# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:52:00 2021
#   Inital geometry file: a 70 line input string
#   Ligand name: (2R,3R)-2-methyl-1-(methylsulfonyl)piperidine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1[C@@H](CCCN1[S](C)(=O)=O)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
 W2A  W2A  (2R,3R)-2-methyl-1-(methylsulfonyl)piperidine-3-carbonitrile  ligand  27  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_W2A
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
 W2A  N1   N  NS    0  -0.263  19.9670  27.7574   2.5183
 W2A  C4   C  CH2   0  -0.436  22.3860  29.1522   6.5172
 W2A  C5   C  CH2   0  -0.445  22.0613  28.7398   5.0886
 W2A  C6   C  CH1   0  -0.347  20.5570  28.4650   4.9575
 W2A  C7   C  CSP   0   0.132  20.2212  28.0675   3.5970
 W2A  C1   C  CH1   0  -0.092  20.0579  27.4128   5.9739
 W2A  C    C  CH3   0  -0.678  20.5653  26.0036   5.6876
 W2A  C3   C  CH2   0  -0.307  21.8673  28.1359   7.5204
 W2A  N    N  N     0  -0.600  20.4389  27.9211   7.2913
 W2A  S    S  S     0   1.347  19.4382  27.7318   8.5828
 W2A  O    O  OS    0  -0.664  18.0731  27.7139   8.0772
 W2A  O1   O  OS    0  -0.664  19.8103  28.7340   9.5709
 W2A  C2   C  CH3   0  -0.797  19.7908  26.1389   9.2924
 W2A  H1   H  HCH2  0   0.259  23.4655  29.2537   6.6376
 W2A  H2   H  HCH2  0   0.240  21.9410  30.1263   6.7334
 W2A  H3   H  HCH2  0   0.251  22.6301  27.8498   4.8105
 W2A  H4   H  HCH2  0   0.274  22.3484  29.5278   4.3918
 W2A  H5   H  HCH1  0   0.329  20.0107  29.3929   5.1546
 W2A  H6   H  HCH1  0   0.300  18.9702  27.4063   5.9207
 W2A  H7   H  HCH3  0   0.253  20.1985  25.3052   6.4391
 W2A  H8   H  HCH3  0   0.255  20.1944  25.6553   4.7238
 W2A  H9   H  HCH3  0   0.241  21.6522  25.9323   5.6692
 W2A  H10  H  HCH2  0   0.246  22.4215  27.1956   7.4326
 W2A  H11  H  HCH2  0   0.280  22.0223  28.5030   8.5325
 W2A  H12  H  HCH3  0   0.307  19.1631  26.0168  10.1737
 W2A  H13  H  HCH3  0   0.289  19.5649  25.3585   8.5699
 W2A  H14  H  HCH3  0   0.292  20.8398  26.0943   9.5790

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
 W2A  N1  C7   triple  1.151  0.020  1.151
 W2A  C7  C6   single  1.457  0.020  1.457
 W2A  C6  C5   single  1.535  0.020  1.535
 W2A  C6  C1   single  1.546  0.020  1.546
 W2A  C5  C4   single  1.522  0.020  1.522
 W2A  C   C1   single  1.525  0.020  1.525
 W2A  C1  N    single  1.463  0.020  1.463
 W2A  C4  C3   single  1.519  0.020  1.519
 W2A  N   C3   single  1.463  0.020  1.463
 W2A  N   S    single  1.645  0.020  1.645
 W2A  O   S    double  1.456  0.020  1.456
 W2A  S   O1   double  1.456  0.020  1.456
 W2A  S   C2   single  1.779  0.020  1.779
 W2A  C4  H1   single  0.970  0.020  1.090
 W2A  C4  H2   single  0.970  0.020  1.090
