# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:19:55 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: (1~{R},3~{S})-5-methyl-2-[(1~{S})-2-naphthalen-1-yloxy-1-oxidanyl-ethyl]cyclohexane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1C[C@@H](O)[C@H]([C@H](O)COc2cccc3ccccc23)[C@@H](O)C1
#
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
 HZS  HZS  "(1R,3S)-5-methyl-2-[(1S)-2-naphthalen-1-yloxy-1-oxidanyl-ethyl]cyclohexane-1,3-diol"
  ligand  47  23  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HZS
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
 HZS  C1   C  CH2   0  -0.186   3.0927  -2.0732  84.0997
 HZS  C2   C  CH1   0   0.025   3.6986  -2.8853  82.9663
 HZS  C4   C  CH1   0  -0.327   4.8402  -3.7779  83.4652
 HZS  C5   C  CH1   0   0.042   4.2858  -4.9453  84.3106
 HZS  C6   C  CH2   0  -0.493   4.2134  -6.2328  83.5004
 HZS  C7   C  CH1   0  -0.215   5.5699  -6.6996  82.9429
 HZS  C8   C  CH2   0  -0.450   6.5045  -5.5067  82.7190
 HZS  C9   C  CH1   0   0.083   5.7209  -4.2762  82.2992
 HZS  C13  C  CR6   0   0.371   1.2396  -0.5961  84.3685
 HZS  C14  C  CR66  0  -0.019   0.0966  -0.0007  83.7534
 HZS  C15  C  CR66  0   0.126  -0.7202   0.8626  84.5275
 HZS  C16  C  CR16  0  -0.343  -0.3913   1.1146  85.8816
 HZS  C17  C  CR16  0  -0.243   0.7070   0.5243  86.4362
 HZS  C18  C  CR16  0  -0.404   1.5341  -0.3365  85.6843
 HZS  C19  C  CR16  0  -0.287  -0.2472  -0.2472  82.4040
 HZS  C20  C  CR16  0  -0.255  -1.3521   0.3413  81.8478
 HZS  C21  C  CR16  0  -0.250  -2.1647   1.1997  82.6134
 HZS  C22  C  CR16  0  -0.315  -1.8535   1.4532  83.9214
 HZS  C23  C  CH3   0  -0.660   6.2343  -7.7650  83.8067
 HZS  O3   O  OH1   0  -0.678   4.2026  -2.0146  81.9706
 HZS  O10  O  OH1   0  -0.667   5.1030  -5.0733  85.4594
 HZS  O11  O  OH1   0  -0.685   6.6323  -3.2911  81.8677
 HZS  O12  O  O2    0  -0.476   1.9642  -1.3988  83.5712
 HZS  H1   H  HCH2  0   0.235   2.7911  -2.7121  84.9355
 HZS  H2   H  HCH2  0   0.232   3.8337  -1.3571  84.4741
 HZS  H3   H  HCH1  0   0.225   2.9177  -3.5321  82.5380
 HZS  H4   H  HCH1  0   0.244   5.4890  -3.1831  84.1205
 HZS  H5   H  HCH1  0   0.217   3.2578  -4.7082  84.6199
 HZS  H6   H  HCH2  0   0.238   3.5109  -6.0579  82.6796
 HZS  H7   H  HCH2  0   0.240   3.7571  -7.0217  84.1074
 HZS  H8   H  HCH1  0   0.225   5.3731  -7.1498  81.9647
 HZS  H9   H  HCH2  0   0.232   7.2386  -5.7537  81.9477
 HZS  H10  H  HCH2  0   0.216   7.0688  -5.2849  83.6304
 HZS  H11  H  HCH1  0   0.185   5.0613  -4.5715  81.4655
 HZS  H12  H  HCR6  0   0.249  -1.0210   1.7747  86.4649
 HZS  H13  H  HCR6  0   0.257   0.9613   0.7124  87.4713
 HZS  H14  H  HCR6  0   0.281   2.3948  -0.7795  86.1664
 HZS  H15  H  HCR6  0   0.253   0.3645  -0.9051  81.8020
 HZS  H16  H  HCR6  0   0.256  -1.6044   0.1445  80.8140
 HZS  H17  H  HCR6  0   0.256  -3.0363   1.6574  82.1637
 HZS  H18  H  HCR6  0   0.254  -2.4762   2.1116  84.5152
