# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 20:07:02 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (2S)-2-benzyl-3-(S-methylsulfonodiimidoyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=N)(=N)C[C@@H](Cc1ccccc1)C(O)=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
 CPM  CPM  '(2S)-2-benzyl-3-(S-methylsulfonodiimidoyl)propanoic acid'  ligand  31  16  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CPM
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
 CPM  CA1   C  CH2    0  -0.601  -0.8359  -0.1278   1.8480
 CPM  CA    C  CH1    0  -0.331  -0.5543   0.2284   0.3921
 CPM  C     C  C      0   0.430  -1.9186   0.4528  -0.3058
 CPM  O     O  O      0  -0.607  -2.6380  -0.5586  -0.4267
 CPM  CB    C  CH2    0  -0.497   0.2533  -0.8620  -0.3207
 CPM  CG    C  CR6    0   0.133   0.5485  -0.5056  -1.7500
 CPM  CD1   C  CR16   0  -0.315   1.6071   0.3462  -2.0628
 CPM  CD2   C  CR16   0  -0.301  -0.2370  -0.9920  -2.7926
 CPM  CE1   C  CR16   0  -0.241   1.8742   0.7033  -3.3775
 CPM  CE2   C  CR16   0  -0.243   0.0267  -0.6403  -4.1103
 CPM  CZ    C  CR16   0  -0.276   1.0830   0.2103  -4.4081
 CPM  OXT   O  OC    -1  -0.602  -2.1927   1.6129  -0.6631
 CPM  S     S  S      0   0.914   0.6181   0.0820   2.9227
 CPM  N1    N  N      0  -0.874   1.2510   1.4848   2.8004
 CPM  N2    N  N      0  -0.870   1.7277  -0.9686   2.6888
 CPM  CM    C  CH3    0  -0.772  -0.1674  -0.1458   4.5297
 CPM  HA11  H  HCH2   0   0.283  -1.1808  -1.1567   1.9700
 CPM  HA12  H  HCH2   0   0.292  -1.5942   0.5343   2.2756
 CPM  HA    H  HCH1   0   0.228   0.0118   1.1640   0.3745
 CPM  HB1   H  HCH2   0   0.249   1.1881  -1.0292   0.2168
 CPM  HB2   H  HCH2   0   0.232  -0.3101  -1.7968  -0.2824
 CPM  HD1   H  HCR6   0   0.240   2.2342   0.7312  -1.2659
 CPM  HD2   H  HCR6   0   0.240  -1.0672  -1.6499  -2.5677
 CPM  HE1   H  HCR6   0   0.249   2.7047   1.3620  -3.5981
 CPM  HE2   H  HCR6   0   0.249  -0.5957  -1.0314  -4.9055
 CPM  HZ    H  HCR6   0   0.250   1.2909   0.4839  -5.4346
 CPM  HN1   H  H      0   0.345   0.5562   2.1969   3.0034
 CPM  HN2   H  H      0   0.344   1.3207  -1.8977   2.6550
 CPM  HM1   H  HCH3   0   0.295   0.6259  -0.0625   5.2701
 CPM  HM2   H  HCH3   0   0.278  -0.9200   0.6224   4.6970
 CPM  HM3   H  HCH3   0   0.278  -0.6234  -1.1332   4.5788

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
 CPM  CA1  CA    single    1.525  0.020  1.525
 CPM  CA1  S     single    1.820  0.020  1.820
 CPM  CA1  HA11  single    0.970  0.020  1.090
 CPM  CA1  HA12  single    0.970  0.020  1.090
 CPM  CA   C     single    1.549  0.020  1.549
 CPM  CA   CB    single    1.533  0.020  1.533
 CPM  CA   HA    single    0.970  0.020  1.090
 CPM  C    O     deloc     1.247  0.020  1.247
 CPM  C    OXT   deloc     1.244  0.020  1.244
 CPM  CB   CG    single    1.502  0.020  1.502
 CPM  CB   HB1   single    0.970  0.020  1.090
 CPM  CB   HB2   single    0.970  0.020  1.090
 CPM  CG   CD1   aromatic  1.394  0.020  1.394
 CPM  CG   CD2   aromatic  1.393  0.020  1.393
 CPM  CD1  CE1   aromatic  1.388  0.020  1.388
 CPM  CD1  HD1   single    0.930  0.020  1.080
 CPM  CD2  CE2   aromatic  1.389  0.020  1.389
 CPM  CD2  HD2   single    0.930  0.020  1.080
 CPM  CE1  CZ    aromatic  1.390  0.020  1.390
 CPM  CE1  HE1   single    0.930  0.020  1.080
 CPM  CE2  CZ    aromatic  1.389  0.020  1.389
 CPM  CE2  HE2   single    0.930  0.020  1.080
 CPM  CZ   HZ    single    0.930  0.020  1.080
 CPM  S    N1    double    1.544  0.020  1.544
 CPM  S    N2    double    1.546  0.020  1.546
 CPM  S    CM    single    1.803  0.020  1.803
 CPM  N1   HN1   single    0.890  0.020  1.040
