# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 22:59:50 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: (3alpha,8alpha)-3-hydroxy-17-(pyridin-3-yl)androsta-5,16-diene-6-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC[C@H](O)CC1=C(C[C@@H]3[C@@H]2CC[C@@]4(C)[C@H]3CC=C4c5cccnc5)C#N
#
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
 3NR  3NR  (3alpha,8alpha)-3-hydroxy-17-(pyridin-3-yl)androsta-5,16-diene-6-carbonitrile  ligand  58  28  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3NR
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
 3NR  C1   C  C     0   0.225  -3.3454   0.2278  -0.0411
 3NR  C2   C  C     0  -0.070  -2.9160   1.4739   0.2203
 3NR  C3   C  CSP   0   0.020  -3.8551   2.5208   0.4693
 3NR  N4   N  NS    0  -0.266  -4.5633   3.4059   0.6876
 3NR  C5   C  CH2   0  -0.465  -1.4761   1.9027   0.2816
 3NR  C6   C  CH1   0  -0.254  -0.5405   0.8631  -0.3149
 3NR  C8   C  CH1   0  -0.188  -0.9447  -0.5335   0.1803
 3NR  C9   C  CT    0  -0.145  -2.3751  -0.9171  -0.2794
 3NR  C10  C  CH3   0  -0.673  -2.4151  -1.2568  -1.7797
 3NR  C11  C  CH2   0  -0.437  -2.8445  -2.1323   0.5529
 3NR  C12  C  CH2   0  -0.486  -4.3183  -2.4769   0.3951
 3NR  C13  C  CH1   0   0.093  -5.1827  -1.2797   0.7474
 3NR  O15  O  OH1   0  -0.674  -6.5595  -1.5232   0.5609
 3NR  C17  C  CH2   0  -0.552  -4.8090  -0.0991  -0.1394
 3NR  C18  C  CH2   0  -0.454   0.0963  -1.6175  -0.1453
 3NR  C19  C  CH2   0  -0.414   1.5379  -1.2410   0.2113
 3NR  C20  C  CT    0  -0.147   1.9010   0.1047  -0.4111
 3NR  C21  C  CH3   0  -0.665   1.8997   0.0274  -1.9479
 3NR  C22  C  CH1   0  -0.207   0.8869   1.1316   0.1202
 3NR  C24  C  CH2   0  -0.464   1.5572   2.4805  -0.1337
 3NR  C25  C  C1    0  -0.291   2.9940   2.1096   0.1060
 3NR  C26  C  C     0   0.165   3.1956   0.7871   0.0251
 3NR  C27  C  CR6   0  -0.009   4.4825   0.1254   0.2579
 3NR  C28  C  CR16  0  -0.121   4.8559  -1.0588  -0.3829
 3NR  N29  N  N     0  -0.398   6.0162  -1.6748  -0.1977
 3NR  C30  C  CR16  0  -0.076   6.8839  -1.1396   0.6513
 3NR  C31  C  CR16  0  -0.313   6.6250   0.0309   1.3500
 3NR  C32  C  CR16  0  -0.208   5.4105   0.6620   1.1547
 3NR  H1   H  HCH2  0   0.266  -1.3624   2.8564  -0.2404
 3NR  H2   H  HCH2  0   0.253  -1.2057   2.0968   1.3264
 3NR  H3   H  HCH1  0   0.238  -0.6211   0.9163  -1.4059
 3NR  H4   H  HCH1  0   0.223  -0.9837  -0.4582   1.2773
 3NR  H5   H  HCH3  0   0.240  -2.0139  -0.4419  -2.3841
 3NR  H6   H  HCH3  0   0.241  -1.8342  -2.1532  -1.9965
 3NR  H7   H  HCH3  0   0.246  -3.4273  -1.4475  -2.1333
 3NR  H8   H  HCH2  0   0.249  -2.2406  -3.0013   0.2859
 3NR  H9   H  HCH2  0   0.234  -2.6394  -1.9290   1.6096
 3NR  H10  H  HCH2  0   0.228  -4.5394  -2.7932  -0.6291
 3NR  H11  H  HCH2  0   0.244  -4.5625  -3.3211   1.0471
 3NR  H12  H  HCH1  0   0.201  -4.9794  -1.0010   1.7933
 3NR  H13  H  HOH1  0   0.450  -6.8136  -2.2540   1.1335
 3NR  H14  H  HCH2  0   0.265  -5.4244   0.7648   0.1172
 3NR  H15  H  HCH2  0   0.262  -5.0507  -0.3556  -1.1769
 3NR  H16  H  HCH2  0   0.245  -0.1650  -2.5346   0.3866
 3NR  H17  H  HCH2  0   0.228   0.0574  -1.8737  -1.2054
 3NR  H18  H  HCH2  0   0.223   1.6511  -1.1758   1.2984
