# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 22:26:08 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (5beta,8alpha,10alpha,13alpha,14beta)-androstane-3,17-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CCC(=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
 5SD  5SD  (5beta,8alpha,10alpha,13alpha,14beta)-androstane-3,17-dione  ligand  49  21  .  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_5SD
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
 5SD  C1    C  CH2   0  -0.432   1.4794   0.5071   2.4223
 5SD  C2    C  CH2   0  -0.565   1.4271   0.2663   3.9341
 5SD  C3    C  C     0   0.420   0.0705   0.5522   4.5178
 5SD  O3    O  O     0  -0.411  -0.0817   1.1945   5.5355
 5SD  C4    C  CH2   0  -0.561  -1.0832  -0.0337   3.7506
 5SD  C5    C  CH1   0  -0.221  -0.9750   0.2392   2.2464
 5SD  C6    C  CH2   0  -0.415  -2.1753  -0.3227   1.4991
 5SD  C7    C  CH2   0  -0.423  -2.1411   0.1041   0.0401
 5SD  C8    C  CH1   0  -0.222  -0.8300  -0.2811  -0.6366
 5SD  C9    C  CH1   0  -0.176   0.3966   0.2201   0.1590
 5SD  C10   C  CT    0  -0.055   0.3720  -0.2216   1.6449
 5SD  C11   C  CH2   0  -0.453   1.7090  -0.1270  -0.5611
 5SD  C12   C  CH2   0  -0.401   1.7592   0.3534  -2.0148
 5SD  C13   C  CT    0  -0.204   0.5388  -0.1396  -2.7755
 5SD  C14   C  CH1   0  -0.198  -0.7323   0.2970  -2.0384
 5SD  C15   C  CH2   0  -0.459  -1.8508   0.0779  -3.0582
 5SD  C16   C  CH2   0  -0.567  -1.2050   0.5645  -4.3627
 5SD  C17   C  C     0   0.432   0.2982   0.4613  -4.1437
 5SD  O17   O  O     0  -0.402   1.1467   0.8040  -4.9322
 5SD  C18   C  CH3   0  -0.665   0.6090  -1.6584  -3.0183
 5SD  C19   C  CH3   0  -0.699   0.5749  -1.7368   1.7648
 5SD  H1C1  H  HCH2  0   0.244   2.4663   0.2014   2.0713
 5SD  H1C2  H  HCH2  0   0.231   1.4012   1.5825   2.2292
 5SD  H2C1  H  HCH2  0   0.263   1.6522  -0.7853   4.1447
 5SD  H2C2  H  HCH2  0   0.263   2.1858   0.8591   4.4469
 5SD  H4C1  H  HCH2  0   0.260  -1.0959  -1.1145   3.9331
 5SD  H4C2  H  HCH2  0   0.259  -2.0222   0.3636   4.1416
 5SD  H5    H  HCH1  0   0.226  -1.0073   1.3308   2.1175
 5SD  H6C1  H  HCH2  0   0.217  -2.1922  -1.4154   1.5789
 5SD  H6C2  H  HCH2  0   0.230  -3.0973   0.0324   1.9685
 5SD  H7C1  H  HCH2  0   0.234  -2.9814  -0.3380  -0.5016
 5SD  H7C2  H  HCH2  0   0.207  -2.2735   1.1914  -0.0201
 5SD  H8    H  HCH1  0   0.215  -0.7999  -1.3757  -0.6989
 5SD  H9    H  HCH1  0   0.205   0.3200   1.3189   0.1699
 5SD  H111  H  HCH2  0   0.241   2.5529   0.3147  -0.0281
 5SD  H112  H  HCH2  0   0.224   1.8707  -1.2079  -0.5320
 5SD  H121  H  HCH2  0   0.226   1.7840   1.4480  -2.0380
 5SD  H122  H  HCH2  0   0.231   2.6845   0.0090  -2.4840
