# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:41:02 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: (3alpha,8alpha)-3-hydroxy-17-(pyridin-3-yl)androsta-5,16-diene-6-carboxamide
#   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)=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
 3NX  3NX  (3alpha,8alpha)-3-hydroxy-17-(pyridin-3-yl)androsta-5,16-diene-6-carboxamide  ligand  61  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3NX
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
 3NX  C1   C  C     0   0.209  -3.1447  -0.0095  -0.1098
 3NX  C2   C  C     0  -0.144  -2.7770   1.2497   0.1456
 3NX  C3   C  C     0   0.420  -3.7598   2.3535   0.3943
 3NX  O4   O  O     0  -0.483  -3.8844   2.8548   1.5043
 3NX  N5   N  NH2   0  -0.779  -4.4161   2.7929  -0.6887
 3NX  C8   C  CH2   0  -0.466  -1.3520   1.7076   0.2694
 3NX  C9   C  CH1   0  -0.252  -0.3647   0.7151  -0.3212
 3NX  C11  C  CH1   0  -0.182  -0.7219  -0.6974   0.1630
 3NX  C12  C  CT    0  -0.130  -2.1315  -1.1317  -0.3145
 3NX  C13  C  CH3   0  -0.672  -2.1294  -1.4959  -1.8090
 3NX  C14  C  CH2   0  -0.434  -2.5640  -2.3533   0.5257
 3NX  C15  C  CH2   0  -0.483  -4.0197  -2.7592   0.3493
 3NX  C16  C  CH1   0   0.095  -4.9321  -1.5900   0.6708
 3NX  O18  O  OH1   0  -0.678  -6.2982  -1.8942   0.4785
 3NX  C20  C  CH2   0  -0.551  -4.5960  -0.4092  -0.2284
 3NX  C21  C  CH2   0  -0.453   0.3665  -1.7399  -0.1454
 3NX  C22  C  CH2   0  -0.414   1.7893  -1.3063   0.2241
 3NX  C23  C  CT    0  -0.146   2.1053   0.0510  -0.3996
 3NX  C24  C  CH3   0  -0.665   2.1140  -0.0295  -1.9360
 3NX  C25  C  CH1   0  -0.202   1.0473   1.0367   0.1249
 3NX  C27  C  CH2   0  -0.464   1.6645   2.4113  -0.1236
 3NX  C28  C  C1    0  -0.292   3.1141   2.0993   0.1196
 3NX  C29  C  C     0   0.164   3.3702   0.7860   0.0389
 3NX  C30  C  CR6   0  -0.007   4.6860   0.1817   0.2666
 3NX  C31  C  CR16  0  -0.122   5.1032  -0.9912  -0.3680
 3NX  N32  N  N     0  -0.398   6.2911  -1.5551  -0.1919
 3NX  C33  C  CR16  0  -0.076   7.1446  -0.9753   0.6422
 3NX  C34  C  CR16  0  -0.313   6.8424   0.1883   1.3350
 3NX  C35  C  CR16  0  -0.209   5.5997   0.7649   1.1488
 3NX  H1   H  HNH2  0   0.401  -5.0763   3.5515  -0.6229
 3NX  H2   H  HNH2  0   0.409  -4.2864   2.3635  -1.5883
 3NX  H3   H  HCH2  0   0.252  -1.2392   2.6811  -0.2190
 3NX  H4   H  HCH2  0   0.239  -1.1200   1.8810   1.3279
 3NX  H5   H  HCH1  0   0.228  -0.4386   0.7722  -1.4130
 3NX  H6   H  HCH1  0   0.214  -0.7794  -0.6236   1.2597
 3NX  H7   H  HCH3  0   0.234  -1.7345  -0.6793  -2.4153
 3NX  H8   H  HCH3  0   0.233  -1.5240  -2.3811  -2.0057
 3NX  H9   H  HCH3  0   0.238  -3.1295  -1.7126  -2.1827
