# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:02:06 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(/C=C/[C@@]1(O)C(=CC(=O)CC1(C)C)C)=C/C(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
 A8S  A8S  '(2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid'  ligand  38  19  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A8S
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
 A8S  C1    C  C      0   0.394   4.4658  -0.0061  -0.8338
 A8S  C2    C  C1     0  -0.458   3.9148   0.7181   0.3733
 A8S  C3    C  C      0   0.140   2.6508   0.8330   0.8237
 A8S  C4    C  C1     0  -0.321   1.4996   0.2161   0.1642
 A8S  C5    C  C1     0  -0.236   0.2423   0.3399   0.5969
 A8S  C6    C  CH3    0  -0.747   2.3829   1.6497   2.0580
 A8S  C7    C  CT     0   0.163  -0.9644  -0.2695  -0.0680
 A8S  O7    O  OH1    0  -0.658  -0.6108  -1.2196  -1.0504
 A8S  C8    C  C      0   0.180  -1.8022  -1.0044   0.9854
 A8S  C9    C  C1     0  -0.417  -3.1403  -1.0327   0.9392
 A8S  C10   C  C      0   0.401  -3.9202  -0.3595  -0.0995
 A8S  O10   O  O      0  -0.429  -5.1382  -0.3477  -0.0679
 A8S  C11   C  CH2    0  -0.550  -3.1381   0.2512  -1.2258
 A8S  O11   O  OC    -1  -0.615   5.6810   0.1983  -1.0429
 A8S  C12   C  CT     0  -0.124  -1.7928   0.8380  -0.7842
 A8S  O12   O  O      0  -0.595   3.7186  -0.7331  -1.5223
 A8S  C13   C  CH3    0  -0.720  -1.0562  -1.7688   2.0319
 A8S  C14   C  CH3    0  -0.636  -1.0600   1.3576  -2.0210
 A8S  C15   C  CH3    0  -0.658  -2.0485   2.0262   0.1513
 A8S  H2    H  H      0   0.209   4.6754   1.2410   0.9470
 A8S  H4    H  H      0   0.255   1.7195  -0.3566  -0.7262
 A8S  H5    H  H      0   0.272   0.0205   0.9172   1.4878
 A8S  H6    H  HCH3   0   0.237   1.7031   2.4782   1.8464
 A8S  H6A   H  HCH3   0   0.236   1.9132   1.0503   2.8411
 A8S  H6B   H  HCH3   0   0.249   3.3020   2.0679   2.4647
 A8S  HO7   H  HOH1   0   0.451  -0.0129  -1.8665  -0.6595
 A8S  H9    H  H      0   0.257  -3.6997  -1.5860   1.6866
 A8S  H11   H  HCH2   0   0.280  -2.9746  -0.5401  -1.9661
 A8S  H11A  H  HCH2   0   0.262  -3.7425   1.0183  -1.7161
 A8S  H13   H  HCH3   0   0.260  -0.5078  -1.1020   2.6992
 A8S  H13A  H  HCH3   0   0.260  -1.7271  -2.3777   2.6347
 A8S  H14   H  HCH3   0   0.233  -0.9447   0.5929  -2.7882
 A8S  H14A  H  HCH3   0   0.228  -1.6311   2.1786  -2.4586
 A8S  H14B  H  HCH3   0   0.237  -0.0706   1.7422  -1.7704
 A8S  H15   H  HCH3   0   0.240  -1.1309   2.5798   0.3532
 A8S  H15A  H  HCH3   0   0.240  -2.7460   2.7182  -0.3237
 A8S  H15B  H  HCH3   0   0.235  -2.4782   1.7337   1.1106
 A8S  H13B  H  HCH3   0   0.248  -0.3116  -2.4306   1.5829

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
 A8S  O11  C1    deloc   1.250  0.020  1.250
