# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 16:09:41 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  34  19  .  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_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   4.4920  -0.9341   0.2055
 DJB  C10  C  C     0   0.526   3.1430  -0.8791  -0.4661
 DJB  O10  O  O     0  -0.499   3.0321  -0.8547  -1.6829
 DJB  N2   N  NH1   0  -0.632   2.0881  -0.8714   0.3736
 DJB  C2   C  CH1   0  -0.136   0.7199  -0.7771  -0.0545
 DJB  C13  C  CH3   0  -0.774   1.9043   3.6239  -0.7612
 DJB  C12  C  C     0   0.566   1.0503   2.7674   0.1223
 DJB  O12  O  O     0  -0.442   0.5802   3.1027   1.1783
 DJB  C3   C  CH1   0   0.012   0.1144   0.5795   0.2936
 DJB  O3   O  O2    0  -0.465   0.8618   1.5605  -0.4200
 DJB  C4   C  CH1   0  -0.016  -1.3570   0.6381  -0.1167
 DJB  O4   O  OH1   0  -0.663  -1.5254   0.5331  -1.5065
 DJB  C5   C  CH1   0  -0.088  -2.0766  -0.5516   0.5167
 DJB  C6   C  C     0   0.516  -3.5076  -0.6292   0.0205
 DJB  O6B  O  O     0  -0.419  -3.9762  -1.5576  -0.5789
 DJB  O6A  O  OH1   0  -0.592  -4.1783   0.4629   0.3538
 DJB  O5   O  O2    0  -0.492  -1.4655  -1.7697   0.1777
 DJB  C1   C  CH1   0   0.256  -0.1250  -1.8887   0.5745
 DJB  O1   O  OH1   0  -0.665   0.0302  -1.8142   1.9535
 DJB  H1   H  HCH3  0   0.268   5.0227  -1.8272  -0.1245
 DJB  H2   H  HCH3  0   0.266   5.0842  -0.0733  -0.1048
 DJB  H3   H  HCH3  0   0.249   4.4419  -0.9436   1.2924
 DJB  H4   H  HNH1  0   0.401   2.2616  -0.8829   1.3663
 DJB  H5   H  HCH1  0   0.287   0.6962  -0.9149  -1.1364
 DJB  H6   H  HCH3  0   0.265   2.1244   4.5698  -0.2752
 DJB  H7   H  HCH3  0   0.272   2.8378   3.1174  -1.0054
 DJB  H8   H  HCH3  0   0.278   1.3895   3.8223  -1.7022
 DJB  H9   H  HCH1  0   0.267   0.1915   0.7571   1.3699
 DJB  H10  H  HCH1  0   0.267  -1.7963   1.5620   0.2784
 DJB  H11  H  HOH1  0   0.461  -1.2245   1.3464  -1.9238
 DJB  H12  H  HCH1  0   0.289  -2.1048  -0.4017   1.6046
 DJB  H13  H  HOH1  0   0.490  -5.0895   0.4100   0.0281
 DJB  H14  H  HCH1  0   0.257   0.1992  -2.8577   0.1835
 DJB  H15  H  HOH1  0   0.472  -0.2826  -2.6307   2.3587

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  1.508  0.020  1.508
 DJB  O10  C10  double  1.222  0.020  1.222
 DJB  C10  N2   single  1.348  0.020  1.348
 DJB  N2   C2   single  1.437  0.020  1.437
 DJB  C2   C1   single  1.531  0.020  1.531
 DJB  C2   C3   single  1.526  0.020  1.526
 DJB  O12  C12  double  1.204  0.020  1.204
 DJB  O3   C12  single  1.336  0.020  1.336
 DJB  O3   C3   single  1.425  0.020  1.425
 DJB  C1   O1   single  1.390  0.020  1.390
 DJB  C1   O5   single  1.403  0.020  1.403
 DJB  C12  C13  single  1.498  0.020  1.498
 DJB  C3   C4   single  1.529  0.020  1.529
 DJB  O4   C4   single  1.404  0.020  1.404
