# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 16:47:23 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (4-benzylpiperidin-1-yl)[2-methoxy-4-(methylsulfanyl)phenyl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(SC)ccc1C(=O)N2CCC(CC2)Cc3ccccc3
#
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
 J8S  J8S  (4-benzylpiperidin-1-yl)[2-methoxy-4-(methylsulfanyl)phenyl]methanone  ligand  50  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 PERFECT
;

data_comp_J8S
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
 J8S  C4   C  CR16  0  -0.394  -3.7369   0.3751  -0.7317
 J8S  C5   C  CR6   0  -0.097  -4.6414  -0.4756  -0.0878
 J8S  C7   C  CH3   0  -0.796  -7.0748  -1.8369   0.1868
 J8S  C8   C  CR16  0  -0.289  -4.3063  -1.0531   1.1296
 J8S  C10  C  CR6   0  -0.212  -2.1553   0.0522   1.0654
 J8S  C15  C  CH2   0  -0.417   1.1913  -0.9240  -0.7952
 J8S  C17  C  CH2   0  -0.501   3.5136  -0.1795  -1.4316
 J8S  C20  C  CR16  0  -0.240   7.0769  -0.8657  -0.3118
 J8S  C21  C  CR16  0  -0.275   7.5758   0.4189  -0.1310
 J8S  C22  C  CR16  0  -0.241   6.7590   1.5108  -0.3904
 J8S  C24  C  CH2   0  -0.415   2.5080   0.4496   0.8185
 J8S  C1   C  CH3   0  -0.442  -1.8282   2.0397  -1.9557
 J8S  C11  C  C     0   0.511  -0.8598   0.4114   1.7319
 J8S  C14  C  CH2   0  -0.310   0.2584  -1.3110   0.3439
 J8S  C16  C  CH1   0  -0.242   2.5938  -0.6045  -0.2826
 J8S  C18  C  CR6   0   0.138   4.9383   0.0363  -1.0027
 J8S  C19  C  CR16  0  -0.308   5.7714  -1.0519  -0.7441
 J8S  C23  C  CR16  0  -0.313   5.4526   1.3180  -0.8229
 J8S  C25  C  CH2   0  -0.311   1.5405   0.0297   1.9175
 J8S  C3   C  CR6   0   0.424  -2.5026   0.6408  -0.1567
 J8S  C9   C  CR16  0  -0.229  -3.0672  -0.7735   1.6951
 J8S  N13  N  NT    0  -0.423   0.2320  -0.2785   1.3644
 J8S  O12  O  O     0  -0.495  -0.8523   1.2878   2.5887
 J8S  O2   O  O2    0  -0.465  -1.5704   1.4416  -0.6993
 J8S  S6   S  S2    0   0.046  -6.1685  -0.7423  -0.9189
 J8S  H1   H  HCR6  0   0.289  -4.0115   0.8216  -1.6789
 J8S  H2   H  HCH3  0   0.276  -7.2726  -1.3674   1.1484
 J8S  H3   H  HCH3  0   0.296  -8.0251  -2.0346  -0.3052
 J8S  H4   H  HCH3  0   0.276  -6.5574  -2.7830   0.3326
 J8S  H5   H  HCR6  0   0.264  -4.9841  -1.7139   1.6497
 J8S  H6   H  HCH2  0   0.239   1.2276  -1.7442  -1.5166
 J8S  H7   H  HCH2  0   0.227   0.7777  -0.0542  -1.3142
 J8S  H8   H  HCH2  0   0.246   3.4783  -0.9484  -2.2094
 J8S  H9   H  HCH2  0   0.237   3.1219   0.7372  -1.8832
 J8S  H11  H  HCR6  0   0.252   8.5939   0.5670   0.2055
 J8S  H12  H  HCR6  0   0.252   7.1377   2.5162  -0.2566
 J8S  H13  H  HCH2  0   0.243   3.4892   0.6225   1.2661
 J8S  H14  H  HCH2  0   0.221   2.1798   1.4043   0.3931
 J8S  H15  H  HCH3  0   0.233  -1.9920   1.2908  -2.7344
 J8S  H16  H  HCH3  0   0.235  -2.6929   2.7064  -1.9175
 J8S  H17  H  HCH3  0   0.263  -0.9449   2.6211  -2.2059
 J8S  H18  H  HCH2  0   0.271  -0.7464  -1.4996  -0.0253
 J8S  H19  H  HCH2  0   0.242   0.6065  -2.2425   0.8039
 J8S  H20  H  HCH1  0   0.225   3.0017  -1.5232   0.1612
