# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 04:33:30 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (1R)-1-[3-(cyclohexylmethoxy)phenyl]propane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC[C@@H](O)c1cccc(OCC2CCCCC2)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
 A9V  A9V  (1R)-1-[3-(cyclohexylmethoxy)phenyl]propane-1,3-diol  ligand  43  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A9V
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
 A9V  O1   O  OH1   0  -0.662  -4.6728  -1.0095   1.0806
 A9V  C2   C  CH1   0  -0.033  -3.6276  -0.1369   0.7171
 A9V  C1   C  CH2   0  -0.499  -4.0746   0.9139  -0.2982
 A9V  C    C  CH2   0  -0.138  -5.2150   1.7765   0.2123
 A9V  O    O  OH1   0  -0.674  -5.5057   2.7553  -0.7630
 A9V  C3   C  CR6   0   0.138  -2.4032  -0.8718   0.2094
 A9V  C15  C  CR16  0  -0.412  -1.1509  -0.3165   0.4210
 A9V  C7   C  CR6   0   0.411   0.0037  -0.9370  -0.0577
 A9V  C6   C  CR16  0  -0.397  -0.1026  -2.1357  -0.7599
 A9V  C5   C  CR16  0  -0.225  -1.3614  -2.6868  -0.9684
 A9V  C4   C  CR16  0  -0.350  -2.5076  -2.0722  -0.4913
 A9V  O2   O  O2    0  -0.480   1.1660  -0.3131   0.2107
 A9V  C8   C  CH2   0  -0.157   2.3840  -0.9266  -0.1787
 A9V  C9   C  CH1   0  -0.278   3.5396  -0.0511   0.2675
 A9V  C14  C  CH2   0  -0.422   4.8606  -0.7703  -0.0112
 A9V  C13  C  CH2   0  -0.430   6.0612   0.0726   0.4057
 A9V  C12  C  CH2   0  -0.429   6.0392   1.4435  -0.2620
 A9V  C11  C  CH2   0  -0.432   4.7246   2.1669   0.0082
 A9V  C10  C  CH2   0  -0.413   3.5235   1.3217  -0.4056
 A9V  H1   H  HOH1  0   0.450  -5.1522  -1.2750   0.2890
 A9V  H2   H  HCH1  0   0.243  -3.3442   0.3806   1.6402
 A9V  H3   H  HCH2  0   0.246  -3.2196   1.5530  -0.5339
 A9V  H4   H  HCH2  0   0.236  -4.3636   0.4190  -1.2332
 A9V  H5   H  HCH2  0   0.194  -6.0926   1.1544   0.4212
 A9V  H6   H  HCH2  0   0.191  -4.9179   2.2358   1.1654
 A9V  H7   H  HOH1  0   0.453  -6.2473   3.2783  -0.4462
 A9V  H8   H  HCR6  0   0.251  -1.0557   0.6109   0.9765
 A9V  H9   H  HCR6  0   0.277   0.7690  -2.6496  -1.1415
 A9V  H10  H  HCR6  0   0.257  -1.4407  -3.6184  -1.5143
 A9V  H11  H  HCR6  0   0.237  -3.4696  -2.5370  -0.6642
 A9V  H12  H  HCH2  0   0.228   2.4663  -1.9210   0.2772
 A9V  H13  H  HCH2  0   0.214   2.4152  -1.0595  -1.2680
 A9V  H14  H  HCH1  0   0.223   3.4579   0.0907   1.3533
 A9V  H15  H  HCH2  0   0.229   4.8788  -1.7313   0.5103
 A9V  H16  H  HCH2  0   0.210   4.9328  -0.9936  -1.0824
 A9V  H17  H  HCH2  0   0.210   6.0554   0.1977   1.4937
 A9V  H18  H  HCH2  0   0.227   6.9872  -0.4521   0.1588
 A9V  H19  H  HCH2  0   0.226   6.8819   2.0455   0.0869
 A9V  H20  H  HCH2  0   0.208   6.1697   1.3216  -1.3429
 A9V  H21  H  HCH2  0   0.209   4.6512   2.3991   1.0764
 A9V  H22  H  HCH2  0   0.226   4.7041   3.1243  -0.5181
 A9V  H23  H  HCH2  0   0.205   3.5346   1.1814  -1.4932
 A9V  H24  H  HCH2  0   0.231   2.5986   1.8515  -0.1682

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
 A9V  C12  C11  single    1.525  0.020  1.525
 A9V  C12  C13  single    1.525  0.020  1.525
 A9V  C11  C10  single    1.526  0.020  1.526
 A9V  C10  C9   single    1.529  0.020  1.529
