# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:13:29 2021
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-(4-phenylpiperidin-1-yl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CN1CCC(CC1)c2ccccc2
#
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
 S3J  S3J  '2-(4-phenylpiperidin-1-yl)ethanoic acid'  ligand  33  16  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S3J
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
 S3J  C4   C  CR16  0  -0.350  -1.5052  65.1626  68.1213
 S3J  C5   C  CR6   0   0.198  -1.8854  63.9718  68.9621
 S3J  C6   C  CR16  0  -0.322  -2.6661  64.1183  70.1092
 S3J  C7   C  CR16  0  -0.238  -3.0105  63.0198  70.8838
 S3J  C8   C  CR16  0  -0.276  -2.5796  61.7480  70.5252
 S3J  C10  C  CR16  0  -0.341  -1.4621  62.6917  68.6139
 S3J  N    N  NR6   0  -0.419  -1.4485  68.0176  67.5403
 S3J  C    C  C     0  -0.417  -2.7248  65.9216  67.5949
 S3J  O    O  O     0  -0.451  -2.3160  70.9987  65.7574
 S3J  C1   C  C     0  -0.289  -2.3022  67.1264  66.7713
 S3J  C11  C  CH2   0  -0.385  -1.1217  69.2083  66.8015
 S3J  C12  C  C     0   0.517  -2.2557  70.1968  66.6574
 S3J  C2   C  C     0  -0.286  -0.2487  67.3339  67.9958
 S3J  C3   C  C     0  -0.417  -0.5957  66.1405  68.8702
 S3J  C9   C  CR16  0  -0.237  -1.8040  61.5877  69.3856
 S3J  O1   O  OH1   0  -0.579  -3.1400  70.1366  67.6410
 S3J  H1   H  HCR6  0   0.237  -0.9457  64.7950  67.2521
 S3J  H2   H  HCR6  0   0.246  -3.0128  65.1021  70.4039
 S3J  H3   H  HCR6  0   0.252  -3.6178  63.1566  71.7697
 S3J  H4   H  HCR6  0   0.252  -2.8471  60.8905  71.1293
 S3J  H5   H  HCR6  0   0.245  -0.8560  62.5558  67.7255
 S3J  H7   H  H     0   0.224  -3.3435  66.2592  68.4313
 S3J  H8   H  H     0   0.240  -3.3446  65.2632  66.9822
 S3J  H9   H  H     0   0.243  -3.1941  67.6674  66.4478
 S3J  H10  H  H     0   0.196  -1.7904  66.7861  65.8538
 S3J  H11  H  HCH2  0   0.237  -0.7309  69.0085  65.7917
 S3J  H12  H  HCH2  0   0.288  -0.3270  69.7483  67.3293
 S3J  H13  H  H     0   0.194   0.3690  66.9921  67.1464
 S3J  H14  H  H     0   0.243   0.3603  68.0414  68.5636
 S3J  H15  H  H     0   0.239   0.3254  65.6408  69.1785
 S3J  H16  H  H     0   0.223  -1.0923  66.4889  69.7810
 S3J  H17  H  HCR6  0   0.252  -1.4646  60.6018  69.0941
 S3J  H18  H  HOH1  0   0.481  -3.8192  70.8153  67.5075

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
 S3J  O    C12  double    1.207  0.020  1.207
 S3J  C11  C12  single    1.511  0.020  1.511
 S3J  C11  N    single    1.439  0.020  1.439
 S3J  C12  O1   single    1.324  0.020  1.324
 S3J  C1   N    single    1.454  0.020  1.454
 S3J  C1   C    single    1.519  0.020  1.519
 S3J  N    C2   single    1.454  0.020  1.454
 S3J  C2   C3   single    1.520  0.020  1.520
 S3J  C    C4   single    1.530  0.020  1.530
 S3J  C4   C3   single    1.531  0.020  1.531
 S3J  C4   C5   single    1.506  0.020  1.506
 S3J  C5   C10  aromatic  1.392  0.020  1.392
 S3J  C5   C6   aromatic  1.395  0.020  1.395
 S3J  C10  C9   aromatic  1.390  0.020  1.390
 S3J  C6   C7   aromatic  1.388  0.020  1.388
 S3J  C9   C8   aromatic  1.388  0.020  1.388
 S3J  C7   C8   aromatic  1.390  0.020  1.390
 S3J  C4   H1   single    0.970  0.020  1.090
 S3J  C6   H2   single    0.930  0.020  1.080
 S3J  C7   H3   single    0.930  0.020  1.080
 S3J  C8   H4   single    0.930  0.020  1.080
 S3J  C10  H5   single    0.930  0.020  1.080
 S3J  C    H7   single    0.970  0.020  1.090
 S3J  C    H8   single    0.970  0.020  1.090
 S3J  C1   H9   single    0.970  0.020  1.090
 S3J  C1   H10  single    0.970  0.020  1.090
 S3J  C11  H11  single    0.970  0.020  1.090
 S3J  C11  H12  single    0.970  0.020  1.090
 S3J  C2   H13  single    0.970  0.020  1.090
 S3J  C2   H14  single    0.970  0.020  1.090
 S3J  C3   H15  single    0.970  0.020  1.090
 S3J  C3   H16  single    0.970  0.020  1.090
 S3J  C9   H17  single    0.930  0.020  1.080
