# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 03:26:33 2021
#   Inital geometry file: a 165 line input string
#   Ligand name: (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(2~{R})-6-methylheptan-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2/C(CCC[C@]12C)=C/C=C3/C[C@@H](O)C[C@H](O)C3=C
#
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
 M9B  M9B  (1~{R},3~{S},5~{Z})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-7~{a}-methyl-1-[(2~{R})-6-methylheptan-2-yl]-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-4-methylidene-cyclohexane-1,3-diol  ligand  73  29  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_M9B
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
 M9B  C4   C  CH2   0  -0.544  -13.2026   5.5708  -14.3841
 M9B  C14  C  CR15  0  -0.244   -9.4950   9.4137  -10.9566
 M9B  C5   C  C     0   0.104  -12.6268   6.8689  -13.8916
 M9B  C6   C  C     0   0.036  -13.2457   8.0550  -14.5193
 M9B  C11  C  CH2   0  -0.438   -7.7933   7.0535  -11.1535
 M9B  C7   C  C1    0  -0.305  -11.6633   6.9082  -12.9564
 M9B  C8   C  C1    0  -0.357  -11.0741   8.1004  -12.3782
 M9B  C9   C  C     0   0.151  -10.0538   8.1399  -11.5067
 M9B  C10  C  CH2   0  -0.504   -9.3141   6.9433  -10.9655
 M9B  C12  C  CH2   0  -0.413   -7.2377   8.3955  -10.6754
 M9B  C13  C  CR5   0  -0.062   -7.9950   9.5661  -11.2966
 M9B  C3   C  CH1   0   0.028  -14.7262   5.5492  -14.2592
 M9B  O    O  OH1   0  -0.671  -15.1402   5.5635  -12.9074
 M9B  C1   C  CH1   0   0.022  -14.7564   8.0764  -14.4054
 M9B  C15  C  CH2   0  -0.451  -10.0935  10.7751  -11.3036
 M9B  C16  C  CH2   0  -0.441   -8.9513  11.7795  -11.0079
 M9B  C17  C  CR15  0  -0.178   -7.7214  10.9272  -10.6291
 M9B  C18  C  CH3   0  -0.673   -7.7847   9.5927  -12.8113
 M9B  C19  C  C2    0  -0.586  -12.5468   8.9784  -15.1763
 M9B  C2   C  CH2   0  -0.484  -15.3339   6.7670  -14.9392
 M9B  C20  C  CH1   0  -0.227   -6.3359  11.5664  -10.8195
 M9B  C21  C  CH3   0  -0.668   -6.0005  12.4442   -9.6124
 M9B  C22  C  CH2   0  -0.428   -6.1404  12.3686  -12.1136
 M9B  C23  C  CH2   0  -0.425   -4.6788  12.4565  -12.5422
 M9B  C24  C  CH2   0  -0.393   -4.4755  13.3236  -13.7786
 M9B  C25  C  CH1   0  -0.232   -3.0213  13.4700  -14.2319
 M9B  C26  C  CH3   0  -0.657   -2.4269  12.1394  -14.6844
 M9B  C27  C  CH3   0  -0.651   -2.9172  14.5029  -15.3500
 M9B  O1   O  OH1   0  -0.665  -15.3644   9.1334  -15.1029
 M9B  H1   H  HCH2  0   0.254  -12.7628   4.7223  -13.8518
 M9B  H2   H  HCH2  0   0.245  -12.9533   5.4369  -15.4431
 M9B  H3   H  HCR5  0   0.229   -9.5388   9.3152   -9.8603
 M9B  H5   H  HCH2  0   0.234   -7.3103   6.2380  -10.6104
 M9B  H6   H  H     0   0.232  -11.3100   5.9497  -12.5889
 M9B  H7   H  H     0   0.230  -11.5082   9.0439  -12.6896
 M9B  H8   H  HCH2  0   0.230   -9.5221   6.8764   -9.8903
 M9B  H9   H  HCH2  0   0.244   -9.6635   6.0087  -11.4040
 M9B  H10  H  HCH2  0   0.226   -6.1681   8.4573  -10.8992
 M9B  H11  H  HCH2  0   0.212   -7.3310   8.4577   -9.5844
