# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 15:38:45 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (2~{S},4~{S},5~{S},6~{S})-5-acetamido-6-[(1~{S},2~{S})-1-acetamido-2-oxidanyl-propyl]-2,4-bis(oxidanyl)oxane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@H](NC(C)=O)[C@@H]1O[C@@](O)(C[C@H](O)[C@@H]1NC(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
 6PZ  6PZ  '(2~{S},4~{S},5~{S},6~{S})-5-acetamido-6-[(1~{S},2~{S})-1-acetamido-2-oxidanyl-propyl]-2,4-bis(oxidanyl)oxane-2-carboxylic acid'  D-saccharide  45  23  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6PZ
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
 6PZ  N1   N  NH1   0  -0.629   2.3632  -0.4532   0.5393
 6PZ  C7   C  CH1   0  -0.167   1.1994  -1.0081  -0.1021
 6PZ  C8   C  CH1   0   0.090   1.2771  -2.5456  -0.1932
 6PZ  C9   C  CH3   0  -0.703   1.3062  -3.2350   1.1574
 6PZ  O8   O  OH1   0  -0.664   2.4505  -2.9254  -0.8812
 6PZ  C6   C  CH1   0  -0.001  -0.0666  -0.5016   0.5919
 6PZ  O6   O  O2    0  -0.503  -1.1490  -0.9367  -0.2161
 6PZ  C5   C  CH1   0  -0.124  -0.0956   1.0179   0.7619
 6PZ  N2   N  NH1   0  -0.628   0.1505   1.6908  -0.4880
 6PZ  C4   C  CH1   0   0.084  -1.4403   1.3996   1.3801
 6PZ  O4   O  OH1   0  -0.655  -1.4922   2.7972   1.4978
 6PZ  C3   C  CH2   0  -0.543  -2.5853   0.8654   0.5223
 6PZ  C2   C  CT    0   0.416  -2.4250  -0.6354   0.2645
 6PZ  C1   C  C     0   0.485  -3.3748  -1.0324  -0.8773
 6PZ  O1B  O  O     0  -0.416  -3.0561  -1.0576  -2.0349
 6PZ  O1A  O  OH1   0  -0.581  -4.5908  -1.2804  -0.4251
 6PZ  C10  C  C     0   0.547   3.3603   0.1641  -0.1249
 6PZ  O10  O  O     0  -0.503   3.3745   0.2959  -1.3408
 6PZ  C11  C  CH3   0  -0.778   4.4614   0.7161   0.7425
 6PZ  C12  C  C     0   0.545   1.1008   2.6311  -0.6595
 6PZ  O12  O  O     0  -0.500   1.8080   3.0450   0.2472
 6PZ  C13  C  CH3   0  -0.780   1.2531   3.1320  -2.0731
 6PZ  H1   H  HNH1  0   0.395   2.4539  -0.5571   1.5373
 6PZ  H2   H  HCH1  0   0.268   1.1891  -0.6207  -1.1240
 6PZ  H3   H  HCH1  0   0.215   0.3878  -2.8869  -0.7373
 6PZ  H4   H  HCH3  0   0.230   0.3782  -3.0750   1.7054
 6PZ  H5   H  HCH3  0   0.249   1.4209  -4.3116   1.0288
 6PZ  H6   H  HCH3  0   0.224   2.1335  -2.8844   1.7768
 6PZ  H7   H  HOH1  0   0.445   2.4638  -2.4796  -1.7342
 6PZ  H8   H  HCH1  0   0.245  -0.1388  -0.9373   1.5969
 6PZ  H9   H  HCH1  0   0.284   0.6969   1.3045   1.4530
 6PZ  H10  H  HNH1  0   0.394  -0.3723   1.3966  -1.2977
 6PZ  H11  H  HCH1  0   0.226  -1.4833   0.9241   2.3688
 6PZ  H12  H  HOH1  0   0.453  -2.2857   3.0283   1.9914
 6PZ  H13  H  HCH2  0   0.278  -3.5483   1.0539   1.0023
 6PZ  H14  H  HCH2  0   0.262  -2.5958   1.4030  -0.4302
 6PZ  O2   O  OH1   0  -0.651  -2.7115  -1.2980   1.4496
 6PZ  H16  H  HOH1  0   0.489  -5.1881  -1.4741  -1.1639
 6PZ  H17  H  HCH3  0   0.244   4.3707   0.4466   1.7931
 6PZ  H18  H  HCH3  0   0.260   5.4271   0.3702   0.3768
 6PZ  H19  H  HCH3  0   0.270   4.4491   1.8034   0.6667
 6PZ  H20  H  HCH3  0   0.244   0.4875   2.7643  -2.7540
 6PZ  H21  H  HCH3  0   0.260   1.2319   4.2209  -2.0828
