# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 12:29:22 2021
#   Inital geometry file: a 80 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[4,6-dimethyl-2,3-bis(oxidanyl)phenyl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c(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
 QO5  QO5  '(2~{R})-2-azanyl-3-[4,6-dimethyl-2,3-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_QO5
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
 QO5  C11  C  CH3   0  -0.737  23.9605  65.7354  83.4913
 QO5  N    N  NH2   0  -0.797  27.5767  65.0528  83.7999
 QO5  CA   C  CH1   0  -0.173  27.4148  64.9375  82.3701
 QO5  CB   C  CH2   0  -0.571  27.5568  66.3093  81.7076
 QO5  SG   S  S2    0  -0.015  26.2537  67.4851  82.2046
 QO5  C    C  C     0   0.545  28.4605  64.0337  81.7376
 QO5  O    O  O     0  -0.449  28.3363  63.5826  80.6252
 QO5  C1   C  CR6   0   0.122  23.8623  66.0678  82.0312
 QO5  C2   C  CR6   0  -0.329  24.8404  66.8198  81.3680
 QO5  C3   C  CR6   0   0.348  24.6960  67.1251  80.0131
 QO5  O3   O  OH1   0  -0.637  25.5838  67.8677  79.3229
 QO5  C4   C  CR6   0   0.255  23.5963  66.6532  79.2923
 QO5  O4   O  OH1   0  -0.628  23.4472  66.9291  77.9774
 QO5  C5   C  CR6   0   0.010  22.6265  65.8909  79.9309
 QO5  C6   C  CR16  0  -0.377  22.7769  65.6208  81.2900
 QO5  C51  C  CH3   0  -0.714  21.4390  65.3896  79.1665
 QO5  H1   H  HCH3  0   0.240  24.7164  64.9711  83.6801
 QO5  H2   H  HCH3  0   0.246  24.2248  66.6033  84.0943
 QO5  H3   H  HCH3  0   0.253  23.0120  65.3467  83.8586
 QO5  H5   H  HNH2  0   0.359  27.3366  64.1812  84.2548
 QO5  H7   H  HCH1  0   0.261  26.4481  64.5185  82.0545
 QO5  H8   H  HCH2  0   0.293  27.5544  66.2188  80.6226
 QO5  H9   H  HCH2  0   0.299  28.4958  66.7779  82.0089
 QO5  H11  H  HOH1  0   0.473  26.1894  68.3104  79.9381
 QO5  H12  H  HOH1  0   0.472  24.1464  67.5220  77.6781
 QO5  H13  H  HCR6  0   0.243  22.0093  65.0399  81.7877
 QO5  H14  H  HCH3  0   0.247  21.7351  64.7344  78.3455
 QO5  H15  H  HCH3  0   0.245  20.7704  64.8276  79.8162
 QO5  H16  H  HCH3  0   0.246  20.8668  66.2086  78.7277
 QO5  OXT  O  OH1   0  -0.573  29.5161  63.8159  82.5017
 QO5  H6   H  HOH1  0   0.482  30.1453  63.2495  82.0295
 QO5  H4   H  HNH2  0   0.358  26.9233  65.7417  84.1525

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
 QO5  O4   C4   single    1.352  0.020  1.352
 QO5  C51  C5   single    1.499  0.020  1.499
 QO5  C4   C5   aromatic  1.389  0.020  1.389
 QO5  C4   C3   aromatic  1.397  0.020  1.397
 QO5  O3   C3   single    1.348  0.020  1.348
 QO5  C5   C6   aromatic  1.394  0.020  1.394
 QO5  C3   C2   aromatic  1.396  0.020  1.396
 QO5  O    C    double    1.231  0.020  1.231
 QO5  C6   C1   aromatic  1.388  0.020  1.388
 QO5  C2   C1   aromatic  1.401  0.020  1.401
 QO5  C2   SG   single    1.772  0.020  1.772
 QO5  C    CA   single    1.525  0.021  1.525
 QO5  CB   SG   single    1.824  0.020  1.824
 QO5  CB   CA   single    1.530  0.020  1.530
 QO5  C1   C11  single    1.501  0.020  1.501
 QO5  CA   N    single    1.458  0.019  1.458
 QO5  C11  H1   single    0.970  0.020  1.090
 QO5  C11  H2   single    0.970  0.020  1.090
 QO5  C11  H3   single    0.970  0.020  1.090
 QO5  N    H4   single    0.890  0.020  1.040
 QO5  N    H5   single    0.890  0.020  1.040
 QO5  CA   H7   single    0.970  0.020  1.090
 QO5  CB   H8   single    0.970  0.020  1.090
 QO5  CB   H9   single    0.970  0.020  1.090
 QO5  O3   H11  single    0.850  0.020  0.980
 QO5  O4   H12  single    0.850  0.020  0.980
 QO5  C6   H13  single    0.930  0.020  1.080
 QO5  C51  H14  single    0.970  0.020  1.090
 QO5  C51  H15  single    0.970  0.020  1.090
