# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 01:17:32 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-[(1R,2R,5S)-5-methyl-2-(prop-1-en-2-yl)cyclohexyl]-5-pentylbenzene-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCc1cc(O)c([C@@H]2C[C@@H](C)CC[C@H]2C(C)=C)c(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
 CD0  CD0  2-[(1R,2R,5S)-5-methyl-2-(prop-1-en-2-yl)cyclohexyl]-5-pentylbenzene-1,3-diol  ligand  55  23  .  2022-03-15  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CD0
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
 CD0  C11  C  CR6   0   0.324  147.0882  107.9696  126.3560
 CD0  C12  C  CR6   0   0.359  146.5672  108.0554  128.6718
 CD0  C21  C  CH2   0  -0.423  144.4154  103.8186  129.4875
 CD0  C22  C  CH2   0  -0.418  143.0861  103.4346  130.1274
 CD0  C03  C  CH1   0  -0.327  149.0611  110.3725  127.2139
 CD0  C04  C  CH1   0  -0.350  147.6011  110.1271  127.6649
 CD0  C05  C  CH2   0  -0.424  149.4500  111.8058  127.5964
 CD0  C06  C  CH2   0  -0.427  148.5232  112.8177  126.9286
 CD0  C07  C  CH2   0  -0.401  146.6627  111.1330  126.9808
 CD0  C08  C  CR6   0  -0.054  147.1016  108.7019  127.5472
 CD0  C09  C  CH1   0  -0.237  147.0486  112.5867  127.2711
 CD0  C10  C  C     0   0.232  150.0212  109.3419  127.7489
 CD0  C13  C  CH3   0  -0.667  146.7145  112.9988  128.7031
 CD0  C14  C  CH3   0  -0.743  150.1672  109.2270  129.2376
 CD0  C15  C  CR6   0   0.142  146.0823  106.0453  127.4265
 CD0  C16  C  CR16  0  -0.443  146.5884  106.6698  126.2963
 CD0  C17  C  CR16  0  -0.478  146.0765  106.7549  128.6218
 CD0  C18  C  CH2   0  -0.506  145.5736  104.6290  127.3238
 CD0  C19  C  C2    0  -0.602  150.7196  108.5669  126.9212
 CD0  C20  C  CH2   0  -0.437  144.2590  104.3205  128.0555
 CD0  C23  C  CH3   0  -0.662  143.2441  102.9449  131.5602
 CD0  O01  O  OH1   0  -0.636  147.5376  108.4618  125.1789
 CD0  O02  O  OH1   0  -0.639  146.5379  108.7462  129.8344
 CD0  H1   H  HCH2  0   0.213  145.0815  102.9489  129.4916
 CD0  H2   H  HCH2  0   0.220  144.9045  104.5696  130.1142
 CD0  H3   H  HCH2  0   0.212  142.4121  104.2963  130.1054
 CD0  H4   H  HCH2  0   0.212  142.6066  102.6594  129.5214
 CD0  H5   H  HCH1  0   0.211  149.1358  110.3406  126.1175
 CD0  H6   H  HCH1  0   0.264  147.5861  110.3649  128.7296
 CD0  H7   H  HCH2  0   0.239  150.4832  111.9947  127.2948
 CD0  H8   H  HCH2  0   0.222  149.4160  111.9227  128.6837
 CD0  H9   H  HCH2  0   0.221  148.6519  112.7466  125.8431
 CD0  H10  H  HCH2  0   0.229  148.8172  113.8335  127.2066
 CD0  H11  H  HCH2  0   0.237  145.6356  110.9494  127.3070
 CD0  H12  H  HCH2  0   0.213  146.6675  110.9808  125.8957
 CD0  H13  H  HCH1  0   0.229  146.4499  113.2201  126.6085
 CD0  H14  H  HCH3  0   0.227  145.6547  112.8455  128.9140
 CD0  H15  H  HCH3  0   0.220  147.2784  112.4392  129.4504
 CD0  H16  H  HCH3  0   0.228  146.9326  114.0564  128.8607
 CD0  H17  H  HCH3  0   0.242  150.9026  108.4686  129.5041
 CD0  H18  H  HCH3  0   0.239  150.4844  110.1712  129.6854
 CD0  H19  H  HCH3  0   0.245  149.2229  108.9573  129.7145
