# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 10:16:59 2021
#   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  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_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  -0.252  24.1643  66.2826  82.0570
 QNW  C2   C  CR6   0  -0.277  25.0931  67.0179  81.3253
 QNW  C3   C  CR6   0   0.323  24.8658  67.2681  79.9730
 QNW  C4   C  CR6   0   0.278  23.7176  66.7632  79.3528
 QNW  C5   C  CR6   0  -0.010  22.7915  66.0201  80.0793
 QNW  C    C  C     0   0.547  28.5742  64.1218  81.8149
 QNW  N    N  NH2   0  -0.796  27.5037  65.1968  83.7609
 QNW  C6   C  CR16  0  -0.312  23.0315  65.7914  81.4340
 QNW  CA   C  CH1   0  -0.179  27.5075  65.0775  82.3226
 QNW  CB   C  CH2   0  -0.568  27.7865  66.4352  81.6739
 QNW  SG   S  S2    0  -0.016  26.5367  67.6975  82.0870
 QNW  O3   O  OH1   0  -0.634  25.7048  67.9798  79.1965
 QNW  O4   O  OH1   0  -0.626  23.4764  66.9873  78.0436
 QNW  C51  C  CH3   0  -0.711  21.5621  65.4905  79.4054
 QNW  H1   H  HCR6  0   0.263  24.3354  66.0979  83.1095
 QNW  H3   H  HNH2  0   0.356  26.8258  65.9004  84.0278
 QNW  H4   H  HNH2  0   0.358  27.1910  64.3327  84.1848
 QNW  H6   H  HCR6  0   0.252  22.3132  65.2166  82.0049
 QNW  H7   H  HCH1  0   0.265  26.5642  64.6996  81.9007
 QNW  H8   H  HCH2  0   0.292  27.8517  66.3386  80.5915
 QNW  H9   H  HCH2  0   0.299  28.7306  66.8468  82.0374
 QNW  H10  H  HOH1  0   0.475  26.3809  68.4044  79.7470
 QNW  H11  H  HOH1  0   0.474  24.1752  67.5279  77.6572
 QNW  H12  H  HCH3  0   0.247  21.8099  64.8076  78.5910
 QNW  H13  H  HCH3  0   0.246  20.9382  64.9491  80.1142
 QNW  H14  H  HCH3  0   0.247  20.9600  66.2926  78.9755
 QNW  OXT  O  OH1   0  -0.573  29.4551  63.7586  82.7303
 QNW  H2   H  HOH1  0   0.482  30.1081  63.1640  82.3307
 QNW  O    O  O     0  -0.450  28.6102  63.7463  80.6682

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    1.350  0.020  1.350
 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    double    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    1.768  0.020  1.768
 QNW  C    CA   single    1.525  0.021  1.525
 QNW  CB   SG   single    1.824  0.020  1.824
 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  single    1.321  0.020  1.321
 QNW  OXT  H2   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
 QNW  H1   C1   C6   120.46  3.000
 QNW  H1   C1   C2   119.72  3.000
 QNW  C6   C1   C2   119.82  3.000
 QNW  SG   C2   C3   118.82  3.000
 QNW  SG   C2   C1   121.42  3.000
 QNW  C3   C2   C1   119.72  3.000
 QNW  O3   C3   C4   116.51  3.000
 QNW  O3   C3   C2   123.55  3.000
 QNW  C4   C3   C2   119.94  3.000
 QNW  O4   C4   C5   118.42  3.000
 QNW  C5   C4   C3   120.48  3.000
 QNW  O4   C4   C3   121.10  3.000
 QNW  C51  C5   C6   121.33  3.000
 QNW  C6   C5   C4   118.69  3.000
 QNW  C51  C5   C4   119.98  3.000
 QNW  OXT  C    O    123.56  3.000
 QNW  OXT  C    CA   114.17  3.000
 QNW  O    C    CA   120.80  1.700
 QNW  H4   N    H3   106.03  3.000
 QNW  H4   N    CA   110.34  3.000
 QNW  H3   N    CA   108.77  3.000
 QNW  H6   C6   C5   119.01  3.000
 QNW  H6   C6   C1   119.64  3.000
 QNW  C5   C6   C1   121.35  3.000
 QNW  H7   CA   CB   107.36  3.000
 QNW  H7   CA   N    114.09  3.000
 QNW  CB   CA   N    110.50  1.700
 QNW  H7   CA   C    104.94  3.000
 QNW  N    CA   C    111.00  2.800
 QNW  CB   CA   C    110.10  1.900
 QNW  H9   CB   H8   108.21  3.000
 QNW  H9   CB   SG   104.84  3.000
 QNW  H8   CB   SG   109.13  3.000
 QNW  H9   CB   CA   110.54  3.000
 QNW  H8   CB   CA   110.71  3.000
 QNW  SG   CB   CA   113.15  3.000
 QNW  CB   SG   C2   101.30  3.000
 QNW  H10  O3   C3   109.79  3.000
 QNW  H11  O4   C4   110.62  3.000
 QNW  H14  C51  H13  107.81  3.000
 QNW  H14  C51  H12  106.94  3.000
 QNW  H13  C51  H12  107.74  3.000
 QNW  H14  C51  C5   111.72  3.000
 QNW  H13  C51  C5   110.68  3.000
 QNW  H12  C51  C5   111.74  3.000
 QNW  H2   OXT  C    109.39  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  CONST_17  H2   OXT  C   CA  180.00   0.0  0
 QNW  Var_01    H12  C51  C5  C4   60.88  30.0  2
 QNW  Var_02    CA   CB   SG  C2  -64.78  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  OXT  0.020
 QNW  plan-2  H2   0.020
 QNW  plan-2  O    0.020

