# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:45:21 2021
#   Inital geometry file: a 86 line input string
#   Ligand name: 2-[4-(2-methoxyphenyl)piperazin-1-yl]ethanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1N2CCN(CC2)CC#N
#
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
 S5J  S5J  2-[4-(2-methoxyphenyl)piperazin-1-yl]ethanenitrile  ligand  34  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S5J
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
 S5J  N1   N  NT    0  -0.410  -20.0091  92.7672  141.1933
 S5J  C4   C  CR16  0  -0.276  -16.3640  93.0836  135.9951
 S5J  C5   C  CR16  0  -0.324  -17.2149  92.8391  137.0693
 S5J  C6   C  CR6   0   0.234  -17.0239  93.4480  138.3040
 S5J  C7   C  CH2   0  -0.300  -18.7360  94.2907  139.7862
 S5J  C8   C  CH2   0  -0.297  -19.3219  94.0456  141.1626
 S5J  C10  C  CH2   0  -0.309  -18.5570  91.9341  139.4295
 S5J  N    N  NT    0  -0.496  -17.8460  93.1969  139.4172
 S5J  C    C  CH3   0  -0.436  -14.6752  95.7373  139.8937
 S5J  C1   C  CR6   0   0.349  -15.9318  94.3321  138.4518
 S5J  C11  C  CH2   0  -0.396  -20.7225  92.5281  142.4153
 S5J  C12  C  CSP   0   0.094  -19.8592  92.4315  143.6117
 S5J  C2   C  CR16  0  -0.388  -15.0977  94.5933  137.3721
 S5J  C3   C  CR16  0  -0.260  -15.3131  93.9676  136.1468
 S5J  C9   C  CH2   0  -0.291  -19.1236  91.6812  140.8144
 S5J  N2   N  NS    0  -0.268  -19.1672  92.3688  144.5290
 S5J  H2   H  HCR6  0   0.249  -16.5365  92.5887  135.0484
 S5J  H3   H  HCR6  0   0.262  -18.0442  92.1568  136.9339
 S5J  H4   H  HCH2  0   0.258  -18.1891  95.2315  139.8037
 S5J  H5   H  HCH2  0   0.213  -19.5500  94.3947  139.0522
 S5J  H6   H  HCH2  0   0.210  -18.5120  94.0986  141.9081
 S5J  H7   H  HCH2  0   0.250  -20.0361  94.8390  141.3936
 S5J  H8   H  HCH2  0   0.210  -19.3834  91.9066  138.7025
 S5J  H9   H  HCH2  0   0.254  -17.8676  91.1265  139.1779
 S5J  H10  H  HCH3  0   0.258  -14.7209  96.0347  140.9386
 S5J  H11  H  HCH3  0   0.226  -13.7167  95.2442  139.7103
 S5J  H12  H  HCH3  0   0.226  -14.7332  96.6346  139.2719
 S5J  H13  H  HCH2  0   0.315  -21.4424  93.3295  142.5941
 S5J  H14  H  HCH2  0   0.315  -21.2907  91.5981  142.3445
 S5J  H15  H  HCR6  0   0.276  -14.2596  95.2698  137.4704
 S5J  H16  H  HCR6  0   0.253  -14.6459  94.1774  135.3209
 S5J  H17  H  HCH2  0   0.251  -19.6906  90.7477  140.8027
 S5J  H18  H  HCH2  0   0.210  -18.2931  91.5562  141.5281
 S5J  O    O  O2    0  -0.463  -15.7669  94.8684  139.6764

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
 S5J  C4   C3   aromatic  1.382  0.020  1.382
 S5J  C4   C5   aromatic  1.392  0.020  1.392
 S5J  C3   C2   aromatic  1.393  0.020  1.393
