# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 03:25:30 2021
#   Inital geometry file: a 58 line input string
#   Ligand name: (2~{S},5~{S})-5-azanyl-3,4,6-tris(oxidanyl)oxane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1[C@@H](O)O[C@@H]([C@H](O)[C@H]1O)C(O)=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
 F8F  F8F  '(2~{S},5~{S})-5-azanyl-3,4,6-tris(oxidanyl)oxane-2-carboxylic acid'  ligand  24  13  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_F8F
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
 F8F  N    N  NH2   0  -0.801  -60.1505  39.4140  16.6763
 F8F  C12  C  CR16  0  -0.222  -60.2546  40.3460  15.5707
 F8F  C13  C  CR16  0   0.024  -59.1245  41.3992  15.4386
 F8F  C14  C  CR16  0  -0.048  -58.1113  40.9797  14.3786
 F8F  C15  C  CR16  0  -0.096  -58.8413  40.7821  13.0377
 F8F  C16  C  CR16  0   0.325  -60.3935  39.5244  14.2857
 F8F  C87  C  C     0   0.527  -58.0466  39.8432  12.1435
 F8F  O1   O  O     0  -0.491  -60.1617  40.3358  13.1682
 F8F  O24  O  OH1   0  -0.593  -56.8756  40.3751  11.8238
 F8F  O25  O  O     0  -0.427  -58.4349  38.7743  11.7544
 F8F  O26  O  OH1   0  -0.665  -57.4910  39.7658  14.7387
 F8F  O27  O  OH1   0  -0.676  -59.6024  42.6611  15.0337
 F8F  H1   H  HNH2  0   0.343  -59.2443  38.9619  16.6688
 F8F  H2   H  HNH2  0   0.357  -60.2169  39.9056  17.5582
 F8F  H4   H  HCR6  0   0.253  -61.1919  40.9004  15.7005
 F8F  H5   H  HCR6  0   0.237  -58.6072  41.4700  16.4076
 F8F  H6   H  HCR6  0   0.265  -57.3673  41.7730  14.2458
 F8F  H7   H  HCR6  0   0.304  -58.8921  41.7522  12.5348
 F8F  H8   H  HCR6  0   0.185  -59.6733  38.6911  14.3070
 F8F  H10  H  HOH1  0   0.485  -56.3741  39.7708  11.2558
 F8F  H11  H  HOH1  0   0.466  -56.8412  39.9421  15.4268
 F8F  H12  H  HOH1  0   0.455  -60.2707  42.9529  15.6615
 F8F  O2   O  OH1   0  -0.662  -61.6822  39.0367  14.1058
 F8F  H3   H  HOH1  0   0.456  -61.9684  38.6656  14.9490

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
 F8F  O25  C87  double  1.202  0.020  1.202
 F8F  O24  C87  single  1.325  0.020  1.325
 F8F  C87  C15  single  1.521  0.020  1.521
 F8F  C15  O1   single  1.400  0.020  1.400
 F8F  C15  C14  single  1.539  0.020  1.539
 F8F  O1   C16  single  1.400  0.020  1.400
 F8F  C16  C12  single  1.532  0.020  1.532
 F8F  C14  O26  single  1.410  0.020  1.410
 F8F  C14  C13  single  1.525  0.020  1.525
 F8F  C13  C12  single  1.550  0.020  1.550
 F8F  C13  O27  single  1.409  0.020  1.409
 F8F  C12  N    single  1.450  0.020  1.450
 F8F  N    H1   single  0.890  0.020  1.040
 F8F  N    H2   single  0.890  0.020  1.040
 F8F  C12  H4   single  0.970  0.020  1.090
 F8F  C13  H5   single  0.970  0.020  1.090
 F8F  C14  H6   single  0.970  0.020  1.090
 F8F  C15  H7   single  0.970  0.020  1.090
 F8F  C16  H8   single  0.970  0.020  1.090
 F8F  O24  H10  single  0.850  0.020  0.980
 F8F  O26  H11  single  0.850  0.020  0.980
 F8F  O27  H12  single  0.850  0.020  0.980
 F8F  C16  O2   single  1.390  0.020  1.390
 F8F  O2   H3   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
 F8F  H2   N    H1   106.38  3.000
 F8F  H2   N    C12  110.35  3.000
 F8F  H1   N    C12  110.22  3.000
 F8F  H4   C12  C16  107.04  3.000
 F8F  H4   C12  C13  106.84  3.000
 F8F  C16  C12  C13  111.04  3.000
 F8F  H4   C12  N    107.22  3.000
 F8F  C13  C12  N    116.70  3.000
 F8F  C16  C12  N    107.55  3.000
 F8F  H5   C13  O27  110.79  3.000
 F8F  H5   C13  C14  108.50  3.000
 F8F  O27  C13  C14  105.78  3.000
 F8F  H5   C13  C12  108.13  3.000
 F8F  O27  C13  C12  112.69  3.000
 F8F  C14  C13  C12  110.89  3.000
 F8F  H6   C14  O26  110.83  3.000
 F8F  H6   C14  C15  108.01  3.000
 F8F  O26  C14  C15  108.70  3.000
 F8F  H6   C14  C13  109.65  3.000
 F8F  O26  C14  C13  110.59  3.000
 F8F  C15  C14  C13  109.00  3.000
 F8F  H7   C15  O1   106.36  3.000
 F8F  H7   C15  C87  107.55  3.000
 F8F  O1   C15  C87  110.54  3.000
 F8F  H7   C15  C14  107.98  3.000
 F8F  O1   C15  C14  114.02  3.000
 F8F  C87  C15  C14  110.10  3.000
 F8F  O2   C16  H8   110.08  3.000
 F8F  O2   C16  O1   104.69  3.000
 F8F  H8   C16  O1   110.22  3.000
 F8F  O2   C16  C12  112.39  3.000
 F8F  H8   C16  C12  109.28  3.000
 F8F  O1   C16  C12  110.11  3.000
 F8F  O25  C87  O24  124.35  3.000
 F8F  O24  C87  C15  110.84  3.000
 F8F  O25  C87  C15  124.80  3.000
 F8F  C16  O1   C15  114.53  3.000
 F8F  H10  O24  C87  110.39  3.000
 F8F  H11  O26  C14  108.77  3.000
 F8F  H12  O27  C13  108.64  3.000
 F8F  H3   O2   C16  107.28  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
 F8F  CONST_01  H10  O24  C87  C15  180.00  0.0  0

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
 F8F  chir_01  C12  C16  C13  N    positiv
 F8F  chir_02  C13  O27  C12  C14  negativ
 F8F  chir_03  C14  O26  C13  C15  positiv
 F8F  chir_04  C15  O1   C14  C87  negativ
 F8F  chir_05  C16  O1   O2   C12  positiv

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
 F8F  plan-1  C15  0.020
 F8F  plan-1  C87  0.020
 F8F  plan-1  O24  0.020
 F8F  plan-1  O25  0.020
 F8F  plan-1  H10  0.020

