# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:10:29 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: [(6S)-6-hydroxy-3-oxocyclohexa-1,4-dien-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C=CC(=O)C=C1CC(O)=O
#
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
 HQ9  HQ9  '[(6S)-6-hydroxy-3-oxocyclohexa-1,4-dien-1-yl]acetic acid'  ligand  19  12  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HQ9
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
 HQ9  C1    C  C      0   0.431   2.3476  -0.2400  -0.3544
 HQ9  C2    C  CH2    0  -0.663   1.4512  -0.3203   0.9139
 HQ9  C1'   C  C      0   0.179   0.0079  -0.1239   0.6166
 HQ9  C2'   C  C1     0  -0.430  -0.8564  -1.1422   0.5032
 HQ9  C3'   C  C      0   0.386  -2.2641  -0.9575   0.1590
 HQ9  O3'   O  O      0  -0.450  -3.0462  -1.8966   0.1025
 HQ9  C4'   C  C1     0  -0.347  -2.6985   0.4158  -0.1403
 HQ9  C5'   C  C1     0  -0.224  -1.8608   1.4425  -0.0094
 HQ9  C6'   C  CH1    0  -0.039  -0.4620   1.2974   0.5006
 HQ9  O6'   O  OH1    0  -0.649   0.4555   2.0388  -0.2679
 HQ9  O1    O  OC    -1  -0.615   3.5049   0.1823  -0.1788
 HQ9  O2    O  O      0  -0.600   1.8479  -0.6552  -1.4136
 HQ9  H21C  H  HCH2   0   0.254   1.5972  -1.3150   1.3461
 HQ9  H22C  H  HCH2   0   0.237   1.7943   0.4022   1.6571
 HQ9  H2'   H  H      0   0.252  -0.5217  -2.1620   0.6595
 HQ9  H4'   H  H      0   0.267  -3.7184   0.5584  -0.4771
 HQ9  H5'   H  H      0   0.279  -2.1901   2.4521  -0.2303
 HQ9  H6'   H  HCH1   0   0.267  -0.4803   1.6728   1.5391
 HQ9  H6'A  H  HOH1   0   0.464   0.4138   2.9584   0.0123

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
 HQ9  C1   C2    single  1.555  0.020  1.555
 HQ9  C1   O1    deloc   1.244  0.020  1.244
 HQ9  C1   O2    deloc   1.243  0.020  1.243
 HQ9  C2   C1'   single  1.487  0.020  1.487
 HQ9  C1'  C2'   double  1.340  0.020  1.340
 HQ9  C1'  C6'   single  1.501  0.020  1.501
 HQ9  C2'  C3'   single  1.461  0.020  1.461
 HQ9  C3'  O3'   double  1.224  0.020  1.224
 HQ9  C3'  C4'   single  1.471  0.020  1.471
 HQ9  C4'  C5'   double  1.331  0.020  1.331
 HQ9  C5'  C6'   single  1.496  0.020  1.496
 HQ9  C6'  O6'   single  1.408  0.020  1.408
 HQ9  C2   H21C  single  0.970  0.020  1.090
 HQ9  C2   H22C  single  0.970  0.020  1.090
 HQ9  C2'  H2'   single  0.930  0.020  1.080
 HQ9  C4'  H4'   single  0.930  0.020  1.080
 HQ9  C5'  H5'   single  0.930  0.020  1.080
 HQ9  C6'  H6'   single  0.970  0.020  1.090
 HQ9  O6'  H6'A  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
 HQ9  O2    C1   O1    127.42  3.000
 HQ9  O2    C1   C2    116.50  3.000
 HQ9  O1    C1   C2    116.01  3.000
 HQ9  H22C  C2   H21C  106.90  3.000
 HQ9  H22C  C2   C1'   110.72  3.000
 HQ9  H21C  C2   C1'   109.18  3.000
 HQ9  H22C  C2   C1    109.87  3.000
 HQ9  H21C  C2   C1    106.99  3.000
 HQ9  C1'   C2   C1    112.94  3.000
 HQ9  C6'   C1'  C2'   120.72  3.000
 HQ9  C6'   C1'  C2    116.38  3.000
 HQ9  C2'   C1'  C2    122.86  3.000
 HQ9  H2'   C2'  C3'   116.76  3.000
 HQ9  H2'   C2'  C1'   120.21  3.000
 HQ9  C3'   C2'  C1'   123.03  3.000
 HQ9  C4'   C3'  O3'   121.22  3.000
 HQ9  C4'   C3'  C2'   116.78  3.000
 HQ9  O3'   C3'  C2'   121.99  3.000
 HQ9  H4'   C4'  C5'   121.42  3.000
 HQ9  H4'   C4'  C3'   117.65  3.000
 HQ9  C5'   C4'  C3'   120.93  3.000
 HQ9  H5'   C5'  C6'   116.33  3.000
 HQ9  H5'   C5'  C4'   120.44  3.000
 HQ9  C6'   C5'  C4'   123.16  3.000
 HQ9  H6'   C6'  O6'   110.19  3.000
 HQ9  H6'   C6'  C5'   105.79  3.000
 HQ9  O6'   C6'  C5'   111.85  3.000
 HQ9  H6'   C6'  C1'   104.73  3.000
 HQ9  O6'   C6'  C1'   109.68  3.000
 HQ9  C5'   C6'  C1'   114.25  3.000
 HQ9  H6'A  O6'  C6'   108.43  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
 HQ9  Var_01  C4'  C3'  C2'  C1'    3.36  30.0  1
 HQ9  Var_02  C5'  C4'  C3'  C2'   -4.50  30.0  1
 HQ9  Var_03  C6'  C1'  C2'  C3'    5.02  30.0  1
 HQ9  Var_04  C6'  C5'  C4'  C3'   -2.86  30.0  1
 HQ9  Var_05  C2'  C1'  C2   C1    99.70  30.0  3
 HQ9  Var_06  O1   C1   C2   C1'  149.81  30.0  2

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
 HQ9  chir_01  C6'  C1'  C5'  O6'  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
 HQ9  plan-1  C2'  0.020
 HQ9  plan-1  C3'  0.020
 HQ9  plan-1  O3'  0.020
 HQ9  plan-1  C4'  0.020
 HQ9  plan-2  C1   0.020
 HQ9  plan-2  C2   0.020
 HQ9  plan-2  O1   0.020
 HQ9  plan-2  O2   0.020

