# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:56:56 2021
#   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  18  9  .  2022-08-11  2022-11-18
;
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  NR15  0  -0.614  -22.8425  74.1126  103.2179
 UYA  CA   C  CR15  0  -0.213  -22.0871  73.4908  102.1533
 UYA  C    C  C     0   0.539  -22.0946  74.1865  100.7977
 UYA  OXT  O  OH1   0  -0.590  -22.9726  75.1750  100.7097
 UYA  CB   C  CH2   0  -0.472  -20.6718  73.4537  102.7330
 UYA  CG   C  CR15  0  -0.011  -20.5667  74.8251  103.3802
 UYA  CD   C  CH2   0  -0.282  -21.9682  75.0169  103.9687
 UYA  OD1  O  OH1   0  -0.667  -20.2819  75.7455  102.3447
 UYA  O    O  O     0  -0.460  -21.4134  73.8236   99.8691
 UYA  H    H  HNR5  0   0.359  -23.6961  74.5520  102.9097
 UYA  HA   H  HCR5  0   0.285  -22.4498  72.4751  101.9558
 UYA  HXT  H  HOH1  0   0.479  -22.9573  75.5507   99.8167
 UYA  HB2  H  HCH2  0   0.261  -20.6128  72.6746  103.4947
 UYA  HB3  H  HCH2  0   0.260  -19.8951  73.2627  101.9940
 UYA  HG2  H  HCR5  0   0.229  -19.7984  74.8616  104.1606
 UYA  HD2  H  HCH2  0   0.230  -22.2838  76.0627  103.9042
 UYA  HD3  H  HCH2  0   0.218  -21.9653  74.7540  105.0309
 UYA  H10  H  HOH1  0   0.451  -20.4270  76.6371  102.6764

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    double  1.231  0.020  1.231
 UYA  OXT  C    single  1.325  0.020  1.325
 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  1.520  0.020  1.520
 UYA  N    CD   single  1.473  0.014  1.473
 UYA  CG   CD   single  1.532  0.020  1.532
 UYA  N    H    single  0.860  0.020  0.860
 UYA  CA   HA   single  0.970  0.020  0.970
 UYA  OXT  HXT  single  0.850  0.020  0.980
 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   113.13  3.000
 UYA  H    N    CA   114.00  3.000
 UYA  CD   N    CA   109.34  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  123.16  3.000
 UYA  OXT  C    CA   120.80  1.700
 UYA  O    C    CA   120.80  1.700
 UYA  HXT  OXT  C    109.88  3.000
 UYA  HB3  CB   HB2  108.06  3.000
 UYA  HB3  CB   CG   113.44  3.000
 UYA  HB2  CB   CG   110.07  3.000
 UYA  HB3  CB   CA   114.01  3.000
 UYA  HB2  CB   CA   109.38  3.000
 UYA  CG   CB   CA   101.74  3.000
 UYA  HG2  CG   OD1  111.01  3.000
 UYA  HG2  CG   CD   111.32  3.000
 UYA  OD1  CG   CD   112.58  3.000
 UYA  HG2  CG   CB   112.45  3.000
 UYA  CD   CG   CB   102.31  3.000
 UYA  OD1  CG   CB   106.82  3.000
 UYA  HD3  CD   HD2  106.72  3.000
 UYA  HD3  CD   CG   109.90  3.000
 UYA  HD2  CD   CG   111.15  3.000
 UYA  HD3  CD   N    110.53  3.000
 UYA  HD2  CD   N    112.81  3.000
 UYA  CG   CD   N    103.20  1.500
 UYA  H10  OD1  CG   108.68  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  CONST_01  HXT  OXT  C  CA  180.00   0.0  0
 UYA  Var_01    CG   CD   N  CA   -5.07  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
 UYA  plan-1  HXT  0.020

