# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 15:22:23 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: (5alpha,8alpha,10alpha,14beta,17alpha)-pregnane-3,20-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]4CC(=O)CC[C@]4(C)[C@H]3CC[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
 CI2  CI2  (5alpha,8alpha,10alpha,14beta,17alpha)-pregnane-3,20-dione  ligand  55  23  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CI2
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
 CI2  C1   C  CH3   0  -0.779   4.7027   2.0707  -1.1889
 CI2  C2   C  C     0   0.407   4.5855   0.7268  -0.5240
 CI2  O3   O  O     0  -0.409   5.4486   0.3128   0.2203
 CI2  C4   C  CH1   0  -0.349   3.3491  -0.0708  -0.8566
 CI2  C5   C  CH2   0  -0.432   3.5231  -1.6025  -0.8258
 CI2  C6   C  CH2   0  -0.448   2.1597  -2.1791  -0.3800
 CI2  C7   C  CH1   0  -0.172   1.2321  -0.9673  -0.3643
 CI2  C8   C  CH1   0  -0.226  -0.0830  -1.0514   0.3940
 CI2  C9   C  CH2   0  -0.427  -0.9507  -2.2006  -0.1154
 CI2  C10  C  CH2   0  -0.435  -2.3158  -2.2373   0.5643
 CI2  C11  C  CH1   0  -0.214  -3.0505  -0.8990   0.4795
 CI2  C12  C  CH2   0  -0.564  -3.5664  -0.6687  -0.9527
 CI2  C13  C  C     0   0.422  -4.1903   0.6827  -1.1704
 CI2  O14  O  O     0  -0.412  -5.2487   0.8269  -1.7450
 CI2  C15  C  CH2   0  -0.562  -3.3932   1.8385  -0.6334
 CI2  C16  C  CH2   0  -0.439  -2.9763   1.5695   0.8117
 CI2  C17  C  CT    0  -0.074  -2.1847   0.2683   1.0069
 CI2  C18  C  CH3   0  -0.665  -1.9817   0.0998   2.5175
 CI2  C19  C  CH1   0  -0.198  -0.8315   0.2884   0.2498
 CI2  C20  C  CH2   0  -0.439   0.0484   1.4932   0.6021
 CI2  C21  C  CH2   0  -0.415   1.3957   1.4951  -0.1242
 CI2  C22  C  CT    0  -0.054   2.1430   0.1856   0.0919
 CI2  C23  C  CH3   0  -0.680   2.5793   0.0506   1.5546
 CI2  H24  H  HCH3  0   0.256   5.4567   2.6948  -0.7130
 CI2  H25  H  HCH3  0   0.271   4.9897   1.9137  -2.2324
 CI2  H26  H  HCH3  0   0.260   3.7491   2.5977  -1.2126
 CI2  H27  H  HCH1  0   0.251   3.0215   0.2348  -1.8570
 CI2  H28  H  HCH2  0   0.240   3.8124  -1.9672  -1.8118
 CI2  H29  H  HCH2  0   0.234   4.3174  -1.8931  -0.1387
 CI2  H30  H  HCH2  0   0.235   1.8059  -2.9647  -1.0487
 CI2  H31  H  HCH2  0   0.221   2.2287  -2.6240   0.6161
 CI2  H32  H  HCH1  0   0.211   0.9714  -0.7475  -1.4119
 CI2  H33  H  HCH1  0   0.212   0.1293  -1.2386   1.4531
 CI2  H34  H  HCH2  0   0.208  -1.0691  -2.1039  -1.2013
 CI2  H35  H  HCH2  0   0.237  -0.4436  -3.1548   0.0477
 CI2  H36  H  HCH2  0   0.230  -2.9339  -3.0230   0.1200
 CI2  H37  H  HCH2  0   0.230  -2.1881  -2.5162   1.6138
 CI2  H38  H  HCH1  0   0.231  -3.9354  -0.9534   1.1255
 CI2  H39  H  HCH2  0   0.261  -2.7441  -0.7486  -1.6728
 CI2  H40  H  HCH2  0   0.261  -4.2860  -1.4466  -1.2158
 CI2  H41  H  HCH2  0   0.260  -2.5077   1.9625  -1.2661