 CPM  N2   HN2   single    0.890  0.020  1.040
 CPM  CM   HM1   single    0.970  0.020  1.090
 CPM  CM   HM2   single    0.970  0.020  1.090
 CPM  CM   HM3   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
 CPM  HA12  CA1  HA11  107.92  3.000
 CPM  HA12  CA1  S     104.67  3.000
 CPM  HA11  CA1  S     107.16  3.000
 CPM  HA12  CA1  CA    111.09  3.000
 CPM  HA11  CA1  CA    112.65  3.000
 CPM  S     CA1  CA    112.91  3.000
 CPM  HA    CA   CB    109.17  3.000
 CPM  HA    CA   C     108.96  3.000
 CPM  CB    CA   C     110.96  3.000
 CPM  HA    CA   CA1   108.10  3.000
 CPM  CB    CA   CA1   112.03  3.000
 CPM  C     CA   CA1   107.54  3.000
 CPM  OXT   C    O     126.95  3.000
 CPM  OXT   C    CA    117.29  3.000
 CPM  O     C    CA    115.75  3.000
 CPM  HB2   CB   HB1   107.07  3.000
 CPM  HB2   CB   CG    109.74  3.000
 CPM  HB1   CB   CG    109.67  3.000
 CPM  HB2   CB   CA    108.71  3.000
 CPM  HB1   CB   CA    109.35  3.000
 CPM  CG    CB   CA    112.16  3.000
 CPM  CD2   CG   CD1   118.26  3.000
 CPM  CD2   CG   CB    121.22  3.000
 CPM  CD1   CG   CB    120.50  3.000
 CPM  HD1   CD1  CE1   119.56  3.000
 CPM  HD1   CD1  CG    119.41  3.000
 CPM  CE1   CD1  CG    121.04  3.000
 CPM  HD2   CD2  CE2   119.76  3.000
 CPM  HD2   CD2  CG    119.28  3.000
 CPM  CE2   CD2  CG    120.96  3.000
 CPM  HE1   CE1  CZ    120.10  3.000
 CPM  HE1   CE1  CD1   119.80  3.000
 CPM  CZ    CE1  CD1   120.11  3.000
 CPM  HE2   CE2  CZ    120.07  3.000
 CPM  HE2   CE2  CD2   119.74  3.000
 CPM  CZ    CE2  CD2   120.20  3.000
 CPM  HZ    CZ   CE2   120.29  3.000
 CPM  HZ    CZ   CE1   120.28  3.000
 CPM  CE2   CZ   CE1   119.43  3.000
 CPM  CM    S    N2    111.21  3.000
 CPM  CM    S    N1    111.35  3.000
 CPM  N2    S    N1    108.13  3.000
 CPM  CM    S    CA1    99.42  3.000
 CPM  N2    S    CA1   113.94  3.000
 CPM  N1    S    CA1   112.67  3.000
 CPM  HN1   N1   S     109.93  3.000
 CPM  HN2   N2   S     109.83  3.000
 CPM  HM3   CM   HM2   110.10  3.000
 CPM  HM3   CM   HM1   110.12  3.000
 CPM  HM2   CM   HM1   110.21  3.000
 CPM  HM3   CM   S     109.70  3.000
 CPM  HM2   CM   S     110.43  3.000
 CPM  HM1   CM   S     106.21  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
 CPM  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 CPM  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 CPM  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 CPM  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 CPM  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 CPM  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 CPM  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 CPM  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 CPM  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 CPM  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 CPM  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 CPM  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 CPM  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 CPM  Var_01    CD1  CG   CB   CA    81.22  30.0  2
 CPM  Var_02    N1   S    CA1  CA    52.82  30.0  3
 CPM  Var_03    HM1  CM   S    CA1  178.76  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
 CPM  chir_01  CA  CA1  C  CB  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
 CPM  plan-1  CB   0.020
 CPM  plan-1  CG   0.020
 CPM  plan-1  CD1  0.020
 CPM  plan-1  CD2  0.020
 CPM  plan-1  CE1  0.020
 CPM  plan-1  CE2  0.020
 CPM  plan-1  CZ   0.020
 CPM  plan-1  HD1  0.020
 CPM  plan-1  HD2  0.020
 CPM  plan-1  HE1  0.020
 CPM  plan-1  HE2  0.020
 CPM  plan-1  HZ   0.020
 CPM  plan-2  CA   0.020
 CPM  plan-2  C    0.020
 CPM  plan-2  O    0.020
 CPM  plan-2  OXT  0.020

