# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 05:06:48 2022
#   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  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_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  -0.623  22.6524  66.4112  78.1283
 QNT  C4   C  CR6    0   0.228  23.2963  66.1833  80.4199
 QNT  C5   C  CR6    0   0.015  24.1842  66.4385  81.4649
 QNT  O4   O  OH1    0  -0.646  22.1563  65.4597  80.5698
 QNT  C6   C  CR6    0  -0.198  25.3202  67.2072  81.1772
 QNT  N    N  NH2    0  -0.805  27.4000  64.8800  83.8344
 QNT  C    C  C      0   0.415  28.6219  63.9948  81.8587
 QNT  O    O  O      0  -0.606  28.9474  64.1486  80.6650
 QNT  C1   C  CR16   0  -0.276  25.5211  67.7065  79.8935
 QNT  C2   C  CR6    0  -0.011  24.6381  67.4492  78.8545
 QNT  C3   C  CR6    0   0.270  23.5157  66.6733  79.1308
 QNT  CA   C  CH1    0  -0.195  27.5279  64.9631  82.3908
 QNT  CB   C  CH2    0  -0.540  27.8454  66.3931  81.9864
 QNT  SG   S  S2     0  -0.048  26.5349  67.5973  82.4127
 QNT  C51  C  CH3    0  -0.776  23.8785  65.8790  82.8233
 QNT  C21  C  CH3    0  -0.710  24.8718  67.9824  77.4725
 QNT  H1   H  HOH1   0   0.470  21.9403  65.8406  78.4428
 QNT  H2   H  HOH1   0   0.486  22.1715  64.9290  81.3736
 QNT  H3   H  HNH2   0   0.335  26.5196  65.2842  84.1245
 QNT  H4   H  HNH2   0   0.334  27.3838  63.9067  84.1058
 QNT  H7   H  HCR6   0   0.251  26.3965  68.3131  79.6949
 QNT  H8   H  HCH1   0   0.204  26.6019  64.6728  81.8636
 QNT  H9   H  HCH2   0   0.263  28.0322  66.4689  80.9173
 QNT  H10  H  HCH2   0   0.257  28.7345  66.7444  82.5157
 QNT  H11  H  HCH3   0   0.253  23.9825  64.7907  82.8473
 QNT  H12  H  HCH3   0   0.266  24.5520  66.2838  83.5729
 QNT  H13  H  HCH3   0   0.255  22.8616  66.1191  83.1420
 QNT  H14  H  HCH3   0   0.241  24.0479  68.6144  77.1370
 QNT  H15  H  HCH3   0   0.244  25.7825  68.5782  77.4397
 QNT  H16  H  HCH3   0   0.242  24.9756  67.1792  76.7408
 QNT  OXT  O  OC    -1  -0.594  29.0497  63.1333  82.6488

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    1.500  0.020  1.500
 QNT  O3   C3   single    1.349  0.020  1.349
 QNT  C2   C3   aromatic  1.392  0.020  1.392
 QNT  C2   C1   aromatic  1.388  0.020  1.388
 QNT  C3   C4   aromatic  1.396  0.020  1.396
 QNT  C1   C6   aromatic  1.392  0.020  1.392
 QNT  C4   O4   single    1.359  0.020  1.359
 QNT  C4   C5   aromatic  1.395  0.020  1.395
 QNT  O    C    deloc     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    1.830  0.020  1.830
 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  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
 QNT  H1   O3   C3   110.18  3.000
 QNT  C3   C4   O4   114.87  3.000
 QNT  O4   C4   C5   123.30  3.000
 QNT  C3   C4   C5   121.83  3.000
 QNT  C51  C5   C6   123.74  3.000
 QNT  C51  C5   C4   118.71  3.000
 QNT  C6   C5   C4   117.55  3.000
 QNT  H2   O4   C4   111.85  3.000
 QNT  SG   C6   C1   117.65  3.000
 QNT  SG   C6   C5   122.15  3.000
 QNT  C1   C6   C5   120.20  3.000
 QNT  H4   N    H3   107.09  3.000
 QNT  H4   N    CA   108.88  3.000
 QNT  H3   N    CA   109.82  3.000
 QNT  OXT  C    CA   117.11  3.000
 QNT  OXT  C    O    127.11  3.000
 QNT  CA   C    O    120.80  1.700
 QNT  H7   C1   C2   118.73  3.000
 QNT  H7   C1   C6   119.11  3.000
 QNT  C2   C1   C6   122.15  3.000
 QNT  C21  C2   C3   120.44  3.000
 QNT  C3   C2   C1   117.89  3.000
 QNT  C21  C2   C1   121.67  3.000
 QNT  C2   C3   C4   120.36  3.000
 QNT  C4   C3   O3   121.16  3.000
 QNT  C2   C3   O3   118.48  3.000
 QNT  H8   CA   CB   107.19  3.000
 QNT  H8   CA   C    105.24  3.000
 QNT  CB   CA   C    110.10  1.900
 QNT  H8   CA   N    112.69  3.000
 QNT  CB   CA   N    110.50  1.700
 QNT  C    CA   N    111.00  2.800
 QNT  H10  CB   H9   108.30  3.000
 QNT  H10  CB   SG   104.97  3.000
 QNT  H9   CB   SG   107.82  3.000
 QNT  H10  CB   CA   110.10  3.000
 QNT  H9   CB   CA   111.28  3.000
 QNT  SG   CB   CA   114.05  3.000
 QNT  CB   SG   C6   100.56  3.000
 QNT  H13  C51  H12  107.10  3.000
 QNT  H13  C51  H11  107.51  3.000
 QNT  H12  C51  H11  107.27  3.000
 QNT  H13  C51  C5   111.83  3.000
 QNT  H12  C51  C5   111.07  3.000
 QNT  H11  C51  C5   111.81  3.000
 QNT  H16  C21  H15  107.63  3.000
 QNT  H16  C21  H14  106.97  3.000
 QNT  H15  C21  H14  107.78  3.000
 QNT  H16  C21  C2   111.78  3.000
 QNT  H15  C21  C2   110.65  3.000
 QNT  H14  C21  C2   111.82  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  Var_01    H11  C51  C5  C4    69.62  30.0  2
 QNT  Var_02    H14  C21  C2  C1  -121.10  30.0  2
 QNT  Var_03    CA   CB   SG  C6   -74.55  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  OXT  0.020

