# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 22:52:43 2021
#   Inital geometry file: a 78 line input string
#   Ligand name: 5-cyclohexyl-3-pyridin-4-yl-1,2,4-oxadiazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCC(CC1)c2onc(n2)c3ccncc3
#
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
 SZ2  SZ2  5-cyclohexyl-3-pyridin-4-yl-1,2,4-oxadiazole  ligand  32  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SZ2
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
 SZ2  N1   N  N     0  -0.149  -41.8847  5.7069  -4.0296
 SZ2  C4   C  CH2   0  -0.417  -38.3959  5.6107  -1.1478
 SZ2  C5   C  CH2   0  -0.440  -36.9377  5.3322  -0.7998
 SZ2  C6   C  CR5   0   0.592  -40.2154  5.1180  -2.7691
 SZ2  C7   C  CR5   0   0.330  -42.2812  5.2937  -2.8634
 SZ2  C8   C  CR6   0   0.097  -43.6911  5.2382  -2.4775
 SZ2  C10  C  CR16  0  -0.053  -45.4006  4.7596  -0.8832
 SZ2  C12  C  CR16  0  -0.352  -44.7017  5.6114  -3.3587
 SZ2  C11  C  CR16  0  -0.054  -46.0156  5.5282  -2.9300
 SZ2  N2   N  N     0  -0.399  -46.3693  5.1121  -1.7185
 SZ2  C9   C  CR16  0  -0.362  -44.0533  4.8025  -1.2088
 SZ2  N    N  N     0  -0.457  -41.2635  4.9149  -2.0414
 SZ2  O    O  O     0  -0.322  -40.5285  5.5918  -3.9701
 SZ2  C3   C  CH1   0  -0.409  -38.7923  4.8679  -2.4300
 SZ2  C2   C  CH2   0  -0.420  -38.5417  3.3594  -2.2796
 SZ2  C1   C  CH2   0  -0.439  -37.0833  3.0894  -1.9279
 SZ2  C    C  CH2   0  -0.433  -36.6700  3.8370  -0.6647
 SZ2  H2   H  HCH2  0   0.230  -39.0417  5.2808  -0.3288
 SZ2  H3   H  HCH2  0   0.218  -36.2947  5.7474  -1.5830
 SZ2  H4   H  HCH2  0   0.237  -36.6767  5.8516   0.1248
 SZ2  H5   H  HCR6  0   0.272  -45.7055  4.4225   0.1006
 SZ2  H6   H  HCR6  0   0.276  -44.4806  5.9580  -4.3587
 SZ2  H7   H  HCR6  0   0.272  -46.8191  5.8112  -3.6003
 SZ2  H8   H  HCR6  0   0.276  -43.3088  4.5022  -0.4847
 SZ2  H9   H  HCH1  0   0.274  -38.1798  5.2424  -3.2568
 SZ2  H10  H  HCH2  0   0.230  -39.1901  2.9710  -1.4882
 SZ2  H11  H  HCH2  0   0.249  -38.8158  2.8402  -3.2002
 SZ2  H12  H  HCH2  0   0.237  -36.9307  2.0152  -1.8030
 SZ2  H13  H  HCH2  0   0.218  -36.4455  3.3995  -2.7626
 SZ2  H14  H  HCH2  0   0.215  -37.2331  3.4441   0.1885
 SZ2  H15  H  HCH2  0   0.234  -35.6138  3.6607  -0.4494
 SZ2  H1   H  HCH2  0   0.248  -38.5602  6.6835  -1.2715

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
 SZ2  N1   O    aromatic  1.362  0.020  1.362
 SZ2  N1   C7   aromatic  1.299  0.020  1.299
 SZ2  O    C6   aromatic  1.328  0.020  1.328
 SZ2  C12  C11  aromatic  1.385  0.020  1.385
 SZ2  C12  C8   aromatic  1.392  0.020  1.392
 SZ2  C11  N2   aromatic  1.329  0.020  1.329
 SZ2  C7   C8   single    1.463  0.020  1.463
 SZ2  C7   N    aromatic  1.362  0.020  1.362