 HZS  H19  H  HCH3  0   0.222   5.5990  -8.6466  83.9071
 HZS  H20  H  HCH3  0   0.221   7.1807  -8.0876  83.3684
 HZS  H21  H  HCH3  0   0.216   6.4457  -7.3885  84.8085
 HZS  H22  H  HOH1  0   0.461   3.4682  -1.6135  81.4955
 HZS  H23  H  HOH1  0   0.446   4.7965  -5.8373  85.9587
 HZS  H24  H  HOH1  0   0.443   6.1007  -2.5255  81.6179

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
 HZS  O11  C9   single    1.410  0.020  1.410
 HZS  O3   C2   single    1.415  0.020  1.415
 HZS  C9   C8   single    1.518  0.020  1.518
 HZS  C9   C4   single    1.544  0.020  1.544
 HZS  C20  C19  aromatic  1.370  0.020  1.370
 HZS  C20  C21  aromatic  1.408  0.020  1.408
 HZS  C8   C7   single    1.532  0.020  1.532
 HZS  C19  C14  aromatic  1.414  0.020  1.414
 HZS  C2   C4   single    1.533  0.020  1.533
 HZS  C2   C1   single    1.520  0.020  1.520
 HZS  C21  C22  aromatic  1.368  0.020  1.368
 HZS  C4   C5   single    1.544  0.020  1.544
 HZS  C7   C6   single    1.539  0.020  1.539
 HZS  C7   C23  single    1.524  0.020  1.524
 HZS  O12  C1   single    1.417  0.020  1.417
 HZS  O12  C13  single    1.343  0.020  1.343
 HZS  C14  C13  aromatic  1.428  0.020  1.428
 HZS  C14  C15  aromatic  1.418  0.020  1.418
 HZS  C6   C5   single    1.523  0.020  1.523
 HZS  C5   O10  single    1.416  0.020  1.416
 HZS  C22  C15  aromatic  1.414  0.020  1.414
 HZS  C13  C18  aromatic  1.373  0.020  1.373
 HZS  C15  C16  aromatic  1.416  0.020  1.416
 HZS  C18  C17  aromatic  1.411  0.020  1.411
 HZS  C16  C17  aromatic  1.365  0.020  1.365
 HZS  C1   H1   single    0.970  0.020  1.090
 HZS  C1   H2   single    0.970  0.020  1.090
 HZS  C2   H3   single    0.970  0.020  1.090
 HZS  C4   H4   single    0.970  0.020  1.090
 HZS  C5   H5   single    0.970  0.020  1.090
 HZS  C6   H6   single    0.970  0.020  1.090
 HZS  C6   H7   single    0.970  0.020  1.090
 HZS  C7   H8   single    0.970  0.020  1.090
 HZS  C8   H9   single    0.970  0.020  1.090
 HZS  C8   H10  single    0.970  0.020  1.090
 HZS  C9   H11  single    0.970  0.020  1.090
 HZS  C16  H12  single    0.930  0.020  1.080
 HZS  C17  H13  single    0.930  0.020  1.080
 HZS  C18  H14  single    0.930  0.020  1.080
 HZS  C19  H15  single    0.930  0.020  1.080
 HZS  C20  H16  single    0.930  0.020  1.080
 HZS  C21  H17  single    0.930  0.020  1.080
 HZS  C22  H18  single    0.930  0.020  1.080
 HZS  C23  H19  single    0.970  0.020  1.090
 HZS  C23  H20  single    0.970  0.020  1.090
 HZS  C23  H21  single    0.970  0.020  1.090
 HZS  O3   H22  single    0.850  0.020  0.980
 HZS  O10  H23  single    0.850  0.020  0.980
 HZS  O11  H24  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
 HZS  H2   C1   H1   107.86  3.000
 HZS  H2   C1   O12  110.77  3.000
 HZS  H1   C1   O12  110.08  3.000
 HZS  H2   C1   C2   109.52  3.000
 HZS  H1   C1   C2   111.55  3.000
 HZS  O12  C1   C2   107.08  3.000
 HZS  H3   C2   O3   109.90  3.000
 HZS  H3   C2   C4   108.23  3.000