 M9B  H12  H  HCH1  0   0.225  -15.0993   4.6479  -14.7642
 M9B  H13  H  HOH1  0   0.448  -14.6755   4.8617  -12.4412
 M9B  H14  H  HCH1  0   0.220  -14.9931   8.1431  -13.3334
 M9B  H15  H  HCH2  0   0.233  -10.9938  10.9815  -10.7231
 M9B  H16  H  HCH2  0   0.222  -10.3834  10.8284  -12.3551
 M9B  H17  H  HCH2  0   0.228   -8.7552  12.3959  -11.8868
 M9B  H18  H  HCH2  0   0.228   -9.2139  12.4701  -10.2054
 M9B  H19  H  HCR5  0   0.209   -7.8031  10.7188   -9.5537
 M9B  H20  H  HCH3  0   0.231   -8.2871  10.4354  -13.2872
 M9B  H21  H  HCH3  0   0.226   -6.7237   9.6594  -13.0603
 M9B  H22  H  HCH3  0   0.239   -8.1706   8.6904  -13.2866
 M9B  H23  H  H     0   0.240  -11.4692   8.9142  -15.2533
 M9B  H24  H  H     0   0.235  -13.0172   9.8196  -15.6683
 M9B  H25  H  HCH2  0   0.251  -16.4194   6.7615  -14.8094
 M9B  H26  H  HCH2  0   0.238  -15.1385   6.7002  -16.0136
 M9B  H27  H  HCH1  0   0.213   -5.6109  10.7408  -10.8307
 M9B  H28  H  HCH3  0   0.223   -5.9955  11.8653   -8.6872
 M9B  H29  H  HCH3  0   0.225   -5.0193  12.9121   -9.7087
 M9B  H30  H  HCH3  0   0.216   -6.7349  13.2451   -9.4988
 M9B  H31  H  HCH2  0   0.208   -6.5419  13.3794  -11.9777
 M9B  H32  H  HCH2  0   0.228   -6.7094  11.9325  -12.9361
 M9B  H33  H  HCH2  0   0.212   -4.3126  11.4416  -12.7276
 M9B  H34  H  HCH2  0   0.208   -4.0686  12.8538  -11.7240
 M9B  H35  H  HCH2  0   0.211   -4.8830  14.3209  -13.5767
 M9B  H36  H  HCH2  0   0.201   -5.0661  12.9198  -14.6110
 M9B  H37  H  HCH1  0   0.207   -2.4363  13.8346  -13.3782
 M9B  H38  H  HCH3  0   0.227   -2.4240  11.3941  -13.8889
 M9B  H39  H  HCH3  0   0.210   -2.9993  11.7302  -15.5210
 M9B  H40  H  HCH3  0   0.223   -1.3949  12.2605  -15.0186
 M9B  H41  H  HCH3  0   0.222   -3.3194  15.4690  -15.0398
 M9B  H42  H  HCH3  0   0.223   -1.8817  14.6582  -15.6578
 M9B  H43  H  HCH3  0   0.211   -3.4770  14.1792  -16.2315
 M9B  H44  H  HOH1  0   0.454  -15.1456   9.9574  -14.6564
 M9B  H4   H  HCH2  0   0.222   -7.5470   6.9010  -12.2074

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
 M9B  O1   C1   single  1.405  0.020  1.405
 M9B  C2   C1   single  1.527  0.020  1.527
 M9B  C2   C3   single  1.521  0.020  1.521
 M9B  C26  C25  single  1.526  0.020  1.526
 M9B  C1   C6   single  1.515  0.020  1.515
 M9B  C27  C25  single  1.526  0.020  1.526
 M9B  C19  C6   double  1.331  0.020  1.331
 M9B  C25  C24  single  1.530  0.020  1.530
 M9B  C6   C5   single  1.478  0.020  1.478
 M9B  C3   C4   single  1.529  0.020  1.529
 M9B  C3   O    single  1.414  0.020  1.414
 M9B  C4   C5   single  1.503  0.020  1.503
 M9B  C24  C23  single  1.524  0.020  1.524
 M9B  C5   C7   double  1.343  0.020  1.343
 M9B  C23  C22  single  1.526  0.020  1.526
 M9B  C18  C13  single  1.529  0.020  1.529
 M9B  C7   C8   single  1.450  0.020  1.450
 M9B  C8   C9   double  1.342  0.020  1.342
 M9B  C22  C20  single  1.535  0.020  1.535
 M9B  C20  C17  single  1.538  0.020  1.538
 M9B  C20  C21  single  1.530  0.020  1.530
 M9B  C13  C12  single  1.526  0.020  1.526
