# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun 29 07:37:54 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: (1R,3R)-5-[(2E)-3-{(1S,3R)-2,2,3-trimethyl-3-[6,6,6-trifluoro-5-hydroxy-5-(trifluoromethyl)hex-3-yn-1-yl]cyclopentyl}prop-2-en-1-ylidene]cyclohexane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)[C@@H](CC[C@]1(C)CCC#CC(O)(C(F)(F)F)C(F)(F)F)/C=C/C=C2/C[C@@H](O)C[C@H](O)C2
#
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
 C5D  C5D  (1R,3R)-5-[(2E)-3-{(1S,3R)-2,2,3-trimethyl-3-[6,6,6-trifluoro-5-hydroxy-5-(trifluoromethyl)hex-3-yn-1-yl]cyclopentyl}prop-2-en-1-ylidene]cyclohexane-1,3-diol  ligand  65  33  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C5D
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
 C5D  C20   C  CH2   0  -0.436  -1.4905   0.8732   0.0544
 C5D  C22   C  CH2   0  -0.658  -2.6311   1.6540   0.7215
 C5D  C23   C  CSP   0   0.131  -3.9294   1.1307   0.3330
 C5D  C24   C  CSP   0   0.075  -4.9891   0.6832  -0.0145
 C5D  C25   C  CT    0  -0.287  -6.2602   0.0849  -0.3991
 C5D  C27   C  CT    0   1.012  -7.3298   1.2017  -0.4622
 C5D  C26   C  CT    0   1.008  -6.0655  -0.6307  -1.7603
 C5D  O3    O  OH1   0  -0.647  -6.7406  -0.8515   0.5122
 C5D  F11   F  F     0  -0.290  -7.0180   2.1364  -1.3569
 C5D  F19   F  F     0  -0.292  -8.5322   0.7225  -0.7700
 C5D  F21   F  F     0  -0.291  -7.4220   1.7896   0.7274
 C5D  F28   F  F     0  -0.294  -5.1530  -1.5907  -1.6217
 C5D  F29   F  F     0  -0.292  -7.1888  -1.2023  -2.1871
 C5D  F30   F  F     0  -0.289  -5.6412   0.2011  -2.7088
 C5D  O2    O  OH1   0  -0.675  10.2587  -2.0821  -0.1665
 C5D  C1    C  CH1   0   0.038   8.5864   1.2266  -0.6475
 C5D  C2    C  CH2   0  -0.486   9.6705   0.1587  -0.6689
 C5D  C3    C  CH1   0   0.078   9.2080  -1.1459  -0.0368
 C5D  C4    C  CH2   0  -0.531   7.9216  -1.6390  -0.7076
 C5D  C5    C  C     0   0.139   6.8619  -0.5766  -0.6757
 C5D  C6    C  C1    0  -0.334   5.6714  -0.7937  -0.0977
 C5D  C8    C  C1    0  -0.185   3.4054  -0.1534   0.6076
 C5D  C10   C  CH2   0  -0.560   7.3016   0.7112  -1.3046
 C5D  C12   C  CH3   0  -0.654   1.3428   0.9132  -1.6277
 C5D  C13   C  CT    0  -0.035   1.0469   0.4927  -0.1926
 C5D  C14   C  CH1   0  -0.286   2.2591   0.7917   0.7345
 C5D  C15   C  CH2   0  -0.431   1.6667   0.8501   2.1559
 C5D  C16   C  CH2   0  -0.443   0.1516   1.0553   1.9883
 C5D  C17   C  CT    0  -0.031  -0.0910   1.3231   0.4904
 C5D  C18   C  CH3   0  -0.683   0.7350  -1.0074  -0.1891
 C5D  C9    C  CH3   0  -0.690   0.0715   2.8210   0.1973
 C5D  H20   H  HCH2  0   0.246  -1.6307  -0.1814   0.2953
 C5D  H20A  H  HCH2  0   0.238  -1.5922   0.9644  -1.0311
