# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 16 05:08:52 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 1-{(5E)-5,6,7-trideoxy-7-[(2,3-dihydroxy-5-nitrobenzoyl)amino]-beta-D-ribo-hept-5-enofuranosyl}pyridin-4(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1\C=C\CNC(=O)c2cc(cc(O)c2O)[N+]([O-])=O)N3C=CC(=O)C=C3
#
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
 OZZ  OZZ  1-{(5E)-5,6,7-trideoxy-7-[(2,3-dihydroxy-5-nitrobenzoyl)amino]-beta-D-ribo-hept-5-enofuranosyl}pyridin-4(1H)-one  ligand  50  31  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OZZ
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
 OZZ  C1    C  CH1    0  -0.042  -3.6886   2.0677   1.2680
 OZZ  C2    C  CH1    0  -0.034  -4.7527   1.1784   0.6148
 OZZ  C3    C  CH1    0   0.150  -4.0724   0.7937  -0.7031
 OZZ  O4    O  O2     0  -0.487  -3.1615   1.8050  -1.0026
 OZZ  C5    C  CH1    0   0.013  -3.0715   2.7584   0.0455
 OZZ  C6    C  C1     0  -0.259  -1.6661   3.2059   0.2613
 OZZ  N7    N  NR6    0  -0.491  -3.3842  -0.5027  -0.6413
 OZZ  O8    O  OH1    0  -0.656  -4.2088   3.0241   2.1445
 OZZ  O9    O  OH1    0  -0.663  -5.8940   1.9242   0.2926
 OZZ  C10   C  C1     0  -0.221  -0.6106   2.8360  -0.4535
 OZZ  C11   C  CH2    0  -0.355   0.7807   3.3255  -0.1862
 OZZ  N12   N  NH1    0  -0.619   1.6977   2.2316   0.0722
 OZZ  C13   C  C      0   0.533   2.2555   1.5111  -0.9109
 OZZ  C14   C  CR6    0  -0.148   3.0770   0.3476  -0.4462
 OZZ  C15   C  CR6    0   0.317   4.3576   0.1502  -0.9593
 OZZ  C16   C  CR6    0   0.299   5.0994  -0.9777  -0.5573
 OZZ  C17   C  CR16   0  -0.404   4.5606  -1.8882   0.3233
 OZZ  C18   C  CR6    0   0.262   3.2767  -1.6728   0.8167
 OZZ  C19   C  CR16   0  -0.316   2.5372  -0.5645   0.4507
 OZZ  N20   N  N      1   0.328   2.7095  -2.6339   1.7349
 OZZ  O21   O  OH1    0  -0.589   4.8725   1.0444  -1.7977
 OZZ  O22   O  OH1    0  -0.636   6.3285  -1.0756  -1.0920
 OZZ  O23   O  O      0  -0.475   2.1039   1.7546  -2.0972
 OZZ  O24   O  O      0  -0.381   3.3831  -3.5880   2.0498
 OZZ  O25   O  O     -1  -0.386   1.5872  -2.4402   2.1470
 OZZ  C26   C  CR16   0   0.056  -4.0297  -1.6045  -1.1048
 OZZ  C27   C  CR16   0  -0.498  -3.5028  -2.8469  -1.0141
 OZZ  C28   C  CR6    0   0.431  -2.2071  -3.0785  -0.4128
 OZZ  C29   C  CR16   0   0.057  -2.1617  -0.6537  -0.0688
 OZZ  C30   C  CR16   0  -0.496  -1.5715  -1.8652   0.0549
 OZZ  O31   O  O      0  -0.510  -1.6927  -4.1966  -0.3129
 OZZ  H1    H  HCH1   0   0.254  -2.9389   1.4409   1.7648
 OZZ  H2    H  HCH1   0   0.264  -4.9989   0.2958   1.2181
 OZZ  H3    H  HCH1   0   0.286  -4.8124   0.6973  -1.5013
 OZZ  H5    H  HCH1   0   0.264  -3.6847   3.6361  -0.2038
 OZZ  H6    H  H      0   0.268  -1.5463   3.9099   1.0807
 OZZ  HO8   H  HOH1   0   0.471  -4.2901   2.6349   3.0213
 OZZ  HO9   H  HOH1   0   0.453  -6.0358   2.5664   0.9996
 OZZ  H10   H  H      0   0.259  -0.7211   2.1507  -1.2875
 OZZ  H11   H  HCH2   0   0.262   1.1522   3.8964  -1.0388
