# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 11:48:07 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: 5-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)-2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cc(ccc1C2=C3C=CC(=O)C=C3Oc4cc(O)ccc24)N5C(=O)C=CC5=O
#
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
 F5M  F5M  '5-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)-2-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoic acid'  ligand  44  32  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F5M
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
 F5M  C1   C  CR6    0   0.380   3.5288  -3.5671   0.2371
 F5M  O1   O  OH1    0  -0.612   4.2082  -4.7095   0.3682
 F5M  C2   C  CR16   0  -0.483   4.1537  -2.3521  -0.0056
 F5M  O2   O  O      0  -0.475   4.0268  -0.0579  -0.3518
 F5M  C3   C  CR66   0   0.376   3.3754  -1.2106  -0.1205
 F5M  O3   O  O      0  -0.511   4.1332   4.5378  -1.1653
 F5M  C4   C  CR66   0   0.419   3.3700   1.1112  -0.5070
 F5M  O4   O  O      0  -0.559   0.9305   0.1348   2.3878
 F5M  C5   C  CR16   0  -0.548   4.1119   2.2213  -0.7618
 F5M  O5   O  OC    -1  -0.574  -1.0580   0.1868   3.4020
 F5M  C6   C  CR6    0   0.373   3.4868   3.5085  -0.9345
 F5M  C7   C  CR16   0  -0.396   2.0303   3.5300  -0.8182
 F5M  C8   C  CR16   0  -0.284   1.3147   2.4153  -0.5654
 F5M  C9   C  CR66   0  -0.070   1.9419   1.1381  -0.4000
 F5M  C10  C  CR6    0   0.311   1.2566  -0.0176  -0.1117
 F5M  C11  C  CR66   0   0.009   1.9830  -1.2434  -0.0009
 F5M  C12  C  CR16   0  -0.320   1.3835  -2.4896   0.2400
 F5M  C13  C  CR16   0  -0.333   2.1303  -3.6337   0.3558
 F5M  C14  C  CR6    0  -0.053  -0.2258  -0.0456  -0.1198
 F5M  C15  C  CR16   0  -0.278  -0.8558  -0.1423  -1.3582
 F5M  C16  C  CR16   0  -0.266  -2.2369  -0.1742  -1.4466
 F5M  C17  C  CR6    0   0.356  -2.9912  -0.1218  -0.2829
 F5M  C18  C  CR16   0  -0.318  -2.3702  -0.0335   0.9519
 F5M  C19  C  CR6    0  -0.110  -0.9852   0.0110   1.0480
 F5M  C20  C  C      0   0.411  -0.3142   0.1214   2.4094
 F5M  NAB  N  NR5    0  -0.704  -4.4022  -0.1513  -0.3575
 F5M  CAZ  C  CR5    0   0.558  -5.1511  -1.2247  -0.8208
 F5M  CBA  C  CR15   0  -0.309  -6.5787  -0.8118  -0.7110
 F5M  CBB  C  CR15   0  -0.308  -6.6280   0.4191  -0.2178
 F5M  CBC  C  CR5    0   0.558  -5.2360   0.8906   0.0273
 F5M  OBJ  O  O      0  -0.388  -4.8738   1.9504   0.4627
 F5M  OBK  O  O      0  -0.388  -4.7056  -2.2666  -1.2210
 F5M  HO1  H  HOH1   0   0.484   5.1576  -4.5597   0.2851
 F5M  H2   H  HCR6   0   0.297   5.2309  -2.2829  -0.1015
 F5M  H5   H  HCR6   0   0.261   5.1900   2.1472  -0.8360
 F5M  H7   H  HCR6   0   0.257   1.5301   4.4833  -0.9391
 F5M  H8   H  HCR6   0   0.266   0.2372   2.4746  -0.4808
 F5M  H12  H  HCR6   0   0.269   0.3077  -2.5502   0.3358
 F5M  H13  H  HCR6   0   0.278   1.6543  -4.5866   0.5453
