# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 11:03:58 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-5-[(E)-(sulfanylmethylidene)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(ccc1C2=C3C=CC(=O)C=C3Oc4cc(O)ccc24)N=CS
#
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
 6B9  6B9  '2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-5-[(E)-(sulfanylmethylidene)amino]benzoic acid'  ligand  41  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6B9
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
 6B9  O    O  O     0  -0.418  -0.6791  -0.1337   2.4283
 6B9  C7   C  C     0   0.511   0.5160   0.0014   2.3685
 6B9  C3   C  CR6   0  -0.077   1.2757   0.1330   1.0981
 6B9  C4   C  CR16  0  -0.318   2.6572   0.2824   1.1145
 6B9  C5   C  CR6   0   0.269   3.3872   0.3828  -0.0661
 6B9  N    N  N     0  -0.386   4.7683   0.5363   0.0392
 6B9  C6   C  C1    0  -0.173   5.5277  -0.0263  -0.7994
 6B9  S    S  S2    0  -0.133   7.2490   0.2285  -0.7050
 6B9  C    C  CR16  0  -0.277   2.7027   0.3668  -1.2796
 6B9  O1   O  OH1   0  -0.591   1.2946   0.0479   3.4427
 6B9  C8   C  CR6   0   0.272  -0.8783  -0.0191  -0.2473
 6B9  C2   C  CR6   0  -0.028   0.5936   0.1003  -0.1257
 6B9  C1   C  CR16  0  -0.258   1.3259   0.2242  -1.2998
 6B9  C16  C  CR66  0   0.009  -1.6834   1.1643  -0.1396
 6B9  C17  C  CR16  0  -0.329  -1.1718   2.4424   0.1196
 6B9  C18  C  CR16  0  -0.330  -1.9928   3.5389   0.2249
 6B9  C19  C  CR6   0   0.379  -3.3762   3.3841   0.0723
 6B9  O4   O  OH1   0  -0.615  -4.1320   4.4860   0.1894
 6B9  C20  C  CR16  0  -0.480  -3.9149   2.1337  -0.1930
 6B9  C15  C  CR66  0   0.380  -3.0660   1.0419  -0.2988
 6B9  O3   O  O     0  -0.476  -3.6356  -0.1434  -0.5628
 6B9  C10  C  CR66  0   0.432  -2.9034  -1.2745  -0.7099
 6B9  C11  C  CR16  0  -0.547  -3.5550  -2.4196  -0.9986
 6B9  C12  C  CR6   0   0.379  -2.8363  -3.6733  -1.1565
 6B9  O2   O  O     0  -0.476  -3.3961  -4.7265  -1.4170
 6B9  C13  C  CR16  0  -0.391  -1.3784  -3.5992  -0.9754
 6B9  C14  C  CR16  0  -0.282  -0.7506  -2.4480  -0.6892
 6B9  C9   C  CR66  0  -0.063  -1.4702  -1.2087  -0.5461
 6B9  H1   H  HCR6  0   0.277   3.1997   0.3177   2.0485
 6B9  H2   H  H     0   0.293   5.1935  -0.6897  -1.6004
 6B9  H3   H  HSH1  0   0.256   7.5725  -0.5653  -1.7297
 6B9  H4   H  HCR6  0   0.287   3.2341   0.4941  -2.2140
 6B9  H5   H  HOH1  0   0.491   0.7506  -0.0469   4.2354
 6B9  H6   H  HCR6  0   0.275   0.8085   0.2211  -2.2503
 6B9  H7   H  HCR6  0   0.272  -0.1048   2.5745   0.2391
 6B9  H8   H  HCR6  0   0.281  -1.5817   4.5178   0.4295
 6B9  H9   H  HOH1  0   0.484  -5.0670   4.2697   0.1372
 6B9  H10  H  HCR6  0   0.298  -4.9814   1.9890  -0.3216
 6B9  H11  H  HCR6  0   0.269  -4.6311  -2.4267  -1.1122
 6B9  H13  H  HCR6  0   0.264  -0.8224  -4.5220  -1.0793
 6B9  H14  H  HCR6  0   0.270   0.3238  -2.4309  -0.5594

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
 6B9  S    C6   single    1.743  0.020  1.743
 6B9  C6   N    double    1.264  0.020  1.264
 6B9  N    C5   single    1.394  0.020  1.394
 6B9  C    C5   aromatic  1.393  0.020  1.393
 6B9  C    C1   aromatic  1.384  0.020  1.384
 6B9  C5   C4   aromatic  1.392  0.020  1.392
 6B9  C1   C2   aromatic  1.389  0.020  1.389
 6B9  C4   C3   aromatic  1.390  0.020  1.390
 6B9  C2   C3   aromatic  1.401  0.020  1.401
 6B9  C2   C8   single    1.482  0.020  1.482
 6B9  C3   C7   single    1.486  0.020  1.486
 6B9  C14  C13  double    1.342  0.020  1.342
