# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 18:55:35 2021
#   Inital geometry file: a 53 line input string
#   Ligand name: 4-chloro-4-deoxy-alpha-D-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@H]1Cl
#
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
 RRJ  RRJ  4-chloro-4-deoxy-alpha-D-galactopyranose  D-saccharide  23  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_RRJ
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
 RRJ  O1   O   OH1   0  -0.665  -66.0123  -19.8444  185.1313
 RRJ  C1   C   CH1   0   0.213  -65.5474  -18.6654  184.5669
 RRJ  O5   O   O2    0  -0.500  -66.1752  -17.5255  185.0954
 RRJ  C5   C   CH1   0   0.051  -65.9690  -17.3158  186.4754
 RRJ  C6   C   CH2   0  -0.159  -66.8157  -16.1399  186.9145
 RRJ  O6   O   OH1   0  -0.701  -68.1672  -16.5256  186.8662
 RRJ  C4   C   CH1   0  -0.388  -64.4904  -17.1443  186.7869
 RRJ  CL4  CL  CL    0  -0.139  -63.8557  -15.6217  186.0580
 RRJ  C3   C   CH1   0   0.037  -63.7165  -18.3418  186.2622
 RRJ  O3   O   OH1   0  -0.607  -62.3517  -18.1454  186.4845
 RRJ  C2   C   CH1   0  -0.022  -64.0337  -18.5754  184.7883
 RRJ  O2   O   OH1   0  -0.657  -63.3558  -19.7451  184.4034
 RRJ  H1   H   HCH1  0   0.184  -65.7681  -18.6246  183.4930
 RRJ  H5   H   HCH1  0   0.218  -66.2947  -18.1910  187.0568
 RRJ  H61  H   HCH2  0   0.245  -66.5091  -15.8623  187.9318
 RRJ  H62  H   HCH2  0   0.267  -66.6146  -15.2777  186.2696
 RRJ  HO6  H   HOH1  0   0.435  -68.6995  -15.7629  187.1022
 RRJ  H4   H   HCH1  0   0.345  -64.3455  -17.0480  187.8638
 RRJ  H3   H   HCH1  0   0.267  -64.0876  -19.2067  186.8360
 RRJ  HO3  H   HOH1  0   0.414  -61.8817  -18.8830  186.0834
 RRJ  H2   H   HCH1  0   0.301  -63.6764  -17.7069  184.2198
 RRJ  HO2  H   HOH1  0   0.410  -63.3181  -19.7850  183.4449
 RRJ  HO1  H   HOH1  0   0.449  -66.9123  -19.9997  184.8300

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
 RRJ  O1  C1   single  1.387  0.020  1.387
 RRJ  C1  C2   single  1.532  0.020  1.532
 RRJ  C1  O5   single  1.405  0.020  1.405
 RRJ  O5  C5   single  1.411  0.020  1.411
 RRJ  C5  C4   single  1.521  0.020  1.521
 RRJ  C5  C6   single  1.514  0.020  1.514
 RRJ  C6  O6   single  1.406  0.020  1.406
 RRJ  C4  C3   single  1.519  0.020  1.519
 RRJ  C4  CL4  single  1.803  0.020  1.803
 RRJ  C3  C2   single  1.526  0.020  1.526
 RRJ  C3  O3   single  1.397  0.020  1.397
 RRJ  C2  O2   single  1.406  0.020  1.406
 RRJ  C1  H1   single  0.970  0.020  1.090
 RRJ  C5  H5   single  0.970  0.020  1.090
 RRJ  C6  H61  single  0.970  0.020  1.090
 RRJ  C6  H62  single  0.970  0.020  1.090
 RRJ  O6  HO6  single  0.850  0.020  0.980
 RRJ  C4  H4   single  0.970  0.020  1.090
 RRJ  C3  H3   single  0.970  0.020  1.090
 RRJ  O3  HO3  single  0.850  0.020  0.980
 RRJ  C2  H2   single  0.970  0.020  1.090
 RRJ  O2  HO2  single  0.850  0.020  0.980
 RRJ  O1  HO1  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
 RRJ  HO1  O1  C1   108.86  3.000
 RRJ  H1   C1  C2   109.75  3.000
 RRJ  H1   C1  O5   104.37  3.000
 RRJ  C2   C1  O5   109.84  3.000
 RRJ  H1   C1  O1   111.25  3.000
 RRJ  O5   C1  O1   112.76  3.000
 RRJ  C2   C1  O1   108.79  3.000
 RRJ  C5   O5  C1   115.04  3.000
 RRJ  H5   C5  C4   105.63  3.000
 RRJ  H5   C5  C6   107.40  3.000
 RRJ  C4   C5  C6   113.37  3.000
 RRJ  H5   C5  O5   110.82  3.000
 RRJ  C6   C5  O5   108.50  3.000
 RRJ  C4   C5  O5   111.05  3.000
 RRJ  H62  C6  H61  107.17  3.000
 RRJ  H62  C6  O6   111.84  3.000
 RRJ  H61  C6  O6   111.69  3.000
 RRJ  H62  C6  C5   109.75  3.000
 RRJ  H61  C6  C5   107.99  3.000
 RRJ  O6   C6  C5   108.33  3.000
 RRJ  HO6  O6  C6   107.86  3.000
 RRJ  H4   C4  C3   110.05  3.000
 RRJ  H4   C4  CL4  106.12  3.000
 RRJ  C3   C4  CL4  110.28  3.000
 RRJ  H4   C4  C5   109.96  3.000
 RRJ  CL4  C4  C5   110.77  3.000
 RRJ  C3   C4  C5   109.61  3.000
 RRJ  H3   C3  C2   108.22  3.000
 RRJ  H3   C3  O3   110.88  3.000
 RRJ  C2   C3  O3   112.24  3.000
 RRJ  H3   C3  C4   105.50  3.000
 RRJ  O3   C3  C4   109.39  3.000
 RRJ  C2   C3  C4   110.39  3.000
 RRJ  HO3  O3  C3   107.65  3.000
 RRJ  H2   C2  O2   111.08  3.000
 RRJ  H2   C2  C3   108.15  3.000
 RRJ  O2   C2  C3   106.96  3.000
 RRJ  H2   C2  C1   107.04  3.000
 RRJ  O2   C2  C1   112.82  3.000
 RRJ  C3   C2  C1   110.73  3.000
 RRJ  HO2  O2  C2   109.08  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
 RRJ  chir_01  C1  O1   C2  O5  positiv
 RRJ  chir_02  C5  O5   C6  C4  positiv
 RRJ  chir_03  C4  CL4  C5  C3  negativ
 RRJ  chir_04  C3  O3   C4  C2  negativ
 RRJ  chir_05  C2  O2   C3  C1  positiv