 S3J  O1   H18  single    0.850  0.020  0.980

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
 S3J  H1   C4   C3   107.37  3.000
 S3J  H1   C4   C    107.47  3.000
 S3J  C3   C4   C    108.96  3.000
 S3J  H1   C4   C5   107.82  3.000
 S3J  C3   C4   C5   112.44  3.000
 S3J  C    C4   C5   112.52  3.000
 S3J  C10  C5   C6   118.18  3.000
 S3J  C6   C5   C4   121.13  3.000
 S3J  C10  C5   C4   120.69  3.000
 S3J  H2   C6   C7   119.17  3.000
 S3J  H2   C6   C5   119.85  3.000
 S3J  C7   C6   C5   120.97  3.000
 S3J  H3   C7   C8   120.04  3.000
 S3J  H3   C7   C6   119.73  3.000
 S3J  C8   C7   C6   120.23  3.000
 S3J  H4   C8   C9   120.32  3.000
 S3J  H4   C8   C7   120.28  3.000
 S3J  C9   C8   C7   119.40  3.000
 S3J  H5   C10  C9   119.54  3.000
 S3J  H5   C10  C5   119.35  3.000
 S3J  C9   C10  C5   121.11  3.000
 S3J  C2   N    C11  111.26  3.000
 S3J  C2   N    C1   111.22  3.000
 S3J  C11  N    C1   111.65  3.000
 S3J  H8   C    H7   107.10  3.000
 S3J  H8   C    C1   109.38  3.000
 S3J  H7   C    C1   109.09  3.000
 S3J  H8   C    C4   110.26  3.000
 S3J  H7   C    C4   109.94  3.000
 S3J  C1   C    C4   110.99  3.000
 S3J  H10  C1   H9   106.56  3.000
 S3J  H10  C1   C    109.57  3.000
 S3J  H9   C1   C    109.04  3.000
 S3J  H10  C1   N    110.86  3.000
 S3J  H9   C1   N    109.42  3.000
 S3J  C    C1   N    111.26  3.000
 S3J  H12  C11  H11  105.88  3.000
 S3J  H12  C11  C12  105.53  3.000
 S3J  H11  C11  C12  107.31  3.000
 S3J  H12  C11  N    108.97  3.000
 S3J  H11  C11  N    113.66  3.000
 S3J  C12  C11  N    114.83  3.000
 S3J  O1   C12  C11  113.61  3.000
 S3J  O1   C12  O    123.42  3.000
 S3J  C11  C12  O    122.90  3.000
 S3J  H14  C2   H13  106.76  3.000
 S3J  H14  C2   C3   109.68  3.000
 S3J  H13  C2   C3   109.10  3.000
 S3J  H14  C2   N    108.56  3.000
 S3J  H13  C2   N    111.47  3.000
 S3J  C3   C2   N    111.17  3.000
 S3J  H16  C3   H15  107.07  3.000
 S3J  H16  C3   C2   109.42  3.000
 S3J  H15  C3   C2   109.21  3.000
 S3J  H16  C3   C4   109.94  3.000
 S3J  H15  C3   C4   110.29  3.000
 S3J  C2   C3   C4   110.84  3.000
 S3J  H17  C9   C10  119.78  3.000
 S3J  H17  C9   C8   120.10  3.000
 S3J  C10  C9   C8   120.11  3.000
 S3J  H18  O1   C12  109.50  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
 S3J  CONST_01  C8   C9   C10  C5     0.00   0.0  0
 S3J  CONST_02  C8   C7   C6   C5     0.00   0.0  0
 S3J  CONST_03  C9   C10  C5   C6     0.00   0.0  0
 S3J  CONST_04  C9   C8   C7   C6     0.00   0.0  0
 S3J  CONST_05  C10  C5   C6   C7     0.00   0.0  0
 S3J  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 S3J  CONST_07  C9   C10  C5   C4   180.00   0.0  0
 S3J  CONST_08  C7   C6   C5   C4   180.00   0.0  0
 S3J  CONST_09  H5   C10  C5   C4     0.00   0.0  0
 S3J  CONST_10  H2   C6   C5   C4     0.00   0.0  0
 S3J  CONST_11  H17  C9   C10  C5   180.00   0.0  0
 S3J  CONST_12  H3   C7   C6   C5   180.00   0.0  0
 S3J  CONST_13  H4   C8   C7   C6   180.00   0.0  0
 S3J  CONST_14  H18  O1   C12  O      0.00   0.0  0
 S3J  Var_01    N    C1   C    C4   -56.85  30.0  1
 S3J  Var_02    N    C2   C3   C4    57.25  30.0  1
 S3J  Var_03    C2   N    C1   C     59.23  30.0  1
 S3J  Var_04    C3   C2   N    C1   -59.46  30.0  1
 S3J  Var_05    C12  C11  N    C1    73.12  30.0  1
 S3J  Var_06    O    C12  C11  N   -155.48  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
 S3J  chir_01  C4  C  C3  C5  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
 S3J  plan-1  C4   0.020
 S3J  plan-1  C5   0.020
 S3J  plan-1  C6   0.020
 S3J  plan-1  C7   0.020
 S3J  plan-1  C8   0.020
 S3J  plan-1  C10  0.020
 S3J  plan-1  C9   0.020
 S3J  plan-1  H2   0.020
 S3J  plan-1  H3   0.020
 S3J  plan-1  H4   0.020
 S3J  plan-1  H5   0.020
 S3J  plan-1  H17  0.020
 S3J  plan-2  O    0.020
 S3J  plan-2  C11  0.020
 S3J  plan-2  C12  0.020
 S3J  plan-2  O1   0.020
 S3J  plan-2  H18  0.020

