# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 12:27:20 2021
#   Inital geometry file: a 80 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[2,5-dimethyl-3,4-bis(oxidanyl)phenyl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(SC[C@H](N)C(O)=O)c(C)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
 QNT  QNT  '(2~{R})-2-azanyl-3-[2,5-dimethyl-3,4-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 GRAND (side chain)
;

data_comp_QNT
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
 QNT  O3   O  OH1   0  -0.624  22.6334  66.4248  78.1463
 QNT  C4   C  CR6   0   0.232  23.3028  66.1743  80.4279
 QNT  C5   C  CR6   0   0.019  24.2026  66.4207  81.4643
 QNT  O4   O  OH1   0  -0.645  22.1688  65.4467  80.5835
 QNT  C6   C  CR6   0  -0.211  25.3346  67.1909  81.1667
 QNT  N    N  NH2   0  -0.797  27.3906  64.8007  83.7302
 QNT  C    C  C     0   0.540  28.6533  64.1056  81.7333
 QNT  O    O  O     0  -0.450  28.7336  63.8435  80.5577
 QNT  C1   C  CR16  0  -0.274  25.5263  67.6983  79.8853
 QNT  C2   C  CR6   0  -0.012  24.6316  67.4468  78.8549
 QNT  C3   C  CR6   0   0.274  23.5095  66.6735  79.1396
 QNT  CA   C  CH1   0  -0.169  27.5340  64.9598  82.3028
 QNT  CB   C  CH2   0  -0.576  27.8728  66.4138  81.9631
 QNT  SG   S  S2    0  -0.012  26.5515  67.5852  82.3986
 QNT  C51  C  CH3   0  -0.783  23.9124  65.8469  82.8205
 QNT  C21  C  CH3   0  -0.710  24.8490  67.9890  77.4741
 QNT  H1   H  HOH1  0   0.474  21.9031  65.8826  78.4679
 QNT  H2   H  HOH1  0   0.489  22.1269  65.0301  81.4507
 QNT  H3   H  HNH2  0   0.356  26.6990  65.4619  84.0620
 QNT  H4   H  HNH2  0   0.357  27.0255  63.8819  83.9461
 QNT  H7   H  HCR6  0   0.255  26.3976  68.3094  79.6823
 QNT  H8   H  HCH1  0   0.258  26.6395  64.6835  81.7259
 QNT  H9   H  HCH2  0   0.290  28.0950  66.5226  80.9022
 QNT  H10  H  HCH2  0   0.291  28.7486  66.7378  82.5297
 QNT  H11  H  HCH3  0   0.259  24.0373  64.7609  82.8358
 QNT  H12  H  HCH3  0   0.269  24.5747  66.2604  83.5752
 QNT  H13  H  HCH3  0   0.258  22.8927  66.0662  83.1455
 QNT  H14  H  HCH3  0   0.244  24.0204  68.6220  77.1525
 QNT  H15  H  HCH3  0   0.244  25.7583  68.5868  77.4355
 QNT  H16  H  HCH3  0   0.245  24.9456  67.1904  76.7364
 QNT  H5   H  HOH1  0   0.481  30.2351  63.1974  82.1925
 QNT  OXT  O  OH1   0  -0.574  29.5399  63.7110  82.6312

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
 QNT  C21  C2   single    1.499  0.020  1.499
 QNT  O3   C3   single    1.348  0.020  1.348
 QNT  C2   C3   aromatic  1.392  0.020  1.392
 QNT  C2   C1   aromatic  1.388  0.020  1.388
 QNT  C3   C4   aromatic  1.397  0.020  1.397
 QNT  C1   C6   aromatic  1.391  0.020  1.391
 QNT  C4   O4   single    1.356  0.020  1.356
 QNT  C4   C5   aromatic  1.394  0.020  1.394
 QNT  O    C    double    1.231  0.020  1.231
 QNT  C6   C5   aromatic  1.401  0.020  1.401
 QNT  C6   SG   single    1.776  0.020  1.776
 QNT  C5   C51  single    1.501  0.020  1.501
 QNT  C    CA   single    1.525  0.021  1.525
 QNT  CB   SG   single    1.819  0.020  1.819
 QNT  CB   CA   single    1.530  0.020  1.530
 QNT  CA   N    single    1.458  0.019  1.458
 QNT  O3   H1   single    0.850  0.020  0.980
 QNT  O4   H2   single    0.850  0.020  0.980
 QNT  N    H3   single    0.890  0.020  1.040
 QNT  N    H4   single    0.890  0.020  1.040
 QNT  C1   H7   single    0.930  0.020  1.080
 QNT  CA   H8   single    0.970  0.020  1.090
 QNT  CB   H9   single    0.970  0.020  1.090
 QNT  CB   H10  single    0.970  0.020  1.090
 QNT  C51  H11  single    0.970  0.020  1.090
 QNT  C51  H12  single    0.970  0.020  1.090
 QNT  C51  H13  single    0.970  0.020  1.090
 QNT  C21  H14  single    0.970  0.020  1.090