 M9B  C13  C14  single  1.546  0.020  1.546
 M9B  C13  C17  single  1.540  0.020  1.540
 M9B  C9   C14  single  1.496  0.020  1.496
 M9B  C9   C10  single  1.507  0.020  1.507
 M9B  C11  C12  single  1.529  0.020  1.529
 M9B  C11  C10  single  1.536  0.020  1.536
 M9B  C15  C16  single  1.549  0.020  1.549
 M9B  C15  C14  single  1.527  0.020  1.527
 M9B  C16  C17  single  1.544  0.020  1.544
 M9B  C4   H1   single  0.970  0.020  1.090
 M9B  C4   H2   single  0.970  0.020  1.090
 M9B  C14  H3   single  0.970  0.020  1.090
 M9B  C11  H4   single  0.970  0.020  1.090
 M9B  C11  H5   single  0.970  0.020  1.090
 M9B  C7   H6   single  0.930  0.020  1.080
 M9B  C8   H7   single  0.930  0.020  1.080
 M9B  C10  H8   single  0.970  0.020  1.090
 M9B  C10  H9   single  0.970  0.020  1.090
 M9B  C12  H10  single  0.970  0.020  1.090
 M9B  C12  H11  single  0.970  0.020  1.090
 M9B  C3   H12  single  0.970  0.020  1.090
 M9B  O    H13  single  0.850  0.020  0.980
 M9B  C1   H14  single  0.970  0.020  1.090
 M9B  C15  H15  single  0.970  0.020  1.090
 M9B  C15  H16  single  0.970  0.020  1.090
 M9B  C16  H17  single  0.970  0.020  1.090
 M9B  C16  H18  single  0.970  0.020  1.090
 M9B  C17  H19  single  0.970  0.020  1.090
 M9B  C18  H20  single  0.970  0.020  1.090
 M9B  C18  H21  single  0.970  0.020  1.090
 M9B  C18  H22  single  0.970  0.020  1.090
 M9B  C19  H23  single  0.930  0.020  1.080
 M9B  C19  H24  single  0.930  0.020  1.080
 M9B  C2   H25  single  0.970  0.020  1.090
 M9B  C2   H26  single  0.970  0.020  1.090
 M9B  C20  H27  single  0.970  0.020  1.090
 M9B  C21  H28  single  0.970  0.020  1.090
 M9B  C21  H29  single  0.970  0.020  1.090
 M9B  C21  H30  single  0.970  0.020  1.090
 M9B  C22  H31  single  0.970  0.020  1.090
 M9B  C22  H32  single  0.970  0.020  1.090
 M9B  C23  H33  single  0.970  0.020  1.090
 M9B  C23  H34  single  0.970  0.020  1.090
 M9B  C24  H35  single  0.970  0.020  1.090
 M9B  C24  H36  single  0.970  0.020  1.090
 M9B  C25  H37  single  0.970  0.020  1.090
 M9B  C26  H38  single  0.970  0.020  1.090
 M9B  C26  H39  single  0.970  0.020  1.090
 M9B  C26  H40  single  0.970  0.020  1.090
 M9B  C27  H41  single  0.970  0.020  1.090
 M9B  C27  H42  single  0.970  0.020  1.090
 M9B  C27  H43  single  0.970  0.020  1.090
 M9B  O1   H44  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
 M9B  H2   C4   H1   106.49  3.000
 M9B  H2   C4   C3   107.69  3.000
 M9B  H1   C4   C3   110.48  3.000
 M9B  H2   C4   C5   109.57  3.000
 M9B  H1   C4   C5   110.88  3.000
 M9B  C3   C4   C5   111.54  3.000
 M9B  H3   C14  C15  106.88  3.000
 M9B  H3   C14  C13  105.45  3.000
 M9B  C15  C14  C13  104.03  3.000
 M9B  H3   C14  C9   105.96  3.000
 M9B  C15  C14  C9   121.95  3.000
 M9B  C13  C14  C9   111.44  3.000
 M9B  C7   C5   C6   124.93  3.000
 M9B  C7   C5   C4   121.88  3.000
 M9B  C6   C5   C4   113.18  3.000
 M9B  C19  C6   C1   123.41  3.000
 M9B  C19  C6   C5   123.13  3.000
 M9B  C1   C6   C5   113.39  3.000
 M9B  H5   C11  H4   106.00  3.000