 3NX  H10  H  HCH2  0   0.241  -1.9203  -3.2026   0.2881
 3NX  H11  H  HCH2  0   0.226  -2.3903  -2.1251   1.5835
 3NX  H12  H  HCH2  0   0.222  -4.2122  -3.0968  -0.6741
 3NX  H13  H  HCH2  0   0.238  -4.2429  -3.6044   1.0080
 3NX  H14  H  HCH1  0   0.193  -4.7502  -1.2879   1.7145
 3NX  H15  H  HOH1  0   0.447  -6.5230  -2.6322   1.0539
 3NX  H16  H  HCH2  0   0.255  -5.2596   0.4222   0.0108
 3NX  H17  H  HCH2  0   0.243  -4.8204  -0.6918  -1.2637
 3NX  H18  H  HCH2  0   0.241   0.1367  -2.6647   0.3880
 3NX  H19  H  HCH2  0   0.226   0.3507  -2.0039  -1.2043
 3NX  H20  H  HCH2  0   0.221   1.8901  -1.2322   1.3119
 3NX  H21  H  HCH2  0   0.228   2.4854  -2.0840  -0.1008
 3NX  H22  H  HCH3  0   0.236   2.9037  -0.6934  -2.2903
 3NX  H23  H  HCH3  0   0.234   1.1781  -0.4070  -2.3466
 3NX  H24  H  HCH3  0   0.237   2.2936   0.9500  -2.3806
 3NX  H25  H  HCH1  0   0.224   1.0566   0.9124   1.2184
 3NX  H26  H  HCH2  0   0.237   1.4990   2.7712  -1.1473
 3NX  H27  H  HCH2  0   0.246   1.2782   3.1853   0.5430
 3NX  H28  H  H     0   0.240   3.8569   2.8653   0.3087
 3NX  H31  H  HCR6  0   0.248   4.4483  -1.4976  -1.0671
 3NX  H32  H  HCR6  0   0.264   8.1077  -1.4571   0.7694
 3NX  H33  H  HCR6  0   0.270   7.5624   0.6238   2.0143
 3NX  H34  H  HCR6  0   0.263   5.3303   1.6602   1.6948

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
 3NX  N5   C3   single    1.340  0.020  1.340
 3NX  C3   O4   double    1.224  0.020  1.224
 3NX  C3   C2   single    1.499  0.020  1.499
 3NX  C2   C8   single    1.502  0.020  1.502
 3NX  C2   C1   double    1.336  0.020  1.336
 3NX  C20  C1   single    1.510  0.020  1.510
 3NX  C20  C16  single    1.522  0.020  1.522
 3NX  C8   C9   single    1.519  0.020  1.519
 3NX  C1   C12  single    1.526  0.020  1.526
 3NX  C27  C25  single    1.527  0.020  1.527
 3NX  C27  C28  single    1.503  0.020  1.503
 3NX  C13  C12  single    1.538  0.020  1.538
 3NX  C9   C25  single    1.515  0.020  1.515
 3NX  C9   C11  single    1.535  0.020  1.535
 3NX  O18  C16  single    1.413  0.020  1.413
 3NX  C16  C15  single    1.518  0.020  1.518
 3NX  C24  C23  single    1.539  0.020  1.539
 3NX  C12  C11  single    1.550  0.020  1.550
 3NX  C12  C14  single    1.544  0.020  1.544
 3NX  C25  C23  single    1.538  0.020  1.538
 3NX  C28  C29  double    1.340  0.020  1.340
 3NX  C11  C21  single    1.538  0.020  1.538
 3NX  C15  C14  single    1.521  0.020  1.521
 3NX  C23  C29  single    1.527  0.020  1.527
 3NX  C23  C22  single    1.527  0.020  1.527
 3NX  C29  C30  single    1.466  0.020  1.466
 3NX  C21  C22  single    1.533  0.020  1.533
 3NX  C30  C35  aromatic  1.398  0.020  1.398
 3NX  C30  C31  aromatic  1.397  0.020  1.397
