# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 05:52:34 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 2-bromanyl-~{N}-[(2~{S},3~{R},4~{R},5~{S})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1O[C@H](NC(=O)CBr)[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
 08U  08U  "2-bromanyl-N-[(2S,3R,4R,5S)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]ethanamide"  L-saccharide  26  14  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_08U
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
 08U  C1   C   CR15  0   0.118  -18.4331  -13.3056  -14.9002
 08U  C2   C   CR15  0  -0.003  -18.1798  -14.4357  -15.9152
 08U  C3   C   CR15  0  -0.028  -16.8207  -14.0533  -16.4836
 08U  C4   C   CR15  0   0.009  -16.8668  -12.5236  -16.4465
 08U  C5   C   CH2   0  -0.172  -15.5553  -11.8636  -16.0814
 08U  C7   C   CH2   0  -0.655  -19.8816  -13.2893  -12.2837
 08U  O2   O   OH1   0  -0.650  -18.1631  -15.7271  -15.3911
 08U  O3   O   OH1   0  -0.661  -16.5806  -14.4840  -17.7967
 08U  O4   O   O     0  -0.482  -17.8831  -12.1687  -15.5087
 08U  O5   O   OH1   0  -0.665  -15.1329  -12.3316  -14.8237
 08U  O6   O   O     0  -0.460  -17.7337  -13.7064  -11.3796
 08U  N1   N   NH1   0  -0.611  -17.8316  -13.5613  -13.6183
 08U  H1   H   HCR5  0   0.261  -19.5003  -13.1366  -14.7621
 08U  H2   H   HCR5  0   0.236  -18.9274  -14.3245  -16.7136
 08U  H3   H   HCR5  0   0.231  -16.0409  -14.4292  -15.8073
 08U  H4   H   HCR5  0   0.244  -17.1620  -12.1543  -17.4359
 08U  H5   H   HCH2  0   0.208  -14.8340  -12.0961  -16.8751
 08U  H6   H   HCH2  0   0.216  -15.6919  -10.7745  -16.0842
 08U  BR   BR  BR    0  -0.088  -20.8300  -14.9664  -12.6365
 08U  H8   H   HCH2  0   0.333  -20.1188  -12.9989  -11.2631
 08U  H9   H   HCH2  0   0.320  -20.2712  -12.5366  -12.9669
 08U  H10  H   HOH1  0   0.454  -19.0635  -15.9930  -15.1792
 08U  H11  H   HOH1  0   0.455  -16.3573  -15.4195  -17.7724
 08U  H12  H   HOH1  0   0.461  -14.2646  -11.9673  -14.6313
 08U  H13  H   HNH1  0   0.400  -16.8298  -13.7122  -13.6145
 08U  C6   C   C     0   0.529  -18.3885  -13.5304  -12.3918

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
 08U  O3  C3   single  1.403  0.020  1.403
 08U  C5  C4   single  1.513  0.020  1.513
 08U  C5  O5   single  1.407  0.020  1.407
 08U  C3  C4   single  1.531  0.020  1.531
 08U  C3  C2   single  1.522  0.020  1.522
 08U  C4  O4   single  1.428  0.020  1.428
 08U  C2  O2   single  1.394  0.020  1.394
 08U  C2  C1   single  1.540  0.020  1.540
 08U  O4  C1   single  1.402  0.020  1.402
 08U  C1  N1   single  1.439  0.020  1.439
 08U  C7  C6   single  1.516  0.020  1.516
 08U  N1  C6   single  1.347  0.020  1.347
 08U  C6  O6   double  1.218  0.020  1.218
 08U  C1  H1   single  0.970  0.020  1.090
 08U  C2  H2   single  0.970  0.020  1.090
 08U  C3  H3   single  0.970  0.020  1.090
 08U  C4  H4   single  0.970  0.020  1.090
 08U  C5  H5   single  0.970  0.020  1.090
 08U  C5  H6   single  0.970  0.020  1.090
 08U  C7  BR   single  1.959  0.020  1.959
 08U  C7  H8   single  0.970  0.020  1.090
 08U  C7  H9   single  0.970  0.020  1.090
 08U  O2  H10  single  0.850  0.020  0.980
 08U  O3  H11  single  0.850  0.020  0.980
 08U  O5  H12  single  0.850  0.020  0.980
 08U  N1  H13  single  0.860  0.020  1.020

