# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:09:00 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: (3S,5S,8R,9S,10S,13S,14S)-10,13-dimethyl-3-oxidanyl-1,2,3,4,5,6,7,8,9,11,12,14,15,16-tetradecahydrocyclopenta[a]phenanthren-17-one
#   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]2CC[C@@]4(C)[C@H]3CCC4=O
#
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
 AOX  AOX  (3S,5S,8R,9S,10S,13S,14S)-10,13-dimethyl-3-oxidanyl-1,2,3,4,5,6,7,8,9,11,12,14,15,16-tetradecahydrocyclopenta[a]phenanthren-17-one  ligand  51  21  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AOX
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
 AOX  C1   C  CH2   0  -0.430  -2.3738  -1.4947   0.4815
 AOX  C2   C  CH2   0  -0.479  -3.8836  -1.4067   0.2730
 AOX  C3   C  CH1   0   0.088  -4.4289  -0.0608   0.7302
 AOX  C4   C  CH2   0  -0.452  -3.6961   1.0754   0.0393
 AOX  C5   C  CH1   0  -0.211  -2.1890   0.9725   0.2586
 AOX  C6   C  CH2   0  -0.417  -1.4445   2.1718  -0.3114
 AOX  C7   C  CH2   0  -0.421   0.0202   2.1337   0.0970
 AOX  C8   C  CH1   0  -0.221   0.6905   0.8209  -0.2954
 AOX  C9   C  CH1   0  -0.175  -0.1066  -0.4064   0.2026
 AOX  C10  C  CT    0  -0.043  -1.5954  -0.3716  -0.2259
 AOX  C11  C  CH2   0  -0.452   0.6085  -1.7168  -0.1607
 AOX  C12  C  CH2   0  -0.401   2.0634  -1.7752   0.3147
 AOX  C13  C  CT    0  -0.203   2.8267  -0.5545  -0.1726
 AOX  C14  C  CH1   0  -0.197   2.0956   0.7170   0.2732
 AOX  C15  C  CH2   0  -0.459   3.1177   1.8334   0.0530
 AOX  C16  C  CH2   0  -0.567   4.4244   1.1810   0.5262
 AOX  C17  C  C     0   0.431   4.1963  -0.3214   0.4270
 AOX  C18  C  CH3   0  -0.666   3.0676  -0.6161  -1.6921
 AOX  C19  C  CH3   0  -0.696  -1.7254  -0.5459  -1.7440
 AOX  O3   O  OH1   0  -0.680  -5.8125   0.0793   0.4681
 AOX  O17  O  O     0  -0.402   4.9797  -1.1732   0.7735
 AOX  H1   H  HCH2  0   0.215  -2.1572  -1.4521   1.5560
 AOX  H2   H  HCH2  0   0.231  -2.0317  -2.4733   0.1397
 AOX  H3   H  HCH2  0   0.220  -4.1332  -1.5573  -0.7822
 AOX  H4   H  HCH2  0   0.231  -4.3727  -2.2151   0.8263
 AOX  H5   H  HCH1  0   0.179  -4.2384   0.0272   1.8123
 AOX  H6   H  HCH2  0   0.215  -3.9354   1.0744  -1.0297
 AOX  H7   H  HCH2  0   0.230  -4.0479   2.0331   0.4359
 AOX  H8   H  HCH1  0   0.206  -2.0273   0.9968   1.3474
 AOX  H9   H  HCH2  0   0.213  -1.5359   2.1938  -1.4031
 AOX  H10  H  HCH2  0   0.223  -1.9065   3.0952   0.0504
 AOX  H11  H  HCH2  0   0.230   0.5610   2.9725  -0.3497
 AOX  H12  H  HCH2  0   0.204   0.0931   2.2655   1.1837
 AOX  H13  H  HCH1  0   0.213   0.7472   0.7951  -1.3904
 AOX  H14  H  HCH1  0   0.200  -0.1078  -0.3384   1.3022
 AOX  H15  H  HCH2  0   0.239   0.0740  -2.5639   0.2736