 3NX  C35  C34  aromatic  1.383  0.020  1.383
 3NX  C31  N32  aromatic  1.327  0.020  1.327
 3NX  C34  C33  aromatic  1.388  0.020  1.388
 3NX  N32  C33  aromatic  1.327  0.020  1.327
 3NX  N5   H1   single    0.860  0.020  1.020
 3NX  N5   H2   single    0.860  0.020  1.020
 3NX  C8   H3   single    0.970  0.020  1.090
 3NX  C8   H4   single    0.970  0.020  1.090
 3NX  C9   H5   single    0.970  0.020  1.090
 3NX  C11  H6   single    0.970  0.020  1.090
 3NX  C13  H7   single    0.970  0.020  1.090
 3NX  C13  H8   single    0.970  0.020  1.090
 3NX  C13  H9   single    0.970  0.020  1.090
 3NX  C14  H10  single    0.970  0.020  1.090
 3NX  C14  H11  single    0.970  0.020  1.090
 3NX  C15  H12  single    0.970  0.020  1.090
 3NX  C15  H13  single    0.970  0.020  1.090
 3NX  C16  H14  single    0.970  0.020  1.090
 3NX  O18  H15  single    0.850  0.020  0.980
 3NX  C20  H16  single    0.970  0.020  1.090
 3NX  C20  H17  single    0.970  0.020  1.090
 3NX  C21  H18  single    0.970  0.020  1.090
 3NX  C21  H19  single    0.970  0.020  1.090
 3NX  C22  H20  single    0.970  0.020  1.090
 3NX  C22  H21  single    0.970  0.020  1.090
 3NX  C24  H22  single    0.970  0.020  1.090
 3NX  C24  H23  single    0.970  0.020  1.090
 3NX  C24  H24  single    0.970  0.020  1.090
 3NX  C25  H25  single    0.970  0.020  1.090
 3NX  C27  H26  single    0.970  0.020  1.090
 3NX  C27  H27  single    0.970  0.020  1.090
 3NX  C28  H28  single    0.930  0.020  1.080
 3NX  C31  H31  single    0.930  0.020  1.080
 3NX  C33  H32  single    0.930  0.020  1.080
 3NX  C34  H33  single    0.930  0.020  1.080
 3NX  C35  H34  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
 3NX  C20  C1   C12  115.66  3.000
 3NX  C12  C1   C2   122.41  3.000
 3NX  C20  C1   C2   121.93  3.000
 3NX  C8   C2   C3   112.58  3.000
 3NX  C8   C2   C1   124.34  3.000
 3NX  C3   C2   C1   123.04  3.000
 3NX  N5   C3   O4   123.26  3.000
 3NX  O4   C3   C2   121.25  3.000
 3NX  N5   C3   C2   115.37  3.000
 3NX  H2   N5   H1   117.68  3.000
 3NX  H2   N5   C3   121.32  3.000
 3NX  H1   N5   C3   120.98  3.000
 3NX  H4   C8   H3   105.54  3.000
 3NX  H4   C8   C9   109.93  3.000
 3NX  H3   C8   C9   109.90  3.000
 3NX  H4   C8   C2   109.17  3.000
 3NX  H3   C8   C2   109.39  3.000
 3NX  C9   C8   C2   112.66  3.000
 3NX  H5   C9   C25  110.19  3.000
 3NX  H5   C9   C11  110.27  3.000
 3NX  C25  C9   C11  108.61  3.000
 3NX  H5   C9   C8   108.03  3.000
 3NX  C11  C9   C8   109.10  3.000
 3NX  C25  C9   C8   110.64  3.000
 3NX  H6   C11  C21  106.39  3.000
 3NX  H6   C11  C12  106.15  3.000
 3NX  C21  C11  C12  113.06  3.000
 3NX  H6   C11  C9   105.35  3.000
 3NX  C21  C11  C9   113.31  3.000
