# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 16:54:00 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 3,4-dihydroxy-9,10-secoandrosta-1(10),2,4-triene-9,17-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(O)c(O)c1CC[C@H]2[C@@H]3CCC(=O)[C@@]3(C)CCC2=O
#
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
 SDT  SDT  3,4-dihydroxy-9,10-secoandrosta-1(10),2,4-triene-9,17-dione  ligand  47  23  .  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_SDT
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
 SDT  OAD   O  O     0  -0.394  -5.5896   1.1626  -0.9432
 SDT  CAP   C  C     0   0.437  -4.4193   1.2126  -0.6543
 SDT  CAI   C  CH2   0  -0.568  -3.4530   2.3182  -1.0497
 SDT  CAL   C  CH2   0  -0.462  -2.0727   1.8669  -0.5527
 SDT  CAV   C  CH1   0  -0.223  -2.2461   0.3551  -0.4045
 SDT  CAW   C  CT    0  -0.214  -3.6607   0.1910   0.1681
 SDT  CAB   C  CH3   0  -0.674  -3.7970   0.6741   1.6235
 SDT  CAN   C  CH2   0  -0.418  -4.1030  -1.2570   0.0324
 SDT  CAJ   C  CH2   0  -0.559  -3.0763  -2.1811   0.7055
 SDT  CAU   C  CH1   0  -0.364  -1.1989  -0.4483   0.3728
 SDT  CAO   C  C     0   0.426  -1.6508  -1.8986   0.2745
 SDT  OAC   O  O     0  -0.391  -0.9339  -2.7767  -0.1501
 SDT  CAM   C  CH2   0  -0.416   0.2235  -0.2071  -0.1154
 SDT  CAK   C  CH2   0  -0.506   1.3053  -0.7594   0.8187
 SDT  CAT   C  CR6   0  -0.009   2.6864  -0.4431   0.3120
 SDT  CAS   C  CR6   0   0.257   3.2669   0.7829   0.6248
 SDT  OAF   O  OH1   0  -0.634   2.5813   1.6493   1.4073
 SDT  CAR   C  CR6   0   0.246   4.5356   1.1214   0.1385
 SDT  OAE   O  OH1   0  -0.653   5.0081   2.3379   0.5089
 SDT  CAH   C  CR16  0  -0.377   5.2172   0.2325  -0.6706
 SDT  CAG   C  CR16  0  -0.322   4.6370  -0.9889  -0.9921
 SDT  CAQ   C  CR6   0   0.040   3.3818  -1.3412  -0.5139
 SDT  CAA   C  CH3   0  -0.748   2.7920  -2.6766  -0.8742
 SDT  HAI   H  HCH2  0   0.282  -3.4741   2.4177  -2.1384
 SDT  HAIA  H  HCH2  0   0.284  -3.7796   3.2775  -0.6439
 SDT  HAL   H  HCH2  0   0.258  -1.2828   2.1264  -1.2559
 SDT  HALA  H  HCH2  0   0.240  -1.8192   2.3297   0.4031
 SDT  HAV   H  HCH1  0   0.251  -2.2782  -0.0517  -1.4271
 SDT  HAB   H  HCH3  0   0.252  -4.8411   0.6132   1.9340
 SDT  HABA  H  HCH3  0   0.251  -3.2191   0.0596   2.3126
 SDT  HABB  H  HCH3  0   0.252  -3.4712   1.7055   1.7637
 SDT  HAN   H  HCH2  0   0.252  -5.0859  -1.4221   0.4775
 SDT  HANA  H  HCH2  0   0.247  -4.1840  -1.5200  -1.0260
 SDT  HAJ   H  HCH2  0   0.266  -3.1218  -2.0502   1.7921
 SDT  HAJA  H  HCH2  0   0.268  -3.3093  -3.2267   0.5022
 SDT  HAU   H  HCH1  0   0.263  -1.2595  -0.1535   1.4293
 SDT  HAM   H  HCH2  0   0.230   0.3503  -0.6175  -1.1211
 SDT  HAMA  H  HCH2  0   0.251   0.3722   0.8710  -0.2083