 C5D  H22   H  HCH2  0   0.284  -2.5489   1.5994   1.8101
 C5D  H22A  H  HCH2  0   0.286  -2.5940   2.7132   0.4598
 C5D  HO3   H  HOH1  0   0.485  -6.0319  -1.1312   1.1029
 C5D  HO2   H  HOH1  0   0.448  10.0062  -2.8806   0.3077
 C5D  H1    H  HCH1  0   0.221   8.9391   2.0929  -1.2238
 C5D  H2    H  HCH2  0   0.231   9.9489  -0.0262  -1.7114
 C5D  H2A   H  HCH2  0   0.247  10.5663   0.5285  -0.1620
 C5D  H3    H  HCH1  0   0.202   8.9880  -0.9695   1.0244
 C5D  H4    H  HCH2  0   0.233   8.1580  -1.8932  -1.7489
 C5D  H4A   H  HCH2  0   0.244   7.5713  -2.5533  -0.2202
 C5D  H6    H  H     0   0.228   5.4927  -1.7788   0.3277
 C5D  H8    H  H     0   0.234   3.2734  -1.1484   1.0290
 C5D  H10   H  HCH2  0   0.256   6.5322   1.4847  -1.2669
 C5D  H10A  H  HCH2  0   0.246   7.5113   0.5427  -2.3671
 C5D  H12   H  HCH3  0   0.229   2.1273   0.2839  -2.0529
 C5D  H12A  H  HCH3  0   0.223   0.4621   0.8152  -2.2660
 C5D  H12B  H  HCH3  0   0.226   1.6882   1.9459  -1.6894
 C5D  H14   H  HCH1  0   0.235   2.6359   1.7834   0.4653
 C5D  H15   H  HCH2  0   0.227   1.8720  -0.0752   2.6984
 C5D  H15A  H  HCH2  0   0.235   2.1317   1.6516   2.7316
 C5D  H16   H  HCH2  0   0.231  -0.3887   0.1567   2.2978
 C5D  H16A  H  HCH2  0   0.233  -0.2281   1.8697   2.6085
 C5D  H18   H  HCH3  0   0.236   1.5869  -1.5718  -0.5717
 C5D  H18A  H  HCH3  0   0.230   0.5091  -1.3961   0.8065
 C5D  H18B  H  HCH3  0   0.234  -0.1092  -1.2437  -0.8378
 C5D  H9    H  HCH3  0   0.235  -0.5773   3.4173   0.8401
 C5D  H9A   H  HCH3  0   0.241   1.0876   3.1760   0.3720
 C5D  H9B   H  HCH3  0   0.231  -0.1855   3.0597  -0.8363
 C5D  C7    C  C1    0  -0.265   4.5708   0.1453   0.0206
 C5D  O1    O  OH1   0  -0.669   8.3663   1.5877   0.7016
 C5D  H7    H  H     0   0.235   4.6990   1.1448  -0.3849
 C5D  HO1   H  HOH1  0   0.447   7.6133   2.1855   0.7378

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
 C5D  C20  C22   single  1.535  0.020  1.535
 C5D  C20  C17   single  1.533  0.020  1.533
 C5D  C22  C23   single  1.453  0.020  1.453
 C5D  C23  C24   triple  1.202  0.020  1.202
 C5D  C24  C25   single  1.457  0.020  1.457
 C5D  C25  C27   single  1.548  0.020  1.548
 C5D  C25  C26   single  1.550  0.020  1.550
 C5D  C25  O3    single  1.392  0.020  1.392
 C5D  C27  F11   single  1.331  0.020  1.331
 C5D  C27  F19   single  1.330  0.020  1.330
 C5D  C27  F21   single  1.330  0.020  1.330
 C5D  C26  F28   single  1.332  0.020  1.332
 C5D  C26  F29   single  1.331  0.020  1.331
 C5D  C26  F30   single  1.331  0.020  1.331
 C5D  O2   C3    single  1.413  0.020  1.413
 C5D  C1   C2    single  1.522  0.020  1.522
