# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 11:56:09 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 1-[(3~{R},5~{R},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]ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@H]1CC[C@H]2[C@@H]3CC[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3CC[C@]12C
#
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
 P9N  P9N  1-[(3~{R},5~{R},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]ethanone  ligand  57  23  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_P9N
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
 P9N  C01  C  CH2   0  -0.431  -2.9348   1.5526   0.9548
 P9N  O01  O  OH1   0  -0.680  -4.7670   0.7835  -2.2406
 P9N  C02  C  CH2   0  -0.476  -3.4290   1.8007  -0.4635
 P9N  O02  O  O     0  -0.405   5.6150   0.2007  -0.1522
 P9N  C03  C  CH1   0   0.085  -4.3148   0.6451  -0.9067
 P9N  C04  C  CH2   0  -0.451  -3.5638  -0.6700  -0.8013
 P9N  C05  C  CH1   0  -0.208  -3.0015  -0.9188   0.6034
 P9N  C06  C  CH2   0  -0.433  -2.2484  -2.2493   0.6558
 P9N  C07  C  CH2   0  -0.423  -0.9084  -2.1937  -0.0697
 P9N  C08  C  CH1   0  -0.224  -0.0345  -1.0435   0.4255
 P9N  C09  C  CH1   0  -0.191  -0.7978   0.2917   0.3306
 P9N  C10  C  CT    0  -0.064  -2.1312   0.2527   1.1223
 P9N  C11  C  CH2   0  -0.438   0.0909   1.4890   0.6832
 P9N  C12  C  CH2   0  -0.407   1.4161   1.5173  -0.0834
 P9N  C13  C  CT    0  -0.063   2.1786   0.2073   0.0741
 P9N  C14  C  CH1   0  -0.169   1.2511  -0.9340  -0.3788
 P9N  C15  C  CH2   0  -0.449   2.1729  -2.1464  -0.4659
 P9N  C16  C  CH2   0  -0.435   3.5166  -1.5607  -0.9517
 P9N  C17  C  CH1   0  -0.350   3.3588  -0.0284  -0.9106
 P9N  C18  C  CH3   0  -0.682   2.6749   0.0358   1.5136
 P9N  C19  C  CH3   0  -0.664  -1.8851   0.0726   2.6248
 P9N  C20  C  C     0   0.399   4.6172   0.7373  -0.5850
 P9N  C21  C  CH3   0  -0.776   4.5829   2.2276  -0.8092
 P9N  H1   H  HCH2  0   0.233  -2.3610   2.4089   1.3158
 P9N  H2   H  HCH2  0   0.218  -3.8094   1.4915   1.6144
 P9N  H3   H  HOH1  0   0.444  -5.2622   1.6062  -2.3037
 P9N  H4   H  HCH2  0   0.230  -3.9943   2.7382  -0.4938
 P9N  H5   H  HCH2  0   0.218  -2.5956   1.9156  -1.1642
 P9N  H6   H  HCH1  0   0.179  -5.1745   0.6050  -0.2178
 P9N  H7   H  HCH2  0   0.230  -4.2371  -1.4947  -1.0557
 P9N  H8   H  HCH2  0   0.218  -2.7652  -0.6801  -1.5495
 P9N  H9   H  HCH1  0   0.212  -3.8630  -0.9921   1.2812
 P9N  H10  H  HCH2  0   0.222  -2.0795  -2.5354   1.6979
 P9N  H11  H  HCH2  0   0.223  -2.8726  -3.0388   0.2264
 P9N  H12  H  HCH2  0   0.231  -0.3851  -3.1447   0.0603
 P9N  H13  H  HCH2  0   0.205  -1.0660  -2.0818  -1.1491
 P9N  H14  H  HCH1  0   0.208   0.2218  -1.2457   1.4725
 P9N  H15  H  HCH1  0   0.208  -1.0502   0.4111  -0.7329
 P9N  H16  H  HCH2  0   0.233  -0.4391   2.4180   0.4616
 P9N  H17  H  HCH2  0   0.217   0.2936   1.5098   1.7577
 P9N  H18  H  HCH2  0   0.216   1.2191   1.6873  -1.1485
