# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 21:08:08 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (8alpha,14beta,17alpha,20Z)-17,20,21-trihydroxypregna-1,4,20-triene-3,11-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC(=O)[C@H]3[C@@H](CCC4=CC(=O)C=C[C@]34C)[C@@H]1CC[C@]2(O)\C(O)=C\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
 PDN  PDN  (8alpha,14beta,17alpha,20Z)-17,20,21-trihydroxypregna-1,4,20-triene-3,11-dione  ligand  52  26  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PDN
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
 PDN  C1    C  C1    0  -0.116   1.6835  -0.0317  -3.1819
 PDN  C2    C  C1    0  -0.383   1.7208  -0.7994  -4.2720
 PDN  C3    C  C     0   0.397   0.5029  -1.1609  -4.9981
 PDN  C4    C  C1    0  -0.467  -0.7430  -0.6234  -4.4615
 PDN  C5    C  C     0   0.251  -0.7951   0.1502  -3.3683
 PDN  C6    C  CH2   0  -0.509  -2.1044   0.6160  -2.8216
 PDN  C7    C  CH2   0  -0.415  -2.2857   0.0774  -1.4052
 PDN  C8    C  CH1   0  -0.258  -1.1168   0.4455  -0.5015
 PDN  C9    C  CH1   0  -0.332   0.2315   0.0021  -1.1374
 PDN  C10   C  CT    0  -0.234   0.4351   0.5469  -2.5875
 PDN  C11   C  C     0   0.425   1.3830   0.2449  -0.1655
 PDN  C12   C  CH2   0  -0.514   1.2146  -0.3861   1.1984
 PDN  C13   C  CT    0  -0.102  -0.0935   0.1142   1.8083
 PDN  C14   C  CH1   0  -0.183  -1.2467  -0.2244   0.8577
 PDN  C15   C  CH2   0  -0.454  -2.4945   0.0515   1.6967
 PDN  C16   C  CH2   0  -0.462  -2.0640  -0.2417   3.1537
 PDN  C17   C  CT    0   0.203  -0.5583  -0.6074   3.1019
 PDN  C18   C  CH3   0  -0.671   0.0251   1.6222   2.0537
 PDN  C19   C  CH3   0  -0.661   0.5717   2.0860  -2.6369
 PDN  C20   C  C     0   0.241   0.2200  -0.2345   4.3441
 PDN  C21   C  C1    0  -0.104   1.2838  -0.9297   4.7533
 PDN  O1    O  O     0  -0.453   0.5292  -1.8700  -5.9954
 PDN  O2    O  O     0  -0.392   2.3702   0.8883  -0.4415
 PDN  O3    O  OH1   0  -0.672  -0.3988  -1.9896   2.8571
 PDN  O4    O  OH1   0  -0.643  -0.2158   0.8773   4.9923
 PDN  O5    O  OH1   0  -0.652   2.0124  -0.4950   5.8273
 PDN  HC1   H  H     0   0.285   2.6138   0.2307  -2.6967
 PDN  HC2   H  H     0   0.262   2.6648  -1.1673  -4.6566
 PDN  HC4   H  H     0   0.252  -1.6568  -0.8830  -4.9860
 PDN  HC61  H  HCH2  0   0.262  -2.9196   0.2799  -3.4633
 PDN  HC62  H  HCH2  0   0.257  -2.1443   1.7095  -2.8048
 PDN  HC71  H  HCH2  0   0.229  -2.3898  -1.0122  -1.4431
 PDN  HC72  H  HCH2  0   0.256  -3.2133   0.4697  -0.9834
 PDN  HC8   H  HCH1  0   0.241  -1.1183   1.5340  -0.3779
 PDN  HC9   H  HCH1  0   0.282   0.1681  -1.0935  -1.2247
 PDN  H121  H  HCH2  0   0.256   2.0770  -0.1374   1.8195
 PDN  H122  H  HCH2  0   0.274   1.1854  -1.4717   1.0713
 PDN  HC41  H  HCH1  0   0.238  -1.2032  -1.3032   0.6682
 PDN  H151  H  HCH2  0   0.230  -2.8083   1.0935   1.5947
