# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 10:08:32 2021
#   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  29  16  .  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_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  -0.796  27.4582  64.5818  83.9591
 QNQ  CA   C  CH1   0  -0.176  27.2693  64.5763  82.5275
 QNQ  CB   C  CH2   0  -0.571  27.2923  66.0059  81.9828
 QNQ  SG   S  S2    0  -0.013  25.9208  67.0385  82.6010
 QNQ  C    C  C     0   0.546  28.3610  63.8101  81.7982
 QNQ  O    O  O     0  -0.449  28.2554  63.4797  80.6423
 QNQ  C1   C  CR6   0   0.338  24.3436  66.7299  80.4190
 QNQ  C2   C  CR6   0   0.288  23.2605  66.2313  79.6855
 QNQ  C3   C  CR16  0  -0.332  22.3831  65.3584  80.3019
 QNQ  C4   C  CR16  0  -0.322  22.5686  64.9889  81.6285
 QNQ  C5   C  CR6   0   0.103  23.6387  65.4625  82.3752
 QNQ  C6   C  CR6   0  -0.304  24.5388  66.3330  81.7429
 QNQ  O1   O  OH1   0  -0.633  25.1587  67.5839  79.7712
 QNQ  O2   O  OH1   0  -0.635  23.0510  66.5875  78.4002
 QNQ  H1   H  HNH2  0   0.359  26.7543  65.1751  84.3815
 QNQ  H2   H  HNH2  0   0.359  27.3027  63.6557  84.3368
 QNQ  H4   H  HCH1  0   0.262  26.3282  64.1116  82.1978
 QNQ  H5   H  HCH2  0   0.300  28.2014  66.5168  82.3059
 QNQ  H6   H  HCH2  0   0.293  27.2701  66.0074  80.8942
 QNQ  H8   H  HCR6  0   0.268  21.5401  64.9727  79.7422
 QNQ  H9   H  HCR6  0   0.252  21.8566  64.3167  82.0902
 QNQ  H10  H  HCH3  0   0.240  24.6213  64.3130  83.9128
 QNQ  H11  H  HCH3  0   0.246  24.0281  65.8712  84.4632
 QNQ  H12  H  HCH3  0   0.254  22.9016  64.5500  84.1647
 QNQ  H13  H  HOH1  0   0.473  25.7495  68.0206  80.4052
 QNQ  H14  H  HOH1  0   0.472  23.6982  67.2464  78.1229
 QNQ  OXT  O  OH1   0  -0.572  29.4296  63.5650  82.5352
 QNQ  H3   H  HOH1  0   0.482  30.0854  63.0852  82.0066
 QNQ  C51  C  CH3   0  -0.734  23.8081  65.0330  83.8029

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    1.350  0.020  1.350
 QNQ  C2   C3   aromatic  1.383  0.020  1.383
 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    double    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    1.825  0.020  1.825
 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  single    1.321  0.020  1.321
 QNQ  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
 QNQ  H2   N    H1   105.87  3.000
 QNQ  H2   N    CA   110.26  3.000
 QNQ  H1   N    CA   108.95  3.000
 QNQ  H4   CA   C    104.93  3.000
 QNQ  H4   CA   CB   107.51  3.000
 QNQ  C    CA   CB   110.10  1.900
 QNQ  H4   CA   N    114.25  3.000
 QNQ  CB   CA   N    110.50  1.700
 QNQ  C    CA   N    111.00  2.800
 QNQ  H6   CB   H5   108.20  3.000
 QNQ  H6   CB   SG   108.82  3.000
 QNQ  H5   CB   SG   105.12  3.000
 QNQ  H6   CB   CA   110.91  3.000
 QNQ  H5   CB   CA   110.14  3.000
 QNQ  SG   CB   CA   113.38  3.000
 QNQ  C6   SG   CB   101.34  3.000
 QNQ  OXT  C    O    123.67  3.000
 QNQ  OXT  C    CA   114.00  3.000
 QNQ  O    C    CA   120.80  1.700
 QNQ  O1   C1   C6   123.50  3.000
 QNQ  C6   C1   C2   120.26  3.000
 QNQ  O1   C1   C2   116.24  3.000
 QNQ  O2   C2   C3   119.51  3.000
 QNQ  C3   C2   C1   118.83  3.000
 QNQ  O2   C2   C1   121.66  3.000
 QNQ  H8   C3   C4   120.18  3.000
 QNQ  H8   C3   C2   119.24  3.000
 QNQ  C4   C3   C2   120.58  3.000
 QNQ  H9   C4   C5   119.31  3.000
 QNQ  H9   C4   C3   118.98  3.000
 QNQ  C5   C4   C3   121.72  3.000
 QNQ  C51  C5   C6   122.28  3.000
 QNQ  C51  C5   C4   120.08  3.000
 QNQ  C6   C5   C4   117.64  3.000
 QNQ  C5   C6   C1   120.94  3.000
 QNQ  C5   C6   SG   121.93  3.000
 QNQ  C1   C6   SG   117.06  3.000
 QNQ  H13  O1   C1   109.85  3.000
 QNQ  H14  O2   C2   110.48  3.000
 QNQ  H3   OXT  C    109.57  3.000
 QNQ  H12  C51  H11  107.94  3.000
 QNQ  H12  C51  H10  107.10  3.000
 QNQ  H11  C51  H10  107.22  3.000
 QNQ  H12  C51  C5   110.43  3.000
 QNQ  H11  C51  C5   112.29  3.000
 QNQ  H10  C51  C5   111.63  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  CONST_17  H3   OXT  C   CA  180.00   0.0  0
 QNQ  Var_01    C1   C6   SG  CB  -80.46  30.0  2
 QNQ  Var_02    H10  C51  C5  C4  105.76  30.0  2
 QNQ  Var_03    H5   CB   SG  C6  168.39  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  O1   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-2  CA   0.020
 QNQ  plan-2  C    0.020
 QNQ  plan-2  O    0.020
 QNQ  plan-2  OXT  0.020
 QNQ  plan-2  H3   0.020