 S5J  C5   C6   aromatic  1.390  0.020  1.390
 S5J  C2   C1   aromatic  1.389  0.020  1.389
 S5J  C6   C1   aromatic  1.413  0.020  1.413
 S5J  C6   N    single    1.406  0.020  1.406
 S5J  C1   O    single    1.347  0.020  1.347
 S5J  N    C10  single    1.449  0.020  1.449
 S5J  N    C7   single    1.458  0.020  1.458
 S5J  C10  C9   single    1.517  0.020  1.517
 S5J  O    C    single    1.412  0.020  1.412
 S5J  C7   C8   single    1.516  0.020  1.516
 S5J  C9   N1   single    1.452  0.020  1.452
 S5J  N1   C8   single    1.452  0.020  1.452
 S5J  N1   C11  single    1.435  0.020  1.435
 S5J  C11  C12  single    1.479  0.020  1.479
 S5J  C12  N2   triple    1.151  0.020  1.151
 S5J  C4   H2   single    0.930  0.020  1.080
 S5J  C5   H3   single    0.930  0.020  1.080
 S5J  C7   H4   single    0.970  0.020  1.090
 S5J  C7   H5   single    0.970  0.020  1.090
 S5J  C8   H6   single    0.970  0.020  1.090
 S5J  C8   H7   single    0.970  0.020  1.090
 S5J  C10  H8   single    0.970  0.020  1.090
 S5J  C10  H9   single    0.970  0.020  1.090
 S5J  C    H10  single    0.970  0.020  1.090
 S5J  C    H11  single    0.970  0.020  1.090
 S5J  C    H12  single    0.970  0.020  1.090
 S5J  C11  H13  single    0.970  0.020  1.090
 S5J  C11  H14  single    0.970  0.020  1.090
 S5J  C2   H15  single    0.930  0.020  1.080
 S5J  C3   H16  single    0.930  0.020  1.080
 S5J  C9   H17  single    0.970  0.020  1.090
 S5J  C9   H18  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
 S5J  C9   N1   C11  113.63  3.000
 S5J  C11  N1   C8   113.58  3.000
 S5J  C9   N1   C8   111.38  3.000
 S5J  H2   C4   C3   120.66  3.000
 S5J  H2   C4   C5   119.82  3.000
 S5J  C3   C4   C5   119.51  3.000
 S5J  H3   C5   C6   119.51  3.000
 S5J  H3   C5   C4   118.85  3.000
 S5J  C6   C5   C4   121.64  3.000
 S5J  C1   C6   N    118.73  3.000
 S5J  N    C6   C5   123.00  3.000
 S5J  C1   C6   C5   118.25  3.000
 S5J  H5   C7   H4   107.50  3.000
 S5J  H5   C7   N    110.70  3.000
 S5J  H4   C7   N    110.24  3.000
 S5J  H5   C7   C8   109.56  3.000
 S5J  H4   C7   C8   108.63  3.000
 S5J  N    C7   C8   110.15  3.000
 S5J  H7   C8   H6   107.61  3.000
 S5J  H7   C8   C7   109.11  3.000
 S5J  H6   C8   C7   108.80  3.000
 S5J  H7   C8   N1   109.01  3.000
 S5J  H6   C8   N1   112.08  3.000
 S5J  C7   C8   N1   110.16  3.000
 S5J  H9   C10  H8   107.67  3.000
 S5J  H9   C10  C9   108.84  3.000
 S5J  H8   C10  C9   108.56  3.000
 S5J  H9   C10  N    109.45  3.000
 S5J  H8   C10  N    112.60  3.000
 S5J  C9   C10  N    109.64  3.000
 S5J  C10  N    C7   110.62  3.000
 S5J  C7   N    C6   115.04  3.000
 S5J  C10  N    C6   116.68  3.000
 S5J  H12  C    H11  108.74  3.000
