# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 25 17:58:49 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: S-[(7R,8R,9S,10R,13S,14S,17R)-10,13-dimethyl-3,5'-dioxo-1,2,3,4',5',6,7,8,9,10,11,12,13,14,15,16-hexadecahydro-3'H-spiro[cyclopenta[a]phenanthrene-17,2'-furan]-7-yl] ethanethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)S[C@@H]1CC2=CC(=O)CC[C@]2(C)[C@H]3CC[C@@]4(C)[C@@H](CC[C@@]45CCC(=O)O5)[C@H]13
#
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
 SNL  SNL  'S-[(7R,8R,9S,10R,13S,14S,17R)-10,13-dimethyl-3,5'-dioxo-1,2,3,4',5',6,7,8,9,10,11,12,13,14,15,16-hexadecahydro-3'H-spiro[cyclopenta[a]phenanthrene-17,2'-furan]-7-yl] ethanethioate'  ligand  61  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SNL
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
 SNL  C8    C  CH2   0  -0.477  -3.3430   1.5017   0.7377
 SNL  C4    C  CH2   0  -0.423  -1.7940  -1.7428  -0.6163
 SNL  C5    C  CT    0  -0.093  -2.2614  -0.6261   0.3129
 SNL  C2    C  CT    0  -0.142   2.0316  -1.7683   0.3309
 SNL  C6    C  CH1   0  -0.199  -1.1851   0.4655   0.3410
 SNL  C1    C  CH2   0  -0.446   2.5494  -2.6314  -0.8292
 SNL  C3    C  CH2   0  -0.450  -0.4355  -2.2867  -0.1689
 SNL  C7    C  CH2   0  -0.446  -1.8433   1.6299   1.0837
 SNL  C9    C  CR5   0   0.291  -3.4623   0.2307  -0.1346
 SNL  C10   C  CH3   0  -0.676  -2.5507  -1.1981   1.7094
 SNL  C11   C  CH3   0  -0.678   1.9453  -2.6120   1.6178
 SNL  C12   C  CH2   0  -0.574   4.0189  -2.9968  -0.7020
 SNL  C13   C  CH2   0  -0.488  -3.5449   0.5837  -1.6268
 SNL  C14   C  CH2   0  -0.622  -5.0392   0.7761  -1.8304
 SNL  C15   C  CR5   0   0.540  -5.6357  -0.1365  -0.7933
 SNL  C16   C  C     0   0.264   2.0503   3.4764  -0.2044
 SNL  C17   C  CH3   0  -0.749   2.4144   4.3349  -1.3821
 SNL  C18   C  C     0   0.405   4.8752  -1.7693  -0.5687
 SNL  C19   C  C1    0  -0.452   4.2688  -0.6394   0.1345
 SNL  C20   C  C     0   0.260   3.0053  -0.6348   0.5883
 SNL  C21   C  CH2   0  -0.491   2.5264   0.4993   1.4379
 SNL  C22   C  CH1   0  -0.380   1.2096   1.0697   0.9323
 SNL  C23   C  CH1   0  -0.248   0.1638  -0.0365   0.8314
 SNL  C24   C  CH1   0  -0.192   0.6382  -1.1938  -0.0664
 SNL  O57   O  O     0  -0.437  -6.7584  -0.5590  -0.7169
 SNL  O58   O  O     0  -0.463  -4.7101  -0.4502   0.1115
 SNL  O59   O  O     0  -0.390   2.1780   3.8198   0.9436
 SNL  O60   O  O     0  -0.436   6.0243  -1.7236  -0.9727
 SNL  S61   S  S2    0   0.002   1.4491   1.8860  -0.6868
 SNL  H81   H  HCH2  0   0.256  -3.9495   1.4021   1.6391
 SNL  H82   H  HCH2  0   0.253  -3.7191   2.3803   0.2108
 SNL  H41   H  HCH2  0   0.226  -1.6865  -1.3678  -1.6376
 SNL  H42   H  HCH2  0   0.237  -2.5242  -2.5561  -0.6547
