# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 03:50:19 2021
#   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  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_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  -0.510  -20.7281  73.8834  103.1168
 UY7  CG   C  CH1   0   0.030  -20.9348  74.5223  104.4858
 UY7  CD   C  CH2   0  -0.303  -22.2772  75.2191  104.3038
 UY7  CA   C  CH1   0  -0.161  -22.1622  73.6073  102.5836
 UY7  C    C  C     0   0.509  -22.2472  74.1074  101.1560
 UY7  N    N  NH1   0  -0.613  -23.0359  74.2368  103.5525
 UY7  OXT  O  OH1   0  -0.584  -22.7204  75.3419  101.0562
 UY7  O    O  O     0  -0.452  -21.8864  73.4553  100.2064
 UY7  O09  O  OH1   0  -0.674  -20.9789  73.4981  105.4549
 UY7  HB2  H  HCH2  0   0.269  -20.1265  72.9769  103.1662
 UY7  HB3  H  HCH2  0   0.262  -20.1943  74.5873  102.4766
 UY7  HG2  H  HCH1  0   0.225  -20.1417  75.2455  104.7091
 UY7  HD2  H  HCH2  0   0.206  -22.1221  76.1704  103.7760
 UY7  HD3  H  HCH2  0   0.237  -22.7618  75.4526  105.2556
 UY7  HA   H  HCH1  0   0.270  -22.3489  72.5306  102.5360
 UY7  H    H  HNH1  0   0.358  -23.8973  74.5947  103.1663
 UY7  HXT  H  HOH1  0   0.482  -22.7257  75.6201  100.1280
 UY7  H10  H  HOH1  0   0.449  -21.1723  73.8983  106.3082

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    double  1.231  0.020  1.231
 UY7  OXT  C    single  1.326  0.020  1.326
 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  1.525  0.020  1.525
 UY7  N    CD   single  1.473  0.014  1.473
 UY7  CD   CG   single  1.523  0.020  1.523
 UY7  CG   O09  single  1.411  0.020  1.411
 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  OXT  HXT  single  0.850  0.020  0.980
 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  107.05  3.000
 UY7  HB3  CB   CA   111.39  3.000
 UY7  HB2  CB   CA   112.16  3.000
 UY7  HB3  CB   CG   108.83  3.000
 UY7  HB2  CB   CG   112.51  3.000
 UY7  CA   CB   CG   104.91  3.000
 UY7  HG2  CG   O09  111.20  3.000
 UY7  HG2  CG   CD   111.11  3.000
 UY7  O09  CG   CD   112.74  3.000
 UY7  HG2  CG   CB   111.18  3.000
 UY7  O09  CG   CB   108.47  3.000
 UY7  CD   CG   CB   101.76  3.000
 UY7  HD3  CD   HD2  107.20  3.000
 UY7  HD3  CD   N    111.33  3.000
 UY7  HD2  CD   N    114.28  3.000
 UY7  HD3  CD   CG   112.60  3.000
 UY7  HD2  CD   CG   109.20  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  123.40  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   113.84  3.000
 UY7  CA   N    CD   108.98  3.000
 UY7  HXT  OXT  C    109.96  3.000
 UY7  H10  O09  CG   108.28  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  CONST_01  HXT  OXT  C   CA  180.00   0.0  0
 UY7  Var_01    CA   N    CD  CG  -38.84  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
 UY7  plan-1  HXT  0.020

