# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:54:42 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: S-[(S)-hydroxy(pyridin-3-yl)methyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CS[C@H](O)c1cccnc1)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
 JJK  JJK  S-[(S)-hydroxy(pyridin-3-yl)methyl]-L-cysteine  L-peptide  26  15  .  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_JJK
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
 JJK  C    C  C      0   0.399  -56.1126  21.5074   6.3791
 JJK  N    N  NH2    0  -0.820  -55.9709  23.8894   7.2067
 JJK  O    O  O      0  -0.602  -55.5113  20.5598   5.8397
 JJK  N1   N  N      0  -0.399  -51.3132  25.4335  12.1931
 JJK  C2   C  CR16   0  -0.089  -52.2975  24.8649  11.5096
 JJK  C3   C  CR6    0   0.004  -52.7277  25.2986  10.2604
 JJK  C4   C  CR16   0  -0.171  -52.0855  26.3978   9.7043
 JJK  C5   C  CR16   0  -0.316  -51.0533  26.9974  10.4086
 JJK  C6   C  CR16   0  -0.070  -50.7036  26.4794  11.6464
 JJK  C7   C  CH1    0  -0.138  -53.8299  24.5845   9.5308
 JJK  O7   O  OH1    0  -0.672  -54.6031  25.4844   8.8383
 JJK  CA   C  CH1    0  -0.177  -55.2145  22.6976   6.8321
 JJK  CB   C  CH2    0  -0.576  -54.3321  22.2277   7.9869
 JJK  SG   S  S2     0  -0.059  -52.9762  23.3494   8.4507
 JJK  OXT  O  OC    -1  -0.589  -57.3316  21.5988   6.6154
 JJK  HN   H  HNH2   0   0.368  -56.2684  24.3758   6.3688
 JJK  HNA  H  HNH2   0   0.358  -56.8329  23.5786   7.6458
 JJK  H2   H  HCR6   0   0.259  -52.7828  24.0131  11.9779
 JJK  H4   H  HCR6   0   0.269  -52.3855  26.7834   8.7387
 JJK  H5   H  HCR6   0   0.269  -50.5286  27.8547  10.0094
 JJK  H6   H  HCR6   0   0.261  -49.9018  26.9288  12.2218
 JJK  H7   H  HCH1   0   0.242  -54.4094  23.9797  10.2446
 JJK  HO7  H  HOH1   0   0.475  -55.1803  24.9522   8.2051
 JJK  HA   H  HCH1   0   0.236  -54.5580  22.9616   5.9990
 JJK  HB   H  HCH2   0   0.263  -54.9350  22.0242   8.8773
 JJK  HBA  H  HCH2   0   0.280  -53.8465  21.2924   7.7093

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
 JJK  C   CA   single    1.525  0.021  1.525
 JJK  C   OXT  deloc     1.245  0.020  1.245
 JJK  N   CA   single    1.458  0.019  1.458
 JJK  N   HN   single    0.890  0.020  1.040
 JJK  N   HNA  single    0.890  0.020  1.040
 JJK  O   C    deloc     1.231  0.020  1.231
 JJK  C2  N1   aromatic  1.326  0.020  1.326
 JJK  C2  H2   single    0.930  0.020  1.080
 JJK  C3  C2   aromatic  1.391  0.020  1.391
 JJK  C4  C3   aromatic  1.389  0.020  1.389
 JJK  C4  C5   aromatic  1.386  0.020  1.386
 JJK  C4  H4   single    0.930  0.020  1.080
 JJK  C5  C6   aromatic  1.387  0.020  1.387
 JJK  C5  H5   single    0.930  0.020  1.080
 JJK  C6  N1   aromatic  1.328  0.020  1.328
 JJK  C6  H6   single    0.930  0.020  1.080
 JJK  C7  C3   single    1.502  0.020  1.502
 JJK  C7  H7   single    0.970  0.020  1.090
 JJK  O7  C7   single    1.374  0.020  1.374
 JJK  O7  HO7  single    0.850  0.020  0.980
 JJK  CA  CB   single    1.530  0.020  1.530
 JJK  CA  HA   single    0.970  0.020  0.970
 JJK  CB  SG   single    1.820  0.020  1.820
 JJK  CB  HB   single    0.970  0.020  1.090
 JJK  CB  HBA  single    0.970  0.020  1.090
 JJK  SG  C7   single    1.850  0.020  1.850