 P9N  H19  H  HCH2  0   0.224   1.9997   2.3716   0.2681
 P9N  H20  H  HCH1  0   0.209   0.9503  -0.6845  -1.4089
 P9N  H21  H  HCH2  0   0.220   2.2806  -2.6189   0.5140
 P9N  H22  H  HCH2  0   0.234   1.7881  -2.9119  -1.1405
 P9N  H23  H  HCH2  0   0.233   4.3419  -1.8887  -0.3202
 P9N  H24  H  HCH2  0   0.238   3.7541  -1.8860  -1.9650
 P9N  H25  H  HCH1  0   0.261   3.0212   0.3285  -1.8915
 P9N  H26  H  HCH3  0   0.241   1.8600  -0.0739   2.2276
 P9N  H27  H  HCH3  0   0.239   3.3238  -0.8329   1.6287
 P9N  H28  H  HCH3  0   0.228   3.2502   0.9092   1.8309
 P9N  H29  H  HCH3  0   0.229  -1.3736  -0.8563   2.8740
 P9N  H30  H  HCH3  0   0.226  -1.2939   0.8903   3.0393
 P9N  H31  H  HCH3  0   0.223  -2.8373   0.0661   3.1610
 P9N  H32  H  HCH3  0   0.264   4.2332   2.7215   0.1011
 P9N  H33  H  HCH3  0   0.269   5.5797   2.6099  -1.0243
 P9N  H34  H  HCH3  0   0.253   3.9022   2.5107  -1.6101

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
 P9N  C06  C05  single  1.530  0.020  1.530
 P9N  C06  C07  single  1.525  0.020  1.525
 P9N  C19  C10  single  1.533  0.020  1.533
 P9N  C05  C10  single  1.549  0.020  1.549
 P9N  C05  C04  single  1.533  0.020  1.533
 P9N  C07  C08  single  1.527  0.020  1.527
 P9N  C10  C01  single  1.537  0.020  1.537
 P9N  C10  C09  single  1.551  0.020  1.551
 P9N  C04  C03  single  1.518  0.020  1.518
 P9N  C01  C02  single  1.522  0.020  1.522
 P9N  C03  C02  single  1.522  0.020  1.522
 P9N  C03  O01  single  1.415  0.020  1.415
 P9N  C08  C09  single  1.541  0.020  1.541
 P9N  C08  C14  single  1.520  0.020  1.520
 P9N  C09  C11  single  1.532  0.020  1.532
 P9N  C15  C14  single  1.526  0.020  1.526
 P9N  C15  C16  single  1.544  0.020  1.544
 P9N  C14  C13  single  1.539  0.020  1.539
 P9N  C18  C13  single  1.532  0.020  1.532
 P9N  C11  C12  single  1.531  0.020  1.531
 P9N  C13  C12  single  1.524  0.020  1.524
 P9N  C13  C17  single  1.555  0.020  1.555
 P9N  C16  C17  single  1.541  0.020  1.541
 P9N  C17  C20  single  1.509  0.020  1.509
 P9N  C20  O02  double  1.213  0.020  1.213
 P9N  C20  C21  single  1.507  0.020  1.507
 P9N  C01  H1   single  0.970  0.020  1.090
 P9N  C01  H2   single  0.970  0.020  1.090
 P9N  O01  H3   single  0.850  0.020  0.980
 P9N  C02  H4   single  0.970  0.020  1.090
 P9N  C02  H5   single  0.970  0.020  1.090
 P9N  C03  H6   single  0.970  0.020  1.090
 P9N  C04  H7   single  0.970  0.020  1.090
 P9N  C04  H8   single  0.970  0.020  1.090
 P9N  C05  H9   single  0.970  0.020  1.090
 P9N  C06  H10  single  0.970  0.020  1.090
 P9N  C06  H11  single  0.970  0.020  1.090
 P9N  C07  H12  single  0.970  0.020  1.090
 P9N  C07  H13  single  0.970  0.020  1.090
 P9N  C08  H14  single  0.970  0.020  1.090
 P9N  C09  H15  single  0.970  0.020  1.090
 P9N  C11  H16  single  0.970  0.020  1.090
 P9N  C11  H17  single  0.970  0.020  1.090
 P9N  C12  H18  single  0.970  0.020  1.090
 P9N  C12  H19  single  0.970  0.020  1.090