 J8S  H21  H  HCR6  0   0.245   5.3952  -2.0585  -0.8881
 J8S  H22  H  HCR6  0   0.245   4.8242   2.1778  -1.0238
 J8S  H23  H  HCH2  0   0.239   1.9227  -0.8638   2.4232
 J8S  H24  H  HCH2  0   0.264   1.4391   0.8096   2.6669
 J8S  H25  H  HCR6  0   0.266  -2.8097  -1.2269   2.6444
 J8S  H10  H  HCR6  0   0.252   7.7074  -1.7245  -0.1193

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
 J8S  O12  C11  double    1.226  0.020  1.226
 J8S  C11  C10  single    1.501  0.020  1.501
 J8S  C11  N13  single    1.343  0.020  1.343
 J8S  C9   C8   aromatic  1.390  0.020  1.390
 J8S  C9   C10  aromatic  1.382  0.020  1.382
 J8S  C8   C5   aromatic  1.388  0.020  1.388
 J8S  C10  C3   aromatic  1.400  0.020  1.400
 J8S  C14  N13  single    1.452  0.020  1.452
 J8S  C14  C15  single    1.522  0.020  1.522
 J8S  C5   C4   aromatic  1.399  0.020  1.399
 J8S  C5   S6   single    1.759  0.020  1.759
 J8S  C3   O2   single    1.343  0.020  1.343
 J8S  C3   C4   aromatic  1.387  0.020  1.387
 J8S  N13  C25  single    1.454  0.020  1.454
 J8S  O2   C1   single    1.415  0.020  1.415
 J8S  S6   C7   single    1.801  0.020  1.801
 J8S  C15  C16  single    1.527  0.020  1.527
 J8S  C25  C24  single    1.523  0.020  1.523
 J8S  C22  C23  aromatic  1.390  0.020  1.390
 J8S  C22  C21  aromatic  1.388  0.020  1.388
 J8S  C16  C24  single    1.527  0.020  1.527
 J8S  C16  C17  single    1.532  0.020  1.532
 J8S  C23  C18  aromatic  1.393  0.020  1.393
 J8S  C21  C20  aromatic  1.390  0.020  1.390
 J8S  C18  C17  single    1.503  0.020  1.503
 J8S  C18  C19  aromatic  1.395  0.020  1.395
 J8S  C20  C19  aromatic  1.388  0.020  1.388
 J8S  C4   H1   single    0.930  0.020  1.080
 J8S  C7   H2   single    0.970  0.020  1.090
 J8S  C7   H3   single    0.970  0.020  1.090
 J8S  C7   H4   single    0.970  0.020  1.090
 J8S  C8   H5   single    0.930  0.020  1.080
 J8S  C15  H6   single    0.970  0.020  1.090
 J8S  C15  H7   single    0.970  0.020  1.090
 J8S  C17  H8   single    0.970  0.020  1.090
 J8S  C17  H9   single    0.970  0.020  1.090
 J8S  C20  H10  single    0.930  0.020  1.080
 J8S  C21  H11  single    0.930  0.020  1.080
 J8S  C22  H12  single    0.930  0.020  1.080
 J8S  C24  H13  single    0.970  0.020  1.090
 J8S  C24  H14  single    0.970  0.020  1.090
 J8S  C1   H15  single    0.970  0.020  1.090
 J8S  C1   H16  single    0.970  0.020  1.090
 J8S  C1   H17  single    0.970  0.020  1.090
 J8S  C14  H18  single    0.970  0.020  1.090
 J8S  C14  H19  single    0.970  0.020  1.090
 J8S  C16  H20  single    0.970  0.020  1.090
 J8S  C19  H21  single    0.930  0.020  1.080
 J8S  C23  H22  single    0.930  0.020  1.080
 J8S  C25  H23  single    0.970  0.020  1.090
 J8S  C25  H24  single    0.970  0.020  1.090
 J8S  C9   H25  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
 J8S  H1   C4   C3   120.62  3.000
 J8S  H1   C4   C5   119.32  3.000
 J8S  C3   C4   C5   120.07  3.000
 J8S  S6   C5   C8   124.11  3.000
 J8S  S6   C5   C4   115.86  3.000
 J8S  C8   C5   C4   120.03  3.000
 J8S  H4   C7   H3   108.53  3.000
