# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 15:54:42 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-5-[(sulfanylcarbonyl)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(NC(S)=O)ccc1C2=C3C=CC(=O)C=C3Oc4cc(O)ccc24
#
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
 52M  52M  '2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)-5-[(sulfanylcarbonyl)amino]benzoic acid'  ligand  41  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_52M
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
 52M  S1   S  S2     0  -0.211  -7.0347   0.9532   0.8828
 52M  C21  C  C      0   0.373  -5.4923   0.5855   0.0418
 52M  N1   N  NH1    0  -0.725  -4.4449   0.6881   0.8919
 52M  C17  C  CR6    0   0.394  -3.0857   0.4828   0.6221
 52M  C18  C  CR16   0  -0.357  -2.5517   0.3212  -0.6525
 52M  C19  C  CR6    0  -0.099  -1.1851   0.1379  -0.8307
 52M  C20  C  C      0   0.412  -0.6235  -0.0396  -2.2341
 52M  O4   O  OC    -1  -0.576  -1.4302  -0.0161  -3.1789
 52M  O5   O  O      0  -0.559   0.6110  -0.1935  -2.2942
 52M  C16  C  CR16   0  -0.332  -2.2300   0.4556   1.7244
 52M  C15  C  CR16   0  -0.266  -0.8733   0.2703   1.5468
 52M  C14  C  CR6    0  -0.066  -0.3362   0.1096   0.2720
 52M  C10  C  CR6    0   0.316   1.1321  -0.0550   0.1644
 52M  C9   C  CR66   0  -0.075   1.7337  -1.2639   0.4257
 52M  C4   C  CR66   0   0.419   3.1620  -1.3585   0.4617
 52M  O2   O  O      0  -0.476   3.9083  -0.2495   0.2720
 52M  C5   C  CR16   0  -0.548   3.8185  -2.5281   0.6858
 52M  C8   C  CR16   0  -0.283   1.0100  -2.4823   0.6303
 52M  C7   C  CR16   0  -0.398   1.6393  -3.6546   0.8522
 52M  C6   C  CR6    0   0.372   3.0960  -3.7572   0.8964
 52M  O3   O  O      0  -0.513   3.6637  -4.8374   1.1014
 52M  C11  C  CR6    0   0.006   1.9573   1.1018   0.0016
 52M  C3   C  CR6    0   0.375   3.3457   0.9530   0.0609
 52M  C2   C  C1     0  -0.483   4.2113   2.0257  -0.0905
 52M  C12  C  C1     0  -0.318   1.4545   2.3934  -0.2220
 52M  C13  C  C1     0  -0.334   2.2883   3.4713  -0.3741
 52M  C1   C  C      0   0.379   3.6800   3.2887  -0.3088
 52M  O1   O  OH1    0  -0.613   4.4458   4.3724  -0.4640
 52M  O6   O  O      0  -0.425  -5.4411   0.2946  -1.1282
 52M  H1   H  HSH1   0   0.265  -7.8147   0.6788  -0.1665
 52M  H2   H  HNH1   0   0.426  -4.6562   0.8919   1.8584
 52M  H3   H  HCR6   0   0.278  -3.1793   0.3352  -1.5281
 52M  H5   H  HCR6   0   0.278  -2.6253   0.5794   2.7256
 52M  H6   H  HCR6   0   0.262  -0.2248   0.2527   2.4138
 52M  H7   H  HCR6   0   0.260   4.9014  -2.5464   0.7068
 52M  H9   H  HCR6   0   0.264  -0.0712  -2.4470   0.5983
 52M  H10  H  HCR6   0   0.255   1.0657  -4.5613   1.0016
 52M  H11  H  H      0   0.296   5.2824   1.8682  -0.0372
 52M  H12  H  H      0   0.269   0.3841   2.5398  -0.2746
 52M  H13  H  H      0   0.277   1.8864   4.4608  -0.5469
 52M  H14  H  HOH1   0   0.484   5.3818   4.1470  -0.4030

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
 52M  O1   C1   single    1.336  0.020  1.336
 52M  C1   C2   aromatic  1.388  0.020  1.388
 52M  C1   C13  aromatic  1.405  0.020  1.405
 52M  C2   C3   aromatic  1.387  0.020  1.387
 52M  C13  C12  aromatic  1.371  0.020  1.371
 52M  C3   O2   single    1.344  0.020  1.344
 52M  C3   C11  aromatic  1.398  0.020  1.398
 52M  C12  C11  aromatic  1.404  0.020  1.404
 52M  O2   C4   single    1.350  0.020  1.350
 52M  C11  C10  single    1.430  0.020  1.430
 52M  O5   C20  deloc     1.246  0.020  1.246
 52M  C4   C5   double    1.360  0.020  1.360
 52M  C4   C9   single    1.432  0.020  1.432