 SNL  H6    H  HCH1  0   0.238  -1.0445   0.7820  -0.7019
 SNL  H11   H  HCH2  0   0.241   2.4055  -2.0863  -1.7673
 SNL  H12   H  HCH2  0   0.251   1.9556  -3.5428  -0.9061
 SNL  H31   H  HCH2  0   0.250  -0.1191  -3.0494  -0.8831
 SNL  H32   H  HCH2  0   0.233  -0.5399  -2.8005   0.7887
 SNL  H71   H  HCH2  0   0.235  -1.6875   1.5439   2.1614
 SNL  H72   H  HCH2  0   0.242  -1.4325   2.5930   0.7788
 SNL  H101  H  HCH3  0   0.236  -1.6547  -1.5983   2.1794
 SNL  H102  H  HCH3  0   0.242  -2.9549  -0.4551   2.3964
 SNL  H103  H  HCH3  0   0.242  -3.2693  -2.0156   1.6498
 SNL  H111  H  HCH3  0   0.247   2.9361  -2.8601   1.9993
 SNL  H112  H  HCH3  0   0.242   1.4091  -2.0973   2.4153
 SNL  H113  H  HCH3  0   0.246   1.4287  -3.5530   1.4277
 SNL  H121  H  HCH2  0   0.269   4.3530  -3.5883  -1.5560
 SNL  H122  H  HCH2  0   0.268   4.1890  -3.6157   0.1862
 SNL  H131  H  HCH2  0   0.268  -2.9602   1.4665  -1.8793
 SNL  H132  H  HCH2  0   0.268  -3.1948  -0.2372  -2.2524
 SNL  H141  H  HCH2  0   0.295  -5.3618   1.7991  -1.6153
 SNL  H142  H  HCH2  0   0.294  -5.3959   0.5261  -2.8281
 SNL  H171  H  HCH3  0   0.285   3.4968   4.2941  -1.5190
 SNL  H172  H  HCH3  0   0.261   1.9455   4.0048  -2.3069
 SNL  H173  H  HCH3  0   0.277   2.1405   5.3706  -1.1867
 SNL  H19   H  H     0   0.252   4.9166   0.2073   0.3384
 SNL  H211  H  HCH2  0   0.273   3.2894   1.2750   1.5121
 SNL  H212  H  HCH2  0   0.276   2.3569   0.1359   2.4587
 SNL  H22   H  HCH1  0   0.311   0.8612   1.8441   1.6173
 SNL  H23   H  HCH1  0   0.250   0.0483  -0.3994   1.8611
 SNL  H24   H  HCH1  0   0.229   0.7546  -0.7758  -1.0783

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
 SNL  C8   C7    single  1.544  0.020  1.544
 SNL  C8   C9    single  1.546  0.020  1.546
 SNL  C8   H81   single  0.970  0.020  1.090
 SNL  C8   H82   single  0.970  0.020  1.090
 SNL  C4   C5    single  1.526  0.020  1.526
 SNL  C4   C3    single  1.530  0.020  1.530
 SNL  C4   H41   single  0.970  0.020  1.090
 SNL  C4   H42   single  0.970  0.020  1.090
 SNL  C5   C6    single  1.533  0.020  1.533
 SNL  C5   C9    single  1.542  0.020  1.542
 SNL  C5   C10   single  1.537  0.020  1.537
 SNL  C2   C1    single  1.536  0.020  1.536
 SNL  C2   C11   single  1.541  0.020  1.541
 SNL  C2   C20   single  1.516  0.020  1.516
 SNL  C2   C24   single  1.559  0.020  1.559
 SNL  C6   C7    single  1.530  0.020  1.530
 SNL  C6   C23   single  1.521  0.020  1.521
 SNL  C6   H6    single  0.970  0.020  1.090
 SNL  C1   C12   single  1.520  0.020  1.520
 SNL  C1   H11   single  0.970  0.020  1.090
 SNL  C1   H12   single  0.970  0.020  1.090
 SNL  C3   C24   single  1.536  0.020  1.536
 SNL  C3   H31   single  0.970  0.020  1.090
