# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 05:51:27 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  37  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  -0.437   5.3882  -1.6932  -0.2749
 17N  OAB   O  O     0  -0.438  -2.5681  -2.2368  -1.3012
 17N  OAC   O  O     0  -0.438  -1.5935  -2.7672   1.4187
 17N  OAD   O  OH1   0  -0.585  -4.2060  -1.4531  -0.0064
 17N  OAE   O  OH1   0  -0.584  -0.1899  -3.8126   0.0347
 17N  CAF   C  CR16  0  -0.220   3.5300   2.0607  -0.0291
 17N  CAG   C  CR16  0  -0.404   4.1928   0.8359  -0.1191
 17N  CAH   C  CR16  0  -0.390   2.1597   2.1437   0.0509
 17N  CAI   C  CR16  0  -0.360  -2.9349   0.9804  -0.0449
 17N  CAJ   C  CR16  0  -0.295   1.2818  -1.4745   0.0661
 17N  CAK   C  CH2   0   0.072  -1.5649   4.2322   0.3868
 17N  OAL   O  O2    0  -0.463   3.9808  -1.5573  -0.1994
 17N  OAM   O  O     0  -0.482  -2.6842   3.4067   0.1134
 17N  OAN   O  O     0  -0.484  -0.4114   3.4286   0.1592
 17N  CAO   C  C     0   0.468  -2.9860  -1.4168  -0.5182
 17N  CAP   C  CR56  0   0.335  -2.2112   2.1401   0.0883
 17N  CAQ   C  CR6   0   0.382   3.4531  -0.3285  -0.1190
 17N  CAR   C  CR6   0  -0.122  -2.2229  -0.2133  -0.1011
 17N  CAS   C  CR6   0  -0.107  -0.0728  -1.4727   0.1336
 17N  CAT   C  CR56  0   0.242  -0.8362   2.1477   0.1176
 17N  CAU   C  CR66  0  -0.060   2.0379  -0.2723  -0.0276
 17N  CAV   C  CR66  0   0.176   1.3797   0.9726   0.0429
 17N  CAW   C  CR66  0   0.124  -0.8150  -0.2399   0.0286
 17N  CAX   C  CR66  0  -0.001  -0.0727   0.9795   0.0780
 17N  CAY   C  C     0   0.463  -0.7235  -2.7326   0.5811
 17N  HAA   H  HCH3  0   0.234   5.8831  -1.2901   0.6121
 17N  HAAA  H  HCH3  0   0.264   5.5891  -2.7592  -0.3369
 17N  HAAB  H  HCH3  0   0.234   5.7941  -1.2036  -1.1630
 17N  HOAD  H  HOH1  0   0.489  -4.7000  -2.1962  -0.3847
 17N  HOAE  H  HOH1  0   0.488  -0.5741  -4.6081   0.4333
 17N  HAF   H  HCR6  0   0.268   4.1163   2.9701  -0.0262
 17N  HAG   H  HCR6  0   0.288   5.2712   0.8234  -0.1869
 17N  HAH   H  HCR6  0   0.269   1.7102   3.1195   0.1127
 17N  HAI   H  HCR6  0   0.296  -4.0103   1.0109  -0.1492
 17N  HAJ   H  HCR6  0   0.278   1.8177  -2.4082   0.1571
 17N  HAK   H  HCH2  0   0.255  -1.5550   5.0864  -0.2882
 17N  HAKA  H  HCH2  0   0.242  -1.5827   4.5606   1.4311

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    1.416  0.020  1.416
 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   double    1.208  0.020  1.208
 17N  OAC  CAY   double    1.208  0.020  1.208
 17N  CAO  OAD   single    1.324  0.020  1.324
 17N  OAD  HOAD  single    0.850  0.020  0.980
 17N  CAY  OAE   single    1.323  0.020  1.323
 17N  OAE  HOAE  single    0.850  0.020  0.980
 17N  CAG  CAF   aromatic  1.396  0.020  1.396
 17N  CAF  CAH   aromatic  1.375  0.020  1.375
 17N  CAF  HAF   single    0.930  0.020  1.080
 17N  CAG  CAQ   aromatic  1.380  0.020  1.380
 17N  CAG  HAG   single    0.930  0.020  1.080
 17N  CAH  CAV   aromatic  1.407  0.020  1.407
 17N  CAH  HAH   single    0.930  0.020  1.080
 17N  CAR  CAI   aromatic  1.391  0.020  1.391
 17N  CAP  CAI   aromatic  1.374  0.020  1.374
 17N  CAI  HAI   single    0.930  0.020  1.080
 17N  CAU  CAJ   aromatic  1.423  0.020  1.423
 17N  CAJ  CAS   aromatic  1.356  0.020  1.356
 17N  CAJ  HAJ   single    0.930  0.020  1.080
 17N  OAN  CAK   single    1.424  0.020  1.424
 17N  CAK  OAM   single    1.417  0.020  1.417
 17N  CAK  HAK   single    0.970  0.020  1.090
 17N  CAK  HAKA  single    0.970  0.020  1.090
 17N  OAL  CAQ   single    1.340  0.020  1.340
 17N  CAP  OAM   single    1.352  0.020  1.352
 17N  CAT  OAN   single    1.350  0.020  1.350
