# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 14:56:02 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: (2S)-2-azanyl-3-(3,5-difluorophenyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cc(F)cc(F)c1)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
 WFP  WFP  '(2S)-2-azanyl-3-(3,5-difluorophenyl)propanoic acid'  L-peptide  22  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_WFP
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
 WFP  C    C  C      0   0.420  -22.5535  -32.1903   5.6304
 WFP  N    N  NH2    0  -0.808  -21.5879  -30.1700   6.6759
 WFP  O    O  O      0  -0.599  -23.1948  -33.2433   5.8048
 WFP  F1   F  F      0  -0.312  -22.1425  -28.2189  11.3846
 WFP  F2   F  F      0  -0.312  -19.3978  -31.9849  11.7101
 WFP  CA   C  CH1    0  -0.214  -21.8577  -31.5829   6.8790
 WFP  CB   C  CH2    0  -0.492  -22.6941  -31.7916   8.1466
 WFP  CG   C  CR6    0   0.161  -22.0337  -31.2077   9.3608
 WFP  CZ   C  CR16   0  -0.577  -20.7420  -30.0789  11.5902
 WFP  CD1  C  CR16   0  -0.481  -22.4101  -29.9532   9.8330
 WFP  CD2  C  CR16   0  -0.478  -21.0061  -31.8977  10.0046
 WFP  CE1  C  CR6    0   0.556  -21.7649  -29.4238  10.9329
 WFP  CE2  C  CR6    0   0.557  -20.3873  -31.3202  11.0946
 WFP  OXT  O  OC    -1  -0.598  -22.3747  -31.5912   4.5516
 WFP  H    H  HNH2   0   0.332  -20.7946  -29.8776   7.2309
 WFP  H2   H  HNH2   0   0.335  -21.3357  -30.0422   5.7045
 WFP  HA   H  HCH1   0   0.204  -20.9286  -32.1669   7.0086
 WFP  HB2  H  HCH2   0   0.232  -23.6746  -31.3298   8.0070
 WFP  HB3  H  HCH2   0   0.239  -22.8545  -32.8598   8.2926
 WFP  HZ   H  HCR6   0   0.295  -20.2466  -29.6466  12.4495
 WFP  HD1  H  HCR6   0   0.269  -23.2044  -29.3985   9.3504
 WFP  HD2  H  HCR6   0   0.270  -20.6967  -32.8765   9.6587

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
 WFP  C    O    deloc     1.231  0.020  1.231
 WFP  C    CA   single    1.525  0.021  1.525
 WFP  C    OXT  deloc     1.247  0.020  1.247
 WFP  N    CA   single    1.458  0.019  1.458
 WFP  F1   CE1  single    1.341  0.020  1.341
 WFP  F2   CE2  single    1.342  0.020  1.342
 WFP  CA   CB   single    1.530  0.020  1.530
 WFP  CB   CG   single    1.500  0.020  1.500
 WFP  CG   CD1  aromatic  1.392  0.020  1.392
 WFP  CG   CD2  aromatic  1.395  0.020  1.395
 WFP  CZ   CE1  aromatic  1.381  0.020  1.381
 WFP  CZ   CE2  aromatic  1.383  0.020  1.383
 WFP  CD1  CE1  aromatic  1.381  0.020  1.381
 WFP  CD2  CE2  aromatic  1.380  0.020  1.380
 WFP  N    H    single    0.860  0.020  0.860
 WFP  N    H2   single    0.890  0.020  1.040
 WFP  CA   HA   single    0.970  0.020  0.970
 WFP  CB   HB2  single    0.970  0.020  1.090
 WFP  CB   HB3  single    0.970  0.020  1.090
 WFP  CZ   HZ   single    0.930  0.020  1.080
 WFP  CD1  HD1  single    0.930  0.020  1.080
 WFP  CD2  HD2  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
 WFP  OXT  C    CA   116.32  3.000
 WFP  OXT  C    O    126.97  3.000
 WFP  CA   C    O    120.80  1.700
 WFP  H2   N    H    107.15  3.000
 WFP  H2   N    CA   107.67  3.000
 WFP  H    N    CA   114.00  3.000
 WFP  HA   CA   CB   109.00  3.000
 WFP  HA   CA   N    110.00  3.000
 WFP  CB   CA   N    110.50  1.700
 WFP  HA   CA   C    109.00  3.000
 WFP  CB   CA   C    110.10  1.900
 WFP  N    CA   C    111.00  2.800
 WFP  HB3  CB   HB2  107.41  3.000
 WFP  HB3  CB   CG   109.74  3.000
 WFP  HB2  CB   CG   109.51  3.000
 WFP  HB3  CB   CA   108.93  3.000
 WFP  HB2  CB   CA   109.05  3.000
 WFP  CG   CB   CA   112.09  3.000
 WFP  CD2  CG   CD1  119.23  3.000
 WFP  CD2  CG   CB   120.34  3.000
 WFP  CD1  CG   CB   120.40  3.000
 WFP  HZ   CZ   CE2  121.72  3.000
 WFP  HZ   CZ   CE1  121.84  3.000
 WFP  CE2  CZ   CE1  116.44  3.000
 WFP  HD1  CD1  CE1  120.10  3.000
 WFP  HD1  CD1  CG   120.60  3.000
 WFP  CE1  CD1  CG   119.30  3.000
 WFP  HD2  CD2  CE2  120.15  3.000
 WFP  HD2  CD2  CG   120.66  3.000
 WFP  CE2  CD2  CG   119.19  3.000
 WFP  CD1  CE1  CZ   122.91  3.000
 WFP  CD1  CE1  F1   118.77  3.000
 WFP  CZ   CE1  F1   118.32  3.000
 WFP  CD2  CE2  CZ   122.93  3.000
 WFP  CD2  CE2  F2   119.06  3.000
 WFP  CZ   CE2  F2   118.00  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
 WFP  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 WFP  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 WFP  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 WFP  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 WFP  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 WFP  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 WFP  CONST_07  CE2  CZ   CE1  F1   180.00   0.0  0
 WFP  CONST_08  CG   CD1  CE1  F1   180.00   0.0  0
 WFP  CONST_09  CE1  CZ   CE2  F2   180.00   0.0  0
 WFP  CONST_10  CG   CD2  CE2  F2   180.00   0.0  0
 WFP  CONST_11  CE1  CD1  CG   CB   180.00   0.0  0
 WFP  CONST_12  CE2  CD2  CG   CB   180.00   0.0  0
 WFP  CONST_13  HD1  CD1  CE1  CZ   180.00   0.0  0
 WFP  CONST_14  HD2  CD2  CE2  CZ   180.00   0.0  0
 WFP  CONST_15  HZ   CZ   CE1  CD1  180.00   0.0  0
 WFP  Var_01    CD1  CG   CB   CA    98.27  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
 WFP  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
 WFP  plan-1  F1   0.020
 WFP  plan-1  F2   0.020
 WFP  plan-1  CB   0.020
 WFP  plan-1  CG   0.020
 WFP  plan-1  CZ   0.020
 WFP  plan-1  CD1  0.020
 WFP  plan-1  CD2  0.020
 WFP  plan-1  CE1  0.020
 WFP  plan-1  CE2  0.020
 WFP  plan-1  HZ   0.020
 WFP  plan-1  HD1  0.020
 WFP  plan-1  HD2  0.020
 WFP  plan-2  C    0.020
 WFP  plan-2  O    0.020
 WFP  plan-2  CA   0.020
 WFP  plan-2  OXT  0.020

