# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 22:11:12 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: S-(2,4,6-trinitrophenyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSc1c(cc(cc1[N+]([O-])=O)[N+]([O-])=O)[N+]([O-])=O)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
 TNB  TNB  S-(2,4,6-trinitrophenyl)-L-cysteine  L-peptide  29  22  .  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_TNB
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
 TNB  CA   C  CH1    0  -0.201   7.2140   7.5864  4.0765
 TNB  C    C  C      0   0.410   6.3914   7.1528  2.8274
 TNB  O    O  O      0  -0.584   5.9090   6.0086  2.8278
 TNB  OXT  O  OC    -1  -0.605   6.3295   8.0090  1.9239
 TNB  N    N  NH2    0  -0.782   7.0555   6.6693  5.1837
 TNB  CB   C  CH2    0  -0.598   8.6586   7.7595  3.5977
 TNB  SG   S  S2     0   0.102   9.8225   8.1861  4.9650
 TNB  C1   C  CR6    0  -0.144  10.5989   9.6383  4.3497
 TNB  C2   C  CR6    0   0.294   9.9051  10.7799  3.9390
 TNB  C3   C  CR16   0  -0.257  10.5092  11.8681  3.3474
 TNB  C4   C  CR6    0   0.266  11.8836  11.8526  3.2036
 TNB  C5   C  CR16   0  -0.265  12.6395  10.7742  3.6159
 TNB  C6   C  CR6    0   0.273  11.9858   9.7036  4.1908
 TNB  N2   N  N      1   0.321   8.4621  10.8906  4.1504
 TNB  N4   N  N      1   0.328  12.5478  12.9986  2.5941
 TNB  N6   N  N      1   0.328  12.8185   8.5908  4.6289
 TNB  O21  O  O      0  -0.332   8.0615  10.7406  5.2744
 TNB  O22  O  O     -1  -0.342   7.7866  11.1593  3.1891
 TNB  O41  O  O      0  -0.352  13.7496  12.9661  2.5119
 TNB  O42  O  O     -1  -0.352  11.8513  13.9041  2.2101
 TNB  O61  O  O      0  -0.339  12.6136   8.1576  5.7335
 TNB  O62  O  O     -1  -0.348  13.6604   8.1969  3.8620
 TNB  HA   H  HCH1   0   0.226   6.8312   8.5580  4.3987
 TNB  H    H  HNH2   0   0.338   7.6095   6.9590  5.9806
 TNB  H2   H  HNH2   0   0.333   7.3633   5.7423  4.9202
 TNB  HB2  H  HCH2   0   0.301   9.0374   6.8142  3.2028
 TNB  HB3  H  HCH2   0   0.288   8.7499   8.4954  2.8011
 TNB  H3   H  HCR6   0   0.346   9.9220  12.7205  3.0338
 TNB  H5   H  HCR6   0   0.346  13.7141  10.7626  3.4962

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
 TNB  CA  C    single    1.525  0.021  1.525
 TNB  CA  N    single    1.458  0.019  1.458
 TNB  CA  CB   single    1.530  0.020  1.530
 TNB  CA  HA   single    0.970  0.020  0.970
 TNB  C   O    deloc     1.231  0.020  1.231
 TNB  C   OXT  deloc     1.246  0.020  1.246
 TNB  N   H    single    0.860  0.020  0.860
 TNB  N   H2   single    0.890  0.020  1.040
 TNB  CB  SG   single    1.846  0.020  1.846
 TNB  CB  HB2  single    0.970  0.020  1.090
 TNB  CB  HB3  single    0.970  0.020  1.090
 TNB  SG  C1   single    1.758  0.020  1.758
 TNB  C1  C2   aromatic  1.398  0.020  1.398
 TNB  C1  C6   aromatic  1.398  0.020  1.398
 TNB  C2  C3   aromatic  1.378  0.020  1.378
 TNB  C2  N2   single    1.463  0.020  1.463
 TNB  C3  C4   aromatic  1.382  0.020  1.382
 TNB  C3  H3   single    0.930  0.020  1.080
 TNB  C4  C5   aromatic  1.380  0.020  1.380
 TNB  C4  N4   single    1.458  0.020  1.458
 TNB  C5  C6   aromatic  1.380  0.020  1.380
 TNB  C5  H5   single    0.930  0.020  1.080
 TNB  C6  N6   single    1.457  0.020  1.457
 TNB  N2  O21  double    1.203  0.020  1.203
 TNB  N2  O22  single    1.205  0.020  1.205
 TNB  N4  O41  double    1.205  0.020  1.205
 TNB  N4  O42  single    1.205  0.020  1.205
 TNB  N6  O61  double    1.204  0.020  1.204
 TNB  N6  O62  single    1.205  0.020  1.205

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
