# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Thu Jun 25 10:49:36 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 5-(acetylamino)-9-(benzoylamino)-3,5,9-trideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@@H](F)[C@](O)(O[C@H]1[C@H](O)[C@H](O)CNC(=O)c2ccccc2)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
 BFN  BFN  '5-(acetylamino)-9-(benzoylamino)-3,5,9-trideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid'  D-saccharide  52  30  .  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_BFN
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
 BFN  O2    O  OH1    0  -0.678   2.4258  -2.3420  -1.4263
 BFN  C1    C  C      0   0.371   2.3304  -3.3058   0.8257
 BFN  F1    F  F      0  -0.380   4.1159  -1.2798   1.4916
 BFN  C2    C  CT     0   0.312   2.5200  -2.0375  -0.0656
 BFN  C3    C  CH1    0   0.148   3.9229  -1.4658   0.1242
 BFN  C4    C  CH1    0   0.021   4.0843  -0.1280  -0.5779
 BFN  O4    O  OH1    0  -0.662   5.3292   0.4626  -0.3118
 BFN  C5    C  CH1    0  -0.134   2.9873   0.8358  -0.1308
 BFN  N5    N  NH1    0  -0.634   3.0405   2.0547  -0.8963
 BFN  C6    C  CH1    0   0.033   1.6131   0.1730  -0.3065
 BFN  O6    O  O2     0  -0.511   1.5660  -1.0906   0.3188
 BFN  C7    C  CH1    0  -0.017   0.4947   0.9812   0.3531
 BFN  O7    O  OH1    0  -0.666   0.6202   0.9541   1.7527
 BFN  C8    C  CH1    0  -0.016  -0.8938   0.4997  -0.1003
 BFN  O8    O  OH1    0  -0.662  -1.0475   0.6450  -1.4972
 BFN  C9    C  CH2    0  -0.279  -2.0038   1.2280   0.6512
 BFN  N9    N  NH1    0  -0.648  -3.2948   0.7949   0.1717
 BFN  C10   C  C      0   0.525   3.3949   3.2565  -0.4017
 BFN  O10   O  O      0  -0.500   3.6457   3.4527   0.7784
 BFN  C11   C  CH3    0  -0.782   3.4599   4.3672  -1.4208
 BFN  C12   C  C      0   0.527  -4.3694   0.6248   0.9580
 BFN  O12   O  O      0  -0.492  -4.3620   0.8430   2.1629
 BFN  C13   C  CR6    0  -0.034  -5.6105   0.1475   0.2704
 BFN  C14   C  CR16   0  -0.270  -6.8407   0.4506   0.8501
 BFN  C15   C  CR16   0  -0.243  -8.0195   0.0279   0.2556
 BFN  C16   C  CR16   0  -0.251  -7.9811  -0.7186  -0.9153
 BFN  C17   C  CR16   0  -0.241  -6.7584  -1.0425  -1.4875
 BFN  C18   C  CR16   0  -0.291  -5.5785  -0.6102  -0.8991
 BFN  O1A   O  OC    -1  -0.604   3.1356  -4.2191   0.5695
 BFN  O1B   O  O      0  -0.572   1.4233  -3.2949   1.6668
 BFN  HO2   H  HOH1   0   0.457   1.6544  -2.8973  -1.5835
 BFN  H3    H  HCH1   0   0.234   4.6697  -2.1841  -0.2222
 BFN  H4    H  HCH1   0   0.228   3.9601  -0.3108  -1.6544
 BFN  HO4   H  HOH1   0   0.456   5.9944   0.0354  -0.8601
 BFN  H5    H  HCH1   0   0.268   3.1381   1.0944   0.9183
 BFN  HN5   H  HNH1   0   0.397   2.8902   1.9800  -1.8905
 BFN  H6    H  HCH1   0   0.227   1.4084   0.0882  -1.3821
 BFN  H7    H  HCH1   0   0.244   0.6008   2.0296   0.0501
 BFN  HO7   H  HOH1   0   0.447   0.7244   0.0305   2.0148
 BFN  H8    H  HCH1   0   0.246  -0.9912  -0.5728   0.0968
 BFN  HO8   H  HOH1   0   0.448  -0.9450   1.5769  -1.7250
