# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 04:27:19 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[6-methyl-2,3-bis(oxidanyl)phenyl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(O)c(O)c1SC[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
 QNQ  QNQ  '(2~{R})-2-azanyl-3-[6-methyl-2,3-bis(oxidanyl)phenyl]sulfanyl-propanoic acid'  L-peptide  28  16  .  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_QNQ
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
 QNQ  N    N  NH2    0  -0.808  27.5197  64.7529  84.0614
 QNQ  CA   C  CH1    0  -0.203  27.3035  64.6306  82.6319
 QNQ  CB   C  CH2    0  -0.536  27.2345  66.0083  81.9983
 QNQ  SG   S  S2     0  -0.045  25.8409  67.0340  82.6141
 QNQ  C    C  C      0   0.425  28.4222  63.7774  81.9666
 QNQ  O    O  O      0  -0.601  28.5325  63.8871  80.7306
 QNQ  C1   C  CR6    0   0.335  24.3020  66.7068  80.4093
 QNQ  C2   C  CR6    0   0.286  23.2393  66.1969  79.6541
 QNQ  C3   C  CR16   0  -0.334  22.3547  65.3209  80.2553
 QNQ  C4   C  CR16   0  -0.324  22.5152  64.9597  81.5883
 QNQ  C5   C  CR6    0   0.098  23.5666  65.4446  82.3542
 QNQ  C6   C  CR6    0  -0.294  24.4743  66.3195  81.7389
 QNQ  O2   O  OH1    0  -0.633  23.0574  66.5460  78.3620
 QNQ  H1   H  HNH2   0   0.337  26.6589  65.0118  84.5252
 QNQ  H2   H  HNH2   0   0.336  27.7968  63.8502  84.4224
 QNQ  H4   H  HCH1   0   0.208  26.3607  64.1105  82.3846
 QNQ  H5   H  HCH2   0   0.265  28.1299  66.5847  82.2410
 QNQ  H6   H  HCH2   0   0.269  27.1555  65.9408  80.9161
 QNQ  H8   H  HCR6   0   0.262  21.5271  64.9254  79.6793
 QNQ  H9   H  HCR6   0   0.247  21.8016  64.2806  82.0373
 QNQ  H10  H  HCH3   0   0.243  24.6186  64.4604  83.9610
 QNQ  H11  H  HCH3   0   0.242  23.7443  65.8966  84.4582
 QNQ  H12  H  HCH3   0   0.249  22.8665  64.4127  84.0945
 QNQ  H13  H  HOH1   0   0.469  25.7155  67.9800  80.4267
 QNQ  H14  H  HOH1   0   0.469  23.7346  67.1749  78.0861
 QNQ  OXT  O  OC    -1  -0.593  29.0766  63.0301  82.7165
 QNQ  C51  C  CH3    0  -0.734  23.7070  65.0351  83.7910
 QNQ  O1   O  OH1    0  -0.635  25.1235  67.5661  79.7769

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
 QNQ  O2   C2   single    1.351  0.020  1.351
 QNQ  C2   C3   aromatic  1.382  0.020  1.382
 QNQ  C2   C1   aromatic  1.400  0.020  1.400
 QNQ  O1   C1   single    1.347  0.020  1.347
 QNQ  C3   C4   aromatic  1.390  0.020  1.390
 QNQ  C1   C6   aromatic  1.396  0.020  1.396
 QNQ  O    C    deloc     1.231  0.020  1.231
 QNQ  C4   C5   aromatic  1.388  0.020  1.388
 QNQ  C    CA   single    1.525  0.021  1.525
 QNQ  C6   C5   aromatic  1.403  0.020  1.403
 QNQ  C6   SG   single    1.773  0.020  1.773
 QNQ  CB   CA   single    1.530  0.020  1.530
 QNQ  CB   SG   single    1.837  0.020  1.837
 QNQ  C5   C51  single    1.501  0.020  1.501
 QNQ  CA   N    single    1.458  0.019  1.458
 QNQ  N    H1   single    0.890  0.020  1.040
 QNQ  N    H2   single    0.890  0.020  1.040
 QNQ  CA   H4   single    0.970  0.020  1.090
 QNQ  CB   H5   single    0.970  0.020  1.090
 QNQ  CB   H6   single    0.970  0.020  1.090
 QNQ  C3   H8   single    0.930  0.020  1.080
 QNQ  C4   H9   single    0.930  0.020  1.080
 QNQ  C51  H10  single    0.970  0.020  1.090
 QNQ  C51  H11  single    0.970  0.020  1.090