 AOX  H16  H  HCH2  0   0.222   0.5740  -1.8664  -1.2434
 AOX  H17  H  HCH2  0   0.224   2.0885  -1.8043   1.4092
 AOX  H18  H  HCH2  0   0.229   2.5297  -2.7004  -0.0342
 AOX  H19  H  HCH1  0   0.223   1.9757   0.6296   1.3651
 AOX  H20  H  HCH2  0   0.230   3.1754   2.1244  -0.9984
 AOX  H21  H  HCH2  0   0.248   2.8774   2.7325   0.6205
 AOX  H22  H  HCH2  0   0.277   5.3102   1.4799  -0.0378
 AOX  H23  H  HCH2  0   0.277   4.6284   1.4203   1.5736
 AOX  H24  H  HCH3  0   0.245   2.1345  -0.6321  -2.2542
 AOX  H25  H  HCH3  0   0.243   3.6470   0.2311  -2.0616
 AOX  H26  H  HCH3  0   0.243   3.6174  -1.5244  -1.9444
 AOX  H27  H  HCH3  0   0.232  -1.0430   0.0988  -2.2974
 AOX  H28  H  HCH3  0   0.231  -1.5034  -1.5738  -2.0360
 AOX  H29  H  HCH3  0   0.235  -2.7300  -0.3271  -2.1057
 AOX  H30  H  HOH1  0   0.444  -6.2725  -0.6553   0.8863

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
 AOX  C16  C15  single  1.535  0.020  1.535
 AOX  C16  C17  single  1.523  0.020  1.523
 AOX  C15  C14  single  1.530  0.020  1.530
 AOX  O17  C17  double  1.208  0.020  1.208
 AOX  C17  C13  single  1.513  0.020  1.513
 AOX  C14  C13  single  1.533  0.020  1.533
 AOX  C14  C8   single  1.519  0.020  1.519
 AOX  C7   C8   single  1.525  0.020  1.525
 AOX  C7   C6   single  1.521  0.020  1.521
 AOX  C13  C12  single  1.520  0.020  1.520
 AOX  C13  C18  single  1.540  0.020  1.540
 AOX  C8   C9   single  1.546  0.020  1.546
 AOX  C12  C11  single  1.532  0.020  1.532
 AOX  C6   C5   single  1.522  0.020  1.522
 AOX  C9   C11  single  1.536  0.020  1.536
 AOX  C9   C10  single  1.550  0.020  1.550
 AOX  C5   C10  single  1.547  0.020  1.547
 AOX  C5   C4   single  1.526  0.020  1.526
 AOX  C10  C1   single  1.539  0.020  1.539
 AOX  C10  C19  single  1.534  0.020  1.534
 AOX  C4   C3   single  1.518  0.020  1.518
 AOX  C1   C2   single  1.527  0.020  1.527
 AOX  C3   C2   single  1.522  0.020  1.522
 AOX  C3   O3   single  1.415  0.020  1.415
 AOX  C1   H1   single  0.970  0.020  1.090
 AOX  C1   H2   single  0.970  0.020  1.090
 AOX  C2   H3   single  0.970  0.020  1.090
 AOX  C2   H4   single  0.970  0.020  1.090
 AOX  C3   H5   single  0.970  0.020  1.090
 AOX  C4   H6   single  0.970  0.020  1.090
 AOX  C4   H7   single  0.970  0.020  1.090
 AOX  C5   H8   single  0.970  0.020  1.090
 AOX  C6   H9   single  0.970  0.020  1.090
 AOX  C6   H10  single  0.970  0.020  1.090
 AOX  C7   H11  single  0.970  0.020  1.090
 AOX  C7   H12  single  0.970  0.020  1.090
 AOX  C8   H13  single  0.970  0.020  1.090
 AOX  C9   H14  single  0.970  0.020  1.090
 AOX  C11  H15  single  0.970  0.020  1.090
 AOX  C11  H16  single  0.970  0.020  1.090
