# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 12:52:32 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 2-phenyl-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: O=C(Cc1ccccc1)N2CCC(CC2)c3onc(n3)c4sccc4
#
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
 LL3  LL3  2-phenyl-1-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}ethanone  ligand  44  25  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LL3
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
 LL3  C34   C  CR16  0  -0.303   6.5571   0.5254   0.4786
 LL3  C43   C  CR16  0  -0.243   7.7965  -0.0110   0.1573
 LL3  C41   C  CR16  0  -0.271   7.9231  -1.3715  -0.0932
 LL3  C39   C  CR16  0  -0.242   6.8030  -2.1889  -0.0177
 LL3  C37   C  CR16  0  -0.309   5.5656  -1.6468   0.3036
 LL3  C36   C  CR6   0   0.177   5.4285  -0.2853   0.5549
 LL3  C01   C  CH2   0  -0.720   4.0911   0.2978   0.9015
 LL3  C04   C  C     0   0.572   3.3503   0.7951  -0.3340
 LL3  O06   O  O     0  -0.489   3.8499   0.6929  -1.4444
 LL3  N05   N  NT    0  -0.452   2.1374   1.3584  -0.1360
 LL3  C18   C  CH2   0  -0.322   1.3233   1.7881  -1.2591
 LL3  C15   C  CH2   0  -0.422   0.0785   0.9195  -1.3875
 LL3  C07   C  CH2   0  -0.330   1.4341   1.4143   1.1319
 LL3  C10   C  CH2   0  -0.418   0.1930   0.5300   1.0986
 LL3  C13   C  CH1   0  -0.410  -0.7098   0.9423  -0.0715
 LL3  C21   C  CR5   0   0.570  -1.9376   0.1114  -0.1357
 LL3  N25   N  N     0  -0.461  -3.1617   0.4809   0.0435
 LL3  O22   O  O     0  -0.328  -1.8374  -1.1852  -0.3951
 LL3  N23   N  N     0  -0.157  -3.1022  -1.7108  -0.3843
 LL3  C24   C  CR5   0   0.340  -3.8552  -0.6842  -0.1193
 LL3  C26   C  CR5   0  -0.278  -5.2932  -0.7457  -0.0009
 LL3  C27   C  CR15  0  -0.210  -6.1232  -1.8238  -0.1415
 LL3  C29   C  CR15  0  -0.169  -7.4838  -1.4852   0.0513
 LL3  C31   C  CR15  0  -0.460  -7.6569  -0.1618   0.3341
 LL3  S33   S  S2    0   0.264  -6.1749   0.6855   0.3683
 LL3  H34   H  HCR6  0   0.248   6.4674   1.5872   0.6763
 LL3  H43   H  HCR6  0   0.254   8.6643   0.6340   0.1058
 LL3  H41   H  HCR6  0   0.254   8.8889  -1.7923  -0.3414
 LL3  H39   H  HCR6  0   0.254   6.8928  -3.2513  -0.2051
 LL3  H37   H  HCR6  0   0.248   4.6976  -2.2929   0.3644
 LL3  H01   H  HCH2  0   0.291   3.4794  -0.4501   1.4135
 LL3  H01A  H  HCH2  0   0.295   4.2146   1.1226   1.6086
 LL3  H18   H  HCH2  0   0.249   1.0310   2.8314  -1.1011
 LL3  H18A  H  HCH2  0   0.273   1.9111   1.7489  -2.1715
 LL3  H15   H  HCH2  0   0.263  -0.5382   1.2966  -2.2053
 LL3  H15A  H  HCH2  0   0.247   0.3742  -0.1020  -1.6390
 LL3  H07   H  HCH2  0   0.285   2.0794   1.1164   1.9525
 LL3  H07A  H  HCH2  0   0.256   1.1433   2.4522   1.3224
 LL3  H10   H  HCH2  0   0.247   0.4984  -0.5148   0.9960
 LL3  H10A  H  HCH2  0   0.264  -0.3431   0.6253   2.0445
 LL3  H13   H  HCH1  0   0.289  -1.0592   1.9638   0.1068
 LL3  H27   H  HCR5  0   0.273  -5.7737  -2.8195  -0.3745
