# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 14:05:38 2021
#   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  53  30  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.651   7.5270  -14.6068  -6.2525
 BFN  C1    C  C     0   0.511   6.1358  -15.3163  -8.0629
 BFN  F1    F  F     0  -0.370   8.2818  -16.5284  -9.1754
 BFN  C2    C  CT    0   0.358   7.3819  -15.6110  -7.2080
 BFN  C3    C  CH1   0   0.136   8.6002  -15.6549  -8.1418
 BFN  C4    C  CH1   0   0.007   9.8288  -16.1562  -7.4108
 BFN  O4    O  OH1   0  -0.658  10.8614  -16.2776  -8.3481
 BFN  C5    C  CH1   0  -0.163   9.5112  -17.4787  -6.7075
 BFN  N5    N  NH1   0  -0.643  10.6688  -17.9227  -5.9677
 BFN  C6    C  CH1   0   0.050   8.2902  -17.2913  -5.7959
 BFN  O6    O  O2    0  -0.496   7.1981  -16.8124  -6.5677
 BFN  C7    C  CH1   0  -0.005   7.8444  -18.5912  -5.1249
 BFN  O7    O  OH1   0  -0.691   7.6122  -19.6164  -6.0567
 BFN  C8    C  CH1   0   0.037   6.5917  -18.4000  -4.2664
 BFN  O8    O  OH1   0  -0.674   6.9656  -17.5036  -3.2439
 BFN  C9    C  CH2   0  -0.341   6.1075  -19.7268  -3.6612
 BFN  N9    N  NH1   0  -0.642   5.3315  -20.5218  -4.5811
 BFN  C10   C  C     0   0.549  11.0409  -19.2113  -5.8615
 BFN  O10   O  O     0  -0.513  10.4115  -20.1299  -6.3819
 BFN  C11   C  CH3   0  -0.773  12.2864  -19.4692  -5.0605
 BFN  C12   C  C     0   0.531   3.9880  -20.5316  -4.5929
 BFN  O12   O  O     0  -0.492   3.3047  -19.9267  -3.7759
 BFN  C13   C  CR6   0  -0.036   3.3462  -21.3381  -5.6785
 BFN  C14   C  CR16  0  -0.270   2.0360  -21.0251  -6.0355
 BFN  C15   C  CR16  0  -0.243   1.3896  -21.7378  -7.0332
 BFN  C16   C  CR16  0  -0.252   2.0392  -22.7850  -7.6744
 BFN  C17   C  CR16  0  -0.240   3.3381  -23.1149  -7.3125
 BFN  C18   C  CR16  0  -0.298   3.9898  -22.3946  -6.3215
 BFN  O1B   O  OH1   0  -0.560   5.2733  -16.3027  -8.1291
 BFN  O1A   O  O     0  -0.438   6.0094  -14.2448  -8.5981
 BFN  HO2   H  HOH1  0   0.468   7.6405  -13.7496  -6.6812
 BFN  H32   H  HCH1  0   0.264   8.7899  -14.6726  -8.5841
 BFN  H4    H  HCH1  0   0.244  10.0678  -15.4022  -6.6460
 BFN  HO4   H  HOH1  0   0.458  11.6887  -16.4246  -7.8792
 BFN  H5    H  HCH1  0   0.279   9.2939  -18.2272  -7.4716
 BFN  HN5   H  HNH1  0   0.411  11.1694  -17.2397  -5.4188
 BFN  H6    H  HCH1  0   0.247   8.5469  -16.5772  -5.0053
 BFN  H7    H  HCH1  0   0.229   8.6456  -18.8704  -4.4253
 BFN  HO7   H  HOH1  0   0.461   8.4776  -19.9767  -6.3095
 BFN  H8    H  HCH1  0   0.229   5.7781  -17.9869  -4.8759
 BFN  HO8   H  HOH1  0   0.459   6.1672  -17.1576  -2.8343
 BFN  H92   H  HCH2  0   0.253   6.9570  -20.3150  -3.3050
 BFN  H91   H  HCH2  0   0.259   5.4840  -19.5084  -2.7948
 BFN  HN9   H  HNH1  0   0.402   5.8340  -20.8867  -5.3734
 BFN  H111  H  HCH3  0   0.275  13.0118  -19.9925  -5.6830
 BFN  H113  H  HCH3  0   0.256  12.7502  -18.5646  -4.6731
 BFN  H112  H  HCH3  0   0.273  12.0447  -20.1235  -4.2233
 BFN  H14   H  HCR6  0   0.259   1.5213  -20.2156  -5.5354
 BFN  H15   H  HCR6  0   0.263   0.3759  -21.4780  -7.3086
 BFN  H16   H  HCR6  0   0.264   1.5319  -23.3449  -8.4493
