# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 03:59:51 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 8-methoxypyrene-1,3,6-trisulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(c2ccc3c4c(ccc1c24)c(cc3[S](O)(=O)=O)[S](O)(=O)=O)[S](O)(=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
 2M9  2M9  '8-methoxypyrene-1,3,6-trisulfonic acid'  ligand  39  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2M9
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
 2M9  OAJ  O  OS    -1  -0.751  -3.8323  -2.9627   1.1634
 2M9  SBD  S  S      0   1.423  -4.0201  -2.1926  -0.0783
 2M9  OAC  O  OS     0  -0.751  -3.7897  -2.9848  -1.2989
 2M9  OAD  O  OS     0  -0.731  -5.2861  -1.4420  -0.1077
 2M9  CAT  C  CR6    0  -0.328  -2.7219  -0.9450  -0.0669
 2M9  CAM  C  CR16   0  -0.306  -3.1067   0.3825  -0.0954
 2M9  CAS  C  CR6    0  -0.326  -2.1750   1.4054  -0.0833
 2M9  SBC  S  S      0   1.423  -2.7929   3.0966  -0.1086
 2M9  OAA  O  OS     0  -0.749  -2.1813   3.7262  -1.2913
 2M9  OAB  O  OS     0  -0.731  -4.2565   2.9758  -0.2115
 2M9  OAI  O  OS    -1  -0.753  -2.3481   3.6887   1.1650
 2M9  CAW  C  CR66   0   0.152  -0.8035   1.1150  -0.0396
 2M9  CAO  C  CR16   0  -0.352   0.2080   2.1278  -0.0144
 2M9  CAP  C  CR16   0  -0.339   1.5222   1.8199   0.0167
 2M9  CAX  C  CR66   0   0.166  -1.3617  -1.2892  -0.0314
 2M9  CBA  C  C      0   0.112  -0.3922  -0.2468  -0.0186
 2M9  CBB  C  CR66   0   0.151   1.0031  -0.5677   0.0146
 2M9  CAY  C  CR6    0   0.130   1.9788   0.4656   0.0276
 2M9  CAQ  C  CR16   0  -0.357  -0.9051  -2.6459  -0.0084
 2M9  CAR  C  CR16   0  -0.282   0.4114  -2.9454   0.0222
 2M9  CAZ  C  CR6    0  -0.070   1.4047  -1.9236   0.0330
 2M9  CAV  C  C      0   0.380   2.7745  -2.2378   0.0607
 2M9  OBF  O  O2     0  -0.459   3.0851  -3.5402   0.0773
 2M9  CAG  C  CH3    0  -0.441   4.4478  -3.9235   0.0990
 2M9  CAN  C  C1     0  -0.438   3.7228  -1.2238   0.0678
 2M9  CAU  C  C      0  -0.320   3.3331   0.1044   0.0517
 2M9  SBE  S  S      0   1.428   4.6438   1.3448   0.0580
 2M9  OAK  O  OS     0  -0.747   4.4473   2.1176  -1.1795
 2M9  OAE  O  OS     0  -0.748   4.4255   2.1294   1.2845
 2M9  OAF  O  OS    -1  -0.729   5.9046   0.5854   0.0734
 2M9  H1   H  HCR6   0   0.280  -4.1583   0.6256  -0.1276
 2M9  H2   H  HCR6   0   0.255  -0.0708   3.1691  -0.0240
 2M9  H3   H  HCR6   0   0.257   2.2322   2.6309   0.0349
 2M9  H4   H  HCR6   0   0.257  -1.6147  -3.4567  -0.0171
 2M9  H5   H  HCR6   0   0.260   0.7133  -3.9830   0.0384
 2M9  H6   H  HCH3   0   0.235   4.9576  -3.5579   0.9933
 2M9  H7   H  HCH3   0   0.266   4.4595  -5.0100   0.1068
 2M9  H8   H  HCH3   0   0.235   4.9819  -3.5700  -0.7860
 2M9  H9   H  H      0   0.299   4.7782  -1.4536   0.0872

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
 2M9  OAA  SBC  deloc     1.473  0.020  1.473
 2M9  OAD  SBD  deloc     1.472  0.020  1.472
