# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 05:23:41 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (2S)-2-(acetylamino)-N-methyl-4-[(S)-methylsulfinyl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@H](CC[S@](C)=O)NC(C)=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
 SSM  SSM  (2S)-2-(acetylamino)-N-methyl-4-[(S)-methylsulfinyl]butanamide  ligand  30  14  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SSM
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
 SSM  C2   C  CH3   0  -0.772   1.4901   3.4910  -0.0905
 SSM  C    C  C     0   0.532   1.3705   1.9951  -0.2201
 SSM  O    O  O     0  -0.501   1.6057   1.4103  -1.2691
 SSM  N    N  NH1   0  -0.626   0.9937   1.3401   0.8913
 SSM  CA   C  CH1   0  -0.190   0.8712  -0.0953   0.9356
 SSM  CB   C  CH2   0  -0.475  -0.3554  -0.6147   0.1772
 SSM  CG   C  CH2   0  -0.602  -1.6215   0.1038   0.6123
 SSM  SD   S  S3    0   0.727  -3.0521  -0.6264  -0.2335
 SSM  OD1  O  O     0  -0.790  -3.1456  -2.0602   0.2396
 SSM  CE   C  CH3   0  -0.804  -4.3251   0.2981   0.6452
 SSM  C3   C  C     0   0.567   2.2138  -0.7358   0.5469
 SSM  O3   O  O     0  -0.501   3.2655  -0.2210   0.8946
 SSM  N2   N  NH1   0  -0.639   2.1669  -1.8969  -0.1128
 SSM  C1   C  CH3   0  -0.513   3.3625  -2.6342  -0.4490
 SSM  H2   H  HCH3  0   0.269   2.5334   3.7802  -0.2214
 SSM  H2A  H  HCH3  0   0.266   0.9190   3.9713  -0.8841
 SSM  H2B  H  HCH3  0   0.250   1.1448   3.8745   0.8673
 SSM  HN   H  HNH1  0   0.407   0.8339   1.8572   1.7389
 SSM  HA   H  HCH1  0   0.306   0.7317  -0.3493   1.9912
 SSM  HB   H  HCH2  0   0.265  -0.2154  -0.5120  -0.9005
 SSM  HBA  H  HCH2  0   0.257  -0.4798  -1.6771   0.3981
 SSM  HG   H  HCH2  0   0.286  -1.7848   0.0134   1.6895
 SSM  HGA  H  HCH2  0   0.285  -1.6037   1.1616   0.3462
 SSM  HE   H  HCH3  0   0.278  -4.2225   1.3586   0.4220
 SSM  HEA  H  HCH3  0   0.293  -5.2930  -0.0524   0.2925
 SSM  HEB  H  HCH3  0   0.282  -4.2316   0.1248   1.7167
 SSM  HN2  H  HNH1  0   0.414   1.2837  -2.2999  -0.3710
 SSM  H1   H  HCH3  0   0.238   3.8955  -2.9687   0.4420
 SSM  H1A  H  HCH3  0   0.250   3.0750  -3.5089  -1.0248
 SSM  H1B  H  HCH3  0   0.240   4.0459  -2.0347  -1.0501

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
 SSM  C2  C    single  1.506  0.020  1.506
 SSM  C   O    double  1.224  0.020  1.224
 SSM  C   N    single  1.344  0.020  1.344
 SSM  N   CA   single  1.441  0.020  1.441
 SSM  CA  CB   single  1.533  0.020  1.533
 SSM  CA  C3   single  1.537  0.020  1.537
 SSM  CB  CG   single  1.519  0.020  1.519
 SSM  CG  SD   single  1.815  0.020  1.815
 SSM  SD  OD1  double  1.513  0.020  1.513
 SSM  SD  CE   single  1.802  0.020  1.802
 SSM  C3  O3   double  1.221  0.020  1.221
 SSM  C3  N2   single  1.336  0.020  1.336
 SSM  N2  C1   single  1.444  0.020  1.444
 SSM  C2  H2   single  0.970  0.020  1.090
 SSM  C2  H2A  single  0.970  0.020  1.090
 SSM  C2  H2B  single  0.970  0.020  1.090
 SSM  N   HN   single  0.860  0.020  1.020
 SSM  CA  HA   single  0.970  0.020  1.090
 SSM  CB  HB   single  0.970  0.020  1.090
 SSM  CB  HBA  single  0.970  0.020  1.090
 SSM  CG  HG   single  0.970  0.020  1.090
 SSM  CG  HGA  single  0.970  0.020  1.090