 SZ2  C6   C3   single    1.484  0.020  1.484
 SZ2  C6   N    aromatic  1.292  0.020  1.292
 SZ2  C8   C9   aromatic  1.389  0.020  1.389
 SZ2  C3   C2   single    1.537  0.020  1.537
 SZ2  C3   C4   single    1.534  0.020  1.534
 SZ2  C2   C1   single    1.524  0.020  1.524
 SZ2  C1   C    single    1.525  0.020  1.525
 SZ2  N2   C10  aromatic  1.327  0.020  1.327
 SZ2  C9   C10  aromatic  1.387  0.020  1.387
 SZ2  C4   C5   single    1.525  0.020  1.525
 SZ2  C5   C    single    1.525  0.020  1.525
 SZ2  C4   H1   single    0.970  0.020  1.090
 SZ2  C4   H2   single    0.970  0.020  1.090
 SZ2  C5   H3   single    0.970  0.020  1.090
 SZ2  C5   H4   single    0.970  0.020  1.090
 SZ2  C10  H5   single    0.930  0.020  1.080
 SZ2  C12  H6   single    0.930  0.020  1.080
 SZ2  C11  H7   single    0.930  0.020  1.080
 SZ2  C9   H8   single    0.930  0.020  1.080
 SZ2  C3   H9   single    0.970  0.020  1.090
 SZ2  C2   H10  single    0.970  0.020  1.090
 SZ2  C2   H11  single    0.970  0.020  1.090
 SZ2  C1   H12  single    0.970  0.020  1.090
 SZ2  C1   H13  single    0.970  0.020  1.090
 SZ2  C    H14  single    0.970  0.020  1.090
 SZ2  C    H15  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
 SZ2  O    N1   C7   103.75  3.000
 SZ2  H2   C4   H1   106.99  3.000
 SZ2  H2   C4   C3   109.10  3.000
 SZ2  H1   C4   C3   110.00  3.000
 SZ2  H2   C4   C5   109.79  3.000
 SZ2  H1   C4   C5   110.43  3.000
 SZ2  C3   C4   C5   110.45  3.000
 SZ2  H4   C5   H3   106.54  3.000
 SZ2  H4   C5   C    110.45  3.000
 SZ2  H3   C5   C    109.40  3.000
 SZ2  H4   C5   C4   109.57  3.000
 SZ2  H3   C5   C4   109.21  3.000
 SZ2  C    C5   C4   111.54  3.000
 SZ2  C3   C6   O    119.52  3.000
 SZ2  C3   C6   N    128.51  3.000
 SZ2  O    C6   N    111.97  3.000
 SZ2  N    C7   C8   123.40  3.000
 SZ2  N    C7   N1   113.71  3.000
 SZ2  C8   C7   N1   122.89  3.000
 SZ2  C9   C8   C12  118.22  3.000
 SZ2  C9   C8   C7   120.26  3.000
 SZ2  C12  C8   C7   121.51  3.000
 SZ2  H5   C10  C9   119.74  3.000
 SZ2  H5   C10  N2   116.66  3.000
 SZ2  C9   C10  N2   123.60  3.000
 SZ2  H6   C12  C11  119.98  3.000
 SZ2  H6   C12  C8   121.54  3.000
 SZ2  C11  C12  C8   118.48  3.000
 SZ2  H7   C11  N2   116.63  3.000
 SZ2  H7   C11  C12  119.75  3.000
 SZ2  N2   C11  C12  123.62  3.000
 SZ2  C11  N2   C10  117.57  3.000
 SZ2  H8   C9   C10  120.21  3.000
 SZ2  H8   C9   C8   121.28  3.000
 SZ2  C10  C9   C8   118.51  3.000
 SZ2  C7   N    C6   102.86  3.000
 SZ2  C6   O    N1   107.71  3.000
 SZ2  H9   C3   C2   108.57  3.000
 SZ2  H9   C3   C6   107.82  3.000
 SZ2  C2   C3   C6   110.13  3.000
 SZ2  H9   C3   C4   108.73  3.000
 SZ2  C2   C3   C4   110.58  3.000
 SZ2  C6   C3   C4   110.93  3.000
 SZ2  H11  C2   H10  106.98  3.000
