# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 23:25:57 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2R,3R,4S,5S,6R)-2-hexoxy-6-(hydroxymethyl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCO[C@@H]1O[C@H](CO)[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
 JZR  JZR  (2R,3R,4S,5S,6R)-2-hexoxy-6-(hydroxymethyl)oxane-3,4,5-triol  D-saccharide  42  18  .  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_JZR
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
 JZR  C1    C  CH1   0   0.299   0.7601   0.3848  -0.1593
 JZR  O1    O  O2    0  -0.503  -0.4776   0.6673   0.3720
 JZR  C2    C  CH1   0  -0.026   1.7236   1.5047   0.2217
 JZR  O2    O  OH1   0  -0.669   1.3529   2.7294  -0.3608
 JZR  C3    C  CH1   0  -0.010   3.1133   1.1506  -0.2885
 JZR  O3    O  OH1   0  -0.673   4.0902   2.0637   0.1523
 JZR  C4    C  CH1   0   0.034   3.5322  -0.2338   0.1932
 JZR  O4    O  OH1   0  -0.672   4.7330  -0.6414  -0.4138
 JZR  C5    C  CH1   0  -0.015   2.4483  -1.2544  -0.1602
 JZR  O5    O  O2    0  -0.496   1.2124  -0.8333   0.3757
 JZR  C6    C  CH2   0  -0.156   2.7600  -2.6248   0.4027
 JZR  O6    O  OH1   0  -0.670   1.7793  -3.5323  -0.0403
 JZR  C1'   C  CH2   0  -0.140  -1.5603  -0.0389  -0.2153
 JZR  C2'   C  CH2   0  -0.464  -2.8636   0.5009   0.3336
 JZR  C3'   C  CH2   0  -0.425  -4.0647  -0.1967  -0.2937
 JZR  C4'   C  CH2   0  -0.406  -5.3970   0.3156   0.2373
 JZR  C5'   C  CH2   0  -0.420  -6.5973  -0.3704  -0.4026
 JZR  C6'   C  CH3   0  -0.662  -7.9279   0.1457   0.1271
 JZR  H1    H  HCH1  0   0.183   0.7059   0.3067  -1.2627
 JZR  H2    H  HCH1  0   0.221   1.7505   1.5750   1.3199
 JZR  HO2   H  HOH1  0   0.455   0.5484   3.0388   0.0671
 JZR  H3    H  HCH1  0   0.215   3.0755   1.1224  -1.3899
 JZR  HO3   H  HOH1  0   0.457   3.9422   2.9074  -0.2862
 JZR  H4    H  HCH1  0   0.211   3.6337  -0.2052   1.2902
 JZR  HO4   H  HOH1  0   0.454   5.4110   0.0100  -0.2053
 JZR  H5    H  HCH1  0   0.222   2.3811  -1.3258  -1.2586
 JZR  H6    H  HCH2  0   0.213   3.7611  -2.9169   0.0695
 JZR  H6A   H  HCH2  0   0.196   2.7904  -2.5590   1.4995
 JZR  HO6   H  HOH1  0   0.456   2.0302  -4.4094   0.2624
 JZR  H1'   H  HCH2  0   0.205  -1.5316   0.0819  -1.3063
 JZR  H1'A  H  HCH2  0   0.210  -1.4801  -1.1118  -0.0076
 JZR  H2'   H  HCH2  0   0.225  -2.8882   0.3697   1.4198
 JZR  H2'A  H  HCH2  0   0.223  -2.9227   1.5766   0.1422
 JZR  H3'   H  HCH2  0   0.214  -4.0342  -0.0654  -1.3808
 JZR  H3'A  H  HCH2  0   0.215  -3.9953  -1.2755  -0.1176
 JZR  H4'   H  HCH2  0   0.209  -5.4351   0.1761   1.3233
 JZR  H4'A  H  HCH2  0   0.209  -5.4649   1.3961   0.0691
 JZR  H5'   H  HCH2  0   0.211  -6.5561  -0.2312  -1.4874
 JZR  H5'A  H  HCH2  0   0.211  -6.5283  -1.4496  -0.2342
 JZR  H6'   H  HCH3  0   0.226  -8.7710  -0.3580  -0.3470
