# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 00:11:52 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: (8R,9S,10R,13S,14S,17R)-13-ethyl-17-ethynyl-17-hydroxy-1,2,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-3H-cyclopenta[a]phenanthren-3-one (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@]12CC[C@H]3[C@@H](CCC4=CC(=O)CC[C@H]34)[C@@H]1CC[C@@]2(O)C#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
 NOG  NOG  '(8R,9S,10R,13S,14S,17R)-13-ethyl-17-ethynyl-17-hydroxy-1,2,6,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-3H-cyclopenta[a]phenanthren-3-one (non-preferred name)'  ligand  51  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NOG
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
 NOG  C1    C  CH2   0  -0.460   1.6087   0.1633   2.9686
 NOG  C2    C  CH2   0  -0.567   1.5470  -0.0537   4.4725
 NOG  C3    C  C     0   0.402   0.2782   0.5044   5.0551
 NOG  C4    C  C1    0  -0.461  -0.9131   0.3674   4.2207
 NOG  C5    C  C     0   0.225  -0.8839  -0.1157   2.9666
 NOG  C6    C  CH2   0  -0.506  -2.1573  -0.4262   2.2447
 NOG  C7    C  CH2   0  -0.418  -2.1700   0.0931   0.8121
 NOG  C8    C  CH1   0  -0.236  -0.9367  -0.3817   0.0575
 NOG  C9    C  CH1   0  -0.199   0.3366   0.0842   0.7775
 NOG  C10   C  CH1   0  -0.282   0.3991  -0.4161   2.2362
 NOG  C11   C  CH2   0  -0.439   1.5929  -0.3029  -0.0081
 NOG  C12   C  CH2   0  -0.436   1.5661   0.1899  -1.4569
 NOG  C13   C  CT    0  -0.084   0.3195  -0.3056  -2.1829
 NOG  C14   C  CH1   0  -0.195  -0.9099   0.1391  -1.3699
 NOG  C15   C  CH2   0  -0.442  -2.0963  -0.1535  -2.2881
 NOG  C16   C  CH2   0  -0.491  -1.5395   0.0841  -3.7063
 NOG  C17   C  CT    0   0.165  -0.0187   0.3754  -3.5403
 NOG  C18   C  CH2   0  -0.436   0.3479  -1.8428  -2.3731
 NOG  C19   C  CH3   0  -0.671   1.6837  -2.4590  -2.7784
 NOG  C20   C  CSP   0   0.342   0.1899   1.8334  -3.4775
 NOG  C21   C  CSP1  0  -0.625   0.3497   3.0254  -3.4873
 NOG  O3    O  O     0  -0.441   0.2249   0.9825   6.1758
 NOG  O17   O  OH1   0  -0.658   0.7715  -0.1432  -4.5826
 NOG  HC11  H  HCH2  0   0.231   1.6689   1.2368   2.7611
 NOG  HC12  H  HCH2  0   0.253   2.5287  -0.2777   2.5860
 NOG  HC21  H  HCH2  0   0.262   2.4112   0.3855   4.9730
 NOG  HC22  H  HCH2  0   0.264   1.5635  -1.1276   4.6944
 NOG  HC4   H  H     0   0.249  -1.8649   0.6076   4.6843
 NOG  HC61  H  HCH2  0   0.253  -3.0132  -0.0496   2.8073
 NOG  HC62  H  HCH2  0   0.252  -2.2596  -1.5182   2.2180
 NOG  HC71  H  HCH2  0   0.221  -2.2088   1.1879   0.8098
 NOG  HC72  H  HCH2  0   0.245  -3.0796  -0.2552   0.3178
 NOG  HC8   H  HCH1  0   0.215  -0.9572  -1.4799   0.0597
 NOG  HC9   H  HCH1  0   0.214   0.2949   1.1835   0.8170
 NOG  H10C  H  HCH1  0   0.253   0.4947  -1.5128   2.2072
 NOG  H111  H  HCH2  0   0.218   1.7151  -1.3917   0.0290
