# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 04:22:42 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (8R,9S,10R,13S,14S,17R)-17-ethynyl-17-hydroxy-13-methyl-1,2,6,7,8,9,10,11,12,14,15,16-dodecahydrocyclopenta[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@@]2(O)C#C
#
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
 NDR  NDR  (8R,9S,10R,13S,14S,17R)-17-ethynyl-17-hydroxy-13-methyl-1,2,6,7,8,9,10,11,12,14,15,16-dodecahydrocyclopenta[a]phenanthren-3-one  ligand  48  22  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NDR
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
 NDR  O22   O  O     0  -0.441  -6.0140   0.4481  -0.9351
 NDR  C21   C  C     0   0.402  -4.9157   0.3831  -0.4088
 NDR  C20   C  CH2   0  -0.567  -4.3795   1.4679   0.4836
 NDR  C19   C  C1    0  -0.461  -4.0685  -0.7997  -0.5414
 NDR  C17   C  C     0   0.225  -2.8334  -0.8823  -0.0179
 NDR  C15   C  CH2   0  -0.506  -2.1007  -2.1861   0.0071
 NDR  C14   C  CH1   0  -0.284  -2.1314   0.2926   0.6111
 NDR  C18   C  CH2   0  -0.460  -2.8711   1.6025   0.3443
 NDR  C8    C  CH1   0  -0.200  -0.6649   0.3720   0.1351
 NDR  C3    C  CH1   0  -0.235   0.0712  -0.9672   0.3049
 NDR  C9    C  CH2   0  -0.417  -0.6557  -2.0627  -0.4625
 NDR  C13   C  CH2   0  -0.442   0.0824   1.5266   0.8122
 NDR  C6    C  CH2   0  -0.416   1.5483   1.6251   0.3836
 NDR  C2    C  CT    0  -0.093   2.2703   0.2983   0.5816
 NDR  C1    C  CH1   0  -0.195   1.5049  -0.7970  -0.1716
 NDR  C7    C  CH3   0  -0.672   2.4082  -0.0020   2.0793
 NDR  C5    C  CT    0   0.164   3.6665   0.1589  -0.0795
 NDR  O12   O  OH1   0  -0.662   4.6379   0.8398   0.6755
 NDR  C10   C  CH2   0  -0.489   3.8646  -1.3825  -0.1340
 NDR  C4    C  CH2   0  -0.443   2.4491  -2.0003  -0.1497
 NDR  C11   C  CSP   0   0.343   3.6679   0.6945  -1.4529
 NDR  C16   C  CSP1  0  -0.624   3.7298   1.1198  -2.5763
 NDR  H201  H  HCH2  0   0.262  -4.8841   2.4106   0.2678
 NDR  H202  H  HCH2  0   0.263  -4.6340   1.1956   1.5150
 NDR  H19   H  H     0   0.249  -4.5105  -1.6647  -1.0257
 NDR  H151  H  HCH2  0   0.251  -2.0947  -2.5336   1.0479
 NDR  H152  H  HCH2  0   0.254  -2.6402  -2.9384  -0.5705
 NDR  H181  H  HCH2  0   0.233  -2.6315   1.9444  -0.6683
 NDR  H182  H  HCH2  0   0.253  -2.5207   2.3788   1.0241
 NDR  H91   H  HCH2  0   0.244  -0.1559  -3.0240  -0.3252
 NDR  H92   H  HCH2  0   0.221  -0.6272  -1.8424  -1.5353
 NDR  H131  H  HCH2  0   0.243  -0.4006   2.4747   0.5692
 NDR  H132  H  HCH2  0   0.219   0.0037   1.4191   1.8993
 NDR  H61   H  HCH2  0   0.227   1.5854   1.9081  -0.6729
 NDR  H62   H  HCH2  0   0.230   2.0413   2.4288   0.9377
 NDR  H71   H  HCH3  0   0.235   1.4394  -0.1852   2.5408
 NDR  H72   H  HCH3  0   0.237   3.0253  -0.8754   2.2888
 NDR  H73   H  HCH3  0   0.237   2.8556   0.8431   2.6025
 NDR  H12   H  HOH1  0   0.451   5.5068   0.6500   0.3056
 NDR  H101  H  HCH2  0   0.249   4.4587  -1.6781  -0.9989
 NDR  H102  H  HCH2  0   0.252   4.4211  -1.6946   0.7514
 NDR  H41   H  HCH2  0   0.230   2.2872  -2.6127   0.7406
 NDR  H42   H  HCH2  0   0.240   2.2990  -2.6538  -1.0096
 NDR  H16   H  H     0   0.282   3.7761   1.5027  -3.5701
 NDR  H23   H  HCH1  0   0.253  -2.1191   0.1041   1.6959
 NDR  H24   H  HCH1  0   0.215  -0.6919   0.5833  -0.9449
 NDR  H25   H  HCH1  0   0.216   0.0600  -1.2439   1.3676
 NDR  H26   H  HCH1  0   0.227   1.4281  -0.4621  -1.2163

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
 NDR  O22  C21   double  1.220  0.020  1.220