 AOX  C12  H17  single  0.970  0.020  1.090
 AOX  C12  H18  single  0.970  0.020  1.090
 AOX  C14  H19  single  0.970  0.020  1.090
 AOX  C15  H20  single  0.970  0.020  1.090
 AOX  C15  H21  single  0.970  0.020  1.090
 AOX  C16  H22  single  0.970  0.020  1.090
 AOX  C16  H23  single  0.970  0.020  1.090
 AOX  C18  H24  single  0.970  0.020  1.090
 AOX  C18  H25  single  0.970  0.020  1.090
 AOX  C18  H26  single  0.970  0.020  1.090
 AOX  C19  H27  single  0.970  0.020  1.090
 AOX  C19  H28  single  0.970  0.020  1.090
 AOX  C19  H29  single  0.970  0.020  1.090
 AOX  O3   H30  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
 AOX  H2   C1   H1   106.24  3.000
 AOX  H2   C1   C10  110.60  3.000
 AOX  H1   C1   C10  108.78  3.000
 AOX  H2   C1   C2   108.60  3.000
 AOX  H1   C1   C2   109.08  3.000
 AOX  C10  C1   C2   113.29  3.000
 AOX  H4   C2   H3   106.48  3.000
 AOX  H4   C2   C3   109.93  3.000
 AOX  H3   C2   C3   109.23  3.000
 AOX  H4   C2   C1   109.28  3.000
 AOX  H3   C2   C1   110.44  3.000
 AOX  C3   C2   C1   111.36  3.000
 AOX  H5   C3   O3   110.05  3.000
 AOX  H5   C3   C4   107.67  3.000
 AOX  O3   C3   C4   108.27  3.000
 AOX  H5   C3   C2   107.67  3.000
 AOX  O3   C3   C2   112.46  3.000
 AOX  C4   C3   C2   110.61  3.000
 AOX  H7   C4   H6   106.51  3.000
 AOX  H7   C4   C5   108.92  3.000
 AOX  H6   C4   C5   110.84  3.000
 AOX  H7   C4   C3   109.56  3.000
 AOX  H6   C4   C3   109.75  3.000
 AOX  C5   C4   C3   111.14  3.000
 AOX  H8   C5   C10  105.81  3.000
 AOX  H8   C5   C6   106.32  3.000
 AOX  C10  C5   C6   112.31  3.000
 AOX  H8   C5   C4   106.59  3.000
 AOX  C10  C5   C4   113.10  3.000
 AOX  C6   C5   C4   112.09  3.000
 AOX  H10  C6   H9   106.10  3.000
 AOX  H10  C6   C7   109.82  3.000
 AOX  H9   C6   C7   110.39  3.000
 AOX  H10  C6   C5   109.55  3.000
 AOX  H9   C6   C5   110.37  3.000
 AOX  C7   C6   C5   110.53  3.000
 AOX  H12  C7   H11  106.23  3.000
 AOX  H12  C7   C8   109.21  3.000
 AOX  H11  C7   C8   109.74  3.000
 AOX  H12  C7   C6   109.08  3.000
 AOX  H11  C7   C6   110.33  3.000
 AOX  C8   C7   C6   112.07  3.000
 AOX  H13  C8   C14  108.92  3.000
 AOX  H13  C8   C9   109.24  3.000
 AOX  C14  C8   C9   107.58  3.000
 AOX  H13  C8   C7   107.45  3.000
 AOX  C9   C8   C7   111.95  3.000
 AOX  C14  C8   C7   111.66  3.000
 AOX  H14  C9   C11  106.81  3.000
 AOX  H14  C9   C10  105.88  3.000
 AOX  C11  C9   C10  113.64  3.000
 AOX  H14  C9   C8   105.85  3.000
 AOX  C10  C9   C8   112.86  3.000
 AOX  C11  C9   C8   111.16  3.000
 AOX  C19  C10  C9   110.64  3.000
 AOX  C19  C10  C5   112.10  3.000
 AOX  C9   C10  C5   107.55  3.000
 AOX  C19  C10  C1   109.22  3.000