 6B9  C14  C9   single    1.440  0.020  1.440
 6B9  C13  C12  single    1.471  0.020  1.471
 6B9  C8   C9   double    1.362  0.020  1.362
 6B9  C8   C16  single    1.435  0.020  1.435
 6B9  O    C7   double    1.204  0.020  1.204
 6B9  C7   O1   single    1.328  0.020  1.328
 6B9  C9   C10  single    1.444  0.020  1.444
 6B9  C17  C16  aromatic  1.401  0.020  1.401
 6B9  C17  C18  aromatic  1.374  0.020  1.374
 6B9  C16  C15  aromatic  1.397  0.020  1.397
 6B9  C12  O2   double    1.221  0.020  1.221
 6B9  C12  C11  single    1.454  0.020  1.454
 6B9  C18  C19  aromatic  1.400  0.020  1.400
 6B9  C10  C11  double    1.349  0.020  1.349
 6B9  C10  O3   single    1.355  0.020  1.355
 6B9  C15  O3   single    1.341  0.020  1.341
 6B9  C15  C20  aromatic  1.387  0.020  1.387
 6B9  C19  C20  aromatic  1.387  0.020  1.387
 6B9  C19  O4   single    1.341  0.020  1.341
 6B9  C4   H1   single    0.930  0.020  1.080
 6B9  C6   H2   single    0.930  0.020  1.080
 6B9  S    H3   single    1.200  0.020  1.300
 6B9  C    H4   single    0.930  0.020  1.080
 6B9  O1   H5   single    0.850  0.020  0.980
 6B9  C1   H6   single    0.930  0.020  1.080
 6B9  C17  H7   single    0.930  0.020  1.080
 6B9  C18  H8   single    0.930  0.020  1.080
 6B9  O4   H9   single    0.850  0.020  0.980
 6B9  C20  H10  single    0.930  0.020  1.080
 6B9  C11  H11  single    0.930  0.020  1.080
 6B9  C13  H13  single    0.930  0.020  1.080
 6B9  C14  H14  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
 6B9  O1   C7   C3   112.88  3.000
 6B9  O1   C7   O    123.08  3.000
 6B9  C3   C7   O    124.04  3.000
 6B9  C2   C3   C4   119.78  3.000
 6B9  C2   C3   C7   119.71  3.000
 6B9  C4   C3   C7   120.51  3.000
 6B9  H1   C4   C5   117.87  3.000
 6B9  H1   C4   C3   120.85  3.000
 6B9  C5   C4   C3   121.28  3.000
 6B9  C    C5   N    123.64  3.000
 6B9  C    C5   C4   118.70  3.000
 6B9  N    C5   C4   117.63  3.000
 6B9  C6   N    C5   119.76  3.000
 6B9  H2   C6   S    115.51  3.000
 6B9  H2   C6   N    124.98  3.000
 6B9  S    C6   N    119.51  3.000
 6B9  H3   S    C6    96.36  3.000
 6B9  H4   C    C1   119.20  3.000
 6B9  H4   C    C5   120.61  3.000
 6B9  C1   C    C5   120.17  3.000
 6B9  H5   O1   C7   109.28  3.000
 6B9  C9   C8   C16  119.53  3.000
 6B9  C16  C8   C2   118.99  3.000
 6B9  C9   C8   C2   121.34  3.000
 6B9  C1   C2   C8   117.47  3.000
 6B9  C8   C2   C3   123.85  3.000
 6B9  C1   C2   C3   118.65  3.000
 6B9  H6   C1   C2   119.35  3.000
 6B9  H6   C1   C    119.25  3.000
 6B9  C2   C1   C    121.40  3.000
 6B9  C15  C16  C17  117.54  3.000
 6B9  C15  C16  C8   118.31  3.000
 6B9  C17  C16  C8   124.14  3.000
 6B9  H7   C17  C18  118.91  3.000
 6B9  H7   C17  C16  119.48  3.000
 6B9  C18  C17  C16  121.61  3.000
 6B9  H8   C18  C19  119.75  3.000
 6B9  H8   C18  C17  120.66  3.000
 6B9  C19  C18  C17  119.58  3.000
 6B9  C20  C19  O4   122.57  3.000
 6B9  O4   C19  C18  117.15  3.000
 6B9  C20  C19  C18  120.28  3.000
 6B9  H9   O4   C19  111.01  3.000
 6B9  H10  C20  C15  119.21  3.000
 6B9  H10  C20  C19  121.68  3.000
 6B9  C15  C20  C19  119.11  3.000
 6B9  O3   C15  C20  116.79  3.000
 6B9  C20  C15  C16  121.87  3.000
 6B9  O3   C15  C16  121.34  3.000
 6B9  C10  O3   C15  121.97  3.000
 6B9  C9   C10  C11  122.85  3.000
 6B9  C11  C10  O3   118.08  3.000
 6B9  C9   C10  O3   119.06  3.000
 6B9  H11  C11  C12  118.33  3.000
 6B9  H11  C11  C10  120.56  3.000
 6B9  C12  C11  C10  121.11  3.000
 6B9  C13  C12  O2   121.62  3.000
