# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 11:58:56 2020
#   Inital geometry file: a 44 line input string
#   Ligand name: 4,4-difluoro-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1CC(F)(F)CN1
#
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
 PDF  PDF  '4,4-difluoro-L-proline   '  ligand  16  10  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PDF
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
 PDF  N    N  NH1    0  -0.594   0.1949  -1.2828  -0.6936
 PDF  CD   C  CH2    0  -0.405  -1.2528  -1.1624  -0.6534
 PDF  CA   C  CH1    0  -0.235   0.7311   0.0590  -0.5045
 PDF  CB   C  CH2    0  -0.571  -0.2375   0.7341   0.4820
 PDF  CG   C  CT     0   0.726  -1.5759   0.1448   0.0914
 PDF  C    C  C      0   0.407   2.1714   0.0766   0.0354
 PDF  O    O  O      0  -0.598   2.5944  -0.9727   0.5572
 PDF  F1   F  F      0  -0.358  -2.2774   0.9982  -0.7216
 PDF  F2   F  F      0  -0.353  -2.3954  -0.0566   1.1683
 PDF  HN   H  HNH1   0   0.341   0.5252  -1.8512   0.0768
 PDF  HD   H  HCH2   0   0.240  -1.6642  -1.0969  -1.6646
 PDF  HDA  H  HCH2   0   0.259  -1.7110  -2.0261  -0.1711
 PDF  HA   H  HCH1   0   0.233   0.7022   0.5967  -1.4592
 PDF  HB   H  HCH2   0   0.255   0.0017   0.4151   1.5002
 PDF  HBA  H  HCH2   0   0.265  -0.2288   1.8233   0.4536
 PDF  O2   O  OC    -1  -0.611   2.7679   1.1650  -0.0621

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
 PDF  N   CD   single  1.453  0.020  1.453
 PDF  N   HN   single  0.890  0.020  1.040
 PDF  CD  HD   single  0.970  0.020  1.090
 PDF  CD  HDA  single  0.970  0.020  1.090
 PDF  CA  N    single  1.457  0.020  1.457
 PDF  CA  CB   single  1.539  0.020  1.539
 PDF  CA  HA   single  0.970  0.020  1.090
 PDF  CB  CG   single  1.514  0.020  1.514
 PDF  CB  HB   single  0.970  0.020  1.090
 PDF  CB  HBA  single  0.970  0.020  1.090
 PDF  CG  CD   single  1.539  0.020  1.539
 PDF  CG  F1   single  1.372  0.020  1.372
 PDF  C   CA   single  1.538  0.020  1.538
 PDF  C   O    deloc   1.246  0.020  1.246
 PDF  C   O2   deloc   1.245  0.020  1.245
 PDF  F2  CG   single  1.368  0.020  1.368

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
 PDF  HN   N   CA  107.34  3.000
 PDF  CA   N   CD  106.66  3.000
 PDF  HN   N   CD  110.51  3.000
 PDF  HDA  CD  HD  107.36  3.000
 PDF  HDA  CD  CG  111.75  3.000
 PDF  HD   CD  CG  108.52  3.000
 PDF  CG   CD  N   107.03  3.000
 PDF  HDA  CD  N   111.42  3.000
 PDF  HD   CD  N   110.74  3.000
 PDF  HA   CA  C   108.95  3.000
 PDF  C    CA  CB  111.06  3.000
 PDF  HA   CA  CB  109.06  3.000
 PDF  C    CA  N   113.61  3.000
 PDF  HA   CA  N   109.21  3.000
 PDF  CB   CA  N   104.81  3.000
 PDF  HBA  CB  HB  108.32  3.000
 PDF  HBA  CB  CG  112.92  3.000
 PDF  HB   CB  CG  108.67  3.000
 PDF  HBA  CB  CA  114.64  3.000
 PDF  HB   CB  CA  109.35  3.000
 PDF  CG   CB  CA  102.73  3.000
 PDF  F2   CG  F1  104.59  3.000
 PDF  F2   CG  CB  112.57  3.000
 PDF  F1   CG  CB  111.28  3.000
 PDF  F2   CG  CD  112.44  3.000
 PDF  F1   CG  CD  110.43  3.000
 PDF  CB   CG  CD  105.66  3.000
 PDF  O2   C   O   127.33  3.000
 PDF  O2   C   CA  115.54  3.000
 PDF  O    C   CA  117.08  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
 PDF  Var_01  CB  CG  CD  N    -0.85  30.0  1
 PDF  Var_02  CA  CB  CG  CD   21.34  30.0  1
 PDF  Var_03  CG  CD  N   CA  -21.60  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
 PDF  chir_01  CA  N  CB  C  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
 PDF  plan-1  CA  0.020
 PDF  plan-1  C   0.020
 PDF  plan-1  O   0.020
 PDF  plan-1  O2  0.020