 SDT  HAK   H  HCH2  0   0.241   1.1592  -0.3393   1.8167
 SDT  HAKA  H  HCH2  0   0.254   1.1914  -1.8373   0.9239
 SDT  HOAF  H  HOH1  0   0.470   3.0946   2.4554   1.5352
 SDT  HOAE  H  HOH1  0   0.480   5.8783   2.4980   0.1284
 SDT  HAH   H  HCR6  0   0.266   6.1982   0.4880  -1.0545
 SDT  HAG   H  HCR6  0   0.242   5.1784  -1.6752  -1.6314
 SDT  HAA   H  HCH3  0   0.243   1.7947  -2.5863  -1.3068
 SDT  HAAA  H  HCH3  0   0.245   3.4233  -3.1938  -1.5957
 SDT  HAAB  H  HCH3  0   0.240   2.6957  -3.3248  -0.0002

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
 SDT  OAD  CAP   double    1.207  0.020  1.207
 SDT  CAP  CAI   single    1.521  0.020  1.521
 SDT  CAP  CAW   single    1.515  0.020  1.515
 SDT  CAI  CAL   single    1.535  0.020  1.535
 SDT  CAL  CAV   single    1.529  0.020  1.529
 SDT  CAV  CAW   single    1.535  0.020  1.535
 SDT  CAV  CAU   single    1.532  0.020  1.532
 SDT  CAW  CAB   single    1.540  0.020  1.540
 SDT  CAW  CAN   single    1.520  0.020  1.520
 SDT  CAN  CAJ   single    1.537  0.020  1.537
 SDT  CAJ  CAO   single    1.516  0.020  1.516
 SDT  CAU  CAO   single    1.522  0.020  1.522
 SDT  CAU  CAM   single    1.523  0.020  1.523
 SDT  CAO  OAC   double    1.211  0.020  1.211
 SDT  CAM  CAK   single    1.532  0.020  1.532
 SDT  CAK  CAT   single    1.505  0.020  1.505
 SDT  CAT  CAS   aromatic  1.392  0.020  1.392
 SDT  CAT  CAQ   aromatic  1.404  0.020  1.404
 SDT  CAS  OAF   single    1.354  0.020  1.354
 SDT  CAS  CAR   aromatic  1.400  0.020  1.400
 SDT  CAR  OAE   single    1.357  0.020  1.357
 SDT  CAR  CAH   aromatic  1.382  0.020  1.382
 SDT  CAH  CAG   aromatic  1.390  0.020  1.390
 SDT  CAG  CAQ   aromatic  1.389  0.020  1.389
 SDT  CAQ  CAA   single    1.504  0.020  1.504
 SDT  CAI  HAI   single    0.970  0.020  1.090
 SDT  CAI  HAIA  single    0.970  0.020  1.090
 SDT  CAL  HAL   single    0.970  0.020  1.090
 SDT  CAL  HALA  single    0.970  0.020  1.090
 SDT  CAV  HAV   single    0.970  0.020  1.090
 SDT  CAB  HAB   single    0.970  0.020  1.090
 SDT  CAB  HABA  single    0.970  0.020  1.090
 SDT  CAB  HABB  single    0.970  0.020  1.090
 SDT  CAN  HAN   single    0.970  0.020  1.090
 SDT  CAN  HANA  single    0.970  0.020  1.090
 SDT  CAJ  HAJ   single    0.970  0.020  1.090
 SDT  CAJ  HAJA  single    0.970  0.020  1.090
 SDT  CAU  HAU   single    0.970  0.020  1.090
 SDT  CAM  HAM   single    0.970  0.020  1.090
 SDT  CAM  HAMA  single    0.970  0.020  1.090
 SDT  CAK  HAK   single    0.970  0.020  1.090
 SDT  CAK  HAKA  single    0.970  0.020  1.090
 SDT  OAF  HOAF  single    0.850  0.020  0.980
 SDT  OAE  HOAE  single    0.850  0.020  0.980
 SDT  CAH  HAH   single    0.930  0.020  1.080
 SDT  CAG  HAG   single    0.930  0.020  1.080
 SDT  CAA  HAA   single    0.970  0.020  1.090
