# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 06:15:00 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (3beta,5alpha,8alpha,9beta,10alpha)-3-hydroxypregnane-11,20-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)[C@H]1CC[C@H]2[C@@H]3CC[C@H]4C[C@H](O)CC[C@]4(C)[C@H]3C(=O)C[C@]12C
#
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
 EY4  EY4  (3beta,5alpha,8alpha,9beta,10alpha)-3-hydroxypregnane-11,20-dione  ligand  56  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EY4
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
 EY4  C10  C  CT    0  -0.040   2.1201   0.3313  -0.4739
 EY4  C11  C  C     0   0.430  -0.2190   1.4745  -0.2359
 EY4  C12  C  CH2   0  -0.532  -1.5922   1.4401   0.4094
 EY4  C13  C  CT    0  -0.091  -2.3295   0.1775  -0.0392
 EY4  C14  C  CH1   0  -0.178  -1.4558  -1.0354   0.3117
 EY4  C15  C  CH2   0  -0.450  -2.3812  -2.2267   0.0856
 EY4  C1   C  CH2   0  -0.412   2.8573   1.5387   0.1350
 EY4  C16  C  CH2   0  -0.433  -3.7728  -1.7019   0.5037
 EY4  C17  C  CH1   0  -0.343  -3.6062  -0.1907   0.7644
 EY4  C18  C  CH3   0  -0.673  -2.6351   0.2648  -1.5367
 EY4  C19  C  CH3   0  -0.693   2.1585   0.4083  -2.0063
 EY4  C2   C  CH2   0  -0.489   4.3549   1.5324  -0.1594
 EY4  C20  C  C     0   0.406  -4.8210   0.6481   0.4376
 EY4  C21  C  CH3   0  -0.778  -4.9751   1.9195   1.2244
 EY4  C3   C  CH1   0   0.050   5.0461   0.2610   0.3147
 EY4  C4   C  CH2   0  -0.448   4.3285  -0.9577  -0.2420
 EY4  C5   C  CH1   0  -0.204   2.8285  -0.9454   0.0486
 EY4  C6   C  CH2   0  -0.420   2.1517  -2.2172  -0.4417
 EY4  C7   C  CH2   0  -0.415   0.7068  -2.2707   0.0275
 EY4  C8   C  CH1   0  -0.242  -0.0898  -1.0273  -0.3568
 EY4  C9   C  CH1   0  -0.335   0.6649   0.2703   0.0495
 EY4  O11  O  O     0  -0.393   0.1063   2.4113  -0.9307
 EY4  O20  O  O     0  -0.403  -5.6329   0.3145  -0.3978
 EY4  O3   O  OH1   0  -0.679   5.0404   0.1534   1.7290
 EY4  H1   H  HCH2  0   0.266  -1.4733   1.4261   1.4986
 EY4  H2   H  HCH2  0   0.257  -2.1252   2.3531   0.1381
 EY4  H3   H  HCH1  0   0.227  -1.2678  -0.9729   1.3942
 EY4  H4   H  HCH2  0   0.227  -2.3740  -2.5298  -0.9648
 EY4  H5   H  HCH2  0   0.242  -2.0768  -3.0990   0.6643
 EY4  H6   H  HCH2  0   0.238   2.4350   2.4706  -0.2395
 EY4  H7   H  HCH2  0   0.211   2.7015   1.5439   1.2195
 EY4  H8   H  HCH2  0   0.239  -4.5114  -1.8807  -0.2769
 EY4  H9   H  HCH2  0   0.244  -4.1378  -2.1992   1.4025
 EY4  H10  H  HCH1  0   0.259  -3.3673  -0.0242   1.8208
 EY4  H11  H  HCH3  0   0.239  -1.7247   0.2899  -2.1370
 EY4  H12  H  HCH3  0   0.247  -3.2260  -0.5799  -1.8904
 EY4  H13  H  HCH3  0   0.240  -3.1889   1.1757  -1.7707
 EY4  H14  H  HCH3  0   0.240   1.8911   1.4044  -2.3543
 EY4  H15  H  HCH3  0   0.229   3.1481   0.1844  -2.4046
 EY4  H16  H  HCH3  0   0.229   1.4696  -0.2937  -2.4759
 EY4  H17  H  HCH2  0   0.225   4.5267   1.6387  -1.2343
