# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 12:20:01 2021
#   Inital geometry file: a 80 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[2,3-dimethyl-5,6-bis(oxidanyl)phenyl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(O)c(O)c(SC[C@H](N)C(O)=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
 QO2  QO2  '(2~{R})-2-azanyl-3-[2,3-dimethyl-5,6-bis(oxidanyl)phenyl]sulfanyl-propanoic acid'  L-peptide  32  17  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QO2
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
 QO2  N    N  NH2   0  -0.796  27.5466  64.9858  83.8152
 QO2  C    C  C     0   0.544  28.5544  64.1497  81.7283
 QO2  C4   C  CR6   0   0.316  24.8505  67.3027  80.0737
 QO2  C5   C  CR6   0  -0.294  24.9174  66.8952  81.4066
 QO2  C6   C  CR6   0   0.059  23.9406  66.0582  81.9682
 QO2  O    O  O     0  -0.448  28.4838  63.7635  80.5872
 QO2  C3   C  CR6   0   0.302  23.8146  66.8396  79.2615
 QO2  C2   C  CR16  0  -0.394  22.8703  65.9886  79.8061
 QO2  C1   C  CR6   0   0.061  22.9130  65.5937  81.1418
 QO2  O3   O  OH1   0  -0.637  23.7129  67.1962  77.9628
 QO2  O4   O  OH1   0  -0.636  25.7499  68.1255  79.4967
 QO2  C61  C  CH3   0  -0.749  24.0039  65.6482  83.4121
 QO2  CA   C  CH1   0  -0.173  27.4615  64.9851  82.3739
 QO2  CB   C  CH2   0  -0.571  27.6179  66.4086  81.8348
 QO2  SG   S  S2    0  -0.018  26.2765  67.5290  82.3571
 QO2  H1   H  HNH2  0   0.359  26.8507  65.6229  84.1831
 QO2  H2   H  HNH2  0   0.359  27.3088  64.0729  84.1825
 QO2  H5   H  HCH3  0   0.244  22.2688  63.7591  82.0908
 QO2  H6   H  HCH3  0   0.245  21.2407  65.1385  82.4368
 QO2  H7   H  HCH3  0   0.252  21.1728  64.3681  80.8580
 QO2  H8   H  HCR6  0   0.259  22.0729  65.6262  79.1676
 QO2  H9   H  HOH1  0   0.472  24.4005  67.8326  77.7343
 QO2  H10  H  HOH1  0   0.471  26.3044  68.5321  80.1813
 QO2  H11  H  HCH3  0   0.244  24.6542  64.7813  83.5521
 QO2  H12  H  HCH3  0   0.251  24.3907  66.4451  84.0444
 QO2  H13  H  HCH3  0   0.258  23.0229  65.3751  83.7949
 QO2  H14  H  HCH1  0   0.262  26.5192  64.5804  81.9762
 QO2  H15  H  HCH2  0   0.293  27.6733  66.4098  80.7471
 QO2  H16  H  HCH2  0   0.300  28.5337  66.8605  82.2215
 QO2  H3   H  HOH1  0   0.482  30.2508  63.3963  82.0382
 QO2  OXT  O  OH1   0  -0.573  29.5884  63.9170  82.5175
 QO2  C7   C  CH3   0  -0.745  21.8466  64.6681  81.6593

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
 QO2  O3   C3   single    1.351  0.020  1.351
 QO2  C3   C2   aromatic  1.383  0.020  1.383
 QO2  C3   C4   aromatic  1.395  0.020  1.395
 QO2  O4   C4   single    1.349  0.020  1.349
 QO2  C2   C1   aromatic  1.393  0.020  1.393
 QO2  C4   C5   aromatic  1.395  0.020  1.395
 QO2  O    C    double    1.231  0.020  1.231
 QO2  C1   C7   single    1.504  0.020  1.504
 QO2  C1   C6   aromatic  1.398  0.020  1.398
 QO2  C5   C6   aromatic  1.404  0.020  1.404
 QO2  C5   SG   single    1.776  0.020  1.776
 QO2  C    CA   single    1.525  0.021  1.525
 QO2  CB   SG   single    1.824  0.020  1.824
 QO2  CB   CA   single    1.530  0.020  1.530
 QO2  C6   C61  single    1.502  0.020  1.502
 QO2  CA   N    single    1.458  0.019  1.458
 QO2  N    H1   single    0.890  0.020  1.040
 QO2  N    H2   single    0.890  0.020  1.040
 QO2  C7   H5   single    0.970  0.020  1.090
 QO2  C7   H6   single    0.970  0.020  1.090
 QO2  C7   H7   single    0.970  0.020  1.090
 QO2  C2   H8   single    0.930  0.020  1.080
 QO2  O3   H9   single    0.850  0.020  0.980
 QO2  O4   H10  single    0.850  0.020  0.980
 QO2  C61  H11  single    0.970  0.020  1.090
 QO2  C61  H12  single    0.970  0.020  1.090
 QO2  C61  H13  single    0.970  0.020  1.090
