# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 03:45:49 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-azido-1-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [N-]=[N+]=NCC(=O)N1CCC(CC1)c2onc(n2)c3sccc3
#
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
 O8G  O8G  2-azido-1-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}ethanone  ligand  36  22  .  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_O8G
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
 O8G  C1    C  CH2    0  -0.424  -0.9952  -1.0200   1.1675
 O8G  C4    C  CH2    0  -0.323  -2.2793  -1.7884   0.8848
 O8G  N7    N  NT     0  -0.449  -3.0525  -1.1354  -0.1588
 O8G  C8    C  CH2    0  -0.335  -2.3330  -0.9924  -1.4126
 O8G  C11   C  CH2    0  -0.419  -1.0512  -0.1956  -1.2091
 O8G  C14   C  CH1    0  -0.411  -0.1885  -0.8573  -0.1269
 O8G  C16   C  C      0   0.541  -4.2480  -0.5803   0.1126
 O8G  O17   O  O      0  -0.489  -4.7794  -0.6258   1.2104
 O8G  C18   C  CH2    0  -0.446  -4.9511   0.1414  -1.0398
 O8G  N21   N  N      0  -0.461   2.2875  -0.5166  -0.1260
 O8G  C22   C  CR5    0   0.570   1.0791  -0.1168   0.0906
 O8G  O23   O  O      0  -0.328   1.0370   1.1242   0.5566
 O8G  N24   N  N      0  -0.156   2.3255   1.5770   0.6524
 O8G  C25   C  CR5    0   0.340   3.0333   0.5684   0.2362
 O8G  C26   C  CR5    0  -0.278   4.4752   0.5745   0.1557
 O8G  C27   C  CR15   0  -0.210   5.3487   1.5784   0.4723
 O8G  C29   C  CR15   0  -0.169   6.6976   1.2063   0.2597
 O8G  C31   C  CR15   0  -0.460   6.8185  -0.0681  -0.2123
 O8G  S33   S  S2     0   0.264   5.3012  -0.8279  -0.4035
 O8G  N34   N  N      0  -0.350  -6.3045   0.5280  -0.6898
 O8G  N36   N  N      1   0.365  -6.4291   1.3290   0.2206
 O8G  N37   N  N     -1  -0.217  -6.6691   2.0700   1.0290
 O8G  H1    H  HCH2   0   0.249  -1.2437  -0.0428   1.5890
 O8G  H1A   H  HCH2   0   0.266  -0.4103  -1.5620   1.9127
 O8G  H4    H  HCH2   0   0.253  -2.0411  -2.8045   0.5550
 O8G  H4A   H  HCH2   0   0.277  -2.8804  -1.8681   1.7860
 O8G  H8    H  HCH2   0   0.261  -2.0971  -1.9893  -1.7977
 O8G  H8A   H  HCH2   0   0.286  -2.9478  -0.5055  -2.1640
 O8G  H11   H  HCH2   0   0.268  -0.5063  -0.1473  -2.1535
 O8G  H11A  H  HCH2   0   0.250  -1.3046   0.8276  -0.9207
 O8G  H14   H  HCH1   0   0.290   0.1071  -1.8500  -0.4787
 O8G  H18   H  HCH2   0   0.290  -4.3602   1.0095  -1.3524
 O8G  H18A  H  HCH2   0   0.299  -5.0438  -0.5096  -1.9071
 O8G  H27   H  HCR5   0   0.274   5.0372   2.5449   0.8423
 O8G  H29   H  HCR5   0   0.276   7.5403   1.8551   0.4477
 O8G  H31   H  HCR5   0   0.305   7.7246  -0.6003  -0.4579

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
 O8G  C1   C14   single    1.534  0.020  1.534
 O8G  C1   H1    single    0.970  0.020  1.090
 O8G  C1   H1A   single    0.970  0.020  1.090
 O8G  C4   C1    single    1.523  0.020  1.523
 O8G  C4   N7    single    1.454  0.020  1.454
 O8G  C4   H4    single    0.970  0.020  1.090
 O8G  C4   H4A   single    0.970  0.020  1.090
 O8G  N7   C8    single    1.453  0.020  1.453
 O8G  C8   C11   single    1.523  0.020  1.523
 O8G  C8   H8    single    0.970  0.020  1.090
