# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 06:14:32 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[2,3-dimethyl-5,6-bis(oxidanyl)phenyl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(O)c(O)c(SC[C@H](N)C(O)=O)c1C
#
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
 QO2  QO2  '(2~{R})-2-azanyl-3-[2,3-dimethyl-5,6-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_QO2
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
 QO2  N    N  NH2    0  -0.812  27.6640  65.2248  83.9082
 QO2  C    C  C      0   0.426  28.5732  64.0986  81.8978
 QO2  C4   C  CR6    0   0.314  24.8103  67.3603  80.0405
 QO2  C5   C  CR6    0  -0.297  24.9006  66.9361  81.3692
 QO2  C6   C  CR6    0   0.068  23.9535  66.0570  81.9146
 QO2  O    O  O      0  -0.599  28.8163  64.1955  80.6803
 QO2  C3   C  CR6    0   0.297  23.7876  66.8782  79.2244
 QO2  C2   C  CR16   0  -0.396  22.8701  65.9891  79.7567
 QO2  C1   C  CR6    0   0.060  22.9341  65.5775  81.0844
 QO2  O3   O  OH1    0  -0.636  23.6706  67.2519  77.9305
 QO2  C61  C  CH3    0  -0.747  24.0025  65.6134  83.3471
 QO2  CA   C  CH1    0  -0.203  27.5088  65.0790  82.4722
 QO2  CB   C  CH2    0  -0.531  27.5966  66.4344  81.7949
 QO2  SG   S  S2     0  -0.057  26.2641  67.5895  82.3011
 QO2  H1   H  HNH2   0   0.336  26.7891  65.4981  84.3344
 QO2  H2   H  HNH2   0   0.336  27.9122  64.3206  84.2874
 QO2  H5   H  HCH3   0   0.241  22.3763  63.7083  82.0089
 QO2  H6   H  HCH3   0   0.241  21.3200  65.0445  82.4196
 QO2  H7   H  HCH3   0   0.250  21.2184  64.3080  80.8251
 QO2  H8   H  HCR6   0   0.255  22.0802  65.6129  79.1166
 QO2  H9   H  HOH1   0   0.468  24.3678  67.8763  77.6983
 QO2  H10  H  HOH1   0   0.466  26.2642  68.5770  80.1670
 QO2  H11  H  HCH3   0   0.244  24.2796  64.5595  83.4300
 QO2  H12  H  HCH3   0   0.252  24.7177  66.1909  83.9265
 QO2  H13  H  HCH3   0   0.249  23.0290  65.7225  83.8275
 QO2  H14  H  HCH1   0   0.213  26.5352  64.6380  82.1940
 QO2  H15  H  HCH2   0   0.268  27.5680  66.3414  80.7120
 QO2  H16  H  HCH2   0   0.263  28.5246  66.9389  82.0725
 QO2  C7   C  CH3    0  -0.735  21.9104  64.6112  81.6093
 QO2  OXT  O  OC    -1  -0.595  29.0538  63.2732  82.6975
 QO2  O4   O  OH1    0  -0.638  25.6798  68.2230  79.4756

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
 QO2  O3   C3   single    1.352  0.020  1.352
 QO2  C3   C2   aromatic  1.384  0.020  1.384
 QO2  C3   C4   aromatic  1.394  0.020  1.394
 QO2  O4   C4   single    1.349  0.020  1.349
 QO2  C2   C1   aromatic  1.392  0.020  1.392
 QO2  C4   C5   aromatic  1.398  0.020  1.398
 QO2  O    C    deloc     1.231  0.020  1.231
 QO2  C1   C7   single    1.502  0.020  1.502
 QO2  C1   C6   aromatic  1.399  0.020  1.399
 QO2  C5   C6   aromatic  1.403  0.020  1.403
 QO2  C5   SG   single    1.776  0.020  1.776
 QO2  C    CA   single    1.525  0.021  1.525
 QO2  CB   SG   single    1.835  0.020  1.835
 QO2  CB   CA   single    1.530  0.020  1.530
 QO2  C6   C61  single    1.500  0.020  1.500
 QO2  CA   N    single    1.458  0.019  1.458
 QO2  N    H1   single    0.890  0.020  1.040
 QO2  N    H2   single    0.890  0.020  1.040
 QO2  C7   H5   single    0.970  0.020  1.090
 QO2  C7   H6   single    0.970  0.020  1.090
 QO2  C7   H7   single    0.970  0.020  1.090
 QO2  C2   H8   single    0.930  0.020  1.080
 QO2  O3   H9   single    0.850  0.020  0.980
 QO2  O4   H10  single    0.850  0.020  0.980
 QO2  C61  H11  single    0.970  0.020  1.090
 QO2  C61  H12  single    0.970  0.020  1.090
 QO2  C61  H13  single    0.970  0.020  1.090
 QO2  CA   H14  single    0.970  0.020  1.090