 OZZ  H11A  H  HCH2   0   0.272   0.8002   3.9870   0.6788
 OZZ  HN12  H  HNH1   0   0.415   1.8746   1.9829   1.0319
 OZZ  H17   H  HCR6   0   0.318   5.1370  -2.7526   0.6254
 OZZ  H19   H  HCR6   0   0.293   1.5435  -0.4067   0.8448
 OZZ  HO21  H  HOH1   0   0.488   5.7768   0.8090  -2.0452
 OZZ  HO22  H  HOH1   0   0.493   6.8071  -1.8380  -0.7463
 OZZ  H26   H  HCR6   0   0.318  -4.9957  -1.4297  -1.5589
 OZZ  H27   H  HCR6   0   0.273  -4.0674  -3.6801  -1.4104
 OZZ  H29   H  HCR6   0   0.303  -1.6664   0.2421   0.2772
 OZZ  H30   H  HCR6   0   0.260  -0.5984  -1.9254   0.5240

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
 OZZ  C1   C2    single    1.533  0.020  1.533
 OZZ  C1   C5    single    1.534  0.020  1.534
 OZZ  C1   O8    single    1.398  0.020  1.398
 OZZ  C2   C3    single    1.532  0.020  1.532
 OZZ  C2   O9    single    1.401  0.020  1.401
 OZZ  C3   O4    single    1.394  0.020  1.394
 OZZ  C3   N7    single    1.469  0.020  1.469
 OZZ  O4   C5    single    1.420  0.020  1.420
 OZZ  C5   C6    single    1.491  0.020  1.491
 OZZ  C6   C10   double    1.327  0.020  1.327
 OZZ  N7   C26   single    1.358  0.020  1.358
 OZZ  N7   C29   single    1.358  0.020  1.358
 OZZ  C10  C11   single    1.499  0.020  1.499
 OZZ  C11  N12   single    1.451  0.020  1.451
 OZZ  N12  C13   single    1.340  0.020  1.340
 OZZ  C13  C14   single    1.498  0.020  1.498
 OZZ  C13  O23   double    1.221  0.020  1.221
 OZZ  C14  C15   aromatic  1.394  0.020  1.394
 OZZ  C14  C19   aromatic  1.388  0.020  1.388
 OZZ  C15  C16   aromatic  1.408  0.020  1.408
 OZZ  C15  O21   single    1.330  0.020  1.330
 OZZ  C16  C17   aromatic  1.377  0.020  1.377
 OZZ  C16  O22   single    1.344  0.020  1.344
 OZZ  C17  C18   aromatic  1.392  0.020  1.392
 OZZ  C18  C19   aromatic  1.382  0.020  1.382
 OZZ  C18  N20   single    1.445  0.020  1.445
 OZZ  N20  O24   double    1.210  0.020  1.210
 OZZ  N20  O25   single    1.211  0.020  1.211
 OZZ  C26  C27   double    1.353  0.020  1.353
 OZZ  C27  C28   single    1.447  0.020  1.447
 OZZ  C28  C30   single    1.447  0.020  1.447
 OZZ  C28  O31   double    1.235  0.020  1.235
 OZZ  C29  C30   double    1.353  0.020  1.353
 OZZ  C1   H1    single    0.970  0.020  1.090
 OZZ  C2   H2    single    0.970  0.020  1.090
 OZZ  C3   H3    single    0.970  0.020  1.090
 OZZ  C5   H5    single    0.970  0.020  1.090
 OZZ  C6   H6    single    0.930  0.020  1.080
 OZZ  O8   HO8   single    0.850  0.020  0.980
 OZZ  O9   HO9   single    0.850  0.020  0.980
 OZZ  C10  H10   single    0.930  0.020  1.080
 OZZ  C11  H11   single    0.970  0.020  1.090
 OZZ  C11  H11A  single    0.970  0.020  1.090
 OZZ  N12  HN12  single    0.860  0.020  1.020
 OZZ  C17  H17   single    0.930  0.020  1.080
 OZZ  C19  H19   single    0.930  0.020  1.080
 OZZ  O21  HO21  single    0.850  0.020  0.980
 OZZ  O22  HO22  single    0.850  0.020  0.980
 OZZ  C26  H26   single    0.930  0.020  1.080
 OZZ  C27  H27   single    0.930  0.020  1.080
 OZZ  C29  H29   single    0.930  0.020  1.080
