# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:47:20 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: 4-cyano-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(cc1)C#N)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
 4CF  4CF  '4-cyano-L-phenylalanine  '  L-peptide  23  14  .  2012-08-28  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_4CF
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
 4CF  C    C  C      0   0.392  30.6056  8.3672   9.0388
 4CF  N    N  NH2    0  -0.804  32.1614  9.7293  10.4238
 4CF  O    O  O      0  -0.605  30.6384  7.2859   8.4196
 4CF  C1   C  CSP    0   0.049  27.9983  3.1945  11.6890
 4CF  N1   N  NS     0  -0.255  27.4915  2.1592  11.7092
 4CF  CA   C  CH1    0  -0.158  31.4780  8.4468  10.3164
 4CF  CB   C  CH2    0  -0.520  30.5843  8.2894  11.5579
 4CF  CG   C  C      0   0.149  29.8909  6.9631  11.6113
 4CF  CZ   C  C      0  -0.015  28.6350  4.4702  11.6632
 4CF  CD1  C  C1     0  -0.290  28.5610  6.8277  11.2168
 4CF  CD2  C  C1     0  -0.299  30.5780  5.8264  12.0388
 4CF  CE1  C  C1     0  -0.227  27.9295  5.5966  11.2405
 4CF  CE2  C  C1     0  -0.225  29.9664  4.5874  12.0660
 4CF  OXT  O  OC    -1  -0.602  29.9249  9.3733   8.7619
 4CF  HN   H  HNH2   0   0.334  32.8283  9.6811  11.1854
 4CF  HNA  H  HNH2   0   0.337  32.7140  9.8915   9.5908
 4CF  HA   H  HCH1   0   0.186  32.1754  7.5964  10.2983
 4CF  HB   H  HCH2   0   0.244  31.2057  8.4054  12.4516
 4CF  HBA  H  HCH2   0   0.241  29.8543  9.1016  11.5663
 4CF  HD1  H  H      0   0.260  28.0127  7.6994  10.8820
 4CF  HD2  H  H      0   0.260  31.6096  5.9144  12.3574
 4CF  HE1  H  H      0   0.275  26.8960  5.5068  10.9329
 4CF  HE2  H  H      0   0.275  30.5123  3.7150  12.3994

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
 4CF  O    C    deloc     1.231  0.020  1.231
 4CF  OXT  C    deloc     1.246  0.020  1.246
 4CF  C    CA   single    1.525  0.021  1.525
 4CF  N    CA   single    1.458  0.019  1.458
 4CF  N    HN   single    0.890  0.020  1.040
 4CF  N    HNA  single    0.890  0.020  1.040
 4CF  N1   C1   triple    1.153  0.020  1.153
 4CF  C1   CZ   single    1.426  0.020  1.426
 4CF  CA   CB   single    1.530  0.020  1.530
 4CF  CA   HA   single    0.970  0.020  0.970
 4CF  CB   CG   single    1.498  0.020  1.498
 4CF  CB   HB   single    0.970  0.020  1.090
 4CF  CB   HBA  single    0.970  0.020  1.090
 4CF  CD1  CG   aromatic  1.394  0.020  1.394
 4CF  CG   CD2  aromatic  1.395  0.020  1.395
 4CF  CE1  CZ   aromatic  1.395  0.020  1.395
 4CF  CZ   CE2  aromatic  1.396  0.020  1.396
 4CF  CE1  CD1  aromatic  1.384  0.020  1.384
 4CF  CD1  HD1  single    0.930  0.020  1.080
 4CF  CE2  CD2  aromatic  1.382  0.020  1.382
 4CF  CD2  HD2  single    0.930  0.020  1.080
 4CF  CE1  HE1  single    0.930  0.020  1.080
 4CF  CE2  HE2  single    0.930  0.020  1.080

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
 4CF  OXT  C    CA   116.71  3.000
 4CF  CA   C    O    120.80  1.700
 4CF  OXT  C    O    127.19  3.000
 4CF  HNA  N    HN   105.46  3.000
 4CF  HNA  N    CA   109.65  3.000
 4CF  HN   N    CA   108.79  3.000
 4CF  CZ   C1   N1   180.00  3.000
 4CF  HA   CA   CB   109.00  3.000
 4CF  HA   CA   N    110.00  3.000
 4CF  CB   CA   N    110.50  1.700
 4CF  HA   CA   C    109.00  3.000
 4CF  CB   CA   C    110.10  1.900
 4CF  N    CA   C    111.00  2.800
 4CF  HBA  CB   HB   107.12  3.000
 4CF  HBA  CB   CG   110.42  3.000
 4CF  HB   CB   CG   109.12  3.000
 4CF  HBA  CB   CA   108.58  3.000
 4CF  HB   CB   CA   108.56  3.000
 4CF  CG   CB   CA   112.86  3.000
 4CF  CD2  CG   CD1  118.52  3.000
 4CF  CD2  CG   CB   120.29  3.000
 4CF  CD1  CG   CB   121.18  3.000
 4CF  CE2  CZ   CE1  120.14  3.000
 4CF  CE2  CZ   C1   119.72  3.000
 4CF  CE1  CZ   C1   120.14  3.000
 4CF  HD1  CD1  CE1  119.37  3.000
 4CF  HD1  CD1  CG   119.50  3.000
 4CF  CE1  CD1  CG   121.13  3.000
 4CF  HD2  CD2  CE2  119.24  3.000
 4CF  HD2  CD2  CG   119.53  3.000
 4CF  CE2  CD2  CG   121.23  3.000
 4CF  HE1  CE1  CD1  120.32  3.000
 4CF  HE1  CE1  CZ   120.15  3.000
 4CF  CD1  CE1  CZ   119.53  3.000
 4CF  HE2  CE2  CD2  120.38  3.000
 4CF  HE2  CE2  CZ   120.17  3.000
 4CF  CD2  CE2  CZ   119.45  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
 4CF  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 4CF  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 4CF  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 4CF  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 4CF  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 4CF  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 4CF  CONST_07  CD1  CE1  CZ   C1   180.00   0.0  0
 4CF  CONST_08  CD2  CE2  CZ   C1   180.00   0.0  0
 4CF  CONST_09  CE1  CD1  CG   CB   180.00   0.0  0
 4CF  CONST_10  CE2  CD2  CG   CB   180.00   0.0  0
 4CF  CONST_11  HE1  CE1  CD1  CG   180.00   0.0  0
 4CF  CONST_12  HE2  CE2  CD2  CG   180.00   0.0  0
 4CF  CONST_13  HD1  CD1  CE1  CZ   180.00   0.0  0
 4CF  CONST_14  HD2  CD2  CE2  CZ   180.00   0.0  0
 4CF  Var_01    CD1  CG   CB   CA   -99.85  30.0  2

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
 4CF  chir_01  CA  C  N  CB  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
 4CF  plan-1  C1   0.020
 4CF  plan-1  N1   0.020
 4CF  plan-1  CB   0.020
 4CF  plan-1  CG   0.020
 4CF  plan-1  CZ   0.020
 4CF  plan-1  CD1  0.020
 4CF  plan-1  CD2  0.020
 4CF  plan-1  CE1  0.020
 4CF  plan-1  CE2  0.020
 4CF  plan-1  HD1  0.020
 4CF  plan-1  HD2  0.020
 4CF  plan-1  HE1  0.020
 4CF  plan-1  HE2  0.020
 4CF  plan-2  C    0.020
 4CF  plan-2  O    0.020
 4CF  plan-2  CA   0.020
 4CF  plan-2  OXT  0.020

