# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:42:47 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: 3-cyano-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cccc(c1)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
 3CF  3CF  '3-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_3CF
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
 3CF  C    C  C      0   0.393  65.0382  10.9621  29.6548
 3CF  N    N  NH2    0  -0.803  64.8687   8.5540  30.2463
 3CF  OXT  O  OC    -1  -0.605  64.2553  11.7985  29.1628
 3CF  C1   C  CSP    0   0.049  65.9650  14.8715  33.1091
 3CF  N1   N  NS     0  -0.252  66.7684  15.6920  33.2061
 3CF  CA   C  CH1    0  -0.162  64.4068   9.8950  30.5834
 3CF  CB   C  CH2    0  -0.510  64.8068  10.1834  32.0373
 3CF  CG   C  CR6    0   0.142  64.4095  11.5590  32.4822
 3CF  CZ   C  CR16   0  -0.263  63.6369  14.1528  33.2480
 3CF  CD1  C  CR16   0  -0.304  65.3566  12.5664  32.6058
 3CF  CD2  C  CR16   0  -0.290  63.0759  11.8687  32.7491
 3CF  CE1  C  CR6    0   0.026  64.9725  13.8522  32.9878
 3CF  CE2  C  CR16   0  -0.228  62.6915  13.1480  33.1240
 3CF  O    O  O      0  -0.603  66.2748  10.9107  29.5054
 3CF  HN   H  HNH2   0   0.334  64.3464   7.8795  30.7937
 3CF  HNA  H  HNH2   0   0.338  64.6390   8.3503  29.2812
 3CF  HA   H  HCH1   0   0.183  63.3135   9.9936  30.5133
 3CF  HB   H  HCH2   0   0.243  64.3380   9.4390  32.6892
 3CF  HBA  H  HCH2   0   0.238  65.8866  10.0568  32.1323
 3CF  HZ   H  HCR6   0   0.276  63.3473  15.1527  33.5421
 3CF  HD1  H  HCR6   0   0.269  66.3991  12.3555  32.4030
 3CF  HD2  H  HCR6   0   0.260  62.3242  11.0933  32.6580
 3CF  HE2  H  HCR6   0   0.268  61.6502  13.3639  33.3219

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
 3CF  O    C    deloc     1.231  0.020  1.231
 3CF  OXT  C    deloc     1.247  0.020  1.247
 3CF  C    CA   single    1.525  0.021  1.525
 3CF  N    CA   single    1.458  0.019  1.458
 3CF  N    HN   single    0.890  0.020  1.040
 3CF  N    HNA  single    0.890  0.020  1.040
 3CF  N1   C1   triple    1.152  0.020  1.152
 3CF  C1   CE1  single    1.428  0.020  1.428
 3CF  CA   CB   single    1.530  0.020  1.530
 3CF  CA   HA   single    0.970  0.020  0.970
 3CF  CB   CG   single    1.499  0.020  1.499
 3CF  CB   HB   single    0.970  0.020  1.090
 3CF  CB   HBA  single    0.970  0.020  1.090
 3CF  CG   CD1  aromatic  1.388  0.020  1.388
 3CF  CG   CD2  aromatic  1.395  0.020  1.395
 3CF  CE1  CZ   aromatic  1.394  0.020  1.394
 3CF  CZ   CE2  aromatic  1.385  0.020  1.385
 3CF  CZ   HZ   single    0.930  0.020  1.080
 3CF  CD1  CE1  aromatic  1.395  0.020  1.395
 3CF  CD1  HD1  single    0.930  0.020  1.080
 3CF  CD2  CE2  aromatic  1.387  0.020  1.387
 3CF  CD2  HD2  single    0.930  0.020  1.080
 3CF  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
 3CF  O    C    CA   120.80  1.700
 3CF  CA   C    OXT  116.27  3.000
 3CF  O    C    OXT  127.10  3.000
 3CF  HNA  N    HN   105.30  3.000
 3CF  HNA  N    CA   109.48  3.000
 3CF  HN   N    CA   108.90  3.000
 3CF  CE1  C1   N1   180.00  3.000
 3CF  HA   CA   CB   109.00  3.000
 3CF  HA   CA   N    110.00  3.000
 3CF  CB   CA   N    110.50  1.700
 3CF  HA   CA   C    109.00  3.000
 3CF  CB   CA   C    110.10  1.900
 3CF  N    CA   C    111.00  2.800
 3CF  HBA  CB   HB   107.03  3.000
 3CF  HBA  CB   CG   110.05  3.000
 3CF  HB   CB   CG   109.49  3.000
 3CF  HBA  CB   CA   108.57  3.000
 3CF  HB   CB   CA   108.94  3.000
 3CF  CG   CB   CA   112.60  3.000
 3CF  CD2  CG   CD1  118.30  3.000
 3CF  CD2  CG   CB   120.92  3.000
 3CF  CD1  CG   CB   120.76  3.000
 3CF  HZ   CZ   CE2  120.80  3.000
 3CF  HZ   CZ   CE1  120.45  3.000
 3CF  CE2  CZ   CE1  118.75  3.000
 3CF  HD1  CD1  CE1  119.72  3.000
 3CF  HD1  CD1  CG   119.92  3.000
 3CF  CE1  CD1  CG   120.35  3.000
 3CF  HD2  CD2  CE2  119.36  3.000
 3CF  HD2  CD2  CG   119.22  3.000
 3CF  CE2  CD2  CG   121.42  3.000
 3CF  CD1  CE1  CZ   120.92  3.000
 3CF  CD1  CE1  C1   119.33  3.000
 3CF  CZ   CE1  C1   119.76  3.000
 3CF  HE2  CE2  CD2  120.01  3.000
 3CF  HE2  CE2  CZ   119.73  3.000
 3CF  CD2  CE2  CZ   120.26  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
 3CF  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 3CF  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 3CF  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 3CF  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 3CF  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 3CF  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 3CF  CONST_07  CE2  CZ   CE1  C1    180.00   0.0  0
 3CF  CONST_08  CG   CD1  CE1  C1    180.00   0.0  0
 3CF  CONST_09  CE1  CD1  CG   CB    180.00   0.0  0
 3CF  CONST_10  CE2  CD2  CG   CB    180.00   0.0  0
 3CF  CONST_11  HE2  CE2  CD2  CG    180.00   0.0  0
 3CF  CONST_12  HD1  CD1  CE1  CZ    180.00   0.0  0
 3CF  CONST_13  HD2  CD2  CE2  CZ    180.00   0.0  0
 3CF  CONST_14  HZ   CZ   CE1  CD1   180.00   0.0  0
 3CF  Var_01    CD1  CG   CB   CA   -104.74  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
 3CF  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
 3CF  plan-1  C1   0.020
 3CF  plan-1  N1   0.020
 3CF  plan-1  CB   0.020
 3CF  plan-1  CG   0.020
 3CF  plan-1  CZ   0.020
 3CF  plan-1  CD1  0.020
 3CF  plan-1  CD2  0.020
 3CF  plan-1  CE1  0.020
 3CF  plan-1  CE2  0.020
 3CF  plan-1  HZ   0.020
 3CF  plan-1  HD1  0.020
 3CF  plan-1  HD2  0.020
 3CF  plan-1  HE2  0.020
 3CF  plan-2  C    0.020
 3CF  plan-2  OXT  0.020
 3CF  plan-2  CA   0.020
 3CF  plan-2  O    0.020