 EY4  H18  H  HCH2  0   0.234   4.8253   2.4079   0.3009
 EY4  H19  H  HCH3  0   0.263  -4.0492   2.4955   1.2311
 EY4  H20  H  HCH3  0   0.258  -5.7833   2.5381   0.8400
 EY4  H21  H  HCH3  0   0.271  -5.1848   1.6671   2.2669
 EY4  H22  H  HCH1  0   0.204   6.0823   0.2637  -0.0534
 EY4  H23  H  HCH2  0   0.222   4.5127  -1.0098  -1.3187
 EY4  H24  H  HCH2  0   0.231   4.7677  -1.8677   0.1797
 EY4  H25  H  HCH1  0   0.212   2.7144  -0.9335   1.1410
 EY4  H26  H  HCH2  0   0.215   2.2042  -2.2816  -1.5341
 EY4  H27  H  HCH2  0   0.226   2.6916  -3.0884  -0.0594
 EY4  H28  H  HCH2  0   0.238   0.2093  -3.1544  -0.3804
 EY4  H29  H  HCH2  0   0.209   0.6880  -2.3829   1.1183
 EY4  H30  H  HCH1  0   0.229  -0.2179  -1.0401  -1.4449
 EY4  H31  H  HCH1  0   0.251   0.7310   0.2353   1.1496
 EY4  H32  H  HOH1  0   0.444   5.3704   0.9805   2.0937

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
 EY4  C2   C3   single  1.523  0.020  1.523
 EY4  C2   C1   single  1.526  0.020  1.526
 EY4  C3   C4   single  1.520  0.020  1.520
 EY4  C3   O3   single  1.418  0.020  1.418
 EY4  C4   C5   single  1.528  0.020  1.528
 EY4  C1   C10  single  1.540  0.020  1.540
 EY4  C19  C10  single  1.535  0.020  1.535
 EY4  C5   C10  single  1.551  0.020  1.551
 EY4  C5   C6   single  1.522  0.020  1.522
 EY4  C10  C9   single  1.548  0.020  1.548
 EY4  C6   C7   single  1.520  0.020  1.520
 EY4  O11  C11  double  1.211  0.020  1.211
 EY4  C9   C11  single  1.521  0.020  1.521
 EY4  C9   C8   single  1.555  0.020  1.555
 EY4  C11  C12  single  1.518  0.020  1.518
 EY4  C7   C8   single  1.526  0.020  1.526
 EY4  C8   C14  single  1.521  0.020  1.521
 EY4  C18  C13  single  1.531  0.020  1.531
 EY4  C12  C13  single  1.529  0.020  1.529
 EY4  C14  C13  single  1.535  0.020  1.535
 EY4  C14  C15  single  1.525  0.020  1.525
 EY4  C13  C17  single  1.553  0.020  1.553
 EY4  C15  C16  single  1.545  0.020  1.545
 EY4  C17  C16  single  1.542  0.020  1.542
 EY4  C17  C20  single  1.512  0.020  1.512
 EY4  C20  O20  double  1.212  0.020  1.212
 EY4  C20  C21  single  1.503  0.020  1.503
 EY4  C12  H1   single  0.970  0.020  1.090
 EY4  C12  H2   single  0.970  0.020  1.090
 EY4  C14  H3   single  0.970  0.020  1.090
 EY4  C15  H4   single  0.970  0.020  1.090
 EY4  C15  H5   single  0.970  0.020  1.090
 EY4  C1   H6   single  0.970  0.020  1.090
 EY4  C1   H7   single  0.970  0.020  1.090
 EY4  C16  H8   single  0.970  0.020  1.090
 EY4  C16  H9   single  0.970  0.020  1.090
 EY4  C17  H10  single  0.970  0.020  1.090
 EY4  C18  H11  single  0.970  0.020  1.090
 EY4  C18  H12  single  0.970  0.020  1.090
 EY4  C18  H13  single  0.970  0.020  1.090
 EY4  C19  H14  single  0.970  0.020  1.090
 EY4  C19  H15  single  0.970  0.020  1.090
 EY4  C19  H16  single  0.970  0.020  1.090
 EY4  C2   H17  single  0.970  0.020  1.090
 EY4  C2   H18  single  0.970  0.020  1.090