 52M  C10  C9   double    1.375  0.020  1.375
 52M  C10  C14  single    1.481  0.020  1.481
 52M  C5   C6   single    1.441  0.020  1.441
 52M  C9   C8   single    1.432  0.020  1.432
 52M  C20  O4   deloc     1.243  0.020  1.243
 52M  C20  C19  single    1.522  0.020  1.522
 52M  C14  C19  aromatic  1.392  0.020  1.392
 52M  C14  C15  aromatic  1.393  0.020  1.393
 52M  C19  C18  aromatic  1.390  0.020  1.390
 52M  C15  C16  aromatic  1.381  0.020  1.381
 52M  C6   O3   double    1.237  0.020  1.237
 52M  C6   C7   single    1.461  0.020  1.461
 52M  C8   C7   double    1.349  0.020  1.349
 52M  C18  C17  aromatic  1.391  0.020  1.391
 52M  C16  C17  aromatic  1.396  0.020  1.396
 52M  C17  N1   single    1.401  0.020  1.401
 52M  N1   C21  single    1.353  0.020  1.353
 52M  C21  O6   double    1.207  0.020  1.207
 52M  C21  S1   single    1.795  0.020  1.795
 52M  S1   H1   single    1.200  0.020  1.300
 52M  N1   H2   single    0.860  0.020  1.020
 52M  C18  H3   single    0.930  0.020  1.080
 52M  C16  H5   single    0.930  0.020  1.080
 52M  C15  H6   single    0.930  0.020  1.080
 52M  C5   H7   single    0.930  0.020  1.080
 52M  C8   H9   single    0.930  0.020  1.080
 52M  C7   H10  single    0.930  0.020  1.080
 52M  C2   H11  single    0.930  0.020  1.080
 52M  C12  H12  single    0.930  0.020  1.080
 52M  C13  H13  single    0.930  0.020  1.080
 52M  O1   H14  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
 52M  H1   S1   C21   95.26  3.000
 52M  O6   C21  N1   126.49  3.000
 52M  O6   C21  S1   122.69  3.000
 52M  N1   C21  S1   110.82  3.000
 52M  H2   N1   C17  114.64  3.000
 52M  H2   N1   C21  117.03  3.000
 52M  C17  N1   C21  128.25  3.000
 52M  C16  C17  C18  119.07  3.000
 52M  C16  C17  N1   116.46  3.000
 52M  C18  C17  N1   124.46  3.000
 52M  H3   C18  C19  118.05  3.000
 52M  H3   C18  C17  121.29  3.000
 52M  C19  C18  C17  120.66  3.000
 52M  C14  C19  C20  120.21  3.000
 52M  C14  C19  C18  120.04  3.000
 52M  C20  C19  C18  119.75  3.000
 52M  O5   C20  O4   127.53  3.000
 52M  O4   C20  C19  117.35  3.000
 52M  O5   C20  C19  115.12  3.000
 52M  H5   C16  C15  119.51  3.000
 52M  H5   C16  C17  120.26  3.000
 52M  C15  C16  C17  120.23  3.000
 52M  H6   C15  C14  120.00  3.000
 52M  H6   C15  C16  119.19  3.000
 52M  C14  C15  C16  120.81  3.000
 52M  C10  C14  C15  117.49  3.000
 52M  C15  C14  C19  119.18  3.000
 52M  C10  C14  C19  123.31  3.000
 52M  C11  C10  C9   118.70  3.000
 52M  C9   C10  C14  121.16  3.000
 52M  C11  C10  C14  119.35  3.000
 52M  C8   C9   C4   116.38  3.000
 52M  C8   C9   C10  123.64  3.000
 52M  C4   C9   C10  119.94  3.000
 52M  C5   C4   O2   117.57  3.000
 52M  C5   C4   C9   122.85  3.000
 52M  O2   C4   C9   119.58  3.000
 52M  C3   O2   C4   121.70  3.000
 52M  H7   C5   C6   118.94  3.000
 52M  H7   C5   C4   120.02  3.000
 52M  C6   C5   C4   121.04  3.000
 52M  H9   C8   C7   119.96  3.000
 52M  H9   C8   C9   118.23  3.000
 52M  C7   C8   C9   121.82  3.000
 52M  H10  C7   C6   117.71  3.000
 52M  H10  C7   C8   120.20  3.000
 52M  C6   C7   C8   122.08  3.000
 52M  O3   C6   C7   121.58  3.000
 52M  C7   C6   C5   115.82  3.000
 52M  O3   C6   C5   122.60  3.000
 52M  C12  C11  C3   117.42  3.000
 52M  C12  C11  C10  123.75  3.000
 52M  C3   C11  C10  118.82  3.000
 52M  C2   C3   C11  122.21  3.000
 52M  C11  C3   O2   121.18  3.000
 52M  C2   C3   O2   116.61  3.000
 52M  H11  C2   C1   121.22  3.000
 52M  H11  C2   C3   119.94  3.000
 52M  C1   C2   C3   118.84  3.000
