# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 22:06:28 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: (3R)-3-[3-(4-chlorophenyl)-1,2,4-oxadiazol-5-yl]piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(cc1)c2noc(n2)[C@@H]3CCCNC3
#
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
 S45  S45  (3R)-3-[3-(4-chlorophenyl)-1,2,4-oxadiazol-5-yl]piperidine  ligand  32  18  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S45
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
 S45  CL1   CL  CL    0  -0.115  -6.1162  -0.5493   0.0094
 S45  C7    C   CR6   0  -0.042  -4.4120  -0.2556   0.0092
 S45  C10   C   CR16  0  -0.194  -3.9481   1.0523   0.0350
 S45  C6    C   CR16  0  -0.284  -2.5846   1.2853   0.0348
 S45  C4    C   CR6   0   0.013  -1.6842   0.2206   0.0091
 S45  C5    C   CR16  0  -0.294  -2.1711  -1.0835  -0.0166
 S45  C9    C   CR16  0  -0.193  -3.5349  -1.3281  -0.0169
 S45  C1    C   CR5   0   0.322  -0.2424   0.4559   0.0089
 S45  N1    N   N     0  -0.464   0.6802  -0.5508   0.0153
 S45  C2    C   CR5   0   0.568   1.8035   0.0858   0.0133
 S45  O1    O   O     0  -0.327   1.6306   1.4029   0.0057
 S45  N2    N   N     0  -0.155   0.2865   1.6430   0.0018
 S45  C3    C   CH1   0  -0.396   3.1796  -0.4666   0.0265
 S45  C11   C   CH2   0  -0.430   3.9419  -0.0610   1.2966
 S45  C13   C   CH2   0  -0.440   5.3631  -0.6101   1.2523
 S45  C12   C   CH2   0  -0.293   6.0581  -0.2077  -0.0392
 S45  N3    N   NH1   0  -0.600   5.2768  -0.6659  -1.1751
 S45  C8    C   CH2   0  -0.268   3.9684  -0.0482  -1.2215
 S45  H10   H   HCR6  0   0.288  -4.6416   1.8812   0.0556
 S45  H6    H   HCR6  0   0.271  -2.2265   2.3061   0.0560
 S45  H5    H   HCR6  0   0.273  -1.4841  -1.9185  -0.0373
 S45  H9    H   HCR6  0   0.287  -3.9053  -2.3439  -0.0375
 S45  H3    H   HCH1  0   0.283   3.0706  -1.5540   0.0104
 S45  H11   H   HCH2  0   0.233   3.9758   1.0299   1.3740
 S45  H11A  H   HCH2  0   0.255   3.4172  -0.4273   2.1812
 S45  H13   H   HCH2  0   0.239   5.9280  -0.2403   2.1102
 S45  H13A  H   HCH2  0   0.223   5.3418  -1.7010   1.3274
 S45  H12   H   HCH2  0   0.191   6.2017   0.8855  -0.0423
 S45  H12A  H   HCH2  0   0.236   7.0501  -0.6600  -0.0907
 S45  HN3   H   HNH1  0   0.358   5.7689  -0.4636  -2.0349
 S45  H8    H   HCH2  0   0.253   3.4483  -0.3888  -2.1191
 S45  H8A   H   HCH2  0   0.203   4.0166   1.0515  -1.2690

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
 S45  CL1  C7    single    1.729  0.020  1.729
 S45  C7   C10   aromatic  1.388  0.020  1.388
 S45  C7   C9    aromatic  1.386  0.020  1.386
 S45  C10  C6    aromatic  1.383  0.020  1.383
 S45  C6   C4    aromatic  1.395  0.020  1.395
 S45  C4   C5    aromatic  1.392  0.020  1.392
 S45  C4   C1    single    1.461  0.020  1.461
 S45  C5   C9    aromatic  1.386  0.020  1.386
