# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 13:03:22 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: 6-[(2~{R})-2-azanyl-3,3-bis(oxidanyl)propyl]sulfanyl-3,4-dimethyl-benzene-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(SC[C@H](N)C(O)O)c(O)c(O)c1C
#
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
 QO8  QO8  6-[(2~{R})-2-azanyl-3,3-bis(oxidanyl)propyl]sulfanyl-3,4-dimethyl-benzene-1,2-diol  L-peptide  34  17  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QO8
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
 QO8  C1   C  CR16  0  -0.308  24.0846  65.5079  82.3865
 QO8  C    C  CH1   0   0.283  28.7202  64.2089  81.6453
 QO8  C2   C  CR6   0  -0.263  24.7576  66.4721  81.6393
 QO8  C3   C  CR6   0   0.326  24.3416  66.7637  80.3451
 QO8  O    O  OH1   0  -0.674  28.6850  62.9105  82.1670
 QO8  O3   O  OH1   0  -0.621  24.9279  67.6911  79.5680
 QO8  C4   C  CR6   0   0.259  23.2585  66.0589  79.8071
 QO8  C5   C  CR6   0  -0.052  22.5918  65.0865  80.5488
 QO8  C6   C  CR6   0   0.060  23.0092  64.8099  81.8617
 QO8  C7   C  CH3   0  -0.749  22.3122  63.7790  82.7051
 QO8  N    N  NH2   0  -0.808  27.7329  65.0217  83.7376
 QO8  CA   C  CH1   0  -0.109  27.5764  64.9849  82.2947
 QO8  CB   C  CH2   0  -0.560  27.5402  66.3970  81.7324
 QO8  SG   S  S2    0  -0.033  26.1152  67.3772  82.3233
 QO8  C51  C  CH3   0  -0.788  21.4342  64.3709  79.9103
 QO8  H1   H  HCR6  0   0.254  24.4181  65.3038  83.3964
 QO8  H2   H  HCH1  0   0.196  28.5416  64.1813  80.5601
 QO8  H4   H  HOH1  0   0.457  29.2603  62.3425  81.6436
 QO8  H5   H  HOH1  0   0.465  25.5836  68.1695  80.0996
 QO8  H7   H  HCH3  0   0.244  22.3551  62.7845  82.2571
 QO8  H8   H  HCH3  0   0.252  22.7727  63.7128  83.6898
 QO8  H9   H  HCH3  0   0.244  21.2574  64.0186  82.8526
 QO8  H10  H  HNH2  0   0.346  26.9814  65.5715  84.1363
 QO8  H11  H  HNH2  0   0.348  27.6213  64.0901  84.1159
 QO8  H13  H  HCH1  0   0.229  26.6537  64.4789  81.9715
 QO8  H14  H  HCH2  0   0.274  27.5214  66.3819  80.6419
 QO8  H15  H  HCH2  0   0.287  28.4173  66.9634  82.0476
 QO8  H16  H  HCH3  0   0.258  21.7328  63.8474  78.9980
 QO8  H17  H  HCH3  0   0.277  21.0014  63.6249  80.5705
 QO8  H18  H  HCH3  0   0.258  20.6274  65.0595  79.6439
 QO8  H3   H  HOH1  0   0.459  30.5771  64.5961  81.2524
 QO8  O4   O  OH1   0  -0.626  22.9130  66.3905  78.5433
 QO8  OXT  O  OH1   0  -0.669  29.9279  64.8558  81.9138
 QO8  H6   H  HOH1  0   0.484  22.1557  65.8737  78.2480

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
 QO8  O4   C4   single    1.351  0.020  1.351
 QO8  O3   C3   single    1.345  0.020  1.345
 QO8  C4   C3   aromatic  1.400  0.020  1.400
 QO8  C4   C5   aromatic  1.393  0.020  1.393
 QO8  C51  C5   single    1.503  0.020  1.503
 QO8  C3   C2   aromatic  1.390  0.020  1.390
 QO8  C5   C6   aromatic  1.405  0.020  1.405
 QO8  O    C    single    1.231  0.020  1.231
 QO8  C2   SG   single    1.769  0.020  1.769
 QO8  C2   C1   aromatic  1.393  0.020  1.393
 QO8  C    CA   single    1.525  0.021  1.525
 QO8  CB   SG   single    1.828  0.020  1.828
 QO8  CB   CA   single    1.530  0.020  1.530
 QO8  C6   C1   aromatic  1.385  0.020  1.385
 QO8  C6   C7   single    1.503  0.020  1.503
 QO8  CA   N    single    1.458  0.019  1.458
 QO8  C1   H1   single    0.930  0.020  1.080
 QO8  C    H2   single    0.970  0.020  1.090
 QO8  O    H4   single    0.850  0.020  0.980
 QO8  O3   H5   single    0.850  0.020  0.980
 QO8  O4   H6   single    0.850  0.020  0.980
 QO8  C7   H7   single    0.970  0.020  1.090
 QO8  C7   H8   single    0.970  0.020  1.090
 QO8  C7   H9   single    0.970  0.020  1.090
 QO8  N    H10  single    0.890  0.020  1.040
 QO8  N    H11  single    0.890  0.020  1.040
 QO8  CA   H13  single    0.970  0.020  1.090