 NDR  C21  C20   single  1.504  0.020  1.504
 NDR  C21  C19   single  1.461  0.020  1.461
 NDR  C20  C18   single  1.521  0.020  1.521
 NDR  C20  H201  single  0.939  0.020  1.096
 NDR  C20  H202  single  0.939  0.020  1.096
 NDR  C19  C17   double  1.344  0.020  1.344
 NDR  C19  H19   single  0.930  0.020  1.086
 NDR  C17  C15   single  1.496  0.020  1.496
 NDR  C17  C14   single  1.506  0.020  1.506
 NDR  C15  C9    single  1.524  0.020  1.524
 NDR  C15  H151  single  0.939  0.020  1.096
 NDR  C15  H152  single  0.939  0.020  1.096
 NDR  C14  C18   single  1.528  0.020  1.528
 NDR  C14  C8    single  1.544  0.020  1.544
 NDR  C18  H181  single  0.939  0.020  1.096
 NDR  C18  H182  single  0.939  0.020  1.096
 NDR  C8   C3    single  1.538  0.020  1.538
 NDR  C8   C13   single  1.533  0.020  1.533
 NDR  C3   C9    single  1.522  0.020  1.522
 NDR  C3   C1    single  1.520  0.020  1.520
 NDR  C9   H91   single  0.939  0.020  1.096
 NDR  C9   H92   single  0.939  0.020  1.096
 NDR  C13  C6    single  1.530  0.020  1.530
 NDR  C13  H131  single  0.939  0.020  1.096
 NDR  C13  H132  single  0.939  0.020  1.096
 NDR  C6   C2    single  1.523  0.020  1.523
 NDR  C6   H61   single  0.939  0.020  1.096
 NDR  C6   H62   single  0.939  0.020  1.096
 NDR  C2   C1    single  1.534  0.020  1.534
 NDR  C2   C7    single  1.534  0.020  1.534
 NDR  C2   C5    single  1.551  0.020  1.551
 NDR  C1   C4    single  1.530  0.020  1.530
 NDR  C7   H71   single  0.939  0.020  1.096
 NDR  C7   H72   single  0.939  0.020  1.096
 NDR  C7   H73   single  0.939  0.020  1.096
 NDR  C5   O12   single  1.406  0.020  1.406
 NDR  C5   C10   single  1.555  0.020  1.555
 NDR  C5   C11   single  1.474  0.020  1.474
 NDR  O12  H12   single  0.832  0.020  0.971
 NDR  C10  C4    single  1.545  0.020  1.545
 NDR  C10  H101  single  0.939  0.020  1.096
 NDR  C10  H102  single  0.939  0.020  1.096
 NDR  C4   H41   single  0.939  0.020  1.096
 NDR  C4   H42   single  0.939  0.020  1.096
 NDR  C11  C16   triple  1.203  0.020  1.203
 NDR  C16  H16   single  0.913  0.020  1.066
 NDR  C14  H23   single  0.939  0.020  1.096
 NDR  C8   H24   single  0.939  0.020  1.096
 NDR  C3   H25   single  0.939  0.020  1.096
 NDR  C1   H26   single  0.939  0.020  1.096

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
 NDR  C19   C21  C20   115.54  3.000
 NDR  C19   C21  O22   121.75  3.000
 NDR  C20   C21  O22   122.60  3.000
 NDR  H202  C20  H201  107.06  3.000
 NDR  H202  C20  C18   109.77  3.000
 NDR  H201  C20  C18   111.36  3.000
 NDR  H202  C20  C21   107.24  3.000
 NDR  H201  C20  C21   109.94  3.000
 NDR  C18   C20  C21   111.29  3.000
 NDR  H19   C19  C17   119.93  3.000
 NDR  H19   C19  C21   116.72  3.000
 NDR  C17   C19  C21   123.19  3.000
 NDR  C14   C17  C15   116.40  3.000
 NDR  C14   C17  C19   122.89  3.000
 NDR  C15   C17  C19   120.68  3.000
 NDR  H152  C15  H151  106.65  3.000
 NDR  H152  C15  C9    111.19  3.000
 NDR  H151  C15  C9    108.22  3.000
 NDR  H152  C15  C17   110.48  3.000
 NDR  H151  C15  C17   107.13  3.000
 NDR  C9    C15  C17   112.87  3.000
 NDR  H23   C14  C8    107.58  3.000
 NDR  H23   C14  C18   108.91  3.000
 NDR  C8    C14  C18   111.22  3.000
 NDR  H23   C14  C17   106.44  3.000
 NDR  C8    C14  C17   110.74  3.000
 NDR  C18   C14  C17   111.73  3.000
 NDR  H182  C18  H181  106.49  3.000
 NDR  H182  C18  C14   110.25  3.000
 NDR  H181  C18  C14   108.85  3.000
 NDR  H182  C18  C20   108.95  3.000
 NDR  H181  C18  C20   109.23  3.000