 OZZ  C30  H30   single    0.930  0.020  1.080

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
 OZZ  H1    C1   O8   111.20  3.000
 OZZ  H1    C1   C5   110.09  3.000
 OZZ  O8    C1   C5   109.96  3.000
 OZZ  H1    C1   C2   109.65  3.000
 OZZ  O8    C1   C2   113.94  3.000
 OZZ  C5    C1   C2   101.59  3.000
 OZZ  H2    C2   O9   111.84  3.000
 OZZ  H2    C2   C3   111.76  3.000
 OZZ  O9    C2   C3   107.31  3.000
 OZZ  H2    C2   C1   112.84  3.000
 OZZ  O9    C2   C1   110.77  3.000
 OZZ  C3    C2   C1   101.77  3.000
 OZZ  H3    C3   N7   105.67  3.000
 OZZ  H3    C3   O4   110.47  3.000
 OZZ  N7    C3   O4   110.07  3.000
 OZZ  H3    C3   C2   110.48  3.000
 OZZ  N7    C3   C2   113.16  3.000
 OZZ  O4    C3   C2   107.03  3.000
 OZZ  C5    O4   C3   111.72  3.000
 OZZ  H5    C5   C6   108.60  3.000
 OZZ  H5    C5   O4   109.47  3.000
 OZZ  C6    C5   O4   111.61  3.000
 OZZ  H5    C5   C1   108.41  3.000
 OZZ  C6    C5   C1   113.52  3.000
 OZZ  O4    C5   C1   105.10  3.000
 OZZ  H6    C6   C10  119.92  3.000
 OZZ  H6    C6   C5   114.05  3.000
 OZZ  C10   C6   C5   126.02  3.000
 OZZ  C29   N7   C26  118.77  3.000
 OZZ  C29   N7   C3   122.51  3.000
 OZZ  C26   N7   C3   118.61  3.000
 OZZ  HO8   O8   C1   109.02  3.000
 OZZ  HO9   O9   C2   107.78  3.000
 OZZ  H10   C10  C11  115.97  3.000
 OZZ  H10   C10  C6   120.59  3.000
 OZZ  C11   C10  C6   123.44  3.000
 OZZ  H11A  C11  H11  107.26  3.000
 OZZ  H11A  C11  N12  107.77  3.000
 OZZ  H11   C11  N12  108.57  3.000
 OZZ  H11A  C11  C10  110.90  3.000
 OZZ  H11   C11  C10  110.33  3.000
 OZZ  N12   C11  C10  111.86  3.000
 OZZ  HN12  N12  C13  119.54  3.000
 OZZ  HN12  N12  C11  117.84  3.000
 OZZ  C13   N12  C11  122.53  3.000
 OZZ  O23   C13  C14  121.63  3.000
 OZZ  O23   C13  N12  123.64  3.000
 OZZ  C14   C13  N12  114.72  3.000
 OZZ  C19   C14  C15  120.14  3.000
 OZZ  C19   C14  C13  119.82  3.000
 OZZ  C15   C14  C13  119.98  3.000
 OZZ  O21   C15  C16  120.97  3.000
 OZZ  O21   C15  C14  119.52  3.000
 OZZ  C16   C15  C14  119.49  3.000
 OZZ  O22   C16  C17  124.35  3.000
 OZZ  O22   C16  C15  115.24  3.000
 OZZ  C17   C16  C15  120.40  3.000
 OZZ  H17   C17  C18  121.07  3.000
 OZZ  H17   C17  C16  119.90  3.000
 OZZ  C18   C17  C16  119.03  3.000
 OZZ  N20   C18  C19  119.45  3.000
 OZZ  N20   C18  C17  118.96  3.000
 OZZ  C19   C18  C17  121.59  3.000
 OZZ  H19   C19  C18  120.84  3.000
 OZZ  H19   C19  C14  119.82  3.000
 OZZ  C18   C19  C14  119.34  3.000
 OZZ  O25   N20  O24  123.61  3.000
 OZZ  O25   N20  C18  118.27  3.000
 OZZ  O24   N20  C18  118.12  3.000
 OZZ  HO21  O21  C15  111.09  3.000
 OZZ  HO22  O22  C16  111.65  3.000
 OZZ  H26   C26  C27  121.64  3.000
 OZZ  H26   C26  N7   115.88  3.000
 OZZ  C27   C26  N7   122.48  3.000
 OZZ  H27   C27  C28  119.76  3.000
 OZZ  H27   C27  C26  118.66  3.000
 OZZ  C28   C27  C26  121.58  3.000
 OZZ  O31   C28  C30  123.36  3.000
 OZZ  O31   C28  C27  123.48  3.000
 OZZ  C30   C28  C27  113.16  3.000