 3NX  C12  C11  C9   111.84  3.000
 3NX  C14  C12  C13  109.98  3.000
 3NX  C14  C12  C11  107.98  3.000
 3NX  C13  C12  C11  111.37  3.000
 3NX  C14  C12  C1   108.83  3.000
 3NX  C11  C12  C1   110.88  3.000
 3NX  C13  C12  C1   107.78  3.000
 3NX  H9   C13  H8   106.65  3.000
 3NX  H9   C13  H7   106.89  3.000
 3NX  H8   C13  H7   107.85  3.000
 3NX  H9   C13  C12  112.28  3.000
 3NX  H8   C13  C12  111.61  3.000
 3NX  H7   C13  C12  111.29  3.000
 3NX  H11  C14  H10  106.17  3.000
 3NX  H11  C14  C15  108.61  3.000
 3NX  H10  C14  C15  109.34  3.000
 3NX  H11  C14  C12  108.42  3.000
 3NX  H10  C14  C12  109.38  3.000
 3NX  C15  C14  C12  114.58  3.000
 3NX  H13  C15  H12  106.78  3.000
 3NX  H13  C15  C16  110.17  3.000
 3NX  H12  C15  C16  109.26  3.000
 3NX  H13  C15  C14  109.35  3.000
 3NX  H12  C15  C14  111.03  3.000
 3NX  C16  C15  C14  110.19  3.000
 3NX  H14  C16  C20  108.09  3.000
 3NX  H14  C16  O18  110.35  3.000
 3NX  C20  C16  O18  107.47  3.000
 3NX  H14  C16  C15  108.23  3.000
 3NX  O18  C16  C15  112.75  3.000
 3NX  C20  C16  C15  109.87  3.000
 3NX  H15  O18  C16  108.03  3.000
 3NX  H17  C20  H16  106.21  3.000
 3NX  H17  C20  C16  108.23  3.000
 3NX  H16  C20  C16  109.12  3.000
 3NX  H17  C20  C1   109.82  3.000
 3NX  H16  C20  C1   111.46  3.000
 3NX  C16  C20  C1   111.79  3.000
 3NX  H19  C21  H18  105.42  3.000
 3NX  H19  C21  C22  108.41  3.000
 3NX  H18  C21  C22  108.50  3.000
 3NX  H19  C21  C11  110.38  3.000
 3NX  H18  C21  C11  109.09  3.000
 3NX  C22  C21  C11  114.63  3.000
 3NX  H21  C22  H20  106.55  3.000
 3NX  H21  C22  C23  112.29  3.000
 3NX  H20  C22  C23  109.06  3.000
 3NX  H21  C22  C21  108.56  3.000
 3NX  H20  C22  C21  110.13  3.000
 3NX  C23  C22  C21  110.19  3.000
 3NX  C29  C23  C25   99.40  3.000
 3NX  C29  C23  C24  107.89  3.000
 3NX  C25  C23  C24  112.21  3.000
 3NX  C29  C23  C22  118.81  3.000
 3NX  C25  C23  C22  106.74  3.000
 3NX  C24  C23  C22  111.26  3.000
 3NX  H24  C24  H23  107.39  3.000
 3NX  H24  C24  H22  107.16  3.000
 3NX  H23  C24  H22  106.78  3.000
 3NX  H24  C24  C23  111.16  3.000
 3NX  H23  C24  C23  112.93  3.000
 3NX  H22  C24  C23  111.12  3.000
 3NX  H25  C25  C27  105.06  3.000
 3NX  H25  C25  C23  105.11  3.000
 3NX  C27  C25  C23  104.08  3.000
 3NX  H25  C25  C9   106.05  3.000
 3NX  C23  C25  C9   113.86  3.000
 3NX  C27  C25  C9   121.31  3.000
 3NX  H27  C27  H26  106.47  3.000
 3NX  H27  C27  C28  112.93  3.000
 3NX  H26  C27  C28  111.37  3.000
 3NX  H27  C27  C25  113.31  3.000
 3NX  H26  C27  C25  112.71  3.000
 3NX  C28  C27  C25  100.18  3.000
 3NX  H28  C28  C29  124.90  3.000
 3NX  H28  C28  C27  122.87  3.000
 3NX  C29  C28  C27  112.21  3.000