 QO5  C51  H16  single    0.970  0.020  1.090
 QO5  C    OXT  single    1.321  0.020  1.321
 QO5  OXT  H6   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
 QO5  H3   C11  H2   108.00  3.000
 QO5  H3   C11  H1   107.16  3.000
 QO5  H2   C11  H1   107.11  3.000
 QO5  H3   C11  C1   110.50  3.000
 QO5  H2   C11  C1   112.21  3.000
 QO5  H1   C11  C1   111.64  3.000
 QO5  H5   N    H4   106.04  3.000
 QO5  H5   N    CA   110.48  3.000
 QO5  H4   N    CA   109.08  3.000
 QO5  H7   CA   C    105.00  3.000
 QO5  H7   CA   CB   107.39  3.000
 QO5  C    CA   CB   110.10  1.900
 QO5  H7   CA   N    114.41  3.000
 QO5  CB   CA   N    110.50  1.700
 QO5  C    CA   N    111.00  2.800
 QO5  H9   CB   H8   108.21  3.000
 QO5  H9   CB   SG   105.23  3.000
 QO5  H8   CB   SG   108.88  3.000
 QO5  H9   CB   CA   110.19  3.000
 QO5  H8   CB   CA   110.90  3.000
 QO5  SG   CB   CA   113.18  3.000
 QO5  C2   SG   CB   101.49  3.000
 QO5  OXT  C    O    123.62  3.000
 QO5  OXT  C    CA   114.02  3.000
 QO5  O    C    CA   120.80  1.700
 QO5  C6   C1   C2   117.78  3.000
 QO5  C2   C1   C11  122.27  3.000
 QO5  C6   C1   C11  119.95  3.000
 QO5  C3   C2   C1   120.31  3.000
 QO5  C1   C2   SG   122.34  3.000
 QO5  C3   C2   SG   117.29  3.000
 QO5  C4   C3   O3   116.13  3.000
 QO5  O3   C3   C2   123.33  3.000
 QO5  C4   C3   C2   120.54  3.000
 QO5  H11  O3   C3   109.75  3.000
 QO5  C5   C4   O4   118.83  3.000
 QO5  C5   C4   C3   119.85  3.000
 QO5  O4   C4   C3   121.32  3.000
 QO5  H12  O4   C4   110.32  3.000
 QO5  C51  C5   C6   121.20  3.000
 QO5  C6   C5   C4   118.64  3.000
 QO5  C51  C5   C4   120.15  3.000
 QO5  H13  C6   C5   118.38  3.000
 QO5  H13  C6   C1   118.76  3.000
 QO5  C5   C6   C1   122.86  3.000
 QO5  H16  C51  H15  107.78  3.000
 QO5  H16  C51  H14  106.88  3.000
 QO5  H15  C51  H14  107.80  3.000
 QO5  H16  C51  C5   111.69  3.000
 QO5  H15  C51  C5   110.79  3.000
 QO5  H14  C51  C5   111.69  3.000
 QO5  H6   OXT  C    109.46  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
 QO5  CONST_01  C4   C5   C6  C1     0.00   0.0  0
 QO5  CONST_02  C4   C3   C2  C1     0.00   0.0  0
 QO5  CONST_03  C5   C4   C3  C2     0.00   0.0  0
 QO5  CONST_04  C5   C6   C1  C2     0.00   0.0  0
 QO5  CONST_05  C6   C5   C4  C3     0.00   0.0  0
 QO5  CONST_06  C6   C1   C2  C3     0.00   0.0  0
 QO5  CONST_07  C5   C6   C1  C11  180.00   0.0  0
 QO5  CONST_08  C3   C2   C1  C11  180.00   0.0  0
 QO5  CONST_09  C4   C3   C2  SG   180.00   0.0  0
 QO5  CONST_10  C6   C1   C2  SG   180.00   0.0  0
 QO5  CONST_11  C51  C5   C6  C1   180.00   0.0  0
 QO5  CONST_12  O3   C3   C2  C1   180.00   0.0  0
 QO5  CONST_13  O4   C4   C3  C2   180.00   0.0  0
 QO5  CONST_14  C51  C5   C4  C3   180.00   0.0  0
 QO5  CONST_15  C5   C4   C3  O3   180.00   0.0  0
 QO5  CONST_16  C6   C5   C4  O4   180.00   0.0  0
 QO5  CONST_17  H13  C6   C1  C2   180.00   0.0  0
 QO5  CONST_18  H6   OXT  C   CA   180.00   0.0  0
 QO5  Var_01    C3   C2   SG  CB   -80.69  30.0  2
 QO5  Var_02    H1   C11  C1  C2   -73.54  30.0  2
 QO5  Var_03    H14  C51  C5  C4    60.84  30.0  2
 QO5  Var_04    H8   CB   SG  C2    52.23  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
 QO5  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
 QO5  plan-1  C11  0.020
 QO5  plan-1  SG   0.020
 QO5  plan-1  C1   0.020
 QO5  plan-1  C2   0.020
 QO5  plan-1  C3   0.020
 QO5  plan-1  O3   0.020
 QO5  plan-1  C4   0.020
 QO5  plan-1  O4   0.020
 QO5  plan-1  C5   0.020
 QO5  plan-1  C6   0.020
 QO5  plan-1  C51  0.020
 QO5  plan-1  H13  0.020
 QO5  plan-2  CA   0.020
 QO5  plan-2  C    0.020
 QO5  plan-2  O    0.020
 QO5  plan-2  OXT  0.020
 QO5  plan-2  H6   0.020

