# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 02:45:34 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: 4-amino-5-hydroxynaphthalene-2,7-disulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 3I0  3I0  "4-amino-5-hydroxynaphthalene-2,7-disulfonic acid"  ligand  27  20  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3I0
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
 3I0  S1  S  S      0   1.411  50.5532  -11.3475   -1.9946
 3I0  C2  C  CR6    0   0.391  53.2509  -13.2021   -4.3520
 3I0  C3  C  CR16   0  -0.408  52.5632  -12.7127   -3.2707
 3I0  C5  C  CR16   0  -0.377  50.9114  -11.7232   -4.7064
 3I0  C6  C  CR66   0   0.143  51.6012  -12.2143   -5.8416
 3I0  C9  C  CR16   0  -0.360  52.8996  -13.1748   -8.1035
 3I0  C   C  CR6    0   0.333  53.4565  -13.4608   -6.8677
 3I0  C1  C  CR66   0  -0.079  52.7958  -12.9741   -5.6865
 3I0  C4  C  CR6    0  -0.192  51.3848  -11.9703   -3.4533
 3I0  C7  C  CR16   0  -0.390  51.0814  -11.9419   -7.1258
 3I0  C8  C  CR6    0  -0.194  51.7286  -12.4209   -8.2294
 3I0  O3  O  OS     0  -0.738  49.2848  -10.7660   -2.4638
 3I0  O4  O  OS     0  -0.750  51.4879  -10.3546   -1.4376
 3I0  O5  O  OS    -1  -0.748  50.3752  -12.5328   -1.1386
 3I0  S   S  S      0   1.408  51.0971  -12.1168   -9.8807
 3I0  H1  H  HCR6   0   0.274  52.9331  -12.9120   -2.2708
 3I0  H2  H  HCR6   0   0.256  50.0040  -11.1534   -4.8570
 3I0  H3  H  HCR6   0   0.259  53.3975  -13.5517   -8.9896
 3I0  H4  H  HNH2   0   0.394  54.8826  -14.6434   -5.9892
 3I0  H5  H  HNH2   0   0.382  54.8773  -14.6483   -7.6735
 3I0  H6  H  HCR6   0   0.252  50.1744  -11.3592   -7.2116
 3I0  H7  H  HOH1   0   0.483  54.5795  -14.0213   -3.2420
 3I0  N   N  NH2    0  -0.867  54.6381  -14.1533   -6.8303
 3I0  O6  O  OH1    0  -0.642  54.3787  -13.9205   -4.1805
 3I0  O   O  OS     0  -0.751  52.1807  -11.3983  -10.5731
 3I0  O1  O  OS    -1  -0.739  49.8746  -11.3150   -9.7044
 3I0  O2  O  OS     0  -0.752  50.8453  -13.4580  -10.4364

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
 3I0  O2  S   deloc     1.473  0.020  1.473
 3I0  O   S   deloc     1.473  0.020  1.473
 3I0  S   O1  deloc     1.473  0.020  1.473
 3I0  S   C8  single    1.794  0.020  1.794
 3I0  C8  C9  aromatic  1.398  0.020  1.398
 3I0  C8  C7  aromatic  1.366  0.020  1.366
 3I0  C9  C   aromatic  1.385  0.020  1.385
 3I0  C7  C6  aromatic  1.412  0.020  1.412
 3I0  C   N   single    1.370  0.020  1.370
 3I0  C   C1  aromatic  1.438  0.020  1.438
 3I0  C6  C1  aromatic  1.424  0.020  1.424
 3I0  C6  C5  aromatic  1.416  0.020  1.416
 3I0  C1  C2  aromatic  1.428  0.020  1.428
