# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 12:44:58 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  41  22  .  2023-02-15  2023-02-15
;
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   0.375  -1.6291   3.4941   0.4582
 6UD  C2   C  C      0   0.182  -1.7212   2.0181   0.0814
 6UD  C3   C  C1     0  -0.423  -2.8501   1.4216  -0.3011
 6UD  C4   C  CH1    0   0.085  -2.9449  -0.0427  -0.6064
 6UD  C5   C  CH1    0  -0.142  -1.7136  -0.7554  -0.0576
 6UD  C6   C  CH1    0   0.026  -0.4698   0.0687  -0.4042
 6UD  C7   C  CH1    0  -0.016   0.8306  -0.5484   0.1065
 6UD  C8   C  CH1    0  -0.013   2.0642   0.2398  -0.3733
 6UD  C9   C  CH2    0  -0.289   3.3554  -0.3703   0.1556
 6UD  C11  C  CH3    0  -0.781  -1.6352  -4.4991  -0.6437
 6UD  N5   N  NH1    0  -0.638  -1.6072  -2.0910  -0.5851
 6UD  O1A  O  OC    -1  -0.592  -0.5122   3.8982   0.8182
 6UD  O1B  O  O      0  -0.590  -2.6861   4.1449   0.3696
 6UD  O4   O  OH1    0  -0.664  -4.0811  -0.6382  -0.0179
 6UD  O6   O  O2     0  -0.484  -0.5424   1.3606   0.1769
 6UD  O7   O  OH1    0  -0.661   0.8131  -0.6925   1.5051
 6UD  O8   O  OH1    0  -0.665   2.0796   0.3297  -1.7848
 6UD  O10  O  O      0  -0.499  -1.9764  -3.2199   1.3429
 6UD  N1   N  NH1    0  -0.475   4.4926   0.4400  -0.2507
 6UD  N2   N  NH1    0  -0.371   5.7423  -0.0100   0.1919
 6UD  N3   N  NH2    0  -0.679   5.9988  -1.3677  -0.1086
 6UD  H1   H  H      0   0.251  -3.7420   2.0282  -0.3884
 6UD  H2   H  HCH1   0   0.211  -2.9711  -0.1885  -1.6978
 6UD  H3   H  HCH1   0   0.270  -1.8044  -0.8304   1.0275
 6UD  H4   H  HCH1   0   0.237  -0.4124   0.1716  -1.4969
 6UD  H5   H  HCH1   0   0.242   0.9062  -1.5630  -0.2998
 6UD  H6   H  HCH1   0   0.237   1.9960   1.2726  -0.0177
 6UD  H7   H  HCH2   0   0.230   3.3231  -0.3858   1.2475
 6UD  H8   H  HCH2   0   0.200   3.4273  -1.4173  -0.1775
 6UD  H9   H  HCH3   0   0.265  -2.5358  -5.0975  -0.5093
 6UD  H10  H  HCH3   0   0.247  -1.4775  -4.3494  -1.7101
 6UD  H11  H  HCH3   0   0.266  -0.7999  -5.0789  -0.2507
 6UD  H12  H  HNH1   0   0.398  -1.4719  -2.1861  -1.5797
 6UD  H14  H  HOH1   0   0.452  -4.8630  -0.2832  -0.4523
 6UD  H15  H  HOH1   0   0.445   0.6796   0.1774   1.8986
 6UD  H16  H  HOH1   0   0.446   2.1668  -0.5593  -2.1475
 6UD  H17  H  HNH1   0   0.340   4.5357   0.4918  -1.2601
 6UD  H18  H  HNH1   0   0.349   5.7716   0.1481   1.1925
 6UD  H19  H  HNH2   0   0.358   6.9969  -1.4662  -0.2328
 6UD  H20  H  HNH2   0   0.344   5.7323  -1.9818   0.6533
 6UD  C10  C  C      0   0.525  -1.7620  -3.2160   0.1399

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   deloc   1.244  0.020  1.244
 6UD  O4   C4   single  1.411  0.020  1.411
 6UD  C3   C4   single  1.499  0.020  1.499
 6UD  C3   C2   double  1.333  0.020  1.333
 6UD  C1   C2   single  1.526  0.020  1.526
 6UD  C1   O1A  deloc   1.241  0.020  1.241
 6UD  C4   C5   single  1.525  0.020  1.525
 6UD  C2   O6   single  1.353  0.020  1.353
 6UD  C5   N5   single  1.440  0.020  1.440
 6UD  C5   C6   single  1.532  0.020  1.532
 6UD  O6   C6   single  1.418  0.020  1.418
 6UD  N5   C10  single  1.347  0.020  1.347
 6UD  C6   C7   single  1.527  0.020  1.527
 6UD  C10  O10  double  1.222  0.020  1.222
 6UD  C10  C11  single  1.509  0.020  1.509
