# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 23:37:57 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2~{R},3~{R},4~{S})-3-acetamido-2-[(1~{R},2~{R})-3-(2-azanylhydrazinyl)-1,2-bis(oxidanyl)propyl]-4-oxidanyl-3,4-dihydro-2~{H}-pyran-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)C=C(O[C@H]1[C@H](O)[C@H](O)CNNN)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
 6UD  6UD  '(2~{R},3~{R},4~{S})-3-acetamido-2-[(1~{R},2~{R})-3-(2-azanylhydrazinyl)-1,2-bis(oxidanyl)propyl]-4-oxidanyl-3,4-dihydro-2~{H}-pyran-6-carboxylic acid'  D-saccharide  42  22  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6UD
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
 6UD  C1   C  C     0   0.506  -1.4624   3.5057   0.1344
 6UD  C2   C  C     0   0.242  -1.6188   2.0448  -0.1042
 6UD  C3   C  C1    0  -0.371  -2.7971   1.5217  -0.4360
 6UD  C4   C  CH1   0   0.075  -2.9851   0.0484  -0.6425
 6UD  C5   C  CH1   0  -0.151  -1.8063  -0.7077  -0.0338
 6UD  C6   C  CH1   0   0.026  -0.4985  -0.0089  -0.4221
 6UD  C7   C  CH1   0  -0.021   0.7408  -0.6740   0.1739
 6UD  C8   C  CH1   0  -0.025   2.0413  -0.0506  -0.3657
 6UD  C9   C  CH2   0  -0.264   3.2704  -0.7091   0.2476
 6UD  C11  C  CH3   0  -0.781  -2.0395  -4.4715  -0.3873
 6UD  N5   N  NH1   0  -0.639  -1.7959  -2.0766  -0.4741
 6UD  O1A  O  OH1   0  -0.583  -0.2182   3.8363   0.4281
 6UD  O1B  O  O     0  -0.431  -2.3765   4.2899   0.0663
 6UD  O4   O  OH1   0  -0.657  -4.1626  -0.4200  -0.0332
 6UD  O6   O  O2    0  -0.488  -0.4852   1.3359   0.0476
 6UD  O7   O  OH1   0  -0.657   0.6960  -0.6774   1.5777
 6UD  O8   O  OH1   0  -0.663   2.0678  -0.1066  -1.7778
 6UD  O10  O  O     0  -0.494  -2.2394  -3.0496   1.5218
 6UD  N1   N  NH1   0  -0.479   4.4733  -0.0572  -0.2268
 6UD  N2   N  NH1   0  -0.373   5.6160  -0.6213   0.3619
 6UD  N3   N  NH2   0  -0.660   6.6471   0.3310   0.4528
 6UD  H1   H  H     0   0.282  -3.6476   2.1782  -0.5630
 6UD  H2   H  HCH1  0   0.236  -3.0074  -0.1531  -1.7239
 6UD  H3   H  HCH1  0   0.281  -1.9067  -0.7011   1.0533
 6UD  H4   H  HCH1  0   0.253  -0.4130   0.0020  -1.5167
 6UD  H5   H  HCH1  0   0.249   0.7251  -1.7262  -0.1300
 6UD  H6   H  HCH1  0   0.238   2.0680   1.0157  -0.1177
 6UD  H7   H  HCH2  0   0.234   3.2341  -0.6038   1.3322
 6UD  H8   H  HCH2  0   0.191   3.2451  -1.7920   0.0342
 6UD  H9   H  HCH3  0   0.267  -1.3264  -5.1390   0.0955
 6UD  H10  H  HCH3  0   0.268  -3.0254  -4.9274  -0.2947
 6UD  H11  H  HCH3  0   0.248  -1.7903  -4.4056  -1.4447
 6UD  H12  H  HNH1  0   0.401  -1.6873  -2.2411  -1.4630
 6UD  H13  H  HOH1  0   0.490  -0.1586   4.7925   0.5750
 6UD  H14  H  HOH1  0   0.459  -4.9109  -0.1718  -0.5847
 6UD  H15  H  HOH1  0   0.447   0.6973   0.2346   1.8898
 6UD  H16  H  HOH1  0   0.447   2.0887  -1.0311  -2.0510
 6UD  H17  H  HNH1  0   0.336   4.5209  -0.1221  -1.2390
 6UD  H18  H  HNH1  0   0.343   5.9219  -1.4229  -0.1826
