# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:53:48 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: S-[(2-aminophenyl)carbonyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSC(=O)c1ccccc1N)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
 CSJ  CSJ  S-[(2-aminophenyl)carbonyl]-L-cysteine  L-peptide  27  16  .  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_CSJ
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
 CSJ  N     N  NH2    0  -0.774  -11.1123   -4.1160  23.9481
 CSJ  CA    C  CH1    0  -0.191  -12.2436   -3.4479  24.5590
 CSJ  C     C  C      0   0.384  -12.0431   -1.9439  24.9143
 CSJ  O     O  O      0  -0.610  -13.0830   -1.3211  25.2096
 CSJ  OXT   O  OC    -1  -0.592  -10.8792   -1.5039  24.8940
 CSJ  CB    C  CH2    0  -0.568  -12.6669   -4.1641  25.8414
 CSJ  SG    S  S2     0  -0.018  -13.1205   -5.8965  25.5800
 CSJ  CO    C  C      0   0.239  -11.5867   -6.7514  25.8818
 CSJ  O2    O  O      0  -0.417  -10.6528   -6.1873  26.4146
 CSJ  C1    C  CR6    0  -0.074  -11.5734   -8.1728  25.5040
 CSJ  C2    C  CR6    0   0.350  -10.5455   -9.0346  25.9747
 CSJ  C3    C  CR16   0  -0.331  -10.5945  -10.3912  25.5891
 CSJ  N2    N  NH2    0  -0.860   -9.5542   -8.6338  26.8016
 CSJ  C4    C  CR16   0  -0.240  -11.5888  -10.8716  24.7717
 CSJ  C5    C  CR16   0  -0.276  -12.5906  -10.0245  24.2922
 CSJ  C6    C  CR16   0  -0.292  -12.5658   -8.6999  24.6616
 CSJ  HN    H  HNH2   0   0.337  -10.9466   -3.7019  23.0389
 CSJ  HNA   H  HNH2   0   0.325  -10.2825   -3.8935  24.4856
 CSJ  HA    H  HCH1   0   0.222  -13.0829   -3.5116  23.8589
 CSJ  HB    H  HCH2   0   0.275  -11.8844   -4.1239  26.6010
 CSJ  HBA   H  HCH2   0   0.282  -13.5546   -3.6919  26.2593
 CSJ  H3    H  HCR6   0   0.262   -9.8195  -11.0584  25.9476
 CSJ  HN2   H  HNH2   0   0.392   -8.7921   -9.2649  26.9789
 CSJ  HN2A  H  HNH2   0   0.402   -9.3749   -7.6529  26.9227
 CSJ  H4    H  HCR6   0   0.260  -11.5843  -11.9180  24.4933
 CSJ  H5    H  HCR6   0   0.252  -13.3645  -10.3969  23.6359
 CSJ  H6    H  HCR6   0   0.260  -13.3308   -8.0420  24.2700

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
 CSJ  CA  N     single    1.458  0.019  1.458
 CSJ  N   HN    single    0.890  0.020  1.040
 CSJ  N   HNA   single    0.890  0.020  1.040
 CSJ  C   CA    single    1.525  0.021  1.525
 CSJ  CA  CB    single    1.530  0.020  1.530
 CSJ  CA  HA    single    0.970  0.020  0.970
 CSJ  O   C     deloc     1.231  0.020  1.231
 CSJ  C   OXT   deloc     1.244  0.020  1.244
 CSJ  SG  CB    single    1.810  0.020  1.810
 CSJ  CB  HB    single    0.970  0.020  1.090
 CSJ  CB  HBA   single    0.970  0.020  1.090
 CSJ  SG  CO    single    1.782  0.020  1.782
 CSJ  C1  CO    single    1.471  0.020  1.471
 CSJ  CO  O2    double    1.214  0.020  1.214
 CSJ  C6  C1    aromatic  1.404  0.020  1.404
 CSJ  C1  C2    aromatic  1.422  0.020  1.422
 CSJ  C3  C2    aromatic  1.411  0.020  1.411
 CSJ  C2  N2    single    1.352  0.020  1.352
 CSJ  C4  C3    aromatic  1.374  0.020  1.374
 CSJ  C3  H3    single    0.930  0.020  1.080
 CSJ  N2  HN2   single    0.890  0.020  1.040
 CSJ  N2  HN2A  single    0.890  0.020  1.040
 CSJ  C5  C4    aromatic  1.397  0.020  1.397
 CSJ  C4  H4    single    0.930  0.020  1.080
 CSJ  C5  C6    aromatic  1.375  0.020  1.375