 5SD  H14   H  HCH1  0   0.225  -0.6494   1.3884  -1.9119
 5SD  H151  H  HCH2  0   0.231  -2.1349  -0.9750  -3.1232
 5SD  H152  H  HCH2  0   0.249  -2.7530   0.6374  -2.8112
 5SD  H161  H  HCH2  0   0.277  -1.5098   0.0123  -5.2539
 5SD  H162  H  HCH2  0   0.277  -1.4432   1.6151  -4.5519
 5SD  H181  H  HCH3  0   0.245   0.6437  -2.2204  -2.0857
 5SD  H182  H  HCH3  0   0.244  -0.2442  -2.0347  -3.5844
 5SD  H183  H  HCH3  0   0.244   1.5103  -1.9035  -3.5823
 5SD  H191  H  HCH3  0   0.236   0.3702  -2.1133   2.7677
 5SD  H192  H  HCH3  0   0.238  -0.0647  -2.2966   1.0833
 5SD  H193  H  HCH3  0   0.237   1.6061  -2.0076   1.5341

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
 5SD  C1   C2    single  1.532  0.020  1.532
 5SD  C1   C10   single  1.537  0.020  1.537
 5SD  C1   H1C1  single  0.970  0.020  1.090
 5SD  C1   H1C2  single  0.970  0.020  1.090
 5SD  C2   C3    single  1.504  0.020  1.504
 5SD  C2   H2C1  single  0.970  0.020  1.090
 5SD  C2   H2C2  single  0.970  0.020  1.090
 5SD  C3   O3    double  1.213  0.020  1.213
 5SD  C3   C4    single  1.504  0.020  1.504
 5SD  C4   C5    single  1.533  0.020  1.533
 5SD  C4   H4C1  single  0.970  0.020  1.090
 5SD  C4   H4C2  single  0.970  0.020  1.090
 5SD  C5   C6    single  1.521  0.020  1.521
 5SD  C5   C10   single  1.546  0.020  1.546
 5SD  C5   H5    single  0.970  0.020  1.090
 5SD  C6   C7    single  1.520  0.020  1.520
 5SD  C6   H6C1  single  0.970  0.020  1.090
 5SD  C6   H6C2  single  0.970  0.020  1.090
 5SD  C7   C8    single  1.525  0.020  1.525
 5SD  C7   H7C1  single  0.970  0.020  1.090
 5SD  C7   H7C2  single  0.970  0.020  1.090
 5SD  C8   C9    single  1.546  0.020  1.546
 5SD  C8   C14   single  1.519  0.020  1.519
 5SD  C8   H8    single  0.970  0.020  1.090
 5SD  C9   C10   single  1.550  0.020  1.550
 5SD  C9   C11   single  1.537  0.020  1.537
 5SD  C9   H9    single  0.970  0.020  1.090
 5SD  C10  C19   single  1.533  0.020  1.533
 5SD  C11  C12   single  1.532  0.020  1.532
 5SD  C11  H111  single  0.970  0.020  1.090
 5SD  C11  H112  single  0.970  0.020  1.090
 5SD  C12  C13   single  1.520  0.020  1.520
 5SD  C12  H121  single  0.970  0.020  1.090
 5SD  C12  H122  single  0.970  0.020  1.090
 5SD  C13  C14   single  1.533  0.020  1.533
 5SD  C13  C17   single  1.514  0.020  1.514
 5SD  C13  C18   single  1.540  0.020  1.540
 5SD  C14  C15   single  1.529  0.020  1.529
 5SD  C14  H14   single  0.970  0.020  1.090
 5SD  C15  C16   single  1.535  0.020  1.535
 5SD  C15  H151  single  0.970  0.020  1.090
 5SD  C15  H152  single  0.970  0.020  1.090
 5SD  C16  C17   single  1.523  0.020  1.523
 5SD  C16  H161  single  0.970  0.020  1.090