 EY4  C21  H19  single  0.970  0.020  1.090
 EY4  C21  H20  single  0.970  0.020  1.090
 EY4  C21  H21  single  0.970  0.020  1.090
 EY4  C3   H22  single  0.970  0.020  1.090
 EY4  C4   H23  single  0.970  0.020  1.090
 EY4  C4   H24  single  0.970  0.020  1.090
 EY4  C5   H25  single  0.970  0.020  1.090
 EY4  C6   H26  single  0.970  0.020  1.090
 EY4  C6   H27  single  0.970  0.020  1.090
 EY4  C7   H28  single  0.970  0.020  1.090
 EY4  C7   H29  single  0.970  0.020  1.090
 EY4  C8   H30  single  0.970  0.020  1.090
 EY4  C9   H31  single  0.970  0.020  1.090
 EY4  O3   H32  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
 EY4  C9   C10  C5   106.45  3.000
 EY4  C9   C10  C19  111.29  3.000
 EY4  C5   C10  C19  111.49  3.000
 EY4  C9   C10  C1   110.32  3.000
 EY4  C5   C10  C1   107.07  3.000
 EY4  C19  C10  C1   110.09  3.000
 EY4  O11  C11  C9   124.35  3.000
 EY4  C9   C11  C12  115.35  3.000
 EY4  O11  C11  C12  120.30  3.000
 EY4  H2   C12  H1   108.11  3.000
 EY4  H2   C12  C13  112.47  3.000
 EY4  H1   C12  C13  109.47  3.000
 EY4  H2   C12  C11  108.50  3.000
 EY4  H1   C12  C11  108.95  3.000
 EY4  C13  C12  C11  109.28  3.000
 EY4  C18  C13  C17  110.83  3.000
 EY4  C17  C13  C14   99.34  3.000
 EY4  C18  C13  C14  112.47  3.000
 EY4  C17  C13  C12  116.12  3.000
 EY4  C14  C13  C12  108.11  3.000
 EY4  C18  C13  C12  109.63  3.000
 EY4  H3   C14  C8   106.18  3.000
 EY4  H3   C14  C15  107.09  3.000
 EY4  C8   C14  C15  118.94  3.000
 EY4  H3   C14  C13  106.09  3.000
 EY4  C15  C14  C13  103.75  3.000
 EY4  C8   C14  C13  113.98  3.000
 EY4  H5   C15  H4   106.64  3.000
 EY4  H5   C15  C16  112.31  3.000
 EY4  H4   C15  C16  111.11  3.000
 EY4  H5   C15  C14  112.13  3.000
 EY4  H4   C15  C14  110.79  3.000
 EY4  C16  C15  C14  103.95  3.000
 EY4  H7   C1   H6   106.33  3.000
 EY4  H7   C1   C2   109.30  3.000
 EY4  H6   C1   C2   108.52  3.000
 EY4  H7   C1   C10  109.08  3.000
 EY4  H6   C1   C10  110.43  3.000
 EY4  C2   C1   C10  112.96  3.000
 EY4  H9   C16  H8   106.80  3.000
 EY4  H9   C16  C17  110.11  3.000
 EY4  H8   C16  C17  110.80  3.000
 EY4  H9   C16  C15  111.70  3.000
 EY4  H8   C16  C15  111.16  3.000
 EY4  C17  C16  C15  106.33  3.000
 EY4  H10  C17  C20  107.41  3.000
 EY4  H10  C17  C16  109.59  3.000
 EY4  C20  C17  C16  114.85  3.000
 EY4  H10  C17  C13  106.48  3.000
 EY4  C20  C17  C13  114.66  3.000
 EY4  C16  C17  C13  103.51  3.000
 EY4  H13  C18  H12  107.58  3.000
 EY4  H13  C18  H11  106.64  3.000
 EY4  H12  C18  H11  106.96  3.000
 EY4  H13  C18  C13  111.02  3.000
 EY4  H12  C18  C13  112.42  3.000
 EY4  H11  C18  C13  111.91  3.000
 EY4  H16  C19  H15  106.50  3.000
 EY4  H16  C19  H14  107.25  3.000
 EY4  H15  C19  H14  107.11  3.000
 EY4  H16  C19  C10  112.46  3.000
 EY4  H15  C19  C10  112.16  3.000
 EY4  H14  C19  C10  111.04  3.000
 EY4  H18  C2   H17  105.54  3.000
 EY4  H18  C2   C3   109.97  3.000