 PDN  H152  H  HCH2  0   0.243  -3.3406  -0.5606   1.3841
 PDN  H161  H  HCH2  0   0.248  -2.2460   0.6243   3.7872
 PDN  H162  H  HCH2  0   0.246  -2.6289  -1.0664   3.5935
 PDN  H181  H  HCH3  0   0.236   0.2414   2.1640   1.1325
 PDN  H182  H  HCH3  0   0.247  -0.8826   2.0580   2.4697
 PDN  H183  H  HCH3  0   0.246   0.8425   1.8393   2.7410
 PDN  H191  H  HCH3  0   0.247   0.5020   2.4313  -3.6685
 PDN  H192  H  HCH3  0   0.246  -0.2104   2.5812  -2.0638
 PDN  H193  H  HCH3  0   0.260   1.5308   2.4050  -2.2386
 PDN  HC12  H  H     0   0.237   1.6219  -1.8148   4.2321
 PDN  HO3   H  HOH1  0   0.445  -0.7804  -2.4716   3.5988
 PDN  HO4   H  HOH1  0   0.462   0.3597   1.0523   5.7471
 PDN  HO5   H  HOH1  0   0.475   2.3806  -1.2522   6.2919

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
 PDN  C1   C2    double  1.334  0.020  1.334
 PDN  C1   C10   single  1.499  0.020  1.499
 PDN  C1   HC1   single  0.930  0.020  1.080
 PDN  C2   C3    single  1.463  0.020  1.463
 PDN  C2   HC2   single  0.930  0.020  1.080
 PDN  C3   C4    single  1.459  0.020  1.459
 PDN  C3   O1    double  1.224  0.020  1.224
 PDN  C4   C5    double  1.340  0.020  1.340
 PDN  C4   HC4   single  0.930  0.020  1.080
 PDN  C5   C6    single  1.493  0.020  1.493
 PDN  C5   C10   single  1.510  0.020  1.510
 PDN  C6   C7    single  1.526  0.020  1.526
 PDN  C6   HC61  single  0.970  0.020  1.090
 PDN  C6   HC62  single  0.970  0.020  1.090
 PDN  C7   C8    single  1.523  0.020  1.523
 PDN  C7   HC71  single  0.970  0.020  1.090
 PDN  C7   HC72  single  0.970  0.020  1.090
 PDN  C8   C9    single  1.555  0.020  1.555
 PDN  C8   C14   single  1.521  0.020  1.521
 PDN  C8   HC8   single  0.970  0.020  1.090
 PDN  C9   C10   single  1.562  0.020  1.562
 PDN  C9   C11   single  1.526  0.020  1.526
 PDN  C9   HC9   single  0.970  0.020  1.090
 PDN  C10  C19   single  1.546  0.020  1.546
 PDN  C11  C12   single  1.512  0.020  1.512
 PDN  C11  O2    double  1.210  0.020  1.210
 PDN  C12  C13   single  1.528  0.020  1.528
 PDN  C12  H121  single  0.970  0.020  1.090
 PDN  C12  H122  single  0.970  0.020  1.090
 PDN  C13  C14   single  1.532  0.020  1.532
 PDN  C13  C17   single  1.552  0.020  1.552
 PDN  C13  C18   single  1.532  0.020  1.532
 PDN  C14  C15   single  1.529  0.020  1.529
 PDN  C14  HC41  single  0.970  0.020  1.090
 PDN  C15  C16   single  1.547  0.020  1.547
 PDN  C15  H151  single  0.970  0.020  1.090
 PDN  C15  H152  single  0.970  0.020  1.090
 PDN  C16  C17   single  1.550  0.020  1.550
 PDN  C16  H161  single  0.970  0.020  1.090
 PDN  C16  H162  single  0.970  0.020  1.090
 PDN  C17  C20   single  1.513  0.020  1.513
 PDN  C17  O3    single  1.413  0.020  1.413
 PDN  C18  H181  single  0.970  0.020  1.090
 PDN  C18  H182  single  0.970  0.020  1.090