 TNB  HA   CA  CB   109.00  3.000
 TNB  HA   CA  N    110.00  3.000
 TNB  CB   CA  N    110.50  1.700
 TNB  HA   CA  C    109.00  3.000
 TNB  CB   CA  C    110.10  1.900
 TNB  N    CA  C    111.00  2.800
 TNB  OXT  C   O    127.88  3.000
 TNB  OXT  C   CA   114.61  3.000
 TNB  O    C   CA   120.80  1.700
 TNB  H2   N   H    107.49  3.000
 TNB  H2   N   CA   110.38  3.000
 TNB  H    N   CA   114.00  3.000
 TNB  HB3  CB  HB2  106.95  3.000
 TNB  HB3  CB  SG   109.45  3.000
 TNB  HB2  CB  SG   104.43  3.000
 TNB  HB3  CB  CA   112.60  3.000
 TNB  HB2  CB  CA   110.02  3.000
 TNB  SG   CB  CA   112.91  3.000
 TNB  C1   SG  CB   102.13  3.000
 TNB  C6   C1  C2   114.90  3.000
 TNB  C6   C1  SG   121.11  3.000
 TNB  C2   C1  SG   123.94  3.000
 TNB  N2   C2  C3   115.78  3.000
 TNB  N2   C2  C1   120.61  3.000
 TNB  C3   C2  C1   123.61  3.000
 TNB  H3   C3  C4   121.23  3.000
 TNB  H3   C3  C2   120.59  3.000
 TNB  C4   C3  C2   118.16  3.000
 TNB  N4   C4  C5   119.31  3.000
 TNB  N4   C4  C3   119.19  3.000
 TNB  C5   C4  C3   121.49  3.000
 TNB  H5   C5  C6   120.58  3.000
 TNB  H5   C5  C4   121.31  3.000
 TNB  C6   C5  C4   118.12  3.000
 TNB  N6   C6  C5   116.55  3.000
 TNB  N6   C6  C1   119.81  3.000
 TNB  C5   C6  C1   123.63  3.000
 TNB  O22  N2  O21  125.91  3.000
 TNB  O22  N2  C2   117.04  3.000
 TNB  O21  N2  C2   117.02  3.000
 TNB  O42  N4  O41  125.09  3.000
 TNB  O42  N4  C4   117.42  3.000
 TNB  O41  N4  C4   117.49  3.000
 TNB  O62  N6  O61  125.81  3.000
 TNB  O62  N6  C6   117.22  3.000
 TNB  O61  N6  C6   116.96  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
 TNB  CONST_01  C4   C3  C2  C1    0.00   0.0  0
 TNB  CONST_02  C4   C5  C6  C1    0.00   0.0  0
 TNB  CONST_03  C5   C6  C1  C2    0.00   0.0  0
 TNB  CONST_04  C5   C4  C3  C2    0.00   0.0  0
 TNB  CONST_05  C6   C1  C2  C3    0.00   0.0  0
 TNB  CONST_06  C6   C5  C4  C3    0.00   0.0  0
 TNB  CONST_07  C3   C2  C1  SG  180.00   0.0  0
 TNB  CONST_08  C5   C6  C1  SG  180.00   0.0  0
 TNB  CONST_09  N6   C6  C1  C2  180.00   0.0  0
 TNB  CONST_10  N4   C4  C3  C2  180.00   0.0  0
 TNB  CONST_11  N2   C2  C3  C4  180.00   0.0  0
 TNB  CONST_12  N6   C6  C5  C4  180.00   0.0  0
 TNB  CONST_13  N2   C2  C1  C6  180.00   0.0  0
 TNB  CONST_14  N4   C4  C5  C6  180.00   0.0  0
 TNB  CONST_15  H3   C3  C2  C1  180.00   0.0  0
 TNB  CONST_16  H5   C5  C6  C1  180.00   0.0  0
 TNB  CONST_23  O41  N4  C4  C3  180.00   0.0  0
 TNB  CONST_24  O42  N4  C4  C3    0.00   0.0  0
 TNB  CONST_25  O41  N4  C4  C5    0.00   0.0  0
 TNB  CONST_26  O42  N4  C4  C5  180.00   0.0  0
 TNB  Var_01    C2   C1  SG  CB   55.51  30.0  2
 TNB  Var_02    HB2  CB  SG  C1  113.85  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
 TNB  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
 TNB  plan-1  SG   0.020
 TNB  plan-1  C1   0.020
 TNB  plan-1  C2   0.020
 TNB  plan-1  C3   0.020
 TNB  plan-1  C4   0.020
 TNB  plan-1  C5   0.020
 TNB  plan-1  C6   0.020
 TNB  plan-1  N2   0.020
 TNB  plan-1  N4   0.020
 TNB  plan-1  N6   0.020
 TNB  plan-1  H3   0.020
 TNB  plan-1  H5   0.020
 TNB  plan-2  C2   0.020
 TNB  plan-2  N2   0.020
 TNB  plan-2  O21  0.020
 TNB  plan-2  O22  0.020
 TNB  plan-3  C4   0.020
 TNB  plan-3  N4   0.020
 TNB  plan-3  O41  0.020
 TNB  plan-3  O42  0.020
 TNB  plan-4  C6   0.020
 TNB  plan-4  N6   0.020
 TNB  plan-4  O61  0.020
 TNB  plan-4  O62  0.020
 TNB  plan-5  CA   0.020
 TNB  plan-5  C    0.020
 TNB  plan-5  O    0.020
 TNB  plan-5  OXT  0.020

