# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 14:02:31 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (8~{R},9~{S},10~{R},13~{S},14~{S},17~{S})-13-methyl-17-oxidanyl-2,6,7,8,9,10,11,12,14,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC[C@H]3[C@@H](CCC4=CC(=O)CC[C@H]34)[C@@H]1CC[C@@H]2O
#
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
 6VW  6VW  (8~{R},9~{S},10~{R},13~{S},14~{S},17~{S})-13-methyl-17-oxidanyl-2,6,7,8,9,10,11,12,14,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-one  ligand  46  20  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_6VW
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
 6VW  C6   C  CH2   0  -0.567   4.1014   1.4067  -0.2011
 6VW  C2   C  C1    0  -0.461   3.7231  -1.0428   0.1727
 6VW  C4   C  CH1   0  -0.283   1.7756   0.4099  -0.4392
 6VW  C5   C  CH2   0  -0.460   2.6208   1.5570   0.1139
 6VW  C1   C  C     0   0.402   4.6331   0.0927   0.3001
 6VW  O1   O  O     0  -0.441   5.7689  -0.0389   0.7243
 6VW  C3   C  C     0   0.224   2.4485  -0.9227  -0.2365
 6VW  C10  C  CH2   0  -0.504   1.6339  -2.1386  -0.5463
 6VW  C11  C  CH2   0  -0.419   0.2482  -2.0947   0.0874
 6VW  C12  C  CH1   0  -0.229  -0.4683  -0.8032  -0.2772
 6VW  C13  C  CH1   0  -0.202   0.3595   0.4094   0.1791
 6VW  C16  C  CH1   0  -0.191  -1.8483  -0.7078   0.3472
 6VW  C17  C  CT    0  -0.104  -2.6049   0.5636  -0.0594
 6VW  C18  C  CH2   0  -0.404  -1.8050   1.7695   0.4200
 6VW  C19  C  CH2   0  -0.444  -0.3641   1.7339  -0.0964
 6VW  C24  C  CH2   0  -0.450  -2.8573  -1.8377   0.1213
 6VW  C25  C  CH2   0  -0.487  -4.2258  -1.1753   0.4018
 6VW  C26  C  CH1   0   0.102  -3.9225   0.3133   0.6781
 6VW  C27  C  CH3   0  -0.670  -2.8540   0.6496  -1.5681
 6VW  O27  O  OH1   0  -0.675  -4.9338   1.2054   0.2773
 6VW  H1   H  HCH2  0   0.263   4.2550   1.4288  -1.2867
 6VW  H2   H  HCH2  0   0.262   4.6825   2.2295   0.2179
 6VW  H3   H  H     0   0.249   4.1403  -2.0277   0.3580
 6VW  H5   H  HCH1  0   0.251   1.6562   0.5459  -1.5254
 6VW  H6   H  HCH2  0   0.232   2.4877   1.6036   1.1999
 6VW  H7   H  HCH2  0   0.254   2.2690   2.5088  -0.2830
 6VW  H9   H  HCH2  0   0.251   1.5139  -2.1856  -1.6357
 6VW  H10  H  HCH2  0   0.252   2.1726  -3.0413  -0.2533
 6VW  H11  H  HCH2  0   0.244  -0.3251  -2.9601  -0.2527
 6VW  H12  H  HCH2  0   0.220   0.3328  -2.1793   1.1764
 6VW  H13  H  HCH1  0   0.215  -0.5643  -0.7738  -1.3715
 6VW  H14  H  HCH1  0   0.213   0.4851   0.3135   1.2683
 6VW  H15  H  HCH1  0   0.214  -1.6903  -0.6344   1.4342
 6VW  H16  H  HCH2  0   0.225  -2.2771   2.7061   0.1092
 6VW  H17  H  HCH2  0   0.213  -1.7950   1.7745   1.5162
 6VW  H18  H  HCH2  0   0.242   0.1843   2.5593   0.3616
 6VW  H19  H  HCH2  0   0.215  -0.3451   1.9263  -1.1744
 6VW  H20  H  HCH2  0   0.222  -2.8073  -2.2086  -0.9057
 6VW  H21  H  HCH2  0   0.233  -2.6650  -2.6902   0.7734
 6VW  H22  H  HCH2  0   0.228  -4.8870  -1.2597  -0.4633
 6VW  H23  H  HCH2  0   0.233  -4.7454  -1.6391   1.2419
 6VW  H24  H  HCH1  0   0.195  -3.7201   0.4360   1.7539
 6VW  H25  H  HCH3  0   0.232  -3.4394   1.5377  -1.8087
 6VW  H26  H  HCH3  0   0.229  -1.9268   0.7149  -2.1366
 6VW  H27  H  HCH3  0   0.230  -3.3988  -0.2134  -1.9533
 6VW  H28  H  HOH1  0   0.447  -5.7201   1.0203   0.7995

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
