# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:58:55 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (2~{S},3~{R},4~{R},5~{R},6~{S})-5-acetamido-4-acetyloxy-3,6-bis(oxidanyl)oxane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@@H](O)O[C@@H]([C@H](O)[C@@H]1OC(C)=O)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
 DJB  DJB  '(2~{S},3~{R},4~{R},5~{R},6~{S})-5-acetamido-4-acetyloxy-3,6-bis(oxidanyl)oxane-2-carboxylic acid'  D-saccharide  33  19  .  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_DJB
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
 DJB  C11  C  CH3    0  -0.780   4.5196  -1.0054   0.1798
 DJB  C10  C  C      0   0.525   3.1809  -0.8797  -0.5045
 DJB  O10  O  O      0  -0.503   3.0891  -0.7938  -1.7207
 DJB  N2   N  NH1    0  -0.630   2.1172  -0.8889   0.3214
 DJB  C2   C  CH1    0  -0.148   0.7533  -0.7398  -0.1109
 DJB  C13  C  CH3    0  -0.774   1.9808   3.6887  -0.6740
 DJB  C12  C  C      0   0.565   1.0986   2.8124   0.1641
 DJB  O12  O  O      0  -0.454   0.5531   3.1523   1.1841
 DJB  C3   C  CH1    0   0.032   0.1814   0.6185   0.2866
 DJB  O3   O  O2     0  -0.458   0.9822   1.6004  -0.3697
 DJB  C4   C  CH1    0   0.002  -1.2779   0.7225  -0.1368
 DJB  O4   O  OH1    0  -0.709  -1.3489   0.7250  -1.5353
 DJB  C5   C  CH1    0  -0.149  -2.0397  -0.4535   0.4792
 DJB  C6   C  C      0   0.448  -3.5116  -0.5337   0.0086
 DJB  O6B  O  O      0  -0.567  -4.3487  -0.9308   0.8253
 DJB  O6A  O  OC    -1  -0.606  -3.7279  -0.2082  -1.1881
 DJB  O5   O  O2     0  -0.506  -1.4565  -1.6946   0.0927
 DJB  C1   C  CH1    0   0.268  -0.1193  -1.8603   0.4660
 DJB  O1   O  OH1    0  -0.669   0.0542  -1.8649   1.8485
 DJB  H1   H  HCH3   0   0.266   5.0115  -1.9185  -0.1562
 DJB  H2   H  HCH3   0   0.265   5.1550  -0.1697  -0.1123
 DJB  H3   H  HCH3   0   0.248   4.4572  -1.0278   1.2659
 DJB  H4   H  HNH1   0   0.398   2.2804  -0.9534   1.3137
 DJB  H5   H  HCH1   0   0.281   0.7333  -0.8338  -1.1970
 DJB  H6   H  HCH3   0   0.261   2.1873   4.6234  -0.1609
 DJB  H7   H  HCH3   0   0.268   2.9198   3.1889  -0.9088
 DJB  H8   H  HCH3   0   0.276   1.4879   3.9116  -1.6216
 DJB  H9   H  HCH1   0   0.257   0.2521   0.7459   1.3711
 DJB  H10  H  HCH1   0   0.222  -1.7070   1.6426   0.2921
 DJB  H11  H  HOH1   0   0.441  -2.2685   0.4095  -1.7141
 DJB  H12  H  HCH1   0   0.220  -2.0221  -0.3449   1.5694
 DJB  H14  H  HCH1   0   0.245   0.1859  -2.8153   0.0249
 DJB  H15  H  HOH1   0   0.467  -0.2961  -2.6859   2.2111

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
 DJB  C11  C10  single  1.509  0.020  1.509
 DJB  O10  C10  double  1.223  0.020  1.223
 DJB  C10  N2   single  1.347  0.020  1.347
 DJB  N2   C2   single  1.439  0.020  1.439
 DJB  C2   C1   single  1.533  0.020  1.533
 DJB  C2   C3   single  1.526  0.020  1.526
 DJB  O12  C12  double  1.206  0.020  1.206
 DJB  O3   C12  single  1.329  0.020  1.329
 DJB  O3   C3   single  1.427  0.020  1.427
 DJB  C1   O1   single  1.393  0.020  1.393
 DJB  C1   O5   single  1.398  0.020  1.398
 DJB  C12  C13  single  1.499  0.020  1.499
 DJB  C3   C4   single  1.523  0.020  1.523
 DJB  O4   C4   single  1.400  0.020  1.400
 DJB  O5   C5   single  1.425  0.020  1.425
 DJB  C4   C5   single  1.531  0.020  1.531
 DJB  C5   C6   single  1.547  0.020  1.547
 DJB  C6   O6B  deloc   1.235  0.020  1.235
 DJB  C6   O6A  deloc   1.259  0.020  1.259
 DJB  C11  H1   single  0.970  0.020  1.090
 DJB  C11  H2   single  0.970  0.020  1.090
 DJB  C11  H3   single  0.970  0.020  1.090
