# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 05:38:18 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 3-[3-(3'-chlorobiphenyl-4-yl)-1,2-oxazol-5-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCc1onc(c1)c2ccc(cc2)c3cccc(Cl)c3
#
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
 0YD  0YD  '3-[3-(3'-chlorobiphenyl-4-yl)-1,2-oxazol-5-yl]propanoic acid'  ligand  36  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0YD
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
 0YD  C1   C   CH2    0  -0.589  -6.0631   0.6362  -0.5087
 0YD  CL1  CL  CL     0  -0.127   6.6466   2.2639  -0.7899
 0YD  C2   C   CH2    0  -0.537  -5.3780   0.0366   0.7189
 0YD  O2   O   O      0  -0.603  -7.9845   0.9664   0.8750
 0YD  C3   C   CR5    0   0.462  -3.9973  -0.4182   0.4229
 0YD  C4   C   CR15   0  -0.551  -2.7752   0.1069   0.6801
 0YD  C5   C   CR5    0   0.261  -1.8719  -0.8091   0.0794
 0YD  C6   C   CR6    0   0.050  -0.4089  -0.7481   0.0407
 0YD  C7   C   CR16   0  -0.270   0.3446  -1.8042  -0.4736
 0YD  C8   C   CR16   0  -0.290   1.7245  -1.7311  -0.5138
 0YD  C9   C   CR6    0   0.080   2.3996  -0.6021  -0.0450
 0YD  C10  C   CR16   0  -0.287   1.6431   0.4497   0.4702
 0YD  C11  C   CR16   0  -0.307   0.2610   0.3778   0.5135
 0YD  C12  C   C      0   0.421  -7.4963   1.1439  -0.2571
 0YD  N12  N   N      0  -0.187  -2.5203  -1.7931  -0.4839
 0YD  O12  O   O      0  -0.339  -3.8408  -1.5515  -0.2713
 0YD  C18  C   CR6    0   0.088   3.8722  -0.5255  -0.0967
 0YD  C19  C   CR16   0  -0.270   4.5019   0.6868  -0.3800
 0YD  C20  C   CR6    0  -0.021   5.8841   0.7495  -0.4261
 0YD  C21  C   CR16   0  -0.226   6.6708  -0.3685  -0.1982
 0YD  C22  C   CR16   0  -0.245   6.0416  -1.5729   0.0827
 0YD  C23  C   CR16   0  -0.301   4.6590  -1.6548   0.1333
 0YD  H1   H   HCH2   0   0.237  -5.4628   1.4657  -0.8950
 0YD  H2   H   HCH2   0   0.239  -6.0982  -0.1015  -1.3165
 0YD  H4   H   HCH2   0   0.257  -5.3199   0.7781   1.5158
 0YD  H5   H   HCH2   0   0.258  -5.9640  -0.7993   1.1064
 0YD  H7   H   HCR5   0   0.280  -2.5571   1.0120   1.2211
 0YD  H8   H   HCR6   0   0.261  -0.1489  -2.6894  -0.8518
 0YD  H9   H   HCR6   0   0.262   2.2806  -2.5583  -0.9356
 0YD  H12  H   HCR6   0   0.263   2.1346   1.3308   0.8621
 0YD  H13  H   HCR6   0   0.261  -0.2917   1.2133   0.9230
 0YD  H19  H   HCR6   0   0.279   3.9150   1.5728  -0.5844
 0YD  H20  H   HCR6   0   0.282   7.7494  -0.3037  -0.2375
 0YD  H21  H   HCR6   0   0.272   6.6406  -2.4536   0.2719
 0YD  H22  H   HCR6   0   0.263   4.1921  -2.6007   0.3754
 0YD  OXT  O   OC    -1  -0.625  -8.0499   1.6940  -1.2303

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
 0YD  C1   C12  single    1.541  0.020  1.541
 0YD  C1   C2   single    1.528  0.020  1.528
 0YD  C12  O2   deloc     1.246  0.020  1.246
 0YD  C2   C3   single    1.483  0.020  1.483
 0YD  C4   C3   aromatic  1.355  0.020  1.355
 0YD  C4   C5   aromatic  1.420  0.020  1.420
 0YD  C3   O12  aromatic  1.338  0.020  1.338
 0YD  C11  C10  aromatic  1.385  0.020  1.385
 0YD  C11  C6   aromatic  1.393  0.020  1.393
 0YD  C10  C9   aromatic  1.394  0.020  1.394
 0YD  C5   C6   single    1.465  0.020  1.465
 0YD  C5   N12  aromatic  1.306  0.020  1.306
 0YD  O12  N12  aromatic  1.359  0.020  1.359
 0YD  C6   C7   aromatic  1.396  0.020  1.396
 0YD  C23  C22  aromatic  1.386  0.020  1.386
