# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 05:35:09 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 1-[(3~{R},5~{S},8~{R},9~{S},10~{S},13~{S},14~{S},17~{S})-10,13-dimethyl-3-oxidanyl-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]-2-oxidanyl-ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC[C@@H](O)C[C@@H]1CC[C@H]3[C@@H]4CC[C@H](C(=O)CO)[C@@]4(C)CC[C@H]23
#
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
 A8Z  A8Z  1-[(3~{R},5~{S},8~{R},9~{S},10~{S},13~{S},14~{S},17~{S})-10,13-dimethyl-3-oxidanyl-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]-2-oxidanyl-ethanone  ligand  58  24  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_A8Z
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
 A8Z  C2   C  CH2   0  -0.487   4.4861  -1.8707   0.0162
 A8Z  C5   C  CH1   0  -0.198   3.1837   0.7436  -0.0464
 A8Z  C4   C  CH2   0  -0.447   4.6732   0.6099   0.2623
 A8Z  C6   C  CH2   0  -0.419   2.6044   2.0457   0.4901
 A8Z  C7   C  CH2   0  -0.416   1.1657   2.2298   0.0281
 A8Z  C8   C  CH1   0  -0.227   0.2843   1.0333   0.3762
 A8Z  C9   C  CH1   0  -0.171   0.9128  -0.2939  -0.0980
 A8Z  C1   C  CH2   0  -0.409   2.9943  -1.7230  -0.2713
 A8Z  C10  C  CT    0  -0.054   2.3660  -0.4899   0.4028
 A8Z  C11  C  CH2   0  -0.443  -0.0151  -1.4731   0.2151
 A8Z  C12  C  CH2   0  -0.417  -1.4244  -1.3022  -0.3575
 A8Z  C13  C  CT    0  -0.051  -2.0522   0.0102   0.0977
 A8Z  C14  C  CH1   0  -0.175  -1.0917   1.1564  -0.2620
 A8Z  C15  C  CH2   0  -0.449  -1.9218   2.4154  -0.0261
 A8Z  C16  C  CH2   0  -0.430  -3.3559   1.9996  -0.4279
 A8Z  C17  C  CH1   0  -0.366  -3.2962   0.4847  -0.7065
 A8Z  C18  C  CH3   0  -0.678  -2.3755  -0.0384   1.5948
 A8Z  C19  C  CH3   0  -0.692   2.3941  -0.6796   1.9252
 A8Z  C20  C  C     0   0.382  -4.5665  -0.2676  -0.4102
 A8Z  C3   C  CH1   0   0.049   5.2890  -0.6321  -0.3649
 A8Z  O2   O  OH1   0  -0.679   5.3148  -0.4332  -1.7695
 A8Z  C21  C  CH2   0  -0.257  -4.8038  -1.4714  -1.2878
 A8Z  H11  H  HCH2  0   0.224   4.6478  -2.0707   1.0789
 A8Z  H12  H  HCH2  0   0.233   4.8817  -2.7466  -0.5092
 A8Z  H14  H  HCH2  0   0.227   5.2011   1.5002  -0.0956
 A8Z  H13  H  HCH2  0   0.220   4.8407   0.5773   1.3425
 A8Z  H15  H  HCH2  0   0.209   2.6590   2.0669   1.5842
 A8Z  H16  H  HCH2  0   0.220   3.2125   2.8859   0.1402
 A8Z  H18  H  HCH2  0   0.228   0.7433   3.1405   0.4615
 A8Z  H17  H  HCH2  0   0.201   1.1572   2.3753  -1.0593
 A8Z  H2   H  HCH1  0   0.209   0.1703   1.0081   1.4668
 A8Z  H3   H  HCH1  0   0.195   0.9832  -0.2226  -1.1953
 A8Z  H9   H  HCH2  0   0.212   2.8360  -1.6546  -1.3532
 A8Z  H10  H  HCH2  0   0.225   2.4863  -2.6350   0.0531
 A8Z  H19  H  HCH2  0   0.236   0.4045  -2.3992  -0.1826
 A8Z  H20  H  HCH2  0   0.219  -0.0802  -1.6158   1.2971
 A8Z  H21  H  HCH2  0   0.217  -1.3749  -1.3160  -1.4527
 A8Z  H22  H  HCH2  0   0.224  -2.0357  -2.1599  -0.0595
 A8Z  H4   H  HCH1  0   0.212  -0.9278   1.0786  -1.3480
 A8Z  H23  H  HCH2  0   0.222  -1.8806   2.7169   1.0239
