# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:03:56 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: (4R)-4-hydroxy-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CN[C@@H](C1)C(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
 HYP  HYP  '(4R)-4-hydroxy-L-proline '  L-peptide  17  9  .  2014-11-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_HYP
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
 HYP  N     N  NR15   0  -0.589  -3.4851  16.5345  44.2720
 HYP  CA    C  CR15   0  -0.208  -2.9672  15.7762  43.1251
 HYP  C     C  C      0   0.389  -1.4308  15.6688  43.0501
 HYP  O     O  O      0  -0.597  -0.7428  16.4310  43.7525
 HYP  CB    C  CH2    0  -0.514  -3.4865  16.5020  41.8462
 HYP  CG    C  CR15   0   0.015  -4.5123  17.5109  42.3581
 HYP  CD    C  CH2    0  -0.340  -3.9536  17.8110  43.7501
 HYP  OD1   O  OH1    0  -0.668  -5.8332  17.0045  42.3931
 HYP  OXT   O  OC    -1  -0.625  -1.0142  14.8259  42.2259
 HYP  H     H  HNR5   0   0.337  -4.2694  16.0358  44.6717
 HYP  HA    H  HCR5   0   0.221  -3.3711  14.7608  43.1639
 HYP  HB2   H  HCH2   0   0.233  -2.6774  17.0429  41.3495
 HYP  HB3   H  HCH2   0   0.239  -3.9106  15.8192  41.1090
 HYP  HG    H  HCR5   0   0.225  -4.5567  18.4048  41.7318
 HYP  HD22  H  HCH2   0   0.233  -4.6838  18.2741  44.4161
 HYP  HD23  H  HCH2   0   0.213  -3.1098  18.5023  43.6556
 HYP  HD1   H  HOH1   0   0.436  -5.8363  16.1717  42.8760

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
 HYP  N    CA    single  1.466  0.015  1.466
 HYP  N    CD    single  1.473  0.014  1.473
 HYP  N    H     single  0.860  0.020  1.020
 HYP  CA   C     single  1.525  0.021  1.525
 HYP  CA   CB    single  1.530  0.020  1.530
 HYP  CA   HA    single  0.970  0.020  0.970
 HYP  C    O     deloc   1.231  0.020  1.231
 HYP  C    OXT   deloc   1.250  0.020  1.250
 HYP  CB   CG    single  1.527  0.020  1.527
 HYP  CB   HB2   single  0.970  0.020  1.090
 HYP  CB   HB3   single  0.970  0.020  1.090
 HYP  CG   CD    single  1.530  0.020  1.530
 HYP  CG   OD1   single  1.415  0.020  1.415
 HYP  CG   HG    single  0.970  0.020  1.090
 HYP  CD   HD22  single  0.970  0.020  1.090
 HYP  CD   HD23  single  0.970  0.020  1.090
 HYP  OD1  HD1   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
 HYP  H     N    CD    108.92  3.000
 HYP  H     N    CA    109.11  3.000
 HYP  CD    N    CA    106.62  3.000
 HYP  HA    CA   CB    109.00  3.000
 HYP  HA    CA   C     109.00  3.000
 HYP  CB    CA   C     110.10  1.900
 HYP  HA    CA   N     110.00  3.000
 HYP  CB    CA   N     103.00  1.100
 HYP  C     CA   N     112.10  2.500
 HYP  OXT   C    O     126.94  3.000
 HYP  OXT   C    CA    114.27  3.000
 HYP  O     C    CA    119.00  3.000
 HYP  HB3   CB   HB2   106.89  3.000
 HYP  HB3   CB   CG    112.28  3.000
 HYP  HB2   CB   CG    108.83  3.000
 HYP  HB3   CB   CA    113.10  3.000
 HYP  HB2   CB   CA    110.89  3.000
 HYP  CG    CB   CA    104.85  3.000
 HYP  HG    CG   OD1   105.61  3.000
 HYP  HG    CG   CD    112.09  3.000
 HYP  OD1   CG   CD    112.87  3.000
 HYP  HG    CG   CB    112.07  3.000
 HYP  OD1   CG   CB    113.51  3.000
 HYP  CD    CG   CB    100.91  3.000
 HYP  HD23  CD   HD22  107.48  3.000
 HYP  HD23  CD   CG    109.08  3.000
 HYP  HD22  CD   CG    113.21  3.000
 HYP  HD23  CD   N     109.66  3.000
 HYP  HD22  CD   N     111.62  3.000
 HYP  CG    CD   N     103.20  1.500
 HYP  HD1   OD1  CG    108.96  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
 HYP  Var_01  CG  CD  N  CA  34.45  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
 HYP  chir_01  CA  N    C   CB  positiv
 HYP  chir_02  CG  OD1  CB  CD  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
 HYP  plan-1  CA   0.020
 HYP  plan-1  C    0.020
 HYP  plan-1  O    0.020
 HYP  plan-1  OXT  0.020

