# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jun  4 00:41:43 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 4-(acetylamino)-5-hydroxynaphthalene-2,7-disulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1cc(cc2cc(cc(O)c12)[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
 Y3  Y3  '4-(acetylamino)-5-hydroxynaphthalene-2,7-disulfonic acid'  ligand  34  23  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y3
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
 Y3  C1    C  CR6   0   0.434   1.6933  -0.0176  -1.1626
 Y3  C2    C  CR16  0  -0.375   1.2649  -0.0674  -2.4657
 Y3  C3    C  CR6   0  -0.217  -0.1052  -0.1324  -2.7457
 Y3  C4    C  CR16  0  -0.314  -1.0379  -0.1532  -1.7535
 Y3  C5    C  CR66  0   0.121  -0.6123  -0.1065  -0.4089
 Y3  C6    C  CR66  0  -0.066   0.7686  -0.0430  -0.0714
 Y3  C7    C  CR6   0   0.406   1.1332  -0.0157   1.3240
 Y3  C8    C  CR16  0  -0.310   0.1395  -0.0494   2.2788
 Y3  C9    C  CR6   0  -0.209  -1.2072  -0.1007   1.8966
 Y3  C10   C  CR16  0  -0.327  -1.6022  -0.1312   0.5963
 Y3  S11   S  S     0   1.471  -0.6313  -0.1761  -4.4336
 Y3  O12   O  OS    0  -0.626   0.4132  -0.7837  -5.2295
 Y3  O13   O  OS    0  -0.629  -1.9875  -0.6674  -4.4934
 Y3  O14   O  OS    0  -0.706  -0.7559   1.3695  -4.8080
 Y3  N15   N  NH1   0  -0.767   2.4742   0.0334   1.6800
 Y3  C16   C  C     0   0.521   3.0427   0.0989   2.9215
 Y3  O17   O  O     0  -0.456   2.4173   0.1418   3.9634
 Y3  C18   C  CH3   0  -0.791   4.5487   0.0781   2.8798
 Y3  S19   S  S     0   1.476  -2.4266  -0.1745   3.1708
 Y3  O20   O  OS    0  -0.629  -3.7346  -0.3572   2.5786
 Y3  O21   O  OS    0  -0.635  -1.9954  -1.0866   4.2110
 Y3  O22   O  OS    0  -0.712  -2.2865   1.3268   3.7000
 Y3  O23   O  OH1   0  -0.652   3.0050   0.0515  -0.8845
 Y3  H2    H  HCR6  0   0.310   1.9950  -0.0632  -3.2655
 Y3  H4    H  HCR6  0   0.295  -2.0973  -0.2104  -1.9628
 Y3  H8    H  HCR6  0   0.319   0.4033  -0.0377   3.3231
 Y3  H10   H  HCR6  0   0.294  -2.6436  -0.1783   0.3100
 Y3  HO4   H  H     0   0.508   0.1003   1.7721  -5.0295
 Y3  HN5   H  HNH1  0   0.442   3.1242   0.0118   0.9085
 Y3  H181  H  HCH3  0   0.272   4.9527   0.4791   3.8055
 Y3  H182  H  HCH3  0   0.281   4.8921  -0.9533   2.7775
 Y3  H183  H  HCH3  0   0.261   4.9522   0.6448   2.0416
 Y3  HO2   H  H     0   0.508  -2.6105   1.4184   4.6135
 Y3  HO3   H  HOH1  0   0.501   3.5444   0.0616  -1.6852

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
 Y3  C1   C2    aromatic  1.373  0.020  1.373
 Y3  C1   C6    aromatic  1.431  0.020  1.431
 Y3  C1   O23   single    1.343  0.020  1.343
 Y3  C2   C3    aromatic  1.400  0.020  1.400
 Y3  C2   H2    single    0.930  0.020  1.080
 Y3  C3   C4    aromatic  1.362  0.020  1.362
 Y3  C3   S11   single    1.768  0.020  1.768
 Y3  C4   C5    aromatic  1.411  0.020  1.411
 Y3  C4   H4    single    0.930  0.020  1.080
 Y3  C5   C6    aromatic  1.423  0.020  1.423
 Y3  C5   C10   aromatic  1.411  0.020  1.411