 6PZ  H22  H  HCH3  0   0.267   2.2265   2.8179  -2.4506
 6PZ  H15  H  HOH1  0   0.459  -2.6461  -2.2529   1.3245

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
 6PZ  O4   C4   single  1.404  0.020  1.404
 6PZ  C13  C12  single  1.507  0.020  1.507
 6PZ  O12  C12  double  1.222  0.020  1.222
 6PZ  C12  N2   single  1.348  0.020  1.348
 6PZ  C4   C3   single  1.527  0.020  1.527
 6PZ  C4   C5   single  1.529  0.020  1.529
 6PZ  N2   C5   single  1.441  0.020  1.441
 6PZ  C3   C2   single  1.531  0.020  1.531
 6PZ  C5   C6   single  1.529  0.020  1.529
 6PZ  C2   C1   single  1.537  0.020  1.537
 6PZ  C2   O6   single  1.396  0.020  1.396
 6PZ  O1B  C1   double  1.201  0.020  1.201
 6PZ  C1   O1A  single  1.321  0.020  1.321
 6PZ  O10  C10  double  1.223  0.020  1.223
 6PZ  C11  C10  single  1.507  0.020  1.507
 6PZ  C6   O6   single  1.419  0.020  1.419
 6PZ  C6   C7   single  1.530  0.020  1.530
 6PZ  C10  N1   single  1.348  0.020  1.348
 6PZ  N1   C7   single  1.440  0.020  1.440
 6PZ  C7   C8   single  1.542  0.020  1.542
 6PZ  C8   O8   single  1.412  0.020  1.412
 6PZ  C8   C9   single  1.517  0.020  1.517
 6PZ  N1   H1   single  0.860  0.020  1.020
 6PZ  C7   H2   single  0.970  0.020  1.090
 6PZ  C8   H3   single  0.970  0.020  1.090
 6PZ  C9   H4   single  0.970  0.020  1.090
 6PZ  C9   H5   single  0.970  0.020  1.090
 6PZ  C9   H6   single  0.970  0.020  1.090
 6PZ  O8   H7   single  0.850  0.020  0.980
 6PZ  C6   H8   single  0.970  0.020  1.090
 6PZ  C5   H9   single  0.970  0.020  1.090
 6PZ  N2   H10  single  0.860  0.020  1.020
 6PZ  C4   H11  single  0.970  0.020  1.090
 6PZ  O4   H12  single  0.850  0.020  0.980
 6PZ  C3   H13  single  0.970  0.020  1.090
 6PZ  C3   H14  single  0.970  0.020  1.090
 6PZ  C2   O2   single  1.388  0.020  1.388
 6PZ  O1A  H16  single  0.850  0.020  0.980
 6PZ  C11  H17  single  0.970  0.020  1.090
 6PZ  C11  H18  single  0.970  0.020  1.090
 6PZ  C11  H19  single  0.970  0.020  1.090
 6PZ  C13  H20  single  0.970  0.020  1.090
 6PZ  C13  H21  single  0.970  0.020  1.090
 6PZ  C13  H22  single  0.970  0.020  1.090
 6PZ  O2   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
 6PZ  H1   N1   C10  117.96  3.000
 6PZ  H1   N1   C7   118.31  3.000
 6PZ  C10  N1   C7   123.70  3.000
 6PZ  H2   C7   C6   107.39  3.000
 6PZ  H2   C7   C8   107.38  3.000
 6PZ  C6   C7   C8   113.49  3.000
 6PZ  H2   C7   N1   106.71  3.000
 6PZ  C8   C7   N1   111.70  3.000
 6PZ  C6   C7   N1   109.83  3.000
 6PZ  H3   C8   O8   110.38  3.000
 6PZ  H3   C8   C9   108.41  3.000
 6PZ  O8   C8   C9   107.19  3.000
 6PZ  H3   C8   C7   107.38  3.000
 6PZ  C9   C8   C7   113.68  3.000
 6PZ  O8   C8   C7   109.80  3.000
 6PZ  H6   C9   H5   107.73  3.000
 6PZ  H6   C9   H4   108.24  3.000
 6PZ  H5   C9   H4   107.10  3.000
 6PZ  H6   C9   C8   111.96  3.000
 6PZ  H5   C9   C8   110.23  3.000
 6PZ  H4   C9   C8   111.39  3.000
 6PZ  H7   O8   C8   108.58  3.000
 6PZ  H8   C6   C5   106.94  3.000
 6PZ  H8   C6   O6   110.45  3.000
 6PZ  C5   C6   O6   110.70  3.000
 6PZ  H8   C6   C7   109.77  3.000
 6PZ  O6   C6   C7   105.75  3.000