 2M9  OAB  SBC  deloc     1.472  0.020  1.472
 2M9  SBC  OAI  deloc     1.473  0.020  1.473
 2M9  SBC  CAS  single    1.801  0.020  1.801
 2M9  CAM  CAS  aromatic  1.384  0.020  1.384
 2M9  CAM  CAT  aromatic  1.383  0.020  1.383
 2M9  OAC  SBD  deloc     1.473  0.020  1.473
 2M9  SBD  CAT  single    1.800  0.020  1.800
 2M9  SBD  OAJ  deloc     1.473  0.020  1.473
 2M9  CAS  CAW  aromatic  1.403  0.020  1.403
 2M9  CAT  CAX  aromatic  1.403  0.020  1.403
 2M9  CAW  CAO  aromatic  1.432  0.020  1.432
 2M9  CAW  CBA  aromatic  1.423  0.020  1.423
 2M9  CAO  CAP  aromatic  1.350  0.020  1.350
 2M9  CAX  CBA  aromatic  1.424  0.020  1.424
 2M9  CAX  CAQ  aromatic  1.432  0.020  1.432
 2M9  CBA  CBB  aromatic  1.432  0.020  1.432
 2M9  CAQ  CAR  aromatic  1.351  0.020  1.351
 2M9  CAP  CAY  aromatic  1.429  0.020  1.429
 2M9  CBB  CAY  aromatic  1.421  0.020  1.421
 2M9  CBB  CAZ  aromatic  1.414  0.020  1.414
 2M9  CAR  CAZ  aromatic  1.425  0.020  1.425
 2M9  CAY  CAU  aromatic  1.402  0.020  1.402
 2M9  CAZ  CAV  aromatic  1.406  0.020  1.406
 2M9  OAE  SBE  deloc     1.472  0.020  1.472
 2M9  CAU  SBE  single    1.805  0.020  1.805
 2M9  CAU  CAN  aromatic  1.384  0.020  1.384
 2M9  CAV  CAN  aromatic  1.388  0.020  1.388
 2M9  CAV  OBF  single    1.339  0.020  1.339
 2M9  SBE  OAK  deloc     1.472  0.020  1.472
 2M9  SBE  OAF  deloc     1.472  0.020  1.472
 2M9  OBF  CAG  single    1.416  0.020  1.416
 2M9  CAM  H1   single    0.930  0.020  1.080
 2M9  CAO  H2   single    0.930  0.020  1.080
 2M9  CAP  H3   single    0.930  0.020  1.080
 2M9  CAQ  H4   single    0.930  0.020  1.080
 2M9  CAR  H5   single    0.930  0.020  1.080
 2M9  CAG  H6   single    0.970  0.020  1.090
 2M9  CAG  H7   single    0.970  0.020  1.090
 2M9  CAG  H8   single    0.970  0.020  1.090
 2M9  CAN  H9   single    0.930  0.020  1.080

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
 2M9  CAT  SBD  OAD  105.48  3.000
 2M9  CAT  SBD  OAC  105.37  3.000
 2M9  OAD  SBD  OAC  113.09  3.000
 2M9  CAT  SBD  OAJ  105.37  3.000
 2M9  OAC  SBD  OAJ  113.41  3.000
 2M9  OAD  SBD  OAJ  113.14  3.000
 2M9  CAX  CAT  CAM  120.38  3.000
 2M9  CAX  CAT  SBD  121.94  3.000
 2M9  CAM  CAT  SBD  117.68  3.000
 2M9  H1   CAM  CAS  119.32  3.000
 2M9  H1   CAM  CAT  119.20  3.000
 2M9  CAS  CAM  CAT  121.48  3.000
 2M9  CAW  CAS  SBC  122.03  3.000
 2M9  CAW  CAS  CAM  120.38  3.000
 2M9  SBC  CAS  CAM  117.59  3.000
 2M9  OAI  SBC  OAB  113.18  3.000
 2M9  OAI  SBC  OAA  113.39  3.000
 2M9  OAB  SBC  OAA  113.06  3.000
 2M9  OAI  SBC  CAS  105.18  3.000
 2M9  OAB  SBC  CAS  105.37  3.000
 2M9  OAA  SBC  CAS  105.68  3.000
 2M9  CBA  CAW  CAO  118.21  3.000
 2M9  CBA  CAW  CAS  118.77  3.000
 2M9  CAO  CAW  CAS  123.02  3.000
 2M9  H2   CAO  CAP  118.18  3.000
 2M9  H2   CAO  CAW  120.03  3.000
 2M9  CAP  CAO  CAW  121.79  3.000
 2M9  H3   CAP  CAY  120.15  3.000