 6UD  H19  H  HNH2  0   0.353   7.2504   0.0529   1.2150
 6UD  H20  H  HNH2  0   0.338   7.2195   0.3349  -0.3856
 6UD  C10  C  C     0   0.527  -2.0387  -3.1395   0.3207

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
 6UD  O1B  C1   double  1.206  0.020  1.206
 6UD  O4   C4   single  1.406  0.020  1.406
 6UD  C3   C4   single  1.499  0.020  1.499
 6UD  C3   C2   double  1.331  0.020  1.331
 6UD  C1   C2   single  1.489  0.020  1.489
 6UD  C1   O1A  single  1.320  0.020  1.320
 6UD  C4   C5   single  1.527  0.020  1.527
 6UD  C2   O6   single  1.346  0.020  1.346
 6UD  C5   N5   single  1.438  0.020  1.438
 6UD  C5   C6   single  1.533  0.020  1.533
 6UD  O6   C6   single  1.424  0.020  1.424
 6UD  N5   C10  single  1.349  0.020  1.349
 6UD  C6   C7   single  1.528  0.020  1.528
 6UD  C10  O10  double  1.221  0.020  1.221
 6UD  C10  C11  single  1.509  0.020  1.509
 6UD  O7   C7   single  1.404  0.020  1.404
 6UD  C7   C8   single  1.540  0.020  1.540
 6UD  C8   O8   single  1.413  0.020  1.413
 6UD  C8   C9   single  1.523  0.020  1.523
 6UD  N3   N2   single  1.406  0.020  1.406
 6UD  C9   N1   single  1.448  0.020  1.448
 6UD  N2   N1   single  1.404  0.020  1.404
 6UD  C3   H1   single  0.930  0.020  1.080
 6UD  C4   H2   single  0.970  0.020  1.090
 6UD  C5   H3   single  0.970  0.020  1.090
 6UD  C6   H4   single  0.970  0.020  1.090
 6UD  C7   H5   single  0.970  0.020  1.090
 6UD  C8   H6   single  0.970  0.020  1.090
 6UD  C9   H7   single  0.970  0.020  1.090
 6UD  C9   H8   single  0.970  0.020  1.090
 6UD  C11  H9   single  0.970  0.020  1.090
 6UD  C11  H10  single  0.970  0.020  1.090
 6UD  C11  H11  single  0.970  0.020  1.090
 6UD  N5   H12  single  0.860  0.020  1.020
 6UD  O1A  H13  single  0.850  0.020  0.980
 6UD  O4   H14  single  0.850  0.020  0.980
 6UD  O7   H15  single  0.850  0.020  0.980
 6UD  O8   H16  single  0.850  0.020  0.980
 6UD  N1   H17  single  0.890  0.020  1.040
 6UD  N2   H18  single  0.890  0.020  1.040
 6UD  N3   H19  single  0.890  0.020  1.040
 6UD  N3   H20  single  0.890  0.020  1.040

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
 6UD  O1B  C1   O1A  124.32  3.000
 6UD  O1A  C1   C2   112.35  3.000
 6UD  O1B  C1   C2   123.32  3.000
 6UD  O6   C2   C3   124.52  3.000
 6UD  O6   C2   C1   114.24  3.000
 6UD  C3   C2   C1   121.24  3.000
 6UD  H1   C3   C4   118.79  3.000
 6UD  H1   C3   C2   119.12  3.000
 6UD  C4   C3   C2   122.10  3.000
 6UD  H2   C4   O4   110.36  3.000
 6UD  H2   C4   C5   108.47  3.000
 6UD  O4   C4   C5   107.98  3.000
 6UD  H2   C4   C3   108.53  3.000
 6UD  C5   C4   C3   109.57  3.000
 6UD  O4   C4   C3   111.87  3.000
 6UD  H3   C5   N5   108.14  3.000
 6UD  H3   C5   C6   109.14  3.000
 6UD  N5   C5   C6   110.50  3.000
 6UD  H3   C5   C4   108.84  3.000
 6UD  C6   C5   C4   109.38  3.000
 6UD  N5   C5   C4   110.79  3.000