 A9V  C13  C14  single    1.525  0.020  1.525
 A9V  C14  C9   single    1.530  0.020  1.530
 A9V  C9   C8   single    1.517  0.020  1.517
 A9V  C8   O2   single    1.418  0.020  1.418
 A9V  C    C1   single    1.518  0.020  1.518
 A9V  C    O    single    1.412  0.020  1.412
 A9V  C1   C2   single    1.528  0.020  1.528
 A9V  C15  C7   aromatic  1.396  0.020  1.396
 A9V  C15  C3   aromatic  1.386  0.020  1.386
 A9V  O2   C7   single    1.346  0.020  1.346
 A9V  C2   C3   single    1.516  0.020  1.516
 A9V  C2   O1   single    1.409  0.020  1.409
 A9V  C7   C6   aromatic  1.393  0.020  1.393
 A9V  C3   C4   aromatic  1.394  0.020  1.394
 A9V  C6   C5   aromatic  1.390  0.020  1.390
 A9V  C4   C5   aromatic  1.385  0.020  1.385
 A9V  O1   H1   single    0.850  0.020  0.980
 A9V  C2   H2   single    0.970  0.020  1.090
 A9V  C1   H3   single    0.970  0.020  1.090
 A9V  C1   H4   single    0.970  0.020  1.090
 A9V  C    H5   single    0.970  0.020  1.090
 A9V  C    H6   single    0.970  0.020  1.090
 A9V  O    H7   single    0.850  0.020  0.980
 A9V  C15  H8   single    0.930  0.020  1.080
 A9V  C6   H9   single    0.930  0.020  1.080
 A9V  C5   H10  single    0.930  0.020  1.080
 A9V  C4   H11  single    0.930  0.020  1.080
 A9V  C8   H12  single    0.970  0.020  1.090
 A9V  C8   H13  single    0.970  0.020  1.090
 A9V  C9   H14  single    0.970  0.020  1.090
 A9V  C14  H15  single    0.970  0.020  1.090
 A9V  C14  H16  single    0.970  0.020  1.090
 A9V  C13  H17  single    0.970  0.020  1.090
 A9V  C13  H18  single    0.970  0.020  1.090
 A9V  C12  H19  single    0.970  0.020  1.090
 A9V  C12  H20  single    0.970  0.020  1.090
 A9V  C11  H21  single    0.970  0.020  1.090
 A9V  C11  H22  single    0.970  0.020  1.090
 A9V  C10  H23  single    0.970  0.020  1.090
 A9V  C10  H24  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
 A9V  H1   O1   C2   109.15  3.000
 A9V  H2   C2   C3   107.60  3.000
 A9V  H2   C2   C1   108.10  3.000
 A9V  C3   C2   C1   110.31  3.000
 A9V  H2   C2   O1   105.49  3.000
 A9V  C3   C2   O1   112.66  3.000
 A9V  C1   C2   O1   112.35  3.000
 A9V  H4   C1   H3   106.63  3.000
 A9V  H4   C1   C    110.19  3.000
 A9V  H3   C1   C    109.13  3.000
 A9V  H4   C1   C2   109.47  3.000
 A9V  H3   C1   C2   108.45  3.000
 A9V  C    C1   C2   112.77  3.000
 A9V  H6   C    H5   106.76  3.000
 A9V  H6   C    O    111.41  3.000
 A9V  H5   C    O    111.12  3.000
 A9V  H6   C    C1   109.03  3.000
 A9V  H5   C    C1   110.07  3.000
 A9V  O    C    C1   108.44  3.000
 A9V  H7   O    C    107.96  3.000
 A9V  C4   C3   C15  119.30  3.000
 A9V  C4   C3   C2   121.70  3.000
 A9V  C15  C3   C2   118.97  3.000
 A9V  H8   C15  C7   118.88  3.000
 A9V  H8   C15  C3   119.98  3.000
 A9V  C7   C15  C3   121.13  3.000
 A9V  O2   C7   C6   124.41  3.000
 A9V  C6   C7   C15  119.50  3.000
 A9V  O2   C7   C15  116.09  3.000
 A9V  H9   C6   C5   119.25  3.000
 A9V  H9   C6   C7   121.69  3.000
 A9V  C5   C6   C7   119.07  3.000
 A9V  H10  C5   C4   119.66  3.000
 A9V  H10  C5   C6   118.89  3.000
 A9V  C4   C5   C6   121.45  3.000
 A9V  H11  C4   C5   119.33  3.000
