# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:28:56 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  28  16  .  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_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  -0.753   4.7554  -0.0095  -0.2342
 DJE  C10  C  C      0   0.485   3.4092  -0.0866   0.4411
 DJE  O10  O  O      0  -0.536   3.3004  -0.3804   1.6209
 DJE  N2   N  NH1    0  -0.588   2.3557   0.1907  -0.3542
 DJE  O1   O  OH1    0  -0.661   0.3829   1.5553  -1.6911
 DJE  C2   C  CH1    0  -0.079   0.9845   0.0953   0.0658
 DJE  C3   C  CH1    0   0.036   0.2826  -1.1306  -0.5185
 DJE  O3   O  OH1    0  -0.693   0.9923  -2.2692  -0.1174
 DJE  C4   C  CH1    0  -0.099  -1.1716  -1.1373  -0.0476
 DJE  O4   O  OH1    0  -0.686  -1.1948  -1.3149   1.3388
 DJE  C5   C  CH1    0   0.006  -1.8255   0.1746  -0.4837
 DJE  C6   C  C      0   0.351  -3.2823   0.3461  -0.0264
 DJE  O6B  O  O      0  -0.671  -3.9748   1.1491  -0.6823
 DJE  O6A  O  OC    -1  -0.644  -3.6812  -0.3355   0.9430
 DJE  O5   O  O2     0  -0.437  -1.1306   1.2903   0.0457
 DJE  C1   C  CH1    0   0.216   0.2257   1.3667  -0.3237
 DJE  H1   H  HCH3   0   0.299   5.3553   0.7634   0.2455
 DJE  H2   H  HCH3   0   0.270   5.2810  -0.9544  -0.1030
 DJE  H3   H  HCH3   0   0.223   4.7044   0.2090  -1.2994
 DJE  H4   H  HNH1   0   0.384   2.5259   0.3764  -1.3283
 DJE  H6   H  HCH1   0   0.281   0.9766   0.0205   1.1538
 DJE  H7   H  HCH1   0   0.243   0.2770  -1.0444  -1.6149
 DJE  H8   H  HOH1   0   0.418   0.7291  -3.0033  -0.6800
 DJE  H9   H  HCH1   0   0.265  -1.7025  -1.9520  -0.5721
 DJE  H10  H  HOH1   0   0.450  -2.1168  -1.1516   1.5954
 DJE  H11  H  HCH1   0   0.228  -1.8173   0.2078  -1.5803
 DJE  H13  H  HCH1   0   0.244   0.6298   2.2165   0.2408
 DJE  H5   H  HOH1   0   0.448   0.1734   2.4636  -1.9264

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   deloc   1.247  0.020  1.247
 DJE  O5   C1   single  1.408  0.020  1.408
 DJE  O5   C5   single  1.417  0.020  1.417
 DJE  C6   C5   single  1.536  0.020  1.536
 DJE  C6   O6A  deloc   1.250  0.020  1.250
 DJE  C1   O1   single  1.389  0.020  1.389
 DJE  C1   C2   single  1.531  0.020  1.531
 DJE  C5   C4   single  1.529  0.020  1.529
 DJE  O10  C10  double  1.221  0.020  1.221
 DJE  C2   N2   single  1.437  0.020  1.437
 DJE  C2   C3   single  1.529  0.020  1.529
 DJE  C10  N2   single  1.349  0.020  1.349
 DJE  C10  C11  single  1.508  0.020  1.508
 DJE  O4   C4   single  1.398  0.020  1.398
 DJE  C4   C3   single  1.529  0.020  1.529
 DJE  C3   O3   single  1.400  0.020  1.400
 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  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   108.34  3.000
 DJE  H3   C11  H1   108.31  3.000
 DJE  H2   C11  H1   107.26  3.000
 DJE  H3   C11  C10  113.99  3.000
 DJE  H2   C11  C10  109.41  3.000
 DJE  H1   C11  C10  109.30  3.000
 DJE  N2   C10  O10  123.35  3.000
 DJE  N2   C10  C11  115.00  3.000
 DJE  O10  C10  C11  121.65  3.000
 DJE  H4   N2   C2   117.16  3.000
 DJE  H4   N2   C10  118.47  3.000
 DJE  C2   N2   C10  124.00  3.000
 DJE  H5   O1   C1   110.16  3.000
 DJE  H6   C2   C1   107.89  3.000
 DJE  H6   C2   C3   108.84  3.000
 DJE  C1   C2   C3   109.94  3.000
 DJE  H6   C2   N2   107.64  3.000
 DJE  C3   C2   N2   112.31  3.000
 DJE  C1   C2   N2   110.09  3.000
 DJE  H7   C3   C4   107.61  3.000
 DJE  H7   C3   O3   110.60  3.000
 DJE  C4   C3   O3   112.98  3.000
 DJE  H7   C3   C2   108.69  3.000
 DJE  O3   C3   C2   108.05  3.000
 DJE  C4   C3   C2   108.82  3.000
 DJE  H8   O3   C3   108.33  3.000
 DJE  H9   C4   C5   106.96  3.000
 DJE  H9   C4   O4   111.66  3.000
 DJE  C5   C4   O4   112.62  3.000
 DJE  H9   C4   C3   108.31  3.000
 DJE  O4   C4   C3   108.78  3.000
 DJE  C5   C4   C3   108.37  3.000
 DJE  H10  O4   C4   104.87  3.000
 DJE  H11  C5   O5   110.24  3.000
 DJE  H11  C5   C6   107.53  3.000
 DJE  O5   C5   C6   105.42  3.000
 DJE  H11  C5   C4   107.93  3.000
 DJE  C6   C5   C4   114.60  3.000
 DJE  O5   C5   C4   111.05  3.000
 DJE  O6A  C6   O6B  125.57  3.000
 DJE  O6A  C6   C5   118.19  3.000
 DJE  O6B  C6   C5   116.23  3.000
 DJE  C1   O5   C5   114.66  3.000
 DJE  H13  C1   O5   105.18  3.000
 DJE  H13  C1   C2   109.25  3.000
 DJE  O5   C1   C2   111.45  3.000
 DJE  H13  C1   O1   111.07  3.000
 DJE  C2   C1   O1   107.89  3.000
 DJE  O5   C1   O1   112.00  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  H4  N2   C10  C11    0.00   0.0  0
 DJE  Var_01    H1  C11  C10  O10  -61.84  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