 P9N  C14  H20  single  0.970  0.020  1.090
 P9N  C15  H21  single  0.970  0.020  1.090
 P9N  C15  H22  single  0.970  0.020  1.090
 P9N  C16  H23  single  0.970  0.020  1.090
 P9N  C16  H24  single  0.970  0.020  1.090
 P9N  C17  H25  single  0.970  0.020  1.090
 P9N  C18  H26  single  0.970  0.020  1.090
 P9N  C18  H27  single  0.970  0.020  1.090
 P9N  C18  H28  single  0.970  0.020  1.090
 P9N  C19  H29  single  0.970  0.020  1.090
 P9N  C19  H30  single  0.970  0.020  1.090
 P9N  C19  H31  single  0.970  0.020  1.090
 P9N  C21  H32  single  0.970  0.020  1.090
 P9N  C21  H33  single  0.970  0.020  1.090
 P9N  C21  H34  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
 P9N  H2   C01  H1   105.29  3.000
 P9N  H2   C01  C10  107.70  3.000
 P9N  H1   C01  C10  110.63  3.000
 P9N  H2   C01  C02  108.08  3.000
 P9N  H1   C01  C02  110.54  3.000
 P9N  C10  C01  C02  114.15  3.000
 P9N  H3   O01  C03  108.05  3.000
 P9N  H5   C02  H4   106.59  3.000
 P9N  H5   C02  C03  109.65  3.000
 P9N  H4   C02  C03  109.97  3.000
 P9N  H5   C02  C01  111.48  3.000
 P9N  H4   C02  C01  109.45  3.000
 P9N  C03  C02  C01  109.66  3.000
 P9N  H6   C03  C04  108.11  3.000
 P9N  H6   C03  C02  107.43  3.000
 P9N  C04  C03  C02  110.47  3.000
 P9N  H6   C03  O01  110.08  3.000
 P9N  C02  C03  O01  112.72  3.000
 P9N  C04  C03  O01  107.95  3.000
 P9N  H8   C04  H7   106.44  3.000
 P9N  H8   C04  C05  110.93  3.000
 P9N  H7   C04  C05  108.43  3.000
 P9N  H8   C04  C03  108.75  3.000
 P9N  H7   C04  C03  109.41  3.000
 P9N  C05  C04  C03  112.68  3.000
 P9N  H9   C05  C10  106.52  3.000
 P9N  H9   C05  C06  107.87  3.000
 P9N  C10  C05  C06  111.70  3.000
 P9N  H9   C05  C04  106.76  3.000
 P9N  C10  C05  C04  112.97  3.000
 P9N  C06  C05  C04  110.67  3.000
 P9N  H11  C06  H10  105.85  3.000
 P9N  H11  C06  C07  109.93  3.000
 P9N  H10  C06  C07  109.09  3.000
 P9N  H11  C06  C05  109.47  3.000
 P9N  H10  C06  C05  109.64  3.000
 P9N  C07  C06  C05  112.62  3.000
 P9N  H13  C07  H12  105.94  3.000
 P9N  H13  C07  C08  108.95  3.000
 P9N  H12  C07  C08  110.04  3.000
 P9N  H13  C07  C06  110.23  3.000
 P9N  H12  C07  C06  109.41  3.000
 P9N  C08  C07  C06  112.09  3.000
 P9N  H14  C08  C14  108.71  3.000
 P9N  H14  C08  C09  109.53  3.000
 P9N  C14  C08  C09  108.89  3.000
 P9N  H14  C08  C07  107.73  3.000
 P9N  C14  C08  C07  111.51  3.000
 P9N  C09  C08  C07  110.44  3.000
 P9N  H15  C09  C11  105.72  3.000
 P9N  H15  C09  C10  107.40  3.000
 P9N  C11  C09  C10  113.63  3.000
 P9N  H15  C09  C08  105.51  3.000
 P9N  C11  C09  C08  112.06  3.000
 P9N  C10  C09  C08  111.87  3.000
 P9N  C19  C10  C09  111.42  3.000
 P9N  C09  C10  C05  109.33  3.000
 P9N  C19  C10  C05  109.25  3.000
 P9N  C09  C10  C01  111.86  3.000
 P9N  C05  C10  C01  108.02  3.000
 P9N  C19  C10  C01  106.86  3.000
 P9N  H17  C11  H16  105.85  3.000
 P9N  H17  C11  C12  109.34  3.000
 P9N  H16  C11  C12  107.62  3.000
