# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 13:13:26 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 5-amino-2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(c(c1)C(O)=O)C2=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
 A4F  A4F  '5-amino-2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid'  ligand  39  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A4F
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
 A4F  O5   O  OH1   0  -0.589  -2.7498   0.3421   2.8672
 A4F  C17  C  C     0   0.498  -1.7683   0.0425   2.0297
 A4F  O4   O  O     0  -0.424  -0.6011   0.0850   2.3318
 A4F  C18  C  CR6   0  -0.073  -2.2515  -0.3541   0.6812
 A4F  C19  C  CR16  0  -0.342  -3.5846  -0.6912   0.4831
 A4F  C20  C  CR6   0   0.342  -4.0502  -1.1067  -0.7689
 A4F  N1   N  NH2   0  -0.860  -5.3500  -1.4999  -0.9404
 A4F  C16  C  CR16  0  -0.304  -3.1325  -1.1580  -1.8251
 A4F  C15  C  CR16  0  -0.261  -1.8095  -0.8153  -1.6251
 A4F  C14  C  CR6   0  -0.038  -1.3410  -0.4132  -0.3785
 A4F  C1   C  CR6   0   0.273   0.0878  -0.0416  -0.2635
 A4F  C13  C  CR66  0  -0.006   1.0667  -1.0654  -0.0856
 A4F  C12  C  CR16  0  -0.318   0.7561  -2.4252   0.0659
 A4F  C11  C  CR16  0  -0.376   1.7395  -3.3678   0.2331
 A4F  C10  C  CR6   0   0.377   3.0873  -2.9735   0.2570
 A4F  O3   O  OH1   0  -0.610   4.0819  -3.8501   0.4106
 A4F  C9   C  CR16  0  -0.435   3.4298  -1.6341   0.1184
 A4F  C8   C  CR66  0   0.381   2.4203  -0.7036  -0.0490
 A4F  O2   O  O     0  -0.473   2.7948   0.5810  -0.1758
 A4F  C2   C  CR66  0  -0.056   0.4990   1.2574  -0.4144
 A4F  C7   C  CR66  0   0.424   1.8989   1.5733  -0.3546
 A4F  C6   C  CR16  0  -0.543   2.3731   2.8396  -0.4731
 A4F  C3   C  CR16  0  -0.291  -0.3973   2.3596  -0.6152
 A4F  C4   C  CR16  0  -0.390   0.0518   3.6239  -0.7334
 A4F  C5   C  CR6   0   0.377   1.4757   3.9529  -0.6659
 A4F  O1   O  O     0  -0.499   1.8733   5.1173  -0.7708
 A4F  H1   H  HOH1  0   0.491  -2.3864   0.5672   3.7368
 A4F  H2   H  HCR6  0   0.275  -4.2825  -0.6493   1.3087
 A4F  H3   H  HNH2  0   0.388  -6.0210  -1.1605  -0.2713
 A4F  H4   H  HNH2  0   0.388  -5.7037  -1.4995  -1.8829
 A4F  H5   H  HCR6  0   0.273  -3.4609  -1.4677  -2.8096
 A4F  H6   H  HCR6  0   0.266  -1.1236  -0.8559  -2.4619
 A4F  H7   H  HCR6  0   0.275  -0.2795  -2.7376   0.0490
 A4F  H8   H  HCR6  0   0.287   1.4770  -4.4123   0.3478
 A4F  H9   H  HOH1  0   0.485   3.7408  -4.7499   0.4780
 A4F  H10  H  HCR6  0   0.292   4.4666  -1.3229   0.1371
 A4F  H11  H  HCR6  0   0.266   3.4389   3.0269  -0.4231
 A4F  H12  H  HCR6  0   0.269  -1.4589   2.1571  -0.6710
 A4F  H13  H  HCR6  0   0.262  -0.6454   4.4390  -0.8829

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
 A4F  O3   C10  single    1.335  0.020  1.335
 A4F  C10  C9   aromatic  1.389  0.020  1.389
 A4F  C10  C11  aromatic  1.405  0.020  1.405
 A4F  C9   C8   aromatic  1.383  0.020  1.383
 A4F  C11  C12  aromatic  1.372  0.020  1.372
 A4F  C8   O2   single    1.344  0.020  1.344
 A4F  C8   C13  aromatic  1.402  0.020  1.402
 A4F  C12  C13  aromatic  1.403  0.020  1.403
 A4F  O2   C7   single    1.349  0.020  1.349
 A4F  C13  C1   single    1.428  0.020  1.428
 A4F  O4   C17  double    1.206  0.020  1.206
 A4F  C7   C6   double    1.357  0.020  1.357
 A4F  C7   C2   single    1.436  0.020  1.436
