# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 01:38:18 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: S-[2-oxo-2-(phenylamino)ethyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCC(=O)Nc1ccccc1)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
 TYX  TYX  S-[2-oxo-2-(phenylamino)ethyl]-L-cysteine  L-peptide  30  17  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_TYX
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
 TYX  N     N  NH2    0  -0.795  -5.4312   -2.1843  19.9585
 TYX  CA    C  CH1    0  -0.196  -5.2899   -2.8939  18.7002
 TYX  C     C  C      0   0.416  -6.1103   -2.2104  17.5743
 TYX  O     O  O      0  -0.602  -6.3450   -2.9032  16.5663
 TYX  CB    C  CH2    0  -0.548  -5.6541   -4.3618  18.8579
 TYX  SG    S  S2     0  -0.024  -7.4104   -4.6577  19.2274
 TYX  C6    C  CR16   0  -0.272  -6.9976  -10.8014  23.0195
 TYX  C5    C  CR16   0  -0.242  -8.2158  -10.3929  22.4917
 TYX  C4    C  CR16   0  -0.346  -8.3936   -9.0868  22.0701
 TYX  C7    C  C      0   0.540  -6.8215   -5.7684  21.6847
 TYX  C8    C  CH2    0  -0.701  -7.4511   -4.5539  21.0420
 TYX  C3    C  CR6    0   0.372  -7.3540   -8.1561  22.1648
 TYX  C1    C  CR16   0  -0.242  -5.9673   -9.8788  23.1177
 TYX  O1    O  O      0  -0.458  -5.6818   -5.7469  22.1146
 TYX  N1    N  NH1    0  -0.725  -7.6251   -6.8635  21.7067
 TYX  C2    C  CR16   0  -0.319  -6.1293   -8.5643  22.6982
 TYX  OXT   O  OC    -1  -0.600  -6.4202   -1.0164  17.7535
 TYX  HN1A  H  HNH2   0   0.333  -4.6296   -2.3580  20.5507
 TYX  HN2   H  HNH2   0   0.337  -5.4513   -1.1927  19.7613
 TYX  HA    H  HCH1   0   0.210  -4.2445   -2.8899  18.3395
 TYX  HB1   H  HCH2   0   0.264  -5.4602   -4.8924  17.9274
 TYX  HB2   H  HCH2   0   0.264  -5.0478   -4.8412  19.6282
 TYX  H4    H  HCR6   0   0.267  -9.3504   -8.7830  21.6608
 TYX  H81   H  HCH2   0   0.308  -6.9246   -3.6537  21.3505
 TYX  H82   H  HCH2   0   0.299  -8.5045   -4.4574  21.3134
 TYX  H1    H  HCR6   0   0.255  -5.0113  -10.1793  23.5275
 TYX  HN1   H  HNH1   0   0.414  -8.5467   -6.7427  21.3126
 TYX  H2    H  HCR6   0   0.279  -5.3065   -7.8752  22.7883
 TYX  H6    H  HCR6   0   0.252  -6.8560  -11.8221  23.3488
 TYX  H5    H  HCR6   0   0.257  -9.0366  -11.0932  22.4060

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
 TYX  N   CA    single    1.458  0.019  1.458
 TYX  N   HN1A  single    0.890  0.020  1.040
 TYX  N   HN2   single    0.890  0.020  1.040
 TYX  CA  C     single    1.525  0.021  1.525
 TYX  CA  CB    single    1.521  0.033  1.521
 TYX  CA  HA    single    0.970  0.020  0.970
 TYX  C   O     deloc     1.231  0.020  1.231
 TYX  C   OXT   deloc     1.247  0.020  1.247
 TYX  CB  SG    single    1.819  0.020  1.819
 TYX  CB  HB1   single    0.970  0.020  1.090
 TYX  CB  HB2   single    0.970  0.020  1.090
 TYX  SG  C8    single    1.818  0.020  1.818
 TYX  C6  C1    aromatic  1.386  0.020  1.386
 TYX  C6  C5    aromatic  1.389  0.020  1.389
 TYX  C6  H6    single    0.930  0.020  1.080
 TYX  C5  C4    aromatic  1.384  0.020  1.384
 TYX  C5  H5    single    0.930  0.020  1.080
 TYX  C4  C3    aromatic  1.399  0.020  1.399
 TYX  C4  H4    single    0.930  0.020  1.080
 TYX  C7  C8    single    1.511  0.020  1.511
 TYX  C7  N1    single    1.359  0.020  1.359
 TYX  C7  O1    double    1.218  0.020  1.218
 TYX  C8  H81   single    0.970  0.020  1.090
 TYX  C8  H82   single    0.970  0.020  1.090
 TYX  C3  N1    single    1.398  0.020  1.398
 TYX  C3  C2    aromatic  1.397  0.020  1.397
 TYX  C1  C2    aromatic  1.389  0.020  1.389
 TYX  C1  H1    single    0.930  0.020  1.080
 TYX  N1  HN1   single    0.860  0.020  1.020
 TYX  C2  H2    single    0.930  0.020  1.080