 LL3  H29   H  HCR5  0   0.276  -8.2973  -2.1920  -0.0177
 LL3  H31   H  HCR5  0   0.305  -8.5825   0.3586   0.5263

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
 LL3  C43  C34   aromatic  1.388  0.020  1.388
 LL3  C34  C36   aromatic  1.392  0.020  1.392
 LL3  C34  H34   single    0.930  0.020  1.080
 LL3  C43  C41   aromatic  1.389  0.020  1.389
 LL3  C43  H43   single    0.930  0.020  1.080
 LL3  C41  C39   aromatic  1.389  0.020  1.389
 LL3  C41  H41   single    0.930  0.020  1.080
 LL3  C39  C37   aromatic  1.389  0.020  1.389
 LL3  C39  H39   single    0.930  0.020  1.080
 LL3  C36  C37   aromatic  1.391  0.020  1.391
 LL3  C37  H37   single    0.930  0.020  1.080
 LL3  C36  C01   single    1.500  0.020  1.500
 LL3  C04  C01   single    1.524  0.020  1.524
 LL3  C01  H01   single    0.970  0.020  1.090
 LL3  C01  H01A  single    0.970  0.020  1.090
 LL3  O06  C04   double    1.222  0.020  1.222
 LL3  C04  N05   single    1.352  0.020  1.352
 LL3  C07  N05   single    1.451  0.020  1.451
 LL3  N05  C18   single    1.452  0.020  1.452
 LL3  C18  C15   single    1.523  0.020  1.523
 LL3  C18  H18   single    0.970  0.020  1.090
 LL3  C18  H18A  single    0.970  0.020  1.090
 LL3  C13  C15   single    1.534  0.020  1.534
 LL3  C15  H15   single    0.970  0.020  1.090
 LL3  C15  H15A  single    0.970  0.020  1.090
 LL3  C07  C10   single    1.524  0.020  1.524
 LL3  C07  H07   single    0.970  0.020  1.090
 LL3  C07  H07A  single    0.970  0.020  1.090
 LL3  C10  C13   single    1.534  0.020  1.534
 LL3  C10  H10   single    0.970  0.020  1.090
 LL3  C10  H10A  single    0.970  0.020  1.090
 LL3  C13  C21   single    1.484  0.020  1.484
 LL3  C13  H13   single    0.970  0.020  1.090
 LL3  N25  C21   aromatic  1.291  0.020  1.291
 LL3  C21  O22   aromatic  1.326  0.020  1.326
 LL3  N25  C24   aromatic  1.366  0.020  1.366
 LL3  O22  N23   aromatic  1.370  0.020  1.370
 LL3  C24  N23   aromatic  1.300  0.020  1.300
 LL3  C26  C24   single    1.444  0.020  1.444
 LL3  C27  C26   aromatic  1.368  0.020  1.368
 LL3  C26  S33   aromatic  1.721  0.020  1.721
 LL3  C29  C27   aromatic  1.415  0.020  1.415
 LL3  C27  H27   single    0.930  0.020  1.080
 LL3  C29  C31   aromatic  1.364  0.020  1.364
 LL3  C29  H29   single    0.930  0.020  1.080
 LL3  C31  S33   aromatic  1.707  0.020  1.707
 LL3  C31  H31   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
 LL3  H34   C34  C36  119.58  3.000
 LL3  H34   C34  C43  119.65  3.000
 LL3  C36   C34  C43  120.77  3.000
 LL3  H43   C43  C41  120.13  3.000
 LL3  H43   C43  C34  119.76  3.000
 LL3  C41   C43  C34  120.11  3.000
 LL3  H41   C41  C39  120.22  3.000
 LL3  H41   C41  C43  120.23  3.000
 LL3  C39   C41  C43  119.55  3.000
 LL3  H39   C39  C37  119.81  3.000
 LL3  H39   C39  C41  120.09  3.000
 LL3  C37   C39  C41  120.10  3.000
 LL3  H37   C37  C36  119.63  3.000
 LL3  H37   C37  C39  119.60  3.000
 LL3  C36   C37  C39  120.77  3.000
