# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 17:49:03 2022
#   Inital geometry file: a 49 line input string
#   Ligand name: S-carbamoyl-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSC(N)=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
 QCS  QCS  'S-carbamoyl-L-cysteine   '  L-peptide  17  10  .  2016-04-26  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_QCS
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
 QCS  N    N  NH2    0  -0.813  5.5640  18.9577   9.3703
 QCS  CA   C  CH1    0  -0.240  6.4743  19.4665   8.3582
 QCS  CB   C  CH2    0  -0.511  7.7440  20.0193   8.9933
 QCS  SG   S  S2     0  -0.071  7.3021  21.3752  10.1236
 QCS  CD   C  C      0   0.412  8.9221  21.9448  10.6183
 QCS  NE2  N  NH2    0  -0.799  8.8608  22.9438  11.5107
 QCS  OE1  O  O      0  -0.456  9.9494  21.4660  10.1856
 QCS  C    C  C      0   0.430  6.8355  18.3563   7.3239
 QCS  O    O  O      0  -0.595  7.8645  18.5434   6.6506
 QCS  OXT  O  OC    -1  -0.592  6.0388  17.4030   7.2388
 QCS  H    H  HNH2   0   0.335  4.9149  19.6761   9.6614
 QCS  H2   H  HNH2   0   0.340  5.0166  18.2238   8.9382
 QCS  H4   H  HCH1   0   0.217  6.0216  20.2792   7.7654
 QCS  H5   H  HCH2   0   0.258  8.2549  19.2418   9.5621
 QCS  H6   H  HCH2   0   0.266  8.4137  20.4054   8.2302
 QCS  H7   H  HNH2   0   0.407  9.7124  23.3615  11.8496
 QCS  H8   H  HNH2   0   0.413  7.9909  23.3171  11.8514

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
 QCS  O    C    deloc   1.231  0.020  1.231
 QCS  C    OXT  deloc   1.245  0.020  1.245
 QCS  C    CA   single  1.525  0.021  1.525
 QCS  CA   CB   single  1.530  0.020  1.530
 QCS  CA   N    single  1.458  0.019  1.458
 QCS  CB   SG   single  1.820  0.020  1.820
 QCS  OE1  CD   double  1.213  0.020  1.213
 QCS  SG   CD   single  1.787  0.020  1.787
 QCS  CD   NE2  single  1.341  0.020  1.341
 QCS  N    H    single  0.860  0.020  0.860
 QCS  N    H2   single  0.890  0.020  1.040
 QCS  CA   H4   single  0.970  0.020  1.090
 QCS  CB   H5   single  0.970  0.020  1.090
 QCS  CB   H6   single  0.970  0.020  1.090
 QCS  NE2  H7   single  0.860  0.020  1.020
 QCS  NE2  H8   single  0.860  0.020  1.020

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
 QCS  H2   N    H    106.91  3.000
 QCS  H2   N    CA   107.17  3.000
 QCS  H    N    CA   114.00  3.000
 QCS  H4   CA   C    105.25  3.000
 QCS  H4   CA   CB   107.38  3.000
 QCS  C    CA   CB   110.10  1.900
 QCS  H4   CA   N    112.03  3.000
 QCS  CB   CA   N    110.50  1.700
 QCS  C    CA   N    111.00  2.800
 QCS  H6   CB   H5   109.34  3.000
 QCS  H6   CB   SG   108.74  3.000
 QCS  H5   CB   SG   108.73  3.000
 QCS  H6   CB   CA   110.48  3.000
 QCS  H5   CB   CA   110.44  3.000
 QCS  SG   CB   CA   109.08  3.000
 QCS  CD   SG   CB   100.91  3.000
 QCS  OE1  CD   NE2  124.76  3.000
 QCS  NE2  CD   SG   112.34  3.000
 QCS  OE1  CD   SG   122.89  3.000
 QCS  H8   NE2  H7   117.59  3.000
 QCS  H8   NE2  CD   122.78  3.000
 QCS  H7   NE2  CD   119.62  3.000
 QCS  OXT  C    O    127.40  3.000
 QCS  OXT  C    CA   116.24  3.000
 QCS  O    C    CA   120.80  1.700

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
 QCS  CONST_01  H7   NE2  CD  OE1    0.00   0.0  0
 QCS  CONST_02  H8   NE2  CD  OE1  180.00   0.0  0
 QCS  Var_01    OE1  CD   SG  CB     1.86  30.0  3
 QCS  Var_02    H5   CB   SG  CD    64.35  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
 QCS  chir_01  CA  C  CB  N  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
 QCS  plan-1  SG   0.020
 QCS  plan-1  CD   0.020
 QCS  plan-1  NE2  0.020
 QCS  plan-1  OE1  0.020
 QCS  plan-1  H7   0.020
 QCS  plan-1  H8   0.020
 QCS  plan-2  CA   0.020
 QCS  plan-2  C    0.020
 QCS  plan-2  O    0.020
 QCS  plan-2  OXT  0.020