 J8S  H4   C7   H2   110.07  3.000
 J8S  H3   C7   H2   108.61  3.000
 J8S  H4   C7   S6   111.81  3.000
 J8S  H3   C7   S6   105.81  3.000
 J8S  H2   C7   S6   111.83  3.000
 J8S  H5   C8   C9   119.11  3.000
 J8S  H5   C8   C5   121.68  3.000
 J8S  C9   C8   C5   119.21  3.000
 J8S  C9   C10  C3   119.02  3.000
 J8S  C3   C10  C11  120.08  3.000
 J8S  C9   C10  C11  120.69  3.000
 J8S  H7   C15  H6   107.23  3.000
 J8S  H7   C15  C16  109.88  3.000
 J8S  H6   C15  C16  110.37  3.000
 J8S  H7   C15  C14  108.99  3.000
 J8S  H6   C15  C14  108.87  3.000
 J8S  C16  C15  C14  111.40  3.000
 J8S  H9   C17  H8   106.48  3.000
 J8S  H9   C17  C18  109.67  3.000
 J8S  H8   C17  C18  109.52  3.000
 J8S  H9   C17  C16  109.08  3.000
 J8S  H8   C17  C16  108.60  3.000
 J8S  C18  C17  C16  113.26  3.000
 J8S  H10  C20  C19  119.79  3.000
 J8S  H10  C20  C21  120.07  3.000
 J8S  C19  C20  C21  120.14  3.000
 J8S  H11  C21  C22  120.26  3.000
 J8S  H11  C21  C20  120.30  3.000
 J8S  C22  C21  C20  119.44  3.000
 J8S  H12  C22  C23  119.75  3.000
 J8S  H12  C22  C21  120.10  3.000
 J8S  C23  C22  C21  120.15  3.000
 J8S  H14  C24  H13  106.88  3.000
 J8S  H14  C24  C25  109.28  3.000
 J8S  H13  C24  C25  108.58  3.000
 J8S  H14  C24  C16  109.78  3.000
 J8S  H13  C24  C16  110.76  3.000
 J8S  C25  C24  C16  111.45  3.000
 J8S  H17  C1   H16  108.95  3.000
 J8S  H17  C1   H15  108.93  3.000
 J8S  H16  C1   H15  108.93  3.000
 J8S  H17  C1   O2   106.41  3.000
 J8S  H16  C1   O2   111.78  3.000
 J8S  H15  C1   O2   111.74  3.000
 J8S  O12  C11  N13  123.63  3.000
 J8S  N13  C11  C10  117.22  3.000
 J8S  O12  C11  C10  119.14  3.000
 J8S  H19  C14  H18  106.79  3.000
 J8S  H19  C14  N13  108.38  3.000
 J8S  H18  C14  N13  110.21  3.000
 J8S  H19  C14  C15  109.60  3.000
 J8S  H18  C14  C15  110.87  3.000
 J8S  N13  C14  C15  110.87  3.000
 J8S  H20  C16  C24  107.87  3.000
 J8S  H20  C16  C17  108.18  3.000
 J8S  C24  C16  C17  112.53  3.000
 J8S  H20  C16  C15  107.56  3.000
 J8S  C17  C16  C15  110.96  3.000
 J8S  C24  C16  C15  109.57  3.000
 J8S  C23  C18  C19  118.26  3.000
 J8S  C19  C18  C17  120.46  3.000
 J8S  C23  C18  C17  121.26  3.000
 J8S  H21  C19  C18  119.50  3.000
 J8S  H21  C19  C20  119.49  3.000
 J8S  C18  C19  C20  121.00  3.000
 J8S  H22  C23  C18  119.48  3.000
 J8S  H22  C23  C22  119.52  3.000
 J8S  C18  C23  C22  121.00  3.000
 J8S  H24  C25  H23  107.43  3.000
 J8S  H24  C25  N13  109.31  3.000
 J8S  H23  C25  N13  108.47  3.000
 J8S  H24  C25  C24  111.04  3.000
 J8S  H23  C25  C24  109.65  3.000
 J8S  N13  C25  C24  110.83  3.000
 J8S  O2   C3   C10  115.53  3.000
 J8S  O2   C3   C4   124.34  3.000
 J8S  C10  C3   C4   120.13  3.000
 J8S  H25  C9   C10  119.51  3.000
 J8S  H25  C9   C8   118.96  3.000
 J8S  C10  C9   C8   121.53  3.000
 J8S  C25  N13  C14  113.69  3.000
 J8S  C25  N13  C11  121.25  3.000
 J8S  C14  N13  C11  124.92  3.000
 J8S  C3   O2   C1   118.95  3.000
 J8S  C7   S6   C5   103.83  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