 CD0  H20  H  HCR6  0   0.244  146.5923  106.1520  125.3440
 CD0  H21  H  HCR6  0   0.256  145.6896  106.3076  129.5294
 CD0  H22  H  HCH2  0   0.247  145.4520  104.3988  126.2636
 CD0  H23  H  HCH2  0   0.242  146.3510  103.9446  127.6819
 CD0  H24  H  H     0   0.226  151.4194  107.8269  127.2908
 CD0  H25  H  H     0   0.227  150.6160  108.6414  125.8451
 CD0  H26  H  HCH2  0   0.221  143.6099  105.2016  128.0365
 CD0  H27  H  HCH2  0   0.228  143.7294  103.5493  127.4884
 CD0  H28  H  HCH3  0   0.227  142.2857  102.6660  131.9995
 CD0  H29  H  HCH3  0   0.216  143.8965  102.0708  131.6086
 CD0  H30  H  HCH3  0   0.216  143.6843  103.7185  132.1926
 CD0  H31  H  HOH1  0   0.471  147.9103  109.3411  125.2830
 CD0  H32  H  HOH1  0   0.474  146.1925  108.1878  130.5392

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
 CD0  O01  C11  single    1.353  0.020  1.353
 CD0  C16  C11  aromatic  1.394  0.020  1.394
 CD0  C16  C15  aromatic  1.387  0.020  1.387
 CD0  C11  C08  aromatic  1.398  0.020  1.398
 CD0  C06  C09  single    1.531  0.020  1.531
 CD0  C06  C05  single    1.526  0.020  1.526
 CD0  C18  C15  single    1.508  0.020  1.508
 CD0  C18  C20  single    1.536  0.020  1.536
 CD0  C07  C09  single    1.532  0.020  1.532
 CD0  C07  C04  single    1.536  0.020  1.536
 CD0  C09  C13  single    1.527  0.020  1.527
 CD0  C15  C17  aromatic  1.390  0.020  1.390
 CD0  C03  C05  single    1.534  0.020  1.534
 CD0  C03  C04  single    1.548  0.020  1.548
 CD0  C03  C10  single    1.507  0.020  1.507
 CD0  C08  C04  single    1.515  0.020  1.515
 CD0  C08  C12  aromatic  1.403  0.020  1.403
 CD0  C19  C10  double    1.332  0.020  1.332
 CD0  C20  C21  single    1.526  0.020  1.526
 CD0  C10  C14  single    1.500  0.020  1.500
 CD0  C17  C12  aromatic  1.391  0.020  1.391
 CD0  C12  O02  single    1.353  0.020  1.353
 CD0  C21  C22  single    1.525  0.020  1.525
 CD0  C22  C23  single    1.522  0.020  1.522
 CD0  C21  H1   single    0.970  0.020  1.090
 CD0  C21  H2   single    0.970  0.020  1.090
 CD0  C22  H3   single    0.970  0.020  1.090
 CD0  C22  H4   single    0.970  0.020  1.090
 CD0  C03  H5   single    0.970  0.020  1.090
 CD0  C04  H6   single    0.970  0.020  1.090
 CD0  C05  H7   single    0.970  0.020  1.090
 CD0  C05  H8   single    0.970  0.020  1.090
 CD0  C06  H9   single    0.970  0.020  1.090
 CD0  C06  H10  single    0.970  0.020  1.090
 CD0  C07  H11  single    0.970  0.020  1.090
 CD0  C07  H12  single    0.970  0.020  1.090
 CD0  C09  H13  single    0.970  0.020  1.090
 CD0  C13  H14  single    0.970  0.020  1.090
 CD0  C13  H15  single    0.970  0.020  1.090
 CD0  C13  H16  single    0.970  0.020  1.090
 CD0  C14  H17  single    0.970  0.020  1.090
 CD0  C14  H18  single    0.970  0.020  1.090
 CD0  C14  H19  single    0.970  0.020  1.090
 CD0  C16  H20  single    0.930  0.020  1.080
 CD0  C17  H21  single    0.930  0.020  1.080
 CD0  C18  H22  single    0.970  0.020  1.090
 CD0  C18  H23  single    0.970  0.020  1.090
 CD0  C19  H24  single    0.930  0.020  1.080