 JZR  H6'A  H  HCH3  0   0.216  -8.0120  -0.0113   1.2041
 JZR  H6'B  H  HCH3  0   0.216  -8.0358   1.2163  -0.0565

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
 JZR  C1   O1    single  1.376  0.020  1.376
 JZR  C1   C2    single  1.526  0.020  1.526
 JZR  C1   O5    single  1.405  0.020  1.405
 JZR  O1   C1'   single  1.420  0.020  1.420
 JZR  C2   O2    single  1.406  0.020  1.406
 JZR  C2   C3    single  1.522  0.020  1.522
 JZR  C3   O3    single  1.408  0.020  1.408
 JZR  C3   C4    single  1.525  0.020  1.525
 JZR  C4   O4    single  1.406  0.020  1.406
 JZR  C4   C5    single  1.530  0.020  1.530
 JZR  C5   O5    single  1.411  0.020  1.411
 JZR  C5   C6    single  1.514  0.020  1.514
 JZR  C6   O6    single  1.408  0.020  1.408
 JZR  C1'  C2'   single  1.514  0.020  1.514
 JZR  C2'  C3'   single  1.524  0.020  1.524
 JZR  C3'  C4'   single  1.523  0.020  1.523
 JZR  C4'  C5'   single  1.523  0.020  1.523
 JZR  C5'  C6'   single  1.522  0.020  1.522
 JZR  C1   H1    single  0.970  0.020  1.090
 JZR  C2   H2    single  0.970  0.020  1.090
 JZR  O2   HO2   single  0.850  0.020  0.980
 JZR  C3   H3    single  0.970  0.020  1.090
 JZR  O3   HO3   single  0.850  0.020  0.980
 JZR  C4   H4    single  0.970  0.020  1.090
 JZR  O4   HO4   single  0.850  0.020  0.980
 JZR  C5   H5    single  0.970  0.020  1.090
 JZR  C6   H6    single  0.970  0.020  1.090
 JZR  C6   H6A   single  0.970  0.020  1.090
 JZR  O6   HO6   single  0.850  0.020  0.980
 JZR  C1'  H1'   single  0.970  0.020  1.090
 JZR  C1'  H1'A  single  0.970  0.020  1.090
 JZR  C2'  H2'   single  0.970  0.020  1.090
 JZR  C2'  H2'A  single  0.970  0.020  1.090
 JZR  C3'  H3'   single  0.970  0.020  1.090
 JZR  C3'  H3'A  single  0.970  0.020  1.090
 JZR  C4'  H4'   single  0.970  0.020  1.090
 JZR  C4'  H4'A  single  0.970  0.020  1.090
 JZR  C5'  H5'   single  0.970  0.020  1.090
 JZR  C5'  H5'A  single  0.970  0.020  1.090
 JZR  C6'  H6'   single  0.970  0.020  1.090
 JZR  C6'  H6'A  single  0.970  0.020  1.090
 JZR  C6'  H6'B  single  0.970  0.020  1.090

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
 JZR  H1    C1   O5    109.51  3.000
 JZR  H1    C1   C2    109.36  3.000
 JZR  O5    C1   C2    109.75  3.000
 JZR  H1    C1   O1    110.81  3.000
 JZR  O5    C1   O1    108.69  3.000
 JZR  C2    C1   O1    108.71  3.000
 JZR  C1'   O1   C1    115.08  3.000
 JZR  H2    C2   C3    109.09  3.000
 JZR  H2    C2   O2    111.36  3.000
 JZR  C3    C2   O2    107.73  3.000
 JZR  H2    C2   C1    108.14  3.000
 JZR  C3    C2   C1    108.79  3.000
 JZR  O2    C2   C1    111.68  3.000
 JZR  HO2   O2   C2    108.43  3.000
 JZR  H3    C3   C4    107.57  3.000
 JZR  H3    C3   O3    110.68  3.000
 JZR  C4    C3   O3    107.42  3.000
 JZR  H3    C3   C2    108.04  3.000
