# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 14:48:56 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: S-[(1S)-1-hydroxy-1-(hydroxyamino)ethyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@](O)(NO)SC[C@H](N)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
 C3Y  C3Y  S-[(1S)-1-hydroxy-1-(hydroxyamino)ethyl]-L-cysteine  L-peptide  23  12  .  2012-08-28  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C3Y
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
 C3Y  N     N  NH2    0  -0.790  32.2140  39.8046  22.7435
 C3Y  CA    C  CH1    0  -0.184  33.5669  40.2676  23.0617
 C3Y  C     C  C      0   0.448  33.5429  41.3575  24.1534
 C3Y  O     O  O      0  -0.573  33.4991  40.9656  25.3264
 C3Y  CB    C  CH2    0  -0.562  34.2448  40.6785  21.7627
 C3Y  SG    S  S2     0  -0.111  35.9474  41.2425  22.0351
 C3Y  C1    C  CH3    0  -0.680  36.9047  43.7257  22.6074
 C3Y  O2    O  OH1    0  -0.673  34.6340  43.6076  21.7823
 C3Y  N1    N  NH1    0  -0.346  36.3373  43.3786  20.3100
 C3Y  O3    O  OH1    0  -0.574  35.6127  42.6309  19.3758
 C3Y  C2    C  CT     0   0.246  35.8945  43.0986  21.6510
 C3Y  OXT   O  OC    -1  -0.622  33.4788  42.5682  23.7919
 C3Y  HN1   H  HNH2   0   0.344  31.7781  39.4361  23.5802
 C3Y  HN2   H  HNH2   0   0.335  31.6468  40.5970  22.4622
 C3Y  HA    H  HCH1   0   0.215  34.1078  39.4078  23.4673
 C3Y  HBC1  H  HCH2   0   0.263  34.2727  39.8241  21.0854
 C3Y  HBC2  H  HCH2   0   0.259  33.6895  41.4676  21.2560
 C3Y  H1C1  H  HCH3   0   0.230  37.8882  43.2587  22.5314
 C3Y  H1C2  H  HCH3   0   0.242  37.0137  44.7899  22.3910
 C3Y  H1C3  H  HCH3   0   0.245  36.5585  43.6151  23.6334
 C3Y  H1    H  HNH1   0   0.358  37.3001  43.0772  20.2052
 C3Y  H3    H  HOH1   0   0.457  35.0725  43.2836  18.9201
 C3Y  H5    H  HOH1   0   0.472  34.1711  43.1937  22.5793

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
 C3Y  O2  H5    single  0.850  0.020  0.980
 C3Y  N   CA    single  1.458  0.019  1.458
 C3Y  CA  C     single  1.525  0.021  1.525
 C3Y  C   O     deloc   1.231  0.020  1.231
 C3Y  CA  CB    single  1.530  0.020  1.530
 C3Y  CB  SG    single  1.814  0.020  1.814
 C3Y  N1  O3    single  1.399  0.020  1.399
 C3Y  SG  C2    single  1.896  0.020  1.896
 C3Y  C1  C2    single  1.526  0.020  1.526
 C3Y  O2  C2    single  1.366  0.020  1.366
 C3Y  N1  C2    single  1.440  0.020  1.440
 C3Y  C   OXT   deloc   1.265  0.020  1.265
 C3Y  N   HN1   single  0.890  0.020  1.040
 C3Y  N   HN2   single  0.890  0.020  1.040
 C3Y  CA  HA    single  0.970  0.020  0.970
 C3Y  CB  HBC1  single  0.970  0.020  1.090
 C3Y  CB  HBC2  single  0.970  0.020  1.090
 C3Y  C1  H1C1  single  0.970  0.020  1.090
 C3Y  C1  H1C2  single  0.970  0.020  1.090
 C3Y  C1  H1C3  single  0.970  0.020  1.090
 C3Y  N1  H1    single  0.890  0.020  1.040
 C3Y  O3  H3    single  0.850  0.020  0.980

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
 C3Y  HN2   N   HN1   105.82  3.000
 C3Y  HN2   N   CA    109.25  3.000
 C3Y  HN1   N   CA    109.45  3.000
 C3Y  HA    CA  CB    109.00  3.000
 C3Y  HA    CA  C     109.00  3.000
 C3Y  CB    CA  C     110.10  1.900
 C3Y  HA    CA  N     110.00  3.000
 C3Y  CB    CA  N     110.50  1.700
 C3Y  C     CA  N     111.00  2.800
 C3Y  OXT   C   O     124.91  3.000
 C3Y  OXT   C   CA    118.33  3.000
 C3Y  O     C   CA    120.80  1.700
 C3Y  HBC2  CB  HBC1  106.95  3.000
 C3Y  HBC2  CB  SG    108.84  3.000
 C3Y  HBC1  CB  SG    108.23  3.000
 C3Y  HBC2  CB  CA    111.43  3.000
 C3Y  HBC1  CB  CA    109.27  3.000
 C3Y  SG    CB  CA    111.96  3.000
 C3Y  C2    SG  CB    104.35  3.000
 C3Y  H1C3  C1  H1C2  108.52  3.000
 C3Y  H1C3  C1  H1C1  107.99  3.000
 C3Y  H1C2  C1  H1C1  108.26  3.000
 C3Y  H1C3  C1  C2    109.78  3.000
 C3Y  H1C2  C1  C2    110.04  3.000
 C3Y  H1C1  C1  C2    112.16  3.000
 C3Y  H5    O2  C2    110.24  3.000
 C3Y  H1    N1  C2    109.30  3.000
 C3Y  H1    N1  O3    105.30  3.000
 C3Y  C2    N1  O3    111.03  3.000
 C3Y  H3    O3  N1    104.16  3.000
 C3Y  N1    C2  O2    107.51  3.000
 C3Y  N1    C2  C1    107.47  3.000
 C3Y  O2    C2  C1    113.43  3.000
 C3Y  N1    C2  SG    111.75  3.000
 C3Y  O2    C2  SG    111.78  3.000
 C3Y  C1    C2  SG    104.88  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
 C3Y  Var_01  HBC1  CB  SG  C2  127.82  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
 C3Y  chir_01  CA  N   C   CB  positiv
 C3Y  chir_02  C2  O2  N1  C1  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
 C3Y  plan-1  CA   0.020
 C3Y  plan-1  C    0.020
 C3Y  plan-1  O    0.020
 C3Y  plan-1  OXT  0.020