 3NR  H19  H  HCH2  0   0.230   2.2003  -2.0434  -0.1236
 3NR  H20  H  HCH3  0   0.237   2.6690  -0.6570  -2.3072
 3NR  H21  H  HCH3  0   0.234   0.9524  -0.3243  -2.3552
 3NR  H22  H  HCH3  0   0.238   2.1030   1.0025  -2.3919
 3NR  H23  H  HCH1  0   0.229   0.8986   1.0085   1.2136
 3NR  H24  H  HCH2  0   0.239   1.4030   2.8452  -1.1572
 3NR  H25  H  HCH2  0   0.247   1.2051   3.2704   0.5334
 3NR  H26  H  H     0   0.241   3.7676   2.8442   0.2962
 3NR  H29  H  HCR6  0   0.248   4.1890  -1.5311  -1.0945
 3NR  H30  H  HCR6  0   0.264   7.8233  -1.6643   0.7860
 3NR  H31  H  HCR6  0   0.271   7.3555   0.4298   2.0403
 3NR  H32  H  HCR6  0   0.264   5.1729   1.5639   1.7048

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
 3NR  N4   C3   triple    1.154  0.020  1.154
 3NR  C3   C2   single    1.428  0.020  1.428
 3NR  C2   C5   single    1.504  0.020  1.504
 3NR  C2   C1   double    1.344  0.020  1.344
 3NR  C17  C1   single    1.503  0.020  1.503
 3NR  C17  C13  single    1.523  0.020  1.523
 3NR  C5   C6   single    1.520  0.020  1.520
 3NR  C1   C9   single    1.519  0.020  1.519
 3NR  C10  C9   single    1.539  0.020  1.539
 3NR  C24  C22  single    1.528  0.020  1.528
 3NR  C24  C25  single    1.503  0.020  1.503
 3NR  C6   C22  single    1.516  0.020  1.516
 3NR  C6   C8   single    1.536  0.020  1.536
 3NR  C21  C20  single    1.539  0.020  1.539
 3NR  O15  C13  single    1.411  0.020  1.411
 3NR  C9   C8   single    1.551  0.020  1.551
 3NR  C9   C11  single    1.546  0.020  1.546
 3NR  C13  C12  single    1.518  0.020  1.518
 3NR  C22  C20  single    1.538  0.020  1.538
 3NR  C25  C26  double    1.340  0.020  1.340
 3NR  C8   C18  single    1.538  0.020  1.538
 3NR  C12  C11  single    1.522  0.020  1.522
 3NR  C20  C26  single    1.527  0.020  1.527
 3NR  C20  C19  single    1.527  0.020  1.527
 3NR  C18  C19  single    1.532  0.020  1.532
 3NR  C26  C27  single    1.466  0.020  1.466
 3NR  C27  C32  aromatic  1.398  0.020  1.398
 3NR  C27  C28  aromatic  1.397  0.020  1.397
 3NR  C32  C31  aromatic  1.383  0.020  1.383
 3NR  C28  N29  aromatic  1.327  0.020  1.327
 3NR  C31  C30  aromatic  1.388  0.020  1.388
 3NR  N29  C30  aromatic  1.327  0.020  1.327
 3NR  C5   H1   single    0.970  0.020  1.090
 3NR  C5   H2   single    0.970  0.020  1.090
 3NR  C6   H3   single    0.970  0.020  1.090
 3NR  C8   H4   single    0.970  0.020  1.090
 3NR  C10  H5   single    0.970  0.020  1.090
 3NR  C10  H6   single    0.970  0.020  1.090
 3NR  C10  H7   single    0.970  0.020  1.090
 3NR  C11  H8   single    0.970  0.020  1.090
 3NR  C11  H9   single    0.970  0.020  1.090
 3NR  C12  H10  single    0.970  0.020  1.090
 3NR  C12  H11  single    0.970  0.020  1.090
 3NR  C13  H12  single    0.970  0.020  1.090
 3NR  O15  H13  single    0.850  0.020  0.980
 3NR  C17  H14  single    0.970  0.020  1.090
 3NR  C17  H15  single    0.970  0.020  1.090
 3NR  C18  H16  single    0.970  0.020  1.090
 3NR  C18  H17  single    0.970  0.020  1.090
 3NR  C19  H18  single    0.970  0.020  1.090
 3NR  C19  H19  single    0.970  0.020  1.090
 3NR  C21  H20  single    0.970  0.020  1.090
 3NR  C21  H21  single    0.970  0.020  1.090
 3NR  C21  H22  single    0.970  0.020  1.090