 NOG  H112  H  HCH2  0   0.243   2.4796   0.1140   0.4732
 NOG  H121  H  HCH2  0   0.237   2.4826  -0.1163  -1.9658
 NOG  H122  H  HCH2  0   0.231   1.5717   1.2838  -1.4517
 NOG  H14C  H  HCH1  0   0.228  -0.8383   1.2323  -1.2795
 NOG  H151  H  HCH2  0   0.229  -2.4346  -1.1859  -2.1719
 NOG  H152  H  HCH2  0   0.241  -2.9505   0.4872  -2.0684
 NOG  H161  H  HCH2  0   0.251  -1.6571  -0.8004  -4.3345
 NOG  H162  H  HCH2  0   0.250  -2.0445   0.9033  -4.2186
 NOG  H181  H  HCH2  0   0.236  -0.4071  -2.1427  -3.1024
 NOG  H182  H  HCH2  0   0.231   0.0366  -2.3197  -1.4420
 NOG  H191  H  HCH3  0   0.225   1.5602  -3.5312  -2.9383
 NOG  H192  H  HCH3  0   0.230   2.0763  -2.0306  -3.6974
 NOG  H193  H  HCH3  0   0.218   2.4414  -2.3377  -2.0038
 NOG  H21C  H  H     0   0.281   0.4966   4.0810  -3.4875
 NOG  H17O  H  HOH1  0   0.451   0.4536   0.2173  -5.4173

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
 NOG  C1   C2    single  1.521  0.020  1.521
 NOG  C1   C10   single  1.528  0.020  1.528
 NOG  C1   HC11  single  0.939  0.020  1.096
 NOG  C1   HC12  single  0.939  0.020  1.096
 NOG  C2   C3    single  1.504  0.020  1.504
 NOG  C2   HC21  single  0.939  0.020  1.096
 NOG  C2   HC22  single  0.939  0.020  1.096
 NOG  C3   C4    single  1.461  0.020  1.461
 NOG  C3   O3    double  1.220  0.020  1.220
 NOG  C4   C5    double  1.344  0.020  1.344
 NOG  C4   HC4   single  0.930  0.020  1.086
 NOG  C5   C6    single  1.496  0.020  1.496
 NOG  C5   C10   single  1.507  0.020  1.507
 NOG  C6   C7    single  1.524  0.020  1.524
 NOG  C6   HC61  single  0.939  0.020  1.096
 NOG  C6   HC62  single  0.939  0.020  1.096
 NOG  C7   C8    single  1.522  0.020  1.522
 NOG  C7   HC71  single  0.939  0.020  1.096
 NOG  C7   HC72  single  0.939  0.020  1.096
 NOG  C8   C9    single  1.535  0.020  1.535
 NOG  C8   C14   single  1.520  0.020  1.520
 NOG  C8   HC8   single  0.939  0.020  1.096
 NOG  C9   C10   single  1.543  0.020  1.543
 NOG  C9   C11   single  1.531  0.020  1.531
 NOG  C9   HC9   single  0.939  0.020  1.096
 NOG  C10  H10C  single  0.939  0.020  1.096
 NOG  C11  C12   single  1.530  0.020  1.530
 NOG  C11  H111  single  0.939  0.020  1.096
 NOG  C11  H112  single  0.939  0.020  1.096
 NOG  C12  C13   single  1.525  0.020  1.525
 NOG  C12  H121  single  0.939  0.020  1.096
 NOG  C12  H122  single  0.939  0.020  1.096
 NOG  C13  C14   single  1.540  0.020  1.540
 NOG  C13  C17   single  1.556  0.020  1.556
 NOG  C13  C18   single  1.549  0.020  1.549
 NOG  C14  C15   single  1.528  0.020  1.528
 NOG  C14  H14C  single  0.939  0.020  1.096
 NOG  C15  C16   single  1.542  0.020  1.542
 NOG  C15  H151  single  0.939  0.020  1.096
 NOG  C15  H152  single  0.939  0.020  1.096
 NOG  C16  C17   single  1.557  0.020  1.557
 NOG  C16  H161  single  0.939  0.020  1.096
 NOG  C16  H162  single  0.939  0.020  1.096