 3I0  C5  C4  aromatic  1.362  0.020  1.362
 3I0  C2  O6  single    1.348  0.020  1.348
 3I0  C2  C3  aromatic  1.372  0.020  1.372
 3I0  C4  C3  aromatic  1.405  0.020  1.405
 3I0  C4  S1  single    1.791  0.020  1.791
 3I0  O3  S1  deloc     1.472  0.020  1.472
 3I0  S1  O4  deloc     1.473  0.020  1.473
 3I0  S1  O5  deloc     1.473  0.020  1.473
 3I0  C3  H1  single    0.930  0.020  1.080
 3I0  C5  H2  single    0.930  0.020  1.080
 3I0  C9  H3  single    0.930  0.020  1.080
 3I0  N   H4  single    0.890  0.020  1.040
 3I0  N   H5  single    0.890  0.020  1.040
 3I0  C7  H6  single    0.930  0.020  1.080
 3I0  O6  H7  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
 3I0  O5  S1  O4  113.54  3.000
 3I0  O5  S1  O3  113.51  3.000
 3I0  O4  S1  O3  113.64  3.000
 3I0  O5  S1  C4  104.45  3.000
 3I0  O4  S1  C4  104.35  3.000
 3I0  O3  S1  C4  106.14  3.000
 3I0  O6  C2  C1  118.07  3.000
 3I0  O6  C2  C3  120.62  3.000
 3I0  C1  C2  C3  121.32  3.000
 3I0  H1  C3  C4  120.21  3.000
 3I0  H1  C3  C2  119.35  3.000
 3I0  C4  C3  C2  120.44  3.000
 3I0  H2  C5  C4  121.00  3.000
 3I0  H2  C5  C6  118.65  3.000
 3I0  C4  C5  C6  120.34  3.000
 3I0  C7  C6  C1  120.71  3.000
 3I0  C1  C6  C5  120.41  3.000
 3I0  C7  C6  C5  118.88  3.000
 3I0  H3  C9  C8  119.90  3.000
 3I0  H3  C9  C   118.22  3.000
 3I0  C8  C9  C   121.88  3.000
 3I0  C1  C   N   123.01  3.000
 3I0  C1  C   C9  118.57  3.000
 3I0  N   C   C9  118.38  3.000
 3I0  C   C1  C6  118.45  3.000
 3I0  C6  C1  C2  117.01  3.000
 3I0  C   C1  C2  124.54  3.000
 3I0  C5  C4  C3  120.47  3.000
 3I0  C3  C4  S1  117.87  3.000
 3I0  C5  C4  S1  121.65  3.000
 3I0  H6  C7  C8  121.48  3.000
 3I0  H6  C7  C6  119.00  3.000
 3I0  C8  C7  C6  119.53  3.000
 3I0  S   C8  C7  121.16  3.000
 3I0  C7  C8  C9  120.86  3.000
 3I0  S   C8  C9  117.97  3.000
 3I0  O2  S   O1  113.51  3.000
 3I0  O1  S   C8  105.92  3.000
 3I0  O2  S   C8  104.66  3.000
 3I0  C8  S   O   104.86  3.000
 3I0  O1  S   O   113.67  3.000
 3I0  O2  S   O   113.10  3.000
 3I0  H5  N   H4  113.83  3.000
 3I0  H5  N   C   115.51  3.000
 3I0  H4  N   C   118.67  3.000
 3I0  H7  O6  C2  110.70  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
 3I0  CONST_01  C9  C   C1  C2   180.00   0.0  0
 3I0  CONST_02  C7  C6  C1  C2   180.00   0.0  0
 3I0  CONST_03  C5  C6  C1  C2     0.00   0.0  0
 3I0  CONST_04  C5  C4  C3  C2     0.00   0.0  0
 3I0  CONST_05  C   C1  C2  C3   180.00   0.0  0
 3I0  CONST_06  C6  C1  C2  C3     0.00   0.0  0
 3I0  CONST_07  C6  C5  C4  C3     0.00   0.0  0
 3I0  CONST_08  C8  C7  C6  C5   180.00   0.0  0