 W2A  C5  H3   single  0.970  0.020  1.090
 W2A  C5  H4   single  0.970  0.020  1.090
 W2A  C6  H5   single  0.970  0.020  1.090
 W2A  C1  H6   single  0.970  0.020  1.090
 W2A  C   H7   single  0.970  0.020  1.090
 W2A  C   H8   single  0.970  0.020  1.090
 W2A  C   H9   single  0.970  0.020  1.090
 W2A  C3  H10  single  0.970  0.020  1.090
 W2A  C3  H11  single  0.970  0.020  1.090
 W2A  C2  H12  single  0.970  0.020  1.090
 W2A  C2  H13  single  0.970  0.020  1.090
 W2A  C2  H14  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
 W2A  H2   C4  H1   107.35  3.000
 W2A  H2   C4  C3   109.07  3.000
 W2A  H1   C4  C3   109.09  3.000
 W2A  H2   C4  C5   109.91  3.000
 W2A  H1   C4  C5   109.87  3.000
 W2A  C3   C4  C5   111.45  3.000
 W2A  H4   C5  H3   106.80  3.000
 W2A  H4   C5  C6   109.44  3.000
 W2A  H3   C5  C6   110.05  3.000
 W2A  H4   C5  C4   110.35  3.000
 W2A  H3   C5  C4   110.41  3.000
 W2A  C6   C5  C4   109.74  3.000
 W2A  H5   C6  C1   107.30  3.000
 W2A  H5   C6  C7   106.53  3.000
 W2A  C1   C6  C7   110.73  3.000
 W2A  H5   C6  C5   108.79  3.000
 W2A  C1   C6  C5   112.47  3.000
 W2A  C7   C6  C5   110.77  3.000
 W2A  C6   C7  N1   180.00  3.000
 W2A  H6   C1  N    107.83  3.000
 W2A  H6   C1  C    108.52  3.000
 W2A  N    C1  C    113.81  3.000
 W2A  H6   C1  C6   107.13  3.000
 W2A  N    C1  C6   105.76  3.000
 W2A  C    C1  C6   113.46  3.000
 W2A  H9   C   H8   107.68  3.000
 W2A  H9   C   H7   107.79  3.000
 W2A  H8   C   H7   106.89  3.000
 W2A  H9   C   C1   113.31  3.000
 W2A  H8   C   C1   110.38  3.000
 W2A  H7   C   C1   110.54  3.000
 W2A  H11  C3  H10  107.00  3.000
 W2A  H11  C3  N    109.54  3.000
 W2A  H10  C3  N    110.83  3.000
 W2A  H11  C3  C4   109.87  3.000
 W2A  H10  C3  C4   110.41  3.000
 W2A  N    C3  C4   109.16  3.000
 W2A  S    N   C3   119.21  3.000
 W2A  S    N   C1   120.58  3.000
 W2A  C3   N   C1   116.52  3.000
 W2A  C2   S   O1   107.16  3.000
 W2A  C2   S   O    108.26  3.000
 W2A  O1   S   O    118.94  3.000
 W2A  C2   S   N    107.20  3.000
 W2A  O1   S   N    107.35  3.000
 W2A  O    S   N    107.41  3.000
 W2A  H14  C2  H13  110.23  3.000
 W2A  H14  C2  H12  109.75  3.000
 W2A  H13  C2  H12  109.73  3.000
 W2A  H14  C2  S    109.43  3.000
 W2A  H13  C2  S    109.66  3.000
 W2A  H12  C2  S    108.00  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
 W2A  Var_01  C1   N   C3  C4   60.21  30.0  1
 W2A  Var_02  N    C3  C4  C5  -54.13  30.0  1
 W2A  Var_03  C3   C4  C5  C6   53.47  30.0  1
 W2A  Var_04  O    S   N   C1  -29.69  30.0  3
 W2A  Var_05  H12  C2  S   N   177.74  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
 W2A  chir_01  C6  C7  C5  C1  positiv
 W2A  chir_02  C1  N   C6  C   negativ

