# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 04:43:53 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 2-(3,6-dihydroxy-9H-xanthen-9-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccccc1[C@@H]2c3ccc(O)cc3Oc4cc(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
 FDS  FDS  '2-(3,6-dihydroxy-9H-xanthen-9-yl)benzoic acid'  ligand  38  25  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_FDS
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
 FDS  C1   C  CR6    0   0.349  -2.6052   0.1216  -3.2637
 FDS  O1   O  OH1    0  -0.633  -3.3458  -0.0430  -4.3769
 FDS  C2   C  CR16   0  -0.442  -1.2649  -0.2345  -3.3249
 FDS  C3   C  CR6    0   0.331  -0.4666  -0.0822  -2.1983
 FDS  O2   O  O2     0  -0.508   0.8337  -0.4551  -2.3436
 FDS  C4   C  C      0   0.326   1.7349  -0.1380  -1.3740
 FDS  C5   C  C1     0  -0.444   3.0672  -0.3593  -1.6992
 FDS  C6   C  C      0   0.351   4.0538  -0.0622  -0.7690
 FDS  O3   O  OH1    0  -0.634   5.3330  -0.2991  -1.1205
 FDS  C7   C  C1     0  -0.384   3.6994   0.4660   0.4731
 FDS  C8   C  C1     0  -0.295   2.3635   0.6720   0.7671
 FDS  C9   C  C      0   0.051   1.3526   0.3707  -0.1402
 FDS  C10  C  CH1    0  -0.440  -0.0995   0.5465   0.2236
 FDS  C11  C  CR6    0   0.080  -0.9653   0.4160  -1.0030
 FDS  C12  C  CR16   0  -0.296  -2.3096   0.7720  -0.9753
 FDS  C13  C  CR16   0  -0.384  -3.1329   0.6339  -2.0779
 FDS  C14  C  CR6    0   0.178  -0.5194  -0.4586   1.2880
 FDS  C15  C  CR16   0  -0.293  -0.5032  -1.8121   0.9459
 FDS  C16  C  CR16   0  -0.255  -0.8965  -2.7917   1.8400
 FDS  C17  C  CR16   0  -0.265  -1.3464  -2.4221   3.1024
 FDS  C18  C  CR16   0  -0.280  -1.3929  -1.0812   3.4410
 FDS  C19  C  CR6    0  -0.126  -0.9606  -0.0837   2.5608
 FDS  C20  C  C      0   0.359  -0.9898   1.3526   3.0711
 FDS  O4   O  O      0  -0.582   0.0099   2.0629   2.8366
 FDS  O5   O  OC    -1  -0.589  -2.0014   1.6828   3.7154
 FDS  HO1  H  HOH1   0   0.475  -4.2542   0.2369  -4.2190
 FDS  H2   H  HCR6   0   0.273  -0.8421  -0.6239  -4.2429
 FDS  H5   H  H      0   0.272   3.3315  -0.7594  -2.6706
 FDS  HO3  H  HOH1   0   0.475   5.9274  -0.0588  -0.4014
 FDS  H7   H  H      0   0.267   4.4612   0.7082   1.2052
 FDS  H8   H  H      0   0.266   2.0774   1.0759   1.7305
 FDS  H10  H  HCH1   0   0.285  -0.2280   1.5495   0.6271
 FDS  H12  H  HCR6   0   0.256  -2.7261   1.1614  -0.0533
 FDS  H13  H  HCR6   0   0.270  -4.1764   0.9199  -2.0171
 FDS  H15  H  HCR6   0   0.245  -0.1748  -2.1072  -0.0445
 FDS  H16  H  HCR6   0   0.249  -0.8602  -3.8347   1.5525
 FDS  H17  H  HCR6   0   0.247  -1.6650  -3.1748   3.8127
 FDS  H18  H  HCR6   0   0.245  -1.7605  -0.7928   4.4174

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
 FDS  C1   O1   single    1.347  0.020  1.347
 FDS  C1   C2   aromatic  1.388  0.020  1.388
 FDS  C1   C13  aromatic  1.395  0.020  1.395
 FDS  O1   HO1  single    0.850  0.020  0.980
 FDS  C2   C3   aromatic  1.389  0.020  1.389
 FDS  C2   H2   single    0.930  0.020  1.080
 FDS  C3   O2   single    1.360  0.020  1.360
 FDS  C3   C11  aromatic  1.388  0.020  1.388
 FDS  O2   C4   single    1.361  0.020  1.361
 FDS  C4   C5   aromatic  1.389  0.020  1.389
 FDS  C4   C9   aromatic  1.388  0.020  1.388
 FDS  C5   C6   aromatic  1.388  0.020  1.388
 FDS  C5   H5   single    0.930  0.020  1.080
 FDS  C6   O3   single    1.348  0.020  1.348
 FDS  C6   C7   aromatic  1.395  0.020  1.395
