# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 18:09:08 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 5,5-difluoro-4-oxo-5-phosphono-D-norvaline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CC(=O)C(F)(F)[P](O)(O)=O)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
 P4F  P4F  5,5-difluoro-4-oxo-5-phosphono-D-norvaline  D-peptide  20  15  .  2016-04-26  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_P4F
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
 P4F  C    C  C      0   0.405   1.1683  -1.4587   0.6918
 P4F  N    N  NH2    0  -0.792  -0.5284  -0.1393  -0.5293
 P4F  O    O  O      0  -0.597   1.7752  -1.5444  -0.3930
 P4F  CA   C  CH1    0  -0.209   0.0367  -0.4001   0.7785
 P4F  CB   C  CH2    0  -0.581   0.6492   0.8364   1.4971
 P4F  CG   C  C      0   0.273  -0.3509   1.9357   1.6984
 P4F  FAA  F  F      0  -0.374  -1.5044   0.7411   3.3674
 P4F  OAB  O  OP    -1  -0.864  -0.8895   3.0845   5.5142
 P4F  PAI  P  P      0   1.111   0.0946   2.7084   4.4154
 P4F  OAJ  O  OP    -1  -0.859   1.0177   1.5383   4.7413
 P4F  FAN  F  F      0  -0.372  -2.1697   2.7715   2.9050
 P4F  OAO  O  O      0  -0.865   0.7575   3.8718   3.6853
 P4F  CD1  C  CT     0   0.377  -1.0401   2.0041   3.0444
 P4F  OD2  O  O      0  -0.412  -0.5966   2.7570   0.8402
 P4F  OXT  O  OC    -1  -0.609   1.3970  -2.0990   1.7358
 P4F  HN   H  HNH2   0   0.332  -1.1505   0.6582  -0.5053
 P4F  HNA  H  HNH2   0   0.326   0.2218   0.0939  -1.1673
 P4F  HA   H  HCH1   0   0.217  -0.7531  -0.8013   1.4181
 P4F  HB   H  HCH2   0   0.252   1.0624   0.5288   2.4573
 P4F  HBA  H  HCH2   0   0.241   1.4660   1.2192   0.8782

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
 P4F  O    C    deloc   1.231  0.020  1.231
 P4F  C    CA   single  1.525  0.021  1.525
 P4F  C    OXT  deloc   1.246  0.020  1.246
 P4F  N    CA   single  1.458  0.019  1.458
 P4F  N    HN   single  0.890  0.020  1.040
 P4F  N    HNA  single  0.890  0.020  1.040
 P4F  CA   CB   single  1.521  0.033  1.521
 P4F  CA   HA   single  0.970  0.020  0.970
 P4F  CB   CG   single  1.500  0.020  1.500
 P4F  CB   HB   single  0.970  0.020  1.090
 P4F  CB   HBA  single  0.970  0.020  1.090
 P4F  OD2  CG   double  1.213  0.020  1.213
 P4F  CG   CD1  single  1.514  0.020  1.514
 P4F  CD1  FAA  single  1.384  0.020  1.384
 P4F  PAI  OAB  deloc   1.522  0.020  1.522
 P4F  CD1  PAI  single  1.914  0.020  1.914
 P4F  OAO  PAI  deloc   1.525  0.020  1.525
 P4F  PAI  OAJ  deloc   1.526  0.020  1.526
 P4F  FAN  CD1  single  1.373  0.020  1.373

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
 P4F  OXT  C    CA   120.80  1.700
 P4F  OXT  C    O    127.21  3.000
 P4F  CA   C    O    120.80  1.700
 P4F  HNA  N    HN   106.80  3.000
 P4F  HNA  N    CA   108.75  3.000
 P4F  HN   N    CA   111.13  3.000
 P4F  HA   CA   CB   109.00  3.000
 P4F  HA   CA   N    110.00  3.000
 P4F  CB   CA   N    110.40  1.500
 P4F  HA   CA   C    110.00  3.000
 P4F  CB   CA   C    110.50  1.500
 P4F  N    CA   C    111.00  2.800
 P4F  HBA  CB   HB   108.31  3.000
 P4F  HBA  CB   CG   108.51  3.000
 P4F  HB   CB   CG   109.97  3.000
 P4F  HBA  CB   CA   108.10  3.000
 P4F  HB   CB   CA   109.39  3.000
 P4F  CG   CB   CA   112.46  3.000
 P4F  OD2  CG   CD1  120.42  3.000
 P4F  CD1  CG   CB   117.14  3.000
 P4F  OD2  CG   CB   122.44  3.000
 P4F  CD1  PAI  OAO  101.27  3.000
 P4F  OAO  PAI  OAJ  115.11  3.000
 P4F  CD1  PAI  OAJ  103.27  3.000
 P4F  OAJ  PAI  OAB  115.25  3.000
 P4F  OAO  PAI  OAB  115.98  3.000
 P4F  CD1  PAI  OAB  102.98  3.000
 P4F  FAN  CD1  PAI  110.79  3.000
 P4F  FAN  CD1  FAA  104.94  3.000
 P4F  PAI  CD1  FAA  111.57  3.000
 P4F  FAN  CD1  CG   108.03  3.000
 P4F  PAI  CD1  CG   112.56  3.000
 P4F  FAA  CD1  CG   108.60  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
 P4F  Var_01  OD2  CG   CB   CA  -84.61  30.0  3
 P4F  Var_02  FAA  CD1  CG   CB  -48.45  30.0  3
 P4F  Var_03  OAB  PAI  CD1  CG  163.13  30.0  3

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
 P4F  chir_01  CA  C  N  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
 P4F  plan-1  CB   0.020
 P4F  plan-1  CG   0.020
 P4F  plan-1  CD1  0.020
 P4F  plan-1  OD2  0.020
 P4F  plan-2  C    0.020
 P4F  plan-2  O    0.020
 P4F  plan-2  CA   0.020
 P4F  plan-2  OXT  0.020

