# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 18:42:26 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: 1-ethanoylpiperidine-4-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCC(CC1)C#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
 S1V  S1V  1-ethanoylpiperidine-4-carbonitrile  ligand  23  11  .  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_S1V
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
 S1V  N1   N  NT    0  -0.445  12.7324  24.0053   1.2525
 S1V  C4   C  CH2   0  -0.489  10.4533  23.4953   1.9639
 S1V  C5   C  CH1   0  -0.349  10.3812  24.7182   2.8983
 S1V  C6   C  CH2   0  -0.452  11.7313  25.4672   2.9294
 S1V  C7   C  CH2   0  -0.307  12.8789  24.5262   2.6045
 S1V  C8   C  CSP   0   0.129   9.3162  25.6243   2.4871
 S1V  C1   C  CH3   0  -0.807  15.1604  24.0196   0.9537
 S1V  C2   C  C     0   0.524  13.7696  23.7806   0.4180
 S1V  C3   C  CH2   0  -0.277  11.3757  23.7419   0.7846
 S1V  N2   N  NS    0  -0.274   8.4805  26.3411   2.1511
 S1V  O1   O  O     0  -0.512  13.5944  23.4010  -0.7341
 S1V  H1   H  HCH2  0   0.282   9.4627  23.2232   1.6003
 S1V  H2   H  HCH2  0   0.272  10.8152  22.6412   2.5379
 S1V  H3   H  HCH1  0   0.331  10.1269  24.3772   3.9043
 S1V  H4   H  HCH2  0   0.279  11.8884  25.9114   3.9114
 S1V  H5   H  HCH2  0   0.262  11.7357  26.2838   2.2043
 S1V  H6   H  HCH2  0   0.248  12.9290  23.7148   3.3384
 S1V  H7   H  HCH2  0   0.281  13.8089  25.0832   2.6859
 S1V  H8   H  HCH3  0   0.269  15.8866  23.6522   0.2330
 S1V  H9   H  HCH3  0   0.269  15.3435  25.0853   1.1040
 S1V  H10  H  HCH3  0   0.263  15.3338  23.5237   1.9086
 S1V  H11  H  HCH2  0   0.240  11.0053  24.5771   0.1798
 S1V  H12  H  HCH2  0   0.264  11.3790  22.8634   0.1415

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
 S1V  O1  C2   double  1.226  0.020  1.226
 S1V  C2  C1   single  1.509  0.020  1.509
 S1V  C2  N1   single  1.350  0.020  1.350
 S1V  C3  N1   single  1.459  0.020  1.459
 S1V  C3  C4   single  1.517  0.020  1.517
 S1V  N1  C7   single  1.456  0.020  1.456
 S1V  C4  C5   single  1.541  0.020  1.541
 S1V  N2  C8   triple  1.151  0.020  1.151
 S1V  C8  C5   single  1.457  0.020  1.457
 S1V  C7  C6   single  1.519  0.020  1.519
 S1V  C5  C6   single  1.544  0.020  1.544
 S1V  C4  H1   single  0.970  0.020  1.090
 S1V  C4  H2   single  0.970  0.020  1.090
 S1V  C5  H3   single  0.970  0.020  1.090
 S1V  C6  H4   single  0.970  0.020  1.090
 S1V  C6  H5   single  0.970  0.020  1.090
 S1V  C7  H6   single  0.970  0.020  1.090
 S1V  C7  H7   single  0.970  0.020  1.090
 S1V  C1  H8   single  0.970  0.020  1.090
 S1V  C1  H9   single  0.970  0.020  1.090
 S1V  C1  H10  single  0.970  0.020  1.090
 S1V  C3  H11  single  0.970  0.020  1.090
 S1V  C3  H12  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
 S1V  C3   N1  C2   119.08  3.000
 S1V  C3   N1  C7   117.12  3.000
 S1V  C2   N1  C7   123.79  3.000
 S1V  H2   C4  H1   106.36  3.000
 S1V  H2   C4  C3   109.54  3.000
 S1V  H1   C4  C3   109.50  3.000
 S1V  H2   C4  C5   108.54  3.000
 S1V  H1   C4  C5   110.98  3.000
 S1V  C3   C4  C5   111.77  3.000
 S1V  H3   C5  C8   106.49  3.000
 S1V  H3   C5  C6   109.66  3.000
 S1V  C8   C5  C6   110.06  3.000
 S1V  H3   C5  C4   108.76  3.000
 S1V  C6   C5  C4   110.87  3.000
 S1V  C8   C5  C4   110.89  3.000
 S1V  H5   C6  H4   107.05  3.000
 S1V  H5   C6  C7   108.55  3.000
 S1V  H4   C6  C7   109.66  3.000
 S1V  H5   C6  C5   110.66  3.000
 S1V  H4   C6  C5   110.00  3.000
 S1V  C7   C6  C5   110.83  3.000
 S1V  H7   C7  H6   106.88  3.000
 S1V  H7   C7  C6   108.23  3.000
 S1V  H6   C7  C6   110.50  3.000
 S1V  H7   C7  N1   109.81  3.000
 S1V  H6   C7  N1   111.21  3.000
 S1V  C6   C7  N1   110.12  3.000
 S1V  N2   C8  C5   180.00  3.000
 S1V  H10  C1  H9   107.27  3.000
 S1V  H10  C1  H8   108.71  3.000
 S1V  H9   C1  H8   108.01  3.000
 S1V  H10  C1  C2   112.67  3.000
 S1V  H9   C1  C2   110.97  3.000
 S1V  H8   C1  C2   109.07  3.000
 S1V  O1   C2  C1   120.95  3.000
 S1V  C1   C2  N1   117.53  3.000
 S1V  O1   C2  N1   121.52  3.000
 S1V  H12  C3  H11  106.86  3.000
 S1V  H12  C3  C4   109.26  3.000
 S1V  H11  C3  C4   110.32  3.000
 S1V  H12  C3  N1   109.41  3.000
 S1V  H11  C3  N1   110.72  3.000
 S1V  C4   C3  N1   110.20  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
 S1V  CONST_01  O1  C2  N1  C7  180.00   0.0  0
 S1V  CONST_02  C1  C2  N1  C7    0.00   0.0  0
 S1V  CONST_03  C3  N1  C2  C1  180.00   0.0  0
 S1V  CONST_04  O1  C2  N1  C3    0.00   0.0  0
 S1V  Var_01    C5  C4  C3  N1   61.02  30.0  1
 S1V  Var_02    C5  C6  C7  N1   62.70  30.0  1
 S1V  Var_03    C7  N1  C3  C4  -24.56  30.0  1
 S1V  Var_04    C3  N1  C7  C6  -35.68  30.0  1
 S1V  Var_05    H8  C1  C2  N1  171.19  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
 S1V  chir_01  C5  C4  C8  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
 S1V  plan-1  N1  0.020
 S1V  plan-1  C7  0.020
 S1V  plan-1  C1  0.020
 S1V  plan-1  C2  0.020
 S1V  plan-1  C3  0.020
 S1V  plan-1  O1  0.020

