# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:23:45 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: [(6R)-6-hydroperoxy-6-hydroxy-3-oxocyclohexa-1,4-dien-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OO[C@]1(O)C=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
 HMQ  HMQ  '[(6R)-6-hydroperoxy-6-hydroxy-3-oxocyclohexa-1,4-dien-1-yl]acetic acid'  ligand  22  14  .  2021-08-11  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HMQ
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
 HMQ  O5    O  O     0  -0.409  -2.4143   2.8792   0.0858
 HMQ  C5    C  C     0   0.404  -1.8396   1.8084   0.1456
 HMQ  C6    C  C1    0  -0.409  -0.5314   1.6047  -0.4962
 HMQ  C4    C  C1    0  -0.354  -2.4049   0.6665   0.8806
 HMQ  C3    C  C1    0  -0.198  -1.8016  -0.5173   0.8922
 HMQ  C2    C  CT    0   0.375  -0.5264  -0.7930   0.1432
 HMQ  O6    O  O2    0  -0.299  -0.8162  -1.6030  -0.9905
 HMQ  O7    O  OH1   0  -0.443  -1.3409  -2.8355  -0.5567
 HMQ  O2    O  OH1   0  -0.640   0.4358  -1.3603   0.9560
 HMQ  C1    C  C     0   0.154   0.0974   0.4315  -0.4888
 HMQ  C7    C  CH2   0  -0.653   1.4592   0.2463  -1.0806
 HMQ  C8    C  C     0   0.561   2.5365   0.3379  -0.0217
 HMQ  OD1   O  O     0  -0.434   2.4974   1.0889   0.9178
 HMQ  OD2   O  OH1   0  -0.587   3.5592  -0.4619  -0.2856
 HMQ  H6    H  H     0   0.281  -0.0782   2.4688  -0.9680
 HMQ  H4    H  H     0   0.285  -3.3337   0.8256   1.4137
 HMQ  H3    H  H     0   0.308  -2.2398  -1.3444   1.4401
 HMQ  H2    H  HOH1  0   0.477   0.0389  -1.9749   1.5854
 HMQ  H71C  H  HCH2  0   0.299   1.5390  -0.6909  -1.6310
 HMQ  H72C  H  HCH2  0   0.320   1.6554   1.0507  -1.7956
 HMQ  HD2   H  HOH1  0   0.483   4.2587  -0.3343   0.3737
 HMQ  H7L   H  HOH1  0   0.479  -0.5810  -3.4290  -0.6489

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
 HMQ  O5   C5    double  1.217  0.020  1.217
 HMQ  C5   C6    single  1.471  0.020  1.471
 HMQ  C5   C4    single  1.471  0.020  1.471
 HMQ  C6   C1    double  1.331  0.020  1.331
 HMQ  C4   C3    double  1.329  0.020  1.329
 HMQ  C3   C2    single  1.504  0.020  1.504
 HMQ  C2   O6    single  1.423  0.020  1.423
 HMQ  C2   O2    single  1.381  0.020  1.381
 HMQ  C2   C1    single  1.513  0.020  1.513
 HMQ  O6   O7    single  1.408  0.020  1.408
 HMQ  C1   C7    single  1.496  0.020  1.496
 HMQ  C7   C8    single  1.513  0.020  1.513
 HMQ  C8   OD1   double  1.203  0.020  1.203
 HMQ  C8   OD2   single  1.325  0.020  1.325
 HMQ  C6   H6    single  0.930  0.020  1.080
 HMQ  C4   H4    single  0.930  0.020  1.080
 HMQ  C3   H3    single  0.930  0.020  1.080
 HMQ  O2   H2    single  0.850  0.020  0.980
 HMQ  C7   H71C  single  0.970  0.020  1.090
 HMQ  C7   H72C  single  0.970  0.020  1.090
 HMQ  OD2  HD2   single  0.850  0.020  0.980
 HMQ  O7   H7L   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
 HMQ  C4    C5   C6    116.89  3.000
 HMQ  C4    C5   O5    121.76  3.000
 HMQ  C6    C5   O5    121.35  3.000
 HMQ  H6    C6   C1    120.50  3.000
 HMQ  H6    C6   C5    116.83  3.000
 HMQ  C1    C6   C5    122.66  3.000
 HMQ  H4    C4   C3    121.07  3.000
 HMQ  H4    C4   C5    117.50  3.000
 HMQ  C3    C4   C5    121.43  3.000
 HMQ  H3    C3   C2    117.01  3.000
 HMQ  H3    C3   C4    120.03  3.000
 HMQ  C2    C3   C4    122.95  3.000
 HMQ  C1    C2   O2    106.92  3.000
 HMQ  C1    C2   O6    102.24  3.000
 HMQ  O2    C2   O6    112.14  3.000
 HMQ  C1    C2   C3    114.15  3.000
 HMQ  O2    C2   C3    111.88  3.000
 HMQ  O6    C2   C3    109.17  3.000
 HMQ  O7    O6   C2    109.19  3.000
 HMQ  H7L   O7   O6    102.39  3.000
 HMQ  H2    O2   C2    111.03  3.000
 HMQ  C7    C1   C2    116.12  3.000
 HMQ  C7    C1   C6    122.47  3.000
 HMQ  C2    C1   C6    121.40  3.000
 HMQ  H72C  C7   H71C  106.81  3.000
 HMQ  H72C  C7   C8    106.57  3.000
 HMQ  H71C  C7   C8    110.69  3.000
 HMQ  H72C  C7   C1    109.31  3.000
 HMQ  H71C  C7   C1    111.89  3.000
 HMQ  C8    C7   C1    111.32  3.000
 HMQ  OD2   C8   OD1   123.88  3.000
 HMQ  OD2   C8   C7    111.93  3.000
 HMQ  OD1   C8   C7    124.12  3.000
 HMQ  HD2   OD2  C8    110.00  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
 HMQ  CONST_01  HD2  OD2  C8  C7  180.00   0.0  0
 HMQ  Var_01    C2   C1   C6  C5    2.36  30.0  1
 HMQ  Var_02    C2   C3   C4  C5   -1.32  30.0  1
 HMQ  Var_03    C3   C4   C5  C6   -4.13  30.0  1
 HMQ  Var_04    C1   C6   C5  C4    3.59  30.0  1
 HMQ  Var_05    C8   C7   C1  C6   96.69  30.0  3
 HMQ  Var_06    OD1  C8   C7  C1  -36.55  30.0  3

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
 HMQ  chir_01  C2  C3  O2  C1  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
 HMQ  plan-1  O5   0.020
 HMQ  plan-1  C5   0.020
 HMQ  plan-1  C6   0.020
 HMQ  plan-1  C4   0.020
 HMQ  plan-2  C7   0.020
 HMQ  plan-2  C8   0.020
 HMQ  plan-2  OD1  0.020
 HMQ  plan-2  OD2  0.020
 HMQ  plan-2  HD2  0.020