 HZS  O3   C2   C4   108.78  3.000
 HZS  H3   C2   C1   108.74  3.000
 HZS  C4   C2   C1   111.43  3.000
 HZS  O3   C2   C1   109.74  3.000
 HZS  H4   C4   C9   106.77  3.000
 HZS  H4   C4   C5   107.16  3.000
 HZS  C9   C4   C5   111.98  3.000
 HZS  H4   C4   C2   108.61  3.000
 HZS  C5   C4   C2   110.55  3.000
 HZS  C9   C4   C2   111.53  3.000
 HZS  H5   C5   O10  109.33  3.000
 HZS  H5   C5   C6   106.71  3.000
 HZS  O10  C5   C6   112.51  3.000
 HZS  H5   C5   C4   109.07  3.000
 HZS  O10  C5   C4   107.78  3.000
 HZS  C6   C5   C4   111.40  3.000
 HZS  H7   C6   H6   105.27  3.000
 HZS  H7   C6   C7   110.46  3.000
 HZS  H6   C6   C7   110.04  3.000
 HZS  H7   C6   C5   109.51  3.000
 HZS  H6   C6   C5   107.12  3.000
 HZS  C7   C6   C5   114.03  3.000
 HZS  H8   C7   C23  107.29  3.000
 HZS  H8   C7   C8   107.42  3.000
 HZS  C23  C7   C8   111.18  3.000
 HZS  H8   C7   C6   106.86  3.000
 HZS  C23  C7   C6   113.02  3.000
 HZS  C8   C7   C6   110.77  3.000
 HZS  H10  C8   H9   106.68  3.000
 HZS  H10  C8   C9   109.40  3.000
 HZS  H9   C8   C9   109.56  3.000
 HZS  H10  C8   C7   110.52  3.000
 HZS  H9   C8   C7   109.69  3.000
 HZS  C9   C8   C7   110.90  3.000
 HZS  H11  C9   O11  110.01  3.000
 HZS  H11  C9   C8   107.50  3.000
 HZS  O11  C9   C8   108.50  3.000
 HZS  H11  C9   C4   108.42  3.000
 HZS  C8   C9   C4   110.32  3.000
 HZS  O11  C9   C4   111.99  3.000
 HZS  O12  C13  C18  124.47  3.000
 HZS  C18  C13  C14  120.37  3.000
 HZS  O12  C13  C14  115.16  3.000
 HZS  C19  C14  C15  119.14  3.000
 HZS  C15  C14  C13  118.66  3.000
 HZS  C19  C14  C13  122.21  3.000
 HZS  C22  C15  C16  121.44  3.000
 HZS  C16  C15  C14  119.77  3.000
 HZS  C22  C15  C14  118.80  3.000
 HZS  H12  C16  C17  120.86  3.000
 HZS  H12  C16  C15  119.24  3.000
 HZS  C17  C16  C15  119.90  3.000
 HZS  H13  C17  C18  118.55  3.000
 HZS  H13  C17  C16  120.17  3.000
 HZS  C18  C17  C16  121.28  3.000
 HZS  H14  C18  C17  118.61  3.000
 HZS  H14  C18  C13  121.37  3.000
 HZS  C17  C18  C13  120.02  3.000
 HZS  H15  C19  C20  119.45  3.000
 HZS  H15  C19  C14  119.98  3.000
 HZS  C20  C19  C14  120.58  3.000
 HZS  H16  C20  C21  119.71  3.000
 HZS  H16  C20  C19  119.85  3.000
 HZS  C21  C20  C19  120.43  3.000
 HZS  H17  C21  C22  120.14  3.000
 HZS  H17  C21  C20  119.77  3.000
 HZS  C22  C21  C20  120.09  3.000
 HZS  H18  C22  C21  120.38  3.000
 HZS  H18  C22  C15  118.65  3.000
 HZS  C21  C22  C15  120.97  3.000
 HZS  H21  C23  H20  107.63  3.000
 HZS  H21  C23  H19  107.89  3.000
 HZS  H20  C23  H19  107.63  3.000
 HZS  H21  C23  C7   111.32  3.000
 HZS  H20  C23  C7   110.91  3.000
 HZS  H19  C23  C7   111.29  3.000
 HZS  H22  O3   C2   109.39  3.000
 HZS  H23  O10  C5   107.99  3.000
 HZS  H24  O11  C9   106.11  3.000
 HZS  C13  O12  C1   119.51  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
 HZS  CONST_01  C20  C19  C14  C13   180.00   0.0  0
 HZS  CONST_02  C22  C15  C14  C13   180.00   0.0  0
