# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 20:13:10 2022
#   Inital geometry file: a 38 line input string
#   Ligand name: D-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CS)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
 DCY  DCY  'D-cysteine               '  D-peptide  13  7  .  2016-04-22  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_DCY
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
 DCY  N    N  NH2    0  -0.801  10.4876  -11.0800  23.1105
 DCY  CA   C  CH1    0  -0.217   9.8953   -9.7559  23.1593
 DCY  C    C  C      0   0.416   9.7159   -9.2691  24.6233
 DCY  O    O  O      0  -0.603   9.4946   -8.0531  24.7740
 DCY  CB   C  CH2    0  -0.524  10.7315   -8.7942  22.3327
 DCY  SG   S  S2     0  -0.273  12.4698   -8.8821  22.8946
 DCY  OXT  O  OC    -1  -0.599   9.7547  -10.1418  25.5120
 DCY  H    H  HNH2   0   0.334  10.2295  -11.5532  22.2547
 DCY  H2   H  HNH2   0   0.338  10.1246  -11.6230  23.8821
 DCY  HA   H  HCH1   0   0.220   8.8834   -9.7338  22.7174
 DCY  HB2  H  HCH2   0   0.251  10.6886   -9.0532  21.2736
 DCY  HB3  H  HCH2   0   0.260  10.3670   -7.7770  22.4511
 DCY  HG   H  HSH1   0   0.198  12.8128   -7.6278  22.5773

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
 DCY  N   CA   single  1.458  0.019  1.458
 DCY  N   H    single  0.860  0.020  0.860
 DCY  N   H2   single  0.890  0.020  1.040
 DCY  CA  C    single  1.525  0.021  1.525
 DCY  CA  CB   single  1.521  0.033  1.521
 DCY  CA  HA   single  0.970  0.020  0.970
 DCY  C   O    deloc   1.231  0.020  1.231
 DCY  C   OXT  deloc   1.246  0.020  1.246
 DCY  CB  SG   single  1.829  0.020  1.829
 DCY  CB  HB2  single  0.970  0.020  1.090
 DCY  CB  HB3  single  0.970  0.020  1.090
 DCY  SG  HG   single  1.200  0.020  1.300

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
 DCY  H2   N   H    107.63  3.000
 DCY  H2   N   CA   108.53  3.000
 DCY  H    N   CA   114.00  3.000
 DCY  HA   CA  CB   109.00  3.000
 DCY  HA   CA  C    110.00  3.000
 DCY  CB   CA  C    110.50  1.500
 DCY  HA   CA  N    110.00  3.000
 DCY  CB   CA  N    110.40  1.500
 DCY  C    CA  N    111.00  2.800
 DCY  OXT  C   O    127.10  3.000
 DCY  OXT  C   CA   120.80  1.700
 DCY  O    C   CA   120.80  1.700
 DCY  HB3  CB  HB2  108.34  3.000
 DCY  HB3  CB  SG   109.28  3.000
 DCY  HB2  CB  SG   108.91  3.000
 DCY  HB3  CB  CA   110.41  3.000
 DCY  HB2  CB  CA   110.87  3.000
 DCY  SG   CB  CA   109.00  3.000
 DCY  HG   SG  CB    97.22  3.000

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
 DCY  chir_01  CA  N  C  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
 DCY  plan-1  CA   0.020
 DCY  plan-1  C    0.020
 DCY  plan-1  O    0.020
 DCY  plan-1  OXT  0.020