 6VW  O27  C26  single  1.407  0.020  1.407
 6VW  C18  C19  single  1.531  0.020  1.531
 6VW  C18  C17  single  1.524  0.020  1.524
 6VW  C19  C13  single  1.534  0.020  1.534
 6VW  C27  C17  single  1.532  0.020  1.532
 6VW  C17  C26  single  1.531  0.020  1.531
 6VW  C17  C16  single  1.534  0.020  1.534
 6VW  C26  C25  single  1.544  0.020  1.544
 6VW  C5   C6   single  1.521  0.020  1.521
 6VW  C5   C4   single  1.528  0.020  1.528
 6VW  C6   C1   single  1.503  0.020  1.503
 6VW  C13  C4   single  1.545  0.020  1.545
 6VW  C13  C12  single  1.537  0.020  1.537
 6VW  C4   C3   single  1.506  0.020  1.506
 6VW  C25  C24  single  1.546  0.020  1.546
 6VW  C16  C12  single  1.518  0.020  1.518
 6VW  C16  C24  single  1.532  0.020  1.532
 6VW  C12  C11  single  1.521  0.020  1.521
 6VW  C1   O1   double  1.219  0.020  1.219
 6VW  C1   C2   single  1.461  0.020  1.461
 6VW  C3   C2   double  1.344  0.020  1.344
 6VW  C3   C10  single  1.496  0.020  1.496
 6VW  C11  C10  single  1.524  0.020  1.524
 6VW  C6   H1   single  0.970  0.020  1.090
 6VW  C6   H2   single  0.970  0.020  1.090
 6VW  C2   H3   single  0.930  0.020  1.080
 6VW  C4   H5   single  0.970  0.020  1.090
 6VW  C5   H6   single  0.970  0.020  1.090
 6VW  C5   H7   single  0.970  0.020  1.090
 6VW  C10  H9   single  0.970  0.020  1.090
 6VW  C10  H10  single  0.970  0.020  1.090
 6VW  C11  H11  single  0.970  0.020  1.090
 6VW  C11  H12  single  0.970  0.020  1.090
 6VW  C12  H13  single  0.970  0.020  1.090
 6VW  C13  H14  single  0.970  0.020  1.090
 6VW  C16  H15  single  0.970  0.020  1.090
 6VW  C18  H16  single  0.970  0.020  1.090
 6VW  C18  H17  single  0.970  0.020  1.090
 6VW  C19  H18  single  0.970  0.020  1.090
 6VW  C19  H19  single  0.970  0.020  1.090
 6VW  C24  H20  single  0.970  0.020  1.090
 6VW  C24  H21  single  0.970  0.020  1.090
 6VW  C25  H22  single  0.970  0.020  1.090
 6VW  C25  H23  single  0.970  0.020  1.090
 6VW  C26  H24  single  0.970  0.020  1.090
 6VW  C27  H25  single  0.970  0.020  1.090
 6VW  C27  H26  single  0.970  0.020  1.090
 6VW  C27  H27  single  0.970  0.020  1.090
 6VW  O27  H28  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
 6VW  H2   C6   H1   106.88  3.000
 6VW  H2   C6   C1   110.05  3.000
 6VW  H1   C6   C1   107.34  3.000
 6VW  H2   C6   C5   111.37  3.000
 6VW  H1   C6   C5   109.83  3.000
 6VW  C1   C6   C5   111.19  3.000
 6VW  H3   C2   C3   119.84  3.000
 6VW  H3   C2   C1   116.80  3.000
 6VW  C3   C2   C1   123.22  3.000
 6VW  H5   C4   C13  107.18  3.000
 6VW  H5   C4   C3   106.88  3.000
 6VW  C13  C4   C3   110.81  3.000
 6VW  H5   C4   C5   108.92  3.000
 6VW  C3   C4   C5   111.60  3.000
 6VW  C13  C4   C5   111.24  3.000
 6VW  H7   C5   H6   106.54  3.000
 6VW  H7   C5   C4   110.20  3.000
 6VW  H6   C5   C4   108.88  3.000
 6VW  H7   C5   C6   108.97  3.000
 6VW  H6   C5   C6   109.14  3.000
 6VW  C4   C5   C6   112.90  3.000
 6VW  O1   C1   C2   121.78  3.000
 6VW  C2   C1   C6   115.46  3.000
 6VW  O1   C1   C6   122.66  3.000
 6VW  C10  C3   C4   116.61  3.000
 6VW  C10  C3   C2   120.45  3.000
 6VW  C4   C3   C2   122.93  3.000
 6VW  H10  C10  H9   106.57  3.000
 6VW  H10  C10  C11  111.16  3.000
 6VW  H9   C10  C11  108.34  3.000
 6VW  H10  C10  C3   110.36  3.000
