# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 18:59:08 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCc1oc(nn1)c2ccccc2
#
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
 HHY  HHY  '3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoic acid'  ligand  25  16  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HHY
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
 HHY  O1   O  OC    -1  -0.623  -4.8488  -1.4807  -1.1696
 HHY  C1   C  CH2    0  -0.544  -2.3402   0.4778   0.7086
 HHY  O2   O  O      0  -0.601  -4.8942  -0.5638   0.8616
 HHY  C2   C  CR5    0   0.476  -0.9566   0.9316   0.4519
 HHY  C3   C  CR5    0   0.477   1.1308   0.7645   0.1362
 HHY  N1   N  N      0  -0.319   0.8371   2.0137   0.0304
 HHY  C4   C  C      0  -0.026   2.4298   0.1243   0.0107
 HHY  C5   C  C1     0  -0.271   3.5471   0.9070  -0.2855
 HHY  C6   C  C1     0  -0.239   4.7935   0.3174  -0.4074
 HHY  C7   C  C1     0  -0.248   4.9382  -1.0543  -0.2341
 HHY  C8   C  C1     0  -0.240   3.8285  -1.8346   0.0603
 HHY  C9   C  C1     0  -0.287   2.5759  -1.2520   0.1825
 HHY  C10  C  C      0   0.425  -4.3504  -0.8374  -0.2248
 HHY  C    C  CH2    0  -0.597  -2.9078  -0.3417  -0.4490
 HHY  O    O  O      0  -0.416   0.0409   0.0280   0.4016
 HHY  N    N  N      0  -0.313  -0.5130   2.1199   0.2351
 HHY  H2   H  HCH2   0   0.266  -2.3579  -0.1060   1.6313
 HHY  H3   H  HCH2   0   0.266  -2.9461   1.3666   0.8803
 HHY  H4   H  H      0   0.265   3.4380   1.9750  -0.4192
 HHY  H5   H  H      0   0.266   5.6548   0.9294  -0.6393
 HHY  H6   H  H      0   0.266   5.9142  -1.5122  -0.3278
 HHY  H7   H  H      0   0.267   3.9357  -2.9026   0.1950
 HHY  H8   H  H      0   0.264   1.7213  -1.8750   0.4109
 HHY  H9   H  HCH2   0   0.243  -2.8841   0.2535  -1.3669
 HHY  H10  H  HCH2   0   0.242  -2.2741  -1.2117  -0.6454

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
 HHY  C8   C7   aromatic  1.388  0.020  1.388
 HHY  C8   C9   aromatic  1.387  0.020  1.387
 HHY  C7   C6   aromatic  1.390  0.020  1.390
 HHY  C9   C4   aromatic  1.395  0.020  1.395
 HHY  C6   C5   aromatic  1.384  0.020  1.384
 HHY  C4   C5   aromatic  1.396  0.020  1.396
 HHY  C4   C3   single    1.454  0.020  1.454
 HHY  C3   O    aromatic  1.342  0.020  1.342
 HHY  C3   N1   aromatic  1.288  0.020  1.288
 HHY  O    C2   aromatic  1.347  0.020  1.347
 HHY  N1   N    aromatic  1.370  0.020  1.370
 HHY  C2   N    aromatic  1.287  0.020  1.287
 HHY  C2   C1   single    1.479  0.020  1.479
 HHY  O2   C10  deloc     1.245  0.020  1.245
 HHY  C1   C    single    1.528  0.020  1.528
 HHY  C10  C    single    1.542  0.020  1.542
 HHY  C10  O1   deloc     1.247  0.020  1.247
 HHY  C1   H2   single    0.970  0.020  1.090
 HHY  C1   H3   single    0.970  0.020  1.090
 HHY  C5   H4   single    0.930  0.020  1.080
 HHY  C6   H5   single    0.930  0.020  1.080
 HHY  C7   H6   single    0.930  0.020  1.080
 HHY  C8   H7   single    0.930  0.020  1.080
 HHY  C9   H8   single    0.930  0.020  1.080
 HHY  C    H9   single    0.970  0.020  1.090
 HHY  C    H10  single    0.970  0.020  1.090

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
 HHY  H3   C1   H2   107.10  3.000
 HHY  H3   C1   C    110.51  3.000
 HHY  H2   C1   C    110.33  3.000
 HHY  H3   C1   C2   107.31  3.000
 HHY  H2   C1   C2   109.03  3.000
 HHY  C    C1   C2   112.38  3.000