 M9B  H5   C11  C12  109.82  3.000
 M9B  H4   C11  C12  110.00  3.000
 M9B  H5   C11  C10  108.86  3.000
 M9B  H4   C11  C10  109.33  3.000
 M9B  C12  C11  C10  112.60  3.000
 M9B  H6   C7   C8   117.30  3.000
 M9B  H6   C7   C5   116.31  3.000
 M9B  C8   C7   C5   126.38  3.000
 M9B  H7   C8   C9   117.72  3.000
 M9B  H7   C8   C7   115.99  3.000
 M9B  C9   C8   C7   126.29  3.000
 M9B  C10  C9   C8   125.64  3.000
 M9B  C10  C9   C14  111.14  3.000
 M9B  C8   C9   C14  123.21  3.000
 M9B  H9   C10  H8   106.33  3.000
 M9B  H9   C10  C9   112.28  3.000
 M9B  H8   C10  C9   107.89  3.000
 M9B  H9   C10  C11  109.24  3.000
 M9B  H8   C10  C11  108.17  3.000
 M9B  C9   C10  C11  112.64  3.000
 M9B  H11  C12  H10  106.46  3.000
 M9B  H11  C12  C13  108.62  3.000
 M9B  H10  C12  C13  111.00  3.000
 M9B  H11  C12  C11  109.26  3.000
 M9B  H10  C12  C11  109.92  3.000
 M9B  C13  C12  C11  111.44  3.000
 M9B  C18  C13  C17  112.92  3.000
 M9B  C17  C13  C12  114.40  3.000
 M9B  C18  C13  C12  110.38  3.000
 M9B  C17  C13  C14   99.45  3.000
 M9B  C12  C13  C14  108.44  3.000
 M9B  C18  C13  C14  110.67  3.000
 M9B  H12  C3   C2   108.40  3.000
 M9B  H12  C3   O    110.39  3.000
 M9B  C2   C3   O    107.60  3.000
 M9B  H12  C3   C4   108.21  3.000
 M9B  O    C3   C4   111.70  3.000
 M9B  C2   C3   C4   110.50  3.000
 M9B  H13  O    C3   108.33  3.000
 M9B  H14  C1   O1   110.20  3.000
 M9B  H14  C1   C2   108.13  3.000
 M9B  O1   C1   C2   107.93  3.000
 M9B  H14  C1   C6   106.78  3.000
 M9B  C2   C1   C6   109.79  3.000
 M9B  O1   C1   C6   113.88  3.000
 M9B  H16  C15  H15  106.50  3.000
 M9B  H16  C15  C16  110.35  3.000
 M9B  H15  C15  C16  112.59  3.000
 M9B  H16  C15  C14  111.49  3.000
 M9B  H15  C15  C14  111.79  3.000
 M9B  C16  C15  C14  104.22  3.000
 M9B  H18  C16  H17  106.15  3.000
 M9B  H18  C16  C17  111.15  3.000
 M9B  H17  C16  C17  111.49  3.000
 M9B  H18  C16  C15  111.92  3.000
 M9B  H17  C16  C15  110.18  3.000
 M9B  C17  C16  C15  106.04  3.000
 M9B  H19  C17  C20  105.49  3.000
 M9B  H19  C17  C16  106.60  3.000
 M9B  C20  C17  C16  117.26  3.000
 M9B  H19  C17  C13  104.09  3.000
 M9B  C16  C17  C13  103.89  3.000
 M9B  C20  C17  C13  118.27  3.000
 M9B  H22  C18  H21  107.16  3.000
 M9B  H22  C18  H20  106.64  3.000
 M9B  H21  C18  H20  107.51  3.000
 M9B  H22  C18  C13  111.64  3.000
 M9B  H21  C18  C13  111.13  3.000
 M9B  H20  C18  C13  112.48  3.000
 M9B  H24  C19  H23  116.53  3.000
 M9B  H24  C19  C6   122.37  3.000
 M9B  H23  C19  C6   121.10  3.000
 M9B  H26  C2   H25  107.08  3.000
 M9B  H26  C2   C1   109.15  3.000
 M9B  H25  C2   C1   109.77  3.000
 M9B  H26  C2   C3   108.59  3.000
 M9B  H25  C2   C3   109.85  3.000
 M9B  C1   C2   C3   112.27  3.000
 M9B  H27  C20  C22  107.45  3.000
 M9B  H27  C20  C21  107.13  3.000
 M9B  C22  C20  C21  109.72  3.000
 M9B  H27  C20  C17  106.46  3.000
 M9B  C21  C20  C17  109.78  3.000
 M9B  C22  C20  C17  115.87  3.000
 M9B  H30  C21  H29  107.41  3.000
 M9B  H30  C21  H28  107.69  3.000
 M9B  H29  C21  H28  107.34  3.000
