# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:42:42 2022
#   Inital geometry file: a 72 line input string
#   Ligand name: 4-ethynyl-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(cc1)C#C)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
 5DW  5DW  4-ethynyl-L-phenylalanine  L-peptide  24  14  .  2019-03-22  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_5DW
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
 5DW  C1   C  CSP    0   0.299  -52.5887   -9.8470  15.4160
 5DW  C2   C  CSP1   0  -0.560  -53.3949  -10.4802  14.7839
 5DW  N    N  NH2    0  -0.807  -46.9477   -7.3867  16.7899
 5DW  CA   C  CH1    0  -0.210  -47.6198   -6.2891  17.4641
 5DW  C    C  C      0   0.413  -46.6081   -5.4060  18.2454
 5DW  O    O  O      0  -0.603  -47.0951   -4.6047  19.0661
 5DW  CB   C  CH2    0  -0.492  -48.7166   -6.8310  18.3916
 5DW  CG   C  CR6    0   0.132  -49.7450   -7.6279  17.6449
 5DW  CD1  C  CR16   0  -0.298  -50.7994   -6.9914  16.9889
 5DW  CD2  C  CR16   0  -0.299  -49.6551   -9.0155  17.5448
 5DW  CE1  C  CR16   0  -0.262  -51.7313   -7.7082  16.2589
 5DW  CE2  C  CR16   0  -0.264  -50.5809   -9.7457  16.8186
 5DW  CZ   C  CR6    0  -0.074  -51.6319   -9.0990  16.1643
 5DW  O1   O  OC    -1  -0.596  -45.4023   -5.5440  17.9604
 5DW  H1   H  H      0   0.281  -54.1107  -11.0387  14.2251
 5DW  H2   H  HNH2   0   0.333  -47.4770   -7.6785  15.9791
 5DW  H3   H  HNH2   0   0.335  -46.0531   -7.0513  16.4580
 5DW  H5   H  HCH1   0   0.202  -48.1152   -5.6058  16.7520
 5DW  H6   H  HCH2   0   0.227  -48.2534   -7.4557  19.1597
 5DW  H7   H  HCH2   0   0.235  -49.1945   -5.9910  18.8956
 5DW  H8   H  HCR6   0   0.250  -50.8946   -5.9137  17.0540
 5DW  H9   H  HCR6   0   0.248  -48.8483   -9.5341  18.0476
 5DW  H10  H  HCR6   0   0.255  -52.5434   -7.1933  15.7620
 5DW  H11  H  HCR6   0   0.255  -50.4925  -10.8227  16.7564

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
 5DW  C2   C1   triple    1.204  0.020  1.204
 5DW  C1   CZ   single    1.426  0.020  1.426
 5DW  CE1  CZ   aromatic  1.398  0.020  1.398
 5DW  CE1  CD1  aromatic  1.384  0.020  1.384
 5DW  CZ   CE2  aromatic  1.397  0.020  1.397
 5DW  N    CA   single    1.458  0.019  1.458
 5DW  CD1  CG   aromatic  1.395  0.020  1.395
 5DW  CE2  CD2  aromatic  1.385  0.020  1.385
 5DW  CA   C    single    1.525  0.021  1.525
 5DW  CA   CB   single    1.521  0.033  1.521
 5DW  CG   CD2  aromatic  1.394  0.020  1.394
 5DW  CG   CB   single    1.500  0.020  1.500
 5DW  C    O    deloc     1.231  0.020  1.231
 5DW  C    O1   deloc     1.247  0.020  1.247
 5DW  C2   H1   single    0.913  0.020  1.066
 5DW  N    H2   single    0.868  0.020  1.013
 5DW  N    H3   single    0.868  0.020  1.013
 5DW  CA   H5   single    0.939  0.020  1.096
 5DW  CB   H6   single    0.939  0.020  1.096
 5DW  CB   H7   single    0.939  0.020  1.096
 5DW  CD1  H8   single    0.929  0.020  1.085