 O8G  C8   H8A   single    0.970  0.020  1.090
 O8G  C11  H11   single    0.970  0.020  1.090
 O8G  C11  H11A  single    0.970  0.020  1.090
 O8G  C14  C11   single    1.534  0.020  1.534
 O8G  C14  C22   single    1.484  0.020  1.484
 O8G  C14  H14   single    0.970  0.020  1.090
 O8G  C16  N7    single    1.346  0.020  1.346
 O8G  C16  C18   single    1.531  0.020  1.531
 O8G  O17  C16   double    1.220  0.020  1.220
 O8G  C18  H18   single    0.970  0.020  1.090
 O8G  C18  H18A  single    0.970  0.020  1.090
 O8G  N21  C22   aromatic  1.291  0.020  1.291
 O8G  N21  C25   aromatic  1.366  0.020  1.366
 O8G  C22  O23   aromatic  1.326  0.020  1.326
 O8G  O23  N24   aromatic  1.369  0.020  1.369
 O8G  C25  N24   aromatic  1.301  0.020  1.301
 O8G  C26  C25   single    1.444  0.020  1.444
 O8G  C26  S33   aromatic  1.721  0.020  1.721
 O8G  C27  C26   aromatic  1.368  0.020  1.368
 O8G  C27  C29   aromatic  1.415  0.020  1.415
 O8G  C27  H27   single    0.930  0.020  1.080
 O8G  C29  C31   aromatic  1.364  0.020  1.364
 O8G  C29  H29   single    0.930  0.020  1.080
 O8G  C31  S33   aromatic  1.708  0.020  1.708
 O8G  C31  H31   single    0.930  0.020  1.080
 O8G  N34  C18   single    1.450  0.020  1.450
 O8G  N36  N34   double    1.219  0.020  1.219
 O8G  N37  N36   double    1.123  0.020  1.123

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
 O8G  H1A   C1   H1   107.60  3.000
 O8G  H1A   C1   C14  110.30  3.000
 O8G  H1    C1   C14  110.50  3.000
 O8G  H1A   C1   C4   109.16  3.000
 O8G  H1    C1   C4   109.33  3.000
 O8G  C14   C1   C4   109.90  3.000
 O8G  H4A   C4   H4   107.59  3.000
 O8G  H4A   C4   N7   109.52  3.000
 O8G  H4    C4   N7   108.45  3.000
 O8G  H4A   C4   C1   110.47  3.000
 O8G  H4    C4   C1   109.93  3.000
 O8G  N7    C4   C1   110.80  3.000
 O8G  C16   N7   C8   125.00  3.000
 O8G  C16   N7   C4   120.86  3.000
 O8G  C8    N7   C4   113.60  3.000
 O8G  H8A   C8   H8   106.67  3.000
 O8G  H8A   C8   C11  109.53  3.000
 O8G  H8    C8   C11  110.01  3.000
 O8G  H8A   C8   N7   111.16  3.000
 O8G  H8    C8   N7   108.71  3.000
 O8G  C11   C8   N7   110.67  3.000
 O8G  H11A  C11  H11  107.62  3.000
 O8G  H11A  C11  C14  110.37  3.000
 O8G  H11   C11  C14  110.41  3.000
 O8G  C14   C11  C8   109.99  3.000
 O8G  H11A  C11  C8   109.27  3.000
 O8G  H11   C11  C8   109.13  3.000
 O8G  H14   C14  C22  105.61  3.000
 O8G  H14   C14  C11  108.45  3.000
 O8G  C22   C14  C11  111.62  3.000
 O8G  H14   C14  C1   108.49  3.000
 O8G  C22   C14  C1   112.24  3.000
 O8G  C11   C14  C1   110.20  3.000
 O8G  C18   C16  O17  119.66  3.000
 O8G  O17   C16  N7   123.56  3.000
 O8G  C18   C16  N7   116.78  3.000
 O8G  H18A  C18  H18  107.01  3.000
 O8G  H18A  C18  N34  105.80  3.000
 O8G  H18   C18  N34  111.16  3.000
 O8G  N34   C18  C16  111.87  3.000
 O8G  H18A  C18  C16  110.92  3.000
 O8G  H18   C18  C16  109.92  3.000
 O8G  C25   N21  C22  102.75  3.000
 O8G  O23   C22  N21  112.23  3.000
 O8G  O23   C22  C14  119.42  3.000
 O8G  N21   C22  C14  128.34  3.000
 O8G  N24   O23  C22  107.71  3.000
 O8G  C25   N24  O23  103.50  3.000
 O8G  C26   C25  N24  123.92  3.000
