# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 19:47:36 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: (8~{S},9~{R},10~{S},11~{S},13~{S},14~{S},16~{S},17~{R})-9-chloranyl-10,13,16-trimethyl-11,17-bis(oxidanyl)-17-(2-oxidanylethanoyl)-6,7,8,11,12,14,15,16-octahydrocyclopenta[a]phenanthren-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1C[C@H]2[C@@H]3CCC4=CC(=O)C=C[C@]4(C)[C@@]3(Cl)[C@@H](O)C[C@]2(C)[C@@]1(O)C(=O)CO
#
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
 GXR  GXR  "(8~{S},9~{R},10~{S},11~{S},13~{S},14~{S},16~{S},17~{R})-9-chloranyl-10,13,16-trimethyl-11,17-bis(oxidanyl)-17-(2-oxidanylethanoyl)-6,7,8,11,12,14,15,16-octahydrocyclopenta[a]phenanthren-3-one"
  ligand  57  28  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GXR
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
 GXR  C5   C   CT    0   0.163  90.1832  119.2053  115.8372
 GXR  C6   C   CH2   0  -0.440  92.1757  119.6465  114.4148
 GXR  C9   C   CH1   0   0.096  91.0438  122.8285  117.2018
 GXR  C4   C   CT    0  -0.127  92.5435  122.7461  116.8203
 GXR  C3   C   CH1   0  -0.234  92.8075  121.9340  115.5390
 GXR  O2   O   OH1   0  -0.653  90.4473  123.7999  116.3782
 GXR  C1   C   CT    0  -0.054  90.5691  120.7245  115.8203
 GXR  C7   C   CH2   0  -0.477  90.3296  121.4714  117.1296
 GXR  C10  C   CT    0  -0.192  93.3057  124.1210  116.8010
 GXR  C11  C   CH2   0  -0.419  94.2989  121.7402  115.2754
 GXR  C12  C   CH3   0  -0.693  89.8779  121.4296  114.6435
 GXR  C13  C   CH2   0  -0.506  95.0950  123.0415  115.3553
 GXR  C14  C   C     0   0.256  94.7693  123.8185  116.5895
 GXR  C15  C   C     0   0.313  88.6752  118.9986  115.7326
 GXR  C16  C   CH3   0  -0.665  90.4280  118.0836  113.4115
 GXR  C17  C   CH3   0  -0.650  92.8885  125.0794  115.6510
 GXR  C18  C   C1    0  -0.119  93.0502  124.8778  118.0656
 GXR  C19  C   C1    0  -0.463  95.7180  124.2486  117.4305
 GXR  C2   C   CH1   0  -0.184  92.0837  120.5956  115.5993
 GXR  C20  C   CH2   0  -0.229  87.9313  118.6961  117.0257
 GXR  C21  C   C1    0  -0.377  94.0047  125.3026  118.8913
 GXR  C22  C   C     0   0.395  95.4188  125.0047  118.6439
 GXR  C8   C   CH1   0  -0.233  91.0758  118.5920  114.6927
 GXR  O1   O   OH1   0  -0.672  90.6090  118.6940  117.0852
 GXR  O3   O   O     0  -0.388  88.0524  119.1255  114.7054
 GXR  O4   O   OH1   0  -0.650  86.5571  118.5498  116.8325
 GXR  O5   O   O     0  -0.442  96.2949  125.3744  119.4128
 GXR  CL1  CL  CL    0  -0.128  93.2860  121.8321  118.2309
 GXR  H1   H   HCH2  0   0.246  93.1546  119.1746  114.3214
 GXR  H2   H   HCH2  0   0.226  91.9839  120.1670  113.4720
 GXR  H3   H   HCH1  0   0.236  90.9911  123.1519  118.2498