 6VW  H9   C10  C3   107.46  3.000
 6VW  C11  C10  C3   112.68  3.000
 6VW  H12  C11  H11  106.79  3.000
 6VW  H12  C11  C12  109.89  3.000
 6VW  H11  C11  C12  110.53  3.000
 6VW  H12  C11  C10  109.93  3.000
 6VW  H11  C11  C10  108.96  3.000
 6VW  C12  C11  C10  110.67  3.000
 6VW  H13  C12  C16  109.18  3.000
 6VW  H13  C12  C13  108.75  3.000
 6VW  C16  C12  C13  108.54  3.000
 6VW  H13  C12  C11  107.61  3.000
 6VW  C16  C12  C11  112.52  3.000
 6VW  C13  C12  C11  110.17  3.000
 6VW  H14  C13  C19  107.86  3.000
 6VW  H14  C13  C12  106.64  3.000
 6VW  C19  C13  C12  111.94  3.000
 6VW  H14  C13  C4   106.94  3.000
 6VW  C12  C13  C4   112.02  3.000
 6VW  C19  C13  C4   111.11  3.000
 6VW  H15  C16  C24  106.82  3.000
 6VW  H15  C16  C17  106.09  3.000
 6VW  C24  C16  C17  104.32  3.000
 6VW  H15  C16  C12  106.26  3.000
 6VW  C24  C16  C12  119.47  3.000
 6VW  C17  C16  C12  113.04  3.000
 6VW  C27  C17  C26  110.11  3.000
 6VW  C26  C17  C18  115.44  3.000
 6VW  C27  C17  C18  110.53  3.000
 6VW  C26  C17  C16   99.28  3.000
 6VW  C27  C17  C16  112.82  3.000
 6VW  C18  C17  C16  108.27  3.000
 6VW  H17  C18  H16  106.51  3.000
 6VW  H17  C18  C19  109.19  3.000
 6VW  H16  C18  C19  109.28  3.000
 6VW  H17  C18  C17  108.84  3.000
 6VW  H16  C18  C17  111.20  3.000
 6VW  C19  C18  C17  111.67  3.000
 6VW  H19  C19  H18  105.75  3.000
 6VW  H19  C19  C18  110.14  3.000
 6VW  H18  C19  C18  108.28  3.000
 6VW  H19  C19  C13  108.68  3.000
 6VW  H18  C19  C13  109.90  3.000
 6VW  C18  C19  C13  113.79  3.000
 6VW  H21  C24  H20  106.77  3.000
 6VW  H21  C24  C25  112.49  3.000
 6VW  H20  C24  C25  110.87  3.000
 6VW  H21  C24  C16  111.86  3.000
 6VW  H20  C24  C16  111.03  3.000
 6VW  C25  C24  C16  103.91  3.000
 6VW  H23  C25  H22  106.78  3.000
 6VW  H23  C25  C26  111.44  3.000
 6VW  H22  C25  C26  109.58  3.000
 6VW  H23  C25  C24  112.28  3.000
 6VW  H22  C25  C24  111.05  3.000
 6VW  C26  C25  C24  105.76  3.000
 6VW  H24  C26  O27  109.86  3.000
 6VW  H24  C26  C25  108.55  3.000
 6VW  O27  C26  C25  114.78  3.000
 6VW  H24  C26  C17  107.11  3.000
 6VW  C25  C26  C17  103.92  3.000
 6VW  O27  C26  C17  112.20  3.000
 6VW  H27  C27  H26  106.75  3.000
 6VW  H27  C27  H25  107.36  3.000
 6VW  H26  C27  H25  107.03  3.000
 6VW  H27  C27  C17  112.62  3.000
 6VW  H26  C27  C17  112.27  3.000
 6VW  H25  C27  C17  110.51  3.000
 6VW  H28  O27  C26  108.12  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
 6VW  Var_01  C3   C2   C1   C6    -6.42  30.0  1
 6VW  Var_02  C5   C6   C1   C2    37.60  30.0  1
 6VW  Var_03  C11  C10  C3   C2   133.02  30.0  1
 6VW  Var_04  C1   C6   C5   C4   -55.99  30.0  1
 6VW  Var_05  C1   C2   C3   C4    -7.95  30.0  1
 6VW  Var_06  C12  C11  C10  C3    52.97  30.0  1
 6VW  Var_07  C17  C18  C19  C13  -51.62  30.0  1
 6VW  Var_08  C26  C25  C24  C16    3.67  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
 6VW  chir_01  C4   C5   C13  C3   positiv
 6VW  chir_02  C12  C11  C16  C13  negativ
 6VW  chir_03  C13  C12  C4   C19  negativ
 6VW  chir_04  C16  C17  C12  C24  positiv
 6VW  chir_05  C17  C26  C16  C18  positiv
 6VW  chir_06  C26  O27  C17  C25  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
 6VW  plan-1  C6  0.020
 6VW  plan-1  C2  0.020
 6VW  plan-1  C1  0.020
 6VW  plan-1  O1  0.020

