# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 22:39:51 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (5E)-1,4-anhydro-5,6,7-trideoxy-7-[(2,3-dihydroxy-5-nitrobenzoyl)amino]-D-ribo-hept-5-enitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CO[C@H](\C=C\CNC(=O)c2cc(cc(O)c2O)[N+]([O-])=O)[C@H]1O
#
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
 OZR  OZR  (5E)-1,4-anhydro-5,6,7-trideoxy-7-[(2,3-dihydroxy-5-nitrobenzoyl)amino]-D-ribo-hept-5-enitol  ligand  40  24  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OZR
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
 OZR  C1    C  CH1    0  -0.022  -5.0117  -0.3938   0.0547
 OZR  C2    C  CH1    0  -0.022  -4.0877  -1.0020  -0.9976
 OZR  C3    C  CH2    0  -0.178  -4.1717   0.0449  -2.1089
 OZR  O4    O  O2     0  -0.499  -4.3508   1.2884  -1.4507
 OZR  C5    C  CH1    0  -0.025  -4.6531   1.0851  -0.0800
 OZR  C6    C  C1     0  -0.259  -3.5093   1.4577   0.8156
 OZR  O7    O  OH1    0  -0.671  -6.3653  -0.5576  -0.2865
 OZR  O8    O  OH1    0  -0.667  -4.5244  -2.2848  -1.3529
 OZR  C9    C  C1     0  -0.204  -2.3068   1.8506   0.4158
 OZR  C10   C  CH2    0  -0.360  -1.2021   2.2140   1.3617
 OZR  N11   N  NH1    0  -0.614  -0.0402   1.3616   1.1952
 OZR  C12   C  C      0   0.537   0.9218   1.6066   0.2935
 OZR  C13   C  CR6    0  -0.164   2.0354   0.6037   0.2882
 OZR  C14   C  CR6    0   0.316   2.4536   0.0378  -0.9146
 OZR  C15   C  CR6    0   0.296   3.5367  -0.8627  -0.9185
 OZR  C16   C  CR16   0  -0.403   4.1848  -1.1782   0.2541
 OZR  C17   C  CR6    0   0.260   3.7480  -0.5996   1.4430
 OZR  C18   C  CR16   0  -0.307   2.6814   0.2789   1.4736
 OZR  N19   N  N      1   0.323   4.4292  -0.9310   2.6741
 OZR  O20   O  OH1    0  -0.590   1.8064   0.3314  -2.0388
 OZR  O21   O  OH1    0  -0.637   3.8602  -1.3622  -2.1241
 OZR  O22   O  O      0  -0.476   0.9288   2.5751  -0.4490
 OZR  O23   O  O      0  -0.384   5.3591  -1.7039   2.6218
 OZR  O24   O  O     -1  -0.385   4.0372  -0.4226   3.7001
 OZR  H1    H  HCH1   0   0.242  -4.7999  -0.7749   1.0618
 OZR  H2    H  HCH1   0   0.226  -3.0677  -1.0258  -0.5926
 OZR  H3    H  HCH2   0   0.231  -3.2668   0.0826  -2.7199
 OZR  H3A   H  HCH2   0   0.213  -5.0199  -0.1679  -2.7698
 OZR  H5    H  HCH1   0   0.261  -5.5196   1.7019   0.1915
 OZR  H6    H  H      0   0.256  -3.7271   1.3963   1.8794
 OZR  HO7   H  HOH1   0   0.451  -6.5198  -1.4898  -0.4749
 OZR  HO8   H  HOH1   0   0.463  -3.9418  -2.6387  -2.0317
 OZR  H9    H  H      0   0.251  -2.0763   1.9254  -0.6420
 OZR  H10   H  HCH2   0   0.260  -0.8922   3.2485   1.2078
 OZR  H10A  H  HCH2   0   0.269  -1.5362   2.1268   2.3957
 OZR  HN11  H  HNH1   0   0.411  -0.0481   0.4719   1.6684
 OZR  H16   H  HCR6   0   0.317   5.0175  -1.8687   0.2411
 OZR  H18   H  HCR6   0   0.303   2.3558   0.7255   2.4019
 OZR  HO20  H  HOH1   0   0.488   2.1695  -0.1625  -2.7860
 OZR  HO21  H  HOH1   0   0.493   4.5920  -1.9873  -2.0669

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
 OZR  C1   C2    single    1.527  0.020  1.527
 OZR  C1   C5    single    1.528  0.020  1.528
 OZR  C1   O7    single    1.406  0.020  1.406
 OZR  C2   C3    single    1.529  0.020  1.529
 OZR  C2   O8    single    1.401  0.020  1.401
 OZR  C3   O4    single    1.418  0.020  1.418