 CI2  H42  H  HCH2  0   0.262  -3.9736   2.7592  -0.7090
 CI2  H43  H  HCH2  0   0.247  -2.4165   2.4251   1.1941
 CI2  H44  H  HCH2  0   0.236  -3.8797   1.5120   1.4293
 CI2  H45  H  HCH3  0   0.227  -2.9460   0.1193   3.0307
 CI2  H46  H  HCH3  0   0.234  -1.4973  -0.8374   2.7864
 CI2  H47  H  HCH3  0   0.231  -1.3814   0.9080   2.9365
 CI2  H48  H  HCH1  0   0.211  -1.0505   0.3856  -0.8241
 CI2  H49  H  HCH2  0   0.235  -0.4704   2.4181   0.3390
 CI2  H50  H  HCH2  0   0.222   0.2164   1.5431   1.6813
 CI2  H51  H  HCH2  0   0.217   1.2315   1.6384  -1.1987
 CI2  H52  H  HCH2  0   0.226   1.9799   2.3529   0.2210
 CI2  H53  H  HCH3  0   0.237   1.7325  -0.0701   2.2284
 CI2  H54  H  HCH3  0   0.240   3.2444  -0.7974   1.7176
 CI2  H55  H  HCH3  0   0.230   3.1148   0.9442   1.8817

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
 CI2  C1   C2   single  1.504  0.020  1.504
 CI2  C1   H24  single  0.970  0.020  1.090
 CI2  C1   H25  single  0.970  0.020  1.090
 CI2  C1   H26  single  0.970  0.020  1.090
 CI2  C2   O3   double  1.213  0.020  1.213
 CI2  C2   C4   single  1.508  0.020  1.508
 CI2  C4   C5   single  1.542  0.020  1.542
 CI2  C4   C22  single  1.556  0.020  1.556
 CI2  C4   H27  single  0.970  0.020  1.090
 CI2  C5   C6   single  1.546  0.020  1.546
 CI2  C5   H28  single  0.970  0.020  1.090
 CI2  C5   H29  single  0.970  0.020  1.090
 CI2  C6   C7   single  1.526  0.020  1.526
 CI2  C6   H30  single  0.970  0.020  1.090
 CI2  C6   H31  single  0.970  0.020  1.090
 CI2  C7   C8   single  1.520  0.020  1.520
 CI2  C7   C22  single  1.538  0.020  1.538
 CI2  C7   H32  single  0.970  0.020  1.090
 CI2  C8   C9   single  1.527  0.020  1.527
 CI2  C8   C19  single  1.541  0.020  1.541
 CI2  C8   H33  single  0.970  0.020  1.090
 CI2  C9   C10  single  1.525  0.020  1.525
 CI2  C9   H34  single  0.970  0.020  1.090
 CI2  C9   H35  single  0.970  0.020  1.090
 CI2  C10  C11  single  1.529  0.020  1.529
 CI2  C10  H36  single  0.970  0.020  1.090
 CI2  C10  H37  single  0.970  0.020  1.090
 CI2  C11  C12  single  1.540  0.020  1.540
 CI2  C11  C17  single  1.546  0.020  1.546
 CI2  C11  H38  single  0.970  0.020  1.090
 CI2  C12  C13  single  1.504  0.020  1.504
 CI2  C12  H39  single  0.970  0.020  1.090
 CI2  C12  H40  single  0.970  0.020  1.090
 CI2  C13  O14  double  1.213  0.020  1.213
 CI2  C13  C15  single  1.503  0.020  1.503
 CI2  C15  C16  single  1.528  0.020  1.528
 CI2  C15  H41  single  0.970  0.020  1.090
 CI2  C15  H42  single  0.970  0.020  1.090
 CI2  C16  C17  single  1.535  0.020  1.535
 CI2  C16  H43  single  0.970  0.020  1.090
 CI2  C16  H44  single  0.970  0.020  1.090
 CI2  C17  C18  single  1.533  0.020  1.533
 CI2  C17  C19  single  1.551  0.020  1.551
 CI2  C18  H45  single  0.970  0.020  1.090
 CI2  C18  H46  single  0.970  0.020  1.090
 CI2  C18  H47  single  0.970  0.020  1.090