 LL3  C01   C36  C37  120.67  3.000
 LL3  C01   C36  C34  120.62  3.000
 LL3  C37   C36  C34  118.70  3.000
 LL3  H01A  C01  H01  106.04  3.000
 LL3  H01A  C01  C04  109.45  3.000
 LL3  H01   C01  C04  109.32  3.000
 LL3  H01A  C01  C36  110.00  3.000
 LL3  H01   C01  C36  109.95  3.000
 LL3  C04   C01  C36  111.90  3.000
 LL3  N05   C04  O06  122.33  3.000
 LL3  N05   C04  C01  116.96  3.000
 LL3  O06   C04  C01  120.71  3.000
 LL3  C07   N05  C18  113.12  3.000
 LL3  C18   N05  C04  120.86  3.000
 LL3  C07   N05  C04  125.37  3.000
 LL3  H18A  C18  H18  107.46  3.000
 LL3  H18A  C18  C15  110.54  3.000
 LL3  H18   C18  C15  109.72  3.000
 LL3  H18A  C18  N05  109.61  3.000
 LL3  H18   C18  N05  108.67  3.000
 LL3  C15   C18  N05  110.77  3.000
 LL3  H15A  C15  H15  107.67  3.000
 LL3  H15A  C15  C13  110.51  3.000
 LL3  H15   C15  C13  110.32  3.000
 LL3  H15A  C15  C18  109.35  3.000
 LL3  H15   C15  C18  109.14  3.000
 LL3  C13   C15  C18  109.82  3.000
 LL3  H07A  C07  H07  106.65  3.000
 LL3  H07A  C07  C10  109.73  3.000
 LL3  H07   C07  C10  109.96  3.000
 LL3  H07A  C07  N05  108.50  3.000
 LL3  H07   C07  N05  111.21  3.000
 LL3  C10   C07  N05  110.68  3.000
 LL3  H10A  C10  H10  107.57  3.000
 LL3  H10A  C10  C13  110.39  3.000
 LL3  H10   C10  C13  110.46  3.000
 LL3  H10A  C10  C07  109.29  3.000
 LL3  H10   C10  C07  109.21  3.000
 LL3  C13   C10  C07  109.87  3.000
 LL3  H13   C13  C21  105.40  3.000
 LL3  H13   C13  C10  108.33  3.000
 LL3  C21   C13  C10  111.68  3.000
 LL3  H13   C13  C15  108.53  3.000
 LL3  C21   C13  C15  112.31  3.000
 LL3  C10   C13  C15  110.35  3.000
 LL3  O22   C21  N25  112.24  3.000
 LL3  O22   C21  C13  119.57  3.000
 LL3  N25   C21  C13  128.19  3.000
 LL3  C24   N25  C21  102.75  3.000
 LL3  N23   O22  C21  107.69  3.000
 LL3  C24   N23  O22  103.49  3.000
 LL3  C26   C24  N23  124.03  3.000
 LL3  C26   C24  N25  122.16  3.000
 LL3  N23   C24  N25  113.81  3.000
 LL3  S33   C26  C27  111.50  3.000
 LL3  S33   C26  C24  119.49  3.000
 LL3  C27   C26  C24  129.01  3.000
 LL3  H27   C27  C29  124.11  3.000
 LL3  H27   C27  C26  123.51  3.000
 LL3  C29   C27  C26  112.38  3.000
 LL3  H29   C29  C31  123.55  3.000
 LL3  H29   C29  C27  123.98  3.000
 LL3  C31   C29  C27  112.47  3.000
 LL3  H31   C31  S33  120.11  3.000
 LL3  H31   C31  C29  127.84  3.000
 LL3  S33   C31  C29  112.05  3.000
 LL3  C31   S33  C26   91.59  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
 LL3  CONST_01  C39  C41  C43  C34     0.00   0.0  0
 LL3  CONST_02  C39  C37  C36  C34     0.00   0.0  0
 LL3  CONST_03  C37  C36  C34  C43     0.00   0.0  0
 LL3  CONST_04  C37  C39  C41  C43     0.00   0.0  0
 LL3  CONST_05  C36  C34  C43  C41     0.00   0.0  0
 LL3  CONST_06  C36  C37  C39  C41     0.00   0.0  0
 LL3  CONST_07  N23  C24  N25  C21     0.00   0.0  0
 LL3  CONST_08  C26  C24  N25  C21   180.00   0.0  0
 LL3  CONST_09  C24  N23  O22  C21     0.00   0.0  0