 Y3  C6   C7    aromatic  1.442  0.020  1.442
 Y3  C7   C8    aromatic  1.378  0.020  1.378
 Y3  C7   N15   single    1.388  0.020  1.388
 Y3  C8   C9    aromatic  1.401  0.020  1.401
 Y3  C8   H8    single    0.930  0.020  1.080
 Y3  C9   C10   aromatic  1.359  0.020  1.359
 Y3  C9   S19   single    1.765  0.020  1.765
 Y3  C10  H10   single    0.930  0.020  1.080
 Y3  S11  O12   double    1.447  0.020  1.447
 Y3  S11  O13   double    1.444  0.020  1.444
 Y3  S11  O14   single    1.595  0.020  1.595
 Y3  O14  HO4   single    0.850  0.020  0.980
 Y3  N15  C16   single    1.367  0.020  1.367
 Y3  N15  HN5   single    0.860  0.020  1.020
 Y3  C16  O17   double    1.216  0.020  1.216
 Y3  C16  C18   single    1.507  0.020  1.507
 Y3  C18  H181  single    0.970  0.020  1.090
 Y3  C18  H182  single    0.970  0.020  1.090
 Y3  C18  H183  single    0.970  0.020  1.090
 Y3  S19  O20   double    1.447  0.020  1.447
 Y3  S19  O21   double    1.449  0.020  1.449
 Y3  S19  O22   single    1.598  0.020  1.598
 Y3  O22  HO2   single    0.850  0.020  0.980
 Y3  O23  HO3   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
 Y3  O23   C1   C6    118.32  3.000
 Y3  O23   C1   C2    120.23  3.000
 Y3  C6    C1   C2    121.45  3.000
 Y3  H2    C2   C3    120.82  3.000
 Y3  H2    C2   C1    119.38  3.000
 Y3  C3    C2   C1    119.80  3.000
 Y3  S11   C3   C4    119.42  3.000
 Y3  S11   C3   C2    118.90  3.000
 Y3  C4    C3   C2    121.68  3.000
 Y3  H4    C4   C5    118.79  3.000
 Y3  H4    C4   C3    122.05  3.000
 Y3  C5    C4   C3    119.15  3.000
 Y3  C10   C5   C6    120.84  3.000
 Y3  C10   C5   C4    117.82  3.000
 Y3  C6    C5   C4    121.34  3.000
 Y3  C7    C6   C5    118.39  3.000
 Y3  C7    C6   C1    125.04  3.000
 Y3  C5    C6   C1    116.56  3.000
 Y3  N15   C7   C8    121.29  3.000
 Y3  N15   C7   C6    119.53  3.000
 Y3  C8    C7   C6    119.17  3.000
 Y3  H8    C8   C9    120.02  3.000
 Y3  H8    C8   C7    119.66  3.000
 Y3  C9    C8   C7    120.32  3.000
 Y3  S19   C9   C10   119.26  3.000
 Y3  S19   C9   C8    117.95  3.000
 Y3  C10   C9   C8    122.76  3.000
 Y3  H10   C10  C9    122.29  3.000
 Y3  H10   C10  C5    119.20  3.000
 Y3  C9    C10  C5    118.51  3.000
 Y3  O14   S11  O13   104.28  3.000
 Y3  O14   S11  O12   109.52  3.000
 Y3  O13   S11  O12   120.82  3.000
 Y3  O14   S11  C3    102.90  3.000
 Y3  O13   S11  C3    109.12  3.000
 Y3  O12   S11  C3    108.70  3.000
 Y3  HO4   O14  S11   112.71  3.000
 Y3  HN5   N15  C16   115.31  3.000
 Y3  HN5   N15  C7    115.17  3.000
 Y3  C16   N15  C7    129.52  3.000
 Y3  C18   C16  O17   122.56  3.000
 Y3  C18   C16  N15   112.95  3.000
 Y3  O17   C16  N15   124.47  3.000
 Y3  H183  C18  H182  107.62  3.000
 Y3  H183  C18  H181  109.02  3.000
 Y3  H182  C18  H181  108.14  3.000
 Y3  H183  C18  C16   112.61  3.000
 Y3  H182  C18  C16   109.27  3.000
 Y3  H181  C18  C16   110.06  3.000
 Y3  O22   S19  O21   109.12  3.000
 Y3  O22   S19  O20   109.47  3.000
 Y3  O21   S19  O20   118.89  3.000