 SDT  CAA  HAAA  single    0.970  0.020  1.090
 SDT  CAA  HAAB  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
 SDT  CAW   CAP  CAI   108.26  3.000
 SDT  CAW   CAP  OAD   125.99  3.000
 SDT  CAI   CAP  OAD   125.75  3.000
 SDT  HAIA  CAI  HAI   106.52  3.000
 SDT  HAIA  CAI  CAL   114.02  3.000
 SDT  HAI   CAI  CAL   111.50  3.000
 SDT  HAIA  CAI  CAP   110.62  3.000
 SDT  HAI   CAI  CAP   108.23  3.000
 SDT  CAL   CAI  CAP   105.87  3.000
 SDT  HALA  CAL  HAL   107.21  3.000
 SDT  HALA  CAL  CAV   111.14  3.000
 SDT  HAL   CAL  CAV   112.37  3.000
 SDT  HALA  CAL  CAI   111.57  3.000
 SDT  HAL   CAL  CAI   111.91  3.000
 SDT  CAV   CAL  CAI   102.72  3.000
 SDT  HAV   CAV  CAU   107.30  3.000
 SDT  HAV   CAV  CAW   106.27  3.000
 SDT  CAU   CAV  CAW   112.63  3.000
 SDT  HAV   CAV  CAL   106.18  3.000
 SDT  CAU   CAV  CAL   119.35  3.000
 SDT  CAW   CAV  CAL   104.27  3.000
 SDT  CAN   CAW  CAB   110.95  3.000
 SDT  CAN   CAW  CAV   109.68  3.000
 SDT  CAB   CAW  CAV   113.62  3.000
 SDT  CAN   CAW  CAP   116.63  3.000
 SDT  CAB   CAW  CAP   104.91  3.000
 SDT  CAV   CAW  CAP   100.77  3.000
 SDT  HABB  CAB  HABA  107.08  3.000
 SDT  HABB  CAB  HAB   107.58  3.000
 SDT  HABA  CAB  HAB   107.23  3.000
 SDT  HABB  CAB  CAW   113.06  3.000
 SDT  HABA  CAB  CAW   111.97  3.000
 SDT  HAB   CAB  CAW   109.65  3.000
 SDT  HANA  CAN  HAN   106.95  3.000
 SDT  HANA  CAN  CAJ   109.19  3.000
 SDT  HAN   CAN  CAJ   109.40  3.000
 SDT  HANA  CAN  CAW   109.70  3.000
 SDT  HAN   CAN  CAW   111.70  3.000
 SDT  CAJ   CAN  CAW   109.84  3.000
 SDT  HAJA  CAJ  HAJ   106.90  3.000
 SDT  HAJA  CAJ  CAO   109.07  3.000
 SDT  HAJ   CAJ  CAO   107.38  3.000
 SDT  HAJA  CAJ  CAN   110.63  3.000
 SDT  HAJ   CAJ  CAN   109.56  3.000
 SDT  CAO   CAJ  CAN   113.06  3.000
 SDT  HAU   CAU  CAM   108.50  3.000
 SDT  HAU   CAU  CAO   107.54  3.000
 SDT  CAM   CAU  CAO   114.04  3.000
 SDT  HAU   CAU  CAV   108.03  3.000
 SDT  CAM   CAU  CAV   113.13  3.000
 SDT  CAO   CAU  CAV   105.30  3.000
 SDT  OAC   CAO  CAU   122.54  3.000
 SDT  OAC   CAO  CAJ   121.43  3.000
 SDT  CAU   CAO  CAJ   116.00  3.000
 SDT  HAMA  CAM  HAM   106.04  3.000
 SDT  HAMA  CAM  CAK   108.15  3.000
 SDT  HAM   CAM  CAK   110.09  3.000
 SDT  HAMA  CAM  CAU   108.10  3.000
 SDT  HAM   CAM  CAU   110.10  3.000
 SDT  CAK   CAM  CAU   114.01  3.000
 SDT  HAKA  CAK  HAK   106.16  3.000
 SDT  HAKA  CAK  CAT   109.67  3.000
 SDT  HAK   CAK  CAT   110.45  3.000
 SDT  HAKA  CAK  CAM   109.99  3.000
 SDT  HAK   CAK  CAM   108.90  3.000
 SDT  CAT   CAK  CAM   111.53  3.000
 SDT  CAQ   CAT  CAS   119.27  3.000
 SDT  CAQ   CAT  CAK   121.20  3.000
 SDT  CAS   CAT  CAK   119.49  3.000
 SDT  CAR   CAS  OAF   120.32  3.000
 SDT  CAR   CAS  CAT   120.84  3.000
