# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 14:40:59 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  17  9  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.389  -1.5833  -0.2341  -0.0313
 HY3  O1   O  O      0  -0.610  -2.1305  -1.3511  -0.0928
 HY3  N1   N  NH1    0  -0.610   0.5880  -1.4630   0.2200
 HY3  C2   C  CH1    0  -0.207  -0.1065  -0.1971   0.3896
 HY3  C3   C  CH1    0   0.044   0.7742   0.8175  -0.3652
 HY3  C4   C  CH2    0  -0.476   2.0957   0.0601  -0.6038
 HY3  C5   C  CH2    0  -0.288   1.9982  -1.1430   0.3271
 HY3  O2   O  OH1    0  -0.682   0.9252   1.9708   0.4379
 HY3  OXT  O  OC    -1  -0.614  -2.1216   0.8736  -0.2337
 HY3  H    H  HNH1   0   0.338   0.2861  -2.1481   0.8983
 HY3  HN   H  HCH1   0   0.206  -0.0917   0.1296   1.4464
 HY3  HB   H  HCH1   0   0.203   0.3194   1.0873  -1.3248
 HY3  HG   H  HCH2   0   0.226   2.1476  -0.2841  -1.6386
 HY3  HGA  H  HCH2   0   0.231   2.9737   0.6823  -0.4214
 HY3  HD   H  HCH2   0   0.186   2.3063  -0.8587   1.3461
 HY3  HDA  H  HCH2   0   0.222   2.6250  -1.9812   0.0151
 HY3  HO1  H  HOH1   0   0.443   1.4488   2.6082  -0.0567

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   deloc   1.245  0.020  1.245
 HY3  C1  C2   single  1.536  0.020  1.536
 HY3  C1  OXT  deloc   1.248  0.020  1.248
 HY3  N1  C2   single  1.454  0.020  1.454
 HY3  N1  C5   single  1.450  0.020  1.450
 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  1.542  0.020  1.542
 HY3  C3  O2   single  1.413  0.020  1.413
 HY3  C3  HB   single  0.970  0.020  1.090
 HY3  C4  C5   single  1.524  0.020  1.524
 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

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  115.95  3.000
 HY3  OXT  C1  O1  126.77  3.000
 HY3  C2   C1  O1  117.23  3.000
 HY3  H    N1  C5  112.99  3.000
 HY3  H    N1  C2  111.69  3.000
 HY3  C5   N1  C2  105.30  3.000
 HY3  HN   C2  C3  105.42  3.000
 HY3  HN   C2  N1  111.24  3.000
 HY3  C3   C2  N1  104.07  3.000
 HY3  HN   C2  C1  106.36  3.000
 HY3  C3   C2  C1  115.54  3.000
 HY3  N1   C2  C1  113.97  3.000
 HY3  HB   C3  O2  109.94  3.000
 HY3  HB   C3  C4  109.95  3.000
 HY3  O2   C3  C4  113.41  3.000
 HY3  HB   C3  C2  110.72  3.000
 HY3  O2   C3  C2  108.66  3.000
 HY3  C4   C3  C2  104.02  3.000
 HY3  HGA  C4  HG  107.45  3.000
 HY3  HGA  C4  C5  113.53  3.000
 HY3  HG   C4  C5  109.46  3.000
 HY3  HGA  C4  C3  112.56  3.000
 HY3  HG   C4  C3  110.02  3.000
 HY3  C5   C4  C3  103.79  3.000
 HY3  HDA  C5  HD  107.56  3.000
 HY3  HDA  C5  C4  113.24  3.000
 HY3  HD   C5  C4  110.08  3.000
 HY3  HDA  C5  N1  111.57  3.000
 HY3  HD   C5  N1  113.41  3.000
 HY3  C4   C5  N1  101.03  3.000
 HY3  HO1  O2  C3  107.87  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  Var_01  C3  C4  C5  N1   37.19  30.0  1
 HY3  Var_02  C4  C5  N1  C2  -47.80  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

