# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 11:59:44 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (2~{S},3~{R},4~{R},5~{R},6~{S})-5-acetamido-3,4,6-tris(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]1O)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
 DJE  DJE  '(2~{S},3~{R},4~{R},5~{R},6~{S})-5-acetamido-3,4,6-tris(oxidanyl)oxane-2-carboxylic acid'  D-saccharide  29  16  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DJE
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
 DJE  C11  C  CH3   0  -0.786   4.7060  -0.0961  -0.2060
 DJE  C10  C  C     0   0.506   3.3603  -0.1262   0.4788
 DJE  O10  O  O     0  -0.498   3.2308  -0.3823   1.6663
 DJE  N2   N  NH1   0  -0.622   2.3257   0.1753  -0.3320
 DJE  O1   O  OH1   0  -0.666   0.4061   1.5793  -1.7337
 DJE  C2   C  CH1   0  -0.128   0.9444   0.1426   0.0664
 DJE  C3   C  CH1   0   0.017   0.2159  -1.0740  -0.5002
 DJE  O3   O  OH1   0  -0.658   0.8192  -2.2275   0.0327
 DJE  C4   C  CH1   0  -0.013  -1.2687  -1.0215  -0.1257
 DJE  O4   O  OH1   0  -0.670  -1.4586  -1.1674   1.2587
 DJE  C5   C  CH1   0  -0.086  -1.8513   0.3305  -0.5290
 DJE  C6   C  C     0   0.514  -3.2694   0.4753  -0.0136
 DJE  O6B  O  O     0  -0.422  -3.6325   1.3043   0.7758
 DJE  O6A  O  OH1   0  -0.593  -4.0621  -0.4342  -0.5613
 DJE  O5   O  O2    0  -0.493  -1.1164   1.3980   0.0107
 DJE  C1   C  CH1   0   0.255   0.2364   1.4303  -0.3607
 DJE  H1   H  HCH3  0   0.265   4.9180   0.9035  -0.5883
 DJE  H2   H  HCH3  0   0.259   5.4919  -0.3761   0.4903
 DJE  H3   H  HCH3  0   0.263   4.7277  -0.7800  -1.0553
 DJE  H4   H  HNH1  0   0.397   2.5177   0.3471  -1.3068
 DJE  H6   H  HCH1  0   0.275   0.9120   0.0986   1.1560
 DJE  H7   H  HCH1  0   0.233   0.2923  -1.0623  -1.5954
 DJE  H8   H  HOH1  0   0.460   0.6011  -2.9771  -0.5308
 DJE  H9   H  HCH1  0   0.246  -1.7942  -1.8070  -0.6877
 DJE  H10  H  HOH1  0   0.453  -0.9694  -1.9478   1.5439
 DJE  H11  H  HCH1  0   0.281  -1.8857   0.3756  -1.6261
 DJE  H12  H  HOH1  0   0.488  -4.9632  -0.3464  -0.2159
 DJE  H13  H  HCH1  0   0.252   0.6570   2.2789   0.1880
 DJE  H5   H  HOH1  0   0.469   0.2026   2.4865  -1.9862

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
 DJE  O6B  C6   double  1.201  0.020  1.201
 DJE  O5   C1   single  1.403  0.020  1.403
 DJE  O5   C5   single  1.404  0.020  1.404
 DJE  C6   C5   single  1.516  0.020  1.516
 DJE  C6   O6A  single  1.325  0.020  1.325
 DJE  C1   O1   single  1.391  0.020  1.391
 DJE  C1   C2   single  1.530  0.020  1.530
 DJE  C5   C4   single  1.526  0.020  1.526
 DJE  O10  C10  double  1.222  0.020  1.222
 DJE  C2   N2   single  1.438  0.020  1.438
 DJE  C2   C3   single  1.527  0.020  1.527
 DJE  C10  N2   single  1.349  0.020  1.349
 DJE  C10  C11  single  1.510  0.020  1.510
 DJE  O4   C4   single  1.405  0.020  1.405
 DJE  C4   C3   single  1.532  0.020  1.532
 DJE  C3   O3   single  1.407  0.020  1.407
 DJE  C11  H1   single  0.970  0.020  1.090
 DJE  C11  H2   single  0.970  0.020  1.090
 DJE  C11  H3   single  0.970  0.020  1.090
 DJE  N2   H4   single  0.860  0.020  1.020