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
 08U  H1   C1  N1  108.92  3.000
 08U  H1   C1  O4  108.27  3.000
 08U  N1   C1  O4  111.52  3.000
 08U  H1   C1  C2  111.01  3.000
 08U  N1   C1  C2  112.83  3.000
 08U  O4   C1  C2  104.15  3.000
 08U  H2   C2  O2  112.02  3.000
 08U  H2   C2  C3  108.10  3.000
 08U  O2   C2  C3  111.25  3.000
 08U  H2   C2  C1  107.02  3.000
 08U  O2   C2  C1  115.72  3.000
 08U  C3   C2  C1  102.05  3.000
 08U  H3   C3  O3  110.47  3.000
 08U  H3   C3  C4  110.39  3.000
 08U  O3   C3  C4  109.55  3.000
 08U  H3   C3  C2  108.55  3.000
 08U  C4   C3  C2  102.42  3.000
 08U  O3   C3  C2  115.18  3.000
 08U  H4   C4  O4  108.50  3.000
 08U  H4   C4  C5  107.71  3.000
 08U  O4   C4  C5  110.49  3.000
 08U  H4   C4  C3  108.83  3.000
 08U  O4   C4  C3  106.60  3.000
 08U  C5   C4  C3  114.56  3.000
 08U  H6   C5  H5  106.87  3.000
 08U  H6   C5  O5  111.70  3.000
 08U  H5   C5  O5  112.25  3.000
 08U  H6   C5  C4  108.93  3.000
 08U  H5   C5  C4  107.62  3.000
 08U  O5   C5  C4  109.32  3.000
 08U  H9   C7  H8  109.05  3.000
 08U  H9   C7  BR  107.80  3.000
 08U  H8   C7  BR  106.98  3.000
 08U  H9   C7  C6  114.68  3.000
 08U  H8   C7  C6  108.92  3.000
 08U  BR   C7  C6  109.14  3.000
 08U  H10  O2  C2  109.12  3.000
 08U  H11  O3  C3  108.34  3.000
 08U  C4   O4  C1  111.27  3.000
 08U  H12  O5  C5  108.91  3.000
 08U  H13  N1  C6  114.12  3.000
 08U  H13  N1  C1  116.31  3.000
 08U  C6   N1  C1  129.35  3.000
 08U  N1   C6  O6  122.06  3.000
 08U  O6   C6  C7  119.54  3.000
 08U  N1   C6  C7  118.40  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
 08U  CONST_01  C7   C6  N1  C1     0.00   0.0  0
 08U  CONST_02  O6   C6  N1  C1   180.00   0.0  0
 08U  CONST_03  H13  N1  C6  C7   180.00   0.0  0
 08U  CONST_04  H13  N1  C6  O6     0.00   0.0  0
 08U  Var_01    BR   C7  C6  O6   -98.71  30.0  1
 08U  Var_02    BR   C7  C6  N1    80.34  30.0  1
 08U  Var_03    H8   C7  C6  O6    17.76  30.0  1
 08U  Var_04    H9   C7  C6  O6   140.25  30.0  1
 08U  Var_05    H8   C7  C6  N1  -163.19  30.0  1
 08U  Var_06    H9   C7  C6  N1   -40.69  30.0  1

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
 08U  chir_01  C1  C2  O4  N1  positiv
 08U  chir_02  C2  O2  C3  C1  positiv
 08U  chir_03  C3  O3  C2  C4  positiv
 08U  chir_04  C4  O4  C3  C5  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
 08U  plan-1  C1   0.020
 08U  plan-1  C7   0.020
 08U  plan-1  O6   0.020
 08U  plan-1  N1   0.020
 08U  plan-1  H13  0.020
 08U  plan-1  C6   0.020