 6UD  H4   C6   O6   108.58  3.000
 6UD  H4   C6   C7   109.27  3.000
 6UD  O6   C6   C7   105.95  3.000
 6UD  H4   C6   C5   108.87  3.000
 6UD  C7   C6   C5   113.26  3.000
 6UD  O6   C6   C5   110.78  3.000
 6UD  H5   C7   O7   105.94  3.000
 6UD  H5   C7   C8   107.68  3.000
 6UD  O7   C7   C8   112.22  3.000
 6UD  H5   C7   C6   107.36  3.000
 6UD  C8   C7   C6   111.85  3.000
 6UD  O7   C7   C6   111.42  3.000
 6UD  H6   C8   O8   105.33  3.000
 6UD  H6   C8   C9   108.06  3.000
 6UD  O8   C8   C9   111.71  3.000
 6UD  H6   C8   C7   109.60  3.000
 6UD  C9   C8   C7   111.43  3.000
 6UD  O8   C8   C7   110.48  3.000
 6UD  H8   C9   H7   106.63  3.000
 6UD  H8   C9   N1   113.41  3.000
 6UD  H7   C9   N1   108.07  3.000
 6UD  H8   C9   C8   109.12  3.000
 6UD  H7   C9   C8   109.38  3.000
 6UD  N1   C9   C8   110.11  3.000
 6UD  H11  C11  H10  108.36  3.000
 6UD  H11  C11  H9   108.52  3.000
 6UD  H10  C11  H9   107.34  3.000
 6UD  H11  C11  C10  113.73  3.000
 6UD  H10  C11  C10  109.26  3.000
 6UD  H9   C11  C10  109.42  3.000
 6UD  H12  N5   C10  117.95  3.000
 6UD  H12  N5   C5   117.15  3.000
 6UD  C10  N5   C5   124.62  3.000
 6UD  H13  O1A  C1   109.79  3.000
 6UD  H14  O4   C4   108.48  3.000
 6UD  C6   O6   C2   116.89  3.000
 6UD  H15  O7   C7   108.74  3.000
 6UD  H16  O8   C8   108.75  3.000
 6UD  H17  N1   N2   110.75  3.000
 6UD  H17  N1   C9   109.68  3.000
 6UD  N2   N1   C9   110.97  3.000
 6UD  H18  N2   N3   110.37  3.000
 6UD  H18  N2   N1   109.71  3.000
 6UD  N3   N2   N1   110.60  3.000
 6UD  H20  N3   H19  106.69  3.000
 6UD  H20  N3   N2   111.26  3.000
 6UD  H19  N3   N2   107.45  3.000
 6UD  O10  C10  N5   123.44  3.000
 6UD  O10  C10  C11  121.78  3.000
 6UD  N5   C10  C11  114.78  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
 6UD  CONST_01  O10  C10  N5   C5      0.00   0.0  0
 6UD  CONST_02  C11  C10  N5   C5    180.00   0.0  0
 6UD  CONST_03  H13  O1A  C1   C2    180.00   0.0  0
 6UD  CONST_04  H12  N5   C10  C11     0.00   0.0  0
 6UD  Var_01    O6   C2   C3   C4      1.68  30.0  1
 6UD  Var_02    O1B  C1   C2   C3      1.26  30.0  2
 6UD  Var_03    N2   N1   C9   C8    178.03  30.0  3
 6UD  Var_04    N3   N2   N1   C9   -151.30  30.0  1
 6UD  Var_05    H9   C11  C10  N5    124.62  30.0  3
 6UD  Var_06    H19  N3   N2   N1    154.64  30.0  2

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
 6UD  chir_01  C4  O4  C3  C5  negativ
 6UD  chir_02  C5  N5  C6  C4  negativ
 6UD  chir_03  C6  O6  C5  C7  positiv
 6UD  chir_04  C7  O7  C8  C6  positiv
 6UD  chir_05  C8  O8  C7  C9  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
 6UD  plan-1  C5   0.020
 6UD  plan-1  C11  0.020
 6UD  plan-1  N5   0.020
 6UD  plan-1  O10  0.020
 6UD  plan-1  H12  0.020
 6UD  plan-1  C10  0.020
 6UD  plan-2  C1   0.020
 6UD  plan-2  C2   0.020
 6UD  plan-2  O1A  0.020
 6UD  plan-2  O1B  0.020
 6UD  plan-2  H13  0.020