 NOG  C17  C20   single  1.474  0.020  1.474
 NOG  C17  O17   single  1.407  0.020  1.407
 NOG  C18  C19   single  1.526  0.020  1.526
 NOG  C18  H181  single  0.939  0.020  1.096
 NOG  C18  H182  single  0.939  0.020  1.096
 NOG  C19  H191  single  0.939  0.020  1.096
 NOG  C19  H192  single  0.939  0.020  1.096
 NOG  C19  H193  single  0.939  0.020  1.096
 NOG  C20  C21   triple  1.203  0.020  1.203
 NOG  C21  H21C  single  0.913  0.020  1.066
 NOG  O17  H17O  single  0.832  0.020  0.971

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
 NOG  HC12  C1   HC11  106.49  3.000
 NOG  HC12  C1   C10   110.28  3.000
 NOG  HC11  C1   C10   108.93  3.000
 NOG  HC12  C1   C2    108.89  3.000
 NOG  HC11  C1   C2    109.24  3.000
 NOG  C10   C1   C2    112.82  3.000
 NOG  HC22  C2   HC21  106.82  3.000
 NOG  HC22  C2   C3    107.33  3.000
 NOG  HC21  C2   C3    109.96  3.000
 NOG  HC22  C2   C1    109.83  3.000
 NOG  HC21  C2   C1    111.35  3.000
 NOG  C3    C2   C1    111.38  3.000
 NOG  O3    C3   C4    121.73  3.000
 NOG  O3    C3   C2    122.58  3.000
 NOG  C4    C3   C2    115.59  3.000
 NOG  HC4   C4   C5    119.80  3.000
 NOG  HC4   C4   C3    116.76  3.000
 NOG  C5    C4   C3    123.29  3.000
 NOG  C10   C5   C6    116.71  3.000
 NOG  C10   C5   C4    122.85  3.000
 NOG  C6    C5   C4    120.41  3.000
 NOG  HC62  C6   HC61  106.43  3.000
 NOG  HC62  C6   C7    108.40  3.000
 NOG  HC61  C6   C7    111.13  3.000
 NOG  HC62  C6   C5    107.31  3.000
 NOG  HC61  C6   C5    110.31  3.000
 NOG  C7    C6   C5    112.95  3.000
 NOG  HC72  C7   HC71  106.75  3.000
 NOG  HC72  C7   C8    110.55  3.000
 NOG  HC71  C7   C8    109.85  3.000
 NOG  HC72  C7   C6    108.89  3.000
 NOG  HC71  C7   C6    110.05  3.000
 NOG  C8    C7   C6    110.68  3.000
 NOG  HC8   C8   C14   110.17  3.000
 NOG  HC8   C8   C9    108.54  3.000
 NOG  C14   C8   C9    108.78  3.000
 NOG  HC8   C8   C7    107.21  3.000
 NOG  C14   C8   C7    111.91  3.000
 NOG  C9    C8   C7    110.18  3.000
 NOG  HC9   C9   C11   107.57  3.000
 NOG  HC9   C9   C10   106.94  3.000
 NOG  C11   C9   C10   111.70  3.000
 NOG  HC9   C9   C8    106.77  3.000
 NOG  C11   C9   C8    111.29  3.000
 NOG  C10   C9   C8    112.24  3.000
 NOG  H10C  C10  C9    107.55  3.000
 NOG  H10C  C10  C5    106.57  3.000
 NOG  C9    C10  C5    111.04  3.000
 NOG  H10C  C10  C1    108.75  3.000
 NOG  C9    C10  C1    111.23  3.000
 NOG  C5    C10  C1    111.48  3.000
 NOG  H112  C11  H111  105.89  3.000
 NOG  H112  C11  C12   107.98  3.000
 NOG  H111  C11  C12   110.72  3.000
 NOG  H112  C11  C9    110.09  3.000
 NOG  H111  C11  C9    108.97  3.000
 NOG  C12   C11  C9    112.94  3.000
 NOG  H122  C12  H121  106.16  3.000
 NOG  H122  C12  C13   109.35  3.000
 NOG  H121  C12  C13   111.90  3.000
 NOG  H122  C12  C11   108.50  3.000