 SNL  C3   H32   single  0.970  0.020  1.090
 SNL  C7   H71   single  0.970  0.020  1.090
 SNL  C7   H72   single  0.970  0.020  1.090
 SNL  C9   C13   single  1.536  0.020  1.536
 SNL  C9   O58   single  1.443  0.020  1.443
 SNL  C10  H101  single  0.970  0.020  1.090
 SNL  C10  H102  single  0.970  0.020  1.090
 SNL  C10  H103  single  0.970  0.020  1.090
 SNL  C11  H111  single  0.970  0.020  1.090
 SNL  C11  H112  single  0.970  0.020  1.090
 SNL  C11  H113  single  0.970  0.020  1.090
 SNL  C12  C18   single  1.503  0.020  1.503
 SNL  C12  H121  single  0.970  0.020  1.090
 SNL  C12  H122  single  0.970  0.020  1.090
 SNL  C13  C14   single  1.520  0.020  1.520
 SNL  C13  H131  single  0.970  0.020  1.090
 SNL  C13  H132  single  0.970  0.020  1.090
 SNL  C14  C15   single  1.505  0.020  1.505
 SNL  C14  H141  single  0.970  0.020  1.090
 SNL  C14  H142  single  0.970  0.020  1.090
 SNL  C15  O57   double  1.202  0.020  1.202
 SNL  C15  O58   single  1.332  0.020  1.332
 SNL  C16  C17   single  1.502  0.020  1.502
 SNL  C16  O59   double  1.205  0.020  1.205
 SNL  C16  S61   single  1.767  0.020  1.767
 SNL  C17  H171  single  0.970  0.020  1.090
 SNL  C17  H172  single  0.970  0.020  1.090
 SNL  C17  H173  single  0.970  0.020  1.090
 SNL  C18  C19   single  1.463  0.020  1.463
 SNL  C18  O60   double  1.219  0.020  1.219
 SNL  C19  C20   double  1.343  0.020  1.343
 SNL  C19  H19   single  0.930  0.020  1.080
 SNL  C20  C21   single  1.496  0.020  1.496
 SNL  C21  C22   single  1.521  0.020  1.521
 SNL  C21  H211  single  0.970  0.020  1.090
 SNL  C21  H212  single  0.970  0.020  1.090
 SNL  C22  C23   single  1.526  0.020  1.526
 SNL  C22  S61   single  1.829  0.020  1.829
 SNL  C22  H22   single  0.970  0.020  1.090
 SNL  C23  C24   single  1.540  0.020  1.540
 SNL  C23  H23   single  0.970  0.020  1.090
 SNL  C24  H24   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
 SNL  H82   C8   H81   106.30  3.000
 SNL  H82   C8   C9    111.27  3.000
 SNL  H81   C8   C9    110.38  3.000
 SNL  H82   C8   C7    112.09  3.000
 SNL  H81   C8   C7    111.24  3.000
 SNL  C9    C8   C7    105.64  3.000
 SNL  H42   C4   H41   106.73  3.000
 SNL  H42   C4   C3    109.80  3.000
 SNL  H41   C4   C3    107.92  3.000
 SNL  H42   C4   C5    111.17  3.000
 SNL  H41   C4   C5    110.36  3.000
 SNL  C3    C4   C5    110.73  3.000
 SNL  C10   C5   C9    108.90  3.000
 SNL  C10   C5   C6    112.37  3.000
 SNL  C9    C5   C6     99.00  3.000
 SNL  C10   C5   C4    109.80  3.000
 SNL  C9    C5   C4    117.94  3.000
 SNL  C6    C5   C4    108.49  3.000
 SNL  C24   C2   C20   109.99  3.000
 SNL  C24   C2   C11   111.38  3.000
 SNL  C20   C2   C11   107.66  3.000