 CI2  C19  C20  single  1.533  0.020  1.533
 CI2  C19  H48  single  0.970  0.020  1.090
 CI2  C20  C21  single  1.531  0.020  1.531
 CI2  C20  H49  single  0.970  0.020  1.090
 CI2  C20  H50  single  0.970  0.020  1.090
 CI2  C21  C22  single  1.523  0.020  1.523
 CI2  C21  H51  single  0.970  0.020  1.090
 CI2  C21  H52  single  0.970  0.020  1.090
 CI2  C22  C23  single  1.532  0.020  1.532
 CI2  C23  H53  single  0.970  0.020  1.090
 CI2  C23  H54  single  0.970  0.020  1.090
 CI2  C23  H55  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
 CI2  H26  C1   H25  106.16  3.000
 CI2  H26  C1   H24  109.78  3.000
 CI2  H25  C1   H24  108.52  3.000
 CI2  H26  C1   C2   111.94  3.000
 CI2  H25  C1   C2   108.30  3.000
 CI2  H24  C1   C2   111.90  3.000
 CI2  C4   C2   O3   122.56  3.000
 CI2  C4   C2   C1   116.03  3.000
 CI2  O3   C2   C1   121.40  3.000
 CI2  H27  C4   C22  106.18  3.000
 CI2  H27  C4   C5   109.20  3.000
 CI2  C22  C4   C5   103.83  3.000
 CI2  H27  C4   C2   107.38  3.000
 CI2  C22  C4   C2   114.45  3.000
 CI2  C5   C4   C2   115.37  3.000
 CI2  H29  C5   H28  106.72  3.000
 CI2  H29  C5   C6   111.19  3.000
 CI2  H28  C5   C6   111.72  3.000
 CI2  H29  C5   C4   111.09  3.000
 CI2  H28  C5   C4   110.13  3.000
 CI2  C6   C5   C4   106.07  3.000
 CI2  H31  C6   H30  106.62  3.000
 CI2  H31  C6   C7   110.62  3.000
 CI2  H30  C6   C7   112.40  3.000
 CI2  H31  C6   C5   111.04  3.000
 CI2  H30  C6   C5   112.20  3.000
 CI2  C7   C6   C5   104.05  3.000
 CI2  H32  C7   C22  105.81  3.000
 CI2  H32  C7   C8   106.30  3.000
 CI2  C22  C7   C8   113.93  3.000
 CI2  H32  C7   C6   107.01  3.000
 CI2  C22  C7   C6   103.78  3.000
 CI2  C8   C7   C6   119.14  3.000
 CI2  H33  C8   C19  109.45  3.000
 CI2  H33  C8   C9   107.69  3.000
 CI2  C19  C8   C9   110.30  3.000
 CI2  H33  C8   C7   108.89  3.000
 CI2  C19  C8   C7   108.98  3.000
 CI2  C9   C8   C7   111.51  3.000
 CI2  H35  C9   H34  105.96  3.000
 CI2  H35  C9   C10  109.13  3.000
 CI2  H34  C9   C10  110.29  3.000
 CI2  H35  C9   C8   110.09  3.000
 CI2  H34  C9   C8   108.98  3.000
 CI2  C10  C9   C8   112.20  3.000
 CI2  H37  C10  H36  105.82  3.000
 CI2  H37  C10  C11  109.44  3.000
 CI2  H36  C10  C11  109.55  3.000
 CI2  H37  C10  C9   109.22  3.000
 CI2  H36  C10  C9   109.99  3.000
 CI2  C11  C10  C9   112.59  3.000
 CI2  H38  C11  C17  106.75  3.000
 CI2  H38  C11  C12  106.55  3.000
 CI2  C17  C11  C12  113.08  3.000
 CI2  H38  C11  C10  108.15  3.000
 CI2  C17  C11  C10  111.89  3.000
 CI2  C12  C11  C10  110.09  3.000
 CI2  H40  C12  H39  106.52  3.000
 CI2  H40  C12  C13  109.38  3.000
 CI2  H39  C12  C13  106.35  3.000
 CI2  H40  C12  C11  109.78  3.000
 CI2  H39  C12  C11  110.42  3.000
 CI2  C13  C12  C11  114.08  3.000
 CI2  C15  C13  O14  122.72  3.000
 CI2  C15  C13  C12  114.78  3.000
 CI2  O14  C13  C12  122.49  3.000