 6B9  O2   C12  C11  122.71  3.000
 6B9  C13  C12  C11  115.67  3.000
 6B9  H13  C13  C14  120.76  3.000
 6B9  H13  C13  C12  117.02  3.000
 6B9  C14  C13  C12  122.21  3.000
 6B9  H14  C14  C9   118.06  3.000
 6B9  H14  C14  C13  120.23  3.000
 6B9  C9   C14  C13  121.71  3.000
 6B9  C14  C9   C10  116.45  3.000
 6B9  C10  C9   C8   119.74  3.000
 6B9  C14  C9   C8   123.80  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
 6B9  CONST_01  C    C5   C4   C3      0.00   0.0  0
 6B9  CONST_02  C    C1   C2   C3      0.00   0.0  0
 6B9  CONST_03  C1   C    C5   C4      0.00   0.0  0
 6B9  CONST_04  C1   C2   C3   C4      0.00   0.0  0
 6B9  CONST_05  C2   C1   C    C5      0.00   0.0  0
 6B9  CONST_06  C2   C3   C4   C5      0.00   0.0  0
 6B9  CONST_07  C19  C18  C17  C16     0.00   0.0  0
 6B9  CONST_08  C19  C20  C15  C16     0.00   0.0  0
 6B9  CONST_09  C20  C15  C16  C17     0.00   0.0  0
 6B9  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 6B9  CONST_11  C15  C16  C17  C18     0.00   0.0  0
 6B9  CONST_12  C15  C20  C19  C18     0.00   0.0  0
 6B9  CONST_13  C8   C2   C3   C4    180.00   0.0  0
 6B9  CONST_14  C8   C2   C1   C     180.00   0.0  0
 6B9  CONST_15  C5   C4   C3   C7    180.00   0.0  0
 6B9  CONST_16  C1   C2   C3   C7    180.00   0.0  0
 6B9  CONST_17  C8   C2   C3   C7      0.00   0.0  0
 6B9  CONST_18  N    C5   C4   C3    180.00   0.0  0
 6B9  CONST_19  C1   C    C5   N     180.00   0.0  0
 6B9  CONST_20  O4   C19  C18  C17   180.00   0.0  0
 6B9  CONST_21  C15  C20  C19  O4    180.00   0.0  0
 6B9  CONST_22  H6   C1   C2   C3    180.00   0.0  0
 6B9  CONST_23  H4   C    C5   C4    180.00   0.0  0
 6B9  CONST_24  H1   C4   C5   C     180.00   0.0  0
 6B9  CONST_25  H7   C17  C16  C8      0.00   0.0  0
 6B9  CONST_26  H8   C18  C17  C16   180.00   0.0  0
 6B9  CONST_27  H10  C20  C15  C16   180.00   0.0  0
 6B9  CONST_28  H5   O1   C7   C3    180.00   0.0  0
 6B9  Var_01    C9   C8   C2   C3   -100.87  30.0  2
 6B9  Var_02    C14  C9   C8   C2      3.81  30.0  1
 6B9  Var_03    C17  C16  C8   C2     -2.16  30.0  1
 6B9  Var_04    C9   C10  O3   C15     1.51  30.0  1
 6B9  Var_05    C4   C3   C7   O    -179.83  30.0  3
 6B9  Var_06    C    C5   N    C6    -38.84  30.0  2
 6B9  Var_07    S    C6   N    C5    177.25   0.0  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
 6B9  plan-1  C7   0.020
 6B9  plan-1  C3   0.020
 6B9  plan-1  C4   0.020
 6B9  plan-1  C5   0.020
 6B9  plan-1  N    0.020
 6B9  plan-1  C    0.020
 6B9  plan-1  C8   0.020
 6B9  plan-1  C2   0.020
 6B9  plan-1  C1   0.020
 6B9  plan-1  H1   0.020
 6B9  plan-1  H4   0.020
 6B9  plan-1  H6   0.020
 6B9  plan-2  C8   0.020
 6B9  plan-2  C16  0.020
 6B9  plan-2  C17  0.020
 6B9  plan-2  C18  0.020
 6B9  plan-2  C19  0.020
 6B9  plan-2  O4   0.020
 6B9  plan-2  C20  0.020
 6B9  plan-2  C15  0.020
 6B9  plan-2  O3   0.020
 6B9  plan-2  H7   0.020
 6B9  plan-2  H8   0.020
 6B9  plan-2  H10  0.020
 6B9  plan-3  C8   0.020
 6B9  plan-3  O3   0.020
 6B9  plan-3  C10  0.020
 6B9  plan-3  C11  0.020
 6B9  plan-3  C12  0.020
 6B9  plan-3  O2   0.020
 6B9  plan-3  C13  0.020
 6B9  plan-3  C14  0.020
 6B9  plan-3  C9   0.020
 6B9  plan-3  H11  0.020
 6B9  plan-3  H13  0.020
 6B9  plan-3  H14  0.020
 6B9  plan-4  O    0.020
 6B9  plan-4  C7   0.020
 6B9  plan-4  C3   0.020
 6B9  plan-4  O1   0.020
 6B9  plan-4  H5   0.020
 6B9  plan-5  C5   0.020
 6B9  plan-5  N    0.020
 6B9  plan-5  C6   0.020
 6B9  plan-5  S    0.020
 6B9  plan-5  H2   0.020

