# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 14:23:09 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (2S)-2-acetamido-3-phenyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1ccccc1)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
 5CR  5CR  '(2S)-2-acetamido-3-phenyl-propanoic acid'  L-peptide  27  15  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5CR
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
 5CR  CAA   C  CH3    0  -0.793  -0.9832   3.0277   0.1439
 5CR  CAL   C  C      0   0.555  -0.8097   1.6498  -0.4516
 5CR  OAB   O  O      0  -0.516  -0.3282   1.4964  -1.5671
 5CR  N     N  NH1    0  -0.641  -1.2198   0.6407   0.3303
 5CR  CA    C  CH1    0  -0.144  -1.1215  -0.7574   0.0017
 5CR  C     C  C      0   0.394  -2.3718  -1.5323   0.4825
 5CR  O     O  O      0  -0.467  -3.1391  -0.9479   1.2697
 5CR  OXT   O  OC    -1  -0.734  -2.4697  -2.6977   0.0570
 5CR  CB    C  CH2    0  -0.592   0.1311  -1.3938   0.6398
 5CR  CG    C  C      0   0.156   1.3947  -0.6726   0.2765
 5CR  CD1   C  C1     0  -0.239   1.8993   0.3369   1.0914
 5CR  CE1   C  C1     0  -0.165   3.0405   1.0415   0.7307
 5CR  CZ    C  C1     0  -0.274   3.6988   0.7421  -0.4544
 5CR  CE2   C  C1     0  -0.272   3.2079  -0.2678  -1.2731
 5CR  CD2   C  C1     0  -0.197   2.0656  -0.9647  -0.9087
 5CR  HAA1  H  HCH3   0   0.288  -0.0010   3.4794   0.2888
 5CR  HAA2  H  HCH3   0   0.287  -1.5309   3.6632  -0.5512
 5CR  HAA3  H  HCH3   0   0.232  -1.5021   3.0307   1.1011
 5CR  H     H  HNH1   0   0.349  -1.6795   0.8546   1.2010
 5CR  HA    H  HCH1   0   0.273  -1.0392  -0.8476  -1.0830
 5CR  HB1C  H  HCH2   0   0.217   0.0078  -1.3935   1.7272
 5CR  HB2C  H  HCH2   0   0.209   0.1834  -2.4369   0.3244
 5CR  HD1   H  H      0   0.188   1.3930   0.5750   2.0200
 5CR  HD2   H  H      0   0.229   1.6856  -1.7474  -1.5558
 5CR  HE1   H  H      0   0.194   3.4188   1.8233   1.3774
 5CR  HZ    H  H      0   0.232   4.5908   1.2869  -0.7367
 5CR  HE2   H  H      0   0.229   3.7170  -0.5131  -2.1968

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
 5CR  CAA  CAL   single    1.511  0.020  1.511
 5CR  CAL  OAB   double    1.225  0.020  1.225
 5CR  CAL  N     single    1.341  0.020  1.341
 5CR  N    CA    single    1.458  0.019  1.458
 5CR  CA   C     single    1.525  0.021  1.525
 5CR  CA   CB    single    1.530  0.020  1.530
 5CR  C    OXT   deloc     1.245  0.020  1.245
 5CR  C    O     deloc     1.231  0.020  1.231
 5CR  CB   CG    single    1.500  0.020  1.500
 5CR  CG   CD1   aromatic  1.392  0.020  1.392
 5CR  CG   CD2   aromatic  1.393  0.020  1.393
 5CR  CD1  CE1   aromatic  1.389  0.020  1.389
 5CR  CE1  CZ    aromatic  1.388  0.020  1.388
 5CR  CZ   CE2   aromatic  1.390  0.020  1.390
 5CR  CE2  CD2   aromatic  1.387  0.020  1.387
 5CR  CAA  HAA1  single    0.970  0.020  1.090
 5CR  CAA  HAA2  single    0.970  0.020  1.090
 5CR  CAA  HAA3  single    0.970  0.020  1.090
 5CR  N    H     single    0.860  0.020  0.860
 5CR  CA   HA    single    0.970  0.020  0.970
 5CR  CB   HB1C  single    0.970  0.020  1.090
 5CR  CB   HB2C  single    0.970  0.020  1.090
 5CR  CD1  HD1   single    0.930  0.020  1.080
 5CR  CD2  HD2   single    0.930  0.020  1.080
 5CR  CE1  HE1   single    0.930  0.020  1.080
 5CR  CZ   HZ    single    0.930  0.020  1.080
 5CR  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
