# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 04:51:55 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (2R)-2-{4-[(3,5-dichloropyridin-2-yl)oxy]phenoxy}propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Oc1ccc(Oc2ncc(Cl)cc2Cl)cc1)C(O)=O
#
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
 O0D  O0D  '(2R)-2-{4-[(3,5-dichloropyridin-2-yl)oxy]phenoxy}propanoic acid'  ligand  31  21  .  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_O0D
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
 O0D  CL01  CL  CL     0  -0.084  -3.8342   2.5371  -0.9575
 O0D  C02   C   CR6    0  -0.200  -3.5813   0.9519  -0.3441
 O0D  C03   C   CR6    0   0.585  -2.2809   0.4855  -0.1119
 O0D  O04   O   O2     0  -0.507  -1.2744   1.3213  -0.3899
 O0D  C05   C   CR6    0   0.331   0.0241   0.9209  -0.1291
 O0D  C06   C   CR16   0  -0.295   0.7975   0.4124  -1.1521
 O0D  C07   C   CR16   0  -0.384   2.1279   0.0794  -0.9237
 O0D  C08   C   CR6    0   0.396   2.6887   0.2576   0.3411
 O0D  O09   O   O2     0  -0.472   3.9619  -0.0053   0.6713
 O0D  C10   C   CH1    0  -0.124   4.8699  -0.5206  -0.2961
 O0D  C11   C   CH3    0  -0.683   4.6852  -2.0225  -0.4619
 O0D  C12   C   C      0   0.401   6.3112  -0.1762   0.1428
 O0D  O13   O   OC    -1  -0.616   7.1891  -0.5839  -0.6428
 O0D  O14   O   O      0  -0.591   6.4707   0.4584   1.1959
 O0D  C15   C   CR16   0  -0.360   1.8849   0.7667   1.3673
 O0D  C16   C   CR16   0  -0.285   0.5629   1.0965   1.1361
 O0D  N17   N   N      0  -0.430  -2.0432  -0.7146   0.3530
 O0D  C18   C   CR16   0  -0.020  -3.0571  -1.5291   0.6214
 O0D  C19   C   CR6    0  -0.141  -4.3700  -1.1505   0.4239
 O0D  CL20  CL  CL     0  -0.107  -5.6571  -2.2380   0.7878
 O0D  C21   C   CR16   0  -0.039  -4.6428   0.1192  -0.0717
 O0D  H1    H   HCR6   0   0.272   0.3755   0.2739  -2.1396
 O0D  H2    H   HCR6   0   0.281   2.7021  -0.3155  -1.7500
 O0D  H3    H   HCH1   0   0.228   4.7006  -0.0254  -1.2605
 O0D  H4    H   HCH3   0   0.229   4.9150  -2.5487   0.4663
 O0D  H5    H   HCH3   0   0.231   3.6657  -2.2812  -0.7508
 O0D  H6    H   HCH3   0   0.236   5.3525  -2.3949  -1.2360
 O0D  H8    H   HCR6   0   0.265   2.3114   0.9110   2.3522
 O0D  H9    H   HCR6   0   0.271  -0.0401   1.4995   1.9401
 O0D  H10   H   HCR6   0   0.295  -2.8117  -2.5117   1.0051
 O0D  H11   H   HCR6   0   0.317  -5.6588   0.4495  -0.2389

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
 O0D  CL20  C19   single    1.724  0.020  1.724
 O0D  C18   C19   aromatic  1.381  0.020  1.381
 O0D  C18   N17   aromatic  1.328  0.020  1.328
 O0D  C19   C21   aromatic  1.390  0.020  1.390
 O0D  N17   C03   aromatic  1.309  0.020  1.309
 O0D  C21   C02   aromatic  1.376  0.020  1.376
 O0D  C03   C02   aromatic  1.401  0.020  1.401
 O0D  C03   O04   single    1.338  0.020  1.338
