# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 16 16:04:22 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 1-{(5E)-5,6,7-trideoxy-7-[(2,3-dihydroxy-5-nitrobenzoyl)amino]-beta-D-ribo-hept-5-enofuranosyl}-4-(trifluoromethyl)-1H-imidazole
#   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)n3cnc(c3)C(F)(F)F
#
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
 OZS  OZS  1-{(5E)-5,6,7-trideoxy-7-[(2,3-dihydroxy-5-nitrobenzoyl)amino]-beta-D-ribo-hept-5-enofuranosyl}-4-(trifluoromethyl)-1H-imidazole  ligand  50  33  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OZS
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
 OZS  C1    C  CH1    0  -0.044  -2.5335  -2.9341  -1.2573
 OZS  C2    C  CH1    0  -0.033  -3.6378  -2.1641  -0.5272
 OZS  C3    C  CH1    0   0.164  -2.8956  -1.7316   0.7348
 OZS  O4    O  O2     0  -0.490  -1.9764  -2.7388   1.0200
 OZS  C5    C  CH1    0   0.016  -1.8079  -3.6171  -0.0891
 OZS  C6    C  C1     0  -0.243  -0.3677  -3.8711  -0.3876
 OZS  N7    N  NR5    0  -0.453  -2.1953  -0.4611   0.5261
 OZS  O8    O  OH1    0  -0.655  -3.0042  -3.8978  -2.1527
 OZS  O9    O  OH1    0  -0.662  -4.6746  -3.0171  -0.1334
 OZS  C10   C  C1     0  -0.242   0.6580  -3.5251   0.3805
 OZS  C11   C  CR15   0   0.118  -0.8750  -0.2602   0.2919
 OZS  C12   C  CR15   0  -0.070  -2.8003   0.7583   0.4928
 OZS  C13   C  CR5    0  -0.186  -1.7935   1.6429   0.2341
 OZS  N14   N  N      0  -0.429  -0.6007   1.0026   0.1130
 OZS  C15   C  CT     0   1.058  -1.8898   3.1102   0.0830
 OZS  C16   C  CH2    0  -0.368   2.0893  -3.6314  -0.0531
 OZS  N17   N  NH1    0  -0.648   2.5788  -2.2908  -0.3387
 OZS  C18   C  C      0   0.642   3.2504  -1.5358   0.5306
 OZS  C19   C  CR6    0  -0.165   3.3667  -0.0802   0.2497
 OZS  C20   C  CR6    0   0.284   4.2607   0.6630   1.0348
 OZS  C21   C  CR6    0   0.324   4.3857   2.0536   0.8348
 OZS  C22   C  CR16   0  -0.379   3.5855   2.6881  -0.0864
 OZS  C23   C  CR6    0   0.278   2.6778   1.9367  -0.8319
 OZS  C24   C  CR16   0  -0.338   2.5650   0.5729  -0.6820
 OZS  N25   N  N      1   0.326   1.8143   2.6124  -1.7741
 OZS  O26   O  OH1    0  -0.623   5.0177   0.1299   1.9816
 OZS  O27   O  OH1    0  -0.623   5.2590   2.7736   1.5556
 OZS  O28   O  O      0  -0.530   3.7627  -2.0058   1.5564
 OZS  F29   F  F      0  -0.317  -1.0831   3.7603   0.9333
 OZS  F30   F  F      0  -0.315  -1.5455   3.5181  -1.1462
 OZS  F31   F  F      0  -0.309  -3.1378   3.5390   0.3090
 OZS  O32   O  O      0  -0.387   1.7863   3.8225  -1.7497
 OZS  O33   O  O     -1  -0.379   1.1697   1.9411  -2.5453
 OZS  H1    H  HCH1   0   0.254  -1.8592  -2.2229  -1.7509
 OZS  H2    H  HCH1   0   0.265  -4.0059  -1.3056  -1.1024
 OZS  H3    H  HCH1   0   0.298  -3.5731  -1.5900   1.5798
 OZS  H5    H  HCH1   0   0.268  -2.3108  -4.5688   0.1288
 OZS  H6    H  H      0   0.271  -0.1882  -4.3629  -1.3405
 OZS  HO8   H  HOH1   0   0.471  -3.1726  -3.4787  -3.0028
 OZS  HO9   H  HOH1   0   0.454  -4.8315  -3.6453  -0.8494
 OZS  H10   H  H      0   0.268   0.4918  -3.0540   1.3445
 OZS  H11   H  HCR5   0   0.276  -0.1561  -1.0623   0.2718