 C5D  C1   C10   single  1.532  0.020  1.532
 C5D  C1   O1    single  1.414  0.020  1.414
 C5D  C2   C3    single  1.522  0.020  1.522
 C5D  C3   C4    single  1.532  0.020  1.532
 C5D  C4   C5    single  1.501  0.020  1.501
 C5D  C5   C6    double  1.341  0.020  1.341
 C5D  C5   C10   single  1.499  0.020  1.499
 C5D  C6   C7    single  1.452  0.020  1.452
 C5D  C7   C8    double  1.339  0.020  1.339
 C5D  C8   C14   single  1.491  0.020  1.491
 C5D  C12  C13   single  1.524  0.020  1.524
 C5D  C13  C14   single  1.555  0.020  1.555
 C5D  C13  C17   single  1.565  0.020  1.565
 C5D  C13  C18   single  1.532  0.020  1.532
 C5D  C14  C15   single  1.541  0.020  1.541
 C5D  C15  C16   single  1.538  0.020  1.538
 C5D  C16  C17   single  1.541  0.020  1.541
 C5D  C17  C9    single  1.535  0.020  1.535
 C5D  C20  H20   single  0.970  0.020  1.090
 C5D  C20  H20A  single  0.970  0.020  1.090
 C5D  C22  H22   single  0.970  0.020  1.090
 C5D  C22  H22A  single  0.970  0.020  1.090
 C5D  O3   HO3   single  0.850  0.020  0.980
 C5D  O2   HO2   single  0.850  0.020  0.980
 C5D  C1   H1    single  0.970  0.020  1.090
 C5D  C2   H2    single  0.970  0.020  1.090
 C5D  C2   H2A   single  0.970  0.020  1.090
 C5D  C3   H3    single  0.970  0.020  1.090
 C5D  C4   H4    single  0.970  0.020  1.090
 C5D  C4   H4A   single  0.970  0.020  1.090
 C5D  C6   H6    single  0.930  0.020  1.080
 C5D  C7   H7    single  0.930  0.020  1.080
 C5D  C8   H8    single  0.930  0.020  1.080
 C5D  C10  H10   single  0.970  0.020  1.090
 C5D  C10  H10A  single  0.970  0.020  1.090
 C5D  C12  H12   single  0.970  0.020  1.090
 C5D  C12  H12A  single  0.970  0.020  1.090
 C5D  C12  H12B  single  0.970  0.020  1.090
 C5D  C14  H14   single  0.970  0.020  1.090
 C5D  C15  H15   single  0.970  0.020  1.090
 C5D  C15  H15A  single  0.970  0.020  1.090
 C5D  C16  H16   single  0.970  0.020  1.090
 C5D  C16  H16A  single  0.970  0.020  1.090
 C5D  C18  H18   single  0.970  0.020  1.090
 C5D  C18  H18A  single  0.970  0.020  1.090
 C5D  C18  H18B  single  0.970  0.020  1.090
 C5D  O1   HO1   single  0.850  0.020  0.980
 C5D  C9   H9    single  0.970  0.020  1.090
 C5D  C9   H9A   single  0.970  0.020  1.090
 C5D  C9   H9B   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
 C5D  H20A  C20  H20   106.72  3.000
 C5D  H20A  C20  C17   110.03  3.000
 C5D  H20   C20  C17   109.77  3.000
 C5D  H20A  C20  C22   108.65  3.000
 C5D  H20   C20  C22   107.48  3.000
 C5D  C17   C20  C22   113.92  3.000
 C5D  H22A  C22  H22   106.54  3.000
 C5D  H22A  C22  C23   108.41  3.000
 C5D  H22   C22  C23   108.40  3.000
 C5D  H22A  C22  C20   111.36  3.000
 C5D  H22   C22  C20   110.58  3.000