 3NX  C30  C29  C28  124.48  3.000
 3NX  C30  C29  C23  126.13  3.000
 3NX  C28  C29  C23  109.30  3.000
 3NX  C35  C30  C31  116.21  3.000
 3NX  C31  C30  C29  122.93  3.000
 3NX  C35  C30  C29  120.86  3.000
 3NX  H31  C31  N32  115.35  3.000
 3NX  H31  C31  C30  120.32  3.000
 3NX  N32  C31  C30  124.33  3.000
 3NX  C33  N32  C31  118.27  3.000
 3NX  H32  C33  C34  120.50  3.000
 3NX  H32  C33  N32  116.80  3.000
 3NX  C34  C33  N32  122.70  3.000
 3NX  H33  C34  C35  121.01  3.000
 3NX  H33  C34  C33  120.42  3.000
 3NX  C35  C34  C33  118.57  3.000
 3NX  H34  C35  C34  120.04  3.000
 3NX  H34  C35  C30  120.05  3.000
 3NX  C34  C35  C30  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
 3NX  CONST_01  C33  C34  C35  C30     0.00   0.0  0
 3NX  CONST_02  C33  N32  C31  C30     0.00   0.0  0
 3NX  CONST_03  C34  C35  C30  C31     0.00   0.0  0
 3NX  CONST_04  C34  C33  N32  C31     0.00   0.0  0
 3NX  CONST_05  C35  C30  C31  N32     0.00   0.0  0
 3NX  CONST_06  C35  C34  C33  N32     0.00   0.0  0
 3NX  CONST_07  C34  C35  C30  C29   180.00   0.0  0
 3NX  CONST_08  N32  C31  C30  C29   180.00   0.0  0
 3NX  CONST_09  H34  C35  C30  C29     0.00   0.0  0
 3NX  CONST_10  H31  C31  C30  C29     0.00   0.0  0
 3NX  CONST_11  H33  C34  C35  C30   180.00   0.0  0
 3NX  CONST_12  H32  C33  N32  C31   180.00   0.0  0
 3NX  CONST_13  H1   N5   C3   C2    180.00   0.0  0
 3NX  CONST_14  H2   N5   C3   C2      0.00   0.0  0
 3NX  Var_01    C9   C8   C2   C1     17.09  30.0  1
 3NX  Var_02    C16  C20  C1   C2   -127.77  30.0  1
 3NX  Var_03    C20  C1   C2   C8   -179.76  30.0  1
 3NX  Var_04    C23  C22  C21  C11   -52.62  30.0  1
 3NX  Var_05    C16  C15  C14  C12   -56.65  30.0  1
 3NX  Var_06    C27  C28  C29  C23     4.96  30.0  1
 3NX  Var_07    C35  C30  C29  C23  -153.62  30.0  2
 3NX  Var_08    C29  C28  C27  C25    18.99  30.0  1
 3NX  Var_09    N5   C3   C2   C1    -73.60  30.0  2

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
 3NX  chir_01  C9   C8   C25  C11  negativ
 3NX  chir_02  C11  C21  C12  C9   positiv
 3NX  chir_03  C12  C1   C11  C14  negativ
 3NX  chir_04  C16  O18  C15  C20  negativ
 3NX  chir_05  C23  C25  C29  C22  negativ
 3NX  chir_06  C25  C23  C9   C27  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
 3NX  plan-1  C29  0.020
 3NX  plan-1  C30  0.020
 3NX  plan-1  C31  0.020
 3NX  plan-1  N32  0.020
 3NX  plan-1  C33  0.020
 3NX  plan-1  C34  0.020
 3NX  plan-1  C35  0.020
 3NX  plan-1  H31  0.020
 3NX  plan-1  H32  0.020
 3NX  plan-1  H33  0.020
 3NX  plan-1  H34  0.020
 3NX  plan-2  C2   0.020
 3NX  plan-2  C3   0.020
 3NX  plan-2  O4   0.020
 3NX  plan-2  N5   0.020
 3NX  plan-2  H1   0.020
 3NX  plan-2  H2   0.020

