# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 08:50:37 2021
#   Inital geometry file: a 74 line input string
#   Ligand name: (2S,3S)-2-methyl-1-(methylsulfonyl)piperidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1[C@H](CCCN1[S](C)(=O)=O)C(N)=O
#
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
 W2Y  W2Y  (2S,3S)-2-methyl-1-(methylsulfonyl)piperidine-3-carboxamide  ligand  30  14  .  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_W2Y
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
 W2Y  N1   N  NH2   0  -0.806  23.1078  35.1519  -24.6189
 W2Y  C4   C  CH2   0  -0.423  26.2912  38.0934  -24.4436
 W2Y  C5   C  CH2   0  -0.308  25.8857  39.2668  -25.3185
 W2Y  C7   C  C     0   0.530  22.7762  36.3997  -24.2692
 W2Y  O2   O  O     0  -0.499  21.6331  36.7182  -23.9654
 W2Y  C2   C  CH1   0  -0.348  23.8888  37.4388  -24.2560
 W2Y  C3   C  CH2   0  -0.489  25.2990  36.9439  -24.5663
 W2Y  N    N  N     0  -0.597  24.5096  39.6520  -25.0061
 W2Y  S    S  S     0   1.345  24.1091  41.2424  -25.0999
 W2Y  O    O  OS    0  -0.667  22.7066  41.3645  -24.7269
 W2Y  O1   O  OS    0  -0.670  25.1014  41.9929  -24.3423
 W2Y  C1   C  CH1   0  -0.088  23.4851  38.6136  -25.1680
 W2Y  C    C  CH3   0  -0.680  23.2658  38.2097  -26.6232
 W2Y  H1   H  HNH2  0   0.402  22.4080  34.4275  -24.6285
 W2Y  H2   H  HNH2  0   0.419  24.0427  34.8884  -24.8755
 W2Y  H4   H  HCH2  0   0.235  26.3478  38.4252  -23.4038
 W2Y  H5   H  HCH2  0   0.242  25.9861  38.9992  -26.3760
 W2Y  H6   H  HCH2  0   0.275  26.5505  40.1092  -25.1358
 W2Y  H7   H  HCH3  0   0.306  24.0623  42.8032  -26.8637
 W2Y  H8   H  HCH3  0   0.289  25.2969  41.5530  -27.1384
 W2Y  H9   H  HCH3  0   0.287  23.5766  41.1840  -27.4204
 W2Y  H10  H  HCH1  0   0.283  23.8947  37.8340  -23.2333
 W2Y  H11  H  HCH2  0   0.237  25.3548  36.5261  -25.5768
 W2Y  H12  H  HCH2  0   0.260  25.5824  36.1470  -23.8753
 W2Y  H13  H  HCH1  0   0.281  22.5514  39.0131  -24.7778
 W2Y  H14  H  HCH3  0   0.250  22.5045  37.4336  -26.7012
 W2Y  H15  H  HCH3  0   0.244  22.9049  39.0560  -27.2075
 W2Y  H16  H  HCH3  0   0.237  24.1683  37.8350  -27.1051
 W2Y  H3   H  HCH2  0   0.252  27.2903  37.7647  -24.7339
 W2Y  C6   C  CH3   0  -0.798  24.2784  41.7378  -26.8026

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
 W2Y  C6  S    single  1.781  0.020  1.781
 W2Y  C   C1   single  1.526  0.020  1.526
 W2Y  C5  N    single  1.463  0.020  1.463
 W2Y  C5  C4   single  1.519  0.020  1.519
 W2Y  S   N    single  1.643  0.020  1.643
 W2Y  S   O    double  1.456  0.020  1.456
 W2Y  S   O1   double  1.457  0.020  1.457
 W2Y  C1  N    single  1.468  0.020  1.468
 W2Y  C1  C2   single  1.541  0.020  1.541
 W2Y  N1  C7   single  1.338  0.020  1.338
 W2Y  C3  C4   single  1.523  0.020  1.523
 W2Y  C3  C2   single  1.526  0.020  1.526
 W2Y  C7  C2   single  1.522  0.020  1.522
 W2Y  C7  O2   double  1.225  0.020  1.225
 W2Y  N1  H1   single  0.860  0.020  1.020
 W2Y  N1  H2   single  0.860  0.020  1.020
 W2Y  C4  H3   single  0.970  0.020  1.090
 W2Y  C4  H4   single  0.970  0.020  1.090
 W2Y  C5  H5   single  0.970  0.020  1.090
