# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 07:10:02 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[4,6-dimethyl-2,3-bis(oxidanyl)phenyl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c(SC[C@H](N)C(O)=O)c(O)c1O
#
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
 QO5  QO5  '(2~{R})-2-azanyl-3-[4,6-dimethyl-2,3-bis(oxidanyl)phenyl]sulfanyl-propanoic acid'  L-peptide  31  17  .  2022-09-22  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_QO5
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
 QO5  C11  C  CH3    0  -0.737  23.9084  65.7892  83.4601
 QO5  N    N  NH2    0  -0.810  27.6399  65.2279  83.8705
 QO5  CA   C  CH1    0  -0.206  27.4601  65.0021  82.4472
 QO5  CB   C  CH2    0  -0.533  27.5398  66.3193  81.6994
 QO5  SG   S  S2     0  -0.048  26.2272  67.5117  82.1740
 QO5  C    C  C      0   0.428  28.5127  63.9881  81.9121
 QO5  O    O  O      0  -0.599  28.7630  64.0387  80.6930
 QO5  C1   C  C      0   0.118  23.8337  66.0917  81.9920
 QO5  C2   C  C      0  -0.320  24.8198  66.8372  81.3336
 QO5  C3   C  C      0   0.346  24.6892  67.1233  79.9732
 QO5  O3   O  OH1    0  -0.637  25.5814  67.8640  79.2870
 QO5  C4   C  C      0   0.251  23.6005  66.6389  79.2439
 QO5  O4   O  OH1    0  -0.628  23.4675  66.8980  77.9226
 QO5  C5   C  C      0   0.009  22.6250  65.8816  79.8788
 QO5  C6   C  C1     0  -0.379  22.7590  65.6305  81.2435
 QO5  C51  C  CH3    0  -0.712  21.4497  65.3637  79.1056
 QO5  H1   H  HCH3   0   0.241  24.7464  65.1320  83.6987
 QO5  H2   H  HCH3   0   0.241  24.0287  66.6922  84.0590
 QO5  H3   H  HCH3   0   0.249  22.9999  65.2883  83.7922
 QO5  H7   H  HCH1   0   0.209  26.4797  64.5519  82.2081
 QO5  H8   H  HCH2   0   0.267  27.4899  66.1690  80.6239
 QO5  H9   H  HCH2   0   0.263  28.4761  66.8321  81.9300
 QO5  H11  H  HOH1   0   0.468  26.1988  68.2778  79.9127
 QO5  H12  H  HOH1   0   0.469  24.1868  67.4641  77.6188
 QO5  H13  H  H      0   0.240  21.9894  65.0491  81.7376
 QO5  H14  H  HCH3   0   0.243  21.7605  64.7298  78.2733
 QO5  H15  H  HCH3   0   0.244  20.7953  64.7748  79.7460
 QO5  H16  H  HCH3   0   0.243  20.8567  66.1761  78.6816
 QO5  OXT  O  OC    -1  -0.596  28.9780  63.1846  82.7423
 QO5  H4   H  HNH2   0   0.337  26.7906  65.5954  84.2787
 QO5  H5   H  HNH2   0   0.337  27.8253  64.3368  84.3111

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
 QO5  O4   C4   single    1.353  0.020  1.353
 QO5  C51  C5   single    1.499  0.020  1.499
 QO5  C4   C5   aromatic  1.389  0.020  1.389
 QO5  C4   C3   aromatic  1.397  0.020  1.397
 QO5  O3   C3   single    1.347  0.020  1.347
 QO5  C5   C6   aromatic  1.394  0.020  1.394
 QO5  C3   C2   aromatic  1.396  0.020  1.396
 QO5  O    C    deloc     1.231  0.020  1.231
 QO5  C6   C1   aromatic  1.389  0.020  1.389
 QO5  C2   C1   aromatic  1.401  0.020  1.401
 QO5  C2   SG   single    1.773  0.020  1.773
 QO5  C    CA   single    1.525  0.021  1.525
 QO5  CB   SG   single    1.836  0.020  1.836
 QO5  CB   CA   single    1.530  0.020  1.530
 QO5  C1   C11  single    1.501  0.020  1.501
 QO5  CA   N    single    1.458  0.019  1.458
 QO5  C11  H1   single    0.970  0.020  1.090
 QO5  C11  H2   single    0.970  0.020  1.090
 QO5  C11  H3   single    0.970  0.020  1.090
 QO5  N    H4   single    0.890  0.020  1.040
 QO5  N    H5   single    0.890  0.020  1.040
 QO5  CA   H7   single    0.970  0.020  1.090
 QO5  CB   H8   single    0.970  0.020  1.090
 QO5  CB   H9   single    0.970  0.020  1.090
 QO5  O3   H11  single    0.850  0.020  0.980
 QO5  O4   H12  single    0.850  0.020  0.980
 QO5  C6   H13  single    0.930  0.020  1.080