 A4F  C1   C2   double    1.371  0.020  1.371
 A4F  C1   C14  single    1.481  0.020  1.481
 A4F  C6   C5   single    1.443  0.020  1.443
 A4F  C2   C3   single    1.435  0.020  1.435
 A4F  C17  C18  single    1.486  0.020  1.486
 A4F  C17  O5   single    1.325  0.020  1.325
 A4F  C14  C18  aromatic  1.398  0.020  1.398
 A4F  C14  C15  aromatic  1.391  0.020  1.391
 A4F  C18  C19  aromatic  1.389  0.020  1.389
 A4F  C5   O1   double    1.235  0.020  1.235
 A4F  C5   C4   single    1.463  0.020  1.463
 A4F  C15  C16  aromatic  1.381  0.020  1.381
 A4F  C3   C4   double    1.347  0.020  1.347
 A4F  C19  C20  aromatic  1.399  0.020  1.399
 A4F  C16  C20  aromatic  1.400  0.020  1.400
 A4F  C20  N1   single    1.369  0.020  1.369
 A4F  O5   H1   single    0.850  0.020  0.980
 A4F  C19  H2   single    0.930  0.020  1.080
 A4F  N1   H3   single    0.890  0.020  1.040
 A4F  N1   H4   single    0.890  0.020  1.040
 A4F  C16  H5   single    0.930  0.020  1.080
 A4F  C15  H6   single    0.930  0.020  1.080
 A4F  C12  H7   single    0.930  0.020  1.080
 A4F  C11  H8   single    0.930  0.020  1.080
 A4F  O3   H9   single    0.850  0.020  0.980
 A4F  C9   H10  single    0.930  0.020  1.080
 A4F  C6   H11  single    0.930  0.020  1.080
 A4F  C3   H12  single    0.930  0.020  1.080
 A4F  C4   H13  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
 A4F  H1   O5   C17  110.00  3.000
 A4F  C18  C17  O4   123.45  3.000
 A4F  C18  C17  O5   113.15  3.000
 A4F  O4   C17  O5   123.41  3.000
 A4F  C14  C18  C19  120.43  3.000
 A4F  C19  C18  C17  120.41  3.000
 A4F  C14  C18  C17  119.15  3.000
 A4F  H2   C19  C20  118.67  3.000
 A4F  H2   C19  C18  120.05  3.000
 A4F  C20  C19  C18  121.28  3.000
 A4F  C16  C20  N1   121.15  3.000
 A4F  N1   C20  C19  120.90  3.000
 A4F  C16  C20  C19  117.89  3.000
 A4F  H4   N1   H3   112.83  3.000
 A4F  H4   N1   C20  116.80  3.000
 A4F  H3   N1   C20  116.93  3.000
 A4F  H5   C16  C15  119.54  3.000
 A4F  H5   C16  C20  119.83  3.000
 A4F  C15  C16  C20  120.63  3.000
 A4F  H6   C15  C14  119.34  3.000
 A4F  H6   C15  C16  119.05  3.000
 A4F  C14  C15  C16  121.61  3.000
 A4F  C1   C14  C15  117.85  3.000
 A4F  C15  C14  C18  118.16  3.000
 A4F  C1   C14  C18  123.97  3.000
 A4F  C2   C1   C13  119.18  3.000
 A4F  C2   C1   C14  121.24  3.000
 A4F  C13  C1   C14  119.43  3.000
 A4F  C8   C13  C12  117.46  3.000
 A4F  C12  C13  C1   123.83  3.000
 A4F  C8   C13  C1   118.71  3.000
 A4F  H7   C12  C11  119.30  3.000
 A4F  H7   C12  C13  119.35  3.000
 A4F  C11  C12  C13  121.35  3.000
 A4F  H8   C11  C10  120.10  3.000
 A4F  H8   C11  C12  120.11  3.000
 A4F  C10  C11  C12  119.79  3.000
 A4F  C9   C10  O3   117.45  3.000
 A4F  C9   C10  C11  120.36  3.000
 A4F  O3   C10  C11  122.19  3.000
 A4F  H9   O3   C10  110.93  3.000
 A4F  H10  C9   C8   120.51  3.000
 A4F  H10  C9   C10  120.76  3.000
 A4F  C8   C9   C10  118.73  3.000
 A4F  O2   C8   C9   116.81  3.000
 A4F  O2   C8   C13  120.89  3.000
 A4F  C9   C8   C13  122.30  3.000
 A4F  C7   O2   C8   122.04  3.000
 A4F  C3   C2   C7   116.47  3.000
 A4F  C3   C2   C1   123.78  3.000
 A4F  C7   C2   C1   119.75  3.000
 A4F  C6   C7   C2   122.83  3.000
 A4F  C2   C7   O2   119.41  3.000
 A4F  C6   C7   O2   117.76  3.000
 A4F  H11  C6   C5   118.99  3.000
 A4F  H11  C6   C7   120.07  3.000