 F5M  H15  H  HCR6   0   0.266  -0.2619  -0.1862  -2.2626
 F5M  H16  H  HCR6   0   0.276  -2.7188  -0.2297  -2.4138
 F5M  H18  H  HCR6   0   0.266  -2.9622  -0.0020   1.8569
 F5M  HBA  H  HCR5   0   0.307  -7.3946  -1.4569  -0.9987
 F5M  HBB  H  HCR5   0   0.307  -7.4935   1.0287  -0.0086

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
 F5M  C1   O1   single    1.336  0.020  1.336
 F5M  C1   C2   aromatic  1.388  0.020  1.388
 F5M  C1   C13  aromatic  1.405  0.020  1.405
 F5M  C2   C3   aromatic  1.386  0.020  1.386
 F5M  O2   C3   single    1.344  0.020  1.344
 F5M  O2   C4   single    1.350  0.020  1.350
 F5M  C3   C11  aromatic  1.398  0.020  1.398
 F5M  O3   C6   double    1.237  0.020  1.237
 F5M  C4   C5   double    1.359  0.020  1.359
 F5M  C4   C9   single    1.432  0.020  1.432
 F5M  O4   C20  deloc     1.245  0.020  1.245
 F5M  C5   C6   single    1.441  0.020  1.441
 F5M  O5   C20  deloc     1.242  0.020  1.242
 F5M  C6   C7   single    1.461  0.020  1.461
 F5M  C7   C8   double    1.349  0.020  1.349
 F5M  C8   C9   single    1.433  0.020  1.433
 F5M  C9   C10  double    1.374  0.020  1.374
 F5M  C10  C11  single    1.429  0.020  1.429
 F5M  C10  C14  single    1.483  0.020  1.483
 F5M  C11  C12  aromatic  1.404  0.020  1.404
 F5M  C12  C13  aromatic  1.371  0.020  1.371
 F5M  C14  C15  aromatic  1.393  0.020  1.393
 F5M  C14  C19  aromatic  1.394  0.020  1.394
 F5M  C15  C16  aromatic  1.384  0.020  1.384
 F5M  C16  C17  aromatic  1.388  0.020  1.388
 F5M  C17  C18  aromatic  1.385  0.020  1.385
 F5M  C17  NAB  single    1.413  0.020  1.413
 F5M  C18  C19  aromatic  1.389  0.020  1.389
 F5M  C19  C20  single    1.522  0.020  1.522
 F5M  NAB  CAZ  single    1.388  0.020  1.388
 F5M  NAB  CBC  single    1.389  0.020  1.389
 F5M  CAZ  CBA  single    1.490  0.020  1.490
 F5M  CAZ  OBK  double    1.202  0.020  1.202
 F5M  CBA  CBB  double    1.327  0.020  1.327
 F5M  CBB  CBC  single    1.490  0.020  1.490
 F5M  CBC  OBJ  double    1.202  0.020  1.202
 F5M  O1   HO1  single    0.850  0.020  0.980
 F5M  C2   H2   single    0.930  0.020  1.080
 F5M  C5   H5   single    0.930  0.020  1.080
 F5M  C7   H7   single    0.930  0.020  1.080
 F5M  C8   H8   single    0.930  0.020  1.080
 F5M  C12  H12  single    0.930  0.020  1.080
 F5M  C13  H13  single    0.930  0.020  1.080
 F5M  C15  H15  single    0.930  0.020  1.080
 F5M  C16  H16  single    0.930  0.020  1.080
 F5M  C18  H18  single    0.930  0.020  1.080
 F5M  CBA  HBA  single    0.930  0.020  1.080
 F5M  CBB  HBB  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
 F5M  C13  C1   C2   120.30  3.000
 F5M  C13  C1   O1   117.22  3.000
 F5M  C2   C1   O1   122.48  3.000
 F5M  HO1  O1   C1   111.06  3.000
 F5M  H2   C2   C3   119.88  3.000
 F5M  H2   C2   C1   121.27  3.000
 F5M  C3   C2   C1   118.86  3.000