 PDN  C18  H183  single  0.970  0.020  1.090
 PDN  C19  H191  single  0.970  0.020  1.090
 PDN  C19  H192  single  0.970  0.020  1.090
 PDN  C19  H193  single  0.970  0.020  1.090
 PDN  C20  C21   double  1.335  0.020  1.335
 PDN  C20  O4    single  1.359  0.020  1.359
 PDN  C21  O5    single  1.369  0.020  1.369
 PDN  C21  HC12  single  0.930  0.020  1.080
 PDN  O3   HO3   single  0.850  0.020  0.980
 PDN  O4   HO4   single  0.850  0.020  0.980
 PDN  O5   HO5   single  0.850  0.020  0.980

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
 PDN  HC1   C1   C10   116.41  3.000
 PDN  HC1   C1   C2    118.83  3.000
 PDN  C10   C1   C2    124.72  3.000
 PDN  HC2   C2   C3    117.71  3.000
 PDN  HC2   C2   C1    120.65  3.000
 PDN  C3    C2   C1    121.63  3.000
 PDN  O1    C3   C4    122.09  3.000
 PDN  O1    C3   C2    121.98  3.000
 PDN  C4    C3   C2    115.93  3.000
 PDN  HC4   C4   C5    119.97  3.000
 PDN  HC4   C4   C3    116.95  3.000
 PDN  C5    C4   C3    123.08  3.000
 PDN  C10   C5   C6    116.30  3.000
 PDN  C10   C5   C4    122.80  3.000
 PDN  C6    C5   C4    120.85  3.000
 PDN  HC62  C6   HC61  106.84  3.000
 PDN  HC62  C6   C7    109.52  3.000
 PDN  HC61  C6   C7    110.39  3.000
 PDN  HC62  C6   C5    110.44  3.000
 PDN  HC61  C6   C5    110.11  3.000
 PDN  C7    C6   C5    109.51  3.000
 PDN  HC72  C7   HC71  106.86  3.000
 PDN  HC72  C7   C8    109.64  3.000
 PDN  HC71  C7   C8    109.51  3.000
 PDN  HC72  C7   C6    109.43  3.000
 PDN  HC71  C7   C6    109.29  3.000
 PDN  C8    C7   C6    111.98  3.000
 PDN  HC8   C8   C14   109.68  3.000
 PDN  HC8   C8   C9    109.31  3.000
 PDN  C14   C8   C9    108.29  3.000
 PDN  HC8   C8   C7    107.83  3.000
 PDN  C14   C8   C7    111.00  3.000
 PDN  C9    C8   C7    110.73  3.000
 PDN  HC9   C9   C11   104.61  3.000
 PDN  HC9   C9   C10   106.32  3.000
 PDN  C11   C9   C10   115.93  3.000
 PDN  HC9   C9   C8    105.44  3.000
 PDN  C11   C9   C8    110.38  3.000
 PDN  C10   C9   C8    113.14  3.000
 PDN  C19   C10  C9    112.85  3.000
 PDN  C19   C10  C5    108.48  3.000
 PDN  C9    C10  C5    106.39  3.000
 PDN  C19   C10  C1    107.34  3.000
 PDN  C9    C10  C1    110.00  3.000
 PDN  C5    C10  C1    111.85  3.000
 PDN  O2    C11  C12   121.23  3.000
 PDN  O2    C11  C9    123.69  3.000
 PDN  C12   C11  C9    115.08  3.000
 PDN  H122  C12  H121  108.27  3.000
 PDN  H122  C12  C13   110.41  3.000
 PDN  H121  C12  C13   112.01  3.000
 PDN  H122  C12  C11   108.21  3.000
 PDN  H121  C12  C11   109.28  3.000
 PDN  C13   C12  C11   108.59  3.000
 PDN  C18   C13  C17   110.31  3.000
 PDN  C18   C13  C14   112.02  3.000
 PDN  C17   C13  C14   100.89  3.000
 PDN  C18   C13  C12   108.66  3.000
 PDN  C17   C13  C12   115.90  3.000
 PDN  C14   C13  C12   108.93  3.000
 PDN  HC41  C14  C15   107.75  3.000