 DJB  O5   C5   single  1.404  0.020  1.404
 DJB  C4   C5   single  1.528  0.020  1.528
 DJB  C5   C6   single  1.517  0.020  1.517
 DJB  C6   O6B  double  1.200  0.020  1.200
 DJB  C6   O6A  single  1.324  0.020  1.324
 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  O6A  H13  single  0.850  0.020  0.980
 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   108.44  3.000
 DJB  H3   C11  H1   108.52  3.000
 DJB  H2   C11  H1   107.24  3.000
 DJB  H3   C11  C10  113.83  3.000
 DJB  H2   C11  C10  109.30  3.000
 DJB  H1   C11  C10  109.31  3.000
 DJB  N2   C10  O10  123.30  3.000
 DJB  N2   C10  C11  115.01  3.000
 DJB  O10  C10  C11  121.69  3.000
 DJB  H4   N2   C2   117.27  3.000
 DJB  H4   N2   C10  118.60  3.000
 DJB  C2   N2   C10  124.05  3.000
 DJB  H5   C2   C1   107.68  3.000
 DJB  H5   C2   C3   109.27  3.000
 DJB  C1   C2   C3   109.44  3.000
 DJB  H5   C2   N2   107.93  3.000
 DJB  C3   C2   N2   111.61  3.000
 DJB  C1   C2   N2   110.81  3.000
 DJB  H8   C13  H7   107.18  3.000
 DJB  H8   C13  H6   108.86  3.000
 DJB  H7   C13  H6   109.36  3.000
 DJB  H8   C13  C12  110.10  3.000
 DJB  H7   C13  C12  110.78  3.000
 DJB  H6   C13  C12  110.47  3.000
 DJB  O3   C12  O12  123.54  3.000
 DJB  O3   C12  C13  110.94  3.000
 DJB  O12  C12  C13  125.51  3.000
 DJB  H9   C3   C4   109.02  3.000
 DJB  H9   C3   O3   110.13  3.000
 DJB  C4   C3   O3   110.13  3.000
 DJB  H9   C3   C2   109.93  3.000
 DJB  C4   C3   C2   110.78  3.000
 DJB  O3   C3   C2   106.84  3.000
 DJB  C3   O3   C12  119.50  3.000
 DJB  H10  C4   C5   108.54  3.000
 DJB  H10  C4   O4   111.82  3.000
 DJB  C5   C4   O4   107.20  3.000
 DJB  H10  C4   C3   108.73  3.000
 DJB  C5   C4   C3   108.19  3.000
 DJB  O4   C4   C3   112.23  3.000
 DJB  H11  O4   C4   109.18  3.000
 DJB  H12  C5   O5   111.62  3.000
 DJB  H12  C5   C6   107.87  3.000
 DJB  O5   C5   C6   106.69  3.000
 DJB  H12  C5   C4   108.45  3.000
 DJB  C6   C5   C4   110.40  3.000
 DJB  O5   C5   C4   111.74  3.000
 DJB  O6A  C6   O6B  124.46  3.000
 DJB  O6A  C6   C5   110.69  3.000
 DJB  O6B  C6   C5   124.85  3.000
 DJB  H13  O6A  C6   110.28  3.000
 DJB  C1   O5   C5   114.90  3.000
 DJB  H14  C1   O1   111.66  3.000
 DJB  H14  C1   O5   104.90  3.000
 DJB  O1   C1   O5   112.51  3.000
 DJB  H14  C1   C2   109.43  3.000
 DJB  O5   C1   C2   110.45  3.000
 DJB  O1   C1   C2   107.88  3.000
 DJB  H15  O1   C1   109.61  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  H13  O6A  C6   C5   180.00   0.0  0
 DJB  CONST_04  H4   N2   C10  C11    0.00   0.0  0
 DJB  Var_01    H1   C11  C10  O10  -58.92  30.0  3
 DJB  Var_02    H6   C13  C12  O12    5.33  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-2  H13  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