 FDS  O3   HO3  single    0.850  0.020  0.980
 FDS  C7   C8   aromatic  1.383  0.020  1.383
 FDS  C7   H7   single    0.930  0.020  1.080
 FDS  C8   C9   aromatic  1.391  0.020  1.391
 FDS  C8   H8   single    0.930  0.020  1.080
 FDS  C9   C10  single    1.507  0.020  1.507
 FDS  C10  C11  single    1.507  0.020  1.507
 FDS  C10  C14  single    1.523  0.020  1.523
 FDS  C10  H10  single    0.970  0.020  1.090
 FDS  C11  C12  aromatic  1.391  0.020  1.391
 FDS  C12  C13  aromatic  1.383  0.020  1.383
 FDS  C12  H12  single    0.930  0.020  1.080
 FDS  C13  H13  single    0.930  0.020  1.080
 FDS  C14  C15  aromatic  1.396  0.020  1.396
 FDS  C14  C19  aromatic  1.398  0.020  1.398
 FDS  C15  C16  aromatic  1.383  0.020  1.383
 FDS  C15  H15  single    0.930  0.020  1.080
 FDS  C16  C17  aromatic  1.390  0.020  1.390
 FDS  C16  H16  single    0.930  0.020  1.080
 FDS  C17  C18  aromatic  1.384  0.020  1.384
 FDS  C17  H17  single    0.930  0.020  1.080
 FDS  C18  C19  aromatic  1.399  0.020  1.399
 FDS  C18  H18  single    0.930  0.020  1.080
 FDS  C19  C20  single    1.525  0.020  1.525
 FDS  C20  O4   deloc     1.248  0.020  1.248
 FDS  C20  O5   deloc     1.244  0.020  1.244

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
 FDS  C13  C1   C2   119.79  3.000
 FDS  C13  C1   O1   122.63  3.000
 FDS  C2   C1   O1   117.58  3.000
 FDS  HO1  O1   C1   110.33  3.000
 FDS  H2   C2   C3   120.16  3.000
 FDS  H2   C2   C1   120.43  3.000
 FDS  C3   C2   C1   119.40  3.000
 FDS  C11  C3   O2   122.26  3.000
 FDS  C11  C3   C2   122.10  3.000
 FDS  O2   C3   C2   115.63  3.000
 FDS  C4   O2   C3   119.53  3.000
 FDS  C9   C4   C5   122.04  3.000
 FDS  C9   C4   O2   122.42  3.000
 FDS  C5   C4   O2   115.54  3.000
 FDS  H5   C5   C6   120.44  3.000
 FDS  H5   C5   C4   120.18  3.000
 FDS  C6   C5   C4   119.39  3.000
 FDS  C7   C6   O3   122.67  3.000
 FDS  C7   C6   C5   119.80  3.000
 FDS  O3   C6   C5   117.53  3.000
 FDS  HO3  O3   C6   110.31  3.000
 FDS  H7   C7   C8   120.13  3.000
 FDS  H7   C7   C6   120.48  3.000
 FDS  C8   C7   C6   119.39  3.000
 FDS  H8   C8   C9   117.96  3.000
 FDS  H8   C8   C7   119.98  3.000
 FDS  C9   C8   C7   122.06  3.000
 FDS  C10  C9   C8   121.15  3.000
 FDS  C10  C9   C4   121.50  3.000
 FDS  C8   C9   C4   117.31  3.000
 FDS  H10  C10  C14  108.45  3.000
 FDS  H10  C10  C11  108.28  3.000
 FDS  C14  C10  C11  110.69  3.000
 FDS  H10  C10  C9   108.09  3.000
 FDS  C14  C10  C9   110.94  3.000
 FDS  C11  C10  C9   110.30  3.000
 FDS  C12  C11  C10  121.12  3.000
 FDS  C12  C11  C3   117.15  3.000
 FDS  C10  C11  C3   121.72  3.000
 FDS  H12  C12  C13  119.03  3.000
 FDS  H12  C12  C11  118.70  3.000
 FDS  C13  C12  C11  122.27  3.000
 FDS  H13  C13  C12  120.14  3.000
 FDS  H13  C13  C1   120.58  3.000
 FDS  C12  C13  C1   119.28  3.000
 FDS  C19  C14  C15  119.12  3.000
 FDS  C19  C14  C10  123.11  3.000
 FDS  C15  C14  C10  117.73  3.000
 FDS  H15  C15  C16  118.93  3.000
 FDS  H15  C15  C14  119.42  3.000
 FDS  C16  C15  C14  121.65  3.000
 FDS  H16  C16  C17  120.54  3.000
 FDS  H16  C16  C15  120.07  3.000
 FDS  C17  C16  C15  119.39  3.000
 FDS  H17  C17  C18  120.21  3.000
 FDS  H17  C17  C16  120.41  3.000
 FDS  C18  C17  C16  119.39  3.000
 FDS  H18  C18  C19  118.86  3.000
 FDS  H18  C18  C17  119.36  3.000
 FDS  C19  C18  C17  121.78  3.000
 FDS  C20  C19  C18  117.08  3.000
 FDS  C20  C19  C14  124.28  3.000
 FDS  C18  C19  C14  118.63  3.000