 NOG  H121  C12  C11   109.64  3.000
 NOG  C13   C12  C11   111.12  3.000
 NOG  C18   C13  C17   109.34  3.000
 NOG  C18   C13  C14   111.47  3.000
 NOG  C17   C13  C14    99.25  3.000
 NOG  C18   C13  C12   111.46  3.000
 NOG  C17   C13  C12   116.79  3.000
 NOG  C14   C13  C12   107.91  3.000
 NOG  H14C  C14  C15   106.88  3.000
 NOG  H14C  C14  C13   106.18  3.000
 NOG  C15   C14  C13   104.32  3.000
 NOG  H14C  C14  C8    105.35  3.000
 NOG  C15   C14  C8    119.01  3.000
 NOG  C13   C14  C8    114.27  3.000
 NOG  H152  C15  H151  106.93  3.000
 NOG  H152  C15  C16   112.19  3.000
 NOG  H151  C15  C16   110.81  3.000
 NOG  H152  C15  C14   112.01  3.000
 NOG  H151  C15  C14   110.94  3.000
 NOG  C16   C15  C14   104.05  3.000
 NOG  H162  C16  H161  106.78  3.000
 NOG  H162  C16  C17   111.22  3.000
 NOG  H161  C16  C17   108.55  3.000
 NOG  H162  C16  C15   112.38  3.000
 NOG  H161  C16  C15   111.45  3.000
 NOG  C17   C16  C15   106.46  3.000
 NOG  O17   C17  C20   108.46  3.000
 NOG  O17   C17  C16   113.61  3.000
 NOG  C20   C17  C16   109.13  3.000
 NOG  O17   C17  C13   111.28  3.000
 NOG  C20   C17  C13   111.41  3.000
 NOG  C16   C17  C13   102.91  3.000
 NOG  H182  C18  H181  104.62  3.000
 NOG  H182  C18  C19   107.45  3.000
 NOG  H181  C18  C19   108.48  3.000
 NOG  H182  C18  C13   108.89  3.000
 NOG  H181  C18  C13   109.99  3.000
 NOG  C19   C18  C13   116.70  3.000
 NOG  H193  C19  H192  107.80  3.000
 NOG  H193  C19  H191  106.98  3.000
 NOG  H192  C19  H191  107.71  3.000
 NOG  H193  C19  C18   112.01  3.000
 NOG  H192  C19  C18   112.43  3.000
 NOG  H191  C19  C18   109.68  3.000
 NOG  C21   C20  C17   180.00  3.000
 NOG  H21C  C21  C20   180.00  3.000
 NOG  H17O  O17  C17   108.58  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
 NOG  Var_01  C6    C5   C4   C3    170.56   0.0  0
 NOG  Var_02  C4    C3   C2   C1     36.42  30.0  1
 NOG  Var_03  C5    C4   C3   C2     -5.58  30.0  1
 NOG  Var_04  C10   C1   C2   C3    -55.77  30.0  1
 NOG  Var_05  C7    C6   C5   C4    134.54  30.0  1
 NOG  Var_06  C8    C7   C6   C5     52.59  30.0  1
 NOG  Var_07  C13   C12  C11  C9    -55.66  30.0  1
 NOG  Var_08  C17   C16  C15  C14     5.11  30.0  1
 NOG  Var_09  H191  C19  C18  C13  -176.62  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
 NOG  chir_01  C8   C7   C9   C14  positiv
 NOG  chir_02  C9   C8   C10  C11  negativ
 NOG  chir_03  C10  C9   C5   C1   positiv
 NOG  chir_04  C13  C17  C14  C12  positiv
 NOG  chir_05  C14  C15  C13  C8   positiv
 NOG  chir_06  C17  C20  C16  C13  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
 NOG  plan-1  C2   0.020
 NOG  plan-1  C3   0.020
 NOG  plan-1  C4   0.020
 NOG  plan-1  O3   0.020
 NOG  plan-2  C3   0.020
 NOG  plan-2  C4   0.020
 NOG  plan-2  C5   0.020
 NOG  plan-2  C6   0.020
 NOG  plan-2  C10  0.020
 NOG  plan-2  HC4  0.020

