# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 14:45:05 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 8-methoxyphenanthro[3,4-d][1,3]dioxole-5,6-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc2c1cc(C(O)=O)c3c(cc4OCOc4c23)C(O)=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
 17N  17N  '8-methoxyphenanthro[3,4-d][1,3]dioxole-5,6-dicarboxylic acid'  ligand  35  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_17N
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
 17N  CAA   C  CH3    0  -0.433   5.4110  -1.6782  -0.1351
 17N  OAB   O  O      0  -0.595  -2.5229  -2.1621  -1.4173
 17N  OAC   O  O      0  -0.598  -1.5809  -2.7062   1.4362
 17N  OAD   O  OC    -1  -0.607  -4.1776  -1.5236  -0.0646
 17N  OAE   O  OC    -1  -0.607  -0.2371  -3.8354   0.0622
 17N  CAF   C  CR16   0  -0.235   3.5507   2.0778   0.0303
 17N  CAG   C  CR16   0  -0.410   4.2125   0.8474  -0.0320
 17N  CAH   C  CR16   0  -0.390   2.1807   2.1568   0.0748
 17N  CAI   C  CR16   0  -0.409  -2.9068   0.9808  -0.1039
 17N  CAJ   C  CR16   0  -0.360   1.2862  -1.4649   0.0846
 17N  CAK   C  CH2    0   0.071  -1.5536   4.2379   0.3284
 17N  OAL   O  O2     0  -0.465   4.0048  -1.5479  -0.0951
 17N  OAM   O  O2     0  -0.491  -2.6641   3.4224   0.0011
 17N  OAN   O  O2     0  -0.497  -0.3944   3.4604   0.0753
 17N  CAO   C  C      0   0.374  -3.0330  -1.4331  -0.5463
 17N  CAP   C  CR6    0   0.326  -2.1854   2.1495   0.0106
 17N  CAQ   C  CR6    0   0.357   3.4704  -0.3141  -0.0397
 17N  CAR   C  CR6    0  -0.121  -2.2083  -0.2171  -0.1411
 17N  CAS   C  CR6    0  -0.106  -0.0694  -1.4732   0.1344
 17N  CAT   C  CR6    0   0.203  -0.8160   2.1622   0.0631
 17N  CAU   C  CR66   0  -0.042   2.0521  -0.2639   0.0151
 17N  CAV   C  CR66   0   0.140   1.3973   0.9832   0.0581
 17N  CAW   C  CR66   0   0.043  -0.7994  -0.2334   0.0123
 17N  CAX   C  CR66   0   0.001  -0.0550   0.9908   0.0591
 17N  CAY   C  C      0   0.369  -0.7117  -2.7925   0.5483
 17N  HAA   H  HCH3   0   0.228   5.8866  -1.2622   0.7573
 17N  HAAA  H  HCH3   0   0.260   5.6200  -2.7442  -0.1783
 17N  HAAB  H  HCH3   0   0.228   5.8402  -1.1992  -1.0189
 17N  HAF   H  HCR6   0   0.256   4.1385   2.9865   0.0398
 17N  HAG   H  HCR6   0   0.278   5.2926   0.8318  -0.0721
 17N  HAH   H  HCR6   0   0.259   1.7249   3.1315   0.1175
 17N  HAI   H  HCR6   0   0.263  -3.9837   0.9968  -0.2031
 17N  HAJ   H  HCR6   0   0.240   1.8086  -2.4075   0.1647
 17N  HAK   H  HCH2   0   0.245  -1.5444   5.1283  -0.2990
 17N  HAKA  H  HCH2   0   0.226  -1.5909   4.5142   1.3896

