# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:34:32 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (4S)-4-(ethynyloxy)-D-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H]1C[C@@H](CN1)OC#C
#
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
 45W  45W  (4S)-4-(ethynyloxy)-D-proline  D-peptide  19  11  .  2019-03-22  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_45W
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
 45W  CB   C  CH2    0  -0.485  -15.4144  32.4627  28.8677
 45W  CD   C  CH2    0  -0.367  -13.2837  31.2990  28.8065
 45W  C    C  C      0   0.408  -13.6760  34.3295  29.0773
 45W  O    O  O      0  -0.610  -14.4832  35.1882  28.6670
 45W  CA   C  CH1    0  -0.276  -14.3394  33.1039  29.7638
 45W  CG   C  CH1    0   0.006  -14.6330  31.4213  28.0666
 45W  N    N  NH1    0  -0.560  -13.4093  32.0183  30.0637
 45W  O48  O  O2     0  -0.422  -15.3416  30.1533  27.9426
 45W  C49  C  CSP    0   0.193  -15.5748  29.5015  29.0260
 45W  C50  C  CSP1   0  -0.434  -15.8119  28.8551  30.0123
 45W  O1   O  OC    -1  -0.591  -12.4356  34.3737  29.0083
 45W  H1   H  HCH2   0   0.251  -15.9342  33.1782  28.2344
 45W  H2   H  HCH2   0   0.246  -16.1667  31.9689  29.4906
 45W  H3   H  HCH2   0   0.252  -12.9775  30.2626  28.9615
 45W  H4   H  HCH2   0   0.246  -12.5115  31.7720  28.1971
 45W  H5   H  HCH1   0   0.246  -14.7861  33.4613  30.6961
 45W  H6   H  HCH1   0   0.268  -14.4977  31.7121  27.0272
 45W  H7   H  HNH1   0   0.338  -13.8462  31.4039  30.7424
 45W  H9   H  H      0   0.290  -16.0236  28.2781  30.8806

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
 45W  O    C    deloc   1.231  0.020  1.231
 45W  O48  CG   single  1.458  0.020  1.458
 45W  O48  C49  single  1.286  0.020  1.286
 45W  CG   CD   single  1.544  0.020  1.544
 45W  CG   CB   single  1.529  0.020  1.529
 45W  C    CA   single  1.525  0.021  1.525
 45W  C49  C50  triple  1.203  0.020  1.203
 45W  CD   N    single  1.473  0.014  1.473
 45W  CB   CA   single  1.521  0.033  1.521
 45W  CA   N    single  1.458  0.019  1.458
 45W  C    O1   deloc   1.243  0.020  1.243
 45W  CB   H1   single  0.939  0.020  1.096
 45W  CB   H2   single  0.939  0.020  1.096
 45W  CD   H3   single  0.939  0.020  1.096
 45W  CD   H4   single  0.939  0.020  1.096
 45W  CA   H5   single  0.939  0.020  1.096
 45W  CG   H6   single  0.939  0.020  1.096
 45W  N    H7   single  0.868  0.020  1.013
 45W  C50  H9   single  0.913  0.020  1.066

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
 45W  H2   CB   H1   107.44  3.000
 45W  H2   CB   CG   110.01  3.000
 45W  H1   CB   CG   112.79  3.000
 45W  H2   CB   CA   109.67  3.000
 45W  H1   CB   CA   113.49  3.000
 45W  CG   CB   CA   103.40  3.000
 45W  H4   CD   H3   106.99  3.000
 45W  H4   CD   N    109.24  3.000
 45W  H3   CD   N    111.79  3.000
 45W  H4   CD   CG   108.44  3.000
 45W  H3   CD   CG   112.85  3.000
 45W  N    CD   CG   103.20  1.500
 45W  O1   C    CA   118.60  3.000
 45W  O1   C    O    127.06  3.000
 45W  CA   C    O    120.80  1.700
 45W  H5   CA   N    109.14  3.000
 45W  H5   CA   C    107.06  3.000
 45W  N    CA   C    111.00  2.800
 45W  H5   CA   CB   110.31  3.000
 45W  N    CA   CB   110.40  1.500
 45W  C    CA   CB   110.50  1.500
 45W  H6   CG   O48  102.22  3.000
 45W  H6   CG   CD   111.75  3.000
 45W  O48  CG   CD   113.37  3.000
 45W  H6   CG   CB   112.47  3.000
 45W  CD   CG   CB   104.45  3.000
 45W  O48  CG   CB   112.87  3.000
 45W  H7   N    CA   108.26  3.000
 45W  H7   N    CD   108.43  3.000
 45W  CA   N    CD   104.19  3.000
 45W  C49  O48  CG   117.23  3.000
 45W  C50  C49  O48  180.00  3.000
 45W  H9   C50  C49  180.00  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
 45W  Var_01  CG  CD  N  CA  -31.65  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
 45W  chir_01  CA  C    CB  N   negativ
 45W  chir_02  CG  O48  CD  CB  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
 45W  plan-1  C   0.020
 45W  plan-1  O   0.020
 45W  plan-1  CA  0.020
 45W  plan-1  O1  0.020