 2M9  H3   CAP  CAO  118.03  3.000
 2M9  CAY  CAP  CAO  121.82  3.000
 2M9  CAQ  CAX  CBA  118.46  3.000
 2M9  CAQ  CAX  CAT  122.81  3.000
 2M9  CBA  CAX  CAT  118.73  3.000
 2M9  CBB  CBA  CAX  119.98  3.000
 2M9  CBB  CBA  CAW  119.77  3.000
 2M9  CAX  CBA  CAW  120.26  3.000
 2M9  CAZ  CBB  CAY  120.13  3.000
 2M9  CAZ  CBB  CBA  119.46  3.000
 2M9  CAY  CBB  CBA  120.41  3.000
 2M9  CAU  CAY  CBB  118.43  3.000
 2M9  CAU  CAY  CAP  123.57  3.000
 2M9  CBB  CAY  CAP  118.00  3.000
 2M9  H4   CAQ  CAR  118.37  3.000
 2M9  H4   CAQ  CAX  120.20  3.000
 2M9  CAR  CAQ  CAX  121.43  3.000
 2M9  H5   CAR  CAZ  119.58  3.000
 2M9  H5   CAR  CAQ  119.05  3.000
 2M9  CAZ  CAR  CAQ  121.37  3.000
 2M9  CAV  CAZ  CAR  121.27  3.000
 2M9  CAV  CAZ  CBB  119.43  3.000
 2M9  CAR  CAZ  CBB  119.30  3.000
 2M9  CAN  CAV  OBF  123.50  3.000
 2M9  OBF  CAV  CAZ  116.34  3.000
 2M9  CAN  CAV  CAZ  120.16  3.000
 2M9  CAG  OBF  CAV  119.13  3.000
 2M9  H8   CAG  H7   108.91  3.000
 2M9  H8   CAG  H6   109.07  3.000
 2M9  H7   CAG  H6   108.89  3.000
 2M9  H8   CAG  OBF  111.75  3.000
 2M9  H7   CAG  OBF  106.33  3.000
 2M9  H6   CAG  OBF  111.78  3.000
 2M9  H9   CAN  CAU  118.64  3.000
 2M9  H9   CAN  CAV  120.80  3.000
 2M9  CAU  CAN  CAV  120.56  3.000
 2M9  SBE  CAU  CAN  117.07  3.000
 2M9  CAN  CAU  CAY  121.29  3.000
 2M9  SBE  CAU  CAY  121.64  3.000
 2M9  OAF  SBE  OAE  113.16  3.000
 2M9  OAF  SBE  OAK  113.20  3.000
 2M9  OAE  SBE  OAK  113.62  3.000
 2M9  OAF  SBE  CAU  105.52  3.000
 2M9  OAK  SBE  CAU  105.13  3.000
 2M9  OAE  SBE  CAU  105.16  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
 2M9  CONST_01  CAW  CAS  CAM  CAT     0.00   0.0  0
 2M9  CONST_02  CAW  CBA  CAX  CAT     0.00   0.0  0
 2M9  CONST_03  CBB  CBA  CAX  CAT   180.00   0.0  0
 2M9  CONST_04  CAR  CAQ  CAX  CAT   180.00   0.0  0
 2M9  CONST_05  CAO  CAW  CAS  CAM   180.00   0.0  0
 2M9  CONST_06  CBA  CAW  CAS  CAM     0.00   0.0  0
 2M9  CONST_07  CBA  CAX  CAT  CAM     0.00   0.0  0
 2M9  CONST_08  CAQ  CAX  CAT  CAM   180.00   0.0  0
 2M9  CONST_09  CAX  CAT  CAM  CAS     0.00   0.0  0
 2M9  CONST_10  CAP  CAO  CAW  CAS   180.00   0.0  0
 2M9  CONST_11  CAX  CBA  CAW  CAS     0.00   0.0  0
 2M9  CONST_12  CBB  CBA  CAW  CAS   180.00   0.0  0
 2M9  CONST_13  CAY  CAP  CAO  CAW     0.00   0.0  0
 2M9  CONST_14  CAQ  CAX  CBA  CAW   180.00   0.0  0
 2M9  CONST_15  CAY  CBB  CBA  CAW     0.00   0.0  0
 2M9  CONST_16  CAZ  CBB  CBA  CAW   180.00   0.0  0
 2M9  CONST_17  CAX  CBA  CAW  CAO   180.00   0.0  0
 2M9  CONST_18  CBB  CBA  CAW  CAO     0.00   0.0  0
 2M9  CONST_19  CBB  CAY  CAP  CAO     0.00   0.0  0
 2M9  CONST_20  CAU  CAY  CAP  CAO   180.00   0.0  0
 2M9  CONST_21  CBA  CAW  CAO  CAP     0.00   0.0  0
 2M9  CONST_22  CBA  CBB  CAY  CAP     0.00   0.0  0
 2M9  CONST_23  CAZ  CBB  CAY  CAP   180.00   0.0  0
 2M9  CONST_24  CAN  CAU  CAY  CAP   180.00   0.0  0
