# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 01:44:52 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-2-(4-nitrophenoxy)-4,5-bis(oxidanyl)oxan-3-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1Oc2ccc(cc2)[N+]([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
 6ZC  6ZC  ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-2-(4-nitrophenoxy)-4,5-bis(oxidanyl)oxan-3-yl]ethanamide  D-saccharide  42  24  .  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_6ZC
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
 6ZC  C1   C  CH1    0   0.244   1.0169   0.0773   0.6395
 6ZC  C2   C  CH1    0  -0.141   2.4292   0.4754   0.2012
 6ZC  C3   C  CH1    0   0.025   2.9789  -0.5316  -0.8017
 6ZC  C4   C  CH1    0  -0.003   2.8629  -1.9373  -0.2179
 6ZC  C5   C  CH1    0  -0.026   1.4175  -2.2262   0.1972
 6ZC  C6   C  CH2    0  -0.165   1.2870  -3.5533   0.9112
 6ZC  N2   N  NH1    0  -0.631   2.4625   1.8134  -0.3254
 6ZC  O1   O  O2     0  -0.486   0.1774   0.2833  -0.4810
 6ZC  O4   O  OH1    0  -0.671   3.2996  -2.8387  -1.2092
 6ZC  O5   O  O2     0  -0.486   0.9649  -1.2231   1.1006
 6ZC  O6   O  OH1    0  -0.665  -0.0723  -3.7992   1.1735
 6ZC  O1'  O  O      0  -0.388  -5.9218   1.1204  -1.1668
 6ZC  O2'  O  O     -1  -0.388  -5.9052   0.4520   0.8589
 6ZC  C4'  C  CR6    0   0.230  -3.9063   0.5989  -0.2335
 6ZC  C3'  C  CR16   0  -0.253  -3.2311   0.9440  -1.3997
 6ZC  C2'  C  CR16   0  -0.346  -1.8604   0.8221  -1.4440
 6ZC  C5'  C  CR16   0  -0.254  -3.2177   0.1272   0.8744
 6ZC  C6'  C  CR16   0  -0.356  -1.8421  -0.0042   0.8272
 6ZC  C1'  C  CR6    0   0.423  -1.1532   0.3544  -0.3327
 6ZC  C7   C  C      0   0.528   2.6249   2.9054   0.4459
 6ZC  C8   C  CH3    0  -0.777   2.6290   4.2201  -0.2904
 6ZC  O3   O  OH1    0  -0.662   4.3129  -0.1889  -1.0661
 6ZC  H1   H  HCH1   0   0.277   0.6912   0.7136   1.4689
 6ZC  H2   H  HCH1   0   0.288   3.0542   0.4435   1.0979
 6ZC  H3   H  HCH1   0   0.224   2.3771  -0.4969  -1.7243
 6ZC  H4   H  HCH1   0   0.232   3.5039  -1.9876   0.6738
 6ZC  H5   H  HCH1   0   0.239   0.7871  -2.2426  -0.7023
 6ZC  H6   H  HCH2   0   0.206   1.7208  -4.3311   0.2717
 6ZC  H7   H  HCH2   0   0.202   1.8860  -3.5223   1.8322
 6ZC  H8   H  HNH1   0   0.404   2.3042   1.9384  -1.3123
 6ZC  H9   H  HOH1   0   0.465   3.7311  -3.5871  -0.7882
 6ZC  H10  H  HOH1   0   0.457  -0.1376  -4.6482   1.6198
 6ZC  H12  H  HCR6   0   0.286  -1.3219   1.0990  -2.3405
 6ZC  H13  H  HCR6   0   0.301  -3.7393  -0.1540   1.7776
 6ZC  H14  H  HCR6   0   0.302  -1.3349  -0.4016   1.6931
 6ZC  H15  H  HCH3   0   0.269   3.5861   4.7173  -0.1325
 6ZC  H16  H  HCH3   0   0.250   2.4649   4.1215  -1.3615
 6ZC  H17  H  HCH3   0   0.267   1.8554   4.8678   0.1214
 6ZC  H18  H  HOH1   0   0.454   4.6557  -0.8137  -1.7140
 6ZC  H11  H  HCR6   0   0.299  -3.7588   1.3133  -2.2666
 6ZC  O7   O  O      0  -0.502   2.7668   2.8419   1.6594
 6ZC  N1'  N  N      1   0.328  -5.3441   0.7323  -0.1764

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
 6ZC  O1'  N1'  double    1.211  0.020  1.211
 6ZC  O2'  N1'  single    1.210  0.020  1.210
 6ZC  N1'  C4'  single    1.445  0.020  1.445
 6ZC  C4'  C3'  aromatic  1.391  0.020  1.391
 6ZC  C4'  C5'  aromatic  1.387  0.020  1.387