 3NR  C22  H23  single    0.970  0.020  1.090
 3NR  C24  H24  single    0.970  0.020  1.090
 3NR  C24  H25  single    0.970  0.020  1.090
 3NR  C25  H26  single    0.930  0.020  1.080
 3NR  C28  H29  single    0.930  0.020  1.080
 3NR  C30  H30  single    0.930  0.020  1.080
 3NR  C31  H31  single    0.930  0.020  1.080
 3NR  C32  H32  single    0.930  0.020  1.080

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
 3NR  C17  C1   C9   116.60  3.000
 3NR  C9   C1   C2   121.68  3.000
 3NR  C17  C1   C2   121.71  3.000
 3NR  C5   C2   C3   114.43  3.000
 3NR  C5   C2   C1   125.34  3.000
 3NR  C3   C2   C1   120.24  3.000
 3NR  N4   C3   C2   180.00  3.000
 3NR  H2   C5   H1   105.96  3.000
 3NR  H2   C5   C6   110.06  3.000
 3NR  H1   C5   C6   110.19  3.000
 3NR  H2   C5   C2   109.00  3.000
 3NR  H1   C5   C2   109.20  3.000
 3NR  C6   C5   C2   112.23  3.000
 3NR  H3   C6   C22  110.27  3.000
 3NR  H3   C6   C8   110.24  3.000
 3NR  C22  C6   C8   108.44  3.000
 3NR  H3   C6   C5   108.19  3.000
 3NR  C8   C6   C5   109.47  3.000
 3NR  C22  C6   C5   110.23  3.000
 3NR  H4   C8   C18  106.46  3.000
 3NR  H4   C8   C9   106.25  3.000
 3NR  C18  C8   C9   112.79  3.000
 3NR  H4   C8   C6   105.58  3.000
 3NR  C18  C8   C6   113.24  3.000
 3NR  C9   C8   C6   111.85  3.000
 3NR  C11  C9   C10  110.09  3.000
 3NR  C11  C9   C8   108.36  3.000
 3NR  C10  C9   C8   111.57  3.000
 3NR  C11  C9   C1   108.30  3.000
 3NR  C8   C9   C1   110.86  3.000
 3NR  C10  C9   C1   107.62  3.000
 3NR  H7   C10  H6   106.66  3.000
 3NR  H7   C10  H5   107.03  3.000
 3NR  H6   C10  H5   107.94  3.000
 3NR  H7   C10  C9   112.29  3.000
 3NR  H6   C10  C9   111.20  3.000
 3NR  H5   C10  C9   111.45  3.000
 3NR  H9   C11  H8   106.26  3.000
 3NR  H9   C11  C12  108.86  3.000
 3NR  H8   C11  C12  109.28  3.000
 3NR  H9   C11  C9   108.46  3.000
 3NR  H8   C11  C9   109.04  3.000
 3NR  C12  C11  C9   114.60  3.000
 3NR  H11  C12  H10  106.83  3.000
 3NR  H11  C12  C13  110.06  3.000
 3NR  H10  C12  C13  109.27  3.000
 3NR  H11  C12  C11  109.22  3.000
 3NR  H10  C12  C11  110.98  3.000
 3NR  C13  C12  C11  110.42  3.000
 3NR  H12  C13  C17  108.15  3.000
 3NR  H12  C13  O15  110.45  3.000
 3NR  C17  C13  O15  107.23  3.000
 3NR  H12  C13  C12  108.35  3.000
 3NR  O15  C13  C12  112.89  3.000
 3NR  C17  C13  C12  109.66  3.000
 3NR  H13  O15  C13  108.07  3.000
 3NR  H15  C17  H14  106.48  3.000
 3NR  H15  C17  C13  108.41  3.000
 3NR  H14  C17  C13  109.78  3.000
 3NR  H15  C17  C1   109.13  3.000
 3NR  H14  C17  C1   111.20  3.000
 3NR  C13  C17  C1   111.68  3.000
 3NR  H17  C18  H16  105.51  3.000
 3NR  H17  C18  C19  108.51  3.000
 3NR  H16  C18  C19  108.55  3.000
 3NR  H17  C18  C8   110.31  3.000
 3NR  H16  C18  C8   109.08  3.000
 3NR  C19  C18  C8   114.49  3.000
 3NR  H19  C19  H18  106.57  3.000
 3NR  H19  C19  C20  112.21  3.000
 3NR  H18  C19  C20  109.13  3.000
 3NR  H19  C19  C18  108.57  3.000
 3NR  H18  C19  C18  110.07  3.000
 3NR  C20  C19  C18  110.21  3.000
 3NR  C26  C20  C22   99.32  3.000
 3NR  C26  C20  C21  107.97  3.000
 3NR  C22  C20  C21  112.21  3.000
 3NR  C26  C20  C19  118.63  3.000
 3NR  C22  C20  C19  106.91  3.000
