# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:17:37 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: S-(pyridin-3-ylcarbonyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSC(=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
 JJJ  JJJ  S-(pyridin-3-ylcarbonyl)-L-cysteine  L-peptide  24  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_JJJ
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
 JJJ  C    C  C      0   0.425  -51.7418  24.4690  -10.8555
 JJJ  N    N  NH2    0  -0.806  -54.2081  24.1990  -10.8318
 JJJ  O    O  O      0  -0.597  -50.6980  24.3253  -11.5182
 JJJ  N1   N  N      0  -0.395  -57.8522  20.8283  -15.3936
 JJJ  C2   C  CR16   0  -0.066  -56.7713  21.4307  -14.9208
 JJJ  C3   C  CR6    0  -0.080  -56.7292  22.7825  -14.5845
 JJJ  C4   C  CR16   0  -0.146  -57.8847  23.5361  -14.7758
 JJJ  C5   C  CR16   0  -0.314  -59.0176  22.9104  -15.2616
 JJJ  C6   C  CR16   0  -0.049  -58.9520  21.5551  -15.5520
 JJJ  C7   C  C      0   0.199  -55.5105  23.4581  -14.0610
 JJJ  O7   O  O      0  -0.374  -55.3803  24.6564  -14.1052
 JJJ  CA   C  CH1    0  -0.207  -52.9661  23.6161  -11.3017
 JJJ  CB   C  CH2    0  -0.543  -52.9820  23.4610  -12.8175
 JJJ  SG   S  S2     0  -0.007  -54.3179  22.3572  -13.3690
 JJJ  OXT  O  OC    -1  -0.593  -51.9039  25.1810   -9.8470
 JJJ  HN   H  HNH2   0   0.334  -54.9074  23.4807  -10.6990
 JJJ  HNA  H  HNH2   0   0.339  -54.0284  24.6119   -9.9258
 JJJ  H4   H  HCR6   0   0.284  -57.9000  24.5914  -14.5377
 JJJ  H5   H  HCR6   0   0.280  -59.9375  23.4575  -15.4131
 JJJ  H6   H  HCR6   0   0.276  -59.8246  21.0353  -15.9311
 JJJ  HA   H  HCH1   0   0.213  -52.7871  22.6144  -10.8742
 JJJ  HB   H  HCH2   0   0.277  -53.1141  24.4228  -13.3135
 JJJ  HBA  H  HCH2   0   0.278  -52.0592  23.0092  -13.1731
 JJJ  H2   H  HCR6   0   0.272  -55.8899  20.8060  -14.8223

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
 JJJ  C   O    deloc     1.231  0.020  1.231
 JJJ  C   OXT  deloc     1.245  0.020  1.245
 JJJ  N   HN   single    0.890  0.020  1.040
 JJJ  N   HNA  single    0.890  0.020  1.040
 JJJ  N1  C6   aromatic  1.328  0.020  1.328
 JJJ  N1  C2   aromatic  1.325  0.020  1.325
 JJJ  C2  C3   aromatic  1.394  0.020  1.394
 JJJ  C2  H2   single    0.930  0.020  1.080
 JJJ  C3  C4   aromatic  1.393  0.020  1.393
 JJJ  C3  C7   single    1.488  0.020  1.488
 JJJ  C4  H4   single    0.930  0.020  1.080
 JJJ  C5  C4   aromatic  1.382  0.020  1.382
 JJJ  C5  H5   single    0.930  0.020  1.080
 JJJ  C6  C5   aromatic  1.388  0.020  1.388
 JJJ  C6  H6   single    0.930  0.020  1.080
 JJJ  C7  SG   single    1.764  0.020  1.764
 JJJ  O7  C7   double    1.206  0.020  1.206
 JJJ  CA  C    single    1.525  0.021  1.525
 JJJ  CA  N    single    1.458  0.019  1.458
 JJJ  CA  HA   single    0.970  0.020  0.970