 3I0  CONST_09  C   C1  C6  C5   180.00   0.0  0
 3I0  CONST_10  C9  C8  C7  C6     0.00   0.0  0
 3I0  CONST_11  C9  C   C1  C6     0.00   0.0  0
 3I0  CONST_12  C7  C8  C9  C      0.00   0.0  0
 3I0  CONST_13  C7  C6  C1  C      0.00   0.0  0
 3I0  CONST_14  C8  C9  C   C1     0.00   0.0  0
 3I0  CONST_15  C8  C7  C6  C1     0.00   0.0  0
 3I0  CONST_16  C4  C5  C6  C1     0.00   0.0  0
 3I0  CONST_17  C4  C3  C2  C1     0.00   0.0  0
 3I0  CONST_18  C7  C6  C5  C4   180.00   0.0  0
 3I0  CONST_19  C6  C5  C4  S1   180.00   0.0  0
 3I0  CONST_20  C2  C3  C4  S1   180.00   0.0  0
 3I0  CONST_21  N   C   C1  C2     0.00   0.0  0
 3I0  CONST_22  S   C8  C7  C6   180.00   0.0  0
 3I0  CONST_23  N   C   C1  C6   180.00   0.0  0
 3I0  CONST_24  O6  C2  C1  C6   180.00   0.0  0
 3I0  CONST_25  C8  C9  C   N    180.00   0.0  0
 3I0  CONST_26  S   C8  C9  C    180.00   0.0  0
 3I0  CONST_27  O6  C2  C1  C      0.00   0.0  0
 3I0  CONST_28  O6  C2  C3  C4   180.00   0.0  0
 3I0  CONST_29  H2  C5  C4  C3   180.00   0.0  0
 3I0  CONST_30  H6  C7  C6  C5     0.00   0.0  0
 3I0  CONST_31  H1  C3  C4  C5   180.00   0.0  0
 3I0  CONST_32  H6  C7  C8  C9   180.00   0.0  0
 3I0  CONST_33  H3  C9  C   C1   180.00   0.0  0
 3I0  CONST_34  H6  C7  C6  C1   180.00   0.0  0
 3I0  CONST_35  H2  C5  C6  C1   180.00   0.0  0
 3I0  CONST_36  H1  C3  C2  C1   180.00   0.0  0
 3I0  CONST_37  H3  C9  C8  C7   180.00   0.0  0
 3I0  CONST_38  H2  C5  C6  C7     0.00   0.0  0
 3I0  Var_01    O3  S1  C4  C3  -173.15  30.0  2
 3I0  Var_02    O4  S1  C4  C3    66.53  30.0  2
 3I0  Var_03    O5  S1  C4  C3   -52.92  30.0  2
 3I0  Var_04    O3  S1  C4  C5     7.79  30.0  2
 3I0  Var_05    O4  S1  C4  C5  -112.54  30.0  2
 3I0  Var_06    O5  S1  C4  C5   128.02  30.0  2
 3I0  Var_07    O2  S   C8  C9    59.60  30.0  2
 3I0  Var_08    O   S   C8  C9   -59.67  30.0  2
 3I0  Var_09    O1  S   C8  C9   179.83  30.0  2
 3I0  Var_10    C7  C8  S   O    120.88  30.0  2
 3I0  Var_11    O2  S   C8  C7  -119.85  30.0  2
 3I0  Var_12    O1  S   C8  C7     0.38  30.0  2

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
 3I0  plan-1  S1  0.020
 3I0  plan-1  C2  0.020
 3I0  plan-1  C3  0.020
 3I0  plan-1  C5  0.020
 3I0  plan-1  C6  0.020
 3I0  plan-1  C9  0.020
 3I0  plan-1  C   0.020
 3I0  plan-1  C1  0.020
 3I0  plan-1  C4  0.020
 3I0  plan-1  C7  0.020
 3I0  plan-1  C8  0.020
 3I0  plan-1  S   0.020
 3I0  plan-1  H1  0.020
 3I0  plan-1  H2  0.020
 3I0  plan-1  H3  0.020
 3I0  plan-1  H6  0.020
 3I0  plan-1  N   0.020
 3I0  plan-1  O6  0.020
 3I0  plan-2  C   0.020
 3I0  plan-2  H4  0.020
 3I0  plan-2  H5  0.020
 3I0  plan-2  N   0.020