 5CR  HAA3  CAA  HAA2  108.65  3.000
 5CR  HAA3  CAA  HAA1  108.13  3.000
 5CR  HAA2  CAA  HAA1  107.21  3.000
 5CR  HAA3  CAA  CAL   113.81  3.000
 5CR  HAA2  CAA  CAL   109.77  3.000
 5CR  HAA1  CAA  CAL   109.06  3.000
 5CR  N     CAL  OAB   123.86  3.000
 5CR  N     CAL  CAA   114.91  3.000
 5CR  OAB   CAL  CAA   121.23  3.000
 5CR  H     N    CA    114.00  3.000
 5CR  H     N    CAL   118.93  3.000
 5CR  CA    N    CAL   125.23  3.000
 5CR  HA    CA   CB    109.00  3.000
 5CR  HA    CA   C     109.00  3.000
 5CR  CB    CA   C     110.10  1.900
 5CR  HA    CA   N     110.00  3.000
 5CR  CB    CA   N     110.50  1.700
 5CR  C     CA   N     111.00  2.800
 5CR  OXT   C    O     127.39  3.000
 5CR  O     C    CA    120.80  1.700
 5CR  OXT   C    CA    115.23  3.000
 5CR  HB2C  CB   HB1C  107.03  3.000
 5CR  HB2C  CB   CG    110.45  3.000
 5CR  HB1C  CB   CG    109.61  3.000
 5CR  HB2C  CB   CA    108.28  3.000
 5CR  HB1C  CB   CA    108.62  3.000
 5CR  CG    CB   CA    112.67  3.000
 5CR  CD2   CG   CD1   118.40  3.000
 5CR  CD2   CG   CB    120.74  3.000
 5CR  CD1   CG   CB    120.82  3.000
 5CR  HD1   CD1  CE1   119.66  3.000
 5CR  HD1   CD1  CG    119.43  3.000
 5CR  CE1   CD1  CG    120.91  3.000
 5CR  HE1   CE1  CZ    119.99  3.000
 5CR  HE1   CE1  CD1   119.89  3.000
 5CR  CZ    CE1  CD1   120.12  3.000
 5CR  HZ    CZ   CE2   120.21  3.000
 5CR  HZ    CZ   CE1   120.31  3.000
 5CR  CE2   CZ   CE1   119.48  3.000
 5CR  HE2   CE2  CD2   119.83  3.000
 5CR  HE2   CE2  CZ    120.07  3.000
 5CR  CD2   CE2  CZ    120.09  3.000
 5CR  HD2   CD2  CE2   119.64  3.000
 5CR  HD2   CD2  CG    119.37  3.000
 5CR  CE2   CD2  CG    120.99  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
 5CR  CONST_01  CZ    CE1  CD1  CG     0.00   0.0  0
 5CR  CONST_02  CZ    CE2  CD2  CG     0.00   0.0  0
 5CR  CONST_03  CE2   CD2  CG   CD1    0.00   0.0  0
 5CR  CONST_04  CE2   CZ   CE1  CD1    0.00   0.0  0
 5CR  CONST_05  CD2   CG   CD1  CE1    0.00   0.0  0
 5CR  CONST_06  CD2   CE2  CZ   CE1    0.00   0.0  0
 5CR  CONST_07  CE1   CD1  CG   CB   180.00   0.0  0
 5CR  CONST_08  CE2   CD2  CG   CB   180.00   0.0  0
 5CR  CONST_09  HE1   CE1  CD1  CG   180.00   0.0  0
 5CR  CONST_10  HE2   CE2  CD2  CG   180.00   0.0  0
 5CR  CONST_11  HD2   CD2  CG   CD1  180.00   0.0  0
 5CR  CONST_12  HZ    CZ   CE1  CD1  180.00   0.0  0
 5CR  CONST_13  HD1   CD1  CE1  CZ   180.00   0.0  0
 5CR  CONST_14  CA    N    CAL  CAA  180.00   0.0  0
 5CR  CONST_15  CA    N    CAL  OAB    0.00   0.0  0
 5CR  CONST_16  H     N    CAL  CAA    0.00   0.0  0
 5CR  Var_01    CD1   CG   CB   CA    92.88  30.0  2
 5CR  Var_02    HAA1  CAA  CAL  OAB  -64.31  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
 5CR  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
 5CR  plan-1  CB   0.020
 5CR  plan-1  CG   0.020
 5CR  plan-1  CD1  0.020
 5CR  plan-1  CE1  0.020
 5CR  plan-1  CZ   0.020
 5CR  plan-1  CE2  0.020
 5CR  plan-1  CD2  0.020
 5CR  plan-1  HD1  0.020
 5CR  plan-1  HD2  0.020
 5CR  plan-1  HE1  0.020
 5CR  plan-1  HZ   0.020
 5CR  plan-1  HE2  0.020
 5CR  plan-2  CAA  0.020
 5CR  plan-2  CAL  0.020
 5CR  plan-2  OAB  0.020
 5CR  plan-2  N    0.020
 5CR  plan-2  CA   0.020
 5CR  plan-2  H    0.020
 5CR  plan-3  CA   0.020
 5CR  plan-3  C    0.020
 5CR  plan-3  O    0.020
 5CR  plan-3  OXT  0.020