 SDT  OAF   CAS  CAT   118.84  3.000
 SDT  HOAF  OAF  CAS   110.01  3.000
 SDT  CAH   CAR  OAE   124.41  3.000
 SDT  CAH   CAR  CAS   119.65  3.000
 SDT  OAE   CAR  CAS   115.94  3.000
 SDT  HOAE  OAE  CAR   110.84  3.000
 SDT  HAH   CAH  CAG   120.19  3.000
 SDT  HAH   CAH  CAR   120.14  3.000
 SDT  CAG   CAH  CAR   119.66  3.000
 SDT  HAG   CAG  CAQ   119.63  3.000
 SDT  HAG   CAG  CAH   119.00  3.000
 SDT  CAQ   CAG  CAH   121.37  3.000
 SDT  CAA   CAQ  CAG   119.82  3.000
 SDT  CAA   CAQ  CAT   120.98  3.000
 SDT  CAG   CAQ  CAT   119.20  3.000
 SDT  HAAB  CAA  HAAA  107.42  3.000
 SDT  HAAB  CAA  HAA   106.60  3.000
 SDT  HAAA  CAA  HAA   107.85  3.000
 SDT  HAAB  CAA  CAQ   111.71  3.000
 SDT  HAAA  CAA  CAQ   110.68  3.000
 SDT  HAA   CAA  CAQ   112.34  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
 SDT  CONST_01  CAH  CAR  CAS  CAT     0.00   0.0  0
 SDT  CONST_02  CAH  CAG  CAQ  CAT     0.00   0.0  0
 SDT  CONST_03  CAG  CAQ  CAT  CAS     0.00   0.0  0
 SDT  CONST_04  CAG  CAH  CAR  CAS     0.00   0.0  0
 SDT  CONST_05  CAQ  CAT  CAS  CAR     0.00   0.0  0
 SDT  CONST_06  CAQ  CAG  CAH  CAR     0.00   0.0  0
 SDT  CONST_07  CAR  CAS  CAT  CAK   180.00   0.0  0
 SDT  CONST_08  CAG  CAQ  CAT  CAK   180.00   0.0  0
 SDT  CONST_09  OAE  CAR  CAS  CAT   180.00   0.0  0
 SDT  CONST_10  CAA  CAQ  CAT  CAS   180.00   0.0  0
 SDT  CONST_11  CAQ  CAT  CAS  OAF   180.00   0.0  0
 SDT  CONST_12  CAH  CAR  CAS  OAF   180.00   0.0  0
 SDT  CONST_13  CAG  CAH  CAR  OAE   180.00   0.0  0
 SDT  CONST_14  CAA  CAQ  CAG  CAH   180.00   0.0  0
 SDT  CONST_15  HAG  CAG  CAQ  CAT   180.00   0.0  0
 SDT  CONST_16  HAH  CAH  CAR  CAS   180.00   0.0  0
 SDT  Var_01    CAV  CAL  CAI  CAP    20.93  30.0  1
 SDT  Var_02    CAW  CAP  CAI  CAL     5.04  30.0  1
 SDT  Var_03    CAO  CAJ  CAN  CAW   -49.78  30.0  1
 SDT  Var_04    CAU  CAO  CAJ  CAN    51.20  30.0  1
 SDT  Var_05    CAT  CAK  CAM  CAU  -177.73  30.0  3
 SDT  Var_06    CAS  CAT  CAK  CAM    85.28  30.0  2
 SDT  Var_07    HAA  CAA  CAQ  CAT    53.83  30.0  2

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
 SDT  chir_01  CAV  CAL  CAW  CAU  positiv
 SDT  chir_02  CAW  CAN  CAV  CAP  negativ
 SDT  chir_03  CAU  CAM  CAO  CAV  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
 SDT  plan-1  CAK  0.020
 SDT  plan-1  CAT  0.020
 SDT  plan-1  CAS  0.020
 SDT  plan-1  OAF  0.020
 SDT  plan-1  CAR  0.020
 SDT  plan-1  OAE  0.020
 SDT  plan-1  CAH  0.020
 SDT  plan-1  CAG  0.020
 SDT  plan-1  CAQ  0.020
 SDT  plan-1  CAA  0.020
 SDT  plan-1  HAH  0.020
 SDT  plan-1  HAG  0.020
 SDT  plan-2  OAD  0.020
 SDT  plan-2  CAP  0.020
 SDT  plan-2  CAI  0.020
 SDT  plan-2  CAW  0.020
 SDT  plan-3  CAJ  0.020
 SDT  plan-3  CAU  0.020
 SDT  plan-3  CAO  0.020
 SDT  plan-3  OAC  0.020