 QO2  CA   H14  single    0.970  0.020  1.090
 QO2  CB   H15  single    0.970  0.020  1.090
 QO2  CB   H16  single    0.970  0.020  1.090
 QO2  C    OXT  single    1.321  0.020  1.321
 QO2  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
 QO2  H2   N    H1   105.91  3.000
 QO2  H2   N    CA   110.36  3.000
 QO2  H1   N    CA   108.81  3.000
 QO2  OXT  C    CA   113.95  3.000
 QO2  OXT  C    O    123.65  3.000
 QO2  CA   C    O    120.80  1.700
 QO2  O4   C4   C3   116.65  3.000
 QO2  O4   C4   C5   123.70  3.000
 QO2  C3   C4   C5   119.64  3.000
 QO2  SG   C5   C6   122.10  3.000
 QO2  SG   C5   C4   116.35  3.000
 QO2  C6   C5   C4   121.53  3.000
 QO2  C61  C6   C1   120.56  3.000
 QO2  C61  C6   C5   121.20  3.000
 QO2  C1   C6   C5   118.24  3.000
 QO2  O3   C3   C2   119.33  3.000
 QO2  C2   C3   C4   118.81  3.000
 QO2  O3   C3   C4   121.86  3.000
 QO2  H8   C2   C1   119.50  3.000
 QO2  H8   C2   C3   118.43  3.000
 QO2  C1   C2   C3   122.07  3.000
 QO2  C2   C1   C7   118.85  3.000
 QO2  C7   C1   C6   121.48  3.000
 QO2  C2   C1   C6   119.66  3.000
 QO2  H9   O3   C3   110.39  3.000
 QO2  H10  O4   C4   109.57  3.000
 QO2  H13  C61  H12  107.45  3.000
 QO2  H13  C61  H11  107.00  3.000
 QO2  H12  C61  H11  107.15  3.000
 QO2  H13  C61  C6   111.64  3.000
 QO2  H12  C61  C6   111.93  3.000
 QO2  H11  C61  C6   111.39  3.000
 QO2  H14  CA   CB   107.60  3.000
 QO2  H14  CA   C    105.09  3.000
 QO2  CB   CA   C    110.10  1.900
 QO2  H14  CA   N    114.31  3.000
 QO2  CB   CA   N    110.50  1.700
 QO2  C    CA   N    111.00  2.800
 QO2  H16  CB   H15  108.09  3.000
 QO2  H16  CB   SG   105.14  3.000
 QO2  H15  CB   SG   108.82  3.000
 QO2  H16  CB   CA   110.24  3.000
 QO2  H15  CB   CA   110.99  3.000
 QO2  SG   CB   CA   113.29  3.000
 QO2  CB   SG   C5   100.97  3.000
 QO2  H3   OXT  C    109.52  3.000
 QO2  H7   C7   H6   107.41  3.000
 QO2  H7   C7   H5   107.51  3.000
 QO2  H6   C7   H5   106.97  3.000
 QO2  H7   C7   C1   110.80  3.000
 QO2  H6   C7   C1   111.92  3.000
 QO2  H5   C7   C1   111.99  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
 QO2  CONST_01  C1   C2   C3  C4    0.00   0.0  0
 QO2  CONST_02  C1   C6   C5  C4    0.00   0.0  0
 QO2  CONST_03  C2   C3   C4  C5    0.00   0.0  0
 QO2  CONST_04  C2   C1   C6  C5    0.00   0.0  0
 QO2  CONST_05  C3   C2   C1  C6    0.00   0.0  0
 QO2  CONST_06  C3   C4   C5  C6    0.00   0.0  0
 QO2  CONST_07  C61  C6   C5  C4  180.00   0.0  0
 QO2  CONST_08  O3   C3   C4  C5  180.00   0.0  0
 QO2  CONST_09  C7   C1   C6  C5  180.00   0.0  0
 QO2  CONST_10  O4   C4   C5  C6  180.00   0.0  0
 QO2  CONST_11  C3   C2   C1  C7  180.00   0.0  0
 QO2  CONST_12  SG   C5   C4  C3  180.00   0.0  0
 QO2  CONST_13  O4   C4   C3  C2  180.00   0.0  0
 QO2  CONST_14  C61  C6   C1  C2  180.00   0.0  0
 QO2  CONST_15  O3   C3   C2  C1  180.00   0.0  0
 QO2  CONST_16  SG   C5   C6  C1  180.00   0.0  0
 QO2  CONST_17  H8   C2   C3  C4  180.00   0.0  0
 QO2  CONST_18  H3   OXT  C   O     0.00   0.0  0
 QO2  Var_01    H11  C61  C6  C5  -84.33  30.0  2
 QO2  Var_02    H5   C7   C1  C6  -56.46  30.0  2
 QO2  Var_03    CA   CB   SG  C5  -70.77  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
 QO2  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
 QO2  plan-1  C4   0.020
 QO2  plan-1  C5   0.020
 QO2  plan-1  C6   0.020
 QO2  plan-1  C3   0.020
 QO2  plan-1  C2   0.020
 QO2  plan-1  C1   0.020
 QO2  plan-1  O3   0.020
 QO2  plan-1  O4   0.020
 QO2  plan-1  C61  0.020
 QO2  plan-1  SG   0.020
 QO2  plan-1  H8   0.020
 QO2  plan-1  C7   0.020
 QO2  plan-2  C    0.020
 QO2  plan-2  O    0.020
 QO2  plan-2  CA   0.020
 QO2  plan-2  H3   0.020
 QO2  plan-2  OXT  0.020