 CD0  C19  H25  single    0.930  0.020  1.080
 CD0  C20  H26  single    0.970  0.020  1.090
 CD0  C20  H27  single    0.970  0.020  1.090
 CD0  C23  H28  single    0.970  0.020  1.090
 CD0  C23  H29  single    0.970  0.020  1.090
 CD0  C23  H30  single    0.970  0.020  1.090
 CD0  O01  H31  single    0.850  0.020  0.980
 CD0  O02  H32  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
 CD0  O01  C11  C16  114.90  3.000
 CD0  C16  C11  C08  121.89  3.000
 CD0  O01  C11  C08  123.20  3.000
 CD0  O02  C12  C17  120.05  3.000
 CD0  O02  C12  C08  117.51  3.000
 CD0  C17  C12  C08  122.44  3.000
 CD0  H2   C21  H1   105.73  3.000
 CD0  H2   C21  C20  110.97  3.000
 CD0  H1   C21  C20  109.09  3.000
 CD0  H2   C21  C22  108.81  3.000
 CD0  H1   C21  C22  109.19  3.000
 CD0  C20  C21  C22  112.80  3.000
 CD0  H4   C22  H3   106.07  3.000
 CD0  H4   C22  C23  109.80  3.000
 CD0  H3   C22  C23  109.64  3.000
 CD0  H4   C22  C21  109.15  3.000
 CD0  H3   C22  C21  109.29  3.000
 CD0  C23  C22  C21  112.68  3.000
 CD0  H5   C03  C10  106.92  3.000
 CD0  H5   C03  C05  104.99  3.000
 CD0  C10  C03  C05  112.90  3.000
 CD0  H5   C03  C04  110.49  3.000
 CD0  C10  C03  C04  112.91  3.000
 CD0  C05  C03  C04  108.35  3.000
 CD0  H6   C04  C08  106.04  3.000
 CD0  H6   C04  C07  106.46  3.000
 CD0  C08  C04  C07  112.33  3.000
 CD0  H6   C04  C03  105.24  3.000
 CD0  C08  C04  C03  115.95  3.000
 CD0  C07  C04  C03  110.04  3.000
 CD0  H8   C05  H7   106.57  3.000
 CD0  H8   C05  C06  110.19  3.000
 CD0  H7   C05  C06  109.80  3.000
 CD0  H8   C05  C03  109.86  3.000
 CD0  H7   C05  C03  109.42  3.000
 CD0  C06  C05  C03  110.89  3.000
 CD0  H10  C06  H9   106.30  3.000
 CD0  H10  C06  C09  110.00  3.000
 CD0  H9   C06  C09  108.96  3.000
 CD0  H10  C06  C05  109.97  3.000
 CD0  H9   C06  C05  108.62  3.000
 CD0  C09  C06  C05  112.76  3.000
 CD0  H12  C07  H11  106.04  3.000
 CD0  H12  C07  C09  108.57  3.000
 CD0  H11  C07  C09  109.85  3.000
 CD0  H12  C07  C04  110.32  3.000
 CD0  H11  C07  C04  109.33  3.000
 CD0  C09  C07  C04  112.53  3.000
 CD0  C04  C08  C12  119.79  3.000
 CD0  C12  C08  C11  115.97  3.000
 CD0  C04  C08  C11  124.20  3.000
 CD0  H13  C09  C13  106.97  3.000
 CD0  H13  C09  C07  107.25  3.000
 CD0  C13  C09  C07  112.25  3.000
 CD0  H13  C09  C06  107.69  3.000
 CD0  C13  C09  C06  112.32  3.000
 CD0  C07  C09  C06  110.08  3.000
 CD0  C19  C10  C14  121.41  3.000
 CD0  C14  C10  C03  117.82  3.000
 CD0  C19  C10  C03  120.77  3.000
 CD0  H16  C13  H15  107.15  3.000
 CD0  H16  C13  H14  107.59  3.000
 CD0  H15  C13  H14  107.31  3.000
 CD0  H16  C13  C09  110.68  3.000
 CD0  H15  C13  C09  113.01  3.000
 CD0  H14  C13  C09  110.84  3.000
 CD0  H19  C14  H18  106.60  3.000
 CD0  H19  C14  H17  107.76  3.000
 CD0  H18  C14  H17  107.78  3.000
 CD0  H19  C14  C10  111.61  3.000
 CD0  H18  C14  C10  111.65  3.000
 CD0  H17  C14  C10  111.21  3.000
 CD0  C18  C15  C17  122.44  3.000
 CD0  C17  C15  C16  118.19  3.000
 CD0  C18  C15  C16  119.36  3.000
 CD0  H20  C16  C15  120.14  3.000