 EY4  H17  C2   C3   108.41  3.000
 EY4  H18  C2   C1   109.70  3.000
 EY4  H17  C2   C1   110.08  3.000
 EY4  C3   C2   C1   112.88  3.000
 EY4  O20  C20  C21  121.67  3.000
 EY4  C21  C20  C17  116.01  3.000
 EY4  O20  C20  C17  122.31  3.000
 EY4  H21  C21  H20  109.01  3.000
 EY4  H21  C21  H19  106.20  3.000
 EY4  H20  C21  H19  109.42  3.000
 EY4  H21  C21  C20  108.89  3.000
 EY4  H20  C21  C20  111.85  3.000
 EY4  H19  C21  C20  111.29  3.000
 EY4  H22  C3   O3   109.74  3.000
 EY4  H22  C3   C4   108.92  3.000
 EY4  O3   C3   C4   107.61  3.000
 EY4  H22  C3   C2   108.75  3.000
 EY4  O3   C3   C2   111.84  3.000
 EY4  C4   C3   C2   109.95  3.000
 EY4  H24  C4   H23  105.79  3.000
 EY4  H24  C4   C5   109.11  3.000
 EY4  H23  C4   C5   110.67  3.000
 EY4  H24  C4   C3   109.63  3.000
 EY4  H23  C4   C3   108.62  3.000
 EY4  C5   C4   C3   112.79  3.000
 EY4  H25  C5   C6   106.45  3.000
 EY4  H25  C5   C4   106.93  3.000
 EY4  C6   C5   C4   111.63  3.000
 EY4  H25  C5   C10  106.18  3.000
 EY4  C6   C5   C10  112.11  3.000
 EY4  C4   C5   C10  113.02  3.000
 EY4  H27  C6   H26  106.14  3.000
 EY4  H27  C6   C7   109.47  3.000
 EY4  H26  C6   C7   110.57  3.000
 EY4  H27  C6   C5   109.48  3.000
 EY4  H26  C6   C5   110.43  3.000
 EY4  C7   C6   C5   110.65  3.000
 EY4  H29  C7   H28  106.29  3.000
 EY4  H29  C7   C8   108.96  3.000
 EY4  H28  C7   C8   109.10  3.000
 EY4  H29  C7   C6   109.08  3.000
 EY4  H28  C7   C6   110.24  3.000
 EY4  C8   C7   C6   112.94  3.000
 EY4  H30  C8   C9   109.02  3.000
 EY4  H30  C8   C7   107.55  3.000
 EY4  C9   C8   C7   111.15  3.000
 EY4  H30  C8   C14  109.36  3.000
 EY4  C7   C8   C14  110.72  3.000
 EY4  C9   C8   C14  108.99  3.000
 EY4  H31  C9   C8   105.26  3.000
 EY4  H31  C9   C11  104.31  3.000
 EY4  C8   C9   C11  109.25  3.000
 EY4  H31  C9   C10  106.40  3.000
 EY4  C8   C9   C10  113.63  3.000
 EY4  C11  C9   C10  116.86  3.000
 EY4  H32  O3   C3   108.13  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
 EY4  Var_01  C3   C2   C1   C10  -56.69  30.0  1
 EY4  Var_02  C9   C11  C12  C13  -57.37  30.0  1
 EY4  Var_03  C17  C16  C15  C14    7.44  30.0  1
 EY4  Var_04  C8   C7   C6   C5    54.11  30.0  1
 EY4  Var_05  H19  C21  C20  C17   48.98  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
 EY4  chir_01  C10  C1   C5   C9   negativ
 EY4  chir_02  C13  C14  C12  C17  positiv
 EY4  chir_03  C14  C8   C13  C15  negativ
 EY4  chir_04  C17  C20  C16  C13  negativ
 EY4  chir_05  C3   O3   C2   C4   positiv
 EY4  chir_06  C5   C4   C10  C6   negativ
 EY4  chir_07  C8   C14  C7   C9   positiv
 EY4  chir_08  C9   C10  C11  C8   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
 EY4  plan-1  C11  0.020
 EY4  plan-1  C12  0.020
 EY4  plan-1  C9   0.020
 EY4  plan-1  O11  0.020
 EY4  plan-2  C17  0.020
 EY4  plan-2  C20  0.020
 EY4  plan-2  C21  0.020
 EY4  plan-2  O20  0.020