 GXR  H4   H   HCH1  0   0.259  92.3959  122.5246  114.7141
 GXR  H5   H   HOH1  0   0.459  89.4923  123.7440  116.4884
 GXR  H6   H   HCH2  0   0.247  89.2615  121.6514  117.3013
 GXR  H7   H   HCH2  0   0.253  90.6719  120.8712  117.9716
 GXR  H8   H   HCH2  0   0.256  94.4304  121.3085  114.2819
 GXR  H9   H   HCH2  0   0.231  94.7079  121.0170  115.9849
 GXR  H10  H   HCH3  0   0.233  88.8508  121.6947  114.8943
 GXR  H11  H   HCH3  0   0.250  90.3848  122.3534  114.3803
 GXR  H12  H   HCH3  0   0.243  89.8417  120.8202  113.7439
 GXR  H13  H   HCH2  0   0.263  96.1647  122.8319  115.3164
 GXR  H14  H   HCH2  0   0.258  94.8666  123.6568  114.4790
 GXR  H16  H   HCH3  0   0.227  89.6873  117.3066  113.5965
 GXR  H17  H   HCH3  0   0.228  89.9554  118.8744  112.8313
 GXR  H18  H   HCH3  0   0.229  91.2075  117.6434  112.7868
 GXR  H19  H   HCH3  0   0.264  91.9291  125.5442  115.8472
 GXR  H20  H   HCH3  0   0.246  93.6386  125.8668  115.5727
 GXR  H21  H   HCH3  0   0.249  92.8314  124.5806  114.6859
 GXR  H22  H   H     0   0.287  92.0175  125.1355  118.2713
 GXR  H24  H   H     0   0.250  96.7618  124.0309  117.2304
 GXR  H26  H   HCH1  0   0.238  92.4903  120.0607  116.4621
 GXR  H27  H   HCH2  0   0.254  88.3011  117.7641  117.4585
 GXR  H28  H   HCH2  0   0.234  88.1749  119.4855  117.7530
 GXR  H29  H   H     0   0.260  93.7606  125.8831  119.7731
 GXR  H31  H   HCH1  0   0.245  91.5615  117.7219  115.1454
 GXR  H32  H   HOH1  0   0.452  90.7035  117.7378  117.0188
 GXR  H33  H   HOH1  0   0.445  86.2375  119.2875  116.3025

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
 GXR  C16  C8   single  1.523  0.020  1.523
 GXR  C6   C8   single  1.549  0.020  1.549
 GXR  C6   C2   single  1.521  0.020  1.521
 GXR  C8   C5   single  1.576  0.020  1.576
 GXR  C12  C1   single  1.536  0.020  1.536
 GXR  O3   C15  double  1.208  0.020  1.208
 GXR  C11  C13  single  1.528  0.020  1.528
 GXR  C11  C3   single  1.527  0.020  1.527
 GXR  C13  C14  single  1.494  0.020  1.494
 GXR  C15  C5   single  1.526  0.020  1.526
 GXR  C15  C20  single  1.522  0.020  1.522
 GXR  C2   C3   single  1.523  0.020  1.523
 GXR  C2   C1   single  1.536  0.020  1.536
 GXR  C5   C1   single  1.567  0.020  1.567
 GXR  C5   O1   single  1.414  0.020  1.414
 GXR  C3   C4   single  1.540  0.020  1.540
 GXR  C17  C10  single  1.554  0.020  1.554
 GXR  C1   C7   single  1.526  0.020  1.526
 GXR  C20  O4   single  1.395  0.020  1.395
 GXR  C14  C10  single  1.509  0.020  1.509
 GXR  C14  C19  double  1.339  0.020  1.339
 GXR  C10  C4   single  1.572  0.020  1.572
 GXR  C10  C18  single  1.496  0.020  1.496
 GXR  C4   C9   single  1.550  0.020  1.550
 GXR  C4   CL1  single  1.838  0.020  1.838
