# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:41:05 2021
#   Inital geometry file: a 93 line input string
#   Ligand name: 3-oxidanylidene-3-[4-(phenylmethyl)piperidin-1-yl]propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CC#N)N1CCC(CC1)Cc2ccccc2
#
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
 SU7  SU7  3-oxidanylidene-3-[4-(phenylmethyl)piperidin-1-yl]propanenitrile  ligand  36  18  .  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_SU7
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
 SU7  N1   N  NS    0  -0.263  42.1887  122.9750  33.6522
 SU7  C4   C  CR16  0  -0.308  51.0629  117.2439  31.2858
 SU7  C5   C  CR16  0  -0.240  52.2711  117.3674  30.6151
 SU7  C6   C  CH2   0  -0.522  49.4237  117.9570  33.0576
 SU7  C7   C  CR16  0  -0.225  48.2375  118.4911  32.2432
 SU7  C8   C  C     0  -0.473  48.3086  120.0083  32.0166
 SU7  C10  C  C     0  -0.306  45.7975  119.0893  32.6127
 SU7  C13  C  CH2   0  -0.707  43.7711  120.9541  33.2360
 SU7  N    N  NR6   0  -0.459  46.1418  120.4400  33.0551
 SU7  C    C  CR16  0  -0.273  53.1886  118.3382  31.0006
 SU7  O    O  O     0  -0.491  45.5142  122.4905  33.7757
 SU7  C1   C  CR16  0  -0.243  52.8861  119.1793  32.0619
 SU7  C11  C  C     0  -0.461  46.9256  118.1311  32.9533
 SU7  C12  C  C     0   0.586  45.2346  121.3679  33.3822
 SU7  C14  C  CSP   0   0.146  42.8994  122.0879  33.4811
 SU7  C2   C  CR16  0  -0.318  51.6741  119.0505  32.7302
 SU7  C3   C  CR6   0   0.143  50.7451  118.0840  32.3533
 SU7  C9   C  C     0  -0.289  47.5632  120.7834  33.0893
 SU7  H1   H  HCR6  0   0.245  50.3581  116.4801  30.9767
 SU7  H2   H  HCR6  0   0.253  52.4985  116.7029  29.7911
 SU7  H3   H  HCH2  0   0.241  49.4637  118.4828  34.0168
 SU7  H4   H  HCH2  0   0.252  49.2354  116.9050  33.2929
 SU7  H5   H  HCR6  0   0.245  48.2485  117.9981  31.2670
 SU7  H6   H  H     0   0.256  49.3445  120.3524  31.9909
 SU7  H7   H  H     0   0.247  47.8845  120.2665  31.0434
 SU7  H8   H  H     0   0.270  44.8912  118.7541  33.1141
 SU7  H9   H  H     0   0.249  45.5970  119.0758  31.5361
 SU7  H10  H  HCH2  0   0.343  43.5580  120.5609  32.2393
 SU7  H11  H  HCH2  0   0.347  43.5158  120.1634  33.9464
 SU7  H12  H  HCR6  0   0.253  54.1331  118.4330  30.4806
 SU7  H13  H  HCR6  0   0.253  53.5947  119.9356  32.3749
 SU7  H14  H  H     0   0.238  47.0707  118.1401  34.0381
 SU7  H15  H  H     0   0.259  46.6176  117.1173  32.6928
 SU7  H16  H  HCR6  0   0.247  51.4512  119.7090  33.5622
 SU7  H17  H  H     0   0.241  47.9769  120.5722  34.0814
 SU7  H18  H  H     0   0.263  47.6713  121.8528  32.9211

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
 SU7  C5   C4   aromatic  1.387  0.020  1.387
 SU7  C5   C    aromatic  1.390  0.020  1.390
 SU7  C4   C3   aromatic  1.395  0.020  1.395
 SU7  C    C1   aromatic  1.388  0.020  1.388
 SU7  C8   C7   single    1.536  0.020  1.536