 O0D  C02   CL01  single    1.718  0.020  1.718
 O0D  O04   C05   single    1.384  0.020  1.384
 O0D  C06   C05   aromatic  1.380  0.020  1.380
 O0D  C06   C07   aromatic  1.390  0.020  1.390
 O0D  C05   C16   aromatic  1.386  0.020  1.386
 O0D  C07   C08   aromatic  1.395  0.020  1.395
 O0D  O14   C12   deloc     1.240  0.020  1.240
 O0D  C16   C15   aromatic  1.382  0.020  1.382
 O0D  C08   C15   aromatic  1.399  0.020  1.399
 O0D  C08   O09   single    1.341  0.020  1.341
 O0D  C12   C10   single    1.545  0.020  1.545
 O0D  C12   O13   deloc     1.247  0.020  1.247
 O0D  C10   O09   single    1.423  0.020  1.423
 O0D  C10   C11   single    1.522  0.020  1.522
 O0D  C06   H1    single    0.930  0.020  1.080
 O0D  C07   H2    single    0.930  0.020  1.080
 O0D  C10   H3    single    0.970  0.020  1.090
 O0D  C11   H4    single    0.970  0.020  1.090
 O0D  C11   H5    single    0.970  0.020  1.090
 O0D  C11   H6    single    0.970  0.020  1.090
 O0D  C15   H8    single    0.930  0.020  1.080
 O0D  C16   H9    single    0.930  0.020  1.080
 O0D  C18   H10   single    0.930  0.020  1.080
 O0D  C21   H11   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
 O0D  C21   C02  C03   118.79  3.000
 O0D  C03   C02  CL01  120.19  3.000
 O0D  C21   C02  CL01  121.01  3.000
 O0D  N17   C03  O04   120.67  3.000
 O0D  O04   C03  C02   117.13  3.000
 O0D  N17   C03  C02   122.19  3.000
 O0D  C05   O04  C03   119.09  3.000
 O0D  C16   C05  C06   120.37  3.000
 O0D  C16   C05  O04   120.01  3.000
 O0D  C06   C05  O04   119.54  3.000
 O0D  H1    C06  C07   119.48  3.000
 O0D  H1    C06  C05   120.32  3.000
 O0D  C07   C06  C05   120.19  3.000
 O0D  H2    C07  C08   121.75  3.000
 O0D  H2    C07  C06   118.05  3.000
 O0D  C08   C07  C06   120.20  3.000
 O0D  C15   C08  O09   115.85  3.000
 O0D  O09   C08  C07   125.43  3.000
 O0D  C15   C08  C07   118.71  3.000
 O0D  C10   O09  C08   120.61  3.000
 O0D  H3    C10  C12   107.03  3.000
 O0D  H3    C10  C11   109.32  3.000
 O0D  C12   C10  C11   111.35  3.000
 O0D  H3    C10  O09   109.60  3.000
 O0D  C11   C10  O09   110.72  3.000
 O0D  C12   C10  O09   108.74  3.000
 O0D  H6    C11  H5    107.68  3.000
 O0D  H6    C11  H4    108.11  3.000
 O0D  H5    C11  H4    107.92  3.000
 O0D  H6    C11  C10   109.93  3.000
 O0D  H5    C11  C10   112.11  3.000
 O0D  H4    C11  C10   110.95  3.000
 O0D  O14   C12  O13   127.74  3.000
 O0D  O13   C12  C10   113.88  3.000
 O0D  O14   C12  C10   118.37  3.000
 O0D  H8    C15  C16   119.81  3.000
 O0D  H8    C15  C08   119.29  3.000
 O0D  C16   C15  C08   120.90  3.000
 O0D  H9    C16  C15   119.82  3.000
 O0D  H9    C16  C05   120.55  3.000
 O0D  C15   C16  C05   119.62  3.000
 O0D  C18   N17  C03   119.71  3.000
 O0D  H10   C18  C19   120.99  3.000
 O0D  H10   C18  N17   117.07  3.000
 O0D  C19   C18  N17   121.94  3.000