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
 17N  CAA  OAL   single    1.413  0.020  1.413
 17N  CAA  HAA   single    0.970  0.020  1.090
 17N  CAA  HAAA  single    0.970  0.020  1.090
 17N  CAA  HAAB  single    0.970  0.020  1.090
 17N  OAB  CAO   deloc     1.245  0.020  1.245
 17N  OAC  CAY   deloc     1.245  0.020  1.245
 17N  CAO  OAD   deloc     1.245  0.020  1.245
 17N  CAY  OAE   deloc     1.245  0.020  1.245
 17N  CAG  CAF   aromatic  1.398  0.020  1.398
 17N  CAF  CAH   aromatic  1.373  0.020  1.373
 17N  CAF  HAF   single    0.930  0.020  1.080
 17N  CAG  CAQ   aromatic  1.378  0.020  1.378
 17N  CAG  HAG   single    0.930  0.020  1.080
 17N  CAH  CAV   aromatic  1.411  0.020  1.411
 17N  CAH  HAH   single    0.930  0.020  1.080
 17N  CAR  CAI   aromatic  1.387  0.020  1.387
 17N  CAP  CAI   aromatic  1.378  0.020  1.378
 17N  CAI  HAI   single    0.930  0.020  1.080
 17N  CAU  CAJ   aromatic  1.426  0.020  1.426
 17N  CAJ  CAS   aromatic  1.357  0.020  1.357
 17N  CAJ  HAJ   single    0.930  0.020  1.080
 17N  OAN  CAK   single    1.419  0.020  1.419
 17N  CAK  OAM   single    1.416  0.020  1.416
 17N  CAK  HAK   single    0.970  0.020  1.090
 17N  CAK  HAKA  single    0.970  0.020  1.090
 17N  OAL  CAQ   single    1.346  0.020  1.346
 17N  CAP  OAM   single    1.360  0.020  1.360
 17N  CAT  OAN   single    1.365  0.020  1.365
 17N  CAR  CAO   single    1.524  0.020  1.524
 17N  CAT  CAP   aromatic  1.370  0.020  1.370
 17N  CAQ  CAU   aromatic  1.420  0.020  1.420
 17N  CAW  CAR   aromatic  1.417  0.020  1.417
 17N  CAS  CAY   single    1.525  0.020  1.525
 17N  CAS  CAW   aromatic  1.444  0.020  1.444
 17N  CAX  CAT   aromatic  1.397  0.020  1.397
 17N  CAU  CAV   aromatic  1.409  0.020  1.409
 17N  CAV  CAX   aromatic  1.452  0.020  1.452
 17N  CAX  CAW   aromatic  1.433  0.020  1.433

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
 17N  HAAB  CAA  HAAA  108.79  3.000
 17N  HAAB  CAA  HAA   108.80  3.000
 17N  HAAA  CAA  HAA   108.77  3.000
 17N  HAAB  CAA  OAL   111.92  3.000
 17N  HAAA  CAA  OAL   106.44  3.000
 17N  HAA   CAA  OAL   112.01  3.000
 17N  HAF   CAF  CAH   119.56  3.000
 17N  HAF   CAF  CAG   118.82  3.000
 17N  CAH   CAF  CAG   121.62  3.000
 17N  HAG   CAG  CAQ   121.70  3.000
 17N  HAG   CAG  CAF   119.16  3.000
 17N  CAQ   CAG  CAF   119.14  3.000
 17N  HAH   CAH  CAV   121.22  3.000
 17N  HAH   CAH  CAF   118.41  3.000
 17N  CAV   CAH  CAF   120.37  3.000
 17N  HAI   CAI  CAR   120.78  3.000
 17N  HAI   CAI  CAP   121.09  3.000