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
 TYX  HN2   N   HN1A  107.35  3.000
 TYX  HN2   N   CA    108.19  3.000
 TYX  HN1A  N   CA    110.27  3.000
 TYX  HA    CA  CB    109.00  3.000
 TYX  HA    CA  C     110.00  3.000
 TYX  CB    CA  C     110.50  1.500
 TYX  HA    CA  N     110.00  3.000
 TYX  CB    CA  N     110.40  1.500
 TYX  C     CA  N     111.00  2.800
 TYX  OXT   C   O     127.03  3.000
 TYX  OXT   C   CA    120.80  1.700
 TYX  O     C   CA    120.80  1.700
 TYX  HB2   CB  HB1   106.88  3.000
 TYX  HB2   CB  SG    108.76  3.000
 TYX  HB1   CB  SG    105.44  3.000
 TYX  HB2   CB  CA    111.36  3.000
 TYX  HB1   CB  CA    109.83  3.000
 TYX  SG    CB  CA    114.17  3.000
 TYX  C8    SG  CB    102.42  3.000
 TYX  H6    C6  C1    120.60  3.000
 TYX  H6    C6  C5    120.52  3.000
 TYX  C1    C6  C5    118.87  3.000
 TYX  H5    C5  C4    119.28  3.000
 TYX  H5    C5  C6    120.32  3.000
 TYX  C4    C5  C6    120.40  3.000
 TYX  H4    C4  C3    119.67  3.000
 TYX  H4    C4  C5    119.53  3.000
 TYX  C3    C4  C5    120.79  3.000
 TYX  N1    C7  O1    124.18  3.000
 TYX  O1    C7  C8    121.71  3.000
 TYX  N1    C7  C8    114.10  3.000
 TYX  H82   C8  H81   108.86  3.000
 TYX  H82   C8  C7    111.54  3.000
 TYX  H81   C8  C7    110.05  3.000
 TYX  H82   C8  SG    105.94  3.000
 TYX  H81   C8  SG    108.64  3.000
 TYX  C7    C8  SG    111.67  3.000
 TYX  C2    C3  N1    124.43  3.000
 TYX  C2    C3  C4    118.89  3.000
 TYX  N1    C3  C4    116.68  3.000
 TYX  H1    C1  C2    118.68  3.000
 TYX  H1    C1  C6    119.88  3.000
 TYX  C2    C1  C6    121.44  3.000
 TYX  HN1   N1  C3    114.56  3.000
 TYX  HN1   N1  C7    115.92  3.000
 TYX  C3    N1  C7    129.49  3.000
 TYX  H2    C2  C1    119.41  3.000
 TYX  H2    C2  C3    120.98  3.000
 TYX  C1    C2  C3    119.61  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
 TYX  CONST_01  C3   C2  C1  C6    0.00   0.0  0
 TYX  CONST_02  C3   C4  C5  C6    0.00   0.0  0
 TYX  CONST_03  C2   C1  C6  C5    0.00   0.0  0
 TYX  CONST_04  C2   C3  C4  C5    0.00   0.0  0
 TYX  CONST_05  C1   C6  C5  C4    0.00   0.0  0
 TYX  CONST_06  C1   C2  C3  C4    0.00   0.0  0
 TYX  CONST_07  N1   C3  C4  C5  180.00   0.0  0
 TYX  CONST_08  N1   C3  C2  C1  180.00   0.0  0
 TYX  CONST_09  H2   C2  C1  C6  180.00   0.0  0
 TYX  CONST_10  H4   C4  C5  C6  180.00   0.0  0
 TYX  CONST_11  H1   C1  C6  C5  180.00   0.0  0
 TYX  CONST_12  H6   C6  C5  C4  180.00   0.0  0
 TYX  CONST_13  H5   C5  C4  C3  180.00   0.0  0
 TYX  CONST_14  C7   N1  C3  C4  180.00   0.0  0
 TYX  CONST_15  C2   C3  N1  C7    0.00   0.0  0
 TYX  CONST_16  HN1  N1  C3  C4    0.00   0.0  0
 TYX  CONST_17  C3   N1  C7  C8  180.00   0.0  0
 TYX  CONST_18  O1   C7  N1  C3    0.00   0.0  0
 TYX  Var_01    C7   C8  SG  CB  -73.06  30.0  3
 TYX  Var_02    N1   C7  C8  SG  -78.62  30.0  2
 TYX  Var_03    HB1  CB  SG  C8  151.56  30.0  1

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
 TYX  chir_01  CA  N  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
 TYX  plan-1  C6   0.020
 TYX  plan-1  C5   0.020
 TYX  plan-1  C4   0.020
 TYX  plan-1  C3   0.020
 TYX  plan-1  C1   0.020
 TYX  plan-1  N1   0.020
 TYX  plan-1  C2   0.020
 TYX  plan-1  H4   0.020
 TYX  plan-1  H1   0.020
 TYX  plan-1  H2   0.020
 TYX  plan-1  H6   0.020
 TYX  plan-1  H5   0.020
 TYX  plan-2  C7   0.020
 TYX  plan-2  C8   0.020
 TYX  plan-2  C3   0.020
 TYX  plan-2  O1   0.020
 TYX  plan-2  N1   0.020
 TYX  plan-2  HN1  0.020
 TYX  plan-3  CA   0.020
 TYX  plan-3  C    0.020
 TYX  plan-3  O    0.020
 TYX  plan-3  OXT  0.020