 5SD  C16  H162  single  0.970  0.020  1.090
 5SD  C17  O17   double  1.208  0.020  1.208
 5SD  C18  H181  single  0.970  0.020  1.090
 5SD  C18  H182  single  0.970  0.020  1.090
 5SD  C18  H183  single  0.970  0.020  1.090
 5SD  C19  H191  single  0.970  0.020  1.090
 5SD  C19  H192  single  0.970  0.020  1.090
 5SD  C19  H193  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
 5SD  H1C2  C1   H1C1  106.43  3.000
 5SD  H1C2  C1   C10   108.96  3.000
 5SD  H1C1  C1   C10   110.87  3.000
 5SD  H1C2  C1   C2    109.02  3.000
 5SD  H1C1  C1   C2    107.72  3.000
 5SD  C10   C1   C2    113.59  3.000
 5SD  H2C2  C2   H2C1  106.76  3.000
 5SD  H2C2  C2   C3    109.97  3.000
 5SD  H2C1  C2   C3    107.04  3.000
 5SD  H2C2  C2   C1    110.78  3.000
 5SD  H2C1  C2   C1    109.48  3.000
 5SD  C3    C2   C1    112.57  3.000
 5SD  C4    C3   O3    122.55  3.000
 5SD  C4    C3   C2    114.81  3.000
 5SD  O3    C3   C2    122.64  3.000
 5SD  H4C2  C4   H4C1  106.81  3.000
 5SD  H4C2  C4   C5    110.32  3.000
 5SD  H4C1  C4   C5    109.87  3.000
 5SD  H4C2  C4   C3    109.58  3.000
 5SD  H4C1  C4   C3    107.94  3.000
 5SD  C5    C4   C3    112.15  3.000
 5SD  H5    C5   C10   106.02  3.000
 5SD  H5    C5   C6    106.61  3.000
 5SD  C10   C5   C6    112.72  3.000
 5SD  H5    C5   C4    106.85  3.000
 5SD  C10   C5   C4    112.98  3.000
 5SD  C6    C5   C4    111.14  3.000
 5SD  H6C2  C6   H6C1  106.23  3.000
 5SD  H6C2  C6   C7    109.86  3.000
 5SD  H6C1  C6   C7    110.50  3.000
 5SD  H6C2  C6   C5    109.53  3.000
 5SD  H6C1  C6   C5    110.16  3.000
 5SD  C7    C6   C5    110.48  3.000
 5SD  H7C2  C7   H7C1  106.32  3.000
 5SD  H7C2  C7   C8    109.26  3.000
 5SD  H7C1  C7   C8    109.80  3.000
 5SD  H7C2  C7   C6    109.16  3.000
 5SD  H7C1  C7   C6    110.16  3.000
 5SD  C8    C7   C6    111.98  3.000
 5SD  H8    C8   C14   109.00  3.000
 5SD  H8    C8   C9    109.34  3.000
 5SD  C14   C8   C9    107.49  3.000
 5SD  H8    C8   C7    107.51  3.000
 5SD  C14   C8   C7    111.62  3.000
 5SD  C9    C8   C7    111.84  3.000
 5SD  H9    C9   C11   106.82  3.000
 5SD  H9    C9   C10   105.88  3.000
 5SD  C11   C9   C10   113.47  3.000
 5SD  H9    C9   C8    105.87  3.000
 5SD  C11   C9   C8    111.30  3.000
 5SD  C10   C9   C8    112.85  3.000
 5SD  C19   C10  C9    110.75  3.000
 5SD  C19   C10  C5    112.30  3.000
 5SD  C9    C10  C5    107.57  3.000
 5SD  C19   C10  C1    109.49  3.000
 5SD  C9    C10  C1    109.77  3.000
 5SD  C5    C10  C1    106.85  3.000
 5SD  H112  C11  H111  105.83  3.000
 5SD  H112  C11  C12   109.30  3.000
 5SD  H111  C11  C12   108.13  3.000
 5SD  H112  C11  C9    109.70  3.000