 BFN  H9    H  HCH2   0   0.260  -1.9366   1.0199   1.7160
 BFN  H9A   H  HCH2   0   0.236  -1.8925   2.3127   0.5256
 BFN  HN9   H  HNH1   0   0.399  -3.4067   0.7380  -0.8280
 BFN  H11   H  HCH3   0   0.248   3.0906   4.0801  -2.4034
 BFN  H11A  H  HCH3   0   0.264   2.8830   5.2210  -1.0676
 BFN  H11B  H  HCH3   0   0.268   4.4941   4.6967  -1.5266
 BFN  H14   H  HCR6   0   0.260  -6.8761   1.0278   1.7645
 BFN  H15   H  HCR6   0   0.262  -8.9700   0.2771   0.7086
 BFN  H16   H  HCR6   0   0.264  -8.9017  -1.0490  -1.3783
 BFN  H17   H  HCR6   0   0.264  -6.7205  -1.6375  -2.3903
 BFN  H18   H  HCR6   0   0.255  -4.6364  -0.8944  -1.3512

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
 BFN  C2   O2    single    1.398  0.020  1.398
 BFN  O2   HO2   single    0.850  0.020  0.980
 BFN  O1B  C1    deloc     1.237  0.020  1.237
 BFN  C1   O1A   deloc     1.244  0.020  1.244
 BFN  C1   C2    single    1.562  0.020  1.562
 BFN  F1   C3    single    1.393  0.020  1.393
 BFN  C3   C2    single    1.527  0.020  1.527
 BFN  C2   O6    single    1.398  0.020  1.398
 BFN  C3   C4    single    1.520  0.020  1.520
 BFN  C3   H3    single    0.970  0.020  1.090
 BFN  O4   C4    single    1.403  0.020  1.403
 BFN  C4   C5    single    1.527  0.020  1.527
 BFN  C4   H4    single    0.970  0.020  1.090
 BFN  O4   HO4   single    0.850  0.020  0.980
 BFN  C5   N5    single    1.440  0.020  1.440
 BFN  C5   C6    single    1.536  0.020  1.536
 BFN  C5   H5    single    0.970  0.020  1.090
 BFN  N5   C10   single    1.347  0.020  1.347
 BFN  N5   HN5   single    0.860  0.020  1.020
 BFN  O6   C6    single    1.411  0.020  1.411
 BFN  C6   C7    single    1.529  0.020  1.529
 BFN  C6   H6    single    0.970  0.020  1.090
 BFN  O7   C7    single    1.405  0.020  1.405
 BFN  C7   C8    single    1.538  0.020  1.538
 BFN  C7   H7    single    0.970  0.020  1.090
 BFN  O7   HO7   single    0.850  0.020  0.980
 BFN  C8   C9    single    1.525  0.020  1.525
 BFN  C8   O8    single    1.413  0.020  1.413
 BFN  C8   H8    single    0.970  0.020  1.090
 BFN  O8   HO8   single    0.850  0.020  0.980
 BFN  N9   C9    single    1.444  0.020  1.444
 BFN  C9   H9    single    0.970  0.020  1.090
 BFN  C9   H9A   single    0.970  0.020  1.090
 BFN  N9   C12   single    1.342  0.020  1.342
 BFN  N9   HN9   single    0.860  0.020  1.020
 BFN  O10  C10   double    1.222  0.020  1.222
 BFN  C10  C11   single    1.509  0.020  1.509
 BFN  C11  H11   single    0.970  0.020  1.090
 BFN  C11  H11A  single    0.970  0.020  1.090
 BFN  C11  H11B  single    0.970  0.020  1.090
 BFN  C13  C12   single    1.497  0.020  1.497
 BFN  C12  O12   double    1.224  0.020  1.224
 BFN  C18  C13   aromatic  1.394  0.020  1.394
 BFN  C13  C14   aromatic  1.393  0.020  1.393
 BFN  C15  C14   aromatic  1.386  0.020  1.386
 BFN  C14  H14   single    0.930  0.020  1.080
 BFN  C16  C15   aromatic  1.389  0.020  1.389
 BFN  C15  H15   single    0.930  0.020  1.080