 C5D  C23   C22  C20   111.39  3.000
 C5D  C24   C23  C22   180.00  3.000
 C5D  C25   C24  C23   180.00  3.000
 C5D  O3    C25  C26   107.92  3.000
 C5D  O3    C25  C27   105.87  3.000
 C5D  C26   C25  C27   112.59  3.000
 C5D  O3    C25  C24   113.86  3.000
 C5D  C26   C25  C24   108.17  3.000
 C5D  C27   C25  C24   108.52  3.000
 C5D  F21   C27  F19   107.67  3.000
 C5D  F21   C27  F11   107.88  3.000
 C5D  F19   C27  F11   108.01  3.000
 C5D  F21   C27  C25   109.29  3.000
 C5D  F19   C27  C25   111.97  3.000
 C5D  F11   C27  C25   111.85  3.000
 C5D  F30   C26  F29   108.00  3.000
 C5D  F30   C26  F28   107.83  3.000
 C5D  F29   C26  F28   107.58  3.000
 C5D  F30   C26  C25   112.17  3.000
 C5D  F29   C26  C25   111.96  3.000
 C5D  F28   C26  C25   109.12  3.000
 C5D  HO3   O3   C25   110.03  3.000
 C5D  HO2   O2   C3    108.02  3.000
 C5D  H1    C1   O1    110.44  3.000
 C5D  H1    C1   C10   108.03  3.000
 C5D  O1    C1   C10   111.38  3.000
 C5D  H1    C1   C2    108.49  3.000
 C5D  O1    C1   C2    107.67  3.000
 C5D  C10   C1   C2    110.80  3.000
 C5D  H2A   C2   H2    106.87  3.000
 C5D  H2A   C2   C3    110.26  3.000
 C5D  H2    C2   C3    109.15  3.000
 C5D  H2A   C2   C1    109.86  3.000
 C5D  H2    C2   C1    108.24  3.000
 C5D  C3    C2   C1    112.29  3.000
 C5D  H3    C3   C4    107.85  3.000
 C5D  H3    C3   C2    108.94  3.000
 C5D  C4    C3   C2    110.44  3.000
 C5D  H3    C3   O2    110.13  3.000
 C5D  C4    C3   O2    111.77  3.000
 C5D  C2    C3   O2    107.69  3.000
 C5D  H4A   C4   H4    107.35  3.000
 C5D  H4A   C4   C5    110.86  3.000
 C5D  H4    C4   C5    109.64  3.000
 C5D  H4A   C4   C3    110.05  3.000
 C5D  H4    C4   C3    108.00  3.000
 C5D  C5    C4   C3    110.83  3.000
 C5D  C10   C5   C6    125.47  3.000
 C5D  C10   C5   C4    113.08  3.000
 C5D  C6    C5   C4    121.42  3.000
 C5D  H6    C6   C7    115.43  3.000
 C5D  H6    C6   C5    117.45  3.000
 C5D  C7    C6   C5    127.12  3.000
 C5D  H8    C8   C14   116.95  3.000
 C5D  H8    C8   C7    118.64  3.000
 C5D  C14   C8   C7    124.42  3.000
 C5D  H10A  C10  H10   106.09  3.000
 C5D  H10A  C10  C5    109.32  3.000
 C5D  H10   C10  C5    112.80  3.000
 C5D  H10A  C10  C1    107.88  3.000
 C5D  H10   C10  C1    109.74  3.000
 C5D  C5    C10  C1    110.79  3.000
 C5D  H12B  C12  H12A  107.90  3.000
 C5D  H12B  C12  H12   107.23  3.000
 C5D  H12A  C12  H12   107.46  3.000
 C5D  H12B  C12  C13   112.08  3.000
 C5D  H12A  C12  C13   111.65  3.000
 C5D  H12   C12  C13   110.31  3.000
 C5D  C18   C13  C17   111.74  3.000
 C5D  C18   C13  C14   110.21  3.000
 C5D  C17   C13  C14   101.80  3.000
