# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:22:36 2021
#   Inital geometry file: a 51 line input string
#   Ligand name: 1,6-dichloro-1,6-dideoxy-beta-D-fructofuranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](O)[C@@](O)(CCl)O[C@@H]1CCl
#
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
 RRY  RRY  1,6-dichloro-1,6-dideoxy-beta-D-fructofuranose  D-saccharide  22  12  .  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_RRY
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
 RRY  O3   O   OH1   0  -0.652  -66.8779  -22.5571  185.7385
 RRY  C3   C   CH1   0  -0.007  -67.8686  -21.9803  184.9512
 RRY  C4   C   CH1   0  -0.025  -69.0213  -21.4935  185.8129
 RRY  O4   O   OH1   0  -0.659  -69.8450  -22.5521  186.2092
 RRY  C5   C   CH1   0   0.040  -69.7100  -20.4974  184.8692
 RRY  C6   C   CH2   0  -0.474  -70.3426  -19.3460  185.6080
 RRY  CL6  CL  CL    0  -0.164  -71.1507  -18.2144  184.4705
 RRY  O5   O   O2    0  -0.503  -68.7041  -20.0303  183.9808
 RRY  C2   C   CT    0   0.460  -67.4784  -20.6907  184.2027
 RRY  C1   C   CH2   0  -0.507  -66.8987  -20.9149  182.8116
 RRY  CL1  CL  CL    0  -0.156  -65.3374  -21.7930  182.9108
 RRY  O2   O   OH1   0  -0.644  -66.6356  -19.9597  185.0195
 RRY  HO3  H   HOH1  0   0.449  -66.2114  -22.9474  185.1639
 RRY  H3   H   HCH1  0   0.237  -68.2705  -22.6886  184.2101
 RRY  H4   H   HCH1  0   0.243  -68.6102  -20.9643  186.6833
 RRY  HO4  H   HOH1  0   0.463  -70.2699  -22.3244  187.0405
 RRY  H5   H   HCH1  0   0.250  -70.4783  -21.0271  184.2939
 RRY  H61  H   HCH2  0   0.290  -71.1047  -19.7100  186.2951
 RRY  H62  H   HCH2  0   0.289  -69.6036  -18.7730  186.1654
 RRY  H11  H   HCH2  0   0.301  -67.5686  -21.5170  182.2023
 RRY  H12  H   HCH2  0   0.309  -66.7078  -19.9692  182.3033
 RRY  HO2  H   HOH1  0   0.460  -66.3682  -19.1497  184.5683

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
 RRY  O3  C3   single  1.391  0.020  1.391
 RRY  C3  C4   single  1.519  0.020  1.519
 RRY  C3  C2   single  1.541  0.020  1.541
 RRY  C4  O4   single  1.399  0.020  1.399
 RRY  C4  C5   single  1.535  0.020  1.535
 RRY  C5  C6   single  1.507  0.020  1.507
 RRY  C5  O5   single  1.421  0.020  1.421
 RRY  C6  CL6  single  1.797  0.020  1.797
 RRY  O5  C2   single  1.410  0.020  1.410
 RRY  C2  C1   single  1.524  0.020  1.524
 RRY  C2  O2   single  1.383  0.020  1.383
 RRY  C1  CL1  single  1.794  0.020  1.794
 RRY  O3  HO3  single  0.850  0.020  0.980
 RRY  C3  H3   single  0.970  0.020  1.090
 RRY  C4  H4   single  0.970  0.020  1.090
 RRY  O4  HO4  single  0.850  0.020  0.980
 RRY  C5  H5   single  0.970  0.020  1.090
 RRY  C6  H61  single  0.970  0.020  1.090
 RRY  C6  H62  single  0.970  0.020  1.090
 RRY  C1  H11  single  0.970  0.020  1.090
 RRY  C1  H12  single  0.970  0.020  1.090
 RRY  O2  HO2  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
 RRY  HO3  O3  C3   108.88  3.000
 RRY  H3   C3  C2   107.68  3.000
 RRY  H3   C3  C4   108.11  3.000
 RRY  C2   C3  C4   101.50  3.000
 RRY  H3   C3  O3   111.98  3.000
 RRY  C2   C3  O3   116.21  3.000
 RRY  C4   C3  O3   110.63  3.000
 RRY  H4   C4  C5   110.02  3.000
 RRY  H4   C4  O4   111.13  3.000
 RRY  C5   C4  O4   113.64  3.000
 RRY  H4   C4  C3   108.65  3.000
 RRY  C5   C4  C3   101.52  3.000
 RRY  O4   C4  C3   111.41  3.000
 RRY  HO4  O4  C4   109.04  3.000
 RRY  H5   C5  O5   109.08  3.000
 RRY  H5   C5  C6   109.41  3.000
 RRY  O5   C5  C6   110.63  3.000
 RRY  H5   C5  C4   108.87  3.000
 RRY  O5   C5  C4   106.26  3.000
 RRY  C6   C5  C4   112.50  3.000
 RRY  H62  C6  H61  109.15  3.000
 RRY  H62  C6  CL6  107.34  3.000
 RRY  H61  C6  CL6  107.18  3.000
 RRY  H62  C6  C5   111.61  3.000
 RRY  H61  C6  C5   110.35  3.000
 RRY  CL6  C6  C5   111.07  3.000
 RRY  C2   O5  C5   111.29  3.000
 RRY  O2   C2  C1   112.66  3.000
 RRY  O2   C2  O5   112.04  3.000
 RRY  C1   C2  O5   104.83  3.000
 RRY  O2   C2  C3   108.05  3.000
 RRY  C1   C2  C3   114.62  3.000
 RRY  O5   C2  C3   104.38  3.000
 RRY  H12  C1  H11  109.08  3.000
 RRY  H12  C1  CL1  107.33  3.000
 RRY  H11  C1  CL1  107.23  3.000
 RRY  H12  C1  C2   111.38  3.000
 RRY  H11  C1  C2   111.01  3.000
 RRY  CL1  C1  C2   110.65  3.000
 RRY  HO2  O2  C2   109.66  3.000

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
 RRY  chir_01  C3  O3  C4  C2  negativ
 RRY  chir_02  C4  O4  C5  C3  positiv
 RRY  chir_03  C5  O5  C4  C6  negativ
 RRY  chir_04  C2  O5  C3  C1  negativ