 SNL  C24   C2   C1    108.42  3.000
 SNL  C20   C2   C1    109.38  3.000
 SNL  C11   C2   C1    110.00  3.000
 SNL  H6    C6   C23   106.71  3.000
 SNL  H6    C6   C7    107.26  3.000
 SNL  C23   C6   C7    118.45  3.000
 SNL  H6    C6   C5    106.11  3.000
 SNL  C23   C6   C5    113.17  3.000
 SNL  C7    C6   C5    104.41  3.000
 SNL  H12   C1   H11   106.52  3.000
 SNL  H12   C1   C12   109.36  3.000
 SNL  H11   C1   C12   108.58  3.000
 SNL  H12   C1   C2    109.84  3.000
 SNL  H11   C1   C2    108.86  3.000
 SNL  C12   C1   C2    113.44  3.000
 SNL  H32   C3   H31   105.82  3.000
 SNL  H32   C3   C24   110.07  3.000
 SNL  H31   C3   C24   109.77  3.000
 SNL  H32   C3   C4    109.81  3.000
 SNL  H31   C3   C4    108.32  3.000
 SNL  C24   C3   C4    112.79  3.000
 SNL  H72   C7   H71   106.96  3.000
 SNL  H72   C7   C6    111.98  3.000
 SNL  H71   C7   C6    110.96  3.000
 SNL  H72   C7   C8    112.12  3.000
 SNL  H71   C7   C8    110.67  3.000
 SNL  C6    C7   C8    104.23  3.000
 SNL  O58   C9   C13   103.16  3.000
 SNL  O58   C9   C5    111.22  3.000
 SNL  C13   C9   C5    116.85  3.000
 SNL  O58   C9   C8    111.01  3.000
 SNL  C13   C9   C8    111.31  3.000
 SNL  C5    C9   C8    103.47  3.000
 SNL  H103  C10  H102  107.54  3.000
 SNL  H103  C10  H101  106.89  3.000
 SNL  H102  C10  H101  106.50  3.000
 SNL  H103  C10  C5    110.71  3.000
 SNL  H102  C10  C5    112.90  3.000
 SNL  H101  C10  C5    111.98  3.000
 SNL  H113  C11  H112  107.58  3.000
 SNL  H113  C11  H111  107.17  3.000
 SNL  H112  C11  H111  107.37  3.000
 SNL  H113  C11  C2    110.69  3.000
 SNL  H112  C11  C2    112.33  3.000
 SNL  H111  C11  C2    111.46  3.000
 SNL  H122  C12  H121  106.30  3.000
 SNL  H122  C12  C18   107.52  3.000
 SNL  H121  C12  C18   109.74  3.000
 SNL  H122  C12  C1    110.72  3.000
 SNL  H121  C12  C1    111.15  3.000
 SNL  C18   C12  C1    111.23  3.000
 SNL  H132  C13  H131  107.77  3.000
 SNL  H132  C13  C14   109.53  3.000
 SNL  H131  C13  C14   113.22  3.000
 SNL  H132  C13  C9    111.55  3.000
 SNL  H131  C13  C9    112.51  3.000
 SNL  C14   C13  C9    102.24  3.000
 SNL  H142  C14  H141  107.35  3.000
 SNL  H142  C14  C15   111.25  3.000
 SNL  H141  C14  C15   108.34  3.000
 SNL  H142  C14  C13   114.57  3.000
 SNL  H141  C14  C13   112.45  3.000
 SNL  C15   C14  C13   102.74  3.000
 SNL  O58   C15  O57   121.55  3.000
 SNL  O58   C15  C14   109.61  3.000
 SNL  O57   C15  C14   128.85  3.000
 SNL  S61   C16  O59   123.54  3.000
 SNL  S61   C16  C17   112.50  3.000
 SNL  O59   C16  C17   123.94  3.000
 SNL  H173  C17  H172  109.43  3.000
 SNL  H173  C17  H171  107.91  3.000
 SNL  H172  C17  H171  108.02  3.000
 SNL  H173  C17  C16   109.99  3.000