 17N  CAR   CAI  CAP   118.09  3.000
 17N  HAJ   CAJ  CAU   118.59  3.000
 17N  HAJ   CAJ  CAS   118.36  3.000
 17N  CAU   CAJ  CAS   122.93  3.000
 17N  HAKA  CAK  HAK   110.58  3.000
 17N  HAKA  CAK  OAN   109.78  3.000
 17N  HAK   CAK  OAN   109.77  3.000
 17N  HAKA  CAK  OAM   109.99  3.000
 17N  HAK   CAK  OAM   110.14  3.000
 17N  OAN   CAK  OAM   106.49  3.000
 17N  CAQ   OAL  CAA   118.75  3.000
 17N  CAP   OAM  CAK   105.15  3.000
 17N  CAT   OAN  CAK   105.69  3.000
 17N  CAR   CAO  OAD   116.91  3.000
 17N  CAR   CAO  OAB   115.56  3.000
 17N  OAD   CAO  OAB   127.20  3.000
 17N  CAT   CAP  OAM   110.08  3.000
 17N  CAT   CAP  CAI   122.28  3.000
 17N  OAM   CAP  CAI   127.51  3.000
 17N  CAU   CAQ  OAL   115.50  3.000
 17N  CAU   CAQ  CAG   120.50  3.000
 17N  OAL   CAQ  CAG   123.99  3.000
 17N  CAW   CAR  CAO   123.88  3.000
 17N  CAW   CAR  CAI   120.51  3.000
 17N  CAO   CAR  CAI   115.06  3.000
 17N  CAY   CAS  CAW   123.57  3.000
 17N  CAW   CAS  CAJ   119.79  3.000
 17N  CAY   CAS  CAJ   115.87  3.000
 17N  CAX   CAT  CAP   122.44  3.000
 17N  CAX   CAT  OAN   129.00  3.000
 17N  CAP   CAT  OAN   108.53  3.000
 17N  CAV   CAU  CAQ   119.77  3.000
 17N  CAV   CAU  CAJ   119.62  3.000
 17N  CAQ   CAU  CAJ   120.56  3.000
 17N  CAX   CAV  CAU   117.98  3.000
 17N  CAX   CAV  CAH   123.42  3.000
 17N  CAU   CAV  CAH   118.59  3.000
 17N  CAX   CAW  CAS   117.90  3.000
 17N  CAX   CAW  CAR   120.66  3.000
 17N  CAS   CAW  CAR   121.44  3.000
 17N  CAW   CAX  CAV   120.98  3.000
 17N  CAW   CAX  CAT   115.68  3.000
 17N  CAV   CAX  CAT   123.30  3.000
 17N  CAS   CAY  OAE   117.28  3.000
 17N  CAS   CAY  OAC   115.32  3.000
 17N  OAE   CAY  OAC   127.05  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
 17N  CONST_01  CAU  CAQ  CAG  CAF    0.00   0.0  0
 17N  CONST_02  CAU  CAV  CAH  CAF    0.00   0.0  0
 17N  CONST_03  CAX  CAV  CAH  CAF  180.00   0.0  0
 17N  CONST_04  CAV  CAH  CAF  CAG    0.00   0.0  0
 17N  CONST_05  CAJ  CAU  CAQ  CAG  180.00   0.0  0
 17N  CONST_06  CAV  CAU  CAQ  CAG    0.00   0.0  0
 17N  CONST_07  CAQ  CAG  CAF  CAH    0.00   0.0  0
 17N  CONST_08  CAJ  CAU  CAV  CAH  180.00   0.0  0
 17N  CONST_09  CAQ  CAU  CAV  CAH    0.00   0.0  0
 17N  CONST_10  CAT  CAX  CAV  CAH    0.00   0.0  0
 17N  CONST_11  CAW  CAX  CAV  CAH  180.00   0.0  0
 17N  CONST_12  CAS  CAW  CAR  CAI  180.00   0.0  0
 17N  CONST_13  CAX  CAW  CAR  CAI    0.00   0.0  0
 17N  CONST_14  CAX  CAT  CAP  CAI    0.00   0.0  0
 17N  CONST_15  CAX  CAV  CAU  CAJ    0.00   0.0  0