 P9N  H17  C11  C09  110.39  3.000
 P9N  H16  C11  C09  109.66  3.000
 P9N  C12  C11  C09  113.65  3.000
 P9N  H19  C12  H18  106.70  3.000
 P9N  H19  C12  C13  111.82  3.000
 P9N  H18  C12  C13  108.88  3.000
 P9N  H19  C12  C11  108.40  3.000
 P9N  H18  C12  C11  109.49  3.000
 P9N  C13  C12  C11  111.43  3.000
 P9N  C18  C13  C17  109.40  3.000
 P9N  C17  C13  C14   99.13  3.000
 P9N  C18  C13  C14  112.88  3.000
 P9N  C17  C13  C12  116.39  3.000
 P9N  C18  C13  C12  110.81  3.000
 P9N  C14  C13  C12  107.79  3.000
 P9N  H20  C14  C15  106.95  3.000
 P9N  H20  C14  C13  105.78  3.000
 P9N  C15  C14  C13  104.01  3.000
 P9N  H20  C14  C08  106.27  3.000
 P9N  C13  C14  C08  114.04  3.000
 P9N  C15  C14  C08  118.93  3.000
 P9N  H22  C15  H21  106.61  3.000
 P9N  H22  C15  C16  112.26  3.000
 P9N  H21  C15  C16  111.11  3.000
 P9N  H22  C15  C14  112.33  3.000
 P9N  H21  C15  C14  110.60  3.000
 P9N  C16  C15  C14  104.02  3.000
 P9N  H24  C16  H23  106.49  3.000
 P9N  H24  C16  C17  110.10  3.000
 P9N  H23  C16  C17  111.19  3.000
 P9N  H24  C16  C15  111.63  3.000
 P9N  H23  C16  C15  111.26  3.000
 P9N  C17  C16  C15  106.24  3.000
 P9N  H25  C17  C20  106.53  3.000
 P9N  H25  C17  C16  109.34  3.000
 P9N  C20  C17  C16  115.15  3.000
 P9N  H25  C17  C13  106.46  3.000
 P9N  C20  C17  C13  114.80  3.000
 P9N  C16  C17  C13  104.20  3.000
 P9N  H28  C18  H27  107.03  3.000
 P9N  H28  C18  H26  106.51  3.000
 P9N  H27  C18  H26  107.21  3.000
 P9N  H28  C18  C13  110.72  3.000
 P9N  H27  C18  C13  112.40  3.000
 P9N  H26  C18  C13  112.63  3.000
 P9N  H31  C19  H30  106.87  3.000
 P9N  H31  C19  H29  106.97  3.000
 P9N  H30  C19  H29  107.33  3.000
 P9N  H31  C19  C10  109.98  3.000
 P9N  H30  C19  C10  111.80  3.000
 P9N  H29  C19  C10  113.56  3.000
 P9N  C21  C20  C17  116.79  3.000
 P9N  C21  C20  O02  120.61  3.000
 P9N  C17  C20  O02  122.60  3.000
 P9N  H34  C21  H33  109.62  3.000
 P9N  H34  C21  H32  107.17  3.000
 P9N  H33  C21  H32  107.38  3.000
 P9N  H34  C21  C20  112.38  3.000
 P9N  H33  C21  C20  110.83  3.000
 P9N  H32  C21  C20  109.27  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
 P9N  Var_01  C10  C01  C02  C03   58.91  30.0  1
 P9N  Var_02  C08  C07  C06  C05   53.66  30.0  1
 P9N  Var_03  C13  C12  C11  C09  -53.73  30.0  1
 P9N  Var_04  C17  C16  C15  C14    8.42  30.0  1
 P9N  Var_05  H32  C21  C20  C17   89.55  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
 P9N  chir_01  C03  C04  C02  O01  negativ
 P9N  chir_02  C05  C04  C10  C06  positiv
 P9N  chir_03  C08  C07  C09  C14  positiv
 P9N  chir_04  C09  C11  C08  C10  negativ
 P9N  chir_05  C10  C05  C01  C09  positiv
 P9N  chir_06  C13  C14  C12  C17  positiv
 P9N  chir_07  C14  C13  C15  C08  negativ
 P9N  chir_08  C17  C20  C16  C13  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
 P9N  plan-1  O02  0.020
 P9N  plan-1  C17  0.020
 P9N  plan-1  C20  0.020
 P9N  plan-1  C21  0.020

