# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 04:53:41 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[4-methyl-2,3-bis(oxidanyl)phenyl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(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
 QNW  QNW  '(2~{R})-2-azanyl-3-[4-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_QNW
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
 QNW  C1   C  CR16   0  -0.255  24.1632  66.3000  82.0313
 QNW  C2   C  CR6    0  -0.270  25.0913  67.0311  81.2951
 QNW  C3   C  CR6    0   0.320  24.8613  67.2676  79.9403
 QNW  C4   C  CR6    0   0.273  23.7141  66.7560  79.3240
 QNW  C5   C  CR6    0  -0.011  22.7911  66.0144  80.0560
 QNW  C    C  C      0   0.424  28.5516  64.0155  82.0680
 QNW  N    N  NH2    0  -0.806  27.5460  65.3665  83.8967
 QNW  C6   C  CR16   0  -0.312  23.0316  65.7990  81.4127
 QNW  CA   C  CH1    0  -0.205  27.5164  65.1055  82.4688
 QNW  CB   C  CH2    0  -0.533  27.7690  66.3895  81.6991
 QNW  SG   S  S2     0  -0.049  26.5437  67.7113  82.0408
 QNW  O3   O  OH1    0  -0.634  25.6984  67.9771  79.1598
 QNW  O4   O  OH1    0  -0.626  23.4715  66.9697  78.0119
 QNW  C51  C  CH3    0  -0.710  21.5659  65.4704  79.3851
 QNW  H1   H  HCR6   0   0.261  24.3360  66.1255  83.0853
 QNW  H3   H  HNH2   0   0.334  26.6790  65.8020  84.1839
 QNW  H4   H  HNH2   0   0.335  27.6069  64.4813  84.3810
 QNW  H6   H  HCR6   0   0.247  22.3140  65.2278  81.9882
 QNW  H7   H  HCH1   0   0.211  26.5417  64.7089  82.1336
 QNW  H8   H  HCH2   0   0.266  27.7866  66.2107  80.6270
 QNW  H9   H  HCH2   0   0.264  28.7266  66.8279  81.9895
 QNW  H10  H  HOH1   0   0.469  26.4042  68.3531  79.7107
 QNW  H11  H  HOH1   0   0.471  24.1753  67.4996  77.6195
 QNW  H12  H  HCH3   0   0.244  21.8192  64.7859  78.5734
 QNW  H13  H  HCH3   0   0.245  20.9475  64.9259  80.0967
 QNW  H14  H  HCH3   0   0.244  20.9547  66.2643  78.9525
 QNW  O    O  O      0  -0.602  28.8576  63.9671  80.8609
 QNW  OXT  O  OC    -1  -0.595  28.9487  63.2592  82.9735

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
 QNW  O4   C4   single    1.351  0.020  1.351
 QNW  C51  C5   single    1.499  0.020  1.499
 QNW  C4   C5   aromatic  1.392  0.020  1.392
 QNW  C4   C3   aromatic  1.399  0.020  1.399
 QNW  O3   C3   single    1.347  0.020  1.347
 QNW  C5   C6   aromatic  1.395  0.020  1.395
 QNW  C3   C2   aromatic  1.394  0.020  1.394
 QNW  O    C    deloc     1.231  0.020  1.231
 QNW  C6   C1   aromatic  1.383  0.020  1.383
 QNW  C2   C1   aromatic  1.392  0.020  1.392
 QNW  C2   SG   single    1.769  0.020  1.769
 QNW  C    CA   single    1.525  0.021  1.525
 QNW  CB   SG   single    1.835  0.020  1.835
 QNW  CB   CA   single    1.530  0.020  1.530
 QNW  CA   N    single    1.458  0.019  1.458
 QNW  C1   H1   single    0.930  0.020  1.080
 QNW  N    H3   single    0.890  0.020  1.040
 QNW  N    H4   single    0.890  0.020  1.040
 QNW  C6   H6   single    0.930  0.020  1.080
 QNW  CA   H7   single    0.970  0.020  1.090
 QNW  CB   H8   single    0.970  0.020  1.090
 QNW  CB   H9   single    0.970  0.020  1.090
 QNW  O3   H10  single    0.850  0.020  0.980
 QNW  O4   H11  single    0.850  0.020  0.980