 A8Z  H24  H  HCH2  0   0.235  -1.5625   3.2643  -0.6087
 A8Z  H26  H  HCH2  0   0.235  -4.0675   2.2176   0.3683
 A8Z  H25  H  HCH2  0   0.242  -3.7016   2.5341  -1.3132
 A8Z  H5   H  HCH1  0   0.253  -3.0594   0.3205  -1.7648
 A8Z  H31  H  HCH3  0   0.238  -1.4776  -0.1441   2.2016
 A8Z  H30  H  HCH3  0   0.239  -2.8886   0.8594   1.9410
 A8Z  H32  H  HCH3  0   0.231  -3.0180  -0.8895   1.8282
 A8Z  H8   H  HCH3  0   0.231   1.8469   0.0997   2.4555
 A8Z  H6   H  HCH3  0   0.229   1.9456  -1.6355   2.2006
 A8Z  H7   H  HCH3  0   0.233   3.4087  -0.6843   2.3227
 A8Z  H    H  HCH1  0   0.203   6.3155  -0.7511   0.0119
 A8Z  H29  H  HOH1  0   0.462  -6.0720  -2.9043  -1.4656
 A8Z  H33  H  HOH1  0   0.444   5.5941  -1.2560  -2.1827
 A8Z  H28  H  HCH2  0   0.240  -4.9056  -1.0913  -2.3163
 A8Z  H27  H  HCH2  0   0.237  -3.8867  -2.0787  -1.2903
 A8Z  H1   H  HCH1  0   0.208   3.0884   0.7877  -1.1398
 A8Z  O    O  O     0  -0.400  -5.3510   0.0515   0.4530
 A8Z  O1   O  OH1   0  -0.659  -5.9258  -2.1771  -0.8541

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
 A8Z  C4   C3   single  1.522  0.020  1.522
 A8Z  C4   C5   single  1.527  0.020  1.527
 A8Z  C3   O2   single  1.419  0.020  1.419
 A8Z  C3   C2   single  1.524  0.020  1.524
 A8Z  C6   C5   single  1.523  0.020  1.523
 A8Z  C6   C7   single  1.522  0.020  1.522
 A8Z  C2   C1   single  1.526  0.020  1.526
 A8Z  C5   C10  single  1.547  0.020  1.547
 A8Z  C19  C10  single  1.534  0.020  1.534
 A8Z  C7   C8   single  1.526  0.020  1.526
 A8Z  C10  C1   single  1.539  0.020  1.539
 A8Z  C10  C9   single  1.549  0.020  1.549
 A8Z  C8   C9   single  1.543  0.020  1.543
 A8Z  C8   C14  single  1.522  0.020  1.522
 A8Z  C9   C11  single  1.533  0.020  1.533
 A8Z  C14  C15  single  1.526  0.020  1.526
 A8Z  C14  C13  single  1.538  0.020  1.538
 A8Z  C11  C12  single  1.531  0.020  1.531
 A8Z  C15  C16  single  1.546  0.020  1.546
 A8Z  C13  C18  single  1.532  0.020  1.532
 A8Z  C13  C12  single  1.524  0.020  1.524
 A8Z  C13  C17  single  1.556  0.020  1.556
 A8Z  C16  C17  single  1.542  0.020  1.542
 A8Z  C17  C20  single  1.506  0.020  1.506
 A8Z  C20  O    double  1.209  0.020  1.209
 A8Z  C20  C21  single  1.508  0.020  1.508
 A8Z  C21  O1   single  1.395  0.020  1.395
 A8Z  C2   H11  single  0.970  0.020  1.090
 A8Z  C2   H12  single  0.970  0.020  1.090
 A8Z  C5   H1   single  0.970  0.020  1.090
 A8Z  C4   H14  single  0.970  0.020  1.090
 A8Z  C4   H13  single  0.970  0.020  1.090
 A8Z  C6   H15  single  0.970  0.020  1.090
 A8Z  C6   H16  single  0.970  0.020  1.090
 A8Z  C7   H18  single  0.970  0.020  1.090
 A8Z  C7   H17  single  0.970  0.020  1.090
 A8Z  C8   H2   single  0.970  0.020  1.090
 A8Z  C9   H3   single  0.970  0.020  1.090
 A8Z  C1   H9   single  0.970  0.020  1.090
 A8Z  C1   H10  single  0.970  0.020  1.090
 A8Z  C11  H19  single  0.970  0.020  1.090
 A8Z  C11  H20  single  0.970  0.020  1.090
 A8Z  C12  H21  single  0.970  0.020  1.090
