    0.930  0.020  1.080
 J6H  C19  H30  single    0.930  0.020  1.080
 J6H  O3   H1   single    0.850  0.020  0.980
 J6H  C4   H22  single    0.970  0.020  1.090
 J6H  C4   H23  single    0.970  0.020  1.090
 J6H  N16  H21  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
 J6H  C4   C2   O3   111.57  3.000
 J6H  C4   C2   O1   124.85  3.000
 J6H  O3   C2   O1   123.56  3.000
 J6H  H20  C5   C4   107.61  3.000
 J6H  H20  C5   C13  107.35  3.000
 J6H  C4   C5   C13  109.86  3.000
 J6H  H20  C5   C6   107.59  3.000
 J6H  C13  C5   C6   109.75  3.000
 J6H  C4   C5   C6   114.39  3.000
 J6H  C12  C6   C7   118.25  3.000
 J6H  C7   C6   C5   122.93  3.000
 J6H  C12  C6   C5   118.79  3.000
 J6H  H24  C7   C8   117.86  3.000
 J6H  H24  C7   C6   120.97  3.000
 J6H  C8   C7   C6   121.17  3.000
 J6H  H25  C8   C9   120.62  3.000
 J6H  H25  C8   C7   120.15  3.000
 J6H  C9   C8   C7   119.23  3.000
 J6H  H26  C11  C9   120.70  3.000
 J6H  H26  C11  C12  120.33  3.000
 J6H  C9   C11  C12  118.97  3.000
 J6H  H27  C12  C11  118.86  3.000
 J6H  H27  C12  C6   119.66  3.000
 J6H  C11  C12  C6   121.48  3.000
 J6H  C19  C13  C14  119.68  3.000
 J6H  C19  C13  C5   120.28  3.000
 J6H  C14  C13  C5   120.04  3.000
 J6H  H28  C14  C15  119.52  3.000
 J6H  H28  C14  C13  122.11  3.000
 J6H  C15  C14  C13  118.36  3.000
 J6H  H29  C15  N16  115.90  3.000
 J6H  H29  C15  C14  123.04  3.000
 J6H  N16  C15  C14  121.07  3.000
 J6H  H30  C19  C17  116.93  3.000
 J6H  H30  C19  C13  120.70  3.000
 J6H  C17  C19  C13  122.37  3.000
 J6H  H1   O3   C2   110.19  3.000
 J6H  H23  C4   H22  105.20  3.000
 J6H  H23  C4   C5   108.83  3.000
 J6H  H22  C4   C5   112.53  3.000
 J6H  H23  C4   C2   107.13  3.000
 J6H  H22  C4   C2   109.84  3.000
 J6H  C5   C4   C2   112.87  3.000
 J6H  CL1  C9   C11  119.55  3.000
 J6H  CL1  C9   C8   119.56  3.000
 J6H  C11  C9   C8   120.89  3.000
 J6H  H21  N16  C17  116.82  3.000
 J6H  H21  N16  C15  118.45  3.000
 J6H  C17  N16  C15  124.72  3.000
 J6H  O18  C17  N16  120.62  3.000
 J6H  O18  C17  C19  125.58  3.000
 J6H  N16  C17  C19  113.80  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
 J6H  CONST_01  C9   C11  C12  C6     0.00   0.0  0
 J6H  CONST_02  C9   C8   C7   C6     0.00   0.0  0
 J6H  CONST_03  C11  C12  C6   C7     0.00   0.0  0
 J6H  CONST_04  C11  C9   C8   C7     0.00   0.0  0
 J6H  CONST_05  C12  C6   C7   C8     0.00   0.0  0
 J6H  CONST_06  C12  C11  C9   C8     0.00   0.0  0
 J6H  CONST_07  C19  C17  N16  C15    0.00   0.0  0
 J6H  CONST_08  C11  C12  C6   C5   180.00   0.0  0
 J6H  CONST_09  C8   C7   C6   C5   180.00   0.0  0
 J6H  CONST_10  CL1  C9   C8   C7   180.00   0.0  0
 J6H  CONST_11  CL1  C9   C11  C12  180.00   0.0  0
 J6H  CONST_12  O18  C17  N16  C15  180.00   0.0  0
 J6H  CONST_13  H26  C11  C12  C6   180.00   0.0  0
 J6H  CONST_14  H25  C8   C7   C6   180.00   0.0  0
 J6H  CONST_15  H27  C12  C6   C7   180.00   0.0  0
 J6H  CONST_16  H24  C7   C6   C12  180.00   0.0  0
 J6H  CONST_17  H21  N16  C17  C19  180.00   0.0  0
 J6H  CONST_18  H1   O3   C2   O1     0.00   0.0  0
 J6H  Var_01    O1   C2   C4   C5    15.20  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 J6H  chir_01  C5  C4  C13  C6  positiv

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
 J6H  plan-1  C5   0.020
 J6H  plan-1  C6   0.020
 J6H  plan-1  C7   0.020
 J6H  plan-1  C8   0.020
 J6H  plan-1  C11  0.020
 J6H  plan-1  C12  0.020
 J6H  plan-1  C9   0.020
 J6H  plan-1  CL1  0.020
 J6H  plan-1  H24  0.020
 J6H  plan-1  H25  0.020
 J6H  plan-1  H26  0.020
 J6H  plan-1  H27  0.020
 J6H  plan-2  C5   0.020
 J6H  plan-2  C13  0.020
 J6H  plan-2  C14  0.020
 J6H  plan-2  C15  0.020
 J6H  plan-2  C19  0.020
 J6H  plan-2  N16  0.020
 J6H  plan-2  C17  0.020
 J6H  plan-2  O18  0.020
 J6H  plan-2  H28  0.020
 J6H  plan-2  H29  0.020
 J6H  plan-2  H30  0.020
 J6H  plan-2  H21  0.020
 J6H  plan-3  C2   0.020
 J6H  plan-3  O1   0.020
 J6H  plan-3  O3   0.020
 J6H  plan-3  C4   0.020
 J6H  plan-3  H1   0.020