 CSJ  C5  H5    single    0.930  0.020  1.080
 CSJ  C6  H6    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
 CSJ  HNA   N   HN   104.62  3.000
 CSJ  HNA   N   CA   108.33  3.000
 CSJ  HN    N   CA   108.52  3.000
 CSJ  HA    CA  CB   109.00  3.000
 CSJ  HA    CA  C    109.00  3.000
 CSJ  CB    CA  C    110.10  1.900
 CSJ  HA    CA  N    110.00  3.000
 CSJ  CB    CA  N    110.50  1.700
 CSJ  C     CA  N    111.00  2.800
 CSJ  OXT   C   O    127.37  3.000
 CSJ  OXT   C   CA   117.24  3.000
 CSJ  O     C   CA   120.80  1.700
 CSJ  HBA   CB  HB   107.55  3.000
 CSJ  HBA   CB  SG   105.44  3.000
 CSJ  HB    CB  SG   108.39  3.000
 CSJ  HBA   CB  CA   110.16  3.000
 CSJ  HB    CB  CA   111.60  3.000
 CSJ  SG    CB  CA   113.37  3.000
 CSJ  CO    SG  CB   102.66  3.000
 CSJ  C1    CO  O2   123.69  3.000
 CSJ  O2    CO  SG   120.90  3.000
 CSJ  C1    CO  SG   115.34  3.000
 CSJ  C6    C1  C2   118.82  3.000
 CSJ  C2    C1  CO   120.49  3.000
 CSJ  C6    C1  CO   120.69  3.000
 CSJ  N2    C2  C3   118.53  3.000
 CSJ  N2    C2  C1   123.57  3.000
 CSJ  C3    C2  C1   117.86  3.000
 CSJ  H3    C3  C4   119.94  3.000
 CSJ  H3    C3  C2   118.47  3.000
 CSJ  C4    C3  C2   121.59  3.000
 CSJ  HN2A  N2  HN2  117.17  3.000
 CSJ  HN2A  N2  C2   119.62  3.000
 CSJ  HN2   N2  C2   118.53  3.000
 CSJ  H4    C4  C5   120.05  3.000
 CSJ  H4    C4  C3   119.20  3.000
 CSJ  C5    C4  C3   120.74  3.000
 CSJ  H5    C5  C6   120.52  3.000
 CSJ  H5    C5  C4   120.86  3.000
 CSJ  C6    C5  C4   118.62  3.000
 CSJ  H6    C6  C5   118.39  3.000
 CSJ  H6    C6  C1   119.23  3.000
 CSJ  C5    C6  C1   122.36  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
 CSJ  CONST_01  C4   C5  C6  C1     0.00   0.0  0
 CSJ  CONST_02  C4   C3  C2  C1     0.00   0.0  0
 CSJ  CONST_03  C5   C6  C1  C2     0.00   0.0  0
 CSJ  CONST_04  C5   C4  C3  C2     0.00   0.0  0
 CSJ  CONST_05  C6   C1  C2  C3     0.00   0.0  0
 CSJ  CONST_06  C6   C5  C4  C3     0.00   0.0  0
 CSJ  CONST_07  C5   C6  C1  CO   180.00   0.0  0
 CSJ  CONST_08  C3   C2  C1  CO   180.00   0.0  0
 CSJ  CONST_09  C6   C1  C2  N2   180.00   0.0  0
 CSJ  CONST_10  C4   C3  C2  N2   180.00   0.0  0
 CSJ  CONST_11  H5   C5  C6  C1   180.00   0.0  0
 CSJ  CONST_12  H3   C3  C2  C1   180.00   0.0  0
 CSJ  CONST_13  H6   C6  C1  C2   180.00   0.0  0
 CSJ  CONST_14  H4   C4  C3  C2   180.00   0.0  0
 CSJ  CONST_15  HN2  N2  C2  C1   180.00   0.0  0
 CSJ  Var_01    C6   C1  CO  SG    15.68  30.0  2
 CSJ  Var_02    C1   CO  SG  CB  -169.18  30.0  3
 CSJ  Var_03    HB   CB  SG  CO   -31.83  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
 CSJ  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
 CSJ  plan-1  CO    0.020
 CSJ  plan-1  C1    0.020
 CSJ  plan-1  C2    0.020
 CSJ  plan-1  C3    0.020
 CSJ  plan-1  N2    0.020
 CSJ  plan-1  C4    0.020
 CSJ  plan-1  C5    0.020
 CSJ  plan-1  C6    0.020
 CSJ  plan-1  H3    0.020
 CSJ  plan-1  H4    0.020
 CSJ  plan-1  H5    0.020
 CSJ  plan-1  H6    0.020
 CSJ  plan-2  C2    0.020
 CSJ  plan-2  N2    0.020
 CSJ  plan-2  HN2   0.020
 CSJ  plan-2  HN2A  0.020
 CSJ  plan-3  CA    0.020
 CSJ  plan-3  C     0.020
 CSJ  plan-3  O     0.020
 CSJ  plan-3  OXT   0.020
 CSJ  plan-4  SG    0.020
 CSJ  plan-4  CO    0.020
 CSJ  plan-4  O2    0.020
 CSJ  plan-4  C1    0.020