 6ZC  C3'  C2'  aromatic  1.377  0.020  1.377
 6ZC  C5'  C6'  aromatic  1.383  0.020  1.383
 6ZC  C2'  C1'  aromatic  1.398  0.020  1.398
 6ZC  C6'  C1'  aromatic  1.396  0.020  1.396
 6ZC  C1'  O1   single    1.341  0.020  1.341
 6ZC  C8   C7   single    1.507  0.020  1.507
 6ZC  O1   C1   single    1.415  0.020  1.415
 6ZC  O7   C7   double    1.223  0.020  1.223
 6ZC  C7   N2   single    1.347  0.020  1.347
 6ZC  C1   O5   single    1.381  0.020  1.381
 6ZC  C1   C2   single    1.531  0.020  1.531
 6ZC  N2   C2   single    1.438  0.020  1.438
 6ZC  O5   C5   single    1.424  0.020  1.424
 6ZC  C2   C3   single    1.524  0.020  1.524
 6ZC  C5   C6   single    1.513  0.020  1.513
 6ZC  C5   C4   single    1.531  0.020  1.531
 6ZC  C6   O6   single    1.406  0.020  1.406
 6ZC  C3   C4   single    1.526  0.020  1.526
 6ZC  C3   O3   single    1.402  0.020  1.402
 6ZC  C4   O4   single    1.409  0.020  1.409
 6ZC  C1   H1   single    0.970  0.020  1.090
 6ZC  C2   H2   single    0.970  0.020  1.090
 6ZC  C3   H3   single    0.970  0.020  1.090
 6ZC  C4   H4   single    0.970  0.020  1.090
 6ZC  C5   H5   single    0.970  0.020  1.090
 6ZC  C6   H6   single    0.970  0.020  1.090
 6ZC  C6   H7   single    0.970  0.020  1.090
 6ZC  N2   H8   single    0.860  0.020  1.020
 6ZC  O4   H9   single    0.850  0.020  0.980
 6ZC  O6   H10  single    0.850  0.020  0.980
 6ZC  C3'  H11  single    0.930  0.020  1.080
 6ZC  C2'  H12  single    0.930  0.020  1.080
 6ZC  C5'  H13  single    0.930  0.020  1.080
 6ZC  C6'  H14  single    0.930  0.020  1.080
 6ZC  C8   H15  single    0.970  0.020  1.090
 6ZC  C8   H16  single    0.970  0.020  1.090
 6ZC  C8   H17  single    0.970  0.020  1.090
 6ZC  O3   H18  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
 6ZC  H1   C1   O5   106.45  3.000
 6ZC  H1   C1   O1   109.80  3.000
 6ZC  O5   C1   O1   112.28  3.000
 6ZC  H1   C1   C2   109.89  3.000
 6ZC  O5   C1   C2   112.03  3.000
 6ZC  O1   C1   C2   106.42  3.000
 6ZC  H2   C2   N2   108.30  3.000
 6ZC  H2   C2   C3   108.32  3.000
 6ZC  N2   C2   C3   111.43  3.000
 6ZC  H2   C2   C1   106.55  3.000
 6ZC  C3   C2   C1   110.45  3.000
 6ZC  N2   C2   C1   111.59  3.000
 6ZC  H3   C3   O3   110.72  3.000
 6ZC  H3   C3   C4   107.92  3.000
 6ZC  O3   C3   C4   111.68  3.000
 6ZC  H3   C3   C2   109.46  3.000
 6ZC  O3   C3   C2   107.80  3.000
 6ZC  C4   C3   C2   109.23  3.000
 6ZC  H4   C4   O4   111.14  3.000
 6ZC  H4   C4   C5   108.77  3.000
 6ZC  O4   C4   C5   111.25  3.000
 6ZC  H4   C4   C3   107.94  3.000
 6ZC  O4   C4   C3   107.25  3.000
 6ZC  C5   C4   C3   110.43  3.000
 6ZC  H5   C5   O5   110.34  3.000
 6ZC  H5   C5   C6   108.90  3.000
 6ZC  O5   C5   C6   106.93  3.000
 6ZC  H5   C5   C4   108.81  3.000
 6ZC  C6   C5   C4   112.02  3.000
 6ZC  O5   C5   C4   109.82  3.000
 6ZC  H7   C6   H6   107.04  3.000
 6ZC  H7   C6   O6   112.06  3.000
 6ZC  H6   C6   O6   111.55  3.000
 6ZC  H7   C6   C5   108.89  3.000
 6ZC  H6   C6   C5   108.24  3.000
 6ZC  O6   C6   C5   108.96  3.000
 6ZC  H8   N2   C7   118.65  3.000
 6ZC  H8   N2   C2   118.06  3.000
 6ZC  C7   N2   C2   123.19  3.000
 6ZC  C1'  O1   C1   120.59  3.000
 6ZC  H9   O4   C4   109.22  3.000
