# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 14:48:37 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: (4R)-4-hydroxy-D-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
 UYA  UYA  '(4R)-4-hydroxy-D-proline '  D-peptide  17  9  .  2022-08-11  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_UYA
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
 UYA  N    N  NH1    0  -0.610  -22.8821  74.4399  103.0719
 UYA  CA   C  CH1    0  -0.195  -22.1299  73.5611  102.1715
 UYA  C    C  C      0   0.400  -22.2633  73.9660  100.6836
 UYA  OXT  O  OC    -1  -0.599  -22.9786  74.9529  100.4150
 UYA  CB   C  CH2    0  -0.492  -20.6649  73.5932  102.6652
 UYA  CG   C  CH1    0   0.021  -20.5657  74.8997  103.4323
 UYA  CD   C  CH2    0  -0.330  -21.9521  74.9519  104.0714
 UYA  OD1  O  OH1    0  -0.668  -20.3578  75.9467  102.5049
 UYA  O    O  O      0  -0.610  -21.6472  73.2451   99.8755
 UYA  H    H  HNH1   0   0.333  -23.2147  75.2047  102.4948
 UYA  HA   H  HCH1   0   0.210  -22.5014  72.5314  102.2471
 UYA  HB2  H  HCH2   0   0.228  -20.4722  72.7696  103.3565
 UYA  HB3  H  HCH2   0   0.237  -19.9385  73.5100  101.8568
 UYA  HG2  H  HCH1   0   0.198  -19.7693  74.8793  104.1879
 UYA  HD2  H  HCH2   0   0.230  -22.2396  75.9528  104.4047
 UYA  HD3  H  HCH2   0   0.203  -21.9496  74.3116  104.9610
 UYA  H10  H  HOH1   0   0.442  -20.4510  76.7840  102.9697

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
 UYA  O    C    deloc   1.231  0.020  1.231
 UYA  OXT  C    deloc   1.248  0.020  1.248
 UYA  C    CA   single  1.525  0.021  1.525
 UYA  CA   CB   single  1.521  0.033  1.521
 UYA  CA   N    single  1.458  0.019  1.458
 UYA  OD1  CG   single  1.414  0.020  1.414
 UYA  CB   CG   single  1.518  0.020  1.518
 UYA  N    CD   single  1.473  0.014  1.473
 UYA  CG   CD   single  1.528  0.020  1.528
 UYA  N    H    single  0.860  0.020  0.860
 UYA  CA   HA   single  0.970  0.020  0.970
 UYA  CB   HB2  single  0.970  0.020  1.090
 UYA  CB   HB3  single  0.970  0.020  1.090
 UYA  CG   HG2  single  0.970  0.020  1.090
 UYA  CD   HD2  single  0.970  0.020  1.090
 UYA  CD   HD3  single  0.970  0.020  1.090
 UYA  OD1  H10  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
 UYA  H    N    CD   109.54  3.000
 UYA  H    N    CA   114.00  3.000
 UYA  CD   N    CA   107.71  3.000
 UYA  HA   CA   CB   109.00  3.000
 UYA  HA   CA   C    110.00  3.000
 UYA  CB   CA   C    110.50  1.500
 UYA  HA   CA   N    110.00  3.000
 UYA  CB   CA   N    110.40  1.500
 UYA  C    CA   N    111.00  2.800
 UYA  O    C    OXT  126.97  3.000
 UYA  OXT  C    CA   120.80  1.700
 UYA  O    C    CA   120.80  1.700
 UYA  HB3  CB   HB2  107.11  3.000
 UYA  HB3  CB   CG   113.38  3.000
 UYA  HB2  CB   CG   108.52  3.000
 UYA  HB3  CB   CA   113.14  3.000
 UYA  HB2  CB   CA   110.71  3.000
 UYA  CG   CB   CA   103.95  3.000
 UYA  HG2  CG   OD1  111.01  3.000
 UYA  HG2  CG   CD   111.77  3.000
 UYA  OD1  CG   CD   112.49  3.000
 UYA  HG2  CG   CB   112.28  3.000
 UYA  CD   CG   CB   100.46  3.000
 UYA  OD1  CG   CB   108.39  3.000
 UYA  HD3  CD   HD2  106.74  3.000
 UYA  HD3  CD   CG   108.52  3.000
 UYA  HD2  CD   CG   113.42  3.000
 UYA  HD3  CD   N    110.65  3.000
 UYA  HD2  CD   N    111.26  3.000
 UYA  CG   CD   N    103.20  1.500
 UYA  H10  OD1  CG   108.26  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
 UYA  Var_01  CG  CD  N  CA  25.05  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
 UYA  chir_01  CA  C    CB  N   negativ
 UYA  chir_02  CG  OD1  CD  CB  negativ

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
 UYA  plan-1  CA   0.020
 UYA  plan-1  C    0.020
 UYA  plan-1  OXT  0.020
 UYA  plan-1  O    0.020