 LL3  CONST_10  N23  O22  C21  N25     0.00   0.0  0
 LL3  CONST_11  O22  N23  C24  N25     0.00   0.0  0
 LL3  CONST_12  C27  C26  C24  N25   180.00   0.0  0
 LL3  CONST_13  S33  C26  C24  N25     0.00   0.0  0
 LL3  CONST_14  C24  N25  C21  O22     0.00   0.0  0
 LL3  CONST_15  C26  C24  N23  O22   180.00   0.0  0
 LL3  CONST_16  C27  C26  C24  N23     0.00   0.0  0
 LL3  CONST_17  S33  C26  C24  N23   180.00   0.0  0
 LL3  CONST_18  C29  C27  C26  C24   180.00   0.0  0
 LL3  CONST_19  C31  S33  C26  C24   180.00   0.0  0
 LL3  CONST_20  C31  C29  C27  C26     0.00   0.0  0
 LL3  CONST_21  C29  C31  S33  C26     0.00   0.0  0
 LL3  CONST_22  C31  S33  C26  C27     0.00   0.0  0
 LL3  CONST_23  S33  C31  C29  C27     0.00   0.0  0
 LL3  CONST_24  S33  C26  C27  C29     0.00   0.0  0
 LL3  CONST_25  C24  N25  C21  C13   180.00   0.0  0
 LL3  CONST_26  N23  O22  C21  C13   180.00   0.0  0
 LL3  CONST_27  C01  C36  C34  C43   180.00   0.0  0
 LL3  CONST_28  C01  C36  C37  C39   180.00   0.0  0
 LL3  CONST_29  H41  C41  C43  C34   180.00   0.0  0
 LL3  CONST_30  H37  C37  C36  C34   180.00   0.0  0
 LL3  CONST_31  H39  C39  C41  C43   180.00   0.0  0
 LL3  CONST_32  H34  C34  C43  C41   180.00   0.0  0
 LL3  CONST_33  H43  C43  C41  C39   180.00   0.0  0
 LL3  CONST_34  H27  C27  C26  C24     0.00   0.0  0
 LL3  CONST_35  H29  C29  C27  C26   180.00   0.0  0
 LL3  CONST_36  H31  C31  S33  C26   180.00   0.0  0
 LL3  CONST_37  C07  N05  C04  C01     0.00   0.0  0
 LL3  CONST_38  C18  N05  C04  C01   180.00   0.0  0
 LL3  CONST_39  C07  N05  C04  O06   180.00   0.0  0
 LL3  CONST_40  C18  N05  C04  O06     0.00   0.0  0
 LL3  Var_01    C13  C10  C07  N05   -56.09  30.0  1
 LL3  Var_02    C13  C15  C18  N05    56.06  30.0  1
 LL3  Var_03    C10  C07  N05  C18    59.21  30.0  1
 LL3  Var_04    C07  N05  C18  C15   -59.25  30.0  1
 LL3  Var_05    C04  C01  C36  C34    87.83  30.0  2
 LL3  Var_06    N05  C04  C01  C36  -179.13  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
 LL3  chir_01  C13  C15  C10  C21  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
 LL3  plan-1  C13  0.020
 LL3  plan-1  C21  0.020
 LL3  plan-1  N25  0.020
 LL3  plan-1  O22  0.020
 LL3  plan-1  N23  0.020
 LL3  plan-1  C24  0.020
 LL3  plan-1  C26  0.020
 LL3  plan-2  C24  0.020
 LL3  plan-2  C26  0.020
 LL3  plan-2  C27  0.020
 LL3  plan-2  C29  0.020
 LL3  plan-2  C31  0.020
 LL3  plan-2  S33  0.020
 LL3  plan-2  H27  0.020
 LL3  plan-2  H29  0.020
 LL3  plan-2  H31  0.020
 LL3  plan-3  C34  0.020
 LL3  plan-3  C43  0.020
 LL3  plan-3  C41  0.020
 LL3  plan-3  C39  0.020
 LL3  plan-3  C37  0.020
 LL3  plan-3  C36  0.020
 LL3  plan-3  C01  0.020
 LL3  plan-3  H34  0.020
 LL3  plan-3  H43  0.020
 LL3  plan-3  H41  0.020
 LL3  plan-3  H39  0.020
 LL3  plan-3  H37  0.020
 LL3  plan-4  C01  0.020
 LL3  plan-4  C04  0.020
 LL3  plan-4  O06  0.020
 LL3  plan-4  N05  0.020
 LL3  plan-4  C18  0.020
 LL3  plan-4  C07  0.020