 W2Y  C5  H6   single  0.970  0.020  1.090
 W2Y  C6  H7   single  0.970  0.020  1.090
 W2Y  C6  H8   single  0.970  0.020  1.090
 W2Y  C6  H9   single  0.970  0.020  1.090
 W2Y  C2  H10  single  0.970  0.020  1.090
 W2Y  C3  H11  single  0.970  0.020  1.090
 W2Y  C3  H12  single  0.970  0.020  1.090
 W2Y  C1  H13  single  0.970  0.020  1.090
 W2Y  C   H14  single  0.970  0.020  1.090
 W2Y  C   H15  single  0.970  0.020  1.090
 W2Y  C   H16  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
 W2Y  H2   N1  H1   117.09  3.000
 W2Y  H2   N1  C7   122.83  3.000
 W2Y  H1   N1  C7   120.07  3.000
 W2Y  H4   C4  H3   107.29  3.000
 W2Y  H4   C4  C3   109.84  3.000
 W2Y  H3   C4  C3   110.34  3.000
 W2Y  H4   C4  C5   109.11  3.000
 W2Y  H3   C4  C5   108.90  3.000
 W2Y  C3   C4  C5   111.26  3.000
 W2Y  H6   C5  H5   107.17  3.000
 W2Y  H6   C5  N    109.56  3.000
 W2Y  H5   C5  N    110.90  3.000
 W2Y  H6   C5  C4   109.76  3.000
 W2Y  H5   C5  C4   110.06  3.000
 W2Y  N    C5  C4   109.36  3.000
 W2Y  C2   C7  O2   120.16  3.000
 W2Y  O2   C7  N1   122.60  3.000
 W2Y  C2   C7  N1   117.25  3.000
 W2Y  H10  C2  C1   106.18  3.000
 W2Y  H10  C2  C3   107.55  3.000
 W2Y  C1   C2  C3   111.65  3.000
 W2Y  H10  C2  C7   104.96  3.000
 W2Y  C3   C2  C7   116.88  3.000
 W2Y  C1   C2  C7   108.89  3.000
 W2Y  H12  C3  H11  107.00  3.000
 W2Y  H12  C3  C2   110.34  3.000
 W2Y  H11  C3  C2   111.01  3.000
 W2Y  H12  C3  C4   109.30  3.000
 W2Y  H11  C3  C4   109.21  3.000
 W2Y  C2   C3  C4   109.92  3.000
 W2Y  C1   N   S    120.56  3.000
 W2Y  C1   N   C5   116.54  3.000
 W2Y  S    N   C5   118.17  3.000
 W2Y  O1   S   O    118.66  3.000
 W2Y  O1   S   N    107.64  3.000
 W2Y  O    S   N    107.54  3.000
 W2Y  O1   S   C6   106.80  3.000
 W2Y  O    S   C6   108.24  3.000
 W2Y  N    S   C6   107.50  3.000
 W2Y  H13  C1  C    108.42  3.000
 W2Y  H13  C1  N    107.44  3.000
 W2Y  C    C1  N    113.13  3.000
 W2Y  H13  C1  C2   107.01  3.000
 W2Y  N    C1  C2   106.93  3.000
 W2Y  C    C1  C2   113.59  3.000
 W2Y  H16  C   H15  107.71  3.000
 W2Y  H16  C   H14  107.58  3.000
 W2Y  H15  C   H14  106.45  3.000
 W2Y  H16  C   C1   113.19  3.000
 W2Y  H15  C   C1   110.68  3.000
 W2Y  H14  C   C1   110.92  3.000
 W2Y  H9   C6  H8   110.02  3.000
 W2Y  H9   C6  H7   109.79  3.000
 W2Y  H8   C6  H7   109.55  3.000
 W2Y  H9   C6  S    109.90  3.000
 W2Y  H8   C6  S    109.68  3.000
 W2Y  H7   C6  S    107.87  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
 W2Y  CONST_01  H1  N1  C7  C2   180.00   0.0  0
 W2Y  CONST_02  H2  N1  C7  C2     0.00   0.0  0
 W2Y  Var_01    C1  N   C5  C4   -58.19  30.0  1
 W2Y  Var_02    C2  C3  C4  C5   -54.92  30.0  1
 W2Y  Var_03    N   C5  C4  C3    53.98  30.0  1
 W2Y  Var_04    C6  S   N   C5    64.48  30.0  1
 W2Y  Var_05    H7  C6  S   N   -177.23  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
 W2Y  chir_01  C2  C1  C3  C7  positiv
 W2Y  chir_02  C1  N   C2  C   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
 W2Y  plan-1  N1  0.020
 W2Y  plan-1  C7  0.020
 W2Y  plan-1  O2  0.020
 W2Y  plan-1  C2  0.020
 W2Y  plan-1  H1  0.020
 W2Y  plan-1  H2  0.020