 GXR  O2   C9   single  1.406  0.020  1.406
 GXR  C19  C22  single  1.461  0.020  1.461
 GXR  C7   C9   single  1.535  0.020  1.535
 GXR  O5   C22  double  1.223  0.020  1.223
 GXR  C22  C21  single  1.466  0.020  1.466
 GXR  C18  C21  double  1.332  0.020  1.332
 GXR  C6   H1   single  0.970  0.020  1.090
 GXR  C6   H2   single  0.970  0.020  1.090
 GXR  C9   H3   single  0.970  0.020  1.090
 GXR  C3   H4   single  0.970  0.020  1.090
 GXR  O2   H5   single  0.850  0.020  0.980
 GXR  C7   H6   single  0.970  0.020  1.090
 GXR  C7   H7   single  0.970  0.020  1.090
 GXR  C11  H8   single  0.970  0.020  1.090
 GXR  C11  H9   single  0.970  0.020  1.090
 GXR  C12  H10  single  0.970  0.020  1.090
 GXR  C12  H11  single  0.970  0.020  1.090
 GXR  C12  H12  single  0.970  0.020  1.090
 GXR  C13  H13  single  0.970  0.020  1.090
 GXR  C13  H14  single  0.970  0.020  1.090
 GXR  C16  H16  single  0.970  0.020  1.090
 GXR  C16  H17  single  0.970  0.020  1.090
 GXR  C16  H18  single  0.970  0.020  1.090
 GXR  C17  H19  single  0.970  0.020  1.090
 GXR  C17  H20  single  0.970  0.020  1.090
 GXR  C17  H21  single  0.970  0.020  1.090
 GXR  C18  H22  single  0.930  0.020  1.080
 GXR  C19  H24  single  0.930  0.020  1.080
 GXR  C2   H26  single  0.970  0.020  1.090
 GXR  C20  H27  single  0.970  0.020  1.090
 GXR  C20  H28  single  0.970  0.020  1.090
 GXR  C21  H29  single  0.930  0.020  1.080
 GXR  C8   H31  single  0.970  0.020  1.090
 GXR  O1   H32  single  0.850  0.020  0.980
 GXR  O4   H33  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
 GXR  O1   C5   C8   109.25  3.000
 GXR  O1   C5   C15  108.01  3.000
 GXR  C8   C5   C15  117.22  3.000
 GXR  O1   C5   C1   106.60  3.000
 GXR  C15  C5   C1   111.96  3.000
 GXR  C8   C5   C1   103.29  3.000
 GXR  H2   C6   H1   106.82  3.000
 GXR  H2   C6   C8   110.74  3.000
 GXR  H1   C6   C8   110.99  3.000
 GXR  H2   C6   C2   111.33  3.000
 GXR  H1   C6   C2   113.02  3.000
 GXR  C8   C6   C2   104.02  3.000
 GXR  H3   C9   C7   106.43  3.000
 GXR  H3   C9   O2   109.58  3.000
 GXR  C7   C9   O2   112.69  3.000
 GXR  H3   C9   C4   107.28  3.000
 GXR  C7   C9   C4   113.05  3.000
 GXR  O2   C9   C4   107.64  3.000
 GXR  CL1  C4   C10  104.39  3.000
 GXR  CL1  C4   C3   107.89  3.000
 GXR  C10  C4   C3   111.59  3.000
 GXR  CL1  C4   C9   103.21  3.000
 GXR  C10  C4   C9   115.19  3.000
 GXR  C3   C4   C9   113.50  3.000
 GXR  H4   C3   C2   108.99  3.000
 GXR  H4   C3   C11  107.80  3.000
 GXR  C2   C3   C11  111.07  3.000
 GXR  H4   C3   C4   106.14  3.000
 GXR  C2   C3   C4   110.43  3.000
 GXR  C11  C3   C4   112.21  3.000
 GXR  H5   O2   C9   108.27  3.000
 GXR  C2   C1   C12  111.83  3.000
 GXR  C2   C1   C7   108.62  3.000