 0YD  C23  C18  aromatic  1.395  0.020  1.395
 0YD  C9   C18  single    1.476  0.020  1.476
 0YD  C9   C8   aromatic  1.396  0.020  1.396
 0YD  C22  C21  aromatic  1.388  0.020  1.388
 0YD  C18  C19  aromatic  1.395  0.020  1.395
 0YD  C7   C8   aromatic  1.382  0.020  1.382
 0YD  C21  C20  aromatic  1.386  0.020  1.386
 0YD  C19  C20  aromatic  1.384  0.020  1.384
 0YD  C20  CL1  single    1.734  0.020  1.734
 0YD  C1   H1   single    0.970  0.020  1.090
 0YD  C1   H2   single    0.970  0.020  1.090
 0YD  C2   H4   single    0.970  0.020  1.090
 0YD  C2   H5   single    0.970  0.020  1.090
 0YD  C4   H7   single    0.930  0.020  1.080
 0YD  C7   H8   single    0.930  0.020  1.080
 0YD  C8   H9   single    0.930  0.020  1.080
 0YD  C10  H12  single    0.930  0.020  1.080
 0YD  C11  H13  single    0.930  0.020  1.080
 0YD  C19  H19  single    0.930  0.020  1.080
 0YD  C21  H20  single    0.930  0.020  1.080
 0YD  C22  H21  single    0.930  0.020  1.080
 0YD  C23  H22  single    0.930  0.020  1.080
 0YD  C12  OXT  deloc     1.247  0.020  1.247

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
 0YD  H2   C1   H1   105.54  3.000
 0YD  H2   C1   C12  108.22  3.000
 0YD  H1   C1   C12  108.55  3.000
 0YD  H2   C1   C2   110.04  3.000
 0YD  H1   C1   C2   109.57  3.000
 0YD  C12  C1   C2   114.52  3.000
 0YD  H5   C2   H4   106.85  3.000
 0YD  H5   C2   C3   109.61  3.000
 0YD  H4   C2   C3   107.75  3.000
 0YD  H5   C2   C1   110.17  3.000
 0YD  H4   C2   C1   110.13  3.000
 0YD  C3   C2   C1   112.16  3.000
 0YD  O12  C3   C4   108.74  3.000
 0YD  O12  C3   C2   118.16  3.000
 0YD  C4   C3   C2   133.06  3.000
 0YD  H7   C4   C5   128.76  3.000
 0YD  H7   C4   C3   127.15  3.000
 0YD  C5   C4   C3   104.09  3.000
 0YD  N12  C5   C6   121.05  3.000
 0YD  N12  C5   C4   110.66  3.000
 0YD  C6   C5   C4   128.29  3.000
 0YD  C11  C6   C7   118.50  3.000
 0YD  C7   C6   C5   121.16  3.000
 0YD  C11  C6   C5   120.34  3.000
 0YD  H8   C7   C8   119.24  3.000
 0YD  H8   C7   C6   120.12  3.000
 0YD  C8   C7   C6   120.64  3.000
 0YD  H9   C8   C9   120.02  3.000
 0YD  H9   C8   C7   118.94  3.000
 0YD  C9   C8   C7   121.04  3.000
 0YD  C18  C9   C10  121.01  3.000
 0YD  C18  C9   C8   120.84  3.000
 0YD  C10  C9   C8   118.14  3.000
 0YD  H12  C10  C11  118.96  3.000
 0YD  H12  C10  C9   120.10  3.000
 0YD  C11  C10  C9   120.93  3.000
 0YD  H13  C11  C10  118.79  3.000
 0YD  H13  C11  C6   120.45  3.000
 0YD  C10  C11  C6   120.76  3.000
 0YD  OXT  C12  O2   126.72  3.000
 0YD  OXT  C12  C1   115.50  3.000
 0YD  O2   C12  C1   117.77  3.000
 0YD  O12  N12  C5   106.32  3.000
 0YD  N12  O12  C3   110.20  3.000
 0YD  C23  C18  C19  118.83  3.000
 0YD  C19  C18  C9   120.17  3.000
 0YD  C23  C18  C9   120.99  3.000
 0YD  H19  C19  C20  119.88  3.000
 0YD  H19  C19  C18  120.33  3.000
 0YD  C20  C19  C18  119.78  3.000
 0YD  C21  C20  C19  121.65  3.000
 0YD  C19  C20  CL1  119.05  3.000
 0YD  C21  C20  CL1  119.30  3.000
 0YD  H20  C21  C22  120.78  3.000
 0YD  H20  C21  C20  120.79  3.000
 0YD  C22  C21  C20  118.43  3.000
 0YD  H21  C22  C23  119.86  3.000
 0YD  H21  C22  C21  119.40  3.000
 0YD  C23  C22  C21  120.73  3.000
 0YD  H22  C23  C22  119.36  3.000
 0YD  H22  C23  C18  120.06  3.000
 0YD  C22  C23  C18  120.57  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