 17N  CAR  CAO   single    1.485  0.020  1.485
 17N  CAT  CAP   aromatic  1.375  0.020  1.375
 17N  CAQ  CAU   aromatic  1.419  0.020  1.419
 17N  CAW  CAR   aromatic  1.414  0.020  1.414
 17N  CAS  CAY   single    1.487  0.020  1.487
 17N  CAS  CAW   aromatic  1.443  0.020  1.443
 17N  CAX  CAT   aromatic  1.396  0.020  1.396
 17N  CAU  CAV   aromatic  1.410  0.020  1.410
 17N  CAV  CAX   aromatic  1.453  0.020  1.453
 17N  CAX  CAW   aromatic  1.428  0.020  1.428

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  108.95  3.000
 17N  HAAB  CAA  HAA   109.04  3.000
 17N  HAAA  CAA  HAA   108.93  3.000
 17N  HAAB  CAA  OAL   111.70  3.000
 17N  HAAA  CAA  OAL   106.32  3.000
 17N  HAA   CAA  OAL   111.80  3.000
 17N  HOAD  OAD  CAO   109.87  3.000
 17N  HOAE  OAE  CAY   109.90  3.000
 17N  HAF   CAF  CAH   119.28  3.000
 17N  HAF   CAF  CAG   118.71  3.000
 17N  CAH   CAF  CAG   122.00  3.000
 17N  HAG   CAG  CAQ   121.69  3.000
 17N  HAG   CAG  CAF   119.22  3.000
 17N  CAQ   CAG  CAF   119.09  3.000
 17N  HAH   CAH  CAV   121.56  3.000
 17N  HAH   CAH  CAF   118.31  3.000
 17N  CAV   CAH  CAF   120.13  3.000
 17N  HAI   CAI  CAR   121.97  3.000
 17N  HAI   CAI  CAP   120.65  3.000
 17N  CAR   CAI  CAP   117.31  3.000
 17N  HAJ   CAJ  CAU   118.16  3.000
 17N  HAJ   CAJ  CAS   119.50  3.000
 17N  CAU   CAJ  CAS   122.19  3.000
 17N  HAKA  CAK  HAK   110.86  3.000
 17N  HAKA  CAK  OAN   109.56  3.000
 17N  HAK   CAK  OAN   109.65  3.000
 17N  HAKA  CAK  OAM   110.23  3.000
 17N  HAK   CAK  OAM   110.16  3.000
 17N  OAN   CAK  OAM   106.27  3.000
 17N  CAQ   OAL  CAA   118.87  3.000
 17N  CAP   OAM  CAK   105.83  3.000
 17N  CAT   OAN  CAK   106.58  3.000
 17N  CAR   CAO  OAD   112.79  3.000
 17N  CAR   CAO  OAB   123.67  3.000
 17N  OAD   CAO  OAB   123.42  3.000
 17N  CAT   CAP  OAM   110.13  3.000
 17N  CAT   CAP  CAI   122.24  3.000
 17N  OAM   CAP  CAI   127.47  3.000
 17N  CAU   CAQ  OAL   115.66  3.000
 17N  CAU   CAQ  CAG   120.09  3.000
 17N  OAL   CAQ  CAG   124.26  3.000
 17N  CAW   CAR  CAO   121.48  3.000
 17N  CAW   CAR  CAI   121.47  3.000
 17N  CAO   CAR  CAI   116.35  3.000
 17N  CAY   CAS  CAW   121.38  3.000
 17N  CAW   CAS  CAJ   120.75  3.000
 17N  CAY   CAS  CAJ   116.80  3.000
 17N  CAX   CAT  CAP   122.79  3.000
 17N  CAX   CAT  OAN   128.51  3.000
 17N  CAP   CAT  OAN   108.69  3.000
 17N  CAV   CAU  CAQ   120.24  3.000
 17N  CAV   CAU  CAJ   119.64  3.000
 17N  CAQ   CAU  CAJ   120.04  3.000
 17N  CAX   CAV  CAU   118.17  3.000
 17N  CAX   CAV  CAH   123.38  3.000
 17N  CAU   CAV  CAH   118.44  3.000
 17N  CAX   CAW  CAS   117.36  3.000
 17N  CAX   CAW  CAR   120.30  3.000
 17N  CAS   CAW  CAR   122.34  3.000
 17N  CAW   CAX  CAV   120.97  3.000
 17N  CAW   CAX  CAT   115.54  3.000
 17N  CAV   CAX  CAT   123.46  3.000
 17N  CAS   CAY  OAE   113.01  3.000
 17N  CAS   CAY  OAC   123.24  3.000
 17N  OAE   CAY  OAC   123.60  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_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  CONST_46  HOAD  OAD  CAO  CAR  180.00   0.0  0
 17N  CONST_47  HOAE  OAE  CAY  CAS  180.00   0.0  0
 17N  Var_01    CAP   CAT  OAN  CAK    9.76  30.0  1
 17N  Var_02    CAT   CAP  OAM  CAK   -9.56  30.0  1
 17N  Var_03    HAK   CAK  OAM  CAP  133.89  30.0  1
 17N  Var_04    CAG   CAQ  OAL  CAA    0.75  30.0  2
 17N  Var_05    CAI   CAR  CAO  OAB  136.33  30.0  2
 17N  Var_06    CAJ   CAS  CAY  OAC  132.73  30.0  2
 17N  Var_07    HAA   CAA  OAL  CAQ   61.50  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-1  HOAD  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
 17N  plan-3  HOAE  0.020