 6ZC  C5   O5   C1   116.08  3.000
 6ZC  H10  O6   C6   107.86  3.000
 6ZC  C5'  C4'  C3'  120.86  3.000
 6ZC  C5'  C4'  N1'  119.59  3.000
 6ZC  C3'  C4'  N1'  119.55  3.000
 6ZC  H11  C3'  C2'  119.40  3.000
 6ZC  H11  C3'  C4'  121.37  3.000
 6ZC  C2'  C3'  C4'  119.23  3.000
 6ZC  H12  C2'  C1'  119.51  3.000
 6ZC  H12  C2'  C3'  119.97  3.000
 6ZC  C1'  C2'  C3'  120.51  3.000
 6ZC  H13  C5'  C6'  118.96  3.000
 6ZC  H13  C5'  C4'  121.11  3.000
 6ZC  C6'  C5'  C4'  119.93  3.000
 6ZC  H14  C6'  C1'  121.96  3.000
 6ZC  H14  C6'  C5'  118.37  3.000
 6ZC  C1'  C6'  C5'  119.67  3.000
 6ZC  C6'  C1'  C2'  119.79  3.000
 6ZC  C6'  C1'  O1   124.62  3.000
 6ZC  C2'  C1'  O1   115.59  3.000
 6ZC  C8   C7   O7   121.98  3.000
 6ZC  O7   C7   N2   122.68  3.000
 6ZC  C8   C7   N2   115.33  3.000
 6ZC  H17  C8   H16  108.59  3.000
 6ZC  H17  C8   H15  107.31  3.000
 6ZC  H16  C8   H15  108.45  3.000
 6ZC  H17  C8   C7   109.39  3.000
 6ZC  H16  C8   C7   113.67  3.000
 6ZC  H15  C8   C7   109.24  3.000
 6ZC  H18  O3   C3   107.87  3.000
 6ZC  C4'  N1'  O2'  118.27  3.000
 6ZC  C4'  N1'  O1'  118.17  3.000
 6ZC  O2'  N1'  O1'  123.56  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
 6ZC  CONST_01  C1'  C2'  C3'  C4'     0.00   0.0  0
 6ZC  CONST_02  C1'  C6'  C5'  C4'     0.00   0.0  0
 6ZC  CONST_03  C6'  C5'  C4'  C3'     0.00   0.0  0
 6ZC  CONST_04  C6'  C1'  C2'  C3'     0.00   0.0  0
 6ZC  CONST_05  C5'  C4'  C3'  C2'     0.00   0.0  0
 6ZC  CONST_06  C5'  C6'  C1'  C2'     0.00   0.0  0
 6ZC  CONST_07  C3'  C2'  C1'  O1    180.00   0.0  0
 6ZC  CONST_08  C5'  C6'  C1'  O1    180.00   0.0  0
 6ZC  CONST_09  C2'  C3'  C4'  N1'   180.00   0.0  0
 6ZC  CONST_10  C6'  C5'  C4'  N1'   180.00   0.0  0
 6ZC  CONST_11  H12  C2'  C3'  C4'   180.00   0.0  0
 6ZC  CONST_12  H14  C6'  C5'  C4'   180.00   0.0  0
 6ZC  CONST_13  H13  C5'  C4'  C3'   180.00   0.0  0
 6ZC  CONST_14  H11  C3'  C4'  C5'   180.00   0.0  0
 6ZC  CONST_15  C3'  C4'  N1'  O1'     0.00   0.0  0
 6ZC  CONST_16  C5'  C4'  N1'  O1'   180.00   0.0  0
 6ZC  CONST_17  C3'  C4'  N1'  O2'   180.00   0.0  0
 6ZC  CONST_18  C5'  C4'  N1'  O2'     0.00   0.0  0
 6ZC  CONST_19  C8   C7   N2   C2    180.00   0.0  0
 6ZC  CONST_20  O7   C7   N2   C2      0.00   0.0  0
 6ZC  CONST_21  H8   N2   C7   O7    180.00   0.0  0
 6ZC  Var_01    C2'  C1'  O1   C1    167.68  30.0  1
 6ZC  Var_02    H15  C8   C7   N2   -119.31  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
 6ZC  chir_01  C1  O1  O5  C2  negativ
 6ZC  chir_02  C2  N2  C3  C1  positiv
 6ZC  chir_03  C3  O3  C2  C4  positiv
 6ZC  chir_04  C4  O4  C3  C5  negativ
 6ZC  chir_05  C5  O5  C4  C6  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
 6ZC  plan-1  O1   0.020
 6ZC  plan-1  C4'  0.020
 6ZC  plan-1  C3'  0.020
 6ZC  plan-1  C2'  0.020
 6ZC  plan-1  C5'  0.020
 6ZC  plan-1  C6'  0.020
 6ZC  plan-1  C1'  0.020
 6ZC  plan-1  H12  0.020
 6ZC  plan-1  H13  0.020
 6ZC  plan-1  H14  0.020
 6ZC  plan-1  H11  0.020
 6ZC  plan-1  N1'  0.020
 6ZC  plan-2  O1'  0.020
 6ZC  plan-2  O2'  0.020
 6ZC  plan-2  C4'  0.020
 6ZC  plan-2  N1'  0.020
 6ZC  plan-3  C2   0.020
 6ZC  plan-3  N2   0.020
 6ZC  plan-3  C7   0.020
 6ZC  plan-3  C8   0.020
 6ZC  plan-3  H8   0.020
 6ZC  plan-3  O7   0.020

