# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 12:57:22 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 2-deoxy-2-fluoro-beta-D-mannopyranosyl fluoride
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](F)[C@@H](F)[C@@H](O)[C@@H]1O
#
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
 FMF  FMF  '2-deoxy-2-fluoro-beta-D-mannopyranosyl fluoride'  D-saccharide  22  12  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_FMF
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
 FMF  C5   C  CH1   0  -0.050  -1.1221  -1.8100  -0.2401
 FMF  C2   C  CH1   0   0.076   1.6895  -2.3085  -0.0747
 FMF  F2   F  F     0  -0.376   2.2065  -1.3581  -0.9520
 FMF  C3   C  CH1   0  -0.037   0.9987  -1.5955   1.0785
 FMF  O3   O  OH1   0  -0.655   1.8806  -0.7708   1.7869
 FMF  C4   C  CH1   0   0.003  -0.2496  -0.8574   0.5900
 FMF  O4   O  OH1   0  -0.664  -0.9522  -0.4026   1.7185
 FMF  C6   C  CH2   0  -0.170  -2.3015  -1.1048  -0.8855
 FMF  O6   O  OH1   0  -0.662  -3.1602  -1.9855  -1.5637
 FMF  O    O  O2    0  -0.495  -0.3612  -2.3889  -1.2933
 FMF  C1   C  CH1   0   0.384   0.6852  -3.1582  -0.8241
 FMF  F1   F  F     0  -0.346   1.2700  -3.7186  -1.9251
 FMF  H5   H  HCH1  0   0.235  -1.4997  -2.6060   0.4214
 FMF  H2   H  HCH1  0   0.261   2.5206  -2.9177   0.2903
 FMF  H3   H  HCH1  0   0.258   0.6775  -2.3711   1.7837
 FMF  HO3  H  HOH1  0   0.448   2.1983  -0.0735   1.2025
 FMF  H4   H  HCH1  0   0.233   0.0593  -0.0178  -0.0496
 FMF  HO4  H  HOH1  0   0.463  -1.3867   0.4272   1.5050
 FMF  H61  H  HCH2  0   0.209  -1.9262  -0.3081  -1.5425
 FMF  H62  H  HCH2  0   0.233  -2.8917  -0.6264  -0.1030
 FMF  HO6  H  HOH1  0   0.450  -2.6808  -2.3653  -2.3065
 FMF  H1   H  HCH1  0   0.202   0.3308  -3.9712  -0.1743

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
 FMF  C5  C4   single  1.536  0.020  1.536
 FMF  C5  C6   single  1.518  0.020  1.518
 FMF  C5  O    single  1.422  0.020  1.422
 FMF  C5  H5   single  0.970  0.020  1.090
 FMF  C2  F2   single  1.393  0.020  1.393
 FMF  C2  C3   single  1.522  0.020  1.522
 FMF  C2  C1   single  1.514  0.020  1.514
 FMF  C2  H2   single  0.970  0.020  1.090
 FMF  C3  O3   single  1.400  0.020  1.400
 FMF  C3  C4   single  1.530  0.020  1.530
 FMF  C3  H3   single  0.970  0.020  1.090
 FMF  O3  HO3  single  0.850  0.020  0.980
 FMF  C4  O4   single  1.405  0.020  1.405
 FMF  C4  H4   single  0.970  0.020  1.090
 FMF  O4  HO4  single  0.850  0.020  0.980
 FMF  C6  O6   single  1.405  0.020  1.405
 FMF  C6  H61  single  0.970  0.020  1.090
 FMF  C6  H62  single  0.970  0.020  1.090
 FMF  O6  HO6  single  0.850  0.020  0.980
 FMF  O   C1   single  1.381  0.020  1.381
 FMF  C1  F1   single  1.367  0.020  1.367
 FMF  C1  H1   single  0.970  0.020  1.090

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
 FMF  H5   C5  O    109.50  3.000
 FMF  H5   C5  C6   108.94  3.000
 FMF  O    C5  C6   106.85  3.000
 FMF  H5   C5  C4   108.57  3.000
 FMF  O    C5  C4   110.41  3.000
 FMF  C6   C5  C4   112.52  3.000
 FMF  H2   C2  C1   110.90  3.000
 FMF  H2   C2  C3   110.68  3.000
 FMF  C1   C2  C3   109.69  3.000
 FMF  H2   C2  F2   107.96  3.000
 FMF  C1   C2  F2   108.50  3.000
 FMF  C3   C2  F2   109.03  3.000
 FMF  H3   C3  C4   107.91  3.000
 FMF  H3   C3  O3   106.01  3.000
 FMF  C4   C3  O3   113.04  3.000
 FMF  H3   C3  C2   106.80  3.000
 FMF  C4   C3  C2   110.76  3.000
 FMF  O3   C3  C2   111.93  3.000
 FMF  HO3  O3  C3   109.10  3.000
 FMF  H4   C4  O4   111.13  3.000
 FMF  H4   C4  C3   108.95  3.000
 FMF  O4   C4  C3   107.92  3.000
 FMF  H4   C4  C5   108.59  3.000
 FMF  O4   C4  C5   110.54  3.000
 FMF  C3   C4  C5   109.69  3.000
 FMF  HO4  O4  C4   109.11  3.000
 FMF  H62  C6  H61  107.21  3.000
 FMF  H62  C6  O6   106.90  3.000
 FMF  H61  C6  O6   112.01  3.000
 FMF  H62  C6  C5   108.61  3.000
 FMF  H61  C6  C5   109.00  3.000
 FMF  O6   C6  C5   112.88  3.000
 FMF  HO6  O6  C6   108.40  3.000
 FMF  C1   O   C5   112.37  3.000
 FMF  H1   C1  F1   108.11  3.000
 FMF  H1   C1  O    111.63  3.000
 FMF  F1   C1  O    106.20  3.000
 FMF  H1   C1  C2   109.65  3.000
 FMF  F1   C1  C2   110.18  3.000
 FMF  O    C1  C2   110.99  3.000

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
 FMF  chir_01  C5  C4  C6  O   negativ
 FMF  chir_02  C2  F2  C1  C3  positiv
 FMF  chir_03  C3  O3  C2  C4  positiv
 FMF  chir_04  C4  O4  C5  C3  positiv
 FMF  chir_05  C1  F1  O   C2  positiv