 HZS  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 HZS  CONST_04  C16  C17  C18  C13     0.00   0.0  0
 HZS  CONST_05  C21  C20  C19  C14     0.00   0.0  0
 HZS  CONST_06  C17  C18  C13  C14     0.00   0.0  0
 HZS  CONST_07  C21  C22  C15  C14     0.00   0.0  0
 HZS  CONST_08  C17  C16  C15  C14     0.00   0.0  0
 HZS  CONST_09  C20  C19  C14  C15     0.00   0.0  0
 HZS  CONST_10  C18  C13  C14  C15     0.00   0.0  0
 HZS  CONST_11  C20  C21  C22  C15     0.00   0.0  0
 HZS  CONST_12  C18  C17  C16  C15     0.00   0.0  0
 HZS  CONST_13  C19  C14  C15  C16   180.00   0.0  0
 HZS  CONST_14  C21  C22  C15  C16   180.00   0.0  0
 HZS  CONST_15  C22  C15  C16  C17   180.00   0.0  0
 HZS  CONST_16  C19  C14  C13  C18   180.00   0.0  0
 HZS  CONST_17  C22  C21  C20  C19     0.00   0.0  0
 HZS  CONST_18  C22  C15  C14  C19     0.00   0.0  0
 HZS  CONST_19  O12  C13  C14  C15   180.00   0.0  0
 HZS  CONST_20  O12  C13  C18  C17   180.00   0.0  0
 HZS  CONST_21  O12  C13  C14  C19     0.00   0.0  0
 HZS  CONST_22  H15  C19  C14  C13     0.00   0.0  0
 HZS  CONST_23  H13  C17  C18  C13   180.00   0.0  0
 HZS  CONST_24  H16  C20  C19  C14   180.00   0.0  0
 HZS  CONST_25  H14  C18  C13  C14   180.00   0.0  0
 HZS  CONST_26  H18  C22  C15  C14   180.00   0.0  0
 HZS  CONST_27  H12  C16  C15  C14   180.00   0.0  0
 HZS  CONST_28  H15  C19  C14  C15   180.00   0.0  0
 HZS  CONST_29  H17  C21  C22  C15   180.00   0.0  0
 HZS  CONST_30  H13  C17  C16  C15   180.00   0.0  0
 HZS  CONST_31  H18  C22  C15  C16     0.00   0.0  0
 HZS  CONST_32  H14  C18  C17  C16   180.00   0.0  0
 HZS  CONST_33  H12  C16  C17  C18   180.00   0.0  0
 HZS  CONST_34  H17  C21  C20  C19   180.00   0.0  0
 HZS  CONST_35  H18  C22  C21  C20   180.00   0.0  0
 HZS  CONST_36  H15  C19  C20  C21   180.00   0.0  0
 HZS  CONST_37  H16  C20  C21  C22   180.00   0.0  0
 HZS  CONST_38  H12  C16  C15  C22     0.00   0.0  0
 HZS  Var_01    C14  C13  O12  C1   -177.88  30.0  2
 HZS  Var_02    C18  C13  O12  C1      2.06  30.0  2
 HZS  Var_03    C13  O12  C1   C2   -179.67  30.0  1
 HZS  Var_04    H1   C1   O12  C13    58.90  30.0  3
 HZS  Var_05    H2   C1   O12  C13   -60.30  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
 HZS  chir_01  C2  O3   C4  C1  negativ
 HZS  chir_02  C4  C9   C2  C5  negativ
 HZS  chir_03  C5  O10  C4  C6  negativ
 HZS  chir_04  C7  C23  C6  C8  negativ
 HZS  chir_05  C9  O11  C4  C8  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
 HZS  plan-1  C13  0.020
 HZS  plan-1  C14  0.020
 HZS  plan-1  C15  0.020
 HZS  plan-1  C16  0.020
 HZS  plan-1  C17  0.020
 HZS  plan-1  C18  0.020
 HZS  plan-1  C19  0.020
 HZS  plan-1  C20  0.020
 HZS  plan-1  C21  0.020
 HZS  plan-1  C22  0.020
 HZS  plan-1  O12  0.020
 HZS  plan-1  H12  0.020
 HZS  plan-1  H13  0.020
 HZS  plan-1  H14  0.020
 HZS  plan-1  H15  0.020
 HZS  plan-1  H16  0.020
 HZS  plan-1  H17  0.020
 HZS  plan-1  H18  0.020

