# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 15:26:01 2022
#   Inital geometry file: a 45 line input string
#   Ligand name: 2-deoxy-beta-D-erythro-pentopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@H](O)[C@H](O)CO1
#
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
 UZJ  UZJ  2-deoxy-beta-D-erythro-pentopyranose  ligand  19  9  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UZJ
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
 UZJ  C4   C  CH1   0  -0.002  23.0126   0.2220  69.5626
 UZJ  C5   C  CH2   0  -0.227  21.5524  -0.1894  69.4174
 UZJ  C1   C  CH1   0   0.261  21.2977  -0.6439  71.7274
 UZJ  C2   C  CH2   0  -0.551  22.7691  -0.3194  71.9797
 UZJ  C3   C  CH1   0   0.058  23.6102  -0.5516  70.7284
 UZJ  O1   O  OH1   0  -0.666  21.0817  -2.0217  71.5378
 UZJ  O3   O  OH1   0  -0.667  24.9535  -0.1655  70.8952
 UZJ  O4   O  OH1   0  -0.667  23.1605   1.5996  69.8164
 UZJ  O5   O  O2    0  -0.481  20.8063   0.0112  70.6030
 UZJ  H41  H  HCH1  0   0.221  23.5271  -0.0690  68.6343
 UZJ  H51  H  HCH2  0   0.216  21.5059  -1.2315  69.0818
 UZJ  H52  H  HCH2  0   0.244  21.0676   0.4144  68.6465
 UZJ  H11  H  HCH1  0   0.217  20.6944  -0.2744  72.5663
 UZJ  H22  H  HCH2  0   0.247  23.1385  -0.9261  72.8128
 UZJ  H23  H  HCH2  0   0.242  22.8482   0.7230  72.2969
 UZJ  H31  H  HCH1  0   0.207  23.5461  -1.6148  70.4574
 UZJ  H12  H  HOH1  0   0.453  21.4680  -2.5015  72.2778
 UZJ  H32  H  HOH1  0   0.447  25.3319  -0.6986  71.6014
 UZJ  H42  H  HOH1  0   0.449  22.7470   2.0870  69.0972

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
 UZJ  C5  O5   single  1.415  0.020  1.415
 UZJ  C4  O4   single  1.409  0.020  1.409
 UZJ  C4  C3   single  1.521  0.020  1.521
 UZJ  O5  C1   single  1.391  0.020  1.391
 UZJ  C3  O3   single  1.408  0.020  1.408
 UZJ  C3  C2   single  1.525  0.020  1.525
 UZJ  C1  C2   single  1.528  0.020  1.528
 UZJ  C1  O1   single  1.407  0.020  1.407
 UZJ  C4  H41  single  0.970  0.020  1.090
 UZJ  C5  H51  single  0.970  0.020  1.090
 UZJ  C5  H52  single  0.970  0.020  1.090
 UZJ  C1  H11  single  0.970  0.020  1.090
 UZJ  C2  H22  single  0.970  0.020  1.090
 UZJ  C2  H23  single  0.970  0.020  1.090
 UZJ  C3  H31  single  0.970  0.020  1.090
 UZJ  O1  H12  single  0.850  0.020  0.980
 UZJ  O3  H32  single  0.850  0.020  0.980
 UZJ  O4  H42  single  0.850  0.020  0.980
 UZJ  C4  C5   single  1.524  0.020  1.524

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
 UZJ  H41  C4  O4   111.19  3.000
 UZJ  H41  C4  C3   109.16  3.000
 UZJ  O4   C4  C3   108.54  3.000
 UZJ  H41  C4  C5   107.23  3.000
 UZJ  C3   C4  C5   108.18  3.000
 UZJ  O4   C4  C5   112.45  3.000
 UZJ  H52  C5  H51  106.90  3.000
 UZJ  H52  C5  O5   106.19  3.000
 UZJ  H51  C5  O5   111.66  3.000
 UZJ  H52  C5  C4   110.07  3.000
 UZJ  H51  C5  C4   109.06  3.000
 UZJ  O5   C5  C4   112.77  3.000
 UZJ  H11  C1  O5   105.37  3.000
 UZJ  H11  C1  O1   110.38  3.000
 UZJ  O5   C1  O1   107.33  3.000
 UZJ  H11  C1  C2   109.38  3.000
 UZJ  O1   C1  C2   112.21  3.000
 UZJ  O5   C1  C2   111.94  3.000
 UZJ  H23  C2  H22  106.46  3.000
 UZJ  H23  C2  C3   110.09  3.000
 UZJ  H22  C2  C3   110.72  3.000
 UZJ  H23  C2  C1   108.69  3.000
 UZJ  H22  C2  C1   109.44  3.000
 UZJ  C3   C2  C1   111.30  3.000
 UZJ  H31  C3  O3   110.50  3.000
 UZJ  H31  C3  C2   108.50  3.000
 UZJ  O3   C3  C2   112.78  3.000
 UZJ  H31  C3  C4   106.27  3.000
 UZJ  C2   C3  C4   109.54  3.000
 UZJ  O3   C3  C4   109.04  3.000
 UZJ  H12  O1  C1   108.82  3.000
 UZJ  H32  O3  C3   108.08  3.000
 UZJ  H42  O4  C4   108.40  3.000
 UZJ  C1   O5  C5   115.10  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
 UZJ  Var_01  H51  C5  O5  C1  66.03  30.0  1

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
 UZJ  chir_01  C4  O4  C3  C5  negativ
 UZJ  chir_02  C1  O5  O1  C2  negativ
 UZJ  chir_03  C3  O3  C4  C2  positiv