 GXR  C12  C1   C7   111.22  3.000
 GXR  C7   C1   C5   115.24  3.000
 GXR  C2   C1   C5    99.38  3.000
 GXR  C12  C1   C5   110.02  3.000
 GXR  H7   C7   H6   105.99  3.000
 GXR  H7   C7   C1   110.13  3.000
 GXR  H6   C7   C1   111.56  3.000
 GXR  H7   C7   C9   107.73  3.000
 GXR  H6   C7   C9   107.49  3.000
 GXR  C1   C7   C9   113.57  3.000
 GXR  C18  C10  C17  105.53  3.000
 GXR  C18  C10  C14  112.67  3.000
 GXR  C17  C10  C14  106.27  3.000
 GXR  C18  C10  C4   110.45  3.000
 GXR  C14  C10  C4   107.25  3.000
 GXR  C17  C10  C4   114.73  3.000
 GXR  H9   C11  H8   106.51  3.000
 GXR  H9   C11  C13  109.56  3.000
 GXR  H8   C11  C13  108.77  3.000
 GXR  H9   C11  C3   109.73  3.000
 GXR  H8   C11  C3   108.97  3.000
 GXR  C13  C11  C3   113.07  3.000
 GXR  H12  C12  H11  106.96  3.000
 GXR  H12  C12  H10  107.18  3.000
 GXR  H11  C12  H10  106.77  3.000
 GXR  H12  C12  C1   113.06  3.000
 GXR  H11  C12  C1   111.47  3.000
 GXR  H10  C12  C1   111.06  3.000
 GXR  H14  C13  H13  106.50  3.000
 GXR  H14  C13  C14  108.87  3.000
 GXR  H13  C13  C14  110.06  3.000
 GXR  H14  C13  C11  109.16  3.000
 GXR  H13  C13  C11  110.22  3.000
 GXR  C14  C13  C11  111.87  3.000
 GXR  C19  C14  C13  122.11  3.000
 GXR  C19  C14  C10  122.32  3.000
 GXR  C13  C14  C10  115.55  3.000
 GXR  O3   C15  C20  119.43  3.000
 GXR  C20  C15  C5   116.85  3.000
 GXR  O3   C15  C5   123.62  3.000
 GXR  H18  C16  H17  107.33  3.000
 GXR  H18  C16  H16  107.16  3.000
 GXR  H17  C16  H16  108.28  3.000
 GXR  H18  C16  C8   108.19  3.000
 GXR  H17  C16  C8   112.98  3.000
 GXR  H16  C16  C8   112.60  3.000
 GXR  H21  C17  H20  107.67  3.000
 GXR  H21  C17  H19  108.10  3.000
 GXR  H20  C17  H19  108.20  3.000
 GXR  H21  C17  C10  112.82  3.000
 GXR  H20  C17  C10  108.29  3.000
 GXR  H19  C17  C10  111.60  3.000
 GXR  H22  C18  C21  119.29  3.000
 GXR  H22  C18  C10  116.32  3.000
 GXR  C21  C18  C10  124.28  3.000
 GXR  H24  C19  C22  117.01  3.000
 GXR  H24  C19  C14  120.10  3.000
 GXR  C22  C19  C14  122.89  3.000
 GXR  H26  C2   C1   107.11  3.000
 GXR  H26  C2   C3   106.53  3.000
 GXR  C1   C2   C3   113.62  3.000
 GXR  H26  C2   C6   106.66  3.000
 GXR  C1   C2   C6   102.95  3.000
 GXR  C3   C2   C6   119.27  3.000
 GXR  H28  C20  H27  105.98  3.000
 GXR  H28  C20  O4   112.62  3.000
 GXR  H27  C20  O4   107.39  3.000
 GXR  H28  C20  C15  108.10  3.000
 GXR  H27  C20  C15  109.92  3.000
 GXR  O4   C20  C15  112.61  3.000
 GXR  H29  C21  C22  117.61  3.000
 GXR  H29  C21  C18  120.94  3.000
 GXR  C22  C21  C18  121.45  3.000
 GXR  O5   C22  C21  121.56  3.000
 GXR  C21  C22  C19  116.29  3.000
 GXR  O5   C22  C19  122.15  3.000
 GXR  H31  C8   C16  105.74  3.000