 SU7  C8   C9   single    1.519  0.020  1.519
 SU7  C10  N    single    1.462  0.020  1.462
 SU7  C10  C11  single    1.519  0.020  1.519
 SU7  C7   C11  single    1.535  0.020  1.535
 SU7  C7   C6   single    1.535  0.020  1.535
 SU7  C9   N    single    1.463  0.020  1.463
 SU7  N    C12  single    1.338  0.020  1.338
 SU7  C3   C6   single    1.503  0.020  1.503
 SU7  C3   C2   aromatic  1.393  0.020  1.393
 SU7  C1   C2   aromatic  1.390  0.020  1.390
 SU7  C12  O    double    1.222  0.020  1.222
 SU7  C12  C13  single    1.528  0.020  1.528
 SU7  C13  C14  single    1.451  0.020  1.451
 SU7  C14  N1   triple    1.149  0.020  1.149
 SU7  C4   H1   single    0.930  0.020  1.080
 SU7  C5   H2   single    0.930  0.020  1.080
 SU7  C6   H3   single    0.970  0.020  1.090
 SU7  C6   H4   single    0.970  0.020  1.090
 SU7  C7   H5   single    0.970  0.020  1.090
 SU7  C8   H6   single    0.970  0.020  1.090
 SU7  C8   H7   single    0.970  0.020  1.090
 SU7  C10  H8   single    0.970  0.020  1.090
 SU7  C10  H9   single    0.970  0.020  1.090
 SU7  C13  H10  single    0.970  0.020  1.090
 SU7  C13  H11  single    0.970  0.020  1.090
 SU7  C    H12  single    0.930  0.020  1.080
 SU7  C1   H13  single    0.930  0.020  1.080
 SU7  C11  H14  single    0.970  0.020  1.090
 SU7  C11  H15  single    0.970  0.020  1.090
 SU7  C2   H16  single    0.930  0.020  1.080
 SU7  C9   H17  single    0.970  0.020  1.090
 SU7  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
 SU7  H1   C4   C3   119.62  3.000
 SU7  H1   C4   C5   119.40  3.000
 SU7  C3   C4   C5   120.98  3.000
 SU7  H2   C5   C    120.07  3.000
 SU7  H2   C5   C4   119.74  3.000
 SU7  C    C5   C4   120.19  3.000
 SU7  H4   C6   H3   106.24  3.000
 SU7  H4   C6   C3   109.47  3.000
 SU7  H3   C6   C3   109.75  3.000
 SU7  H4   C6   C7   108.40  3.000
 SU7  H3   C6   C7   109.03  3.000
 SU7  C3   C6   C7   113.67  3.000
 SU7  H5   C7   C11  108.41  3.000
 SU7  H5   C7   C8   108.25  3.000
 SU7  C11  C7   C8   109.86  3.000
 SU7  H5   C7   C6   107.99  3.000
 SU7  C11  C7   C6   109.49  3.000
 SU7  C8   C7   C6   112.73  3.000
 SU7  H7   C8   H6   105.83  3.000
 SU7  H7   C8   C9   108.54  3.000
 SU7  H6   C8   C9   108.74  3.000
 SU7  H7   C8   C7   110.30  3.000
 SU7  H6   C8   C7   111.03  3.000
 SU7  C9   C8   C7   112.16  3.000
 SU7  H9   C10  H8   107.25  3.000
 SU7  H9   C10  C11  110.41  3.000
 SU7  H8   C10  C11  108.71  3.000
 SU7  H9   C10  N    110.60  3.000
 SU7  H8   C10  N    109.94  3.000
 SU7  C11  C10  N    109.88  3.000
 SU7  H11  C13  H10  106.67  3.000
 SU7  H11  C13  C14  108.37  3.000
 SU7  H10  C13  C14  108.55  3.000
 SU7  H11  C13  C12  110.94  3.000
 SU7  H10  C13  C12  111.82  3.000
 SU7  C14  C13  C12  110.35  3.000
 SU7  C9   N    C12  119.36  3.000
 SU7  C12  N    C10  123.69  3.000
 SU7  C9   N    C10  116.92  3.000
 SU7  H12  C    C1   120.31  3.000
