# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 14:58:27 2022
#   Inital geometry file: a 46 line input string
#   Ligand name: (4S)-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
 UY7  UY7  '(4S)-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_UY7
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
 UY7  CB   C  CH2    0  -0.479  -20.7304  74.0064  103.0681
 UY7  CG   C  CH1    0   0.008  -20.9043  74.4546  104.5081
 UY7  CD   C  CH2    0  -0.296  -22.2094  75.2418  104.4220
 UY7  CA   C  CH1    0  -0.181  -22.1655  73.6762  102.6274
 UY7  C    C  C      0   0.392  -22.3590  73.8827  101.1122
 UY7  N    N  NH1    0  -0.623  -23.0326  74.5116  103.4604
 UY7  OXT  O  OC    -1  -0.597  -23.1741  74.7534  100.7449
 UY7  O    O  O      0  -0.611  -21.6618  73.1516  100.3817
 UY7  O09  O  OH1    0  -0.675  -21.0176  73.3011  105.3191
 UY7  HB2  H  HCH2   0   0.236  -20.0377  73.1713  102.9604
 UY7  HB3  H  HCH2   0   0.225  -20.3294  74.8432  102.4893
 UY7  HG2  H  HCH1   0   0.212  -20.0790  75.0923  104.8506
 UY7  HD2  H  HCH2   0   0.201  -21.9819  76.2650  104.0976
 UY7  HD3  H  HCH2   0   0.211  -22.6948  75.3256  105.4013
 UY7  HA   H  HCH1   0   0.202  -22.3589  72.6155  102.8353
 UY7  H    H  HNH1   0   0.333  -23.5209  75.1482  102.8433
 UY7  H10  H  HOH1   0   0.443  -21.3032  73.5761  106.1957

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
 UY7  O    C    deloc   1.231  0.020  1.231
 UY7  OXT  C    deloc   1.248  0.020  1.248
 UY7  C    CA   single  1.525  0.021  1.525
 UY7  CA   CB   single  1.521  0.033  1.521
 UY7  CA   N    single  1.458  0.019  1.458
 UY7  CB   CG   single  1.518  0.020  1.518
 UY7  N    CD   single  1.473  0.014  1.473
 UY7  CD   CG   single  1.527  0.020  1.527
 UY7  CG   O09  single  1.415  0.020  1.415
 UY7  CB   HB2  single  0.970  0.020  1.090
 UY7  CB   HB3  single  0.970  0.020  1.090
 UY7  CG   HG2  single  0.970  0.020  1.090
 UY7  CD   HD2  single  0.970  0.020  1.090
 UY7  CD   HD3  single  0.970  0.020  1.090
 UY7  CA   HA   single  0.970  0.020  0.970
 UY7  N    H    single  0.860  0.020  0.860
 UY7  O09  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
 UY7  HB3  CB   HB2  107.51  3.000
 UY7  HB3  CB   CA   110.80  3.000
 UY7  HB2  CB   CA   113.60  3.000
 UY7  HB3  CB   CG   108.55  3.000
 UY7  HB2  CB   CG   113.11  3.000
 UY7  CA   CB   CG   103.20  3.000
 UY7  HG2  CG   O09  110.79  3.000
 UY7  HG2  CG   CD   111.15  3.000
 UY7  O09  CG   CD   112.60  3.000
 UY7  HG2  CG   CB   112.42  3.000
 UY7  O09  CG   CB   108.19  3.000
 UY7  CD   CG   CB   101.34  3.000
 UY7  HD3  CD   HD2  106.53  3.000
 UY7  HD3  CD   N    112.13  3.000
 UY7  HD2  CD   N    112.84  3.000
 UY7  HD3  CD   CG   111.57  3.000
 UY7  HD2  CD   CG   108.68  3.000
 UY7  N    CD   CG   103.20  1.500
 UY7  HA   CA   N    110.00  3.000
 UY7  HA   CA   C    110.00  3.000
 UY7  N    CA   C    111.00  2.800
 UY7  HA   CA   CB   109.00  3.000
 UY7  N    CA   CB   110.40  1.500
 UY7  C    CA   CB   110.50  1.500
 UY7  O    C    OXT  127.02  3.000
 UY7  OXT  C    CA   120.80  1.700
 UY7  O    C    CA   120.80  1.700
 UY7  H    N    CA   114.00  3.000
 UY7  H    N    CD   111.03  3.000
 UY7  CA   N    CD   109.02  3.000
 UY7  H10  O09  CG   108.25  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
 UY7  Var_01  CA  N  CD  CG  -20.73  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
 UY7  chir_01  CG  CB  CD  O09  negativ
 UY7  chir_02  CA  N   CB  C    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
 UY7  plan-1  CA   0.020
 UY7  plan-1  C    0.020
 UY7  plan-1  OXT  0.020
 UY7  plan-1  O    0.020