 QNQ  C51  H12  single    0.970  0.020  1.090
 QNQ  O1   H13  single    0.850  0.020  0.980
 QNQ  O2   H14  single    0.850  0.020  0.980
 QNQ  C    OXT  deloc     1.245  0.020  1.245

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
 QNQ  H2   N    H1   107.34  3.000
 QNQ  H2   N    CA   108.51  3.000
 QNQ  H1   N    CA   110.28  3.000
 QNQ  H4   CA   C    105.05  3.000
 QNQ  H4   CA   CB   107.16  3.000
 QNQ  C    CA   CB   110.10  1.900
 QNQ  H4   CA   N    112.79  3.000
 QNQ  CB   CA   N    110.50  1.700
 QNQ  C    CA   N    111.00  2.800
 QNQ  H6   CB   H5   108.28  3.000
 QNQ  H6   CB   SG   108.26  3.000
 QNQ  H5   CB   SG   104.64  3.000
 QNQ  H6   CB   CA   111.25  3.000
 QNQ  H5   CB   CA   110.42  3.000
 QNQ  SG   CB   CA   113.67  3.000
 QNQ  C6   SG   CB   101.21  3.000
 QNQ  OXT  C    O    127.17  3.000
 QNQ  OXT  C    CA   116.71  3.000
 QNQ  O    C    CA   120.80  1.700
 QNQ  O1   C1   C6   123.31  3.000
 QNQ  C6   C1   C2   120.44  3.000
 QNQ  O1   C1   C2   116.25  3.000
 QNQ  O2   C2   C3   119.58  3.000
 QNQ  C3   C2   C1   118.81  3.000
 QNQ  O2   C2   C1   121.61  3.000
 QNQ  H8   C3   C4   120.21  3.000
 QNQ  H8   C3   C2   119.28  3.000
 QNQ  C4   C3   C2   120.51  3.000
 QNQ  H9   C4   C5   119.31  3.000
 QNQ  H9   C4   C3   118.97  3.000
 QNQ  C5   C4   C3   121.71  3.000
 QNQ  C51  C5   C6   121.98  3.000
 QNQ  C51  C5   C4   120.25  3.000
 QNQ  C6   C5   C4   117.77  3.000
 QNQ  C5   C6   C1   120.73  3.000
 QNQ  C5   C6   SG   122.25  3.000
 QNQ  C1   C6   SG   116.98  3.000
 QNQ  H14  O2   C2   110.34  3.000
 QNQ  H12  C51  H11  107.91  3.000
 QNQ  H12  C51  H10  107.48  3.000
 QNQ  H11  C51  H10  107.00  3.000
 QNQ  H12  C51  C5   110.53  3.000
 QNQ  H11  C51  C5   111.93  3.000
 QNQ  H10  C51  C5   111.78  3.000
 QNQ  H13  O1   C1   109.24  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
 QNQ  CONST_01  C4   C3   C2  C1    0.00   0.0  0
 QNQ  CONST_02  C4   C5   C6  C1    0.00   0.0  0
 QNQ  CONST_03  C5   C4   C3  C2    0.00   0.0  0
 QNQ  CONST_04  C5   C6   C1  C2    0.00   0.0  0
 QNQ  CONST_05  C6   C1   C2  C3    0.00   0.0  0
 QNQ  CONST_06  C6   C5   C4  C3    0.00   0.0  0
 QNQ  CONST_07  C2   C1   C6  SG  180.00   0.0  0
 QNQ  CONST_08  C4   C5   C6  SG  180.00   0.0  0
 QNQ  CONST_09  C51  C5   C6  C1  180.00   0.0  0
 QNQ  CONST_10  O1   C1   C2  C3  180.00   0.0  0
 QNQ  CONST_11  C51  C5   C4  C3  180.00   0.0  0
 QNQ  CONST_12  O2   C2   C3  C4  180.00   0.0  0
 QNQ  CONST_13  O1   C1   C6  C5  180.00   0.0  0
 QNQ  CONST_14  O2   C2   C1  C6  180.00   0.0  0
 QNQ  CONST_15  H8   C3   C2  C1  180.00   0.0  0
 QNQ  CONST_16  H9   C4   C3  C2  180.00   0.0  0
 QNQ  Var_01    C1   C6   SG  CB  -79.53  30.0  2
 QNQ  Var_02    H10  C51  C5  C4  115.70  30.0  2
 QNQ  Var_03    H5   CB   SG  C6  162.48  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
 QNQ  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
 QNQ  plan-1  SG   0.020
 QNQ  plan-1  C1   0.020
 QNQ  plan-1  C2   0.020
 QNQ  plan-1  C3   0.020
 QNQ  plan-1  C4   0.020
 QNQ  plan-1  C5   0.020
 QNQ  plan-1  C6   0.020
 QNQ  plan-1  O2   0.020
 QNQ  plan-1  H8   0.020
 QNQ  plan-1  H9   0.020
 QNQ  plan-1  C51  0.020
 QNQ  plan-1  O1   0.020
 QNQ  plan-2  CA   0.020
 QNQ  plan-2  C    0.020
 QNQ  plan-2  O    0.020
 QNQ  plan-2  OXT  0.020