 OZS  H12   H  HCR5   0   0.320  -3.8582   0.8859   0.6531
 OZS  H16   H  HCH2   0   0.276   2.7154  -4.0784   0.7163
 OZS  H16A  H  HCH2   0   0.278   2.1872  -4.2341  -0.9556
 OZS  HN17  H  HNH1   0   0.422   2.2366  -1.8748  -1.1895
 OZS  H22   H  HCR6   0   0.308   3.6716   3.7583  -0.2152
 OZS  H24   H  HCR6   0   0.276   1.8267   0.0408  -1.2618
 OZS  HO26  H  HOH1   0   0.491   4.7245  -0.8176   2.0774
 OZS  HO27  H  HOH1   0   0.481   5.7581   2.2046   2.1550

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
 OZS  C1   C2    single    1.531  0.020  1.531
 OZS  C1   C5    single    1.535  0.020  1.535
 OZS  C1   O8    single    1.397  0.020  1.397
 OZS  C2   C3    single    1.527  0.020  1.527
 OZS  C2   O9    single    1.399  0.020  1.399
 OZS  C3   O4    single    1.393  0.020  1.393
 OZS  C3   N7    single    1.466  0.020  1.466
 OZS  O4   C5    single    1.425  0.020  1.425
 OZS  C5   C6    single    1.493  0.020  1.493
 OZS  C6   C10   double    1.327  0.020  1.327
 OZS  N7   C11   aromatic  1.356  0.020  1.356
 OZS  N7   C12   aromatic  1.362  0.020  1.362
 OZS  C10  C16   single    1.499  0.020  1.499
 OZS  C11  N14   aromatic  1.305  0.020  1.305
 OZS  C12  C13   aromatic  1.365  0.020  1.365
 OZS  C13  N14   aromatic  1.359  0.020  1.359
 OZS  C13  C15   single    1.478  0.020  1.478
 OZS  C15  F29   single    1.340  0.020  1.340
 OZS  C15  F30   single    1.340  0.020  1.340
 OZS  C15  F31   single    1.339  0.020  1.339
 OZS  C16  N17   single    1.455  0.020  1.455
 OZS  N17  C18   single    1.333  0.020  1.333
 OZS  C18  C19   single    1.487  0.020  1.487
 OZS  C18  O28   double    1.239  0.020  1.239
 OZS  C19  C20   aromatic  1.403  0.020  1.403
 OZS  C19  C24   aromatic  1.392  0.020  1.392
 OZS  C20  C21   aromatic  1.410  0.020  1.410
 OZS  C20  O26   single    1.324  0.020  1.324
 OZS  C21  C22   aromatic  1.375  0.020  1.375
 OZS  C21  O27   single    1.342  0.020  1.342
 OZS  C22  C23   aromatic  1.394  0.020  1.394
 OZS  C23  C24   aromatic  1.377  0.020  1.377
 OZS  C23  N25   single    1.446  0.020  1.446
 OZS  N25  O32   double    1.211  0.020  1.211
 OZS  N25  O33   single    1.209  0.020  1.209
 OZS  C1   H1    single    0.970  0.020  1.090
 OZS  C2   H2    single    0.970  0.020  1.090
 OZS  C3   H3    single    0.970  0.020  1.090
 OZS  C5   H5    single    0.970  0.020  1.090
 OZS  C6   H6    single    0.930  0.020  1.080
 OZS  O8   HO8   single    0.850  0.020  0.980
 OZS  O9   HO9   single    0.850  0.020  0.980
 OZS  C10  H10   single    0.930  0.020  1.080
 OZS  C11  H11   single    0.930  0.020  1.080
 OZS  C12  H12   single    0.930  0.020  1.080
 OZS  C16  H16   single    0.970  0.020  1.090
 OZS  C16  H16A  single    0.970  0.020  1.090
 OZS  N17  HN17  single    0.860  0.020  1.020
 OZS  C22  H22   single    0.930  0.020  1.080
 OZS  C24  H24   single    0.930  0.020  1.080
 OZS  O26  HO26  single    0.850  0.020  0.980
 OZS  O27  HO27  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
 OZS  H1    C1   O8   111.45  3.000
 OZS  H1    C1   C5   109.88  3.000
 OZS  O8    C1   C5   109.87  3.000
 OZS  H1    C1   C2   109.37  3.000