 BFN  H17   H  HCR6  0   0.264   3.8460  -23.9381  -7.7970
 BFN  H18   H  HCR6  0   0.261   4.9944  -22.6883  -6.0441
 BFN  HO1B  H  HOH1  0   0.492   4.5161  -16.0446  -8.6788

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    1.394  0.020  1.394
 BFN  O2   HO2   single    0.850  0.020  0.980
 BFN  O1A  C1    double    1.204  0.020  1.204
 BFN  C1   O1B   single    1.312  0.020  1.312
 BFN  C1   C2    single    1.540  0.020  1.540
 BFN  F1   C3    single    1.390  0.020  1.390
 BFN  C3   C2    single    1.536  0.020  1.536
 BFN  C2   O6    single    1.374  0.020  1.374
 BFN  C3   C4    single    1.515  0.020  1.515
 BFN  C3   H32   single    0.970  0.020  1.090
 BFN  O4   C4    single    1.400  0.020  1.400
 BFN  C4   C5    single    1.531  0.020  1.531
 BFN  C4   H4    single    0.970  0.020  1.090
 BFN  O4   HO4   single    0.850  0.020  0.980
 BFN  C5   N5    single    1.444  0.020  1.444
 BFN  C5   C6    single    1.535  0.020  1.535
 BFN  C5   H5    single    0.970  0.020  1.090
 BFN  N5   C10   single    1.345  0.020  1.345
 BFN  N5   HN5   single    0.860  0.020  1.020
 BFN  O6   C6    single    1.420  0.020  1.420
 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    1.531  0.020  1.531
 BFN  C7   H7    single    0.970  0.020  1.090
 BFN  O7   HO7   single    0.850  0.020  0.980
 BFN  C8   C9    single    1.537  0.020  1.537
 BFN  C8   O8    single    1.410  0.020  1.410
 BFN  C8   H8    single    0.970  0.020  1.090
 BFN  O8   HO8   single    0.850  0.020  0.980
 BFN  N9   C9    single    1.442  0.020  1.442
 BFN  C9   H92   single    0.970  0.020  1.090
 BFN  C9   H91   single    0.970  0.020  1.090
 BFN  N9   C12   single    1.344  0.020  1.344
 BFN  N9   HN9   single    0.860  0.020  1.020
 BFN  O10  C10   double    1.229  0.020  1.229
 BFN  C10  C11   single    1.503  0.020  1.503
 BFN  C11  H111  single    0.970  0.020  1.090
 BFN  C11  H113  single    0.970  0.020  1.090
 BFN  C11  H112  single    0.970  0.020  1.090
 BFN  C13  C12   single    1.497  0.020  1.497
 BFN  C12  O12   double    1.225  0.020  1.225
 BFN  C18  C13   aromatic  1.394  0.020  1.394
 BFN  C13  C14   aromatic  1.394  0.020  1.394
 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
 BFN  O1B  HO1B  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
 BFN  HO2   O2   C2    110.34  3.000
 BFN  O1A   C1   O1B   125.27  3.000
 BFN  O1B   C1   C2    114.60  3.000
 BFN  O1A   C1   C2    120.13  3.000
 BFN  O6    C2   C3    111.38  3.000
 BFN  O6    C2   C1    108.54  3.000
 BFN  C3    C2   C1    108.06  3.000
 BFN  O6    C2   O2    108.93  3.000
 BFN  C3    C2   O2    110.79  3.000
 BFN  C1    C2   O2    109.09  3.000
 BFN  H32   C3   C4    110.58  3.000
 BFN  H32   C3   C2    110.96  3.000
 BFN  C4    C3   C2    111.06  3.000
 BFN  H32   C3   F1    107.66  3.000
 BFN  C4    C3   F1    109.67  3.000
 BFN  C2    C3   F1    106.76  3.000
 BFN  H4    C4   C5    108.52  3.000
 BFN  H4    C4   O4    111.38  3.000
 BFN  C5    C4   O4    112.68  3.000
 BFN  H4    C4   C3    106.55  3.000
 BFN  C5    C4   C3    109.83  3.000
 BFN  O4    C4   C3    107.69  3.000