 S5J  H12  C    H10  108.66  3.000
 S5J  H11  C    H10  108.75  3.000
 S5J  H12  C    O    112.12  3.000
 S5J  H11  C    O    111.99  3.000
 S5J  H10  C    O    106.48  3.000
 S5J  C2   C1   O    123.94  3.000
 S5J  O    C1   C6   116.03  3.000
 S5J  C2   C1   C6   120.03  3.000
 S5J  H14  C11  H13  107.01  3.000
 S5J  H14  C11  C12  107.50  3.000
 S5J  H13  C11  C12  107.49  3.000
 S5J  H14  C11  N1   110.20  3.000
 S5J  H13  C11  N1   110.17  3.000
 S5J  C12  C11  N1   114.19  3.000
 S5J  N2   C12  C11  180.00  3.000
 S5J  H15  C2   C3   118.74  3.000
 S5J  H15  C2   C1   120.81  3.000
 S5J  C3   C2   C1   120.43  3.000
 S5J  H16  C3   C2   119.27  3.000
 S5J  H16  C3   C4   120.61  3.000
 S5J  C2   C3   C4   120.12  3.000
 S5J  H18  C9   H17  107.53  3.000
 S5J  H18  C9   C10  109.18  3.000
 S5J  H17  C9   C10  109.06  3.000
 S5J  H18  C9   N1   112.05  3.000
 S5J  H17  C9   N1   109.00  3.000
 S5J  C10  C9   N1   109.95  3.000
 S5J  C1   O    C    118.65  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
 S5J  CONST_01  C1   C2   C3  C4     0.00   0.0  0
 S5J  CONST_02  C1   C6   C5  C4     0.00   0.0  0
 S5J  CONST_03  C2   C3   C4  C5     0.00   0.0  0
 S5J  CONST_04  C2   C1   C6  C5     0.00   0.0  0
 S5J  CONST_05  C3   C4   C5  C6     0.00   0.0  0
 S5J  CONST_06  C3   C2   C1  C6     0.00   0.0  0
 S5J  CONST_07  N    C6   C5  C4   180.00   0.0  0
 S5J  CONST_08  C2   C1   C6  N    180.00   0.0  0
 S5J  CONST_09  O    C1   C6  C5   180.00   0.0  0
 S5J  CONST_10  O    C1   C6  N      0.00   0.0  0
 S5J  CONST_11  C3   C2   C1  O    180.00   0.0  0
 S5J  CONST_12  H15  C2   C3  C4   180.00   0.0  0
 S5J  CONST_13  H16  C3   C4  C5   180.00   0.0  0
 S5J  CONST_14  H2   C4   C5  C6   180.00   0.0  0
 S5J  CONST_15  H3   C5   C6  N      0.00   0.0  0
 S5J  Var_01    N    C10  C9  N1    58.30  30.0  1
 S5J  Var_02    N    C7   C8  N1   -56.60  30.0  1
 S5J  Var_03    C10  N    C6  C5    23.71  30.0  2
 S5J  Var_04    C9   C10  N   C6   166.82  30.0  1
 S5J  Var_05    C8   C7   N   C6  -166.68  30.0  1
 S5J  Var_06    C9   N1   C8  C7    56.89  30.0  1
 S5J  Var_07    C10  C9   N1  C8   -57.74  30.0  1
 S5J  Var_08    C12  C11  N1  C8   -64.06  30.0  3
 S5J  Var_09    C2   C1   O   C     -0.80  30.0  2
 S5J  Var_10    H10  C    O   C1  -178.95  30.0  3

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
 S5J  plan-1  C4   0.020
 S5J  plan-1  C5   0.020
 S5J  plan-1  C6   0.020
 S5J  plan-1  N    0.020
 S5J  plan-1  C1   0.020
 S5J  plan-1  C2   0.020
 S5J  plan-1  C3   0.020
 S5J  plan-1  H2   0.020
 S5J  plan-1  H3   0.020
 S5J  plan-1  H15  0.020
 S5J  plan-1  H16  0.020
 S5J  plan-1  O    0.020