 O8G  C26   C25  N21  122.27  3.000
 O8G  N24   C25  N21  113.81  3.000
 O8G  S33   C26  C27  111.52  3.000
 O8G  C27   C26  C25  128.89  3.000
 O8G  S33   C26  C25  119.60  3.000
 O8G  H27   C27  C29  124.14  3.000
 O8G  H27   C27  C26  123.47  3.000
 O8G  C29   C27  C26  112.39  3.000
 O8G  H29   C29  C31  123.52  3.000
 O8G  H29   C29  C27  124.02  3.000
 O8G  C31   C29  C27  112.46  3.000
 O8G  H31   C31  S33  120.08  3.000
 O8G  H31   C31  C29  127.86  3.000
 O8G  S33   C31  C29  112.06  3.000
 O8G  C31   S33  C26   91.58  3.000
 O8G  N36   N34  C18  116.79  3.000
 O8G  N37   N36  N34  173.42  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
 O8G  CONST_01  N24  O23  C22  N21    0.00   0.0  0
 O8G  CONST_02  O23  N24  C25  N21    0.00   0.0  0
 O8G  CONST_03  S33  C26  C25  N21    0.00   0.0  0
 O8G  CONST_04  C27  C26  C25  N21  180.00   0.0  0
 O8G  CONST_05  N24  C25  N21  C22    0.00   0.0  0
 O8G  CONST_06  C26  C25  N21  C22  180.00   0.0  0
 O8G  CONST_07  C25  N24  O23  C22    0.00   0.0  0
 O8G  CONST_08  C25  N21  C22  O23    0.00   0.0  0
 O8G  CONST_09  C26  C25  N24  O23  180.00   0.0  0
 O8G  CONST_10  S33  C26  C25  N24  180.00   0.0  0
 O8G  CONST_11  C27  C26  C25  N24    0.00   0.0  0
 O8G  CONST_12  C31  S33  C26  C25  180.00   0.0  0
 O8G  CONST_13  C29  C27  C26  C25  180.00   0.0  0
 O8G  CONST_14  C29  C31  S33  C26    0.00   0.0  0
 O8G  CONST_15  C31  C29  C27  C26    0.00   0.0  0
 O8G  CONST_16  C31  S33  C26  C27    0.00   0.0  0
 O8G  CONST_17  S33  C31  C29  C27    0.00   0.0  0
 O8G  CONST_18  S33  C26  C27  C29    0.00   0.0  0
 O8G  CONST_19  C25  N21  C22  C14  180.00   0.0  0
 O8G  CONST_20  N24  O23  C22  C14  180.00   0.0  0
 O8G  CONST_21  H27  C27  C26  C25    0.00   0.0  0
 O8G  CONST_22  H31  C31  S33  C26  180.00   0.0  0
 O8G  CONST_23  H29  C29  C27  C26  180.00   0.0  0
 O8G  CONST_24  C18  C16  N7   C4   180.00   0.0  0
 O8G  CONST_25  O17  C16  N7   C4     0.00   0.0  0
 O8G  CONST_26  C18  C16  N7   C8     0.00   0.0  0
 O8G  CONST_27  O17  C16  N7   C8   180.00   0.0  0
 O8G  Var_01    C8   N7   C4   C1    58.37  30.0  1
 O8G  Var_02    C11  C8   N7   C4   -58.35  30.0  1
 O8G  Var_03    C14  C1   C4   N7   -55.76  30.0  1
 O8G  Var_04    C14  C11  C8   N7    55.85  30.0  1
 O8G  Var_05    N34  C18  C16  N7   171.66  30.0  3

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
 O8G  chir_01  C14  C1  C11  C22  negativ

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
 O8G  plan-1  C14  0.020
 O8G  plan-1  N21  0.020
 O8G  plan-1  C22  0.020
 O8G  plan-1  O23  0.020
 O8G  plan-1  N24  0.020
 O8G  plan-1  C25  0.020
 O8G  plan-1  C26  0.020
 O8G  plan-2  C25  0.020
 O8G  plan-2  C26  0.020
 O8G  plan-2  C27  0.020
 O8G  plan-2  C29  0.020
 O8G  plan-2  C31  0.020
 O8G  plan-2  S33  0.020
 O8G  plan-2  H27  0.020
 O8G  plan-2  H29  0.020
 O8G  plan-2  H31  0.020
 O8G  plan-3  C4   0.020
 O8G  plan-3  N7   0.020
 O8G  plan-3  C8   0.020
 O8G  plan-3  C16  0.020
 O8G  plan-3  O17  0.020
 O8G  plan-3  C18  0.020
 O8G  plan-4  C18  0.020
 O8G  plan-4  N34  0.020
 O8G  plan-4  N36  0.020
 O8G  plan-4  N37  0.020