 S45  C1   N1    aromatic  1.365  0.020  1.365
 S45  C1   N2    aromatic  1.300  0.020  1.300
 S45  N1   C2    aromatic  1.291  0.020  1.291
 S45  C2   O1    aromatic  1.328  0.020  1.328
 S45  C2   C3    single    1.483  0.020  1.483
 S45  O1   N2    aromatic  1.365  0.020  1.365
 S45  C3   C11   single    1.536  0.020  1.536
 S45  C3   C8    single    1.534  0.020  1.534
 S45  C11  C13   single    1.524  0.020  1.524
 S45  C13  C12   single    1.521  0.020  1.521
 S45  C12  N3    single    1.453  0.020  1.453
 S45  N3   C8    single    1.448  0.020  1.448
 S45  C10  H10   single    0.930  0.020  1.080
 S45  C6   H6    single    0.930  0.020  1.080
 S45  C5   H5    single    0.930  0.020  1.080
 S45  C9   H9    single    0.930  0.020  1.080
 S45  C3   H3    single    0.970  0.020  1.090
 S45  C11  H11   single    0.970  0.020  1.090
 S45  C11  H11A  single    0.970  0.020  1.090
 S45  C13  H13   single    0.970  0.020  1.090
 S45  C13  H13A  single    0.970  0.020  1.090
 S45  C12  H12   single    0.970  0.020  1.090
 S45  C12  H12A  single    0.970  0.020  1.090
 S45  N3   HN3   single    0.890  0.020  1.040
 S45  C8   H8    single    0.970  0.020  1.090
 S45  C8   H8A   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
 S45  C9    C7   C10  121.20  3.000
 S45  C9    C7   CL1  119.50  3.000
 S45  C10   C7   CL1  119.30  3.000
 S45  H10   C10  C6   120.21  3.000
 S45  H10   C10  C7   120.56  3.000
 S45  C6    C10  C7   119.23  3.000
 S45  H6    C6   C4   120.46  3.000
 S45  H6    C6   C10  119.03  3.000
 S45  C4    C6   C10  120.51  3.000
 S45  C1    C4   C5   119.74  3.000
 S45  C1    C4   C6   120.94  3.000
 S45  C5    C4   C6   119.32  3.000
 S45  H5    C5   C9   119.27  3.000
 S45  H5    C5   C4   120.10  3.000
 S45  C9    C5   C4   120.63  3.000
 S45  H9    C9   C5   120.20  3.000
 S45  H9    C9   C7   120.70  3.000
 S45  C5    C9   C7   119.10  3.000
 S45  N2    C1   N1   113.49  3.000
 S45  N2    C1   C4   123.28  3.000
 S45  N1    C1   C4   123.23  3.000
 S45  C2    N1   C1   102.96  3.000
 S45  C3    C2   O1   119.35  3.000
 S45  C3    C2   N1   128.59  3.000
 S45  O1    C2   N1   112.06  3.000
 S45  N2    O1   C2   107.61  3.000
 S45  O1    N2   C1   103.88  3.000
 S45  H3    C3   C8   108.10  3.000
 S45  H3    C3   C11  108.93  3.000
 S45  C8    C3   C11  110.21  3.000
 S45  H3    C3   C2   106.13  3.000
 S45  C8    C3   C2   111.60  3.000
 S45  C11   C3   C2   111.69  3.000
 S45  H11A  C11  H11  106.98  3.000
 S45  H11A  C11  C13  110.53  3.000
 S45  H11   C11  C13  109.41  3.000
 S45  H11A  C11  C3   110.06  3.000
 S45  H11   C11  C3   109.71  3.000
 S45  C13   C11  C3   110.10  3.000
 S45  H13A  C13  H13  107.10  3.000
 S45  H13A  C13  C12  109.34  3.000
 S45  H13   C13  C12  109.95  3.000
 S45  H13A  C13  C11  109.82  3.000
 S45  H13   C13  C11  109.73  3.000