 SU7  H12  C    C5   120.25  3.000
 SU7  C1   C    C5   119.44  3.000
 SU7  H13  C1   C2   119.76  3.000
 SU7  H13  C1   C    120.13  3.000
 SU7  C2   C1   C    120.11  3.000
 SU7  H15  C11  H14  106.36  3.000
 SU7  H15  C11  C10  108.85  3.000
 SU7  H14  C11  C10  108.39  3.000
 SU7  H15  C11  C7   110.42  3.000
 SU7  H14  C11  C7   110.08  3.000
 SU7  C10  C11  C7   112.53  3.000
 SU7  O    C12  N    124.09  3.000
 SU7  O    C12  C13  119.92  3.000
 SU7  N    C12  C13  115.99  3.000
 SU7  C13  C14  N1   180.00  3.000
 SU7  H16  C2   C3   119.48  3.000
 SU7  H16  C2   C1   119.47  3.000
 SU7  C3   C2   C1   121.05  3.000
 SU7  C2   C3   C6   121.22  3.000
 SU7  C2   C3   C4   118.24  3.000
 SU7  C6   C3   C4   120.53  3.000
 SU7  H18  C9   H17  106.98  3.000
 SU7  H18  C9   N    108.89  3.000
 SU7  H17  C9   N    110.06  3.000
 SU7  H18  C9   C8   110.10  3.000
 SU7  H17  C9   C8   110.85  3.000
 SU7  N    C9   C8   109.91  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
 SU7  CONST_01  C1   C    C5   C4      0.00   0.0  0
 SU7  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 SU7  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 SU7  CONST_04  C2   C1   C    C5      0.00   0.0  0
 SU7  CONST_05  C3   C4   C5   C       0.00   0.0  0
 SU7  CONST_06  C3   C2   C1   C       0.00   0.0  0
 SU7  CONST_07  C6   C3   C4   C5    180.00   0.0  0
 SU7  CONST_08  C1   C2   C3   C6    180.00   0.0  0
 SU7  CONST_09  H12  C    C5   C4    180.00   0.0  0
 SU7  CONST_10  H16  C2   C3   C4    180.00   0.0  0
 SU7  CONST_11  H13  C1   C    C5    180.00   0.0  0
 SU7  CONST_12  H1   C4   C5   C     180.00   0.0  0
 SU7  CONST_13  H2   C5   C    C1    180.00   0.0  0
 SU7  CONST_14  O    C12  N    C10   180.00   0.0  0
 SU7  CONST_15  C13  C12  N    C10     0.00   0.0  0
 SU7  CONST_16  C9   N    C12  C13   180.00   0.0  0
 SU7  CONST_17  C9   N    C12  O       0.00   0.0  0
 SU7  Var_01    N    C9   C8   C7    -62.51  30.0  1
 SU7  Var_02    N    C10  C11  C7    -61.96  30.0  1
 SU7  Var_03    C10  N    C9   C8     30.33  30.0  1
 SU7  Var_04    C9   N    C10  C11    29.08  30.0  1
 SU7  Var_05    C7   C6   C3   C4    -73.48  30.0  2
 SU7  Var_06    C14  C13  C12  N    -173.85  30.0  3
 SU7  Var_07    C12  C13  C14  N1    143.81  30.0  1

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
 SU7  chir_01  C7  C8  C11  C6  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
 SU7  plan-1  C4   0.020
 SU7  plan-1  C5   0.020
 SU7  plan-1  C6   0.020
 SU7  plan-1  C    0.020
 SU7  plan-1  C1   0.020
 SU7  plan-1  C2   0.020
 SU7  plan-1  C3   0.020
 SU7  plan-1  H1   0.020
 SU7  plan-1  H2   0.020
 SU7  plan-1  H12  0.020
 SU7  plan-1  H13  0.020
 SU7  plan-1  H16  0.020
 SU7  plan-2  C10  0.020
 SU7  plan-2  C13  0.020
 SU7  plan-2  N    0.020
 SU7  plan-2  O    0.020
 SU7  plan-2  C12  0.020
 SU7  plan-2  C9   0.020