 JZR  C4    C3   C2    110.87  3.000
 JZR  O3    C3   C2    112.19  3.000
 JZR  HO3   O3   C3    108.61  3.000
 JZR  H4    C4   C5    108.21  3.000
 JZR  H4    C4   O4    111.01  3.000
 JZR  C5    C4   O4    108.18  3.000
 JZR  H4    C4   C3    108.43  3.000
 JZR  C5    C4   C3    109.76  3.000
 JZR  O4    C4   C3    111.20  3.000
 JZR  HO4   O4   C4    108.17  3.000
 JZR  H5    C5   C6    108.92  3.000
 JZR  H5    C5   O5    110.13  3.000
 JZR  C6    C5   O5    108.01  3.000
 JZR  H5    C5   C4    108.44  3.000
 JZR  C6    C5   C4    111.85  3.000
 JZR  O5    C5   C4    109.49  3.000
 JZR  C5    O5   C1    113.32  3.000
 JZR  H6A   C6   H6    107.12  3.000
 JZR  H6A   C6   O6    111.84  3.000
 JZR  H6    C6   O6    111.67  3.000
 JZR  H6A   C6   C5    108.81  3.000
 JZR  H6    C6   C5    108.45  3.000
 JZR  O6    C6   C5    108.85  3.000
 JZR  HO6   O6   C6    107.90  3.000
 JZR  H1'A  C1'  H1'   107.11  3.000
 JZR  H1'A  C1'  C2'   110.09  3.000
 JZR  H1'   C1'  C2'   110.09  3.000
 JZR  H1'A  C1'  O1    110.66  3.000
 JZR  H1'   C1'  O1    109.65  3.000
 JZR  C2'   C1'  O1    109.22  3.000
 JZR  H2'A  C2'  H2'   106.87  3.000
 JZR  H2'A  C2'  C3'   109.60  3.000
 JZR  H2'   C2'  C3'   109.64  3.000
 JZR  H2'A  C2'  C1'   109.49  3.000
 JZR  H2'   C2'  C1'   109.66  3.000
 JZR  C3'   C2'  C1'   111.47  3.000
 JZR  H3'A  C3'  H3'   106.02  3.000
 JZR  H3'A  C3'  C4'   109.31  3.000
 JZR  H3'   C3'  C4'   109.27  3.000
 JZR  H3'A  C3'  C2'   109.55  3.000
 JZR  H3'   C3'  C2'   109.38  3.000
 JZR  C4'   C3'  C2'   113.07  3.000
 JZR  H4'A  C4'  H4'   106.00  3.000
 JZR  H4'A  C4'  C5'   109.31  3.000
 JZR  H4'   C4'  C5'   109.37  3.000
 JZR  H4'A  C4'  C3'   109.41  3.000
 JZR  H4'   C4'  C3'   109.46  3.000
 JZR  C5'   C4'  C3'   113.04  3.000
 JZR  H5'A  C5'  H5'   106.00  3.000
 JZR  H5'A  C5'  C6'   109.63  3.000
 JZR  H5'   C5'  C6'   109.55  3.000
 JZR  H5'A  C5'  C4'   109.25  3.000
 JZR  H5'   C5'  C4'   109.23  3.000
 JZR  C6'   C5'  C4'   112.94  3.000
 JZR  H6'B  C6'  H6'A  107.42  3.000
 JZR  H6'B  C6'  H6'   107.67  3.000
 JZR  H6'A  C6'  H6'   107.63  3.000
 JZR  H6'B  C6'  C5'   111.13  3.000
 JZR  H6'A  C6'  C5'   111.22  3.000
 JZR  H6'   C6'  C5'   111.58  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
 JZR  Var_01  C2'  C1'  O1   C1   -172.55  30.0  3
 JZR  Var_02  C3'  C2'  C1'  O1    178.40  30.0  3
 JZR  Var_03  C4'  C3'  C2'  C1'   179.78  30.0  3
 JZR  Var_04  C5'  C4'  C3'  C2'   179.30  30.0  3
 JZR  Var_05  C6'  C5'  C4'  C3'  -179.85  30.0  3
 JZR  Var_06  H6'  C6'  C5'  C4'   179.86  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
 JZR  chir_01  C1  O1  C2  O5  negativ
 JZR  chir_02  C2  O2  C1  C3  negativ
 JZR  chir_03  C3  O3  C2  C4  positiv
 JZR  chir_04  C4  O4  C5  C3  positiv
 JZR  chir_05  C5  O5  C4  C6  negativ