 6UD  O7   C7   single  1.406  0.020  1.406
 6UD  C7   C8   single  1.540  0.020  1.540
 6UD  C8   O8   single  1.414  0.020  1.414
 6UD  C8   C9   single  1.523  0.020  1.523
 6UD  N3   N2   single  1.414  0.020  1.414
 6UD  C9   N1   single  1.454  0.020  1.454
 6UD  N2   N1   single  1.400  0.020  1.400
 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  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  127.93  3.000
 6UD  O1A  C1   C2   116.15  3.000
 6UD  O1B  C1   C2   115.92  3.000
 6UD  O6   C2   C3   122.73  3.000
 6UD  O6   C2   C1   113.58  3.000
 6UD  C3   C2   C1   123.69  3.000
 6UD  H1   C3   C4   118.62  3.000
 6UD  H1   C3   C2   118.06  3.000
 6UD  C4   C3   C2   123.31  3.000
 6UD  H2   C4   O4   109.76  3.000
 6UD  H2   C4   C5   108.30  3.000
 6UD  O4   C4   C5   107.62  3.000
 6UD  H2   C4   C3   109.43  3.000
 6UD  C5   C4   C3   109.41  3.000
 6UD  O4   C4   C3   112.22  3.000
 6UD  H3   C5   N5   107.86  3.000
 6UD  H3   C5   C6   109.23  3.000
 6UD  N5   C5   C6   110.86  3.000
 6UD  H3   C5   C4   108.83  3.000
 6UD  C6   C5   C4   108.83  3.000
 6UD  N5   C5   C4   111.19  3.000
 6UD  H4   C6   O6   108.95  3.000
 6UD  H4   C6   C7   109.02  3.000
 6UD  O6   C6   C7   105.94  3.000
 6UD  H4   C6   C5   108.52  3.000
 6UD  C7   C6   C5   113.48  3.000
 6UD  O6   C6   C5   110.84  3.000
 6UD  H5   C7   O7   105.95  3.000
 6UD  H5   C7   C8   107.64  3.000
 6UD  O7   C7   C8   111.85  3.000
 6UD  H5   C7   C6   108.00  3.000
 6UD  C8   C7   C6   111.77  3.000
 6UD  O7   C7   C6   111.31  3.000
 6UD  H6   C8   O8   105.36  3.000
 6UD  H6   C8   C9   108.54  3.000
 6UD  O8   C8   C9   111.27  3.000
 6UD  H6   C8   C7   109.38  3.000
 6UD  C9   C8   C7   111.46  3.000
 6UD  O8   C8   C7   110.62  3.000
 6UD  H8   C9   H7   106.91  3.000
 6UD  H8   C9   N1   113.22  3.000
 6UD  H7   C9   N1   108.08  3.000
 6UD  H8   C9   C8   109.34  3.000
 6UD  H7   C9   C8   109.13  3.000
 6UD  N1   C9   C8   110.04  3.000
 6UD  H11  C11  H10  108.38  3.000
 6UD  H11  C11  H9   107.26  3.000
 6UD  H10  C11  H9   108.44  3.000
 6UD  H11  C11  C10  109.23  3.000
 6UD  H10  C11  C10  113.84  3.000
 6UD  H9   C11  C10  109.48  3.000
 6UD  H12  N5   C10  117.88  3.000
 6UD  H12  N5   C5   117.30  3.000
 6UD  C10  N5   C5   124.67  3.000
 6UD  H14  O4   C4   108.08  3.000
 6UD  C6   O6   C2   117.27  3.000
 6UD  H15  O7   C7   108.37  3.000
 6UD  H16  O8   C8   108.53  3.000
 6UD  H17  N1   N2   107.09  3.000
 6UD  H17  N1   C9   109.92  3.000
 6UD  N2   N1   C9   115.50  3.000
 6UD  H18  N2   N3   110.76  3.000
 6UD  H18  N2   N1   106.73  3.000
 6UD  N3   N2   N1   113.79  3.000
 6UD  H20  N3   H19  107.03  3.000
 6UD  H20  N3   N2   111.97  3.000
 6UD  H19  N3   N2   107.39  3.000
 6UD  O10  C10  N5   123.55  3.000
 6UD  O10  C10  C11  121.56  3.000
 6UD  N5   C10  C11  114.89  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  H12  N5   C10  C11     0.00   0.0  0
 6UD  Var_01    O6   C2   C3   C4      2.72  30.0  1
 6UD  Var_02    O1B  C1   C2   C3     -1.14  30.0  3
 6UD  Var_03    N2   N1   C9   C8    179.18  30.0  3
 6UD  Var_04    N3   N2   N1   C9     52.10  30.0  1
 6UD  Var_05    H9   C11  C10  N5   -124.11  30.0  3
 6UD  Var_06    H19  N3   N2   N1    149.64  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

