# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 08:43:16 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-[4-(3-phenylpropyl)piperazin-1-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CCCc2ccccc2)CC1
#
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
 O3J  O3J  1-[4-(3-phenylpropyl)piperazin-1-yl]ethan-1-one  ligand  40  18  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_O3J
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
 O3J  N1   N  NR6   0  -0.430   1.1274   0.5896  -0.0502
 O3J  C4   C  CH2   0  -0.259  -0.0598   1.0917   0.6182
 O3J  C5   C  CH2   0  -0.434  -1.3384   0.4011   0.1638
 O3J  C6   C  CH2   0  -0.510  -2.5649   0.9653   0.8829
 O3J  C7   C  CR6   0   0.139  -3.8452   0.3676   0.3713
 O3J  C8   C  CR16  0  -0.315  -4.5716   0.9967  -0.6373
 O3J  C10  C  CR16  0  -0.275  -6.1885  -0.7865  -0.6453
 O3J  C13  C  C     0  -0.290   1.5442  -0.7029   0.4596
 O3J  N    N  NR6   0  -0.445   3.8176  -0.2874  -0.3225
 O3J  C    C  CH3   0  -0.807   6.1308   0.4347   0.0121
 O3J  O    O  O     0  -0.511   5.3455  -1.7814   0.3973
 O3J  C1   C  C     0   0.515   5.0682  -0.6403   0.0458
 O3J  C11  C  CR16  0  -0.240  -5.4727  -1.4248   0.3600
 O3J  C12  C  CR16  0  -0.311  -4.3122  -0.8508   0.8618
 O3J  C14  C  C     0  -0.305   2.7274  -1.2443  -0.3242
 O3J  C2   C  C     0  -0.315   3.4163   1.0270  -0.7825
 O3J  C3   C  C     0  -0.275   2.2281   1.5304   0.0194
 O3J  C9   C  CR16  0  -0.240  -5.7337   0.4279  -1.1425
 O3J  H2   H  HCH2  0   0.194   0.0336   1.0202   1.7158
 O3J  H3   H  HCH2  0   0.231  -0.1492   2.1574   0.3903
 O3J  H4   H  HCH2  0   0.228  -1.4491   0.5350  -0.9157
 O3J  H5   H  HCH2  0   0.231  -1.2859  -0.6767   0.3421
 O3J  H6   H  HCH2  0   0.241  -2.4699   0.7815   1.9566
 O3J  H7   H  HCH2  0   0.239  -2.5901   2.0510   0.7531
 O3J  H8   H  HCR6  0   0.244  -4.2268   1.9466  -1.0300
 O3J  H9   H  HCR6  0   0.252  -7.0950  -1.2309  -1.0357
 O3J  H10  H  H     0   0.198   1.8136  -0.6478   1.5287
 O3J  H11  H  H     0   0.246   0.7239  -1.4173   0.3729
 O3J  H12  H  HCH3  0   0.264   5.8975   1.2570   0.6896
 O3J  H13  H  HCH3  0   0.268   7.0798   0.0015   0.3170
 O3J  H14  H  HCH3  0   0.265   6.2527   0.8570  -0.9860
 O3J  H15  H  HCR6  0   0.252  -5.8194  -2.3708   0.7562
 O3J  H16  H  HCR6  0   0.245  -3.7605  -1.3551   1.6473
 O3J  H17  H  H     0   0.263   3.0620  -2.1813   0.1119
 O3J  H18  H  H     0   0.237   2.4223  -1.4439  -1.3570
 O3J  H19  H  H     0   0.274   4.2333   1.7371  -0.6963
 O3J  H20  H  H     0   0.240   3.1406   0.9711  -1.8410
 O3J  H21  H  H     0   0.245   1.9098   2.4872  -0.4001
 O3J  H22  H  H     0   0.197   2.5496   1.7200   1.0582
 O3J  H23  H  HCR6  0   0.252  -6.2863   0.9362  -1.9224

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
 O3J  C9   C10  aromatic  1.389  0.020  1.389
 O3J  C9   C8   aromatic  1.389  0.020  1.389
 O3J  C10  C11  aromatic  1.389  0.020  1.389
 O3J  C8   C7   aromatic  1.393  0.020  1.393
 O3J  C11  C12  aromatic  1.389  0.020  1.389
 O3J  C7   C12  aromatic  1.394  0.020  1.394
 O3J  C7   C6   single    1.503  0.020  1.503