 BFN  C17  C16   aromatic  1.388  0.020  1.388
 BFN  C16  H16   single    0.930  0.020  1.080
 BFN  C17  C18   aromatic  1.388  0.020  1.388
 BFN  C17  H17   single    0.930  0.020  1.080
 BFN  C18  H18   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
 BFN  HO2   O2   C2    109.78  3.000
 BFN  O1B   C1   O1A   128.39  3.000
 BFN  O1A   C1   C2    113.58  3.000
 BFN  O1B   C1   C2    118.03  3.000
 BFN  O6    C2   C3    109.83  3.000
 BFN  O6    C2   C1    108.08  3.000
 BFN  C3    C2   C1    110.16  3.000
 BFN  O6    C2   O2    111.67  3.000
 BFN  C3    C2   O2    105.34  3.000
 BFN  C1    C2   O2    111.75  3.000
 BFN  H3    C3   C4    111.08  3.000
 BFN  H3    C3   C2    110.03  3.000
 BFN  C4    C3   C2    111.70  3.000
 BFN  H3    C3   F1    107.72  3.000
 BFN  C4    C3   F1    108.73  3.000
 BFN  C2    C3   F1    107.41  3.000
 BFN  H4    C4   C5    108.09  3.000
 BFN  H4    C4   O4    110.85  3.000
 BFN  C5    C4   O4    108.43  3.000
 BFN  H4    C4   C3    107.11  3.000
 BFN  C5    C4   C3    110.13  3.000
 BFN  O4    C4   C3    112.15  3.000
 BFN  HO4   O4   C4    108.57  3.000
 BFN  H5    C5   C6    109.63  3.000
 BFN  H5    C5   N5    107.78  3.000
 BFN  C6    C5   N5    109.72  3.000
 BFN  H5    C5   C4    109.38  3.000
 BFN  C6    C5   C4    109.69  3.000
 BFN  N5    C5   C4    110.61  3.000
 BFN  HN5   N5   C10   117.86  3.000
 BFN  HN5   N5   C5    117.13  3.000
 BFN  C10   N5   C5    124.72  3.000
 BFN  H6    C6   C7    109.09  3.000
 BFN  H6    C6   O6    111.02  3.000
 BFN  C7    C6   O6    104.94  3.000
 BFN  H6    C6   C5    108.19  3.000
 BFN  C7    C6   C5    112.15  3.000
 BFN  O6    C6   C5    111.45  3.000
 BFN  C6    O6   C2    117.52  3.000
 BFN  H7    C7   C8    107.78  3.000
 BFN  H7    C7   O7    106.56  3.000
 BFN  C8    C7   O7    111.60  3.000
 BFN  H7    C7   C6    108.38  3.000
 BFN  C8    C7   C6    111.57  3.000
 BFN  O7    C7   C6    110.73  3.000
 BFN  HO7   O7   C7    107.36  3.000
 BFN  H8    C8   C9    108.32  3.000
 BFN  H8    C8   O8    105.61  3.000
 BFN  C9    C8   O8    111.03  3.000
 BFN  H8    C8   C7    109.51  3.000
 BFN  O8    C8   C7    110.94  3.000
 BFN  C9    C8   C7    111.23  3.000
 BFN  HO8   O8   C8    108.74  3.000
 BFN  H9A   C9   H9    107.16  3.000
 BFN  H9A   C9   N9    110.43  3.000
 BFN  H9    C9   N9    108.85  3.000
 BFN  H9A   C9   C8    109.98  3.000
 BFN  H9    C9   C8    110.26  3.000
 BFN  N9    C9   C8    110.11  3.000
 BFN  HN9   N9   C12   119.02  3.000
 BFN  HN9   N9   C9    116.47  3.000
 BFN  C12   N9   C9    124.01  3.000
 BFN  C11   C10  O10   121.68  3.000
 BFN  C11   C10  N5    114.84  3.000
 BFN  O10   C10  N5    123.48  3.000
 BFN  H11B  C11  H11A  107.27  3.000
 BFN  H11B  C11  H11   108.30  3.000
 BFN  H11A  C11  H11   108.65  3.000
 BFN  H11B  C11  C10   109.20  3.000
 BFN  H11A  C11  C10   109.58  3.000
 BFN  H11   C11  C10   113.65  3.000
 BFN  C13   C12  O12   120.92  3.000
 BFN  O12   C12  N9    123.29  3.000