 GXR  H31  C8   C6   107.48  3.000
 GXR  C16  C8   C6   112.23  3.000
 GXR  H31  C8   C5   105.09  3.000
 GXR  C6   C8   C5   105.52  3.000
 GXR  C16  C8   C5   120.00  3.000
 GXR  H32  O1   C5   109.13  3.000
 GXR  H33  O4   C20  108.83  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
 GXR  Var_01  C22  C19  C14  C10     2.15   0.0  0
 GXR  Var_02  C22  C19  C14  C13  -179.76   0.0  0
 GXR  Var_03  C14  C13  C11  C3     48.35  30.0  1
 GXR  Var_04  C11  C13  C14  C10   -54.35  30.0  1
 GXR  Var_05  C22  C21  C18  C10    -2.58  30.0  1
 GXR  Var_06  C19  C14  C13  C11   127.43  30.0  1
 GXR  Var_07  C21  C22  C19  C14    -1.25  30.0  1
 GXR  Var_08  C19  C22  C21  C18     1.43  30.0  1
 GXR  Var_09  O5   C22  C19  C14   178.92  30.0  1
 GXR  Var_10  O5   C22  C21  C18  -178.74  30.0  1
 GXR  Var_11  H24  C19  C14  C10  -178.49   0.0  0
 GXR  Var_12  H24  C19  C14  C13    -0.39   0.0  0
 GXR  Var_13  H13  C13  C11  C3    171.16  30.0  1
 GXR  Var_14  H14  C13  C11  C3    -72.20  30.0  1
 GXR  Var_15  H13  C13  C14  C10  -177.24  30.0  1
 GXR  Var_16  H14  C13  C14  C10    66.37  30.0  1
 GXR  Var_17  H29  C21  C18  C10   177.41  30.0  1
 GXR  Var_18  H8   C11  C13  C14   169.55  30.0  1
 GXR  Var_19  H9   C11  C13  C14   -74.39  30.0  1
 GXR  Var_20  H13  C13  C14  C19     4.54  30.0  1
 GXR  Var_21  H14  C13  C14  C19  -111.84  30.0  1
 GXR  Var_22  H29  C21  C22  C19  -178.56  30.0  1
 GXR  Var_23  H24  C19  C22  C21   179.36  30.0  1
 GXR  Var_24  H22  C18  C21  C22  -178.75  30.0  1
 GXR  Var_25  H24  C19  C22  O5     -0.46  30.0  1
 GXR  Var_26  H29  C21  C22  O5      1.27  30.0  1
 GXR  Var_27  O4   C20  C15  C5    178.80  30.0  3
 GXR  Var_28  H27  C20  C15  C5    -61.51  30.0  3
 GXR  Var_29  H28  C20  C15  C5     53.74  30.0  3
 GXR  Var_30  O4   C20  C15  O3      2.30  30.0  3
 GXR  Var_31  H27  C20  C15  O3    121.99  30.0  3
 GXR  Var_32  H28  C20  C15  O3   -122.76  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
 GXR  chir_01  C5   C8   C1   O1   positiv
 GXR  chir_02  C9   O2   C4   C7   positiv
 GXR  chir_03  C4   C3   C10  C9   negativ
 GXR  chir_04  C3   C4   C2   C11  positiv
 GXR  chir_05  C1   C5   C2   C7   positiv
 GXR  chir_06  C10  C14  C4   C18  negativ
 GXR  chir_07  C2   C1   C3   C6   positiv
 GXR  chir_08  C8   C16  C6   C5   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
 GXR  plan-1  C5   0.020
 GXR  plan-1  C15  0.020
 GXR  plan-1  C20  0.020
 GXR  plan-1  O3   0.020
 GXR  plan-2  C19  0.020
 GXR  plan-2  C21  0.020
 GXR  plan-2  C22  0.020
 GXR  plan-2  O5   0.020
 GXR  plan-3  C10  0.020
 GXR  plan-3  C13  0.020
 GXR  plan-3  C14  0.020
 GXR  plan-3  C19  0.020
 GXR  plan-3  C22  0.020
 GXR  plan-3  H24  0.020