 A4F  C5   C6   C7   120.94  3.000
 A4F  H12  C3   C4   119.88  3.000
 A4F  H12  C3   C2   118.45  3.000
 A4F  C4   C3   C2   121.68  3.000
 A4F  H13  C4   C5   117.62  3.000
 A4F  H13  C4   C3   120.26  3.000
 A4F  C5   C4   C3   122.11  3.000
 A4F  O1   C5   C4   121.44  3.000
 A4F  C4   C5   C6   115.98  3.000
 A4F  O1   C5   C6   122.59  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
 A4F  CONST_01  C16  C15  C14  C18     0.00   0.0  0
 A4F  CONST_02  C16  C20  C19  C18     0.00   0.0  0
 A4F  CONST_03  C15  C14  C18  C19     0.00   0.0  0
 A4F  CONST_04  C15  C16  C20  C19     0.00   0.0  0
 A4F  CONST_05  C14  C18  C19  C20     0.00   0.0  0
 A4F  CONST_06  C14  C15  C16  C20     0.00   0.0  0
 A4F  CONST_07  C10  C9   C8   C13     0.00   0.0  0
 A4F  CONST_08  C10  C11  C12  C13     0.00   0.0  0
 A4F  CONST_09  C9   C10  C11  C12     0.00   0.0  0
 A4F  CONST_10  C9   C8   C13  C12     0.00   0.0  0
 A4F  CONST_11  C8   C9   C10  C11     0.00   0.0  0
 A4F  CONST_12  C8   C13  C12  C11     0.00   0.0  0
 A4F  CONST_13  C1   C14  C18  C19   180.00   0.0  0
 A4F  CONST_14  C1   C14  C15  C16   180.00   0.0  0
 A4F  CONST_15  C1   C14  C18  C17     0.00   0.0  0
 A4F  CONST_16  C15  C14  C18  C17   180.00   0.0  0
 A4F  CONST_17  C20  C19  C18  C17   180.00   0.0  0
 A4F  CONST_18  N1   C20  C19  C18   180.00   0.0  0
 A4F  CONST_19  C15  C16  C20  N1    180.00   0.0  0
 A4F  CONST_20  O3   C10  C11  C12   180.00   0.0  0
 A4F  CONST_21  C8   C9   C10  O3    180.00   0.0  0
 A4F  CONST_22  H6   C15  C14  C18   180.00   0.0  0
 A4F  CONST_23  H5   C16  C20  C19   180.00   0.0  0
 A4F  CONST_24  H2   C19  C20  C16   180.00   0.0  0
 A4F  CONST_25  H7   C12  C13  C1      0.00   0.0  0
 A4F  CONST_26  H10  C9   C8   C13   180.00   0.0  0
 A4F  CONST_27  H8   C11  C12  C13   180.00   0.0  0
 A4F  CONST_30  H1   O5   C17  C18   180.00   0.0  0
 A4F  Var_01    C13  C1   C14  C18    98.58  30.0  2
 A4F  Var_02    C8   C13  C1   C14   176.69  30.0  1
 A4F  Var_03    C7   C2   C1   C14  -177.28  30.0  1
 A4F  Var_04    C6   C7   O2   C8   -179.97  30.0  1
 A4F  Var_05    C14  C18  C17  O5    166.15  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
 A4F  plan-1  C17  0.020
 A4F  plan-1  C18  0.020
 A4F  plan-1  C19  0.020
 A4F  plan-1  C20  0.020
 A4F  plan-1  N1   0.020
 A4F  plan-1  C16  0.020
 A4F  plan-1  C15  0.020
 A4F  plan-1  C14  0.020
 A4F  plan-1  C1   0.020
 A4F  plan-1  H2   0.020
 A4F  plan-1  H5   0.020
 A4F  plan-1  H6   0.020
 A4F  plan-2  C1   0.020
 A4F  plan-2  C13  0.020
 A4F  plan-2  C12  0.020
 A4F  plan-2  C11  0.020
 A4F  plan-2  C10  0.020
 A4F  plan-2  O3   0.020
 A4F  plan-2  C9   0.020
 A4F  plan-2  C8   0.020
 A4F  plan-2  O2   0.020
 A4F  plan-2  H7   0.020
 A4F  plan-2  H8   0.020
 A4F  plan-2  H10  0.020
 A4F  plan-3  C20  0.020
 A4F  plan-3  N1   0.020
 A4F  plan-3  H3   0.020
 A4F  plan-3  H4   0.020
 A4F  plan-4  C1   0.020
 A4F  plan-4  O2   0.020
 A4F  plan-4  C2   0.020
 A4F  plan-4  C7   0.020
 A4F  plan-4  C6   0.020
 A4F  plan-4  C3   0.020
 A4F  plan-4  C4   0.020
 A4F  plan-4  C5   0.020
 A4F  plan-4  O1   0.020
 A4F  plan-4  H11  0.020
 A4F  plan-4  H12  0.020
 A4F  plan-4  H13  0.020
 A4F  plan-5  O5   0.020
 A4F  plan-5  C17  0.020
 A4F  plan-5  O4   0.020
 A4F  plan-5  C18  0.020
 A4F  plan-5  H1   0.020