 QNT  C21  H15  single    0.970  0.020  1.090
 QNT  C21  H16  single    0.970  0.020  1.090
 QNT  C    OXT  single    1.322  0.020  1.322
 QNT  OXT  H5   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
 QNT  H1   O3   C3   110.50  3.000
 QNT  C3   C4   O4   114.91  3.000
 QNT  O4   C4   C5   123.30  3.000
 QNT  C3   C4   C5   121.79  3.000
 QNT  C51  C5   C6   123.94  3.000
 QNT  C51  C5   C4   118.63  3.000
 QNT  C6   C5   C4   117.43  3.000
 QNT  H2   O4   C4   111.82  3.000
 QNT  SG   C6   C1   117.61  3.000
 QNT  SG   C6   C5   121.89  3.000
 QNT  C1   C6   C5   120.48  3.000
 QNT  H4   N    H3   106.05  3.000
 QNT  H4   N    CA   110.29  3.000
 QNT  H3   N    CA   108.66  3.000
 QNT  OXT  C    CA   114.04  3.000
 QNT  OXT  C    O    123.51  3.000
 QNT  CA   C    O    120.80  1.700
 QNT  H7   C1   C2   118.79  3.000
 QNT  H7   C1   C6   119.27  3.000
 QNT  C2   C1   C6   121.93  3.000
 QNT  C21  C2   C3   120.40  3.000
 QNT  C3   C2   C1   117.94  3.000
 QNT  C21  C2   C1   121.66  3.000
 QNT  C2   C3   C4   120.42  3.000
 QNT  C4   C3   O3   121.17  3.000
 QNT  C2   C3   O3   118.41  3.000
 QNT  H8   CA   CB   107.59  3.000
 QNT  H8   CA   C    105.16  3.000
 QNT  CB   CA   C    110.10  1.900
 QNT  H8   CA   N    114.22  3.000
 QNT  CB   CA   N    110.50  1.700
 QNT  C    CA   N    111.00  2.800
 QNT  H10  CB   H9   108.18  3.000
 QNT  H10  CB   SG   105.50  3.000
 QNT  H9   CB   SG   108.48  3.000
 QNT  H10  CB   CA   110.13  3.000
 QNT  H9   CB   CA   110.85  3.000
 QNT  SG   CB   CA   113.44  3.000
 QNT  CB   SG   C6   100.88  3.000
 QNT  H13  C51  H12  106.62  3.000
 QNT  H13  C51  H11  107.57  3.000
 QNT  H12  C51  H11  107.39  3.000
 QNT  H13  C51  C5   111.87  3.000
 QNT  H12  C51  C5   111.38  3.000
 QNT  H11  C51  C5   111.74  3.000
 QNT  H16  C21  H15  107.69  3.000
 QNT  H16  C21  H14  107.01  3.000
 QNT  H15  C21  H14  107.77  3.000
 QNT  H16  C21  C2   111.76  3.000
 QNT  H15  C21  C2   110.62  3.000
 QNT  H14  C21  C2   111.78  3.000
 QNT  H5   OXT  C    109.37  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
 QNT  CONST_01  C1   C2   C3  C4     0.00   0.0  0
 QNT  CONST_02  C1   C6   C5  C4     0.00   0.0  0
 QNT  CONST_03  C2   C3   C4  C5     0.00   0.0  0
 QNT  CONST_04  C2   C1   C6  C5     0.00   0.0  0
 QNT  CONST_05  C3   C2   C1  C6     0.00   0.0  0
 QNT  CONST_06  C3   C4   C5  C6     0.00   0.0  0
 QNT  CONST_07  C1   C2   C3  O3   180.00   0.0  0
 QNT  CONST_08  C5   C4   C3  O3   180.00   0.0  0
 QNT  CONST_09  C21  C2   C3  C4   180.00   0.0  0
 QNT  CONST_10  SG   C6   C5  C4   180.00   0.0  0
 QNT  CONST_11  C2   C3   C4  O4   180.00   0.0  0
 QNT  CONST_12  C6   C5   C4  O4   180.00   0.0  0
 QNT  CONST_13  C21  C2   C1  C6   180.00   0.0  0
 QNT  CONST_14  C51  C5   C6  C1   180.00   0.0  0
 QNT  CONST_15  SG   C6   C1  C2   180.00   0.0  0
 QNT  CONST_16  C51  C5   C4  C3   180.00   0.0  0
 QNT  CONST_17  H7   C1   C6  C5   180.00   0.0  0
 QNT  CONST_18  H5   OXT  C   O      0.00   0.0  0
 QNT  Var_01    H11  C51  C5  C4    70.74  30.0  2
 QNT  Var_02    H14  C21  C2  C1  -121.11  30.0  2
 QNT  Var_03    CA   CB   SG  C6   -71.65  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
 QNT  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
 QNT  plan-1  O3   0.020
 QNT  plan-1  C4   0.020
 QNT  plan-1  C5   0.020
 QNT  plan-1  O4   0.020
 QNT  plan-1  C6   0.020
 QNT  plan-1  C1   0.020
 QNT  plan-1  C2   0.020
 QNT  plan-1  C3   0.020
 QNT  plan-1  SG   0.020
 QNT  plan-1  C51  0.020
 QNT  plan-1  C21  0.020
 QNT  plan-1  H7   0.020
 QNT  plan-2  C    0.020
 QNT  plan-2  O    0.020
 QNT  plan-2  CA   0.020
 QNT  plan-2  H5   0.020
 QNT  plan-2  OXT  0.020