 A8Z  C12  H22  single  0.970  0.020  1.090
 A8Z  C14  H4   single  0.970  0.020  1.090
 A8Z  C15  H23  single  0.970  0.020  1.090
 A8Z  C15  H24  single  0.970  0.020  1.090
 A8Z  C16  H26  single  0.970  0.020  1.090
 A8Z  C16  H25  single  0.970  0.020  1.090
 A8Z  C17  H5   single  0.970  0.020  1.090
 A8Z  C18  H31  single  0.970  0.020  1.090
 A8Z  C18  H30  single  0.970  0.020  1.090
 A8Z  C18  H32  single  0.970  0.020  1.090
 A8Z  C19  H8   single  0.970  0.020  1.090
 A8Z  C19  H6   single  0.970  0.020  1.090
 A8Z  C19  H7   single  0.970  0.020  1.090
 A8Z  C3   H    single  0.970  0.020  1.090
 A8Z  O1   H29  single  0.850  0.020  0.980
 A8Z  O2   H33  single  0.850  0.020  0.980
 A8Z  C21  H28  single  0.970  0.020  1.090
 A8Z  C21  H27  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
 A8Z  H12  C2   H11  105.46  3.000
 A8Z  H12  C2   C3   109.85  3.000
 A8Z  H11  C2   C3   108.28  3.000
 A8Z  H12  C2   C1   109.87  3.000
 A8Z  H11  C2   C1   110.20  3.000
 A8Z  C3   C2   C1   112.89  3.000
 A8Z  H1   C5   C10  105.98  3.000
 A8Z  H1   C5   C6   106.46  3.000
 A8Z  C10  C5   C6   112.25  3.000
 A8Z  H1   C5   C4   106.81  3.000
 A8Z  C10  C5   C4   112.78  3.000
 A8Z  C6   C5   C4   112.01  3.000
 A8Z  H13  C4   H14  105.86  3.000
 A8Z  H13  C4   C3   108.71  3.000
 A8Z  H14  C4   C3   109.50  3.000
 A8Z  H13  C4   C5   110.58  3.000
 A8Z  H14  C4   C5   109.45  3.000
 A8Z  C3   C4   C5   112.51  3.000
 A8Z  H16  C6   H15  106.06  3.000
 A8Z  H16  C6   C7   109.59  3.000
 A8Z  H15  C6   C7   110.35  3.000
 A8Z  H16  C6   C5   109.42  3.000
 A8Z  H15  C6   C5   110.45  3.000
 A8Z  C7   C6   C5   110.86  3.000
 A8Z  H17  C7   H18  106.22  3.000
 A8Z  H17  C7   C8   109.00  3.000
 A8Z  H18  C7   C8   109.84  3.000
 A8Z  H17  C7   C6   108.91  3.000
 A8Z  H18  C7   C6   110.22  3.000
 A8Z  C8   C7   C6   112.44  3.000
 A8Z  H2   C8   C14  108.95  3.000
 A8Z  H2   C8   C9   109.16  3.000
 A8Z  C14  C8   C9   108.00  3.000
 A8Z  H2   C8   C7   107.74  3.000
 A8Z  C14  C8   C7   111.29  3.000
 A8Z  C9   C8   C7   111.65  3.000
 A8Z  H3   C9   C11  106.97  3.000
 A8Z  H3   C9   C10  105.67  3.000
 A8Z  C11  C9   C10  113.85  3.000
 A8Z  H3   C9   C8   106.04  3.000
 A8Z  C11  C9   C8   110.63  3.000
 A8Z  C10  C9   C8   113.04  3.000
 A8Z  H10  C1   H9   106.14  3.000
 A8Z  H10  C1   C10  110.41  3.000
 A8Z  H9   C1   C10  108.87  3.000
 A8Z  H10  C1   C2   108.51  3.000
 A8Z  H9   C1   C2   109.47  3.000
 A8Z  C10  C1   C2   113.20  3.000
 A8Z  C19  C10  C1   109.15  3.000
 A8Z  C1   C10  C9   110.03  3.000
 A8Z  C19  C10  C9   110.70  3.000
 A8Z  C9   C10  C5   107.52  3.000
 A8Z  C1   C10  C5   107.21  3.000
 A8Z  C19  C10  C5   112.15  3.000
 A8Z  H20  C11  H19  105.82  3.000
 A8Z  H20  C11  C12  109.26  3.000
 A8Z  H19  C11  C12  108.20  3.000
 A8Z  H20  C11  C9   109.79  3.000
 A8Z  H19  C11  C9   110.21  3.000
 A8Z  C12  C11  C9   113.27  3.000
 A8Z  H22  C12  H21  106.69  3.000
 A8Z  H22  C12  C13  111.30  3.000
 A8Z  H21  C12  C13  109.13  3.000