 OZS  O8    C1   C2   114.17  3.000
 OZS  C5    C1   C2   101.64  3.000
 OZS  H2    C2   O9   112.09  3.000
 OZS  H2    C2   C3   112.02  3.000
 OZS  O9    C2   C3   107.48  3.000
 OZS  H2    C2   C1   112.67  3.000
 OZS  O9    C2   C1   111.22  3.000
 OZS  C3    C2   C1   100.72  3.000
 OZS  H3    C3   N7   107.11  3.000
 OZS  H3    C3   O4   110.15  3.000
 OZS  N7    C3   O4   109.91  3.000
 OZS  H3    C3   C2   112.01  3.000
 OZS  N7    C3   C2   111.11  3.000
 OZS  O4    C3   C2   106.57  3.000
 OZS  C5    O4   C3   111.37  3.000
 OZS  H5    C5   C6   109.52  3.000
 OZS  H5    C5   O4   109.00  3.000
 OZS  C6    C5   O4   112.00  3.000
 OZS  H5    C5   C1   108.66  3.000
 OZS  C6    C5   C1   112.31  3.000
 OZS  O4    C5   C1   105.20  3.000
 OZS  H6    C6   C10  119.83  3.000
 OZS  H6    C6   C5   114.30  3.000
 OZS  C10   C6   C5   125.85  3.000
 OZS  C12   N7   C11  107.20  3.000
 OZS  C12   N7   C3   124.57  3.000
 OZS  C11   N7   C3   128.20  3.000
 OZS  HO8   O8   C1   108.94  3.000
 OZS  HO9   O9   C2   107.96  3.000
 OZS  H10   C10  C16  115.70  3.000
 OZS  H10   C10  C6   120.57  3.000
 OZS  C16   C10  C6   123.50  3.000
 OZS  H11   C11  N14  125.30  3.000
 OZS  H11   C11  N7   122.87  3.000
 OZS  N14   C11  N7   111.83  3.000
 OZS  H12   C12  C13  132.50  3.000
 OZS  H12   C12  N7   122.59  3.000
 OZS  C13   C12  N7   104.91  3.000
 OZS  C15   C13  N14  121.04  3.000
 OZS  C15   C13  C12  127.93  3.000
 OZS  N14   C13  C12  111.03  3.000
 OZS  C13   N14  C11  105.03  3.000
 OZS  F31   C15  F30  107.26  3.000
 OZS  F31   C15  F29  107.37  3.000
 OZS  F30   C15  F29  106.24  3.000
 OZS  F31   C15  C13  111.18  3.000
 OZS  F30   C15  C13  112.28  3.000
 OZS  F29   C15  C13  112.18  3.000
 OZS  H16A  C16  H16  107.87  3.000
 OZS  H16A  C16  N17  108.47  3.000
 OZS  H16   C16  N17  108.88  3.000
 OZS  H16A  C16  C10  111.38  3.000
 OZS  H16   C16  C10  111.96  3.000
 OZS  N17   C16  C10  108.21  3.000
 OZS  HN17  N17  C18  119.23  3.000
 OZS  HN17  N17  C16  115.59  3.000
 OZS  C18   N17  C16  124.28  3.000
 OZS  O28   C18  C19  119.69  3.000
 OZS  O28   C18  N17  122.23  3.000
 OZS  C19   C18  N17  118.07  3.000
 OZS  C24   C19  C20  119.54  3.000
 OZS  C24   C19  C18  122.74  3.000
 OZS  C20   C19  C18  117.56  3.000
 OZS  O26   C20  C21  116.59  3.000
 OZS  O26   C20  C19  123.44  3.000
 OZS  C21   C20  C19  119.97  3.000
 OZS  O27   C21  C22  119.40  3.000
 OZS  O27   C21  C20  120.70  3.000
 OZS  C22   C21  C20  119.89  3.000
 OZS  H22   C22  C23  121.43  3.000
 OZS  H22   C22  C21  119.34  3.000
 OZS  C23   C22  C21  119.22  3.000
 OZS  N25   C23  C24  119.02  3.000
 OZS  N25   C23  C22  119.04  3.000
 OZS  C24   C23  C22  121.93  3.000
 OZS  H24   C24  C23  119.08  3.000
 OZS  H24   C24  C19  121.49  3.000
 OZS  C23   C24  C19  119.38  3.000
 OZS  O33   N25  O32  123.75  3.000
 OZS  O33   N25  C23  118.35  3.000
 OZS  O32   N25  C23  117.89  3.000
 OZS  HO26  O26  C20  106.46  3.000
 OZS  HO27  O27  C21  110.71  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
 OZS  CONST_01  C13   N14  C11  N7      0.00   0.0  0
