# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 23:24:37 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-deoxy-2-fluoro-beta-D-mannopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](O)[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
 MBF  MBF  2-deoxy-2-fluoro-beta-D-mannopyranose  D-saccharide  23  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 PERFECT
;

data_comp_MBF
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
 MBF  O1    O  OH1   0  -0.657  -2.7489  -0.2372  -0.7828
 MBF  C1    C  CH1   0   0.250  -1.4564  -0.5937  -0.4739
 MBF  C2    C  CH1   0   0.118  -0.5375  -0.1967  -1.6158
 MBF  F2    F  F     0  -0.375  -0.6747   1.1657  -1.8524
 MBF  C3    C  CH1   0  -0.039   0.8999  -0.5078  -1.2345
 MBF  O3    O  OH1   0  -0.669   1.8215  -0.0487  -2.1904
 MBF  C4    C  CH1   0   0.031   1.2640   0.1236   0.1075
 MBF  O4    O  OH1   0  -0.672   2.5187  -0.3278   0.5518
 MBF  C5    C  CH1   0  -0.018   0.2194  -0.2705   1.1554
 MBF  O5    O  O2    0  -0.499  -1.0717   0.0773   0.7012
 MBF  C6    C  CH2   0  -0.153   0.4509   0.4364   2.4739
 MBF  O6    O  OH1   0  -0.671  -0.4878  -0.0338   3.4115
 MBF  H1    H  HOH1  0   0.466  -3.3522  -0.6799  -0.1763
 MBF  HA    H  HCH1  0   0.197  -1.3554  -1.6830  -0.3237
 MBF  H2    H  HCH1  0   0.241  -0.8178  -0.7272  -2.5314
 MBF  H3    H  HCH1  0   0.230   0.9659  -1.5993  -1.1114
 MBF  HB    H  HOH1  0   0.461   1.8396  -0.6622  -2.9313
 MBF  H4    H  HCH1  0   0.218   1.2542   1.2186  -0.0007
 MBF  HC    H  HOH1  0   0.455   3.1777  -0.0742  -0.1031
 MBF  H5    H  HCH1  0   0.221   0.2849  -1.3597   1.3152
 MBF  H6C1  H  HCH2  0   0.197   0.3604   1.5200   2.3141
 MBF  H6C2  H  HCH2  0   0.213   1.4789   0.2425   2.7971
 MBF  H6    H  HOH1  0   0.457  -0.2919   0.3771   4.2580

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
 MBF  O1  C1    single  1.376  0.020  1.376
 MBF  O1  H1    single  0.850  0.020  0.980
 MBF  C1  C2    single  1.518  0.020  1.518
 MBF  C1  O5    single  1.407  0.020  1.407
 MBF  C1  HA    single  0.970  0.020  1.090
 MBF  C2  F2    single  1.390  0.020  1.390
 MBF  C2  C3    single  1.519  0.020  1.519
 MBF  C2  H2    single  0.970  0.020  1.090
 MBF  C3  O3    single  1.405  0.020  1.405
 MBF  C3  C4    single  1.527  0.020  1.527
 MBF  C3  H3    single  0.970  0.020  1.090
 MBF  O3  HB    single  0.850  0.020  0.980
 MBF  C4  O4    single  1.405  0.020  1.405
 MBF  C4  C5    single  1.531  0.020  1.531
 MBF  C4  H4    single  0.970  0.020  1.090
 MBF  O4  HC    single  0.850  0.020  0.980
 MBF  C5  O5    single  1.412  0.020  1.412
 MBF  C5  C6    single  1.514  0.020  1.514
 MBF  C5  H5    single  0.970  0.020  1.090
 MBF  C6  O6    single  1.408  0.020  1.408
 MBF  C6  H6C1  single  0.970  0.020  1.090
 MBF  C6  H6C2  single  0.970  0.020  1.090
 MBF  O6  H6    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
 MBF  H1    O1  C1    109.15  3.000
 MBF  HA    C1  O5    109.38  3.000
 MBF  HA    C1  C2    107.75  3.000
 MBF  O5    C1  C2    109.76  3.000
 MBF  HA    C1  O1    111.84  3.000
 MBF  O5    C1  O1    108.71  3.000
 MBF  C2    C1  O1    109.38  3.000
 MBF  H2    C2  C3    110.67  3.000
 MBF  H2    C2  F2    107.90  3.000
 MBF  C3    C2  F2    109.68  3.000
 MBF  H2    C2  C1    110.33  3.000
 MBF  C3    C2  C1    109.29  3.000
 MBF  F2    C2  C1    108.95  3.000
 MBF  H3    C3  C4    107.31  3.000
 MBF  H3    C3  O3    111.16  3.000
 MBF  C4    C3  O3    107.84  3.000
 MBF  H3    C3  C2    106.73  3.000
 MBF  C4    C3  C2    111.19  3.000
 MBF  O3    C3  C2    112.52  3.000
 MBF  HB    O3  C3    109.14  3.000
 MBF  H4    C4  C5    108.50  3.000
 MBF  H4    C4  O4    111.01  3.000
 MBF  C5    C4  O4    108.06  3.000
 MBF  H4    C4  C3    108.84  3.000
 MBF  C5    C4  C3    109.41  3.000
 MBF  O4    C4  C3    110.97  3.000
 MBF  HC    O4  C4    108.14  3.000
 MBF  H5    C5  C6    109.02  3.000
 MBF  H5    C5  O5    110.13  3.000
 MBF  C6    C5  O5    107.75  3.000
 MBF  H5    C5  C4    108.23  3.000
 MBF  C6    C5  C4    111.81  3.000
 MBF  O5    C5  C4    109.89  3.000
 MBF  C5    O5  C1    113.65  3.000
 MBF  H6C2  C6  H6C1  107.15  3.000
 MBF  H6C2  C6  O6    111.73  3.000
 MBF  H6C1  C6  O6    111.80  3.000
 MBF  H6C2  C6  C5    108.54  3.000
 MBF  H6C1  C6  C5    108.73  3.000
 MBF  O6    C6  C5    108.79  3.000
 MBF  H6    O6  C6    107.93  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
 MBF  chir_01  C1  O1  C2  O5  negativ
 MBF  chir_02  C2  F2  C3  C1  negativ
 MBF  chir_03  C3  O3  C2  C4  positiv
 MBF  chir_04  C4  O4  C5  C3  positiv
 MBF  chir_05  C5  O5  C4  C6  negativ