 A8Z  H22  C12  C11  108.96  3.000
 A8Z  H21  C12  C11  109.31  3.000
 A8Z  C13  C12  C11  111.32  3.000
 A8Z  C18  C13  C17  110.25  3.000
 A8Z  C17  C13  C14   98.69  3.000
 A8Z  C18  C13  C14  112.57  3.000
 A8Z  C17  C13  C12  115.95  3.000
 A8Z  C18  C13  C12  110.57  3.000
 A8Z  C14  C13  C12  108.33  3.000
 A8Z  H4   C14  C15  106.96  3.000
 A8Z  H4   C14  C13  105.72  3.000
 A8Z  C15  C14  C13  103.83  3.000
 A8Z  H4   C14  C8   105.86  3.000
 A8Z  C13  C14  C8   113.97  3.000
 A8Z  C15  C14  C8   119.58  3.000
 A8Z  H24  C15  H23  106.62  3.000
 A8Z  H24  C15  C16  112.09  3.000
 A8Z  H23  C15  C16  111.01  3.000
 A8Z  H24  C15  C14  112.36  3.000
 A8Z  H23  C15  C14  110.82  3.000
 A8Z  C16  C15  C14  104.03  3.000
 A8Z  H25  C16  H26  106.74  3.000
 A8Z  H25  C16  C17  110.32  3.000
 A8Z  H26  C16  C17  110.72  3.000
 A8Z  H25  C16  C15  111.92  3.000
 A8Z  H26  C16  C15  111.22  3.000
 A8Z  C17  C16  C15  105.98  3.000
 A8Z  H5   C17  C20  107.29  3.000
 A8Z  H5   C17  C16  109.26  3.000
 A8Z  C20  C17  C16  115.01  3.000
 A8Z  H5   C17  C13  106.30  3.000
 A8Z  C20  C17  C13  114.87  3.000
 A8Z  C16  C17  C13  103.73  3.000
 A8Z  H32  C18  H30  107.28  3.000
 A8Z  H32  C18  H31  106.89  3.000
 A8Z  H30  C18  H31  106.92  3.000
 A8Z  H32  C18  C13  110.96  3.000
 A8Z  H30  C18  C13  112.54  3.000
 A8Z  H31  C18  C13  111.94  3.000
 A8Z  H7   C19  H6   106.67  3.000
 A8Z  H7   C19  H8   107.04  3.000
 A8Z  H6   C19  H8   107.28  3.000
 A8Z  H7   C19  C10  112.30  3.000
 A8Z  H6   C19  C10  110.56  3.000
 A8Z  H8   C19  C10  112.66  3.000
 A8Z  C21  C20  C17  114.64  3.000
 A8Z  C21  C20  O    121.59  3.000
 A8Z  C17  C20  O    123.77  3.000
 A8Z  H    C3   O2   109.71  3.000
 A8Z  H    C3   C4   108.95  3.000
 A8Z  O2   C3   C4   107.52  3.000
 A8Z  H    C3   C2   108.54  3.000
 A8Z  O2   C3   C2   111.78  3.000
 A8Z  C4   C3   C2   110.31  3.000
 A8Z  H33  O2   C3   108.09  3.000
 A8Z  H27  C21  H28  105.40  3.000
 A8Z  H27  C21  O1   113.09  3.000
 A8Z  H28  C21  O1   113.00  3.000
 A8Z  H27  C21  C20  108.10  3.000
 A8Z  H28  C21  C20  106.41  3.000
 A8Z  O1   C21  C20  110.45  3.000
 A8Z  H29  O1   C21  107.90  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
 A8Z  Var_01  C8   C7   C6   C5    54.11  30.0  1
 A8Z  Var_02  C13  C12  C11  C9   -54.61  30.0  1
 A8Z  Var_03  C3   C2   C1   C10  -55.50  30.0  1
 A8Z  Var_04  C17  C16  C15  C14    6.67  30.0  1
 A8Z  Var_05  O1   C21  C20  C17  174.02  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
 A8Z  chir_01  C5   C4   C6   C10  positiv
 A8Z  chir_02  C8   C7   C9   C14  positiv
 A8Z  chir_03  C9   C11  C8   C10  negativ
 A8Z  chir_04  C10  C5   C1   C9   positiv
 A8Z  chir_05  C13  C14  C12  C17  positiv
 A8Z  chir_06  C14  C13  C15  C8   negativ
 A8Z  chir_07  C17  C20  C16  C13  negativ
 A8Z  chir_08  C3   C4   O2   C2   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
 A8Z  plan-1  C17  0.020
 A8Z  plan-1  C20  0.020
 A8Z  plan-1  C21  0.020
 A8Z  plan-1  O    0.020

