# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 18:30:27 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{S},6~{S})-2-methyl-6-(4-nitrophenoxy)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H](Oc2ccc(cc2)[N+]([O-])=O)[C@@H](O)[C@H](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
 JFZ  JFZ  (2~{S},3~{S},4~{R},5~{S},6~{S})-2-methyl-6-(4-nitrophenoxy)oxane-3,4,5-triol  L-saccharide  35  20  .  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_JFZ
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
 JFZ  C1   C  CH1    0   0.203   1.2911   0.2609  -0.8324
 JFZ  C2   C  CH1    0  -0.019   2.6278   0.9903  -0.6660
 JFZ  O2   O  OH1    0  -0.665   2.4644   2.3843  -0.6589
 JFZ  C3   C  CH1    0   0.023   3.3056   0.5803   0.6378
 JFZ  O3   O  OH1    0  -0.669   4.5892   1.1365   0.7516
 JFZ  C4   C  CH1    0  -0.007   3.4132  -0.9367   0.7079
 JFZ  O4   O  OH1    0  -0.671   4.3066  -1.3643  -0.2908
 JFZ  C5   C  CH1    0   0.007   2.0174  -1.5407   0.5428
 JFZ  C6   C  CH3    0  -0.705   2.0202  -3.0542   0.5219
 JFZ  O5   O  O2     0  -0.488   1.4201  -1.1068  -0.6810
 JFZ  O1'  O  O2     0  -0.480   0.3975   0.8095   0.1213
 JFZ  C1'  C  CR6    0   0.430  -0.9163   0.5707   0.0336
 JFZ  C2'  C  CR16   0  -0.364  -1.5185  -0.2367  -0.9343
 JFZ  C3'  C  CR16   0  -0.253  -2.8925  -0.3871  -0.9450
 JFZ  C4'  C  CR6    0   0.228  -3.6667   0.2499   0.0136
 JFZ  C5'  C  CR16   0  -0.252  -3.0776   1.0447   0.9920
 JFZ  C6'  C  CR16   0  -0.348  -1.7101   1.2015   0.9977
 JFZ  N1'  N  N      1   0.328  -5.1014   0.0848  -0.0033
 JFZ  O2'  O  O      0  -0.389  -5.5888  -0.6119  -0.8651
 JFZ  O3'  O  O     -1  -0.389  -5.7523   0.6522   0.8454
 JFZ  H1   H  HCH1   0   0.267   0.8997   0.4295  -1.8421
 JFZ  H2   H  HCH1   0   0.245   3.2608   0.6699  -1.5028
 JFZ  H3   H  HOH1   0   0.461   2.3789   2.6951  -1.5651
 JFZ  H4   H  HCH1   0   0.239   3.7737  -1.2134   1.7092
 JFZ  H5   H  HOH1   0   0.458   4.5419  -2.2818  -0.1242
 JFZ  H6   H  HCH1   0   0.231   1.4113  -1.2083   1.3951
 JFZ  H7   H  HCH3   0   0.231   2.5893  -3.4500  -0.3203
 JFZ  H8   H  HCH3   0   0.240   2.4578  -3.4382   1.4436
 JFZ  H9   H  HCH3   0   0.252   1.0035  -3.4399   0.4526
 JFZ  H10  H  HCR6   0   0.301  -0.9433  -0.7602  -1.6830
 JFZ  H11  H  HCR6   0   0.300  -3.3450  -1.0087  -1.7039
 JFZ  H12  H  HCR6   0   0.298  -3.6726   1.5420   1.7438
 JFZ  H13  H  HCR6   0   0.285  -1.2395   1.8204   1.7502
 JFZ  H14  H  HCH1   0   0.224   2.6704   0.8967   1.4790
 JFZ  H15  H  HOH1   0   0.451   4.4982   2.0949   0.7429

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
 JFZ  O3'  N1'  single    1.211  0.020  1.211
 JFZ  O2'  N1'  double    1.211  0.020  1.211
 JFZ  N1'  C4'  single    1.444  0.020  1.444
