# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 13:16:36 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: (3S)-3-hydroxy-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCN[C@@H]1C(O)=O
#
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
 HY3  HY3  '(3S)-3-hydroxy-L-proline '  L-peptide  18  9  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_HY3
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
 HY3  C1   C  C     0   0.549  -1.2891  -0.4784  -0.2681
 HY3  O1   O  O     0  -0.431  -1.3031  -1.5564  -0.8030
 HY3  N1   N  NH1   0  -0.583   0.6472  -1.0792   1.0888
 HY3  C2   C  CH1   0  -0.280  -0.2115   0.0105   0.6775
 HY3  C3   C  CH1   0   0.042   0.7079   1.0164  -0.0414
 HY3  C4   C  CH2   0  -0.534   1.6388   0.0695  -0.7910
 HY3  C5   C  CH2   0  -0.281   1.7712  -1.1477   0.1435
 HY3  O2   O  OH1   0  -0.669   1.3736   1.7368   0.9710
 HY3  OXT  O  OH1   0  -0.595  -2.2258   0.4458  -0.4559
 HY3  H    H  HNH1  0   0.362   0.9964  -0.8790   2.0145
 HY3  HN   H  HCH1  0   0.299  -0.7014   0.4703   1.5405
 HY3  HB   H  HCH1  0   0.231   0.1678   1.6906  -0.7163
 HY3  HG   H  HCH2  0   0.245   1.1841  -0.2149  -1.7420
 HY3  HGA  H  HCH2  0   0.258   2.5994   0.5297  -1.0284
 HY3  HD   H  HCH2  0   0.231   2.7171  -1.1340   0.6863
 HY3  HDA  H  HCH2  0   0.223   1.7454  -2.0765  -0.4290
 HY3  HO1  H  HOH1  0   0.453   2.0901   2.2329   0.5629
 HY3  HXT  H  HOH1  0   0.481  -2.8930   0.1226  -1.0797

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
 HY3  C1   O1   double  1.204  0.020  1.204
 HY3  C1   C2   single  1.515  0.020  1.515
 HY3  C1   OXT  single  1.329  0.020  1.329
 HY3  N1   C2   single  1.447  0.020  1.447
 HY3  N1   C5   single  1.470  0.020  1.470
 HY3  N1   H    single  0.890  0.020  1.040
 HY3  C2   C3   single  1.541  0.020  1.541
 HY3  C2   HN   single  0.970  0.020  1.090
 HY3  C3   C4   single  1.525  0.020  1.525
 HY3  C3   O2   single  1.410  0.020  1.410
 HY3  C3   HB   single  0.970  0.020  1.090
 HY3  C4   C5   single  1.540  0.020  1.540
 HY3  C4   HG   single  0.970  0.020  1.090
 HY3  C4   HGA  single  0.970  0.020  1.090
 HY3  C5   HD   single  0.970  0.020  1.090
 HY3  C5   HDA  single  0.970  0.020  1.090
 HY3  O2   HO1  single  0.850  0.020  0.980
 HY3  OXT  HXT  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
 HY3  OXT  C1   C2  111.42  3.000
 HY3  OXT  C1   O1  123.49  3.000
 HY3  C2   C1   O1  125.09  3.000
 HY3  H    N1   C5  109.53  3.000
 HY3  H    N1   C2  108.46  3.000
 HY3  C5   N1   C2  107.82  3.000
 HY3  HN   C2   C3  111.16  3.000
 HY3  HN   C2   N1  110.98  3.000
 HY3  C3   C2   N1  105.67  3.000
 HY3  HN   C2   C1  108.04  3.000
 HY3  C3   C2   C1  110.12  3.000
 HY3  N1   C2   C1  110.89  3.000
 HY3  HB   C3   O2  111.13  3.000
 HY3  HB   C3   C4  112.33  3.000
 HY3  O2   C3   C4  112.46  3.000
 HY3  HB   C3   C2  113.25  3.000
 HY3  O2   C3   C2  106.28  3.000
 HY3  C4   C3   C2  100.85  3.000
 HY3  HGA  C4   HG  106.67  3.000
 HY3  HGA  C4   C5  112.93  3.000
 HY3  HG   C4   C5  111.00  3.000
 HY3  HGA  C4   C3  112.49  3.000
 HY3  HG   C4   C3  109.61  3.000
 HY3  C5   C4   C3  104.18  3.000
 HY3  HDA  C5   HD  106.99  3.000
 HY3  HDA  C5   C4  110.62  3.000
 HY3  HD   C5   C4  111.50  3.000
 HY3  HDA  C5   N1  111.03  3.000
 HY3  HD   C5   N1  110.03  3.000
 HY3  C4   C5   N1  106.71  3.000
 HY3  HO1  O2   C3  108.10  3.000
 HY3  HXT  OXT  C1  110.14  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
 HY3  CONST_01  HXT  OXT  C1  C2  180.00   0.0  0
 HY3  Var_01    C3   C4   C5  N1   18.19  30.0  1
 HY3  Var_02    C4   C5   N1  C2    6.17  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
 HY3  chir_01  C2  C1  N1  C3  negativ
 HY3  chir_02  C3  O2  C2  C4  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 HY3  plan-1  C1   0.020
 HY3  plan-1  O1   0.020
 HY3  plan-1  C2   0.020
 HY3  plan-1  OXT  0.020
 HY3  plan-1  HXT  0.020

