# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 16:15:46 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  40  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  -0.562  -0.6892  -0.0579   2.3800
 6B9  C7   C  C      0   0.406   0.5381   0.1369   2.4714
 6B9  C3   C  C      0  -0.101   1.2814   0.2298   1.1477
 6B9  C4   C  C1     0  -0.349   2.6571   0.4071   1.1263
 6B9  C5   C  C      0   0.256   3.3656   0.4706  -0.0704
 6B9  N    N  N      0  -0.385   4.7504   0.6488  -0.0016
 6B9  C6   C  C1     0  -0.177   5.4959   0.0680  -0.8407
 6B9  S    S  S2     0  -0.143   7.2189   0.3496  -0.7980
 6B9  C    C  C1     0  -0.295   2.6640   0.3909  -1.2741
 6B9  O1   O  OC    -1  -0.576   1.2079   0.2627   3.5103
 6B9  C8   C  CR6    0   0.314  -0.8810  -0.0180  -0.1359
 6B9  C2   C  C      0  -0.062   0.5908   0.1339  -0.0617
 6B9  C1   C  C1     0  -0.269   1.2898   0.2214  -1.2624
 6B9  C16  C  CR66   0   0.011  -1.7123   1.1455  -0.0984
 6B9  C17  C  CR16   0  -0.319  -1.2294   2.4409   0.1328
 6B9  C18  C  CR16   0  -0.378  -2.0726   3.5238   0.1719
 6B9  C19  C  CR6    0   0.373  -3.4515   3.3403  -0.0192
 6B9  O4   O  OH1    0  -0.613  -4.3170   4.3579   0.0139
 6B9  C20  C  CR16   0  -0.437  -3.9627   2.0711  -0.2551
 6B9  C15  C  CR66   0   0.373  -3.0900   0.9970  -0.2932
 6B9  O3   O  O      0  -0.476  -3.6313  -0.2117  -0.5290
 6B9  C10  C  CR66   0   0.420  -2.8722  -1.3235  -0.6239
 6B9  C11  C  CR16   0  -0.548  -3.5040  -2.4959  -0.8980
 6B9  C12  C  CR6    0   0.373  -2.7670  -3.7297  -1.0086
 6B9  O2   O  O      0  -0.512  -3.3122  -4.8121  -1.2569
 6B9  C13  C  CR16   0  -0.398  -1.3237  -3.6294  -0.8052
 6B9  C14  C  CR16   0  -0.283  -0.7182  -2.4548  -0.5352
 6B9  C9   C  CR66   0  -0.078  -1.4553  -1.2309  -0.4354
 6B9  H1   H  H      0   0.252   3.1952   0.4894   2.0616
 6B9  H2   H  H      0   0.288   5.1506  -0.6229  -1.6130
 6B9  H3   H  HSH1   0   0.253   7.5352  -0.4860  -1.7922
 6B9  H4   H  H      0   0.273   3.1816   0.4876  -2.2203
 6B9  H6   H  H      0   0.260   0.7534   0.1671  -2.2019
 6B9  H7   H  HCR6   0   0.272  -0.1687   2.5910   0.2829
 6B9  H8   H  HCR6   0   0.285  -1.6760   4.5148   0.3545
 6B9  H9   H  HOH1   0   0.484  -3.8598   5.1921   0.1725
 6B9  H10  H  HCR6   0   0.289  -5.0240   1.9214  -0.4073
 6B9  H11  H  HCR6   0   0.260  -4.5788  -2.5133  -1.0338
 6B9  H13  H  HCR6   0   0.256  -0.7403  -4.5394  -0.8739
 6B9  H14  H  HCR6   0   0.266   0.3533  -2.4211  -0.3858

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    1.746  0.020  1.746
 6B9  C6   N    double    1.264  0.020  1.264
 6B9  N    C5   single    1.398  0.020  1.398
 6B9  C    C5   aromatic  1.395  0.020  1.395
 6B9  C    C1   aromatic  1.385  0.020  1.385
 6B9  C5   C4   aromatic  1.392  0.020  1.392
 6B9  C1   C2   aromatic  1.392  0.020  1.392
 6B9  C4   C3   aromatic  1.387  0.020  1.387
 6B9  C2   C3   aromatic  1.396  0.020  1.396
 6B9  C2   C8   single    1.481  0.020  1.481
 6B9  C3   C7   single    1.521  0.020  1.521
 6B9  C14  C13  double    1.349  0.020  1.349
 6B9  C14  C9   single    1.432  0.020  1.432
 6B9  C13  C12  single    1.461  0.020  1.461
 6B9  C8   C9   double    1.375  0.020  1.375
 6B9  C8   C16  single    1.430  0.020  1.430
 6B9  O    C7   deloc     1.246  0.020  1.246
 6B9  C7   O1   deloc     1.243  0.020  1.243
 6B9  C9   C10  single    1.432  0.020  1.432
 6B9  C17  C16  aromatic  1.402  0.020  1.402