 JJJ  CB  CA   single    1.530  0.020  1.530
 JJJ  CB  HB   single    0.970  0.020  1.090
 JJJ  CB  HBA  single    0.970  0.020  1.090
 JJJ  SG  CB   single    1.819  0.020  1.819

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
 JJJ  OXT  C   CA  116.29  3.000
 JJJ  CA   C   O   120.80  1.700
 JJJ  OXT  C   O   127.33  3.000
 JJJ  HNA  N   HN  107.17  3.000
 JJJ  HNA  N   CA  107.58  3.000
 JJJ  HN   N   CA  110.44  3.000
 JJJ  C6   N1  C2  118.00  3.000
 JJJ  H2   C2  C3  120.80  3.000
 JJJ  H2   C2  N1  115.69  3.000
 JJJ  C3   C2  N1  123.50  3.000
 JJJ  C7   C3  C4  118.82  3.000
 JJJ  C7   C3  C2  123.36  3.000
 JJJ  C4   C3  C2  117.81  3.000
 JJJ  H4   C4  C5  120.48  3.000
 JJJ  C5   C4  C3  118.90  3.000
 JJJ  H4   C4  C3  120.61  3.000
 JJJ  H5   C5  C6  120.35  3.000
 JJJ  C6   C5  C4  118.49  3.000
 JJJ  H5   C5  C4  121.17  3.000
 JJJ  H6   C6  C5  120.23  3.000
 JJJ  H6   C6  N1  116.48  3.000
 JJJ  C5   C6  N1  123.29  3.000
 JJJ  SG   C7  O7  124.15  3.000
 JJJ  O7   C7  C3  121.76  3.000
 JJJ  SG   C7  C3  114.09  3.000
 JJJ  HA   CA  CB  109.00  3.000
 JJJ  CB   CA  N   110.50  1.700
 JJJ  HA   CA  N   110.00  3.000
 JJJ  CB   CA  C   110.10  1.900
 JJJ  HA   CA  C   109.00  3.000
 JJJ  N    CA  C   111.00  2.800
 JJJ  HBA  CB  HB  108.70  3.000
 JJJ  HBA  CB  SG  105.79  3.000
 JJJ  HB   CB  SG  107.97  3.000
 JJJ  SG   CB  CA  111.78  3.000
 JJJ  HBA  CB  CA  111.02  3.000
 JJJ  HB   CB  CA  111.35  3.000
 JJJ  CB   SG  C7  103.70  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
 JJJ  CONST_01  C4  C5  C6  N1    0.00   0.0  0
 JJJ  CONST_02  C4  C3  C2  N1    0.00   0.0  0
 JJJ  CONST_03  C5  C6  N1  C2    0.00   0.0  0
 JJJ  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 JJJ  CONST_05  C6  N1  C2  C3    0.00   0.0  0
 JJJ  CONST_06  C6  C5  C4  C3    0.00   0.0  0
 JJJ  CONST_07  C7  C3  C2  N1  180.00   0.0  0
 JJJ  CONST_08  C7  C3  C4  C5  180.00   0.0  0
 JJJ  CONST_09  H5  C5  C6  N1  180.00   0.0  0
 JJJ  CONST_10  H6  C6  N1  C2  180.00   0.0  0
 JJJ  CONST_11  H4  C4  C3  C2  180.00   0.0  0
 JJJ  CONST_12  H2  C2  C3  C4  180.00   0.0  0
 JJJ  Var_01    SG  C7  C3  C2  -20.43  30.0  2
 JJJ  Var_02    CA  CB  SG  C7  105.81  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
 JJJ  chir_01  CA  C  N  CB  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
 JJJ  plan-1  N1   0.020
 JJJ  plan-1  C2   0.020
 JJJ  plan-1  C3   0.020
 JJJ  plan-1  C4   0.020
 JJJ  plan-1  C5   0.020
 JJJ  plan-1  C6   0.020
 JJJ  plan-1  C7   0.020
 JJJ  plan-1  H4   0.020
 JJJ  plan-1  H5   0.020
 JJJ  plan-1  H6   0.020
 JJJ  plan-1  H2   0.020
 JJJ  plan-2  C    0.020
 JJJ  plan-2  O    0.020
 JJJ  plan-2  CA   0.020
 JJJ  plan-2  OXT  0.020
 JJJ  plan-3  C3   0.020
 JJJ  plan-3  C7   0.020
 JJJ  plan-3  O7   0.020
 JJJ  plan-3  SG   0.020