 QNW  C51  H12  single    0.970  0.020  1.090
 QNW  C51  H13  single    0.970  0.020  1.090
 QNW  C51  H14  single    0.970  0.020  1.090
 QNW  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
 QNW  H1   C1   C6   120.52  3.000
 QNW  H1   C1   C2   119.55  3.000
 QNW  C6   C1   C2   119.93  3.000
 QNW  SG   C2   C3   118.68  3.000
 QNW  SG   C2   C1   121.77  3.000
 QNW  C3   C2   C1   119.53  3.000
 QNW  O3   C3   C4   116.56  3.000
 QNW  O3   C3   C2   123.36  3.000
 QNW  C4   C3   C2   120.08  3.000
 QNW  O4   C4   C5   118.41  3.000
 QNW  C5   C4   C3   120.45  3.000
 QNW  O4   C4   C3   121.14  3.000
 QNW  C51  C5   C6   121.35  3.000
 QNW  C6   C5   C4   118.66  3.000
 QNW  C51  C5   C4   120.00  3.000
 QNW  OXT  C    O    127.06  3.000
 QNW  OXT  C    CA   116.78  3.000
 QNW  O    C    CA   120.80  1.700
 QNW  H4   N    H3   107.01  3.000
 QNW  H4   N    CA   108.36  3.000
 QNW  H3   N    CA   109.81  3.000
 QNW  H6   C6   C5   118.96  3.000
 QNW  H6   C6   C1   119.69  3.000
 QNW  C5   C6   C1   121.34  3.000
 QNW  H7   CA   CB   107.26  3.000
 QNW  H7   CA   N    112.41  3.000
 QNW  CB   CA   N    110.50  1.700
 QNW  H7   CA   C    104.91  3.000
 QNW  N    CA   C    111.00  2.800
 QNW  CB   CA   C    110.10  1.900
 QNW  H9   CB   H8   108.30  3.000
 QNW  H9   CB   SG   104.28  3.000
 QNW  H8   CB   SG   108.24  3.000
 QNW  H9   CB   CA   110.52  3.000
 QNW  H8   CB   CA   111.33  3.000
 QNW  SG   CB   CA   113.81  3.000
 QNW  CB   SG   C2   101.12  3.000
 QNW  H10  O3   C3   109.09  3.000
 QNW  H11  O4   C4   110.54  3.000
 QNW  H14  C51  H13  107.74  3.000
 QNW  H14  C51  H12  106.94  3.000
 QNW  H13  C51  H12  107.71  3.000
 QNW  H14  C51  C5   111.79  3.000
 QNW  H13  C51  C5   110.69  3.000
 QNW  H12  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
 QNW  CONST_01  C4   C5   C6  C1    0.00   0.0  0
 QNW  CONST_02  C4   C3   C2  C1    0.00   0.0  0
 QNW  CONST_03  C5   C4   C3  C2    0.00   0.0  0
 QNW  CONST_04  C5   C6   C1  C2    0.00   0.0  0
 QNW  CONST_05  C6   C5   C4  C3    0.00   0.0  0
 QNW  CONST_06  C6   C1   C2  C3    0.00   0.0  0
 QNW  CONST_07  C51  C5   C6  C1  180.00   0.0  0
 QNW  CONST_08  O3   C3   C2  C1  180.00   0.0  0
 QNW  CONST_09  O4   C4   C3  C2  180.00   0.0  0
 QNW  CONST_10  C51  C5   C4  C3  180.00   0.0  0
 QNW  CONST_11  SG   C2   C3  C4  180.00   0.0  0
 QNW  CONST_12  O3   C3   C4  C5  180.00   0.0  0
 QNW  CONST_13  O4   C4   C5  C6  180.00   0.0  0
 QNW  CONST_14  SG   C2   C1  C6  180.00   0.0  0
 QNW  CONST_15  H6   C6   C1  C2  180.00   0.0  0
 QNW  CONST_16  H1   C1   C2  C3  180.00   0.0  0
 QNW  Var_01    H12  C51  C5  C4   60.49  30.0  2
 QNW  Var_02    CA   CB   SG  C2  -68.71  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
 QNW  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
 QNW  plan-1  C1   0.020
 QNW  plan-1  C2   0.020
 QNW  plan-1  C3   0.020
 QNW  plan-1  C4   0.020
 QNW  plan-1  C5   0.020
 QNW  plan-1  C6   0.020
 QNW  plan-1  SG   0.020
 QNW  plan-1  O3   0.020
 QNW  plan-1  O4   0.020
 QNW  plan-1  C51  0.020
 QNW  plan-1  H1   0.020
 QNW  plan-1  H6   0.020
 QNW  plan-2  C    0.020
 QNW  plan-2  CA   0.020
 QNW  plan-2  O    0.020
 QNW  plan-2  OXT  0.020