 F5M  C4   O2   C3   121.79  3.000
 F5M  C11  C3   O2   121.17  3.000
 F5M  C11  C3   C2   122.19  3.000
 F5M  O2   C3   C2   116.64  3.000
 F5M  C9   C4   C5   122.88  3.000
 F5M  C9   C4   O2   119.52  3.000
 F5M  C5   C4   O2   117.60  3.000
 F5M  H5   C5   C6   118.99  3.000
 F5M  H5   C5   C4   120.01  3.000
 F5M  C6   C5   C4   121.00  3.000
 F5M  C7   C6   C5   115.84  3.000
 F5M  C7   C6   O3   121.56  3.000
 F5M  C5   C6   O3   122.60  3.000
 F5M  H7   C7   C8   120.22  3.000
 F5M  H7   C7   C6   117.66  3.000
 F5M  C8   C7   C6   122.12  3.000
 F5M  H8   C8   C9   118.40  3.000
 F5M  H8   C8   C7   119.84  3.000
 F5M  C9   C8   C7   121.76  3.000
 F5M  C10  C9   C8   123.76  3.000
 F5M  C10  C9   C4   119.81  3.000
 F5M  C8   C9   C4   116.40  3.000
 F5M  C14  C10  C11  119.50  3.000
 F5M  C14  C10  C9   120.89  3.000
 F5M  C11  C10  C9   118.95  3.000
 F5M  C12  C11  C10  123.90  3.000
 F5M  C12  C11  C3   117.44  3.000
 F5M  C10  C11  C3   118.66  3.000
 F5M  H12  C12  C13  119.17  3.000
 F5M  H12  C12  C11  119.32  3.000
 F5M  C13  C12  C11  121.51  3.000
 F5M  H13  C13  C12  120.67  3.000
 F5M  H13  C13  C1   119.63  3.000
 F5M  C12  C13  C1   119.69  3.000
 F5M  C19  C14  C15  120.09  3.000
 F5M  C19  C14  C10  122.63  3.000
 F5M  C15  C14  C10  117.28  3.000
 F5M  H15  C15  C16  119.53  3.000
 F5M  H15  C15  C14  119.83  3.000
 F5M  C16  C15  C14  120.64  3.000
 F5M  H16  C16  C17  120.63  3.000
 F5M  H16  C16  C15  120.17  3.000
 F5M  C17  C16  C15  119.20  3.000
 F5M  NAB  C17  C18  119.74  3.000
 F5M  NAB  C17  C16  119.84  3.000
 F5M  C18  C17  C16  120.42  3.000
 F5M  H18  C18  C19  119.13  3.000
 F5M  H18  C18  C17  120.15  3.000
 F5M  C19  C18  C17  120.72  3.000
 F5M  C20  C19  C18  120.26  3.000
 F5M  C20  C19  C14  120.81  3.000
 F5M  C18  C19  C14  118.93  3.000
 F5M  C19  C20  O5   117.05  3.000
 F5M  C19  C20  O4   115.22  3.000
 F5M  O5   C20  O4   127.73  3.000
 F5M  CBC  NAB  CAZ  110.40  3.000
 F5M  CBC  NAB  C17  124.68  3.000
 F5M  CAZ  NAB  C17  124.91  3.000
 F5M  OBK  CAZ  CBA  128.31  3.000
 F5M  OBK  CAZ  NAB  125.55  3.000
 F5M  CBA  CAZ  NAB  106.14  3.000
 F5M  HBA  CBA  CBB  128.72  3.000
 F5M  HBA  CBA  CAZ  122.62  3.000
 F5M  CBB  CBA  CAZ  108.66  3.000
 F5M  HBB  CBB  CBC  122.59  3.000
 F5M  HBB  CBB  CBA  128.75  3.000
 F5M  CBC  CBB  CBA  108.66  3.000
 F5M  OBJ  CBC  CBB  128.34  3.000
 F5M  OBJ  CBC  NAB  125.53  3.000
 F5M  CBB  CBC  NAB  106.13  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
 F5M  CONST_01  C11  C3   C2   C1      0.00   0.0  0
 F5M  CONST_02  C11  C12  C13  C1      0.00   0.0  0
 F5M  CONST_03  C12  C13  C1   C2      0.00   0.0  0
 F5M  CONST_04  C12  C11  C3   C2      0.00   0.0  0
 F5M  CONST_05  C13  C1   C2   C3      0.00   0.0  0
 F5M  CONST_06  C13  C12  C11  C3      0.00   0.0  0