 M9B  H30  C21  C20  110.81  3.000
 M9B  H29  C21  C20  111.93  3.000
 M9B  H28  C21  C20  111.44  3.000
 M9B  H32  C22  H31  105.72  3.000
 M9B  H32  C22  C23  108.11  3.000
 M9B  H31  C22  C23  109.43  3.000
 M9B  H32  C22  C20  111.11  3.000
 M9B  H31  C22  C20  109.31  3.000
 M9B  C23  C22  C20  112.89  3.000
 M9B  H34  C23  H33  106.05  3.000
 M9B  H34  C23  C24  108.99  3.000
 M9B  H33  C23  C24  110.21  3.000
 M9B  H34  C23  C22  110.17  3.000
 M9B  H33  C23  C22  108.34  3.000
 M9B  C24  C23  C22  112.87  3.000
 M9B  H36  C24  H35  105.93  3.000
 M9B  H36  C24  C25  108.78  3.000
 M9B  H35  C24  C25  108.71  3.000
 M9B  H36  C24  C23  109.52  3.000
 M9B  H35  C24  C23  108.58  3.000
 M9B  C25  C24  C23  114.93  3.000
 M9B  H37  C25  C27  107.99  3.000
 M9B  H37  C25  C26  108.22  3.000
 M9B  C27  C25  C26  110.27  3.000
 M9B  H37  C25  C24  107.94  3.000
 M9B  C27  C25  C24  110.28  3.000
 M9B  C26  C25  C24  111.99  3.000
 M9B  H40  C26  H39  107.59  3.000
 M9B  H40  C26  H38  107.27  3.000
 M9B  H39  C26  H38  107.70  3.000
 M9B  H40  C26  C25  111.24  3.000
 M9B  H39  C26  C25  110.45  3.000
 M9B  H38  C26  C25  112.39  3.000
 M9B  H43  C27  H42  107.49  3.000
 M9B  H43  C27  H41  107.61  3.000
 M9B  H42  C27  H41  107.69  3.000
 M9B  H43  C27  C25  110.83  3.000
 M9B  H42  C27  C25  111.57  3.000
 M9B  H41  C27  C25  111.46  3.000
 M9B  H44  O1   C1   108.39  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
 M9B  Var_01  C1   C6   C5   C4     53.55  30.0  1
 M9B  Var_02  C11  C10  C9   C14   -52.45  30.0  1
 M9B  Var_03  C17  C16  C15  C14     4.96  30.0  1
 M9B  Var_04  C3   C4   C5   C6    -52.90  30.0  1
 M9B  Var_05  C12  C11  C10  C9     49.44  30.0  1
 M9B  Var_06  C13  C12  C11  C10   -52.19  30.0  1
 M9B  Var_07  C8   C7   C5   C4   -177.64   0.0  2
 M9B  Var_08  C7   C8   C9   C14   179.75   0.0  2
 M9B  Var_09  C9   C8   C7   C5   -175.48  30.0  2
 M9B  Var_10  H23  C19  C6   C5     -1.99   0.0  2
 M9B  Var_11  C24  C23  C22  C20  -176.48  30.0  2
 M9B  Var_12  C25  C24  C23  C22   178.69  30.0  1
 M9B  Var_13  C26  C25  C24  C23    64.53  30.0  1
 M9B  Var_14  H38  C26  C25  C24   -60.54  30.0  3
 M9B  Var_15  H41  C27  C25  C24    56.92  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
 M9B  chir_01  C14  C13  C9   C15  positiv
 M9B  chir_02  C13  C12  C14  C17  negativ
 M9B  chir_03  C3   O    C4   C2   positiv
 M9B  chir_04  C1   O1   C2   C6   negativ
 M9B  chir_05  C17  C16  C13  C20  negativ
 M9B  chir_06  C20  C22  C17  C21  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
 M9B  plan-1  C5   0.020
 M9B  plan-1  C6   0.020
 M9B  plan-1  C1   0.020
 M9B  plan-1  C19  0.020
 M9B  plan-1  H23  0.020
 M9B  plan-1  H24  0.020
 M9B  plan-2  C4   0.020
 M9B  plan-2  C5   0.020
 M9B  plan-2  C6   0.020
 M9B  plan-2  C7   0.020
 M9B  plan-2  C8   0.020
 M9B  plan-2  H6   0.020
 M9B  plan-3  C14  0.020
 M9B  plan-3  C7   0.020
 M9B  plan-3  C8   0.020
 M9B  plan-3  C9   0.020
 M9B  plan-3  C10  0.020
 M9B  plan-3  H7   0.020