 Y3  O22   S19  C9     98.00  3.000
 Y3  O21   S19  C9    109.81  3.000
 Y3  O20   S19  C9    109.53  3.000
 Y3  HO2   O22  S19   111.71  3.000
 Y3  HO3   O23  C1    112.00  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
 Y3  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 Y3  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 Y3  CONST_03  C10   C5   C6   C1    180.00   0.0  0
 Y3  CONST_04  C8    C7   C6   C1    180.00   0.0  0
 Y3  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 Y3  CONST_06  C7    C6   C1   C2    180.00   0.0  0
 Y3  CONST_07  C5    C4   C3   C2      0.00   0.0  0
 Y3  CONST_08  C6    C1   C2   C3      0.00   0.0  0
 Y3  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 Y3  CONST_10  C10   C5   C4   C3    180.00   0.0  0
 Y3  CONST_11  C7    C6   C5   C4    180.00   0.0  0
 Y3  CONST_12  C9    C10  C5   C4    180.00   0.0  0
 Y3  CONST_13  C8    C7   C6   C5      0.00   0.0  0
 Y3  CONST_14  C8    C9   C10  C5      0.00   0.0  0
 Y3  CONST_15  C9    C10  C5   C6      0.00   0.0  0
 Y3  CONST_16  C9    C8   C7   C6      0.00   0.0  0
 Y3  CONST_17  C10   C5   C6   C7      0.00   0.0  0
 Y3  CONST_18  C10   C9   C8   C7      0.00   0.0  0
 Y3  CONST_19  S11   C3   C2   C1    180.00   0.0  0
 Y3  CONST_20  N15   C7   C6   C1      0.00   0.0  0
 Y3  CONST_21  O23   C1   C2   C3    180.00   0.0  0
 Y3  CONST_22  S11   C3   C4   C5    180.00   0.0  0
 Y3  CONST_23  O23   C1   C6   C5    180.00   0.0  0
 Y3  CONST_24  N15   C7   C6   C5    180.00   0.0  0
 Y3  CONST_25  S19   C9   C10  C5    180.00   0.0  0
 Y3  CONST_26  O23   C1   C6   C7      0.00   0.0  0
 Y3  CONST_27  S19   C9   C8   C7    180.00   0.0  0
 Y3  CONST_28  N15   C7   C8   C9    180.00   0.0  0
 Y3  CONST_29  H4    C4   C3   C2    180.00   0.0  0
 Y3  CONST_30  H2    C2   C3   C4    180.00   0.0  0
 Y3  CONST_31  H10   C10  C5   C4      0.00   0.0  0
 Y3  CONST_32  H8    C8   C7   C6    180.00   0.0  0
 Y3  CONST_33  C16   N15  C7   C6    180.00   0.0  0
 Y3  CONST_34  C16   N15  C7   C8      0.00   0.0  0
 Y3  CONST_35  HN5   N15  C7   C6      0.00   0.0  0
 Y3  CONST_36  O17   C16  N15  C7      0.00   0.0  0
 Y3  CONST_37  C18   C16  N15  C7    180.00   0.0  0
 Y3  Var_01    O12   S11  C3   C2     28.05  30.0  2
 Y3  Var_02    O20   S19  C9   C8   -174.26  30.0  2
 Y3  Var_03    H181  C18  C16  N15   159.87  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
 Y3  plan-1  C1   0.020
 Y3  plan-1  C2   0.020
 Y3  plan-1  C3   0.020
 Y3  plan-1  C4   0.020
 Y3  plan-1  C5   0.020
 Y3  plan-1  C6   0.020
 Y3  plan-1  C7   0.020
 Y3  plan-1  C8   0.020
 Y3  plan-1  C9   0.020
 Y3  plan-1  C10  0.020
 Y3  plan-1  S11  0.020
 Y3  plan-1  N15  0.020
 Y3  plan-1  S19  0.020
 Y3  plan-1  O23  0.020
 Y3  plan-1  H2   0.020
 Y3  plan-1  H4   0.020
 Y3  plan-1  H8   0.020
 Y3  plan-1  H10  0.020
 Y3  plan-2  C7   0.020
 Y3  plan-2  N15  0.020
 Y3  plan-2  C16  0.020
 Y3  plan-2  O17  0.020
 Y3  plan-2  C18  0.020
 Y3  plan-2  HN5  0.020