 2M9  CONST_25  CAY  CBB  CBA  CAX   180.00   0.0  0
 2M9  CONST_26  CAZ  CBB  CBA  CAX     0.00   0.0  0
 2M9  CONST_27  CAZ  CAR  CAQ  CAX     0.00   0.0  0
 2M9  CONST_28  CAR  CAQ  CAX  CBA     0.00   0.0  0
 2M9  CONST_29  CAU  CAY  CBB  CBA   180.00   0.0  0
 2M9  CONST_30  CAR  CAZ  CBB  CBA     0.00   0.0  0
 2M9  CONST_31  CAV  CAZ  CBB  CBA   180.00   0.0  0
 2M9  CONST_32  CAQ  CAX  CBA  CBB     0.00   0.0  0
 2M9  CONST_33  CAN  CAU  CAY  CBB     0.00   0.0  0
 2M9  CONST_34  CAQ  CAR  CAZ  CBB     0.00   0.0  0
 2M9  CONST_35  CAN  CAV  CAZ  CBB     0.00   0.0  0
 2M9  CONST_36  CAR  CAZ  CBB  CAY   180.00   0.0  0
 2M9  CONST_37  CAV  CAZ  CBB  CAY     0.00   0.0  0
 2M9  CONST_38  CAV  CAN  CAU  CAY     0.00   0.0  0
 2M9  CONST_39  CAV  CAZ  CAR  CAQ   180.00   0.0  0
 2M9  CONST_40  CAN  CAV  CAZ  CAR   180.00   0.0  0
 2M9  CONST_41  CAU  CAY  CBB  CAZ     0.00   0.0  0
 2M9  CONST_42  CAU  CAN  CAV  CAZ     0.00   0.0  0
 2M9  CONST_43  CAS  CAM  CAT  SBD   180.00   0.0  0
 2M9  CONST_44  CBA  CAX  CAT  SBD   180.00   0.0  0
 2M9  CONST_45  CAQ  CAX  CAT  SBD     0.00   0.0  0
 2M9  CONST_46  SBC  CAS  CAM  CAT   180.00   0.0  0
 2M9  CONST_47  CAO  CAW  CAS  SBC     0.00   0.0  0
 2M9  CONST_48  CBA  CAW  CAS  SBC   180.00   0.0  0
 2M9  CONST_49  SBE  CAU  CAY  CAP     0.00   0.0  0
 2M9  CONST_50  SBE  CAU  CAY  CBB   180.00   0.0  0
 2M9  CONST_51  OBF  CAV  CAZ  CBB   180.00   0.0  0
 2M9  CONST_52  OBF  CAV  CAZ  CAR     0.00   0.0  0
 2M9  CONST_53  SBE  CAU  CAN  CAV   180.00   0.0  0
 2M9  CONST_54  CAU  CAN  CAV  OBF   180.00   0.0  0
 2M9  CONST_55  H4   CAQ  CAX  CAT     0.00   0.0  0
 2M9  CONST_56  H2   CAO  CAW  CAS     0.00   0.0  0
 2M9  CONST_57  H1   CAM  CAS  CAW   180.00   0.0  0
 2M9  CONST_58  H3   CAP  CAO  CAW   180.00   0.0  0
 2M9  CONST_59  H5   CAR  CAQ  CAX   180.00   0.0  0
 2M9  CONST_60  H9   CAN  CAU  CAY   180.00   0.0  0
 2M9  Var_01    CAM  CAT  SBD  OAJ  -120.37  30.0  2
 2M9  Var_02    OAA  SBC  CAS  CAM  -122.90  30.0  3
 2M9  Var_03    OAE  SBE  CAU  CAY    60.59  30.0  2
 2M9  Var_04    CAN  CAV  OBF  CAG    -0.22  30.0  2
 2M9  Var_05    H6   CAG  OBF  CAV    61.45  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
 2M9  plan-1  SBD  0.020
 2M9  plan-1  CAT  0.020
 2M9  plan-1  CAM  0.020
 2M9  plan-1  CAS  0.020
 2M9  plan-1  SBC  0.020
 2M9  plan-1  CAW  0.020
 2M9  plan-1  CAO  0.020
 2M9  plan-1  CAP  0.020
 2M9  plan-1  CAX  0.020
 2M9  plan-1  CBA  0.020
 2M9  plan-1  CBB  0.020
 2M9  plan-1  CAY  0.020
 2M9  plan-1  CAQ  0.020
 2M9  plan-1  CAR  0.020
 2M9  plan-1  CAZ  0.020
 2M9  plan-1  CAV  0.020
 2M9  plan-1  OBF  0.020
 2M9  plan-1  CAN  0.020
 2M9  plan-1  CAU  0.020
 2M9  plan-1  SBE  0.020
 2M9  plan-1  H1   0.020
 2M9  plan-1  H2   0.020
 2M9  plan-1  H3   0.020
 2M9  plan-1  H4   0.020
 2M9  plan-1  H5   0.020
 2M9  plan-1  H9   0.020