 QO8  CB   H14  single    0.970  0.020  1.090
 QO8  CB   H15  single    0.970  0.020  1.090
 QO8  C51  H16  single    0.970  0.020  1.090
 QO8  C51  H17  single    0.970  0.020  1.090
 QO8  C51  H18  single    0.970  0.020  1.090
 QO8  C    OXT  single    1.396  0.020  1.396
 QO8  OXT  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
 QO8  H1   C1   C6   119.83  3.000
 QO8  H1   C1   C2   118.80  3.000
 QO8  C6   C1   C2   121.37  3.000
 QO8  OXT  C    H2   109.98  3.000
 QO8  OXT  C    CA   109.31  3.000
 QO8  H2   C    CA   108.10  3.000
 QO8  OXT  C    O    112.33  3.000
 QO8  H2   C    O    109.90  3.000
 QO8  CA   C    O    120.80  1.700
 QO8  SG   C2   C3   118.83  3.000
 QO8  SG   C2   C1   121.16  3.000
 QO8  C3   C2   C1   119.99  3.000
 QO8  C4   C3   O3   117.56  3.000
 QO8  C4   C3   C2   118.92  3.000
 QO8  O3   C3   C2   123.52  3.000
 QO8  H4   O    C    109.24  3.000
 QO8  H5   O3   C3   108.55  3.000
 QO8  C5   C4   O4   123.15  3.000
 QO8  C5   C4   C3   121.15  3.000
 QO8  O4   C4   C3   115.70  3.000
 QO8  C51  C5   C6   122.13  3.000
 QO8  C6   C5   C4   119.52  3.000
 QO8  C51  C5   C4   118.34  3.000
 QO8  C7   C6   C5   121.43  3.000
 QO8  C7   C6   C1   119.53  3.000
 QO8  C5   C6   C1   119.04  3.000
 QO8  H9   C7   H8   107.44  3.000
 QO8  H9   C7   H7   107.07  3.000
 QO8  H8   C7   H7   107.40  3.000
 QO8  H9   C7   C6   111.92  3.000
 QO8  H8   C7   C6   110.66  3.000
 QO8  H7   C7   C6   112.10  3.000
 QO8  H11  N    H10  105.71  3.000
 QO8  H11  N    CA   109.65  3.000
 QO8  H10  N    CA   108.96  3.000
 QO8  H13  CA   CB   107.36  3.000
 QO8  H13  CA   N    113.19  3.000
 QO8  CB   CA   N    110.50  1.700
 QO8  H13  CA   C    105.63  3.000
 QO8  N    CA   C    111.00  2.800
 QO8  CB   CA   C    110.10  1.900
 QO8  H15  CB   H14  108.06  3.000
 QO8  H15  CB   SG   104.78  3.000
 QO8  H14  CB   SG   108.49  3.000
 QO8  H15  CB   CA   110.88  3.000
 QO8  H14  CB   CA   110.93  3.000
 QO8  SG   CB   CA   113.40  3.000
 QO8  CB   SG   C2   101.47  3.000
 QO8  H18  C51  H17  106.65  3.000
 QO8  H18  C51  H16  107.45  3.000
 QO8  H17  C51  H16  106.69  3.000
 QO8  H18  C51  C5   111.82  3.000
 QO8  H17  C51  C5   112.06  3.000
 QO8  H16  C51  C5   111.83  3.000
 QO8  H6   O4   C4   110.86  3.000
 QO8  H3   OXT  C    109.04  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
 QO8  CONST_01  C4   C3   C2  C1     0.00   0.0  0
 QO8  CONST_02  C4   C5   C6  C1     0.00   0.0  0
 QO8  CONST_03  C5   C4   C3  C2     0.00   0.0  0
 QO8  CONST_04  C5   C6   C1  C2     0.00   0.0  0
 QO8  CONST_05  C6   C5   C4  C3     0.00   0.0  0
 QO8  CONST_06  C6   C1   C2  C3     0.00   0.0  0
 QO8  CONST_07  O3   C3   C2  C1   180.00   0.0  0
 QO8  CONST_08  C51  C5   C6  C1   180.00   0.0  0
 QO8  CONST_09  O4   C4   C3  C2   180.00   0.0  0
 QO8  CONST_10  C7   C6   C1  C2   180.00   0.0  0
 QO8  CONST_11  C51  C5   C4  C3   180.00   0.0  0
 QO8  CONST_12  C5   C4   C3  O3   180.00   0.0  0
 QO8  CONST_13  C6   C5   C4  O4   180.00   0.0  0
 QO8  CONST_14  SG   C2   C3  C4   180.00   0.0  0
 QO8  CONST_15  C7   C6   C5  C4   180.00   0.0  0
 QO8  CONST_16  SG   C2   C1  C6   180.00   0.0  0
 QO8  CONST_17  H1   C1   C2  C3   180.00   0.0  0
 QO8  Var_01    H7   C7   C6  C1  -119.62  30.0  2
 QO8  Var_02    H16  C51  C5  C4    59.28  30.0  2
 QO8  Var_03    CA   CB   SG  C2   -64.09  30.0  2

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
 QO8  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
 QO8  plan-1  C1   0.020
 QO8  plan-1  C2   0.020
 QO8  plan-1  C3   0.020
 QO8  plan-1  O3   0.020
 QO8  plan-1  C4   0.020
 QO8  plan-1  C5   0.020
 QO8  plan-1  C6   0.020
 QO8  plan-1  C7   0.020
 QO8  plan-1  SG   0.020
 QO8  plan-1  C51  0.020
 QO8  plan-1  H1   0.020
 QO8  plan-1  O4   0.020