 J8S  CONST_01  C9   C8   C5   C4      0.00   0.0  0
 J8S  CONST_02  C9   C10  C3   C4      0.00   0.0  0
 J8S  CONST_03  C10  C9   C8   C5      0.00   0.0  0
 J8S  CONST_04  C10  C3   C4   C5      0.00   0.0  0
 J8S  CONST_05  C3   C10  C9   C8      0.00   0.0  0
 J8S  CONST_06  C3   C4   C5   C8      0.00   0.0  0
 J8S  CONST_07  C23  C22  C21  C20     0.00   0.0  0
 J8S  CONST_08  C23  C18  C19  C20     0.00   0.0  0
 J8S  CONST_09  C18  C23  C22  C21     0.00   0.0  0
 J8S  CONST_10  C18  C19  C20  C21     0.00   0.0  0
 J8S  CONST_11  C19  C18  C23  C22     0.00   0.0  0
 J8S  CONST_12  C19  C20  C21  C22     0.00   0.0  0
 J8S  CONST_13  C11  C10  C3   C4    180.00   0.0  0
 J8S  CONST_14  O2   C3   C4   C5    180.00   0.0  0
 J8S  CONST_15  C11  C10  C9   C8    180.00   0.0  0
 J8S  CONST_16  C22  C23  C18  C17   180.00   0.0  0
 J8S  CONST_17  C20  C19  C18  C17   180.00   0.0  0
 J8S  CONST_18  S6   C5   C4   C3    180.00   0.0  0
 J8S  CONST_19  S6   C5   C8   C9    180.00   0.0  0
 J8S  CONST_20  O2   C3   C10  C9    180.00   0.0  0
 J8S  CONST_21  C14  N13  C11  C10     0.00   0.0  0
 J8S  CONST_22  C25  N13  C11  C10   180.00   0.0  0
 J8S  CONST_23  H5   C8   C5   C4    180.00   0.0  0
 J8S  CONST_24  H25  C9   C8   C5    180.00   0.0  0
 J8S  CONST_25  H1   C4   C5   C8    180.00   0.0  0
 J8S  CONST_26  H12  C22  C21  C20   180.00   0.0  0
 J8S  CONST_27  H22  C23  C22  C21   180.00   0.0  0
 J8S  CONST_28  H21  C19  C20  C21   180.00   0.0  0
 J8S  CONST_29  H10  C20  C21  C22   180.00   0.0  0
 J8S  CONST_30  H11  C21  C20  C19   180.00   0.0  0
 J8S  CONST_31  O12  C11  N13  C14   180.00   0.0  0
 J8S  CONST_32  O12  C11  N13  C25     0.00   0.0  0
 J8S  Var_01    C25  N13  C14  C15   -57.17  30.0  1
 J8S  Var_02    C14  N13  C25  C24    57.05  30.0  1
 J8S  Var_03    N13  C14  C15  C16    55.08  30.0  1
 J8S  Var_04    N13  C25  C24  C16   -54.89  30.0  1
 J8S  Var_05    C23  C18  C17  C16  -102.90  30.0  1
 J8S  Var_06    N13  C11  C10  C3    -86.23  30.0  2
 J8S  Var_07    C8   C5   S6   C7      1.18  30.0  2
 J8S  Var_08    H2   C7   S6   C5     62.66  30.0  3
 J8S  Var_09    H15  C1   O2   C3    -60.19  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
 J8S  chir_01  C16  C15  C24  C17  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
 J8S  plan-1  C17  0.020
 J8S  plan-1  C20  0.020
 J8S  plan-1  C21  0.020
 J8S  plan-1  C22  0.020
 J8S  plan-1  C18  0.020
 J8S  plan-1  C19  0.020
 J8S  plan-1  C23  0.020
 J8S  plan-1  H11  0.020
 J8S  plan-1  H12  0.020
 J8S  plan-1  H21  0.020
 J8S  plan-1  H22  0.020
 J8S  plan-1  H10  0.020
 J8S  plan-2  C4   0.020
 J8S  plan-2  C5   0.020
 J8S  plan-2  C8   0.020
 J8S  plan-2  C10  0.020
 J8S  plan-2  C11  0.020
 J8S  plan-2  C3   0.020
 J8S  plan-2  C9   0.020
 J8S  plan-2  O2   0.020
 J8S  plan-2  S6   0.020
 J8S  plan-2  H1   0.020
 J8S  plan-2  H5   0.020
 J8S  plan-2  H25  0.020
 J8S  plan-3  C10  0.020
 J8S  plan-3  C11  0.020
 J8S  plan-3  C14  0.020
 J8S  plan-3  C25  0.020
 J8S  plan-3  N13  0.020
 J8S  plan-3  O12  0.020