 NDR  C14   C18  C20   112.85  3.000
 NDR  H24   C8   C13   107.50  3.000
 NDR  H24   C8   C3    106.69  3.000
 NDR  C13   C8   C3    111.96  3.000
 NDR  H24   C8   C14   106.81  3.000
 NDR  C13   C8   C14   111.45  3.000
 NDR  C3    C8   C14   112.08  3.000
 NDR  H25   C3   C1    109.94  3.000
 NDR  H25   C3   C9    107.56  3.000
 NDR  C1    C3   C9    111.89  3.000
 NDR  H25   C3   C8    108.75  3.000
 NDR  C1    C3   C8    108.62  3.000
 NDR  C9    C3   C8    110.03  3.000
 NDR  H92   C9   H91   106.75  3.000
 NDR  H92   C9   C3    109.66  3.000
 NDR  H91   C9   C3    110.58  3.000
 NDR  H92   C9   C15   110.04  3.000
 NDR  H91   C9   C15   108.89  3.000
 NDR  C3    C9   C15   110.83  3.000
 NDR  H132  C13  H131  105.93  3.000
 NDR  H132  C13  C6    110.68  3.000
 NDR  H131  C13  C6    107.79  3.000
 NDR  H132  C13  C8    109.23  3.000
 NDR  H131  C13  C8    109.89  3.000
 NDR  C6    C13  C8    113.06  3.000
 NDR  H62   C6   H61   106.49  3.000
 NDR  H62   C6   C2    111.13  3.000
 NDR  H61   C6   C2    109.55  3.000
 NDR  H62   C6   C13   109.70  3.000
 NDR  H61   C6   C13   108.63  3.000
 NDR  C2    C6   C13   111.19  3.000
 NDR  C5    C2   C7    108.53  3.000
 NDR  C5    C2   C1    100.12  3.000
 NDR  C7    C2   C1    112.61  3.000
 NDR  C5    C2   C6    116.71  3.000
 NDR  C7    C2   C6    109.88  3.000
 NDR  C1    C2   C6    108.76  3.000
 NDR  H26   C1   C4    107.23  3.000
 NDR  H26   C1   C2    106.49  3.000
 NDR  C4    C1   C2    104.28  3.000
 NDR  H26   C1   C3    105.43  3.000
 NDR  C4    C1   C3    119.31  3.000
 NDR  C2    C1   C3    113.37  3.000
 NDR  H73   C7   H72   107.26  3.000
 NDR  H73   C7   H71   106.99  3.000
 NDR  H72   C7   H71   106.71  3.000
 NDR  H73   C7   C2    110.72  3.000
 NDR  H72   C7   C2    113.30  3.000
 NDR  H71   C7   C2    111.53  3.000
 NDR  C11   C5   C10   109.11  3.000
 NDR  C11   C5   O12   108.88  3.000
 NDR  C10   C5   O12   114.25  3.000
 NDR  C11   C5   C2    111.42  3.000
 NDR  C10   C5   C2    102.64  3.000
 NDR  O12   C5   C2    110.45  3.000
 NDR  H12   O12  C5    108.76  3.000
 NDR  H102  C10  H101  106.75  3.000
 NDR  H102  C10  C4    111.18  3.000
 NDR  H101  C10  C4    112.52  3.000
 NDR  H102  C10  C5    108.67  3.000
 NDR  H101  C10  C5    111.47  3.000
 NDR  C4    C10  C5    106.27  3.000
 NDR  H42   C4   H41   106.64  3.000
 NDR  H42   C4   C10   111.96  3.000
 NDR  H41   C4   C10   110.59  3.000
 NDR  H42   C4   C1    112.04  3.000
 NDR  H41   C4   C1    111.17  3.000
 NDR  C10   C4   C1    104.55  3.000
 NDR  C16   C11  C5    180.00  3.000
 NDR  H16   C16  C11   180.00  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
 NDR  Var_01  C14  C18  C20  C21  -55.74  30.0  1
 NDR  Var_02  C15  C17  C19  C21  170.06  30.0  1
 NDR  Var_03  C17  C19  C21  C20   -6.30  30.0  1
 NDR  Var_04  C18  C20  C21  C19   37.33  30.0  1
 NDR  Var_05  C9   C15  C17  C19  133.74  30.0  1
 NDR  Var_06  C3   C9   C15  C17   52.59  30.0  1
 NDR  Var_07  C2   C6   C13  C8   -53.60  30.0  1
 NDR  Var_08  C5   C10  C4   C1     2.61  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
 NDR  chir_01  C14  C17  C18  C8   positiv
 NDR  chir_02  C8   C13  C3   C14  negativ
 NDR  chir_03  C3   C8   C9   C1   negativ
 NDR  chir_04  C2   C5   C1   C6   positiv
 NDR  chir_05  C1   C3   C2   C4   negativ
 NDR  chir_06  C5   C2   C10  C11  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
 NDR  plan-1  O22  0.020
 NDR  plan-1  C21  0.020
 NDR  plan-1  C20  0.020
 NDR  plan-1  C19  0.020

