# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 11:00:40 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2R,3R,4R,5S)-2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1N[C@H](CO)[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
 DIG  DIG  (2R,3R,4R,5S)-2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol  saccharide  24  11  .  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_DIG
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
 DIG  C1   C  CH2   0  -0.147   0.4675   0.0174   2.5125
 DIG  O1   O  OH1   0  -0.676   1.7221  -0.5712   2.7944
 DIG  C2   C  CH1   0  -0.125   0.0466  -0.4336   1.1318
 DIG  C3   C  CH1   0   0.031  -1.3527   0.0023   0.6952
 DIG  O3   O  OH1   0  -0.675  -1.6436   1.2701   1.2373
 DIG  C4   C  CH1   0   0.009  -1.2522   0.0255  -0.8543
 DIG  O4   O  OH1   0  -0.670  -2.0540  -0.9212  -1.5143
 DIG  C5   C  CH1   0  -0.110   0.2219  -0.2696  -1.1557
 DIG  C6   C  CH2   0  -0.149   0.7364   0.4870  -2.3587
 DIG  O6   O  OH1   0  -0.674   2.0755   0.1115  -2.5934
 DIG  N5   N  NH1   0  -0.616   0.8889   0.1082   0.0765
 DIG  H11  H  HCH2  0   0.194  -0.2929  -0.2944   3.2407
 DIG  H12  H  HCH2  0   0.197   0.5260   1.1099   2.5450
 DIG  HO1  H  HOH1  0   0.455   2.0455  -0.2039   3.6217
 DIG  H2   H  HCH1  0   0.216   0.0491  -1.5380   1.1236
 DIG  H3   H  HCH1  0   0.219  -2.0963  -0.7405   1.0101
 DIG  HO3  H  HOH1  0   0.452  -2.5449   1.5031   0.9946
 DIG  H4   H  HCH1  0   0.215  -1.4919   1.0459  -1.1879
 DIG  HO4  H  HOH1  0   0.453  -2.9722  -0.6425  -1.4477
 DIG  H5   H  HCH1  0   0.212   0.3070  -1.3523  -1.3539
 DIG  H61  H  HCH2  0   0.196   0.0956   0.2583  -3.2208
 DIG  H62  H  HCH2  0   0.189   0.6464   1.5634  -2.1609
 DIG  HO6  H  HOH1  0   0.455   2.4101   0.6292  -3.3309
 DIG  HN5  H  HNH1  0   0.349   1.8306  -0.2576   0.1195

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
 DIG  C1  O1   single  1.414  0.020  1.414
 DIG  C1  C2   single  1.512  0.020  1.512
 DIG  C1  H11  single  0.970  0.020  1.090
 DIG  C1  H12  single  0.970  0.020  1.090
 DIG  O1  HO1  single  0.850  0.020  0.980
 DIG  C2  C3   single  1.529  0.020  1.529
 DIG  C2  N5   single  1.455  0.020  1.455
 DIG  C2  H2   single  0.970  0.020  1.090
 DIG  C3  O3   single  1.409  0.020  1.409
 DIG  C3  C4   single  1.553  0.020  1.553
 DIG  C3  H3   single  0.970  0.020  1.090
 DIG  O3  HO3  single  0.850  0.020  0.980
 DIG  C4  O4   single  1.405  0.020  1.405
 DIG  C4  C5   single  1.533  0.020  1.533
 DIG  C4  H4   single  0.970  0.020  1.090
 DIG  O4  HO4  single  0.850  0.020  0.980
 DIG  C5  C6   single  1.511  0.020  1.511
 DIG  C5  N5   single  1.451  0.020  1.451
 DIG  C5  H5   single  0.970  0.020  1.090
 DIG  C6  O6   single  1.410  0.020  1.410
 DIG  C6  H61  single  0.970  0.020  1.090
 DIG  C6  H62  single  0.970  0.020  1.090
 DIG  O6  HO6  single  0.850  0.020  0.980
 DIG  N5  HN5  single  0.890  0.020  1.040

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
 DIG  H12  C1  H11  107.50  3.000
 DIG  H12  C1  C2   109.86  3.000
 DIG  H11  C1  C2   109.15  3.000
 DIG  H12  C1  O1   111.23  3.000
 DIG  H11  C1  O1   111.35  3.000
 DIG  C2   C1  O1   107.75  3.000
 DIG  HO1  O1  C1   108.12  3.000
 DIG  H2   C2  N5   111.45  3.000
 DIG  H2   C2  C3   106.56  3.000
 DIG  N5   C2  C3   102.50  3.000
 DIG  H2   C2  C1   107.72  3.000
 DIG  N5   C2  C1   112.96  3.000
 DIG  C3   C2  C1   115.49  3.000
 DIG  H3   C3  C4   109.90  3.000
 DIG  H3   C3  O3   111.02  3.000
 DIG  C4   C3  O3   112.57  3.000
 DIG  H3   C3  C2   110.20  3.000
 DIG  C4   C3  C2   103.29  3.000
 DIG  O3   C3  C2   109.60  3.000
 DIG  HO3  O3  C3   108.31  3.000
 DIG  H4   C4  C5   109.17  3.000
 DIG  H4   C4  O4   110.99  3.000
 DIG  C5   C4  O4   109.06  3.000
 DIG  H4   C4  C3   107.60  3.000
 DIG  C5   C4  C3   104.80  3.000
 DIG  O4   C4  C3   114.94  3.000
 DIG  HO4  O4  C4   108.48  3.000
 DIG  H5   C5  N5   111.86  3.000
 DIG  H5   C5  C6   108.77  3.000
 DIG  N5   C5  C6   112.90  3.000
 DIG  H5   C5  C4   107.34  3.000
 DIG  N5   C5  C4   102.99  3.000
 DIG  C6   C5  C4   112.79  3.000
 DIG  H62  C6  H61  107.32  3.000
 DIG  H62  C6  O6   111.64  3.000
 DIG  H61  C6  O6   111.59  3.000
 DIG  H62  C6  C5   108.63  3.000
 DIG  H61  C6  C5   108.78  3.000
 DIG  O6   C6  C5   108.80  3.000
 DIG  HO6  O6  C6   108.35  3.000
 DIG  HN5  N5  C5   111.71  3.000
 DIG  HN5  N5  C2   111.94  3.000
 DIG  C5   N5  C2   104.65  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
 DIG  chir_01  C2  C1  C3  N5  negativ
 DIG  chir_02  C3  O3  C4  C2  negativ
 DIG  chir_03  C4  O4  C3  C5  negativ
 DIG  chir_04  C5  N5  C4  C6  negativ