 O0D  C21   C19  CL20  120.34  3.000
 O0D  C21   C19  C18   119.22  3.000
 O0D  CL20  C19  C18   120.45  3.000
 O0D  H11   C21  C19   121.23  3.000
 O0D  H11   C21  C02   120.62  3.000
 O0D  C19   C21  C02   118.16  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
 O0D  CONST_01  C18   C19  C21  C02      0.00   0.0  0
 O0D  CONST_02  C18   N17  C03  C02      0.00   0.0  0
 O0D  CONST_03  C19   C18  N17  C03      0.00   0.0  0
 O0D  CONST_04  C19   C21  C02  C03      0.00   0.0  0
 O0D  CONST_05  C08   C07  C06  C05      0.00   0.0  0
 O0D  CONST_06  C08   C15  C16  C05      0.00   0.0  0
 O0D  CONST_07  C15   C16  C05  C06      0.00   0.0  0
 O0D  CONST_08  C15   C08  C07  C06      0.00   0.0  0
 O0D  CONST_09  C16   C05  C06  C07      0.00   0.0  0
 O0D  CONST_10  C16   C15  C08  C07      0.00   0.0  0
 O0D  CONST_11  C21   C19  C18  N17      0.00   0.0  0
 O0D  CONST_12  C21   C02  C03  N17      0.00   0.0  0
 O0D  CONST_13  C19   C21  C02  CL01   180.00   0.0  0
 O0D  CONST_14  N17   C03  C02  CL01   180.00   0.0  0
 O0D  CONST_15  CL20  C19  C21  C02    180.00   0.0  0
 O0D  CONST_16  C18   N17  C03  O04    180.00   0.0  0
 O0D  CONST_17  C21   C02  C03  O04    180.00   0.0  0
 O0D  CONST_18  C07   C06  C05  O04    180.00   0.0  0
 O0D  CONST_19  C15   C16  C05  O04    180.00   0.0  0
 O0D  CONST_20  O09   C08  C07  C06    180.00   0.0  0
 O0D  CONST_21  C16   C15  C08  O09    180.00   0.0  0
 O0D  CONST_22  CL20  C19  C18  N17    180.00   0.0  0
 O0D  CONST_23  H10   C18  N17  C03    180.00   0.0  0
 O0D  CONST_24  H11   C21  C02  C03    180.00   0.0  0
 O0D  CONST_25  H2    C07  C06  C05    180.00   0.0  0
 O0D  CONST_26  H8    C15  C16  C05    180.00   0.0  0
 O0D  CONST_27  H9    C16  C05  C06    180.00   0.0  0
 O0D  CONST_28  H1    C06  C07  C08    180.00   0.0  0
 O0D  Var_01    C06   C05  O04  C03     98.02  30.0  2
 O0D  Var_02    N17   C03  O04  C05     -2.57  30.0  2
 O0D  Var_03    C15   C08  O09  C10   -179.72  30.0  2

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
 O0D  chir_01  C10  C12  O09  C11  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
 O0D  plan-1  O04   0.020
 O0D  plan-1  C05   0.020
 O0D  plan-1  C06   0.020
 O0D  plan-1  C07   0.020
 O0D  plan-1  C08   0.020
 O0D  plan-1  O09   0.020
 O0D  plan-1  C15   0.020
 O0D  plan-1  C16   0.020
 O0D  plan-1  H1    0.020
 O0D  plan-1  H2    0.020
 O0D  plan-1  H8    0.020
 O0D  plan-1  H9    0.020
 O0D  plan-2  CL01  0.020
 O0D  plan-2  C02   0.020
 O0D  plan-2  C03   0.020
 O0D  plan-2  O04   0.020
 O0D  plan-2  N17   0.020
 O0D  plan-2  C18   0.020
 O0D  plan-2  C19   0.020
 O0D  plan-2  CL20  0.020
 O0D  plan-2  C21   0.020
 O0D  plan-2  H10   0.020
 O0D  plan-2  H11   0.020
 O0D  plan-3  C10   0.020
 O0D  plan-3  C12   0.020
 O0D  plan-3  O13   0.020
 O0D  plan-3  O14   0.020