 52M  H12  C12  C13  119.34  3.000
 52M  H12  C12  C11  119.12  3.000
 52M  C13  C12  C11  121.54  3.000
 52M  H13  C13  C1   119.62  3.000
 52M  H13  C13  C12  120.71  3.000
 52M  C1   C13  C12  119.67  3.000
 52M  O1   C1   C13  117.19  3.000
 52M  C13  C1   C2   120.32  3.000
 52M  O1   C1   C2   122.49  3.000
 52M  H14  O1   C1   111.06  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
 52M  CONST_01  C14  C19  C18  C17     0.00   0.0  0
 52M  CONST_02  C14  C15  C16  C17     0.00   0.0  0
 52M  CONST_03  C15  C14  C19  C18     0.00   0.0  0
 52M  CONST_04  C15  C16  C17  C18     0.00   0.0  0
 52M  CONST_05  C16  C15  C14  C19     0.00   0.0  0
 52M  CONST_06  C16  C17  C18  C19     0.00   0.0  0
 52M  CONST_07  C1   C2   C3   C11     0.00   0.0  0
 52M  CONST_08  C1   C13  C12  C11     0.00   0.0  0
 52M  CONST_09  C13  C1   C2   C3      0.00   0.0  0
 52M  CONST_10  C13  C12  C11  C3      0.00   0.0  0
 52M  CONST_11  C12  C13  C1   C2      0.00   0.0  0
 52M  CONST_12  C12  C11  C3   C2      0.00   0.0  0
 52M  CONST_13  C10  C14  C19  C18   180.00   0.0  0
 52M  CONST_14  C10  C14  C15  C16   180.00   0.0  0
 52M  CONST_15  C19  C18  C17  N1    180.00   0.0  0
 52M  CONST_16  C15  C16  C17  N1    180.00   0.0  0
 52M  CONST_17  C20  C19  C18  C17   180.00   0.0  0
 52M  CONST_18  C10  C14  C19  C20     0.00   0.0  0
 52M  CONST_19  C15  C14  C19  C20   180.00   0.0  0
 52M  CONST_20  O1   C1   C2   C3    180.00   0.0  0
 52M  CONST_21  O1   C1   C13  C12   180.00   0.0  0
 52M  CONST_22  H6   C15  C16  C17   180.00   0.0  0
 52M  CONST_23  H5   C16  C17  C18   180.00   0.0  0
 52M  CONST_24  H3   C18  C17  C16   180.00   0.0  0
 52M  CONST_25  H12  C12  C11  C10     0.00   0.0  0
 52M  CONST_26  H11  C2   C3   O2      0.00   0.0  0
 52M  CONST_27  H13  C13  C12  C11   180.00   0.0  0
 52M  CONST_28  C18  C17  N1   C21     0.00   0.0  0
 52M  CONST_29  C16  C17  N1   C21   180.00   0.0  0
 52M  CONST_30  H2   N1   C17  C18   180.00   0.0  0
 52M  CONST_31  O6   C21  N1   C17     0.00   0.0  0
 52M  CONST_32  C17  N1   C21  S1    180.00   0.0  0
 52M  Var_01    C11  C10  C14  C19    88.11  30.0  2
 52M  Var_02    C3   C11  C10  C14   172.46  30.0  1
 52M  Var_03    C4   C9   C10  C14  -172.96  30.0  1
 52M  Var_04    C2   C3   O2   C4    178.57  30.0  1
 52M  Var_05    O5   C20  C19  C18   179.80  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
 52M  plan-1  N1   0.020
 52M  plan-1  C17  0.020
 52M  plan-1  C18  0.020
 52M  plan-1  C19  0.020
 52M  plan-1  C20  0.020
 52M  plan-1  C16  0.020
 52M  plan-1  C15  0.020
 52M  plan-1  C14  0.020
 52M  plan-1  C10  0.020
 52M  plan-1  H3   0.020
 52M  plan-1  H5   0.020
 52M  plan-1  H6   0.020
 52M  plan-2  C10  0.020
 52M  plan-2  O2   0.020
 52M  plan-2  C11  0.020
 52M  plan-2  C3   0.020
 52M  plan-2  C2   0.020
 52M  plan-2  C12  0.020
 52M  plan-2  C13  0.020
 52M  plan-2  C1   0.020
 52M  plan-2  O1   0.020
 52M  plan-2  H11  0.020
 52M  plan-2  H12  0.020
 52M  plan-2  H13  0.020
 52M  plan-3  S1   0.020
 52M  plan-3  C21  0.020
 52M  plan-3  N1   0.020
 52M  plan-3  C17  0.020
 52M  plan-3  O6   0.020
 52M  plan-3  H2   0.020
 52M  plan-4  C10  0.020
 52M  plan-4  C9   0.020
 52M  plan-4  C4   0.020
 52M  plan-4  O2   0.020
 52M  plan-4  C5   0.020
 52M  plan-4  C8   0.020
 52M  plan-4  C7   0.020
 52M  plan-4  C6   0.020
 52M  plan-4  O3   0.020
 52M  plan-4  H7   0.020
 52M  plan-4  H9   0.020
 52M  plan-4  H10  0.020
 52M  plan-5  C19  0.020
 52M  plan-5  C20  0.020
 52M  plan-5  O4   0.020
 52M  plan-5  O5   0.020