 F5M  CONST_07  C17  C16  C15  C14     0.00   0.0  0
 F5M  CONST_08  C17  C18  C19  C14     0.00   0.0  0
 F5M  CONST_09  C18  C19  C14  C15     0.00   0.0  0
 F5M  CONST_10  C18  C17  C16  C15     0.00   0.0  0
 F5M  CONST_11  C19  C14  C15  C16     0.00   0.0  0
 F5M  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 F5M  CONST_13  C16  C15  C14  C10   180.00   0.0  0
 F5M  CONST_14  C18  C19  C14  C10   180.00   0.0  0
 F5M  CONST_15  NAB  C17  C16  C15   180.00   0.0  0
 F5M  CONST_16  NAB  C17  C18  C19   180.00   0.0  0
 F5M  CONST_17  CBA  CAZ  NAB  C17   180.00   0.0  0
 F5M  CONST_18  CBC  NAB  CAZ  CBA     0.00   0.0  0
 F5M  CONST_19  C3   C2   C1   O1    180.00   0.0  0
 F5M  CONST_20  C12  C13  C1   O1    180.00   0.0  0
 F5M  CONST_21  C20  C19  C14  C10     0.00   0.0  0
 F5M  CONST_22  C20  C19  C14  C15   180.00   0.0  0
 F5M  CONST_23  C20  C19  C18  C17   180.00   0.0  0
 F5M  CONST_24  OBK  CAZ  NAB  C17     0.00   0.0  0
 F5M  CONST_25  OBK  CAZ  NAB  CBC   180.00   0.0  0
 F5M  CONST_26  H12  C12  C13  C1    180.00   0.0  0
 F5M  CONST_27  H13  C13  C1   C2    180.00   0.0  0
 F5M  CONST_28  H2   C2   C3   O2      0.00   0.0  0
 F5M  CONST_29  H15  C15  C14  C10     0.00   0.0  0
 F5M  CONST_30  H16  C16  C15  C14   180.00   0.0  0
 F5M  CONST_31  H18  C18  C19  C14   180.00   0.0  0
 F5M  Var_01    C6   C5   C4   O2   -179.73   0.0  0
 F5M  Var_02    C11  C10  C9   C4     -3.60   0.0  0
 F5M  Var_03    C15  C14  C10  C9     79.59  30.0  2
 F5M  Var_04    CAZ  NAB  C17  C16    65.00  30.0  2
 F5M  Var_05    C14  C19  C20  O4     -1.05  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
 F5M  plan-1  C17  0.020
 F5M  plan-1  NAB  0.020
 F5M  plan-1  CAZ  0.020
 F5M  plan-1  CBA  0.020
 F5M  plan-1  CBB  0.020
 F5M  plan-1  CBC  0.020
 F5M  plan-1  OBJ  0.020
 F5M  plan-1  OBK  0.020
 F5M  plan-1  HBA  0.020
 F5M  plan-1  HBB  0.020
 F5M  plan-2  C1   0.020
 F5M  plan-2  O1   0.020
 F5M  plan-2  C2   0.020
 F5M  plan-2  O2   0.020
 F5M  plan-2  C3   0.020
 F5M  plan-2  O3   0.020
 F5M  plan-2  C4   0.020
 F5M  plan-2  C5   0.020
 F5M  plan-2  C6   0.020
 F5M  plan-2  C7   0.020
 F5M  plan-2  C8   0.020
 F5M  plan-2  C9   0.020
 F5M  plan-2  C10  0.020
 F5M  plan-2  C11  0.020
 F5M  plan-2  C12  0.020
 F5M  plan-2  C13  0.020
 F5M  plan-2  C14  0.020
 F5M  plan-2  H2   0.020
 F5M  plan-2  H5   0.020
 F5M  plan-2  H7   0.020
 F5M  plan-2  H8   0.020
 F5M  plan-2  H12  0.020
 F5M  plan-2  H13  0.020
 F5M  plan-3  C10  0.020
 F5M  plan-3  C14  0.020
 F5M  plan-3  C15  0.020
 F5M  plan-3  C16  0.020
 F5M  plan-3  C17  0.020
 F5M  plan-3  C18  0.020
 F5M  plan-3  C19  0.020
 F5M  plan-3  C20  0.020
 F5M  plan-3  NAB  0.020
 F5M  plan-3  H15  0.020
 F5M  plan-3  H16  0.020
 F5M  plan-3  H18  0.020
 F5M  plan-4  O4   0.020
 F5M  plan-4  O5   0.020
 F5M  plan-4  C19  0.020
 F5M  plan-4  C20  0.020