 S45  C12   C13  C11  110.82  3.000
 S45  H12A  C12  H12  107.00  3.000
 S45  H12A  C12  N3   108.73  3.000
 S45  H12   C12  N3   112.37  3.000
 S45  H12A  C12  C13  110.23  3.000
 S45  H12   C12  C13  108.92  3.000
 S45  N3    C12  C13  109.56  3.000
 S45  HN3   N3   C8   109.10  3.000
 S45  HN3   N3   C12  109.88  3.000
 S45  C8    N3   C12  112.12  3.000
 S45  H8A   C8   H8   107.26  3.000
 S45  H8A   C8   N3   112.81  3.000
 S45  H8    C8   N3   108.89  3.000
 S45  H8A   C8   C3   109.25  3.000
 S45  H8    C8   C3   109.80  3.000
 S45  N3    C8   C3   108.79  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
 S45  CONST_01  C4   C6   C10  C7     0.00   0.0  0
 S45  CONST_02  C4   C5   C9   C7     0.00   0.0  0
 S45  CONST_03  C5   C9   C7   C10    0.00   0.0  0
 S45  CONST_04  C5   C4   C6   C10    0.00   0.0  0
 S45  CONST_05  C1   C4   C6   C10  180.00   0.0  0
 S45  CONST_06  C9   C7   C10  C6     0.00   0.0  0
 S45  CONST_07  C9   C5   C4   C6     0.00   0.0  0
 S45  CONST_08  N1   C1   C4   C6   180.00   0.0  0
 S45  CONST_09  N2   C1   C4   C6     0.00   0.0  0
 S45  CONST_10  C2   N1   C1   C4   180.00   0.0  0
 S45  CONST_11  O1   N2   C1   C4   180.00   0.0  0
 S45  CONST_12  N1   C1   C4   C5     0.00   0.0  0
 S45  CONST_13  N2   C1   C4   C5   180.00   0.0  0
 S45  CONST_14  C1   C4   C5   C9   180.00   0.0  0
 S45  CONST_15  O1   C2   N1   C1     0.00   0.0  0
 S45  CONST_16  C2   O1   N2   C1     0.00   0.0  0
 S45  CONST_17  O1   N2   C1   N1     0.00   0.0  0
 S45  CONST_18  N2   O1   C2   N1     0.00   0.0  0
 S45  CONST_19  N2   C1   N1   C2     0.00   0.0  0
 S45  CONST_20  C3   C2   N1   C1   180.00   0.0  0
 S45  CONST_21  C3   C2   O1   N2   180.00   0.0  0
 S45  CONST_22  C6   C10  C7   CL1  180.00   0.0  0
 S45  CONST_23  C5   C9   C7   CL1  180.00   0.0  0
 S45  CONST_24  H6   C6   C10  C7   180.00   0.0  0
 S45  CONST_25  H5   C5   C9   C7   180.00   0.0  0
 S45  CONST_26  H9   C9   C7   C10  180.00   0.0  0
 S45  CONST_27  H10  C10  C6   C4   180.00   0.0  0
 S45  Var_01    C12  C13  C11  C3    53.04  30.0  1
 S45  Var_02    C12  N3   C8   C3   -63.25  30.0  1
 S45  Var_03    N3   C12  C13  C11  -56.66  30.0  1
 S45  Var_04    C8   N3   C12  C13   62.81  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
 S45  chir_01  C3  C2  C11  C8  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
 S45  plan-1  C4   0.020
 S45  plan-1  C1   0.020
 S45  plan-1  N1   0.020
 S45  plan-1  C2   0.020
 S45  plan-1  O1   0.020
 S45  plan-1  N2   0.020
 S45  plan-1  C3   0.020
 S45  plan-2  CL1  0.020
 S45  plan-2  C7   0.020
 S45  plan-2  C10  0.020
 S45  plan-2  C6   0.020
 S45  plan-2  C4   0.020
 S45  plan-2  C5   0.020
 S45  plan-2  C9   0.020
 S45  plan-2  C1   0.020
 S45  plan-2  H10  0.020
 S45  plan-2  H6   0.020
 S45  plan-2  H5   0.020
 S45  plan-2  H9   0.020