 OZZ  H29   C29  C30  120.87  3.000
 OZZ  H29   C29  N7   117.09  3.000
 OZZ  C30   C29  N7   122.04  3.000
 OZZ  H30   C30  C29  118.79  3.000
 OZZ  H30   C30  C28  119.24  3.000
 OZZ  C29   C30  C28  121.96  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
 OZZ  CONST_01  C17   C16  C15  C14     0.00   0.0  0
 OZZ  CONST_02  C17   C18  C19  C14     0.00   0.0  0
 OZZ  CONST_03  C18   C19  C14  C15     0.00   0.0  0
 OZZ  CONST_04  C18   C17  C16  C15     0.00   0.0  0
 OZZ  CONST_05  C19   C14  C15  C16     0.00   0.0  0
 OZZ  CONST_06  C19   C18  C17  C16     0.00   0.0  0
 OZZ  CONST_07  C16   C15  C14  C13   180.00   0.0  0
 OZZ  CONST_08  C18   C19  C14  C13   180.00   0.0  0
 OZZ  CONST_09  O22   C16  C15  C14   180.00   0.0  0
 OZZ  CONST_10  N20   C18  C19  C14   180.00   0.0  0
 OZZ  CONST_11  N20   C18  C17  C16   180.00   0.0  0
 OZZ  CONST_12  O21   C15  C16  C17   180.00   0.0  0
 OZZ  CONST_13  O22   C16  C17  C18   180.00   0.0  0
 OZZ  CONST_14  O21   C15  C14  C19   180.00   0.0  0
 OZZ  CONST_15  H19   C19  C14  C15   180.00   0.0  0
 OZZ  CONST_16  H17   C17  C16  C15   180.00   0.0  0
 OZZ  CONST_17  O24   N20  C18  C17     0.00   0.0  0
 OZZ  CONST_18  O25   N20  C18  C17   180.00   0.0  0
 OZZ  CONST_19  O24   N20  C18  C19   180.00   0.0  0
 OZZ  CONST_20  O25   N20  C18  C19     0.00   0.0  0
 OZZ  CONST_21  C14   C13  N12  C11   180.00   0.0  0
 OZZ  CONST_22  HN12  N12  C13  C14     0.00   0.0  0
 OZZ  CONST_23  O23   C13  N12  C11     0.00   0.0  0
 OZZ  Var_01    C15   C14  C13  N12  -131.33  30.0  2
 OZZ  Var_02    C11   C10  C6   C5    179.89   0.0  2
 OZZ  Var_03    N12   C11  C10  C6    122.12  30.0  3
 OZZ  Var_04    C13   N12  C11  C10    81.15  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
 OZZ  chir_01  C1  C2  C5  O8  negativ
 OZZ  chir_02  C2  O9  C3  C1  negativ
 OZZ  chir_03  C3  O4  N7  C2  negativ
 OZZ  chir_04  C5  O4  C6  C1  positiv

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
 OZZ  plan-1  C3    0.020
 OZZ  plan-1  N7    0.020
 OZZ  plan-1  C26   0.020
 OZZ  plan-1  C27   0.020
 OZZ  plan-1  C28   0.020
 OZZ  plan-1  C29   0.020
 OZZ  plan-1  C30   0.020
 OZZ  plan-1  O31   0.020
 OZZ  plan-1  H26   0.020
 OZZ  plan-1  H27   0.020
 OZZ  plan-1  H29   0.020
 OZZ  plan-1  H30   0.020
 OZZ  plan-2  C13   0.020
 OZZ  plan-2  C14   0.020
 OZZ  plan-2  C15   0.020
 OZZ  plan-2  C16   0.020
 OZZ  plan-2  C17   0.020
 OZZ  plan-2  C18   0.020
 OZZ  plan-2  C19   0.020
 OZZ  plan-2  N20   0.020
 OZZ  plan-2  O21   0.020
 OZZ  plan-2  O22   0.020
 OZZ  plan-2  H17   0.020
 OZZ  plan-2  H19   0.020
 OZZ  plan-3  C18   0.020
 OZZ  plan-3  N20   0.020
 OZZ  plan-3  O24   0.020
 OZZ  plan-3  O25   0.020
 OZZ  plan-4  C11   0.020
 OZZ  plan-4  N12   0.020
 OZZ  plan-4  C13   0.020
 OZZ  plan-4  C14   0.020
 OZZ  plan-4  O23   0.020
 OZZ  plan-4  HN12  0.020
 OZZ  plan-5  C5    0.020
 OZZ  plan-5  C6    0.020
 OZZ  plan-5  C10   0.020
 OZZ  plan-5  C11   0.020
 OZZ  plan-5  H6    0.020
 OZZ  plan-5  H10   0.020