 QO5  C51  H14  single    0.970  0.020  1.090
 QO5  C51  H15  single    0.970  0.020  1.090
 QO5  C51  H16  single    0.970  0.020  1.090
 QO5  C    OXT  deloc     1.246  0.020  1.246

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
 QO5  H3   C11  H2   107.79  3.000
 QO5  H3   C11  H1   107.27  3.000
 QO5  H2   C11  H1   107.10  3.000
 QO5  H3   C11  C1   110.45  3.000
 QO5  H2   C11  C1   112.08  3.000
 QO5  H1   C11  C1   111.93  3.000
 QO5  H5   N    H4   107.36  3.000
 QO5  H5   N    CA   108.22  3.000
 QO5  H4   N    CA   110.37  3.000
 QO5  H7   CA   C    105.09  3.000
 QO5  H7   CA   CB   107.08  3.000
 QO5  C    CA   CB   110.10  1.900
 QO5  H7   CA   N    112.66  3.000
 QO5  CB   CA   N    110.50  1.700
 QO5  C    CA   N    111.00  2.800
 QO5  H9   CB   H8   108.25  3.000
 QO5  H9   CB   SG   104.68  3.000
 QO5  H8   CB   SG   108.23  3.000
 QO5  H9   CB   CA   110.41  3.000
 QO5  H8   CB   CA   111.42  3.000
 QO5  SG   CB   CA   113.52  3.000
 QO5  C2   SG   CB   101.42  3.000
 QO5  OXT  C    O    127.12  3.000
 QO5  OXT  C    CA   116.34  3.000
 QO5  O    C    CA   120.80  1.700
 QO5  C6   C1   C2   117.92  3.000
 QO5  C2   C1   C11  122.15  3.000
 QO5  C6   C1   C11  119.93  3.000
 QO5  C3   C2   C1   120.08  3.000
 QO5  C1   C2   SG   122.59  3.000
 QO5  C3   C2   SG   117.27  3.000
 QO5  C4   C3   O3   116.15  3.000
 QO5  O3   C3   C2   123.16  3.000
 QO5  C4   C3   C2   120.69  3.000
 QO5  H11  O3   C3   109.08  3.000
 QO5  C5   C4   O4   118.81  3.000
 QO5  C5   C4   C3   119.85  3.000
 QO5  O4   C4   C3   121.33  3.000
 QO5  H12  O4   C4   110.29  3.000
 QO5  C51  C5   C6   121.20  3.000
 QO5  C6   C5   C4   118.58  3.000
 QO5  C51  C5   C4   120.22  3.000
 QO5  H13  C6   C5   118.34  3.000
 QO5  H13  C6   C1   118.82  3.000
 QO5  C5   C6   C1   122.84  3.000
 QO5  H16  C51  H15  107.73  3.000
 QO5  H16  C51  H14  106.90  3.000
 QO5  H15  C51  H14  107.80  3.000
 QO5  H16  C51  C5   111.66  3.000
 QO5  H15  C51  C5   110.77  3.000
 QO5  H14  C51  C5   111.76  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
 QO5  CONST_01  C4   C5   C6  C1     0.00   0.0  0
 QO5  CONST_02  C4   C3   C2  C1     0.00   0.0  0
 QO5  CONST_03  C5   C4   C3  C2     0.00   0.0  0
 QO5  CONST_04  C5   C6   C1  C2     0.00   0.0  0
 QO5  CONST_05  C6   C5   C4  C3     0.00   0.0  0
 QO5  CONST_06  C6   C1   C2  C3     0.00   0.0  0
 QO5  CONST_07  C5   C6   C1  C11  180.00   0.0  0
 QO5  CONST_08  C3   C2   C1  C11  180.00   0.0  0
 QO5  CONST_09  C4   C3   C2  SG   180.00   0.0  0
 QO5  CONST_10  C6   C1   C2  SG   180.00   0.0  0
 QO5  CONST_11  C51  C5   C6  C1   180.00   0.0  0
 QO5  CONST_12  O3   C3   C2  C1   180.00   0.0  0
 QO5  CONST_13  O4   C4   C3  C2   180.00   0.0  0
 QO5  CONST_14  C51  C5   C4  C3   180.00   0.0  0
 QO5  CONST_15  C5   C4   C3  O3   180.00   0.0  0
 QO5  CONST_16  C6   C5   C4  O4   180.00   0.0  0
 QO5  CONST_17  H13  C6   C1  C2   180.00   0.0  0
 QO5  Var_01    C3   C2   SG  CB   -80.58  30.0  2
 QO5  Var_02    H1   C11  C1  C2   -66.27  30.0  2
 QO5  Var_03    H14  C51  C5  C4    58.56  30.0  2
 QO5  Var_04    H8   CB   SG  C2    48.24  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
 QO5  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
 QO5  plan-1  C11  0.020
 QO5  plan-1  SG   0.020
 QO5  plan-1  C1   0.020
 QO5  plan-1  C2   0.020
 QO5  plan-1  C3   0.020
 QO5  plan-1  O3   0.020
 QO5  plan-1  C4   0.020
 QO5  plan-1  O4   0.020
 QO5  plan-1  C5   0.020
 QO5  plan-1  C6   0.020
 QO5  plan-1  C51  0.020
 QO5  plan-1  H13  0.020
 QO5  plan-2  CA   0.020
 QO5  plan-2  C    0.020
 QO5  plan-2  O    0.020
 QO5  plan-2  OXT  0.020

