# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 06:36:36 2022
#   Inital geometry file: a 52 line input string
#   Ligand name: S-(2-hydroxyethyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCCO)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
 OCY  OCY  S-(2-hydroxyethyl)-L-cysteine  L-peptide  20  10  .  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_OCY
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
 OCY  N    N  NH2    0  -0.797  49.7036  46.4459  61.7320
 OCY  CA   C  CH1    0  -0.193  49.4915  47.2019  60.5114
 OCY  CB   C  CH2    0  -0.543  50.5155  46.8296  59.4491
 OCY  SG   S  S2     0  -0.052  50.3545  45.1322  58.8170
 OCY  CD   C  CH2    0  -0.587  51.4821  44.2129  59.9051
 OCY  CE   C  CH2    0  -0.137  52.9448  44.3346  59.5445
 OCY  OZ   O  OH1    0  -0.663  53.1610  43.7748  58.2710
 OCY  C    C  C      0   0.414  48.0402  47.0372  59.9886
 OCY  O    O  O      0  -0.603  47.8423  47.3638  58.8031
 OCY  OXT  O  OC    -1  -0.600  47.1903  46.6376  60.8087
 OCY  H    H  HNH2   0   0.336  48.8461  46.4636  62.2678
 OCY  H2   H  HNH2   0   0.331  50.4222  46.8818  62.2945
 OCY  HA   H  HCH1   0   0.205  49.6183  48.2883  60.6745
 OCY  HB2  H  HCH2   0   0.255  50.4089  47.4872  58.5879
 OCY  HB3  H  HCH2   0   0.254  51.5339  46.9640  59.8223
 OCY  HD2  H  HCH2   0   0.270  51.3174  44.5508  60.9272
 OCY  HD3  H  HCH2   0   0.262  51.1703  43.1669  59.8549
 OCY  HE2  H  HCH2   0   0.197  53.2480  45.3894  59.5835
 OCY  HE3  H  HCH2   0   0.201  53.5265  43.8135  60.3180
 OCY  HZ   H  HOH1   0   0.451  54.0889  43.8890  58.0473

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
 OCY  N   CA   single  1.458  0.019  1.458
 OCY  N   H    single  0.860  0.020  0.860
 OCY  N   H2   single  0.890  0.020  1.040
 OCY  CA  CB   single  1.530  0.020  1.530
 OCY  CA  C    single  1.525  0.021  1.525
 OCY  CA  HA   single  0.970  0.020  0.970
 OCY  CB  SG   single  1.818  0.020  1.818
 OCY  CB  HB2  single  0.970  0.020  1.090
 OCY  CB  HB3  single  0.970  0.020  1.090
 OCY  SG  CD   single  1.817  0.020  1.817
 OCY  CD  CE   single  1.511  0.020  1.511
 OCY  CD  HD2  single  0.970  0.020  1.090
 OCY  CD  HD3  single  0.970  0.020  1.090
 OCY  CE  OZ   single  1.408  0.020  1.408
 OCY  CE  HE2  single  0.970  0.020  1.090
 OCY  CE  HE3  single  0.970  0.020  1.090
 OCY  OZ  HZ   single  0.850  0.020  0.980
 OCY  C   O    deloc   1.231  0.020  1.231
 OCY  C   OXT  deloc   1.247  0.020  1.247

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
 OCY  H2   N   H    107.47  3.000
 OCY  H2   N   CA   110.32  3.000
 OCY  H    N   CA   114.00  3.000
 OCY  HA   CA  C    109.00  3.000
 OCY  HA   CA  CB   109.00  3.000
 OCY  C    CA  CB   110.10  1.900
 OCY  HA   CA  N    110.00  3.000
 OCY  C    CA  N    111.00  2.800
 OCY  CB   CA  N    110.50  1.700
 OCY  HB3  CB  HB2  106.68  3.000
 OCY  HB3  CB  SG   108.42  3.000
 OCY  HB2  CB  SG   106.27  3.000
 OCY  HB3  CB  CA   111.02  3.000
 OCY  HB2  CB  CA   109.79  3.000
 OCY  SG   CB  CA   114.30  3.000
 OCY  CD   SG  CB   102.08  3.000
 OCY  HD3  CD  HD2  107.28  3.000
 OCY  HD3  CD  CE   110.01  3.000
 OCY  HD2  CD  CE   110.20  3.000
 OCY  HD3  CD  SG   106.25  3.000
 OCY  HD2  CD  SG   108.14  3.000
 OCY  CE   CD  SG   114.64  3.000
 OCY  HE3  CE  HE2  106.52  3.000
 OCY  HE3  CE  OZ   111.52  3.000
 OCY  HE2  CE  OZ   111.81  3.000
 OCY  HE3  CE  CD   107.82  3.000
 OCY  HE2  CE  CD   109.64  3.000
 OCY  OZ   CE  CD   109.41  3.000
 OCY  HZ   OZ  CE   108.15  3.000
 OCY  OXT  C   O    127.00  3.000
 OCY  OXT  C   CA   116.75  3.000
 OCY  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
 OCY  Var_01  CE   CD  SG  CB  -79.29  30.0  3
 OCY  Var_02  OZ   CE  CD  SG  -63.39  30.0  3
 OCY  Var_03  HB2  CB  SG  CD  146.36  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
 OCY  chir_01  CA  N  CB  C  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
 OCY  plan-1  CA   0.020
 OCY  plan-1  C    0.020
 OCY  plan-1  O    0.020
 OCY  plan-1  OXT  0.020