 17N  CONST_16  CAR  CAW  CAS  CAJ  180.00   0.0  0
 17N  CONST_17  CAX  CAW  CAS  CAJ    0.00   0.0  0
 17N  CONST_18  CAW  CAR  CAI  CAP    0.00   0.0  0
 17N  CONST_19  CAV  CAX  CAT  CAP  180.00   0.0  0
 17N  CONST_20  CAW  CAX  CAT  CAP    0.00   0.0  0
 17N  CONST_21  CAS  CAJ  CAU  CAQ  180.00   0.0  0
 17N  CONST_22  CAX  CAV  CAU  CAQ  180.00   0.0  0
 17N  CONST_23  CAT  CAP  CAI  CAR    0.00   0.0  0
 17N  CONST_24  CAT  CAX  CAW  CAR    0.00   0.0  0
 17N  CONST_25  CAV  CAX  CAW  CAR  180.00   0.0  0
 17N  CONST_26  CAV  CAU  CAJ  CAS    0.00   0.0  0
 17N  CONST_27  CAT  CAX  CAW  CAS  180.00   0.0  0
 17N  CONST_28  CAV  CAX  CAW  CAS    0.00   0.0  0
 17N  CONST_29  CAU  CAV  CAX  CAT  180.00   0.0  0
 17N  CONST_30  CAW  CAS  CAJ  CAU    0.00   0.0  0
 17N  CONST_31  CAW  CAX  CAV  CAU    0.00   0.0  0
 17N  CONST_32  OAL  CAQ  CAG  CAF  180.00   0.0  0
 17N  CONST_33  OAL  CAQ  CAU  CAJ    0.00   0.0  0
 17N  CONST_34  CAV  CAU  CAQ  OAL  180.00   0.0  0
 17N  CONST_35  CAP  CAI  CAR  CAO  180.00   0.0  0
 17N  CONST_39  CAY  CAS  CAJ  CAU  180.00   0.0  0
 17N  CONST_41  HAH  CAH  CAF  CAG  180.00   0.0  0
 17N  CONST_42  HAG  CAG  CAF  CAH  180.00   0.0  0
 17N  CONST_43  HAI  CAI  CAP  OAM    0.00   0.0  0
 17N  CONST_44  HAF  CAF  CAG  CAQ  180.00   0.0  0
 17N  CONST_45  HAJ  CAJ  CAU  CAQ    0.00   0.0  0
 17N  Var_01    CAP  CAT  OAN  CAK   12.68  30.0  1
 17N  Var_02    CAT  CAP  OAM  CAK  -11.78  30.0  1
 17N  Var_03    HAK  CAK  OAM  CAP  138.25  30.0  1
 17N  Var_04    CAG  CAQ  OAL  CAA    0.65  30.0  2
 17N  Var_05    CAI  CAR  CAO  OAB  132.10  30.0  2
 17N  Var_06    CAJ  CAS  CAY  OAC  131.28  30.0  2
 17N  Var_07    HAA  CAA  OAL  CAQ   61.33  30.0  3

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
 17N  plan-1  OAB  0.020
 17N  plan-1  OAD  0.020
 17N  plan-1  CAO  0.020
 17N  plan-1  CAR  0.020
 17N  plan-2  CAF  0.020
 17N  plan-2  CAG  0.020
 17N  plan-2  CAH  0.020
 17N  plan-2  CAI  0.020
 17N  plan-2  CAJ  0.020
 17N  plan-2  OAL  0.020
 17N  plan-2  OAM  0.020
 17N  plan-2  OAN  0.020
 17N  plan-2  CAO  0.020
 17N  plan-2  CAP  0.020
 17N  plan-2  CAQ  0.020
 17N  plan-2  CAR  0.020
 17N  plan-2  CAS  0.020
 17N  plan-2  CAT  0.020
 17N  plan-2  CAU  0.020
 17N  plan-2  CAV  0.020
 17N  plan-2  CAW  0.020
 17N  plan-2  CAX  0.020
 17N  plan-2  CAY  0.020
 17N  plan-2  HAF  0.020
 17N  plan-2  HAG  0.020
 17N  plan-2  HAH  0.020
 17N  plan-2  HAI  0.020
 17N  plan-2  HAJ  0.020
 17N  plan-3  OAC  0.020
 17N  plan-3  OAE  0.020
 17N  plan-3  CAS  0.020
 17N  plan-3  CAY  0.020