 DJE  O1   H5   single  0.850  0.020  0.980
 DJE  C2   H6   single  0.970  0.020  1.090
 DJE  C3   H7   single  0.970  0.020  1.090
 DJE  O3   H8   single  0.850  0.020  0.980
 DJE  C4   H9   single  0.970  0.020  1.090
 DJE  O4   H10  single  0.850  0.020  0.980
 DJE  C5   H11  single  0.970  0.020  1.090
 DJE  O6A  H12  single  0.850  0.020  0.980
 DJE  C1   H13  single  0.970  0.020  1.090

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
 DJE  H3   C11  H2   108.84  3.000
 DJE  H3   C11  H1   107.32  3.000
 DJE  H2   C11  H1   108.66  3.000
 DJE  H3   C11  C10  111.00  3.000
 DJE  H2   C11  C10  110.41  3.000
 DJE  H1   C11  C10  110.51  3.000
 DJE  N2   C10  O10  123.36  3.000
 DJE  N2   C10  C11  113.99  3.000
 DJE  O10  C10  C11  122.65  3.000
 DJE  H4   N2   C2   117.05  3.000
 DJE  H4   N2   C10  118.24  3.000
 DJE  C2   N2   C10  124.42  3.000
 DJE  H5   O1   C1   109.49  3.000
 DJE  H6   C2   C1   107.39  3.000
 DJE  H6   C2   C3   108.92  3.000
 DJE  C1   C2   C3   110.25  3.000
 DJE  H6   C2   N2   107.83  3.000
 DJE  C3   C2   N2   111.94  3.000
 DJE  C1   C2   N2   110.36  3.000
 DJE  H7   C3   C4   108.11  3.000
 DJE  H7   C3   O3   110.90  3.000
 DJE  C4   C3   O3   110.56  3.000
 DJE  H7   C3   C2   109.17  3.000
 DJE  O3   C3   C2   107.95  3.000
 DJE  C4   C3   C2   110.14  3.000
 DJE  H8   O3   C3   108.64  3.000
 DJE  H9   C4   C5   108.38  3.000
 DJE  H9   C4   O4   111.40  3.000
 DJE  C5   C4   O4   107.50  3.000
 DJE  H9   C4   C3   108.28  3.000
 DJE  O4   C4   C3   111.61  3.000
 DJE  C5   C4   C3   109.61  3.000
 DJE  H10  O4   C4   107.87  3.000
 DJE  H11  C5   O5   111.66  3.000
 DJE  H11  C5   C6   107.84  3.000
 DJE  O5   C5   C6   106.64  3.000
 DJE  H11  C5   C4   108.19  3.000
 DJE  C6   C5   C4   110.60  3.000
 DJE  O5   C5   C4   111.85  3.000
 DJE  O6A  C6   O6B  124.37  3.000
 DJE  O6A  C6   C5   110.71  3.000
 DJE  O6B  C6   C5   124.92  3.000
 DJE  H12  O6A  C6   110.30  3.000
 DJE  C1   O5   C5   114.86  3.000
 DJE  H13  C1   O5   104.81  3.000
 DJE  H13  C1   C2   109.55  3.000
 DJE  O5   C1   C2   110.66  3.000
 DJE  H13  C1   O1   111.39  3.000
 DJE  C2   C1   O1   108.00  3.000
 DJE  O5   C1   O1   112.41  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
 DJE  CONST_01  C2   N2   C10  C11   180.00   0.0  0
 DJE  CONST_02  C2   N2   C10  O10     0.00   0.0  0
 DJE  CONST_03  H12  O6A  C6   C5    180.00   0.0  0
 DJE  CONST_04  H4   N2   C10  C11     0.00   0.0  0
 DJE  Var_01    H1   C11  C10  O10  -117.50  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
 DJE  chir_01  C2  C1  N2  C3  positiv
 DJE  chir_02  C3  O3  C2  C4  positiv
 DJE  chir_03  C4  O4  C3  C5  positiv
 DJE  chir_04  C5  O5  C4  C6  negativ
 DJE  chir_05  C1  O5  O1  C2  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
 DJE  plan-1  C11  0.020
 DJE  plan-1  C10  0.020
 DJE  plan-1  O10  0.020
 DJE  plan-1  N2   0.020
 DJE  plan-1  C2   0.020
 DJE  plan-1  H4   0.020
 DJE  plan-2  C5   0.020
 DJE  plan-2  C6   0.020
 DJE  plan-2  O6B  0.020
 DJE  plan-2  O6A  0.020
 DJE  plan-2  H12  0.020