 CI2  H42  C15  H41  107.13  3.000
 CI2  H42  C15  C16  111.05  3.000
 CI2  H41  C15  C16  110.22  3.000
 CI2  H42  C15  C13  110.00  3.000
 CI2  H41  C15  C13  108.02  3.000
 CI2  C16  C15  C13  110.32  3.000
 CI2  H44  C16  H43  105.45  3.000
 CI2  H44  C16  C17  108.00  3.000
 CI2  H43  C16  C17  110.81  3.000
 CI2  H44  C16  C15  108.50  3.000
 CI2  H43  C16  C15  109.46  3.000
 CI2  C17  C16  C15  114.21  3.000
 CI2  C19  C17  C18  111.52  3.000
 CI2  C19  C17  C16  112.14  3.000
 CI2  C18  C17  C16  106.66  3.000
 CI2  C19  C17  C11  109.38  3.000
 CI2  C18  C17  C11  109.10  3.000
 CI2  C16  C17  C11  107.92  3.000
 CI2  H47  C18  H46  107.34  3.000
 CI2  H47  C18  H45  106.98  3.000
 CI2  H46  C18  H45  106.98  3.000
 CI2  H47  C18  C17  111.71  3.000
 CI2  H46  C18  C17  113.38  3.000
 CI2  H45  C18  C17  110.12  3.000
 CI2  H48  C19  C20  105.61  3.000
 CI2  H48  C19  C17  107.70  3.000
 CI2  C20  C19  C17  113.50  3.000
 CI2  H48  C19  C8   105.35  3.000
 CI2  C20  C19  C8   112.51  3.000
 CI2  C17  C19  C8   111.52  3.000
 CI2  H50  C20  H49  105.78  3.000
 CI2  H50  C20  C21  109.45  3.000
 CI2  H49  C20  C21  107.62  3.000
 CI2  H50  C20  C19  110.54  3.000
 CI2  H49  C20  C19  109.72  3.000
 CI2  C21  C20  C19  113.40  3.000
 CI2  H52  C21  H51  106.66  3.000
 CI2  H52  C21  C22  111.56  3.000
 CI2  H51  C21  C22  108.96  3.000
 CI2  H52  C21  C20  108.75  3.000
 CI2  H51  C21  C20  109.48  3.000
 CI2  C22  C21  C20  111.32  3.000
 CI2  C23  C22  C21  110.54  3.000
 CI2  C23  C22  C7   112.68  3.000
 CI2  C21  C22  C7   108.16  3.000
 CI2  C23  C22  C4   110.28  3.000
 CI2  C21  C22  C4   115.83  3.000
 CI2  C7   C22  C4    98.90  3.000
 CI2  H55  C23  H54  107.01  3.000
 CI2  H55  C23  H53  106.66  3.000
 CI2  H54  C23  H53  107.20  3.000
 CI2  H55  C23  C22  110.71  3.000
 CI2  H54  C23  C22  112.65  3.000
 CI2  H53  C23  C22  112.27  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
 CI2  Var_01  C7   C6   C5   C4     7.42  30.0  1
 CI2  Var_02  C11  C10  C9   C8    53.19  30.0  1
 CI2  Var_03  C15  C13  C12  C11   46.94  30.0  1
 CI2  Var_04  C16  C15  C13  C12  -49.44  30.0  1
 CI2  Var_05  C17  C16  C15  C13   56.25  30.0  1
 CI2  Var_06  C22  C21  C20  C19  -53.72  30.0  1
 CI2  Var_07  H24  C1   C2   C4   164.60  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
 CI2  chir_01  C4   C2   C5   C22  negativ
 CI2  chir_02  C7   C22  C8   C6   positiv
 CI2  chir_03  C8   C7   C9   C19  positiv
 CI2  chir_04  C11  C10  C12  C17  positiv
 CI2  chir_05  C17  C19  C16  C11  negativ
 CI2  chir_06  C19  C8   C17  C20  negativ
 CI2  chir_07  C22  C21  C7   C4   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
 CI2  plan-1  C1   0.020
 CI2  plan-1  C2   0.020
 CI2  plan-1  O3   0.020
 CI2  plan-1  C4   0.020
 CI2  plan-2  C12  0.020
 CI2  plan-2  C13  0.020
 CI2  plan-2  O14  0.020
 CI2  plan-2  C15  0.020