 3NR  C21  C20  C19  111.27  3.000
 3NR  H22  C21  H21  107.37  3.000
 3NR  H22  C21  H20  107.19  3.000
 3NR  H21  C21  H20  106.71  3.000
 3NR  H22  C21  C20  111.20  3.000
 3NR  H21  C21  C20  112.98  3.000
 3NR  H20  C21  C20  111.10  3.000
 3NR  H23  C22  C24  105.03  3.000
 3NR  H23  C22  C20  105.16  3.000
 3NR  C24  C22  C20  104.06  3.000
 3NR  H23  C22  C6   105.98  3.000
 3NR  C20  C22  C6   113.79  3.000
 3NR  C24  C22  C6   121.45  3.000
 3NR  H25  C24  H24  106.50  3.000
 3NR  H25  C24  C25  112.90  3.000
 3NR  H24  C24  C25  111.40  3.000
 3NR  H25  C24  C22  113.31  3.000
 3NR  H24  C24  C22  112.75  3.000
 3NR  C25  C24  C22  100.08  3.000
 3NR  H26  C25  C26  124.90  3.000
 3NR  H26  C25  C24  122.90  3.000
 3NR  C26  C25  C24  112.18  3.000
 3NR  C27  C26  C25  124.60  3.000
 3NR  C27  C26  C20  126.02  3.000
 3NR  C25  C26  C20  109.31  3.000
 3NR  C32  C27  C28  116.25  3.000
 3NR  C28  C27  C26  122.98  3.000
 3NR  C32  C27  C26  120.77  3.000
 3NR  H29  C28  N29  115.31  3.000
 3NR  H29  C28  C27  120.40  3.000
 3NR  N29  C28  C27  124.28  3.000
 3NR  C30  N29  C28  118.29  3.000
 3NR  H30  C30  C31  120.48  3.000
 3NR  H30  C30  N29  116.80  3.000
 3NR  C31  C30  N29  122.72  3.000
 3NR  H31  C31  C32  121.01  3.000
 3NR  H31  C31  C30  120.44  3.000
 3NR  C32  C31  C30  118.55  3.000
 3NR  H32  C32  C31  120.08  3.000
 3NR  H32  C32  C27  120.01  3.000
 3NR  C31  C32  C27  119.91  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
 3NR  CONST_01  C30  C31  C32  C27     0.00   0.0  0
 3NR  CONST_02  C30  N29  C28  C27     0.00   0.0  0
 3NR  CONST_03  C31  C32  C27  C28     0.00   0.0  0
 3NR  CONST_04  C31  C30  N29  C28     0.00   0.0  0
 3NR  CONST_05  C32  C27  C28  N29     0.00   0.0  0
 3NR  CONST_06  C32  C31  C30  N29     0.00   0.0  0
 3NR  CONST_07  C31  C32  C27  C26   180.00   0.0  0
 3NR  CONST_08  N29  C28  C27  C26   180.00   0.0  0
 3NR  CONST_09  H32  C32  C27  C26     0.00   0.0  0
 3NR  CONST_10  H29  C28  C27  C26     0.00   0.0  0
 3NR  CONST_11  H31  C31  C32  C27   180.00   0.0  0
 3NR  CONST_12  H30  C30  N29  C28   180.00   0.0  0
 3NR  Var_01    C6   C5   C2   C1     14.05  30.0  1
 3NR  Var_02    C13  C17  C1   C2   -128.28  30.0  1
 3NR  Var_03    C17  C1   C2   C5   -177.39  30.0  1
 3NR  Var_04    C20  C19  C18  C8    -52.72  30.0  1
 3NR  Var_05    C13  C12  C11  C9    -56.74  30.0  1
 3NR  Var_06    C24  C25  C26  C20     5.01  30.0  1
 3NR  Var_07    C32  C27  C26  C20  -152.58  30.0  2
 3NR  Var_08    C26  C25  C24  C22    19.10  30.0  1
 3NR  Var_09    C5   C2   C3   N4     -8.23  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
 3NR  chir_01  C6   C5   C22  C8   negativ
 3NR  chir_02  C8   C18  C9   C6   positiv
 3NR  chir_03  C9   C1   C8   C11  negativ
 3NR  chir_04  C13  O15  C17  C12  positiv
 3NR  chir_05  C20  C26  C22  C19  positiv
 3NR  chir_06  C22  C20  C6   C24  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
 3NR  plan-1  C26  0.020
 3NR  plan-1  C27  0.020
 3NR  plan-1  C28  0.020
 3NR  plan-1  N29  0.020
 3NR  plan-1  C30  0.020
 3NR  plan-1  C31  0.020
 3NR  plan-1  C32  0.020
 3NR  plan-1  H29  0.020
 3NR  plan-1  H30  0.020
 3NR  plan-1  H31  0.020
 3NR  plan-1  H32  0.020