 6B9  C17  C18  aromatic  1.373  0.020  1.373
 6B9  C16  C15  aromatic  1.399  0.020  1.399
 6B9  C12  O2   double    1.237  0.020  1.237
 6B9  C12  C11  single    1.441  0.020  1.441
 6B9  C18  C19  aromatic  1.404  0.020  1.404
 6B9  C10  C11  double    1.360  0.020  1.360
 6B9  C10  O3   single    1.350  0.020  1.350
 6B9  C15  O3   single    1.345  0.020  1.345
 6B9  C15  C20  aromatic  1.385  0.020  1.385
 6B9  C19  C20  aromatic  1.388  0.020  1.388
 6B9  C19  O4   single    1.336  0.020  1.336
 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  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   117.26  3.000
 6B9  O1   C7   O    127.45  3.000
 6B9  C3   C7   O    115.29  3.000
 6B9  C2   C3   C4   119.08  3.000
 6B9  C2   C3   C7   120.53  3.000
 6B9  C4   C3   C7   120.39  3.000
 6B9  H1   C4   C5   119.10  3.000
 6B9  H1   C4   C3   119.31  3.000
 6B9  C5   C4   C3   121.59  3.000
 6B9  C    C5   N    123.22  3.000
 6B9  C    C5   C4   118.88  3.000
 6B9  N    C5   C4   117.88  3.000
 6B9  C6   N    C5   119.54  3.000
 6B9  H2   C6   S    115.54  3.000
 6B9  H2   C6   N    125.01  3.000
 6B9  S    C6   N    119.45  3.000
 6B9  H3   S    C6    96.57  3.000
 6B9  H4   C    C1   119.52  3.000
 6B9  H4   C    C5   120.55  3.000
 6B9  C1   C    C5   119.91  3.000
 6B9  C9   C8   C16  118.71  3.000
 6B9  C16  C8   C2   119.51  3.000
 6B9  C9   C8   C2   121.09  3.000
 6B9  C1   C2   C8   117.52  3.000
 6B9  C8   C2   C3   122.82  3.000
 6B9  C1   C2   C3   119.63  3.000
 6B9  H6   C1   C2   119.75  3.000
 6B9  H6   C1   C    119.36  3.000
 6B9  C2   C1   C    120.88  3.000
 6B9  C15  C16  C17  117.40  3.000
 6B9  C15  C16  C8   118.83  3.000
 6B9  C17  C16  C8   123.77  3.000
 6B9  H7   C17  C18  119.27  3.000
 6B9  H7   C17  C16  119.27  3.000
 6B9  C18  C17  C16  121.46  3.000
 6B9  H8   C18  C19  120.14  3.000
 6B9  H8   C18  C17  120.11  3.000
 6B9  C19  C18  C17  119.75  3.000
 6B9  C20  C19  O4   117.50  3.000
 6B9  O4   C19  C18  122.22  3.000
 6B9  C20  C19  C18  120.27  3.000
 6B9  H9   O4   C19  110.83  3.000
 6B9  H10  C20  C15  120.45  3.000
 6B9  H10  C20  C19  120.75  3.000
 6B9  C15  C20  C19  118.81  3.000
 6B9  O3   C15  C20  116.64  3.000
 6B9  C20  C15  C16  122.30  3.000
 6B9  O3   C15  C16  121.06  3.000
 6B9  C10  O3   C15  121.75  3.000
 6B9  C9   C10  C11  122.82  3.000
 6B9  C11  C10  O3   117.59  3.000
 6B9  C9   C10  O3   119.59  3.000
 6B9  H11  C11  C12  118.94  3.000
 6B9  H11  C11  C10  120.01  3.000
 6B9  C12  C11  C10  121.05  3.000
 6B9  C13  C12  O2   121.56  3.000
 6B9  O2   C12  C11  122.61  3.000
 6B9  C13  C12  C11  115.83  3.000
 6B9  H13  C13  C14  120.17  3.000
 6B9  H13  C13  C12  117.74  3.000
 6B9  C14  C13  C12  122.09  3.000
 6B9  H14  C14  C9   118.24  3.000
 6B9  H14  C14  C13  119.95  3.000
 6B9  C9   C14  C13  121.81  3.000
 6B9  C14  C9   C10  116.40  3.000
 6B9  C10  C9   C8   119.93  3.000
 6B9  C14  C9   C8   123.64  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  Var_01    C9   C8   C2   C3   -104.15  30.0  2
 6B9  Var_02    C14  C9   C8   C2      7.87  30.0  1
 6B9  Var_03    C17  C16  C8   C2     -6.27  30.0  1
 6B9  Var_04    C9   C10  O3   C15     1.67  30.0  1
 6B9  Var_05    C4   C3   C7   O    -178.16  30.0  3
 6B9  Var_06    C    C5   N    C6    -38.13  30.0  2
 6B9  Var_07    S    C6   N    C5    177.23   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-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