 FDS  O5   C20  O4   126.69  3.000
 FDS  O5   C20  C19  116.04  3.000
 FDS  O4   C20  C19  117.24  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
 FDS  CONST_01  C11  C3   C2   C1      0.00   0.0  0
 FDS  CONST_02  C11  C12  C13  C1      0.00   0.0  0
 FDS  CONST_03  C12  C13  C1   C2      0.00   0.0  0
 FDS  CONST_04  C12  C11  C3   C2      0.00   0.0  0
 FDS  CONST_05  C13  C1   C2   C3      0.00   0.0  0
 FDS  CONST_06  C13  C12  C11  C3      0.00   0.0  0
 FDS  CONST_07  C7   C6   C5   C4      0.00   0.0  0
 FDS  CONST_08  C7   C8   C9   C4      0.00   0.0  0
 FDS  CONST_09  C8   C9   C4   C5      0.00   0.0  0
 FDS  CONST_10  C8   C7   C6   C5      0.00   0.0  0
 FDS  CONST_11  C9   C4   C5   C6      0.00   0.0  0
 FDS  CONST_12  C9   C8   C7   C6      0.00   0.0  0
 FDS  CONST_13  C17  C16  C15  C14     0.00   0.0  0
 FDS  CONST_14  C17  C18  C19  C14     0.00   0.0  0
 FDS  CONST_15  C18  C19  C14  C15     0.00   0.0  0
 FDS  CONST_16  C18  C17  C16  C15     0.00   0.0  0
 FDS  CONST_17  C19  C14  C15  C16     0.00   0.0  0
 FDS  CONST_18  C19  C18  C17  C16     0.00   0.0  0
 FDS  CONST_19  C16  C15  C14  C10   180.00   0.0  0
 FDS  CONST_20  C18  C19  C14  C10   180.00   0.0  0
 FDS  CONST_21  C3   C2   C1   O1    180.00   0.0  0
 FDS  CONST_22  C12  C13  C1   O1    180.00   0.0  0
 FDS  CONST_23  O3   C6   C5   C4    180.00   0.0  0
 FDS  CONST_24  C8   C7   C6   O3    180.00   0.0  0
 FDS  CONST_25  C20  C19  C14  C10     0.00   0.0  0
 FDS  CONST_26  C20  C19  C14  C15   180.00   0.0  0
 FDS  CONST_27  C20  C19  C18  C17   180.00   0.0  0
 FDS  CONST_28  H12  C12  C13  C1    180.00   0.0  0
 FDS  CONST_29  H13  C13  C1   C2    180.00   0.0  0
 FDS  CONST_30  H2   C2   C3   O2      0.00   0.0  0
 FDS  CONST_31  H5   C5   C4   O2      0.00   0.0  0
 FDS  CONST_32  H8   C8   C9   C4    180.00   0.0  0
 FDS  CONST_33  H7   C7   C6   C5    180.00   0.0  0
 FDS  CONST_34  H15  C15  C14  C10     0.00   0.0  0
 FDS  CONST_35  H16  C16  C15  C14   180.00   0.0  0
 FDS  CONST_36  H18  C18  C19  C14   180.00   0.0  0
 FDS  CONST_37  H17  C17  C16  C15   180.00   0.0  0
 FDS  Var_01    C5   C4   O2   C3   -169.86  30.0  1
 FDS  Var_02    C11  C3   O2   C4    -10.92  30.0  1
 FDS  Var_03    O4   C20  C19  C14   -43.94  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 FDS  chir_01  C10  C9  C11  C14  negativ

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
 FDS  plan-1  C10  0.020
 FDS  plan-1  C14  0.020
 FDS  plan-1  C15  0.020
 FDS  plan-1  C16  0.020
 FDS  plan-1  C17  0.020
 FDS  plan-1  C18  0.020
 FDS  plan-1  C19  0.020
 FDS  plan-1  C20  0.020
 FDS  plan-1  H15  0.020
 FDS  plan-1  H16  0.020
 FDS  plan-1  H17  0.020
 FDS  plan-1  H18  0.020
 FDS  plan-2  C1   0.020
 FDS  plan-2  O1   0.020
 FDS  plan-2  C2   0.020
 FDS  plan-2  C3   0.020
 FDS  plan-2  O2   0.020
 FDS  plan-2  C10  0.020
 FDS  plan-2  C11  0.020
 FDS  plan-2  C12  0.020
 FDS  plan-2  C13  0.020
 FDS  plan-2  H2   0.020
 FDS  plan-2  H12  0.020
 FDS  plan-2  H13  0.020
 FDS  plan-3  O2   0.020
 FDS  plan-3  C4   0.020
 FDS  plan-3  C5   0.020
 FDS  plan-3  C6   0.020
 FDS  plan-3  O3   0.020
 FDS  plan-3  C7   0.020
 FDS  plan-3  C8   0.020
 FDS  plan-3  C9   0.020
 FDS  plan-3  C10  0.020
 FDS  plan-3  H5   0.020
 FDS  plan-3  H7   0.020
 FDS  plan-3  H8   0.020
 FDS  plan-4  C19  0.020
 FDS  plan-4  C20  0.020
 FDS  plan-4  O4   0.020
 FDS  plan-4  O5   0.020