 C5D  C18   C13  C12   108.16  3.000
 C5D  C17   C13  C12   113.92  3.000
 C5D  C14   C13  C12   110.91  3.000
 C5D  H14   C14  C15   108.96  3.000
 C5D  H14   C14  C13   107.21  3.000
 C5D  C15   C14  C13   104.92  3.000
 C5D  H14   C14  C8    106.78  3.000
 C5D  C15   C14  C8    113.46  3.000
 C5D  C13   C14  C8    115.25  3.000
 C5D  H15A  C15  H15   106.28  3.000
 C5D  H15A  C15  C16   112.29  3.000
 C5D  H15   C15  C16   110.63  3.000
 C5D  H15A  C15  C14   110.53  3.000
 C5D  H15   C15  C14   110.72  3.000
 C5D  C16   C15  C14   106.45  3.000
 C5D  H16A  C16  H16   106.29  3.000
 C5D  H16A  C16  C17   111.58  3.000
 C5D  H16   C16  C17   109.90  3.000
 C5D  H16A  C16  C15   112.34  3.000
 C5D  H16   C16  C15   110.26  3.000
 C5D  C17   C16  C15   106.51  3.000
 C5D  C9    C17  C16   109.79  3.000
 C5D  C9    C17  C13   110.94  3.000
 C5D  C16   C17  C13   102.56  3.000
 C5D  C9    C17  C20   109.19  3.000
 C5D  C16   C17  C20   111.66  3.000
 C5D  C13   C17  C20   112.56  3.000
 C5D  H18B  C18  H18A  107.75  3.000
 C5D  H18B  C18  H18   106.48  3.000
 C5D  H18A  C18  H18   107.28  3.000
 C5D  H18B  C18  C13   111.61  3.000
 C5D  H18A  C18  C13   113.11  3.000
 C5D  H18   C18  C13   110.29  3.000
 C5D  H9B   C9   H9A   107.45  3.000
 C5D  H9B   C9   H9    107.37  3.000
 C5D  H9A   C9   H9    106.38  3.000
 C5D  H9B   C9   C17   111.67  3.000
 C5D  H9A   C9   C17   112.69  3.000
 C5D  H9    C9   C17   110.98  3.000
 C5D  H7    C7   C8    118.15  3.000
 C5D  H7    C7   C6    118.38  3.000
 C5D  C8    C7   C6    123.47  3.000
 C5D  HO1   O1   C1    108.44  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
 C5D  Var_01  C4   C5   C10  C1    -55.76  30.0  1
 C5D  Var_02  C10  C5   C4   C3     56.19  30.0  1
 C5D  Var_03  C17  C16  C15  C14    -8.23  30.0  1
 C5D  Var_04  C7   C6   C5   C4    179.05  30.0  2
 C5D  Var_05  H12  C12  C13  C14    67.10  30.0  3
 C5D  Var_06  H18  C18  C13  C14   -61.51  30.0  3
 C5D  Var_07  C14  C8   C7   C6   -179.67   0.0  2
 C5D  Var_08  C17  C20  C22  C23  -176.51  30.0  2
 C5D  Var_09  C8   C7   C6   C5    179.55  30.0  2
 C5D  Var_10  C27  C25  C24  C23   142.91  30.0  3
 C5D  Var_11  F11  C27  C25  C24    60.48  30.0  3
 C5D  Var_12  F28  C26  C25  C24    61.27  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
 C5D  chir_01  C1   C2   C10  O1   negativ
 C5D  chir_02  C3   O2   C4   C2   positiv
 C5D  chir_03  C14  C8   C13  C15  negativ
 C5D  chir_04  C17  C16  C13  C20  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
 C5D  plan-1  C6   0.020
 C5D  plan-1  C8   0.020
 C5D  plan-1  C14  0.020
 C5D  plan-1  H8   0.020
 C5D  plan-1  C7   0.020
 C5D  plan-1  H7   0.020