 O3J  C6   C5   single    1.530  0.020  1.530
 O3J  C5   C4   single    1.523  0.020  1.523
 O3J  N1   C4   single    1.452  0.020  1.452
 O3J  N1   C3   single    1.450  0.020  1.450
 O3J  N1   C13  single    1.451  0.020  1.451
 O3J  C3   C2   single    1.519  0.020  1.519
 O3J  C13  C14  single    1.519  0.020  1.519
 O3J  C2   N    single    1.449  0.020  1.449
 O3J  C14  N    single    1.451  0.020  1.451
 O3J  N    C1   single    1.351  0.020  1.351
 O3J  C1   O    double    1.226  0.020  1.226
 O3J  C1   C    single    1.512  0.020  1.512
 O3J  C4   H2   single    0.970  0.020  1.090
 O3J  C4   H3   single    0.970  0.020  1.090
 O3J  C5   H4   single    0.970  0.020  1.090
 O3J  C5   H5   single    0.970  0.020  1.090
 O3J  C6   H6   single    0.970  0.020  1.090
 O3J  C6   H7   single    0.970  0.020  1.090
 O3J  C8   H8   single    0.930  0.020  1.080
 O3J  C10  H9   single    0.930  0.020  1.080
 O3J  C13  H10  single    0.970  0.020  1.090
 O3J  C13  H11  single    0.970  0.020  1.090
 O3J  C    H12  single    0.970  0.020  1.090
 O3J  C    H13  single    0.970  0.020  1.090
 O3J  C    H14  single    0.970  0.020  1.090
 O3J  C11  H15  single    0.930  0.020  1.080
 O3J  C12  H16  single    0.930  0.020  1.080
 O3J  C14  H17  single    0.970  0.020  1.090
 O3J  C14  H18  single    0.970  0.020  1.090
 O3J  C2   H19  single    0.970  0.020  1.090
 O3J  C2   H20  single    0.970  0.020  1.090
 O3J  C3   H21  single    0.970  0.020  1.090
 O3J  C3   H22  single    0.970  0.020  1.090
 O3J  C9   H23  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
 O3J  C3   N1   C13  110.07  3.000
 O3J  C13  N1   C4   112.41  3.000
 O3J  C3   N1   C4   111.99  3.000
 O3J  H3   C4   H2   106.10  3.000
 O3J  H3   C4   C5   108.13  3.000
 O3J  H2   C4   C5   109.79  3.000
 O3J  H3   C4   N1   107.93  3.000
 O3J  H2   C4   N1   111.48  3.000
 O3J  C5   C4   N1   113.10  3.000
 O3J  H5   C5   H4   106.65  3.000
 O3J  H5   C5   C6   108.99  3.000
 O3J  H4   C5   C6   109.74  3.000
 O3J  H5   C5   C4   110.98  3.000
 O3J  H4   C5   C4   108.91  3.000
 O3J  C6   C5   C4   111.45  3.000
 O3J  H7   C6   H6   106.58  3.000
 O3J  H7   C6   C7   109.56  3.000
 O3J  H6   C6   C7   109.96  3.000
 O3J  H7   C6   C5   109.21  3.000
 O3J  H6   C6   C5   109.26  3.000
 O3J  C7   C6   C5   112.11  3.000
 O3J  C12  C7   C8   118.35  3.000
 O3J  C12  C7   C6   120.88  3.000
 O3J  C8   C7   C6   120.73  3.000
 O3J  H8   C8   C9   119.55  3.000
 O3J  H8   C8   C7   119.48  3.000
 O3J  C9   C8   C7   120.97  3.000
 O3J  H9   C10  C9   120.27  3.000
 O3J  H9   C10  C11  120.25  3.000
 O3J  C9   C10  C11  119.47  3.000
 O3J  H11  C13  H10  107.04  3.000
 O3J  H11  C13  C14  108.13  3.000
 O3J  H10  C13  C14  109.12  3.000
 O3J  H11  C13  N1   109.84  3.000
 O3J  H10  C13  N1   111.47  3.000
 O3J  C14  C13  N1   111.10  3.000
 O3J  C2   N    C14  112.95  3.000
 O3J  C14  N    C1   121.59  3.000
 O3J  C2   N    C1   125.44  3.000
 O3J  H14  C    H13  108.27  3.000
 O3J  H14  C    H12  107.49  3.000
 O3J  H13  C    H12  108.24  3.000
 O3J  H14  C    C1   111.98  3.000