 SZ2  H11  C2   C1   110.52  3.000
 SZ2  H10  C2   C1   109.70  3.000
 SZ2  H11  C2   C3   110.09  3.000
 SZ2  H10  C2   C3   108.82  3.000
 SZ2  C1   C2   C3   110.64  3.000
 SZ2  H13  C1   H12  106.51  3.000
 SZ2  H13  C1   C    109.56  3.000
 SZ2  H12  C1   C    110.47  3.000
 SZ2  H13  C1   C2   109.33  3.000
 SZ2  H12  C1   C2   109.53  3.000
 SZ2  C    C1   C2   111.32  3.000
 SZ2  H15  C    H14  106.60  3.000
 SZ2  H15  C    C1   110.25  3.000
 SZ2  H14  C    C1   109.28  3.000
 SZ2  H15  C    C5   110.21  3.000
 SZ2  H14  C    C5   109.30  3.000
 SZ2  C1   C    C5   111.08  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
 SZ2  CONST_01  N    C6   O    N1     0.00   0.0  0
 SZ2  CONST_02  C12  C8   C7   N1     0.00   0.0  0
 SZ2  CONST_03  C9   C8   C7   N1   180.00   0.0  0
 SZ2  CONST_04  C6   N    C7   N1     0.00   0.0  0
 SZ2  CONST_05  C7   N1   O    C6     0.00   0.0  0
 SZ2  CONST_06  C8   C7   N    C6   180.00   0.0  0
 SZ2  CONST_07  C11  C12  C8   C7   180.00   0.0  0
 SZ2  CONST_08  C10  C9   C8   C7   180.00   0.0  0
 SZ2  CONST_09  O    C6   N    C7     0.00   0.0  0
 SZ2  CONST_10  N2   C11  C12  C8     0.00   0.0  0
 SZ2  CONST_11  O    N1   C7   C8   180.00   0.0  0
 SZ2  CONST_12  N2   C10  C9   C8     0.00   0.0  0
 SZ2  CONST_13  C12  C11  N2   C10    0.00   0.0  0
 SZ2  CONST_14  C12  C8   C9   C10    0.00   0.0  0
 SZ2  CONST_15  N    C7   C8   C12  180.00   0.0  0
 SZ2  CONST_16  C9   C8   C12  C11    0.00   0.0  0
 SZ2  CONST_17  C9   C10  N2   C11    0.00   0.0  0
 SZ2  CONST_18  N    C7   C8   C9     0.00   0.0  0
 SZ2  CONST_19  O    N1   C7   N      0.00   0.0  0
 SZ2  CONST_20  C3   C6   O    N1   180.00   0.0  0
 SZ2  CONST_21  C3   C6   N    C7   180.00   0.0  0
 SZ2  CONST_22  H6   C12  C8   C7     0.00   0.0  0
 SZ2  CONST_23  H8   C9   C8   C7     0.00   0.0  0
 SZ2  CONST_24  H7   C11  C12  C8   180.00   0.0  0
 SZ2  CONST_25  H5   C10  C9   C8   180.00   0.0  0
 SZ2  Var_01    C1   C    C5   C4    55.57  30.0  1
 SZ2  Var_02    C2   C1   C    C5   -55.46  30.0  1
 SZ2  Var_03    C    C1   C2   C3    56.26  30.0  1
 SZ2  Var_04    C    C5   C4   C3   -56.29  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
 SZ2  chir_01  C3  C6  C2  C4  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
 SZ2  plan-1  N1   0.020
 SZ2  plan-1  C6   0.020
 SZ2  plan-1  C7   0.020
 SZ2  plan-1  C8   0.020
 SZ2  plan-1  N    0.020
 SZ2  plan-1  O    0.020
 SZ2  plan-1  C3   0.020
 SZ2  plan-2  C7   0.020
 SZ2  plan-2  C8   0.020
 SZ2  plan-2  C10  0.020
 SZ2  plan-2  C12  0.020
 SZ2  plan-2  C11  0.020
 SZ2  plan-2  N2   0.020
 SZ2  plan-2  C9   0.020
 SZ2  plan-2  H5   0.020
 SZ2  plan-2  H6   0.020
 SZ2  plan-2  H7   0.020
 SZ2  plan-2  H8   0.020