 CD0  H20  C16  C11  118.80  3.000
 CD0  C15  C16  C11  121.05  3.000
 CD0  H21  C17  C15  120.74  3.000
 CD0  H21  C17  C12  118.81  3.000
 CD0  C15  C17  C12  120.45  3.000
 CD0  H23  C18  H22  105.35  3.000
 CD0  H23  C18  C20  109.03  3.000
 CD0  H22  C18  C20  108.96  3.000
 CD0  H23  C18  C15  108.96  3.000
 CD0  H22  C18  C15  107.56  3.000
 CD0  C20  C18  C15  116.41  3.000
 CD0  H25  C19  H24  116.58  3.000
 CD0  H25  C19  C10  121.81  3.000
 CD0  H24  C19  C10  121.61  3.000
 CD0  H27  C20  H26  105.75  3.000
 CD0  H27  C20  C18  108.00  3.000
 CD0  H26  C20  C18  109.74  3.000
 CD0  H27  C20  C21  107.71  3.000
 CD0  H26  C20  C21  109.99  3.000
 CD0  C18  C20  C21  115.18  3.000
 CD0  H30  C23  H29  107.49  3.000
 CD0  H30  C23  H28  107.59  3.000
 CD0  H29  C23  H28  107.61  3.000
 CD0  H30  C23  C22  111.05  3.000
 CD0  H29  C23  C22  111.18  3.000
 CD0  H28  C23  C22  111.73  3.000
 CD0  H31  O01  C11  111.56  3.000
 CD0  H32  O02  C12  109.91  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
 CD0  CONST_01  C17  C15  C16  C11     0.00   0.0  0
 CD0  CONST_02  C17  C12  C08  C11     0.00   0.0  0
 CD0  CONST_03  C16  C11  C08  C12     0.00   0.0  0
 CD0  CONST_04  C16  C15  C17  C12     0.00   0.0  0
 CD0  CONST_05  C15  C16  C11  C08     0.00   0.0  0
 CD0  CONST_06  C15  C17  C12  C08     0.00   0.0  0
 CD0  CONST_07  C16  C11  C08  C04   180.00   0.0  0
 CD0  CONST_08  C17  C12  C08  C04   180.00   0.0  0
 CD0  CONST_09  C18  C15  C16  C11   180.00   0.0  0
 CD0  CONST_10  O02  C12  C08  C11   180.00   0.0  0
 CD0  CONST_11  O01  C11  C08  C12   180.00   0.0  0
 CD0  CONST_12  C18  C15  C17  C12   180.00   0.0  0
 CD0  CONST_13  O01  C11  C08  C04     0.00   0.0  0
 CD0  CONST_14  O02  C12  C08  C04     0.00   0.0  0
 CD0  CONST_15  O01  C11  C16  C15   180.00   0.0  0
 CD0  CONST_16  O02  C12  C17  C15   180.00   0.0  0
 CD0  CONST_17  H20  C16  C11  C08   180.00   0.0  0
 CD0  CONST_18  H21  C17  C12  C08   180.00   0.0  0
 CD0  Var_01    C09  C06  C05  C03    57.15  30.0  1
 CD0  Var_02    C20  C18  C15  C16  -137.22  30.0  1
 CD0  Var_03    C15  C18  C20  C21   -91.50  30.0  1
 CD0  Var_04    H24  C19  C10  C03   179.52   0.0  2
 CD0  Var_05    H17  C14  C10  C03  -178.65  30.0  3
 CD0  Var_06    C18  C20  C21  C22  -175.87  30.0  1
 CD0  Var_07    C23  C22  C21  C20  -179.53  30.0  3
 CD0  Var_08    H28  C23  C22  C21  -179.48  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
 CD0  chir_01  C03  C05  C04  C10  positiv
 CD0  chir_02  C04  C07  C03  C08  positiv
 CD0  chir_03  C09  C13  C07  C06  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
 CD0  plan-1  C11  0.020
 CD0  plan-1  C12  0.020
 CD0  plan-1  C04  0.020
 CD0  plan-1  C08  0.020
 CD0  plan-1  C15  0.020
 CD0  plan-1  C16  0.020
 CD0  plan-1  C17  0.020
 CD0  plan-1  C18  0.020
 CD0  plan-1  O01  0.020
 CD0  plan-1  O02  0.020
 CD0  plan-1  H20  0.020
 CD0  plan-1  H21  0.020
 CD0  plan-2  C03  0.020
 CD0  plan-2  C10  0.020
 CD0  plan-2  C14  0.020
 CD0  plan-2  C19  0.020
 CD0  plan-2  H24  0.020
 CD0  plan-2  H25  0.020