 A8S  O12  C1    deloc   1.249  0.020  1.249
 A8S  C1   C2    single  1.512  0.020  1.512
 A8S  C2   C3    double  1.347  0.020  1.347
 A8S  C2   H2    single  0.930  0.020  1.080
 A8S  C3   C4    single  1.463  0.020  1.463
 A8S  C3   C6    single  1.504  0.020  1.504
 A8S  C4   C5    double  1.335  0.020  1.335
 A8S  C4   H4    single  0.930  0.020  1.080
 A8S  C5   C7    single  1.506  0.020  1.506
 A8S  C5   H5    single  0.930  0.020  1.080
 A8S  C6   H6    single  0.970  0.020  1.090
 A8S  C6   H6A   single  0.970  0.020  1.090
 A8S  C6   H6B   single  0.970  0.020  1.090
 A8S  O7   C7    single  1.412  0.020  1.412
 A8S  C7   C12   single  1.557  0.020  1.557
 A8S  C7   C8    single  1.534  0.020  1.534
 A8S  O7   HO7   single  0.850  0.020  0.980
 A8S  C8   C13   single  1.495  0.020  1.495
 A8S  C8   C9    double  1.339  0.020  1.339
 A8S  C9   C10   single  1.463  0.020  1.463
 A8S  C9   H9    single  0.930  0.020  1.080
 A8S  C11  C10   single  1.501  0.020  1.501
 A8S  C10  O10   double  1.219  0.020  1.219
 A8S  C12  C11   single  1.533  0.020  1.533
 A8S  C11  H11   single  0.970  0.020  1.090
 A8S  C11  H11A  single  0.970  0.020  1.090
 A8S  C15  C12   single  1.534  0.020  1.534
 A8S  C14  C12   single  1.529  0.020  1.529
 A8S  C13  H13   single  0.970  0.020  1.090
 A8S  C13  H13A  single  0.970  0.020  1.090
 A8S  C14  H14   single  0.970  0.020  1.090
 A8S  C14  H14A  single  0.970  0.020  1.090
 A8S  C14  H14B  single  0.970  0.020  1.090
 A8S  C15  H15   single  0.970  0.020  1.090
 A8S  C15  H15A  single  0.970  0.020  1.090
 A8S  C15  H15B  single  0.970  0.020  1.090
 A8S  C13  H13B  single  0.970  0.020  1.090

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
 A8S  O12   C1   O11   125.76  3.000
 A8S  O12   C1   C2    120.05  3.000
 A8S  O11   C1   C2    114.18  3.000
 A8S  H2    C2   C3    116.06  3.000
 A8S  H2    C2   C1    113.39  3.000
 A8S  C3    C2   C1    130.55  3.000
 A8S  C6    C3   C4    117.31  3.000
 A8S  C6    C3   C2    119.21  3.000
 A8S  C4    C3   C2    123.48  3.000
 A8S  H4    C4   C5    120.49  3.000
 A8S  H4    C4   C3    115.75  3.000
 A8S  C5    C4   C3    123.75  3.000
 A8S  H5    C5   C7    114.46  3.000
 A8S  H5    C5   C4    120.54  3.000
 A8S  C7    C5   C4    125.00  3.000
 A8S  H6B   C6   H6A   107.82  3.000
 A8S  H6B   C6   H6    107.84  3.000
 A8S  H6A   C6   H6    106.71  3.000
 A8S  H6B   C6   C3    111.40  3.000
 A8S  H6A   C6   C3    111.53  3.000
 A8S  H6    C6   C3    111.32  3.000
 A8S  C12   C7   C8    111.47  3.000
 A8S  C8    C7   O7    107.00  3.000
 A8S  C12   C7   O7    106.96  3.000
 A8S  C8    C7   C5    109.17  3.000
 A8S  C12   C7   C5    109.96  3.000
 A8S  O7    C7   C5    112.26  3.000
 A8S  HO7   O7   C7    108.96  3.000