 A9V  H11  C4   C3   121.11  3.000
 A9V  C5   C4   C3   119.56  3.000
 A9V  C8   O2   C7   119.09  3.000
 A9V  H13  C8   H12  107.48  3.000
 A9V  H13  C8   C9   109.88  3.000
 A9V  H12  C8   C9   110.11  3.000
 A9V  H13  C8   O2   110.44  3.000
 A9V  H12  C8   O2   110.03  3.000
 A9V  C9   C8   O2   108.89  3.000
 A9V  H14  C9   C10  108.58  3.000
 A9V  H14  C9   C14  107.76  3.000
 A9V  C10  C9   C14  110.55  3.000
 A9V  H14  C9   C8   107.98  3.000
 A9V  C14  C9   C8   109.45  3.000
 A9V  C10  C9   C8   112.38  3.000
 A9V  H16  C14  H15  106.61  3.000
 A9V  H16  C14  C13  109.13  3.000
 A9V  H15  C14  C13  110.02  3.000
 A9V  H16  C14  C9   109.30  3.000
 A9V  H15  C14  C9   109.92  3.000
 A9V  C13  C14  C9   111.73  3.000
 A9V  H18  C13  H17  106.49  3.000
 A9V  H18  C13  C12  110.18  3.000
 A9V  H17  C13  C12  109.40  3.000
 A9V  H18  C13  C14  109.88  3.000
 A9V  H17  C13  C14  109.30  3.000
 A9V  C12  C13  C14  111.46  3.000
 A9V  H20  C12  H19  106.53  3.000
 A9V  H20  C12  C11  109.29  3.000
 A9V  H19  C12  C11  110.30  3.000
 A9V  H20  C12  C13  109.28  3.000
 A9V  H19  C12  C13  110.14  3.000
 A9V  C11  C12  C13  111.18  3.000
 A9V  H22  C11  H21  106.42  3.000
 A9V  H22  C11  C10  109.87  3.000
 A9V  H21  C11  C10  109.21  3.000
 A9V  H22  C11  C12  110.28  3.000
 A9V  H21  C11  C12  109.34  3.000
 A9V  C10  C11  C12  111.58  3.000
 A9V  H24  C10  H23  106.64  3.000
 A9V  H24  C10  C11  109.82  3.000
 A9V  H23  C10  C11  109.38  3.000
 A9V  H24  C10  C9   110.41  3.000
 A9V  H23  C10  C9   108.76  3.000
 A9V  C11  C10  C9   111.69  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
 A9V  CONST_01  C6   C7   C15  C3      0.00   0.0  0
 A9V  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 A9V  CONST_03  C5   C6   C7   C15     0.00   0.0  0
 A9V  CONST_04  C5   C4   C3   C15     0.00   0.0  0
 A9V  CONST_05  C4   C3   C15  C7      0.00   0.0  0
 A9V  CONST_06  C4   C5   C6   C7      0.00   0.0  0
 A9V  CONST_07  C7   C15  C3   C2    180.00   0.0  0
 A9V  CONST_08  C5   C4   C3   C2    180.00   0.0  0
 A9V  CONST_09  O2   C7   C15  C3    180.00   0.0  0
 A9V  CONST_10  O2   C7   C6   C5    180.00   0.0  0
 A9V  CONST_11  H10  C5   C4   C3    180.00   0.0  0
 A9V  CONST_12  H9   C6   C7   C15   180.00   0.0  0
 A9V  CONST_13  H11  C4   C3   C15   180.00   0.0  0
 A9V  CONST_14  H8   C15  C7   C6    180.00   0.0  0
 A9V  Var_01    C12  C11  C10  C9     55.20  30.0  1
 A9V  Var_02    C12  C13  C14  C9    -55.41  30.0  1
 A9V  Var_03    C11  C12  C13  C14    54.79  30.0  1
 A9V  Var_04    C10  C11  C12  C13   -54.72  30.0  1
 A9V  Var_05    C9   C8   O2   C7   -178.44  30.0  1
 A9V  Var_06    O    C    C1   C2    176.93  30.0  1

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
 A9V  chir_01  C2  C1   C3   O1  positiv
 A9V  chir_02  C9  C10  C14  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
 A9V  plan-1  C2   0.020
 A9V  plan-1  C3   0.020
 A9V  plan-1  C15  0.020
 A9V  plan-1  C7   0.020
 A9V  plan-1  C6   0.020
 A9V  plan-1  C5   0.020
 A9V  plan-1  C4   0.020
 A9V  plan-1  O2   0.020
 A9V  plan-1  H8   0.020
 A9V  plan-1  H9   0.020
 A9V  plan-1  H10  0.020
 A9V  plan-1  H11  0.020