 BFN  C13   C12  N9    115.79  3.000
 BFN  C18   C13  C14   119.18  3.000
 BFN  C14   C13  C12   118.13  3.000
 BFN  C18   C13  C12   122.66  3.000
 BFN  H14   C14  C15   119.82  3.000
 BFN  H14   C14  C13   119.78  3.000
 BFN  C15   C14  C13   120.40  3.000
 BFN  H15   C15  C16   120.06  3.000
 BFN  H15   C15  C14   119.82  3.000
 BFN  C16   C15  C14   120.12  3.000
 BFN  H16   C16  C17   120.11  3.000
 BFN  H16   C16  C15   120.08  3.000
 BFN  C17   C16  C15   119.81  3.000
 BFN  H17   C17  C18   119.69  3.000
 BFN  H17   C17  C16   120.21  3.000
 BFN  C18   C17  C16   120.10  3.000
 BFN  H18   C18  C17   118.75  3.000
 BFN  H18   C18  C13   120.86  3.000
 BFN  C17   C18  C13   120.37  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
 BFN  CONST_01  C16  C17  C18  C13    0.00   0.0  0
 BFN  CONST_02  C16  C15  C14  C13    0.00   0.0  0
 BFN  CONST_03  C17  C18  C13  C14    0.00   0.0  0
 BFN  CONST_04  C17  C16  C15  C14    0.00   0.0  0
 BFN  CONST_05  C18  C13  C14  C15    0.00   0.0  0
 BFN  CONST_06  C18  C17  C16  C15    0.00   0.0  0
 BFN  CONST_07  C17  C18  C13  C12  180.00   0.0  0
 BFN  CONST_08  C15  C14  C13  C12  180.00   0.0  0
 BFN  CONST_09  H17  C17  C18  C13  180.00   0.0  0
 BFN  CONST_10  H15  C15  C14  C13  180.00   0.0  0
 BFN  CONST_11  H18  C18  C13  C14  180.00   0.0  0
 BFN  CONST_12  H16  C16  C15  C14  180.00   0.0  0
 BFN  CONST_13  H14  C14  C15  C16  180.00   0.0  0
 BFN  CONST_14  O10  C10  N5   C5     0.00   0.0  0
 BFN  CONST_15  C11  C10  N5   C5   180.00   0.0  0
 BFN  CONST_16  C13  C12  N9   C9   180.00   0.0  0
 BFN  CONST_17  HN9  N9   C12  C13    0.00   0.0  0
 BFN  CONST_18  O12  C12  N9   C9     0.00   0.0  0
 BFN  CONST_19  HN5  N5   C10  O10  180.00   0.0  0
 BFN  Var_01    C18  C13  C12  N9    26.95  30.0  2
 BFN  Var_02    C12  N9   C9   C8   142.58  30.0  1
 BFN  Var_03    H11  C11  C10  N5     7.26  30.0  3

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
 BFN  chir_01  C2  C1  C3  O6  positiv
 BFN  chir_02  C3  F1  C2  C4  negativ
 BFN  chir_03  C4  O4  C3  C5  negativ
 BFN  chir_04  C5  N5  C6  C4  negativ
 BFN  chir_05  C6  O6  C7  C5  negativ
 BFN  chir_06  C7  O7  C6  C8  negativ
 BFN  chir_07  C8  O8  C7  C9  negativ

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
 BFN  plan-1  C12  0.020
 BFN  plan-1  C13  0.020
 BFN  plan-1  C14  0.020
 BFN  plan-1  C15  0.020
 BFN  plan-1  C16  0.020
 BFN  plan-1  C17  0.020
 BFN  plan-1  C18  0.020
 BFN  plan-1  H14  0.020
 BFN  plan-1  H15  0.020
 BFN  plan-1  H16  0.020
 BFN  plan-1  H17  0.020
 BFN  plan-1  H18  0.020
 BFN  plan-2  C9   0.020
 BFN  plan-2  N9   0.020
 BFN  plan-2  C12  0.020
 BFN  plan-2  O12  0.020
 BFN  plan-2  C13  0.020
 BFN  plan-2  HN9  0.020
 BFN  plan-3  C5   0.020
 BFN  plan-3  N5   0.020
 BFN  plan-3  C10  0.020
 BFN  plan-3  O10  0.020
 BFN  plan-3  C11  0.020
 BFN  plan-3  HN5  0.020
 BFN  plan-4  C1   0.020
 BFN  plan-4  C2   0.020
 BFN  plan-4  O1A  0.020
 BFN  plan-4  O1B  0.020