 HHY  N    C2   O    110.97  3.000
 HHY  N    C2   C1   129.44  3.000
 HHY  O    C2   C1   119.58  3.000
 HHY  O    C3   C4   120.08  3.000
 HHY  O    C3   N1   111.31  3.000
 HHY  C4   C3   N1   128.61  3.000
 HHY  N    N1   C3   106.73  3.000
 HHY  C9   C4   C5   119.71  3.000
 HHY  C5   C4   C3   119.12  3.000
 HHY  C9   C4   C3   121.17  3.000
 HHY  H4   C5   C6   120.03  3.000
 HHY  H4   C5   C4   119.93  3.000
 HHY  C6   C5   C4   120.04  3.000
 HHY  H5   C6   C7   120.14  3.000
 HHY  H5   C6   C5   119.66  3.000
 HHY  C7   C6   C5   120.20  3.000
 HHY  H6   C7   C8   120.10  3.000
 HHY  H6   C7   C6   120.04  3.000
 HHY  C8   C7   C6   119.86  3.000
 HHY  H7   C8   C9   119.56  3.000
 HHY  H7   C8   C7   120.14  3.000
 HHY  C9   C8   C7   120.30  3.000
 HHY  H8   C9   C8   119.34  3.000
 HHY  H8   C9   C4   120.76  3.000
 HHY  C8   C9   C4   119.89  3.000
 HHY  C    C10  O2   117.70  3.000
 HHY  C    C10  O1   115.45  3.000
 HHY  O2   C10  O1   126.85  3.000
 HHY  H10  C    H9   105.63  3.000
 HHY  H10  C    C10  108.21  3.000
 HHY  H9   C    C10  108.49  3.000
 HHY  H10  C    C1   110.32  3.000
 HHY  H9   C    C1   109.62  3.000
 HHY  C10  C    C1   114.20  3.000
 HHY  C3   O    C2   103.93  3.000
 HHY  N1   N    C2   107.06  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
 HHY  CONST_01  C4   C3  O    C2  180.00   0.0  0
 HHY  CONST_02  N1   C3  O    C2    0.00   0.0  0
 HHY  CONST_03  C3   N1  N    C2    0.00   0.0  0
 HHY  CONST_04  C8   C9  C4   C3  180.00   0.0  0
 HHY  CONST_05  C6   C5  C4   C3  180.00   0.0  0
 HHY  CONST_06  N    C2  O    C3    0.00   0.0  0
 HHY  CONST_07  C9   C4  C3   N1  180.00   0.0  0
 HHY  CONST_08  C5   C4  C3   N1    0.00   0.0  0
 HHY  CONST_09  O    C2  N    N1    0.00   0.0  0
 HHY  CONST_10  C7   C8  C9   C4    0.00   0.0  0
 HHY  CONST_11  C7   C6  C5   C4    0.00   0.0  0
 HHY  CONST_12  N    N1  C3   C4  180.00   0.0  0
 HHY  CONST_13  C8   C7  C6   C5    0.00   0.0  0
 HHY  CONST_14  C8   C9  C4   C5    0.00   0.0  0
 HHY  CONST_15  O    C3  C4   C5  180.00   0.0  0
 HHY  CONST_16  C9   C8  C7   C6    0.00   0.0  0
 HHY  CONST_17  C9   C4  C5   C6    0.00   0.0  0
 HHY  CONST_18  O    C3  C4   C9    0.00   0.0  0
 HHY  CONST_19  N    N1  C3   O     0.00   0.0  0
 HHY  CONST_20  C3   O   C2   C1  180.00   0.0  0
 HHY  CONST_21  N1   N   C2   C1  180.00   0.0  0
 HHY  CONST_22  H8   C9  C4   C3    0.00   0.0  0
 HHY  CONST_23  H4   C5  C4   C3    0.00   0.0  0
 HHY  CONST_24  H7   C8  C9   C4  180.00   0.0  0
 HHY  CONST_25  H5   C6  C5   C4  180.00   0.0  0
 HHY  CONST_26  H6   C7  C6   C5  180.00   0.0  0
 HHY  Var_01    O    C2  C1   C   -68.03  30.0  2
 HHY  Var_02    C10  C   C1   C2  179.98  30.0  3
 HHY  Var_03    C1   C   C10  O1  178.29  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
 HHY  plan-1  C1   0.020
 HHY  plan-1  C2   0.020
 HHY  plan-1  C3   0.020
 HHY  plan-1  N1   0.020
 HHY  plan-1  C4   0.020
 HHY  plan-1  O    0.020
 HHY  plan-1  N    0.020
 HHY  plan-2  C3   0.020
 HHY  plan-2  C4   0.020
 HHY  plan-2  C5   0.020
 HHY  plan-2  C6   0.020
 HHY  plan-2  C7   0.020
 HHY  plan-2  C8   0.020
 HHY  plan-2  C9   0.020
 HHY  plan-2  H4   0.020
 HHY  plan-2  H5   0.020
 HHY  plan-2  H6   0.020
 HHY  plan-2  H7   0.020
 HHY  plan-2  H8   0.020
 HHY  plan-3  O1   0.020
 HHY  plan-3  O2   0.020
 HHY  plan-3  C10  0.020
 HHY  plan-3  C    0.020