 SNL  H172  C17  C16   112.86  3.000
 SNL  H171  C17  C16   108.50  3.000
 SNL  O60   C18  C19   121.42  3.000
 SNL  O60   C18  C12   122.58  3.000
 SNL  C19   C18  C12   115.94  3.000
 SNL  H19   C19  C20   119.71  3.000
 SNL  H19   C19  C18   116.46  3.000
 SNL  C20   C19  C18   123.74  3.000
 SNL  C21   C20  C19   119.73  3.000
 SNL  C21   C20  C2    117.23  3.000
 SNL  C19   C20  C2    122.99  3.000
 SNL  H212  C21  H211  106.29  3.000
 SNL  H212  C21  C22   107.44  3.000
 SNL  H211  C21  C22   111.19  3.000
 SNL  H212  C21  C20   109.08  3.000
 SNL  H211  C21  C20   110.73  3.000
 SNL  C22   C21  C20   111.88  3.000
 SNL  H22   C22  S61   106.30  3.000
 SNL  H22   C22  C23   109.71  3.000
 SNL  S61   C22  C23   110.78  3.000
 SNL  H22   C22  C21   109.51  3.000
 SNL  S61   C22  C21   110.37  3.000
 SNL  C23   C22  C21   110.09  3.000
 SNL  H23   C23  C24   109.32  3.000
 SNL  H23   C23  C22   104.46  3.000
 SNL  C24   C23  C22   111.86  3.000
 SNL  H23   C23  C6    108.55  3.000
 SNL  C24   C23  C6    109.48  3.000
 SNL  C22   C23  C6    112.96  3.000
 SNL  H24   C24  C23   106.45  3.000
 SNL  H24   C24  C3    106.42  3.000
 SNL  C23   C24  C3    111.01  3.000
 SNL  H24   C24  C2    106.24  3.000
 SNL  C23   C24  C2    113.82  3.000
 SNL  C3    C24  C2    112.32  3.000
 SNL  C15   O58  C9    111.97  3.000
 SNL  C22   S61  C16   101.80  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
 SNL  Var_01  C24   C3   C4   C5   -55.81  30.0  1
 SNL  Var_02  C18   C12  C1   C2   -56.02  30.0  1
 SNL  Var_03  C18   C19  C20  C2    -4.64  30.0  1
 SNL  Var_04  C22   C21  C20  C2   -52.48  30.0  1
 SNL  Var_05  C9    C8   C7   C6     2.44  30.0  1
 SNL  Var_06  C19   C18  C12  C1    32.76  30.0  1
 SNL  Var_07  C15   C14  C13  C9   -28.88  30.0  1
 SNL  Var_08  C14   C15  O58  C9     3.25  30.0  1
 SNL  Var_09  C20   C19  C18  C12   -3.28  30.0  1
 SNL  Var_10  O58   C15  C14  C13   17.16  30.0  1
 SNL  Var_11  O59   C16  S61  C22   -2.18  30.0  2
 SNL  Var_12  H171  C17  C16  O59   78.85  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
 SNL  chir_01  C5   C6   C9   C4   negativ
 SNL  chir_02  C2   C20  C24  C1   negativ
 SNL  chir_03  C6   C5   C7   C23  negativ
 SNL  chir_04  C9   C13  C5   C8   negativ
 SNL  chir_05  C22  S61  C21  C23  positiv
 SNL  chir_06  C23  C6   C22  C24  positiv
 SNL  chir_07  C24  C2   C3   C23  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
 SNL  plan-1  C12  0.020
 SNL  plan-1  C18  0.020
 SNL  plan-1  C19  0.020
 SNL  plan-1  O60  0.020
 SNL  plan-2  C14  0.020
 SNL  plan-2  C15  0.020
 SNL  plan-2  O57  0.020
 SNL  plan-2  O58  0.020
 SNL  plan-3  C16  0.020
 SNL  plan-3  C17  0.020
 SNL  plan-3  O59  0.020
 SNL  plan-3  S61  0.020