 A8S  C13   C8   C9    120.79  3.000
 A8S  C9    C8   C7    122.16  3.000
 A8S  C13   C8   C7    116.94  3.000
 A8S  H9    C9   C10   116.67  3.000
 A8S  H9    C9   C8    120.14  3.000
 A8S  C10   C9   C8    123.19  3.000
 A8S  C11   C10  O10   122.44  3.000
 A8S  O10   C10  C9    121.26  3.000
 A8S  C11   C10  C9    116.25  3.000
 A8S  H11A  C11  H11   106.64  3.000
 A8S  H11A  C11  C12   110.24  3.000
 A8S  H11   C11  C12   109.88  3.000
 A8S  H11A  C11  C10   109.52  3.000
 A8S  H11   C11  C10   106.91  3.000
 A8S  C12   C11  C10   113.39  3.000
 A8S  C15   C12  C14   108.06  3.000
 A8S  C14   C12  C11   108.53  3.000
 A8S  C15   C12  C11   109.03  3.000
 A8S  C14   C12  C7    111.02  3.000
 A8S  C15   C12  C7    111.04  3.000
 A8S  C11   C12  C7    109.10  3.000
 A8S  H13B  C13  H13A  107.99  3.000
 A8S  H13B  C13  H13   106.19  3.000
 A8S  H13A  C13  H13   108.24  3.000
 A8S  H13B  C13  C8    111.23  3.000
 A8S  H13A  C13  C8    111.48  3.000
 A8S  H13   C13  C8    111.49  3.000
 A8S  H14B  C14  H14A  107.55  3.000
 A8S  H14B  C14  H14   108.26  3.000
 A8S  H14A  C14  H14   107.52  3.000
 A8S  H14B  C14  C12   111.64  3.000
 A8S  H14A  C14  C12   109.22  3.000
 A8S  H14   C14  C12   112.45  3.000
 A8S  H15B  C15  H15A  107.51  3.000
 A8S  H15B  C15  H15   107.74  3.000
 A8S  H15A  C15  H15   107.25  3.000
 A8S  H15B  C15  C12   113.22  3.000
 A8S  H15A  C15  C12   109.41  3.000
 A8S  H15   C15  C12   111.46  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
 A8S  Var_01  C10  C11  C12  C7    55.84  30.0  1
 A8S  Var_02  C10  C9   C8   C7    -0.74  30.0  1
 A8S  Var_03  C11  C10  C9   C8     6.76  30.0  1
 A8S  Var_04  C12  C11  C10  C9   -35.31  30.0  1
 A8S  Var_05  H15  C15  C12  C7    69.57  30.0  3
 A8S  Var_06  H14  C14  C12  C7    64.70  30.0  3
 A8S  Var_07  H13  C13  C8   C7    67.80  30.0  3
 A8S  Var_08  C7   C5   C4   C3   179.28   0.0  2
 A8S  Var_09  C4   C3   C2   C1     0.31   0.0  2
 A8S  Var_10  C5   C4   C3   C2  -179.16  30.0  2
 A8S  Var_11  O11  C1   C2   C3   173.12  30.0  3
 A8S  Var_12  H6   C6   C3   C2   120.00  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
 A8S  chir_01  C7  O7  C12  C8  negativ

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
 A8S  plan-1  C9   0.020
 A8S  plan-1  C10  0.020
 A8S  plan-1  O10  0.020
 A8S  plan-1  C11  0.020
 A8S  plan-2  C1   0.020
 A8S  plan-2  C2   0.020
 A8S  plan-2  O11  0.020
 A8S  plan-2  O12  0.020
 A8S  plan-3  C1   0.020
 A8S  plan-3  C2   0.020
 A8S  plan-3  C3   0.020
 A8S  plan-3  C4   0.020
 A8S  plan-3  C6   0.020
 A8S  plan-3  H2   0.020
 A8S  plan-4  C3   0.020
 A8S  plan-4  C4   0.020
 A8S  plan-4  C5   0.020
 A8S  plan-4  C7   0.020
 A8S  plan-4  H4   0.020
 A8S  plan-4  H5   0.020

