# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar  4 16:03:52 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2S)-amino(phenyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](C(O)=O)c1ccccc1
#
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
 004  004  '(2S)-amino(phenyl)ethanoic acid'  L-peptide  19  11  .  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
;

data_comp_004
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
 004  C    C  C      0   0.408  30.7797   2.4184  52.6942
 004  N    N  NH2    0  -0.804  32.2461   0.6198  53.5997
 004  O    O  O      0  -0.591  31.4760   3.1699  53.4008
 004  CA   C  CH1    0  -0.297  31.2046   0.9146  52.6343
 004  CB   C  CR6    0   0.172  29.9962   0.0351  52.8450
 004  CE   C  CR16   0  -0.277  27.6949  -1.5239  53.2362
 004  CD1  C  CR16   0  -0.242  28.3991  -1.0237  54.3249
 004  CD2  C  CR16   0  -0.243  28.1412  -1.2423  51.9521
 004  CG1  C  CR16   0  -0.293  29.5376  -0.2537  54.1295
 004  CG2  C  CR16   0  -0.326  29.2810  -0.4712  51.7636
 004  OXT  O  OC    -1  -0.593  29.8013   2.7283  51.9926
 004  HN   H  HNH2   0   0.333  32.8126  -0.1535  53.2782
 004  HNA  H  HNH2   0   0.338  32.8455   1.4299  53.6796
 004  HA   H  HCH1   0   0.217  31.5389   0.7611  51.5951
 004  HE   H  HCR6   0   0.244  26.8119  -2.1314  53.3879
 004  HD1  H  HCR6   0   0.242  28.0608  -1.2377  55.3314
 004  HD2  H  HCR6   0   0.243  27.6032  -1.6266  51.0943
 004  HG1  H  HCR6   0   0.235  30.0898   0.1152  54.9841
 004  HG2  H  HCR6   0   0.234  29.6262  -0.2668  50.7561

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
 004  C    O    deloc     1.231  0.020  1.231
 004  C    OXT  deloc     1.243  0.020  1.243
 004  N    HN   single    0.890  0.020  1.040
 004  N    HNA  single    0.890  0.020  1.040
 004  CA   C    single    1.525  0.021  1.525
 004  CA   N    single    1.458  0.019  1.458
 004  CA   CB   single    1.521  0.033  1.521
 004  CA   HA   single    0.970  0.020  0.970
 004  CB   CG1  aromatic  1.394  0.020  1.394
 004  CE   CD1  aromatic  1.390  0.020  1.390
 004  CE   HE   single    0.930  0.020  1.080
 004  CD1  HD1  single    0.930  0.020  1.080
 004  CD2  CE   aromatic  1.388  0.020  1.388
 004  CD2  HD2  single    0.930  0.020  1.080
 004  CG1  CD1  aromatic  1.388  0.020  1.388
 004  CG1  HG1  single    0.930  0.020  1.080
 004  CG2  CB   aromatic  1.392  0.020  1.392
 004  CG2  CD2  aromatic  1.389  0.020  1.389
 004  CG2  HG2  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
 004  OXT  C    CA   120.80  1.700
 004  CA   C    O    120.80  1.700
 004  OXT  C    O    127.60  3.000
 004  HNA  N    HN   107.80  3.000
 004  HNA  N    CA   108.39  3.000
 004  HN   N    CA   110.25  3.000
 004  HA   CA   CB   109.00  3.000
 004  HA   CA   N    110.00  3.000
 004  CB   CA   N    110.40  1.500
 004  HA   CA   C    110.00  3.000
 004  CB   CA   C    110.50  1.500
 004  N    CA   C    111.00  2.800
 004  CG2  CB   CG1  118.13  3.000
 004  CG2  CB   CA   120.99  3.000
 004  CG1  CB   CA   120.84  3.000
 004  HE   CE   CD2  120.38  3.000
 004  CD2  CE   CD1  119.26  3.000
 004  HE   CE   CD1  120.37  3.000
 004  HD1  CD1  CG1  119.77  3.000
 004  CG1  CD1  CE   120.33  3.000
 004  HD1  CD1  CE   119.91  3.000
 004  HD2  CD2  CG2  119.81  3.000
 004  CG2  CD2  CE   120.13  3.000
 004  HD2  CD2  CE   120.06  3.000
 004  HG1  CG1  CD1  119.76  3.000
 004  HG1  CG1  CB   119.28  3.000
 004  CD1  CG1  CB   120.95  3.000
 004  HG2  CG2  CD2  119.47  3.000
 004  HG2  CG2  CB   119.32  3.000
 004  CD2  CG2  CB   121.21  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
 004  CONST_01  CE   CD1  CG1  CB     0.00  0.0  0
 004  CONST_02  CE   CD2  CG2  CB     0.00  0.0  0
 004  CONST_03  CG2  CD2  CE   CD1    0.00  0.0  0
 004  CONST_04  CG2  CB   CG1  CD1    0.00  0.0  0
 004  CONST_05  CG1  CD1  CE   CD2    0.00  0.0  0
 004  CONST_06  CG1  CB   CG2  CD2    0.00  0.0  0
 004  CONST_07  CD1  CG1  CB   CA   180.00  0.0  0
 004  CONST_08  CD2  CG2  CB   CA   180.00  0.0  0
 004  CONST_09  HD1  CD1  CG1  CB   180.00  0.0  0
 004  CONST_10  HD2  CD2  CG2  CB   180.00  0.0  0
 004  CONST_11  HG1  CG1  CD1  CE   180.00  0.0  0
 004  CONST_12  HG2  CG2  CD2  CE   180.00  0.0  0
 004  CONST_13  HE   CE   CD1  CG1  180.00  0.0  0

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
 004  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
 004  plan-1  CA   0.020
 004  plan-1  CB   0.020
 004  plan-1  CE   0.020
 004  plan-1  CD1  0.020
 004  plan-1  CD2  0.020
 004  plan-1  CG1  0.020
 004  plan-1  CG2  0.020
 004  plan-1  HE   0.020
 004  plan-1  HD1  0.020
 004  plan-1  HD2  0.020
 004  plan-1  HG1  0.020
 004  plan-1  HG2  0.020
 004  plan-2  C    0.020
 004  plan-2  O    0.020
 004  plan-2  CA   0.020
 004  plan-2  OXT  0.020