 OZS  CONST_02  N14   C13  C12  N7      0.00   0.0  0
 OZS  CONST_03  C13   C12  N7   C11     0.00   0.0  0
 OZS  CONST_04  C12   C13  N14  C11     0.00   0.0  0
 OZS  CONST_05  N14   C11  N7   C12     0.00   0.0  0
 OZS  CONST_06  C22   C21  C20  C19     0.00   0.0  0
 OZS  CONST_07  C22   C23  C24  C19     0.00   0.0  0
 OZS  CONST_08  C23   C24  C19  C20     0.00   0.0  0
 OZS  CONST_09  C23   C22  C21  C20     0.00   0.0  0
 OZS  CONST_10  C24   C19  C20  C21     0.00   0.0  0
 OZS  CONST_11  C24   C23  C22  C21     0.00   0.0  0
 OZS  CONST_12  N14   C11  N7   C3    180.00   0.0  0
 OZS  CONST_13  C13   C12  N7   C3    180.00   0.0  0
 OZS  CONST_14  C15   C13  C12  N7    180.00   0.0  0
 OZS  CONST_15  C15   C13  N14  C11   180.00   0.0  0
 OZS  CONST_16  C21   C20  C19  C18   180.00   0.0  0
 OZS  CONST_17  C23   C24  C19  C18   180.00   0.0  0
 OZS  CONST_18  O27   C21  C20  C19   180.00   0.0  0
 OZS  CONST_19  N25   C23  C24  C19   180.00   0.0  0
 OZS  CONST_20  N25   C23  C22  C21   180.00   0.0  0
 OZS  CONST_21  O26   C20  C21  C22   180.00   0.0  0
 OZS  CONST_22  O27   C21  C22  C23   180.00   0.0  0
 OZS  CONST_23  O26   C20  C19  C24   180.00   0.0  0
 OZS  CONST_24  H11   C11  N7   C3      0.00   0.0  0
 OZS  CONST_25  H12   C12  N7   C3      0.00   0.0  0
 OZS  CONST_26  H24   C24  C19  C20   180.00   0.0  0
 OZS  CONST_27  H22   C22  C21  C20   180.00   0.0  0
 OZS  CONST_28  O32   N25  C23  C22     0.00   0.0  0
 OZS  CONST_29  O33   N25  C23  C22   180.00   0.0  0
 OZS  CONST_30  O32   N25  C23  C24   180.00   0.0  0
 OZS  CONST_31  O33   N25  C23  C24     0.00   0.0  0
 OZS  CONST_33  HN17  N17  C18  C19     0.00   0.0  0
 OZS  Var_01    F29   C15  C13  C12   123.77  30.0  2
 OZS  Var_02    C20   C19  C18  N17  -169.22  30.0  2
 OZS  Var_03    C16   C10  C6   C5   -171.11   0.0  2
 OZS  Var_04    N17   C16  C10  C6    105.68  30.0  3
 OZS  Var_05    C18   N17  C16  C10    95.58  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
 OZS  chir_01  C1  C2  C5  O8  negativ
 OZS  chir_02  C2  O9  C3  C1  negativ
 OZS  chir_03  C3  O4  N7  C2  negativ
 OZS  chir_04  C5  O4  C1  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
 OZS  plan-1  C3    0.020
 OZS  plan-1  N7    0.020
 OZS  plan-1  C11   0.020
 OZS  plan-1  C12   0.020
 OZS  plan-1  C13   0.020
 OZS  plan-1  N14   0.020
 OZS  plan-1  C15   0.020
 OZS  plan-1  H11   0.020
 OZS  plan-1  H12   0.020
 OZS  plan-2  C18   0.020
 OZS  plan-2  C19   0.020
 OZS  plan-2  C20   0.020
 OZS  plan-2  C21   0.020
 OZS  plan-2  C22   0.020
 OZS  plan-2  C23   0.020
 OZS  plan-2  C24   0.020
 OZS  plan-2  N25   0.020
 OZS  plan-2  O26   0.020
 OZS  plan-2  O27   0.020
 OZS  plan-2  H22   0.020
 OZS  plan-2  H24   0.020
 OZS  plan-3  C23   0.020
 OZS  plan-3  N25   0.020
 OZS  plan-3  O32   0.020
 OZS  plan-3  O33   0.020
 OZS  plan-4  C16   0.020
 OZS  plan-4  N17   0.020
 OZS  plan-4  C18   0.020
 OZS  plan-4  C19   0.020
 OZS  plan-4  O28   0.020
 OZS  plan-4  HN17  0.020
 OZS  plan-5  C5    0.020
 OZS  plan-5  C6    0.020
 OZS  plan-5  C10   0.020
 OZS  plan-5  C16   0.020
 OZS  plan-5  H6    0.020
 OZS  plan-5  H10   0.020