 SSM  CE  HE   single  0.970  0.020  1.090
 SSM  CE  HEA  single  0.970  0.020  1.090
 SSM  CE  HEB  single  0.970  0.020  1.090
 SSM  N2  HN2  single  0.860  0.020  1.020
 SSM  C1  H1   single  0.970  0.020  1.090
 SSM  C1  H1A  single  0.970  0.020  1.090
 SSM  C1  H1B  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
 SSM  H2B  C2  H2A  108.64  3.000
 SSM  H2B  C2  H2   108.41  3.000
 SSM  H2A  C2  H2   107.29  3.000
 SSM  H2B  C2  C    113.61  3.000
 SSM  H2A  C2  C    109.49  3.000
 SSM  H2   C2  C    109.20  3.000
 SSM  N    C   O    121.99  3.000
 SSM  N    C   C2   115.79  3.000
 SSM  O    C   C2   122.22  3.000
 SSM  HN   N   CA   118.20  3.000
 SSM  HN   N   C    119.41  3.000
 SSM  CA   N   C    122.32  3.000
 SSM  HA   CA  C3   104.98  3.000
 SSM  HA   CA  CB   107.25  3.000
 SSM  C3   CA  CB   115.63  3.000
 SSM  HA   CA  N    105.76  3.000
 SSM  C3   CA  N    109.45  3.000
 SSM  CB   CA  N    112.97  3.000
 SSM  HBA  CB  HB   107.81  3.000
 SSM  HBA  CB  CG   107.89  3.000
 SSM  HB   CB  CG   110.19  3.000
 SSM  HBA  CB  CA   108.70  3.000
 SSM  HB   CB  CA   110.73  3.000
 SSM  CG   CB  CA   111.41  3.000
 SSM  HGA  CG  HG   108.84  3.000
 SSM  HGA  CG  SD   106.82  3.000
 SSM  HG   CG  SD   107.95  3.000
 SSM  HGA  CG  CB   112.03  3.000
 SSM  HG   CG  CB   111.56  3.000
 SSM  SD   CG  CB   109.46  3.000
 SSM  CE   SD  OD1  106.86  3.000
 SSM  CE   SD  CG    97.07  3.000
 SSM  OD1  SD  CG   106.52  3.000
 SSM  HEB  CE  HEA  110.11  3.000
 SSM  HEB  CE  HE   110.40  3.000
 SSM  HEA  CE  HE   109.33  3.000
 SSM  HEB  CE  SD   109.72  3.000
 SSM  HEA  CE  SD   107.76  3.000
 SSM  HE   CE  SD   109.47  3.000
 SSM  N2   C3  O3   122.48  3.000
 SSM  N2   C3  CA   117.14  3.000
 SSM  O3   C3  CA   120.29  3.000
 SSM  HN2  N2  C1   117.60  3.000
 SSM  HN2  N2  C3   120.42  3.000
 SSM  C1   N2  C3   121.96  3.000
 SSM  H1B  C1  H1A  108.46  3.000
 SSM  H1B  C1  H1   108.24  3.000
 SSM  H1A  C1  H1   108.39  3.000
 SSM  H1B  C1  N2   111.51  3.000
 SSM  H1A  C1  N2   108.38  3.000
 SSM  H1   C1  N2   111.77  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
 SSM  CONST_01  CA   N   C   C2   180.00   0.0  0
 SSM  CONST_02  CA   N   C   O      0.00   0.0  0
 SSM  CONST_03  C1   N2  C3  CA   180.00   0.0  0
 SSM  CONST_04  C1   N2  C3  O3     0.00   0.0  0
 SSM  CONST_05  HN   N   C   C2     0.00   0.0  0
 SSM  CONST_06  HN2  N2  C3  CA     0.00   0.0  0
 SSM  Var_01    SD   CG  CB  CA  -176.21  30.0  3
 SSM  Var_02    OD1  SD  CG  CB    63.61  30.0  3
 SSM  Var_03    H2   C2  C   O    -65.18  30.0  3
 SSM  Var_04    HE   CE  SD  CG    63.90  30.0  3
 SSM  Var_05    H1   C1  N2  C3    63.60  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
 SSM  chir_01  CA  N  CB  C3  negativ

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
 SSM  plan-1  C2   0.020
 SSM  plan-1  C    0.020
 SSM  plan-1  O    0.020
 SSM  plan-1  N    0.020
 SSM  plan-1  CA   0.020
 SSM  plan-1  HN   0.020
 SSM  plan-2  CA   0.020
 SSM  plan-2  C3   0.020
 SSM  plan-2  O3   0.020
 SSM  plan-2  N2   0.020
 SSM  plan-2  C1   0.020
 SSM  plan-2  HN2  0.020
 SSM  plan-3  CG   0.020
 SSM  plan-3  SD   0.020
 SSM  plan-3  OD1  0.020
 SSM  plan-3  CE   0.020