 PDN  HC41  C14  C13   107.14  3.000
 PDN  C15   C14  C13   103.52  3.000
 PDN  HC41  C14  C8    106.00  3.000
 PDN  C15   C14  C8    118.74  3.000
 PDN  C13   C14  C8    113.13  3.000
 PDN  H152  C15  H151  106.60  3.000
 PDN  H152  C15  C16   112.31  3.000
 PDN  H151  C15  C16   110.39  3.000
 PDN  H152  C15  C14   112.01  3.000
 PDN  H151  C15  C14   110.80  3.000
 PDN  C16   C15  C14   104.81  3.000
 PDN  H162  C16  H161  106.26  3.000
 PDN  H162  C16  C17   109.73  3.000
 PDN  H161  C16  C17   111.69  3.000
 PDN  H162  C16  C15   112.23  3.000
 PDN  H161  C16  C15   110.54  3.000
 PDN  C17   C16  C15   106.46  3.000
 PDN  O3    C17  C20   108.99  3.000
 PDN  O3    C17  C16   110.26  3.000
 PDN  C20   C17  C16   114.47  3.000
 PDN  O3    C17  C13   106.06  3.000
 PDN  C20   C17  C13   114.56  3.000
 PDN  C16   C17  C13   102.06  3.000
 PDN  H183  C18  H182  107.72  3.000
 PDN  H183  C18  H181  106.57  3.000
 PDN  H182  C18  H181  106.81  3.000
 PDN  H183  C18  C13   110.79  3.000
 PDN  H182  C18  C13   112.97  3.000
 PDN  H181  C18  C13   111.66  3.000
 PDN  H193  C19  H192  107.92  3.000
 PDN  H193  C19  H191  108.08  3.000
 PDN  H192  C19  H191  107.95  3.000
 PDN  H193  C19  C10   111.02  3.000
 PDN  H192  C19  C10   111.87  3.000
 PDN  H191  C19  C10   109.87  3.000
 PDN  O4    C20  C21   122.37  3.000
 PDN  O4    C20  C17   115.37  3.000
 PDN  C21   C20  C17   122.23  3.000
 PDN  HC12  C21  O5    118.15  3.000
 PDN  HC12  C21  C20   121.84  3.000
 PDN  O5    C21  C20   119.95  3.000
 PDN  HO3   O3   C17   108.14  3.000
 PDN  HO4   O4   C20   109.29  3.000
 PDN  HO5   O5   C21   109.44  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
 PDN  Var_01  C4   C3   C2   C1      0.42  30.0  1
 PDN  Var_02  C5   C4   C3   C2     -0.34  30.0  1
 PDN  Var_03  C10  C1   C2   C3     -0.46  30.0  1
 PDN  Var_04  C6   C5   C4   C3   -176.83  30.0  1
 PDN  Var_05  C7   C6   C5   C4    118.54  30.0  1
 PDN  Var_06  C8   C7   C6   C5     54.68  30.0  1
 PDN  Var_07  C13  C12  C11  C9    -56.42  30.0  1
 PDN  Var_08  C17  C16  C15  C14     2.79  30.0  1
 PDN  Var_09  O5   C21  C20  C17   175.21   0.0  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
 PDN  chir_01  C8   C7   C9   C14  positiv
 PDN  chir_02  C9   C11  C10  C8   positiv
 PDN  chir_03  C10  C9   C5   C1   positiv
 PDN  chir_04  C13  C14  C17  C12  negativ
 PDN  chir_05  C14  C15  C13  C8   positiv
 PDN  chir_06  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
 PDN  plan-1  C2    0.020
 PDN  plan-1  C3    0.020
 PDN  plan-1  C4    0.020
 PDN  plan-1  O1    0.020
 PDN  plan-2  C9    0.020
 PDN  plan-2  C11   0.020
 PDN  plan-2  C12   0.020
 PDN  plan-2  O2    0.020
 PDN  plan-3  C17   0.020
 PDN  plan-3  C20   0.020
 PDN  plan-3  C21   0.020
 PDN  plan-3  O4    0.020
 PDN  plan-3  O5    0.020
 PDN  plan-3  HC12  0.020