 5SD  H111  C11  C9    109.88  3.000
 5SD  C12   C11  C9    113.69  3.000
 5SD  H122  C12  H121  106.66  3.000
 5SD  H122  C12  C13   111.26  3.000
 5SD  H121  C12  C13   109.38  3.000
 5SD  H122  C12  C11   109.64  3.000
 5SD  H121  C12  C11   109.53  3.000
 5SD  C13   C12  C11   110.29  3.000
 5SD  C18   C13  C17   104.85  3.000
 5SD  C18   C13  C14   113.24  3.000
 5SD  C17   C13  C14   100.94  3.000
 5SD  C18   C13  C12   111.24  3.000
 5SD  C17   C13  C12   116.82  3.000
 5SD  C14   C13  C12   109.43  3.000
 5SD  H14   C14  C15   105.87  3.000
 5SD  H14   C14  C13   105.96  3.000
 5SD  C15   C14  C13   104.18  3.000
 5SD  H14   C14  C8    106.01  3.000
 5SD  C15   C14  C8    120.91  3.000
 5SD  C13   C14  C8    112.86  3.000
 5SD  H152  C15  H151  107.03  3.000
 5SD  H152  C15  C16   112.22  3.000
 5SD  H151  C15  C16   111.37  3.000
 5SD  H152  C15  C14   112.37  3.000
 5SD  H151  C15  C14   111.59  3.000
 5SD  C16   C15  C14   102.34  3.000
 5SD  H162  C16  H161  106.48  3.000
 5SD  H162  C16  C17   107.76  3.000
 5SD  H161  C16  C17   111.03  3.000
 5SD  H162  C16  C15   111.09  3.000
 5SD  H161  C16  C15   114.58  3.000
 5SD  C17   C16  C15   105.76  3.000
 5SD  O17   C17  C16   125.47  3.000
 5SD  O17   C17  C13   126.24  3.000
 5SD  C16   C17  C13   108.30  3.000
 5SD  H183  C18  H182  107.48  3.000
 5SD  H183  C18  H181  107.48  3.000
 5SD  H182  C18  H181  106.94  3.000
 5SD  H183  C18  C13   109.92  3.000
 5SD  H182  C18  C13   112.73  3.000
 5SD  H181  C18  C13   112.04  3.000
 5SD  H193  C19  H192  107.16  3.000
 5SD  H193  C19  H191  106.62  3.000
 5SD  H192  C19  H191  106.72  3.000
 5SD  H193  C19  C10   110.73  3.000
 5SD  H192  C19  C10   112.41  3.000
 5SD  H191  C19  C10   112.85  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
 5SD  Var_01  C4   C3   C2   C1    46.48  30.0  1
 5SD  Var_02  C5   C4   C3   C2   -47.41  30.0  1
 5SD  Var_03  C10  C1   C2   C3   -52.34  30.0  1
 5SD  Var_04  C8   C7   C6   C5    55.03  30.0  1
 5SD  Var_05  C13  C12  C11  C9   -52.98  30.0  1
 5SD  Var_06  C15  C16  C17  C13    2.92  30.0  1
 5SD  Var_07  C17  C16  C15  C14   22.87  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
 5SD  chir_01  C5   C4   C6   C10  positiv
 5SD  chir_02  C8   C14  C9   C7   negativ
 5SD  chir_03  C9   C11  C10  C8   positiv
 5SD  chir_04  C10  C5   C9   C1   negativ
 5SD  chir_05  C13  C14  C17  C12  negativ
 5SD  chir_06  C14  C8   C13  C15  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
 5SD  plan-1  C2   0.020
 5SD  plan-1  C3   0.020
 5SD  plan-1  O3   0.020
 5SD  plan-1  C4   0.020
 5SD  plan-2  C13  0.020
 5SD  plan-2  C16  0.020
 5SD  plan-2  C17  0.020
 5SD  plan-2  O17  0.020