 OZR  O4   C5    single    1.418  0.020  1.418
 OZR  C5   C6    single    1.500  0.020  1.500
 OZR  C6   C9    double    1.327  0.020  1.327
 OZR  C9   C10   single    1.499  0.020  1.499
 OZR  C10  N11   single    1.451  0.020  1.451
 OZR  N11  C12   single    1.341  0.020  1.341
 OZR  C12  C13   single    1.499  0.020  1.499
 OZR  C12  O22   double    1.220  0.020  1.220
 OZR  C13  C14   aromatic  1.394  0.020  1.394
 OZR  C13  C18   aromatic  1.389  0.020  1.389
 OZR  C14  C15   aromatic  1.409  0.020  1.409
 OZR  C14  O20   single    1.330  0.020  1.330
 OZR  C15  C16   aromatic  1.376  0.020  1.376
 OZR  C15  O21   single    1.345  0.020  1.345
 OZR  C16  C17   aromatic  1.393  0.020  1.393
 OZR  C17  C18   aromatic  1.382  0.020  1.382
 OZR  C17  N19   single    1.445  0.020  1.445
 OZR  N19  O23   double    1.210  0.020  1.210
 OZR  N19  O24   single    1.210  0.020  1.210
 OZR  C1   H1    single    0.970  0.020  1.090
 OZR  C2   H2    single    0.970  0.020  1.090
 OZR  C3   H3    single    0.970  0.020  1.090
 OZR  C3   H3A   single    0.970  0.020  1.090
 OZR  C5   H5    single    0.970  0.020  1.090
 OZR  C6   H6    single    0.930  0.020  1.080
 OZR  O7   HO7   single    0.850  0.020  0.980
 OZR  O8   HO8   single    0.850  0.020  0.980
 OZR  C9   H9    single    0.930  0.020  1.080
 OZR  C10  H10   single    0.970  0.020  1.090
 OZR  C10  H10A  single    0.970  0.020  1.090
 OZR  N11  HN11  single    0.860  0.020  1.020
 OZR  C16  H16   single    0.930  0.020  1.080
 OZR  C18  H18   single    0.930  0.020  1.080
 OZR  O20  HO20  single    0.850  0.020  0.980
 OZR  O21  HO21  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
 OZR  H1    C1   O7   111.60  3.000
 OZR  H1    C1   C5   111.83  3.000
 OZR  O7    C1   C5   108.51  3.000
 OZR  H1    C1   C2   112.17  3.000
 OZR  O7    C1   C2   111.66  3.000
 OZR  C5    C1   C2   100.54  3.000
 OZR  H2    C2   O8   111.31  3.000
 OZR  H2    C2   C3   109.52  3.000
 OZR  O8    C2   C3   115.18  3.000
 OZR  H2    C2   C1   108.46  3.000
 OZR  O8    C2   C1   110.54  3.000
 OZR  C3    C2   C1   101.23  3.000
 OZR  H3A   C3   H3   108.08  3.000
 OZR  H3A   C3   O4   110.63  3.000
 OZR  H3    C3   O4   109.50  3.000
 OZR  H3A   C3   C2   110.36  3.000
 OZR  H3    C3   C2   112.62  3.000
 OZR  O4    C3   C2   105.67  3.000
 OZR  C5    O4   C3   110.47  3.000
 OZR  H5    C5   C6   108.34  3.000
 OZR  H5    C5   O4   109.07  3.000
 OZR  C6    C5   O4   112.27  3.000
 OZR  H5    C5   C1   109.69  3.000
 OZR  C6    C5   C1   111.52  3.000
 OZR  O4    C5   C1   105.91  3.000
 OZR  H6    C6   C9   119.53  3.000
 OZR  H6    C6   C5   114.67  3.000
 OZR  C9    C6   C5   125.79  3.000
 OZR  HO7   O7   C1   108.34  3.000
 OZR  HO8   O8   C2   109.08  3.000
 OZR  H9    C9   C10  116.22  3.000
 OZR  H9    C9   C6   120.44  3.000
 OZR  C10   C9   C6   123.34  3.000
 OZR  H10A  C10  H10  107.26  3.000
 OZR  H10A  C10  N11  107.89  3.000
 OZR  H10   C10  N11  108.27  3.000
 OZR  H10A  C10  C9   110.69  3.000
 OZR  H10   C10  C9   110.50  3.000
 OZR  N11   C10  C9   112.05  3.000
 OZR  HN11  N11  C12  118.86  3.000
 OZR  HN11  N11  C10  117.30  3.000
 OZR  C12   N11  C10  122.98  3.000
 OZR  O22   C12  C13  121.64  3.000
 OZR  O22   C12  N11  123.93  3.000
 OZR  C13   C12  N11  114.40  3.000
