# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 14:28:55 2022
#   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  32  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  CH1    0  -0.344  -1.5185  65.1419  68.1500
 S3J  C5   C  CR6    0   0.199  -1.9065  63.9611  69.0017
 S3J  C6   C  CR16   0  -0.322  -2.6688  64.1276  70.1590
 S3J  C7   C  CR16   0  -0.236  -3.0320  63.0391  70.9389
 S3J  C8   C  CR16   0  -0.275  -2.6391  61.7564  70.5763
 S3J  C10  C  CR16   0  -0.341  -1.5208  62.6701  68.6507
 S3J  N    N  NT     0  -0.404  -1.5179  67.9958  67.5310
 S3J  C    C  CH2    0  -0.414  -2.7360  65.8655  67.5691
 S3J  O    O  O      0  -0.619  -2.1627  71.0719  65.7209
 S3J  C1   C  CH2    0  -0.279  -2.3116  67.0709  66.7454
 S3J  C11  C  CH2    0  -0.406  -1.2118  69.2006  66.7913
 S3J  C12  C  C      0   0.387  -2.3922  70.1723  66.5554
 S3J  C2   C  CH2    0  -0.272  -0.3174  67.3457  68.0190
 S3J  C3   C  CH2    0  -0.414  -0.6521  66.1541  68.9033
 S3J  C9   C  CR16   0  -0.236  -1.8812  61.5756  69.4282
 S3J  O1   O  OC    -1  -0.598  -3.4314  70.0151  67.2213
 S3J  H1   H  HCH1   0   0.231  -0.9255  64.7693  67.3053
 S3J  H2   H  HCR6   0   0.245  -2.9857  65.1200  70.4582
 S3J  H3   H  HCR6   0   0.249  -3.6251  63.1926  71.8317
 S3J  H4   H  HCR6   0   0.249  -2.9231  60.9066  71.1837
 S3J  H5   H  HCR6   0   0.243  -0.9294  62.5173  67.7551
 S3J  H7   H  HCH2   0   0.216  -3.3894  66.1991  68.3807
 S3J  H8   H  HCH2   0   0.230  -3.3186  65.1824  66.9466
 S3J  H9   H  HCH2   0   0.234  -3.1969  67.5888  66.3768
 S3J  H10  H  HCH2   0   0.172  -1.7510  66.7229  65.8566
 S3J  H11  H  HCH2   0   0.178  -0.7397  68.9764  65.8183
 S3J  H12  H  HCH2   0   0.226  -0.4570  69.7608  67.3560
 S3J  H13  H  HCH2   0   0.175   0.3277  67.0047  67.1872
 S3J  H14  H  HCH2   0   0.228   0.2688  68.0707  68.5897
 S3J  H15  H  HCH2   0   0.231   0.2720  65.6809  69.2441
 S3J  H16  H  HCH2   0   0.217  -1.1824  66.5046  69.7936
 S3J  H17  H  HCR6   0   0.249  -1.5701  60.5811  69.1342

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  deloc     1.248  0.020  1.248
 S3J  C11  C12  single    1.547  0.020  1.547
 S3J  C11  N    single    1.446  0.020  1.446
 S3J  C12  O1   deloc     1.244  0.020  1.244
 S3J  C1   N    single    1.450  0.020  1.450
 S3J  C1   C    single    1.520  0.020  1.520
 S3J  N    C2   single    1.450  0.020  1.450
 S3J  C2   C3   single    1.521  0.020  1.521
 S3J  C    C4   single    1.531  0.020  1.531
 S3J  C4   C3   single    1.531  0.020  1.531
 S3J  C4   C5   single    1.507  0.020  1.507
 S3J  C5   C10  aromatic  1.392  0.020  1.392
 S3J  C5   C6   aromatic  1.396  0.020  1.396
 S3J  C10  C9   aromatic  1.390  0.020  1.390
 S3J  C6   C7   aromatic  1.387  0.020  1.387
 S3J  C9   C8   aromatic  1.387  0.020  1.387
 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

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   107.31  3.000
 S3J  H1   C4   C    107.35  3.000
 S3J  C3   C4   C    108.93  3.000
 S3J  H1   C4   C5   107.95  3.000
 S3J  C3   C4   C5   112.70  3.000
 S3J  C    C4   C5   112.34  3.000
 S3J  C10  C5   C6   118.09  3.000
 S3J  C6   C5   C4   121.06  3.000
 S3J  C10  C5   C4   120.85  3.000
 S3J  H2   C6   C7   119.12  3.000
 S3J  H2   C6   C5   119.85  3.000
 S3J  C7   C6   C5   121.03  3.000
 S3J  H3   C7   C8   120.06  3.000
 S3J  H3   C7   C6   119.71  3.000
 S3J  C8   C7   C6   120.23  3.000
 S3J  H4   C8   C9   120.35  3.000
 S3J  H4   C8   C7   120.27  3.000
 S3J  C9   C8   C7   119.38  3.000
 S3J  H5   C10  C9   119.51  3.000
 S3J  H5   C10  C5   119.34  3.000
 S3J  C9   C10  C5   121.15  3.000
 S3J  C2   N    C11  111.74  3.000
 S3J  C2   N    C1   110.46  3.000
 S3J  C11  N    C1   111.72  3.000
 S3J  H8   C    H7   107.15  3.000
 S3J  H8   C    C1   109.63  3.000
 S3J  H7   C    C1   109.08  3.000
 S3J  H8   C    C4   110.17  3.000
 S3J  H7   C    C4   109.74  3.000
 S3J  C1   C    C4   111.00  3.000
 S3J  H10  C1   H9   106.81  3.000
 S3J  H10  C1   C    109.10  3.000
 S3J  H9   C1   C    109.47  3.000
 S3J  H10  C1   N    111.00  3.000
 S3J  H9   C1   N    108.95  3.000
 S3J  C    C1   N    111.41  3.000
 S3J  H12  C11  H11  105.25  3.000
 S3J  H12  C11  C12  106.43  3.000
 S3J  H11  C11  C12  108.62  3.000
 S3J  H12  C11  N    107.93  3.000
 S3J  H11  C11  N    111.83  3.000
 S3J  C12  C11  N    116.08  3.000
 S3J  O1   C12  C11  118.45  3.000
 S3J  O1   C12  O    127.04  3.000
 S3J  C11  C12  O    114.47  3.000
 S3J  H14  C2   H13  106.51  3.000
 S3J  H14  C2   C3   109.52  3.000
 S3J  H13  C2   C3   108.90  3.000
 S3J  H14  C2   N    108.81  3.000
 S3J  H13  C2   N    111.58  3.000
 S3J  C3   C2   N    111.39  3.000
 S3J  H16  C3   H15  107.15  3.000
 S3J  H16  C3   C2   109.19  3.000
 S3J  H15  C3   C2   109.54  3.000
 S3J  H16  C3   C4   109.76  3.000
 S3J  H15  C3   C4   110.23  3.000
 S3J  C2   C3   C4   110.88  3.000
 S3J  H17  C9   C10  119.79  3.000
 S3J  H17  C9   C8   120.09  3.000
 S3J  C10  C9   C8   120.12  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  Var_01    N    C1   C    C4   -57.25  30.0  1
 S3J  Var_02    N    C2   C3   C4    57.46  30.0  1
 S3J  Var_03    C2   N    C1   C     60.13  30.0  1
 S3J  Var_04    C3   C2   N    C1   -60.26  30.0  1
 S3J  Var_05    C12  C11  N    C1    71.68  30.0  2
 S3J  Var_06    O    C12  C11  N   -167.74  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