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
 JJK  OXT  C   CA  116.94  3.000
 JJK  OXT  C   O   127.65  3.000
 JJK  CA   C   O   120.80  1.700
 JJK  HNA  N   HN  104.78  3.000
 JJK  HNA  N   CA  107.49  3.000
 JJK  HN   N   CA  109.37  3.000
 JJK  C6   N1  C2  117.78  3.000
 JJK  H2   C2  C3  119.58  3.000
 JJK  C3   C2  N1  123.97  3.000
 JJK  H2   C2  N1  116.45  3.000
 JJK  C7   C3  C4  121.39  3.000
 JJK  C7   C3  C2  121.00  3.000
 JJK  C4   C3  C2  117.61  3.000
 JJK  H4   C4  C5  120.38  3.000
 JJK  H4   C4  C3  120.73  3.000
 JJK  C5   C4  C3  118.90  3.000
 JJK  H5   C5  C6  120.21  3.000
 JJK  H5   C5  C4  121.12  3.000
 JJK  C6   C5  C4  118.67  3.000
 JJK  H6   C6  C5  120.35  3.000
 JJK  H6   C6  N1  116.57  3.000
 JJK  C5   C6  N1  123.07  3.000
 JJK  H7   C7  SG  104.76  3.000
 JJK  SG   C7  O7  113.75  3.000
 JJK  H7   C7  O7  112.99  3.000
 JJK  SG   C7  C3  105.21  3.000
 JJK  O7   C7  C3  110.27  3.000
 JJK  H7   C7  C3  109.43  3.000
 JJK  HO7  O7  C7  107.03  3.000
 JJK  HA   CA  CB  109.00  3.000
 JJK  HA   CA  N   110.00  3.000
 JJK  CB   CA  N   110.50  1.700
 JJK  HA   CA  C   109.00  3.000
 JJK  CB   CA  C   110.10  1.900
 JJK  N    CA  C   111.00  2.800
 JJK  HBA  CB  HB  107.04  3.000
 JJK  HBA  CB  SG  105.19  3.000
 JJK  HB   CB  SG  108.52  3.000
 JJK  HBA  CB  CA  109.20  3.000
 JJK  HB   CB  CA  110.73  3.000
 JJK  SG   CB  CA  115.69  3.000
 JJK  CB   SG  C7  102.51  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
 JJK  CONST_01  C4  C3  C2  N1    0.00   0.0  0
 JJK  CONST_02  C4  C5  C6  N1    0.00   0.0  0
 JJK  CONST_03  C5  C6  N1  C2    0.00   0.0  0
 JJK  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 JJK  CONST_05  C6  N1  C2  C3    0.00   0.0  0
 JJK  CONST_06  C6  C5  C4  C3    0.00   0.0  0
 JJK  CONST_07  C7  C3  C2  N1  180.00   0.0  0
 JJK  CONST_08  C7  C3  C4  C5  180.00   0.0  0
 JJK  CONST_09  H5  C5  C6  N1  180.00   0.0  0
 JJK  CONST_10  H6  C6  N1  C2  180.00   0.0  0
 JJK  CONST_11  H4  C4  C3  C2  180.00   0.0  0
 JJK  CONST_12  H2  C2  C3  C4  180.00   0.0  0
 JJK  Var_01    CA  CB  SG  C7   81.87  30.0  2

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
 JJK  chir_01  C7  C3  O7  SG  negativ
 JJK  chir_02  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
 JJK  plan-1  N1   0.020
 JJK  plan-1  C2   0.020
 JJK  plan-1  C3   0.020
 JJK  plan-1  C4   0.020
 JJK  plan-1  C5   0.020
 JJK  plan-1  C6   0.020
 JJK  plan-1  C7   0.020
 JJK  plan-1  H2   0.020
 JJK  plan-1  H4   0.020
 JJK  plan-1  H5   0.020
 JJK  plan-1  H6   0.020
 JJK  plan-2  C    0.020
 JJK  plan-2  O    0.020
 JJK  plan-2  CA   0.020
 JJK  plan-2  OXT  0.020