 0YD  CONST_01  C6   C5   C4   C3    180.00   0.0  0
 0YD  CONST_02  N12  C5   C4   C3      0.00   0.0  0
 0YD  CONST_03  C5   N12  O12  C3      0.00   0.0  0
 0YD  CONST_04  N12  O12  C3   C4      0.00   0.0  0
 0YD  CONST_05  C11  C6   C5   C4      0.00   0.0  0
 0YD  CONST_06  C7   C6   C5   C4    180.00   0.0  0
 0YD  CONST_07  O12  N12  C5   C4      0.00   0.0  0
 0YD  CONST_08  O12  C3   C4   C5      0.00   0.0  0
 0YD  CONST_09  C10  C11  C6   C5    180.00   0.0  0
 0YD  CONST_10  C8   C7   C6   C5    180.00   0.0  0
 0YD  CONST_11  C9   C10  C11  C6      0.00   0.0  0
 0YD  CONST_12  O12  N12  C5   C6    180.00   0.0  0
 0YD  CONST_13  C9   C8   C7   C6      0.00   0.0  0
 0YD  CONST_14  C10  C11  C6   C7      0.00   0.0  0
 0YD  CONST_15  N12  C5   C6   C7      0.00   0.0  0
 0YD  CONST_16  C10  C9   C8   C7      0.00   0.0  0
 0YD  CONST_17  C18  C9   C8   C7    180.00   0.0  0
 0YD  CONST_18  C11  C10  C9   C8      0.00   0.0  0
 0YD  CONST_21  C11  C6   C7   C8      0.00   0.0  0
 0YD  CONST_22  C22  C23  C18  C9    180.00   0.0  0
 0YD  CONST_23  C20  C19  C18  C9    180.00   0.0  0
 0YD  CONST_26  C18  C9   C10  C11   180.00   0.0  0
 0YD  CONST_27  N12  C5   C6   C11   180.00   0.0  0
 0YD  CONST_28  C21  C22  C23  C18     0.00   0.0  0
 0YD  CONST_29  C21  C20  C19  C18     0.00   0.0  0
 0YD  CONST_30  C22  C23  C18  C19     0.00   0.0  0
 0YD  CONST_31  C22  C21  C20  C19     0.00   0.0  0
 0YD  CONST_32  C23  C22  C21  C20     0.00   0.0  0
 0YD  CONST_33  C23  C18  C19  C20     0.00   0.0  0
 0YD  CONST_34  C22  C21  C20  CL1   180.00   0.0  0
 0YD  CONST_35  C18  C19  C20  CL1   180.00   0.0  0
 0YD  CONST_36  C5   C4   C3   C2    180.00   0.0  0
 0YD  CONST_37  N12  O12  C3   C2    180.00   0.0  0
 0YD  CONST_38  H13  C11  C6   C5      0.00   0.0  0
 0YD  CONST_39  H8   C7   C6   C5      0.00   0.0  0
 0YD  CONST_40  H12  C10  C11  C6    180.00   0.0  0
 0YD  CONST_41  H7   C4   C5   C6      0.00   0.0  0
 0YD  CONST_42  H9   C8   C7   C6    180.00   0.0  0
 0YD  CONST_43  H22  C23  C18  C9      0.00   0.0  0
 0YD  CONST_44  H19  C19  C18  C9      0.00   0.0  0
 0YD  CONST_45  H21  C22  C23  C18   180.00   0.0  0
 0YD  CONST_46  H20  C21  C20  C19   180.00   0.0  0
 0YD  Var_01    C4   C3   C2   C1    102.57  30.0  2
 0YD  Var_02    C12  C1   C2   C3   -179.25  30.0  1
 0YD  Var_03    O2   C12  C1   C2     -3.43  30.0  3

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
 0YD  plan-1  C2   0.020
 0YD  plan-1  C3   0.020
 0YD  plan-1  C4   0.020
 0YD  plan-1  C5   0.020
 0YD  plan-1  C6   0.020
 0YD  plan-1  N12  0.020
 0YD  plan-1  O12  0.020
 0YD  plan-1  H7   0.020
 0YD  plan-2  C5   0.020
 0YD  plan-2  C6   0.020
 0YD  plan-2  C7   0.020
 0YD  plan-2  C8   0.020
 0YD  plan-2  C9   0.020
 0YD  plan-2  C10  0.020
 0YD  plan-2  C11  0.020
 0YD  plan-2  C18  0.020
 0YD  plan-2  H8   0.020
 0YD  plan-2  H9   0.020
 0YD  plan-2  H12  0.020
 0YD  plan-2  H13  0.020
 0YD  plan-3  CL1  0.020
 0YD  plan-3  C9   0.020
 0YD  plan-3  C18  0.020
 0YD  plan-3  C19  0.020
 0YD  plan-3  C20  0.020
 0YD  plan-3  C21  0.020
 0YD  plan-3  C22  0.020
 0YD  plan-3  C23  0.020
 0YD  plan-3  H19  0.020
 0YD  plan-3  H20  0.020
 0YD  plan-3  H21  0.020
 0YD  plan-3  H22  0.020
 0YD  plan-4  C1   0.020
 0YD  plan-4  O2   0.020
 0YD  plan-4  C12  0.020
 0YD  plan-4  OXT  0.020