 OZR  C18   C13  C14  120.15  3.000
 OZR  C18   C13  C12  119.95  3.000
 OZR  C14   C13  C12  119.85  3.000
 OZR  O20   C14  C15  120.87  3.000
 OZR  O20   C14  C13  119.60  3.000
 OZR  C15   C14  C13  119.52  3.000
 OZR  O21   C15  C16  124.43  3.000
 OZR  O21   C15  C14  115.15  3.000
 OZR  C16   C15  C14  120.42  3.000
 OZR  H16   C16  C17  121.12  3.000
 OZR  H16   C16  C15  119.90  3.000
 OZR  C17   C16  C15  118.98  3.000
 OZR  N19   C17  C18  119.37  3.000
 OZR  N19   C17  C16  118.95  3.000
 OZR  C18   C17  C16  121.67  3.000
 OZR  H18   C18  C17  120.95  3.000
 OZR  H18   C18  C13  119.78  3.000
 OZR  C17   C18  C13  119.26  3.000
 OZR  O24   N19  O23  123.63  3.000
 OZR  O24   N19  C17  118.23  3.000
 OZR  O23   N19  C17  118.14  3.000
 OZR  HO20  O20  C14  110.96  3.000
 OZR  HO21  O21  C15  111.73  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
 OZR  CONST_01  C16   C15  C14  C13     0.00   0.0  0
 OZR  CONST_02  C16   C17  C18  C13     0.00   0.0  0
 OZR  CONST_03  C17   C18  C13  C14     0.00   0.0  0
 OZR  CONST_04  C17   C16  C15  C14     0.00   0.0  0
 OZR  CONST_05  C18   C13  C14  C15     0.00   0.0  0
 OZR  CONST_06  C18   C17  C16  C15     0.00   0.0  0
 OZR  CONST_07  C15   C14  C13  C12   180.00   0.0  0
 OZR  CONST_08  C17   C18  C13  C12   180.00   0.0  0
 OZR  CONST_09  O21   C15  C14  C13   180.00   0.0  0
 OZR  CONST_10  N19   C17  C18  C13   180.00   0.0  0
 OZR  CONST_11  N19   C17  C16  C15   180.00   0.0  0
 OZR  CONST_12  O20   C14  C15  C16   180.00   0.0  0
 OZR  CONST_13  O21   C15  C16  C17   180.00   0.0  0
 OZR  CONST_14  O20   C14  C13  C18   180.00   0.0  0
 OZR  CONST_15  H18   C18  C13  C14   180.00   0.0  0
 OZR  CONST_16  H16   C16  C15  C14   180.00   0.0  0
 OZR  CONST_17  O23   N19  C17  C16     0.00   0.0  0
 OZR  CONST_18  O24   N19  C17  C16   180.00   0.0  0
 OZR  CONST_19  O23   N19  C17  C18   180.00   0.0  0
 OZR  CONST_20  O24   N19  C17  C18     0.00   0.0  0
 OZR  CONST_21  C13   C12  N11  C10   180.00   0.0  0
 OZR  CONST_22  HN11  N11  C12  C13     0.00   0.0  0
 OZR  CONST_23  O22   C12  N11  C10     0.00   0.0  0
 OZR  Var_01    H3    C3   O4   C5   -133.27  30.0  1
 OZR  Var_02    C14   C13  C12  N11   130.78  30.0  2
 OZR  Var_03    C10   C9   C6   C5    179.84   0.0  2
 OZR  Var_04    N11   C10  C9   C6    119.41  30.0  3
 OZR  Var_05    C12   N11  C10  C9     85.89  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
 OZR  chir_01  C1  C2  C5  O7  negativ
 OZR  chir_02  C2  O8  C1  C3  positiv
 OZR  chir_03  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
 OZR  plan-1  C12   0.020
 OZR  plan-1  C13   0.020
 OZR  plan-1  C14   0.020
 OZR  plan-1  C15   0.020
 OZR  plan-1  C16   0.020
 OZR  plan-1  C17   0.020
 OZR  plan-1  C18   0.020
 OZR  plan-1  N19   0.020
 OZR  plan-1  O20   0.020
 OZR  plan-1  O21   0.020
 OZR  plan-1  H16   0.020
 OZR  plan-1  H18   0.020
 OZR  plan-2  C17   0.020
 OZR  plan-2  N19   0.020
 OZR  plan-2  O23   0.020
 OZR  plan-2  O24   0.020
 OZR  plan-3  C10   0.020
 OZR  plan-3  N11   0.020
 OZR  plan-3  C12   0.020
 OZR  plan-3  C13   0.020
 OZR  plan-3  O22   0.020
 OZR  plan-3  HN11  0.020
 OZR  plan-4  C5    0.020
 OZR  plan-4  C6    0.020
 OZR  plan-4  C9    0.020
 OZR  plan-4  C10   0.020
 OZR  plan-4  H6    0.020
 OZR  plan-4  H9    0.020