 5DW  CD2  H9   single    0.929  0.020  1.085
 5DW  CE1  H10  single    0.929  0.020  1.085
 5DW  CE2  H11  single    0.929  0.020  1.085

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
 5DW  CZ   C1   C2   180.00  3.000
 5DW  H1   C2   C1   180.00  3.000
 5DW  H3   N    H2   107.19  3.000
 5DW  H3   N    CA   108.12  3.000
 5DW  H2   N    CA   110.36  3.000
 5DW  H5   CA   CB   106.71  3.000
 5DW  H5   CA   C    105.35  3.000
 5DW  CB   CA   C    110.50  1.500
 5DW  H5   CA   N    112.07  3.000
 5DW  CB   CA   N    110.40  1.500
 5DW  C    CA   N    111.00  2.800
 5DW  O1   C    O    126.85  3.000
 5DW  O1   C    CA   116.87  3.000
 5DW  O    C    CA   120.80  1.700
 5DW  H7   CB   H6   107.54  3.000
 5DW  H7   CB   CG   109.81  3.000
 5DW  H6   CB   CG   109.68  3.000
 5DW  H7   CB   CA   108.70  3.000
 5DW  H6   CB   CA   108.88  3.000
 5DW  CG   CB   CA   112.12  3.000
 5DW  CD2  CG   CD1  117.97  3.000
 5DW  CD2  CG   CB   121.35  3.000
 5DW  CD1  CG   CB   120.65  3.000
 5DW  H8   CD1  CE1  119.18  3.000
 5DW  H8   CD1  CG   119.45  3.000
 5DW  CE1  CD1  CG   121.37  3.000
 5DW  H9   CD2  CE2  119.28  3.000
 5DW  H9   CD2  CG   119.43  3.000
 5DW  CE2  CD2  CG   121.29  3.000
 5DW  H10  CE1  CZ   119.72  3.000
 5DW  H10  CE1  CD1  120.07  3.000
 5DW  CZ   CE1  CD1  120.22  3.000
 5DW  H11  CE2  CZ   119.68  3.000
 5DW  H11  CE2  CD2  120.01  3.000
 5DW  CZ   CE2  CD2  120.31  3.000
 5DW  CE2  CZ   CE1  118.85  3.000
 5DW  CE2  CZ   C1   120.51  3.000
 5DW  CE1  CZ   C1   120.64  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
 5DW  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 5DW  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 5DW  CONST_03  CE2  CZ   CE1  CD1    0.00   0.0  0
 5DW  CONST_04  CE2  CD2  CG   CD1    0.00   0.0  0
 5DW  CONST_05  CE1  CZ   CE2  CD2    0.00   0.0  0
 5DW  CONST_06  CE1  CD1  CG   CD2    0.00   0.0  0
 5DW  CONST_07  CD1  CE1  CZ   C1   180.00   0.0  0
 5DW  CONST_08  CD2  CE2  CZ   C1   180.00   0.0  0
 5DW  CONST_09  CE1  CD1  CG   CB   180.00   0.0  0
 5DW  CONST_10  CE2  CD2  CG   CB   180.00   0.0  0
 5DW  CONST_11  H10  CE1  CD1  CG   180.00   0.0  0
 5DW  CONST_12  H11  CE2  CD2  CG   180.00   0.0  0
 5DW  CONST_13  H9   CD2  CG   CD1  180.00   0.0  0
 5DW  CONST_14  H8   CD1  CG   CD2  180.00   0.0  0
 5DW  Var_01    CD1  CG   CB   CA   -83.00  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
 5DW  chir_01  CA  N  C  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
 5DW  plan-1  C1   0.020
 5DW  plan-1  C2   0.020
 5DW  plan-1  CB   0.020
 5DW  plan-1  CG   0.020
 5DW  plan-1  CD1  0.020
 5DW  plan-1  CD2  0.020
 5DW  plan-1  CE1  0.020
 5DW  plan-1  CE2  0.020
 5DW  plan-1  CZ   0.020
 5DW  plan-1  H8   0.020
 5DW  plan-1  H9   0.020
 5DW  plan-1  H10  0.020
 5DW  plan-1  H11  0.020
 5DW  plan-2  CA   0.020
 5DW  plan-2  C    0.020
 5DW  plan-2  O    0.020
 5DW  plan-2  O1   0.020