 JFZ  C3'  C4'  aromatic  1.387  0.020  1.387
 JFZ  C3'  C2'  aromatic  1.382  0.020  1.382
 JFZ  C4'  C5'  aromatic  1.391  0.020  1.391
 JFZ  C2'  C1'  aromatic  1.397  0.020  1.397
 JFZ  C5'  C6'  aromatic  1.376  0.020  1.376
 JFZ  C1'  C6'  aromatic  1.399  0.020  1.399
 JFZ  C1'  O1'  single    1.338  0.020  1.338
 JFZ  O1'  C1   single    1.417  0.020  1.417
 JFZ  C5   C6   single    1.514  0.020  1.514
 JFZ  C5   O5   single    1.429  0.020  1.429
 JFZ  C5   C4   single    1.530  0.020  1.530
 JFZ  C1   O5   single    1.382  0.020  1.382
 JFZ  C1   C2   single    1.532  0.020  1.532
 JFZ  C4   C3   single    1.522  0.020  1.522
 JFZ  C4   O4   single    1.407  0.020  1.407
 JFZ  O2   C2   single    1.404  0.020  1.404
 JFZ  C2   C3   single    1.526  0.020  1.526
 JFZ  C3   O3   single    1.404  0.020  1.404
 JFZ  C1   H1   single    0.970  0.020  1.090
 JFZ  C2   H2   single    0.970  0.020  1.090
 JFZ  O2   H3   single    0.850  0.020  0.980
 JFZ  C4   H4   single    0.970  0.020  1.090
 JFZ  O4   H5   single    0.850  0.020  0.980
 JFZ  C5   H6   single    0.970  0.020  1.090
 JFZ  C6   H7   single    0.970  0.020  1.090
 JFZ  C6   H8   single    0.970  0.020  1.090
 JFZ  C6   H9   single    0.970  0.020  1.090
 JFZ  C2'  H10  single    0.930  0.020  1.080
 JFZ  C3'  H11  single    0.930  0.020  1.080
 JFZ  C5'  H12  single    0.930  0.020  1.080
 JFZ  C6'  H13  single    0.930  0.020  1.080
 JFZ  C3   H14  single    0.970  0.020  1.090
 JFZ  O3   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
 JFZ  H1   C1   O1'  109.59  3.000
 JFZ  H1   C1   O5   106.65  3.000
 JFZ  O1'  C1   O5   111.60  3.000
 JFZ  H1   C1   C2   109.79  3.000
 JFZ  O5   C1   C2   112.20  3.000
 JFZ  O1'  C1   C2   107.02  3.000
 JFZ  H2   C2   C3   108.48  3.000
 JFZ  H2   C2   O2   111.17  3.000
 JFZ  C3   C2   O2   108.32  3.000
 JFZ  H2   C2   C1   106.36  3.000
 JFZ  C3   C2   C1   110.64  3.000
 JFZ  O2   C2   C1   111.83  3.000
 JFZ  H3   O2   C2   109.05  3.000
 JFZ  H14  C3   C4   106.98  3.000
 JFZ  H14  C3   O3   110.60  3.000
 JFZ  C4   C3   O3   109.06  3.000
 JFZ  H14  C3   C2   108.64  3.000
 JFZ  O3   C3   C2   111.66  3.000
 JFZ  C4   C3   C2   109.79  3.000
 JFZ  H15  O3   C3   107.90  3.000
 JFZ  H4   C4   C5   107.34  3.000
 JFZ  H4   C4   O4   111.21  3.000
 JFZ  C5   C4   O4   112.51  3.000
 JFZ  H4   C4   C3   108.41  3.000
 JFZ  O4   C4   C3   108.37  3.000
 JFZ  C5   C4   C3   108.90  3.000
 JFZ  H5   O4   C4   108.81  3.000
 JFZ  H6   C5   O5   110.01  3.000
 JFZ  H6   C5   C6   108.33  3.000
 JFZ  O5   C5   C6   107.01  3.000
 JFZ  H6   C5   C4   107.49  3.000
 JFZ  O5   C5   C4   110.73  3.000
 JFZ  C6   C5   C4   113.24  3.000
 JFZ  H9   C6   H8   107.68  3.000