 O3J  H13  C    C1   108.90  3.000
 O3J  H12  C    C1   111.83  3.000
 O3J  O    C1   C    120.62  3.000
 O3J  C    C1   N    117.31  3.000
 O3J  O    C1   N    122.06  3.000
 O3J  H15  C11  C12  119.77  3.000
 O3J  H15  C11  C10  120.08  3.000
 O3J  C12  C11  C10  120.15  3.000
 O3J  H16  C12  C11  119.66  3.000
 O3J  H16  C12  C7   119.40  3.000
 O3J  C11  C12  C7   120.94  3.000
 O3J  H18  C14  H17  107.89  3.000
 O3J  H18  C14  N    109.31  3.000
 O3J  H17  C14  N    109.70  3.000
 O3J  H18  C14  C13  109.54  3.000
 O3J  H17  C14  C13  109.89  3.000
 O3J  N    C14  C13  110.47  3.000
 O3J  H20  C2   H19  107.43  3.000
 O3J  H20  C2   C3   109.28  3.000
 O3J  H19  C2   C3   109.26  3.000
 O3J  H20  C2   N    109.27  3.000
 O3J  H19  C2   N    111.07  3.000
 O3J  C3   C2   N    110.46  3.000
 O3J  H22  C3   H21  107.21  3.000
 O3J  H22  C3   C2   109.02  3.000
 O3J  H21  C3   C2   108.39  3.000
 O3J  H22  C3   N1   112.20  3.000
 O3J  H21  C3   N1   109.19  3.000
 O3J  C2   C3   N1   110.70  3.000
 O3J  H23  C9   C10  120.09  3.000
 O3J  H23  C9   C8   119.78  3.000
 O3J  C10  C9   C8   120.13  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
 O3J  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 O3J  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 O3J  CONST_03  C11  C10  C9   C8      0.00   0.0  0
 O3J  CONST_04  C11  C12  C7   C8      0.00   0.0  0
 O3J  CONST_05  C9   C10  C11  C12     0.00   0.0  0
 O3J  CONST_06  C9   C8   C7   C12     0.00   0.0  0
 O3J  CONST_07  C9   C8   C7   C6    180.00   0.0  0
 O3J  CONST_08  C11  C12  C7   C6    180.00   0.0  0
 O3J  CONST_09  H23  C9   C8   C7    180.00   0.0  0
 O3J  CONST_10  H15  C11  C12  C7    180.00   0.0  0
 O3J  CONST_11  H9   C10  C9   C8    180.00   0.0  0
 O3J  CONST_12  H16  C12  C7   C8    180.00   0.0  0
 O3J  CONST_13  H8   C8   C9   C10   180.00   0.0  0
 O3J  CONST_14  C2   N    C1   C       0.00   0.0  0
 O3J  CONST_15  C14  N    C1   C     180.00   0.0  0
 O3J  CONST_16  C2   N    C1   O     180.00   0.0  0
 O3J  CONST_17  C14  N    C1   O       0.00   0.0  0
 O3J  Var_01    N    C2   C3   N1    -56.27  30.0  1
 O3J  Var_02    N    C14  C13  N1     55.32  30.0  1
 O3J  Var_03    C2   C3   N1   C13    58.75  30.0  1
 O3J  Var_04    C2   N    C14  C13   -53.64  30.0  1
 O3J  Var_05    C3   N1   C13  C14   -58.42  30.0  1
 O3J  Var_06    C3   C2   N    C14    54.19  30.0  1
 O3J  Var_07    C8   C7   C6   C5    -93.74  30.0  2
 O3J  Var_08    C6   C5   C4   N1   -179.56  30.0  2
 O3J  Var_09    C7   C6   C5   C4    175.68  30.0  2
 O3J  Var_10    H12  C    C1   N      61.28  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
 O3J  plan-1  C6   0.020
 O3J  plan-1  C7   0.020
 O3J  plan-1  C8   0.020
 O3J  plan-1  C10  0.020
 O3J  plan-1  C11  0.020
 O3J  plan-1  C12  0.020
 O3J  plan-1  C9   0.020
 O3J  plan-1  H8   0.020
 O3J  plan-1  H9   0.020
 O3J  plan-1  H15  0.020
 O3J  plan-1  H16  0.020
 O3J  plan-1  H23  0.020
 O3J  plan-2  N    0.020
 O3J  plan-2  C    0.020
 O3J  plan-2  O    0.020
 O3J  plan-2  C1   0.020
 O3J  plan-2  C14  0.020
 O3J  plan-2  C2   0.020