 BFN  HO4   O4   C4    108.74  3.000
 BFN  H5    C5   C6    109.94  3.000
 BFN  H5    C5   N5    107.91  3.000
 BFN  C6    C5   N5    111.78  3.000
 BFN  H5    C5   C4    108.18  3.000
 BFN  C6    C5   C4    109.41  3.000
 BFN  N5    C5   C4    109.56  3.000
 BFN  HN5   N5   C10   117.91  3.000
 BFN  HN5   N5   C5    117.92  3.000
 BFN  C10   N5   C5    123.83  3.000
 BFN  H6    C6   C7    107.79  3.000
 BFN  H6    C6   O6    110.64  3.000
 BFN  C7    C6   O6    107.51  3.000
 BFN  H6    C6   C5    108.76  3.000
 BFN  C7    C6   C5    112.87  3.000
 BFN  O6    C6   C5    109.27  3.000
 BFN  C6    O6   C2    116.44  3.000
 BFN  H7    C7   C8    105.74  3.000
 BFN  H7    C7   O7    110.92  3.000
 BFN  C8    C7   O7    109.15  3.000
 BFN  H7    C7   C6    106.41  3.000
 BFN  C8    C7   C6    112.24  3.000
 BFN  O7    C7   C6    112.17  3.000
 BFN  HO7   O7   C7    107.23  3.000
 BFN  H8    C8   C9    108.07  3.000
 BFN  H8    C8   O8    111.10  3.000
 BFN  C9    C8   O8    110.29  3.000
 BFN  H8    C8   C7    110.02  3.000
 BFN  O8    C8   C7    105.61  3.000
 BFN  C9    C8   C7    111.77  3.000
 BFN  HO8   O8   C8    108.50  3.000
 BFN  H91   C9   H92   107.07  3.000
 BFN  H91   C9   N9    108.04  3.000
 BFN  H92   C9   N9    109.24  3.000
 BFN  H91   C9   C8    108.69  3.000
 BFN  H92   C9   C8    110.37  3.000
 BFN  N9    C9   C8    113.22  3.000
 BFN  HN9   N9   C12   119.31  3.000
 BFN  HN9   N9   C9    115.67  3.000
 BFN  C12   N9   C9    123.20  3.000
 BFN  C11   C10  O10   121.45  3.000
 BFN  C11   C10  N5    115.82  3.000
 BFN  O10   C10  N5    122.74  3.000
 BFN  H112  C11  H113  108.68  3.000
 BFN  H112  C11  H111  107.35  3.000
 BFN  H113  C11  H111  108.60  3.000
 BFN  H112  C11  C10   109.18  3.000
 BFN  H113  C11  C10   113.60  3.000
 BFN  H111  C11  C10   109.24  3.000
 BFN  C13   C12  O12   120.70  3.000
 BFN  O12   C12  N9    123.26  3.000
 BFN  C13   C12  N9    116.04  3.000
 BFN  C18   C13  C14   119.08  3.000
 BFN  C14   C13  C12   117.90  3.000
 BFN  C18   C13  C12   123.01  3.000
 BFN  H14   C14  C15   119.72  3.000
 BFN  H14   C14  C13   119.80  3.000
 BFN  C15   C14  C13   120.49  3.000
 BFN  H15   C15  C16   120.11  3.000
 BFN  H15   C15  C14   119.77  3.000
 BFN  C16   C15  C14   120.12  3.000
 BFN  H16   C16  C17   120.15  3.000
 BFN  H16   C16  C15   120.09  3.000
 BFN  C17   C16  C15   119.76  3.000
 BFN  H17   C17  C18   119.62  3.000
 BFN  H17   C17  C16   120.22  3.000
 BFN  C18   C17  C16   120.15  3.000
 BFN  H18   C18  C17   118.55  3.000
 BFN  H18   C18  C13   121.04  3.000
 BFN  C17   C18  C13   120.39  3.000
 BFN  HO1B  O1B  C1    109.97  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  HO1B  O1B  C1   C2    180.00   0.0  0
 BFN  CONST_19  O12   C12  N9   C9      0.00   0.0  0
 BFN  CONST_20  HN5   N5   C10  O10   180.00   0.0  0
 BFN  Var_01    C18   C13  C12  N9     23.46  30.0  3
 BFN  Var_02    C12   N9   C9   C8    -97.62  30.0  1
 BFN  Var_03    H111  C11  C10  N5   -122.40  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  O1B   0.020
 BFN  plan-4  O1A   0.020
 BFN  plan-4  HO1B  0.020