 JFZ  H9   C6   H7   108.01  3.000
 JFZ  H8   C6   H7   108.40  3.000
 JFZ  H9   C6   C5   110.68  3.000
 JFZ  H8   C6   C5   109.95  3.000
 JFZ  H7   C6   C5   111.99  3.000
 JFZ  C5   O5   C1   115.68  3.000
 JFZ  C1'  O1'  C1   120.38  3.000
 JFZ  C6'  C1'  C2'  119.57  3.000
 JFZ  C6'  C1'  O1'  115.56  3.000
 JFZ  C2'  C1'  O1'  124.88  3.000
 JFZ  H10  C2'  C3'  118.13  3.000
 JFZ  H10  C2'  C1'  122.08  3.000
 JFZ  C3'  C2'  C1'  119.79  3.000
 JFZ  H11  C3'  C4'  121.06  3.000
 JFZ  H11  C3'  C2'  118.97  3.000
 JFZ  C4'  C3'  C2'  119.96  3.000
 JFZ  N1'  C4'  C5'  119.61  3.000
 JFZ  C5'  C4'  C3'  120.79  3.000
 JFZ  N1'  C4'  C3'  119.59  3.000
 JFZ  H12  C5'  C6'  119.47  3.000
 JFZ  H12  C5'  C4'  121.28  3.000
 JFZ  C6'  C5'  C4'  119.25  3.000
 JFZ  H13  C6'  C5'  120.00  3.000
 JFZ  H13  C6'  C1'  119.36  3.000
 JFZ  C5'  C6'  C1'  120.63  3.000
 JFZ  O3'  N1'  O2'  123.52  3.000
 JFZ  O2'  N1'  C4'  118.29  3.000
 JFZ  O3'  N1'  C4'  118.18  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
 JFZ  CONST_01  C4'  C3'  C2'  C1'    0.00   0.0  0
 JFZ  CONST_02  C4'  C5'  C6'  C1'    0.00   0.0  0
 JFZ  CONST_03  C5'  C4'  C3'  C2'    0.00   0.0  0
 JFZ  CONST_04  C5'  C6'  C1'  C2'    0.00   0.0  0
 JFZ  CONST_05  C6'  C5'  C4'  C3'    0.00   0.0  0
 JFZ  CONST_06  C6'  C1'  C2'  C3'    0.00   0.0  0
 JFZ  CONST_07  C3'  C2'  C1'  O1'  180.00   0.0  0
 JFZ  CONST_08  C5'  C6'  C1'  O1'  180.00   0.0  0
 JFZ  CONST_09  N1'  C4'  C3'  C2'  180.00   0.0  0
 JFZ  CONST_10  N1'  C4'  C5'  C6'  180.00   0.0  0
 JFZ  CONST_11  H11  C3'  C2'  C1'  180.00   0.0  0
 JFZ  CONST_12  H12  C5'  C6'  C1'  180.00   0.0  0
 JFZ  CONST_13  H13  C6'  C1'  C2'  180.00   0.0  0
 JFZ  CONST_14  H10  C2'  C3'  C4'  180.00   0.0  0
 JFZ  CONST_15  O3'  N1'  C4'  C3'  180.00   0.0  0
 JFZ  CONST_16  O2'  N1'  C4'  C3'    0.00   0.0  0
 JFZ  CONST_17  O3'  N1'  C4'  C5'    0.00   0.0  0
 JFZ  CONST_18  O2'  N1'  C4'  C5'  180.00   0.0  0
 JFZ  Var_01    C2'  C1'  O1'  C1     1.91  30.0  2

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
 JFZ  chir_01  C1  O1'  O5  C2  positiv
 JFZ  chir_02  C2  O2   C1  C3  positiv
 JFZ  chir_03  C3  O3   C2  C4  negativ
 JFZ  chir_04  C4  O4   C3  C5  negativ
 JFZ  chir_05  C5  O5   C4  C6  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
 JFZ  plan-1  O1'  0.020
 JFZ  plan-1  C1'  0.020
 JFZ  plan-1  C2'  0.020
 JFZ  plan-1  C3'  0.020
 JFZ  plan-1  C4'  0.020
 JFZ  plan-1  C5'  0.020
 JFZ  plan-1  C6'  0.020
 JFZ  plan-1  N1'  0.020
 JFZ  plan-1  H10  0.020
 JFZ  plan-1  H11  0.020
 JFZ  plan-1  H12  0.020
 JFZ  plan-1  H13  0.020
 JFZ  plan-2  C4'  0.020
 JFZ  plan-2  N1'  0.020
 JFZ  plan-2  O2'  0.020
 JFZ  plan-2  O3'  0.020