 AOX  C5   C10  C1   107.22  3.000
 AOX  C9   C10  C1   110.03  3.000
 AOX  H16  C11  H15  105.80  3.000
 AOX  H16  C11  C12  109.40  3.000
 AOX  H15  C11  C12  108.18  3.000
 AOX  H16  C11  C9   109.64  3.000
 AOX  H15  C11  C9   109.87  3.000
 AOX  C12  C11  C9   113.65  3.000
 AOX  H18  C12  H17  106.66  3.000
 AOX  H18  C12  C13  111.29  3.000
 AOX  H17  C12  C13  109.28  3.000
 AOX  H18  C12  C11  109.78  3.000
 AOX  H17  C12  C11  109.45  3.000
 AOX  C13  C12  C11  110.30  3.000
 AOX  C18  C13  C17  104.81  3.000
 AOX  C18  C13  C14  113.26  3.000
 AOX  C17  C13  C14  100.88  3.000
 AOX  C18  C13  C12  111.27  3.000
 AOX  C14  C13  C12  109.48  3.000
 AOX  C17  C13  C12  116.82  3.000
 AOX  H19  C14  C15  105.86  3.000
 AOX  H19  C14  C13  105.92  3.000
 AOX  C15  C14  C13  104.17  3.000
 AOX  H19  C14  C8   106.00  3.000
 AOX  C13  C14  C8   112.89  3.000
 AOX  C15  C14  C8   120.94  3.000
 AOX  H21  C15  H20  107.03  3.000
 AOX  H21  C15  C16  112.19  3.000
 AOX  H20  C15  C16  111.40  3.000
 AOX  H21  C15  C14  112.32  3.000
 AOX  H20  C15  C14  111.61  3.000
 AOX  C16  C15  C14  102.37  3.000
 AOX  H23  C16  H22  106.46  3.000
 AOX  H23  C16  C17  107.83  3.000
 AOX  H22  C16  C17  110.98  3.000
 AOX  H23  C16  C15  111.16  3.000
 AOX  H22  C16  C15  114.52  3.000
 AOX  C17  C16  C15  105.77  3.000
 AOX  O17  C17  C16  125.44  3.000
 AOX  O17  C17  C13  126.30  3.000
 AOX  C16  C17  C13  108.26  3.000
 AOX  H26  C18  H25  107.49  3.000
 AOX  H26  C18  H24  107.46  3.000
 AOX  H25  C18  H24  106.95  3.000
 AOX  H26  C18  C13  109.89  3.000
 AOX  H25  C18  C13  112.72  3.000
 AOX  H24  C18  C13  112.07  3.000
 AOX  H29  C19  H28  106.72  3.000
 AOX  H29  C19  H27  106.85  3.000
 AOX  H28  C19  H27  107.09  3.000
 AOX  H29  C19  C10  112.57  3.000
 AOX  H28  C19  C10  110.77  3.000
 AOX  H27  C19  C10  112.49  3.000
 AOX  H30  O3   C3   108.14  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
 AOX  Var_01  C10  C1   C2   C3   -56.67  30.0  1
 AOX  Var_02  C8   C7   C6   C5    54.94  30.0  1
 AOX  Var_03  C13  C12  C11  C9   -53.20  30.0  1
 AOX  Var_04  C15  C16  C17  C13    3.53  30.0  1
 AOX  Var_05  C17  C16  C15  C14   22.42  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
 AOX  chir_01  C3   C4   C2   O3   positiv
 AOX  chir_02  C5   C4   C10  C6   negativ
 AOX  chir_03  C8   C9   C7   C14  negativ
 AOX  chir_04  C9   C10  C11  C8   negativ
 AOX  chir_05  C10  C5   C1   C9   positiv
 AOX  chir_06  C13  C12  C14  C17  negativ
 AOX  chir_07  C14  C15  C13  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
 AOX  plan-1  C13  0.020
 AOX  plan-1  C16  0.020
 AOX  plan-1  C17  0.020
 AOX  plan-1  O17  0.020