 QO2  CB   H15  single    0.970  0.020  1.090
 QO2  CB   H16  single    0.970  0.020  1.090
 QO2  C    OXT  deloc     1.246  0.020  1.246

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
 QO2  H2   N    H1   107.22  3.000
 QO2  H2   N    CA   107.90  3.000
 QO2  H1   N    CA   110.59  3.000
 QO2  OXT  C    CA   116.37  3.000
 QO2  OXT  C    O    127.15  3.000
 QO2  CA   C    O    120.80  1.700
 QO2  O4   C4   C3   116.67  3.000
 QO2  O4   C4   C5   123.40  3.000
 QO2  C3   C4   C5   119.93  3.000
 QO2  SG   C5   C6   123.02  3.000
 QO2  SG   C5   C4   115.90  3.000
 QO2  C6   C5   C4   121.08  3.000
 QO2  C61  C6   C1   119.27  3.000
 QO2  C61  C6   C5   122.31  3.000
 QO2  C1   C6   C5   118.43  3.000
 QO2  O3   C3   C2   119.23  3.000
 QO2  C2   C3   C4   118.89  3.000
 QO2  O3   C3   C4   121.88  3.000
 QO2  H8   C2   C1   119.62  3.000
 QO2  H8   C2   C3   118.61  3.000
 QO2  C1   C2   C3   121.77  3.000
 QO2  C2   C1   C7   119.49  3.000
 QO2  C7   C1   C6   120.63  3.000
 QO2  C2   C1   C6   119.88  3.000
 QO2  H9   O3   C3   110.30  3.000
 QO2  H13  C61  H12  107.41  3.000
 QO2  H13  C61  H11  106.81  3.000
 QO2  H12  C61  H11  107.77  3.000
 QO2  H13  C61  C6   111.20  3.000
 QO2  H12  C61  C6   111.93  3.000
 QO2  H11  C61  C6   111.46  3.000
 QO2  H14  CA   CB   107.17  3.000
 QO2  H14  CA   C    104.97  3.000
 QO2  CB   CA   C    110.10  1.900
 QO2  H14  CA   N    112.55  3.000
 QO2  CB   CA   N    110.50  1.700
 QO2  C    CA   N    111.00  2.800
 QO2  H16  CB   H15  108.36  3.000
 QO2  H16  CB   SG   104.84  3.000
 QO2  H15  CB   SG   108.03  3.000
 QO2  H16  CB   CA   110.38  3.000
 QO2  H15  CB   CA   111.50  3.000
 QO2  SG   CB   CA   113.40  3.000
 QO2  CB   SG   C5   100.44  3.000
 QO2  H7   C7   H6   107.53  3.000
 QO2  H7   C7   H5   107.73  3.000
 QO2  H6   C7   H5   106.69  3.000
 QO2  H7   C7   C1   111.13  3.000
 QO2  H6   C7   C1   111.86  3.000
 QO2  H5   C7   C1   111.65  3.000
 QO2  H10  O4   C4   108.82  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
 QO2  CONST_01  C1   C2   C3  C4     0.00   0.0  0
 QO2  CONST_02  C1   C6   C5  C4     0.00   0.0  0
 QO2  CONST_03  C2   C3   C4  C5     0.00   0.0  0
 QO2  CONST_04  C2   C1   C6  C5     0.00   0.0  0
 QO2  CONST_05  C3   C2   C1  C6     0.00   0.0  0
 QO2  CONST_06  C3   C4   C5  C6     0.00   0.0  0
 QO2  CONST_07  C61  C6   C5  C4   180.00   0.0  0
 QO2  CONST_08  O3   C3   C4  C5   180.00   0.0  0
 QO2  CONST_09  C7   C1   C6  C5   180.00   0.0  0
 QO2  CONST_10  O4   C4   C5  C6   180.00   0.0  0
 QO2  CONST_11  C3   C2   C1  C7   180.00   0.0  0
 QO2  CONST_12  SG   C5   C4  C3   180.00   0.0  0
 QO2  CONST_13  O4   C4   C3  C2   180.00   0.0  0
 QO2  CONST_14  C61  C6   C1  C2   180.00   0.0  0
 QO2  CONST_15  O3   C3   C2  C1   180.00   0.0  0
 QO2  CONST_16  SG   C5   C6  C1   180.00   0.0  0
 QO2  CONST_17  H8   C2   C3  C4   180.00   0.0  0
 QO2  Var_01    H11  C61  C6  C5  -109.85  30.0  2
 QO2  Var_02    H5   C7   C1  C6   -57.26  30.0  2
 QO2  Var_03    CA   CB   SG  C5   -76.49  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
 QO2  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
 QO2  plan-1  C4   0.020
 QO2  plan-1  C5   0.020
 QO2  plan-1  C6   0.020
 QO2  plan-1  C3   0.020
 QO2  plan-1  C2   0.020
 QO2  plan-1  C1   0.020
 QO2  plan-1  O3   0.020
 QO2  plan-1  C61  0.020
 QO2  plan-1  SG   0.020
 QO2  plan-1  H8   0.020
 QO2  plan-1  C7   0.020
 QO2  plan-1  O4   0.020
 QO2  plan-2  C    0.020
 QO2  plan-2  O    0.020
 QO2  plan-2  CA   0.020
 QO2  plan-2  OXT  0.020