 6PZ  C5   C6   C7   113.27  3.000
 6PZ  C2   O6   C6   115.78  3.000
 6PZ  H9   C5   C4   108.51  3.000
 6PZ  H9   C5   N2   107.65  3.000
 6PZ  C4   C5   N2   112.62  3.000
 6PZ  H9   C5   C6   108.54  3.000
 6PZ  N2   C5   C6   111.37  3.000
 6PZ  C4   C5   C6   108.05  3.000
 6PZ  H10  N2   C12  117.85  3.000
 6PZ  H10  N2   C5   118.18  3.000
 6PZ  C12  N2   C5   123.83  3.000
 6PZ  H11  C4   C3   108.96  3.000
 6PZ  H11  C4   O4   110.75  3.000
 6PZ  C3   C4   O4   111.58  3.000
 6PZ  H11  C4   C5   106.89  3.000
 6PZ  C3   C4   C5   110.18  3.000
 6PZ  O4   C4   C5   108.37  3.000
 6PZ  H12  O4   C4   108.21  3.000
 6PZ  H14  C3   H13  106.82  3.000
 6PZ  H14  C3   C2   109.64  3.000
 6PZ  H13  C3   C2   109.60  3.000
 6PZ  H14  C3   C4   108.93  3.000
 6PZ  H13  C3   C4   110.72  3.000
 6PZ  C2   C3   C4   111.03  3.000
 6PZ  O2   C2   C1   112.54  3.000
 6PZ  O2   C2   C3   107.62  3.000
 6PZ  C1   C2   C3   108.26  3.000
 6PZ  O2   C2   O6   112.31  3.000
 6PZ  C1   C2   O6   104.67  3.000
 6PZ  C3   C2   O6   111.42  3.000
 6PZ  O1A  C1   O1B  124.78  3.000
 6PZ  O1A  C1   C2   111.28  3.000
 6PZ  O1B  C1   C2   123.87  3.000
 6PZ  H16  O1A  C1   110.11  3.000
 6PZ  C11  C10  O10  121.63  3.000
 6PZ  C11  C10  N1   115.14  3.000
 6PZ  O10  C10  N1   123.22  3.000
 6PZ  H19  C11  H18  107.67  3.000
 6PZ  H19  C11  H17  108.25  3.000
 6PZ  H18  C11  H17  108.63  3.000
 6PZ  H19  C11  C10  108.49  3.000
 6PZ  H18  C11  C10  109.78  3.000
 6PZ  H17  C11  C10  113.84  3.000
 6PZ  C13  C12  O12  121.65  3.000
 6PZ  O12  C12  N2   123.36  3.000
 6PZ  C13  C12  N2   114.99  3.000
 6PZ  H22  C13  H21  107.59  3.000
 6PZ  H22  C13  H20  108.31  3.000
 6PZ  H21  C13  H20  108.56  3.000
 6PZ  H22  C13  C12  108.62  3.000
 6PZ  H21  C13  C12  109.79  3.000
 6PZ  H20  C13  C12  113.78  3.000
 6PZ  H15  O2   C2   110.34  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
 6PZ  CONST_01  C13  C12  N2   C5   180.00   0.0  0
 6PZ  CONST_02  O12  C12  N2   C5     0.00   0.0  0
 6PZ  CONST_03  H16  O1A  C1   C2   180.00   0.0  0
 6PZ  CONST_04  O10  C10  N1   C7     0.00   0.0  0
 6PZ  CONST_05  C11  C10  N1   C7   180.00   0.0  0
 6PZ  CONST_06  H1   N1   C10  O10  180.00   0.0  0
 6PZ  CONST_07  H10  N2   C12  O12  180.00   0.0  0
 6PZ  Var_01    H17  C11  C10  N1     6.67  30.0  3
 6PZ  Var_02    H20  C13  C12  N2     7.55  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
 6PZ  chir_01  C7  C6  N1  C8  negativ
 6PZ  chir_02  C8  O8  C7  C9  positiv
 6PZ  chir_03  C6  O6  C5  C7  positiv
 6PZ  chir_04  C5  N2  C4  C6  negativ
 6PZ  chir_05  C4  O4  C5  C3  positiv
 6PZ  chir_06  C2  O6  C3  C1  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
 6PZ  plan-1  N1   0.020
 6PZ  plan-1  C7   0.020
 6PZ  plan-1  C10  0.020
 6PZ  plan-1  O10  0.020
 6PZ  plan-1  C11  0.020
 6PZ  plan-1  H1   0.020
 6PZ  plan-2  C5   0.020
 6PZ  plan-2  N2   0.020
 6PZ  plan-2  C12  0.020
 6PZ  plan-2  O12  0.020
 6PZ  plan-2  C13  0.020
 6PZ  plan-2  H10  0.020
 6PZ  plan-3  C2   0.020
 6PZ  plan-3  C1   0.020
 6PZ  plan-3  O1B  0.020
 6PZ  plan-3  O1A  0.020
 6PZ  plan-3  H16  0.020