 DJB  N2   H4   single  0.860  0.020  1.020
 DJB  C2   H5   single  0.970  0.020  1.090
 DJB  C13  H6   single  0.970  0.020  1.090
 DJB  C13  H7   single  0.970  0.020  1.090
 DJB  C13  H8   single  0.970  0.020  1.090
 DJB  C3   H9   single  0.970  0.020  1.090
 DJB  C4   H10  single  0.970  0.020  1.090
 DJB  O4   H11  single  0.850  0.020  0.980
 DJB  C5   H12  single  0.970  0.020  1.090
 DJB  C1   H14  single  0.970  0.020  1.090
 DJB  O1   H15  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
 DJB  H3   C11  H2   108.46  3.000
 DJB  H3   C11  H1   108.44  3.000
 DJB  H2   C11  H1   107.25  3.000
 DJB  H3   C11  C10  113.81  3.000
 DJB  H2   C11  C10  109.39  3.000
 DJB  H1   C11  C10  109.29  3.000
 DJB  N2   C10  O10  123.45  3.000
 DJB  N2   C10  C11  114.96  3.000
 DJB  O10  C10  C11  121.57  3.000
 DJB  H4   N2   C2   117.13  3.000
 DJB  H4   N2   C10  118.46  3.000
 DJB  C2   N2   C10  124.32  3.000
 DJB  H5   C2   C1   107.55  3.000
 DJB  H5   C2   C3   109.22  3.000
 DJB  C1   C2   C3   109.83  3.000
 DJB  H5   C2   N2   107.92  3.000
 DJB  C3   C2   N2   111.66  3.000
 DJB  C1   C2   N2   110.54  3.000
 DJB  H8   C13  H7   107.21  3.000
 DJB  H8   C13  H6   108.68  3.000
 DJB  H7   C13  H6   109.43  3.000
 DJB  H8   C13  C12  109.82  3.000
 DJB  H7   C13  C12  111.07  3.000
 DJB  H6   C13  C12  110.53  3.000
 DJB  O3   C12  O12  123.85  3.000
 DJB  O3   C12  C13  111.09  3.000
 DJB  O12  C12  C13  125.06  3.000
 DJB  H9   C3   C4   109.23  3.000
 DJB  H9   C3   O3   109.84  3.000
 DJB  C4   C3   O3   111.28  3.000
 DJB  H9   C3   C2   109.72  3.000
 DJB  C4   C3   C2   110.32  3.000
 DJB  O3   C3   C2   106.40  3.000
 DJB  C3   O3   C12  119.46  3.000
 DJB  H10  C4   C5   106.92  3.000
 DJB  H10  C4   O4   111.56  3.000
 DJB  C5   C4   O4   112.22  3.000
 DJB  H10  C4   C3   108.77  3.000
 DJB  C5   C4   C3   108.21  3.000
 DJB  O4   C4   C3   109.04  3.000
 DJB  H11  O4   C4   103.13  3.000
 DJB  H12  C5   O5   110.46  3.000
 DJB  H12  C5   C6   108.85  3.000
 DJB  O5   C5   C6   105.17  3.000
 DJB  H12  C5   C4   108.44  3.000
 DJB  C6   C5   C4   113.01  3.000
 DJB  O5   C5   C4   110.88  3.000
 DJB  O6A  C6   O6B  126.53  3.000
 DJB  O6A  C6   C5   116.04  3.000
 DJB  O6B  C6   C5   117.41  3.000
 DJB  C1   O5   C5   114.98  3.000
 DJB  H14  C1   O1   111.22  3.000
 DJB  H14  C1   O5   105.21  3.000
 DJB  O1   C1   O5   112.61  3.000
 DJB  H14  C1   C2   109.09  3.000
 DJB  O5   C1   C2   110.94  3.000
 DJB  O1   C1   C2   107.75  3.000
 DJB  H15  O1   C1   109.33  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
 DJB  CONST_01  C2  N2   C10  C11  180.00   0.0  0
 DJB  CONST_02  C2  N2   C10  O10    0.00   0.0  0
 DJB  CONST_03  H4  N2   C10  C11    0.00   0.0  0
 DJB  Var_01    H1  C11  C10  O10  -61.24  30.0  3
 DJB  Var_02    H6  C13  C12  O12    8.75  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
 DJB  chir_01  C2  N2  C1  C3  negativ
 DJB  chir_02  C3  O3  C4  C2  negativ
 DJB  chir_03  C4  O4  C3  C5  positiv
 DJB  chir_04  C5  O5  C4  C6  negativ
 DJB  chir_05  C1  O1  O5  C2  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
 DJB  plan-1  C11  0.020
 DJB  plan-1  C10  0.020
 DJB  plan-1  O10  0.020
 DJB  plan-1  N2   0.020
 DJB  plan-1  C2   0.020
 DJB  plan-1  H4   0.020
 DJB  plan-2  C5   0.020
 DJB  plan-2  C6   0.020
 DJB  plan-2  O6B  0.020
 DJB  plan-2  O6A  0.020
 DJB  plan-3  C13  0.020
 DJB  plan-3  C12  0.020
 DJB  plan-3  O12  0.020
 DJB  plan-3  O3   0.020

