# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 00:20:17 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2R)-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
 PG9  PG9  '(2R)-amino(phenyl)ethanoic acid'  D-peptide  19  11  .  2016-04-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PG9
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
 PG9  N    N  NH2    0  -0.796  28.6646  44.7998  190.1224
 PG9  CA   C  CH1    0  -0.286  28.9026  46.2083  190.3964
 PG9  CB   C  CR6    0   0.136  29.5638  46.4132  191.7404
 PG9  CG1  C  CR16   0  -0.293  30.3038  47.5689  191.9914
 PG9  CD1  C  CR16   0  -0.243  30.8751  47.7973  193.2347
 PG9  CE   C  CR16   0  -0.277  30.7098  46.8753  194.2612
 PG9  CD2  C  CR16   0  -0.239  29.9766  45.7212  194.0234
 PG9  CG2  C  CR16   0  -0.319  29.4140  45.4910  192.7734
 PG9  C    C  C      0   0.397  27.6102  47.0889  190.3893
 PG9  O    O  O      0  -0.596  27.7703  48.3043  190.1766
 PG9  OXT  O  OC    -1  -0.592  26.5432  46.4936  190.6309
 PG9  H    H  HNH2   0   0.331  27.7521  44.5746  190.5052
 PG9  H2   H  HNH2   0   0.342  28.5541  44.6856  189.1223
 PG9  HA   H  HCH1   0   0.231  29.5785  46.5979  189.6304
 PG9  HG1  H  HCR6   0   0.234  30.4398  48.2971  191.2013
 PG9  HD1  H  HCR6   0   0.244  31.4532  48.6975  193.4032
 PG9  HE   H  HCR6   0   0.245  31.1524  47.0528  195.2331
 PG9  HD2  H  HCR6   0   0.244  29.8437  44.9919  194.8131
 PG9  HG2  H  HCR6   0   0.237  28.8607  44.5765  192.6028

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
 PG9  N    CA   single    1.458  0.019  1.458
 PG9  N    H    single    0.860  0.020  0.860
 PG9  N    H2   single    0.890  0.020  1.040
 PG9  CA   CB   single    1.521  0.033  1.521
 PG9  CA   C    single    1.525  0.021  1.525
 PG9  CA   HA   single    0.970  0.020  0.970
 PG9  CB   CG1  aromatic  1.395  0.020  1.395
 PG9  CB   CG2  aromatic  1.393  0.020  1.393
 PG9  CG1  CD1  aromatic  1.387  0.020  1.387
 PG9  CG1  HG1  single    0.930  0.020  1.080
 PG9  CD1  CE   aromatic  1.390  0.020  1.390
 PG9  CD1  HD1  single    0.930  0.020  1.080
 PG9  CE   CD2  aromatic  1.388  0.020  1.388
 PG9  CE   HE   single    0.930  0.020  1.080
 PG9  CD2  CG2  aromatic  1.390  0.020  1.390
 PG9  CD2  HD2  single    0.930  0.020  1.080
 PG9  CG2  HG2  single    0.930  0.020  1.080
 PG9  C    O    deloc     1.231  0.020  1.231
 PG9  C    OXT  deloc     1.246  0.020  1.246

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
 PG9  H2   N    H    104.44  3.000
 PG9  H2   N    CA   108.24  3.000
 PG9  H    N    CA   114.00  3.000
 PG9  HA   CA   C    110.00  3.000
 PG9  HA   CA   CB   109.00  3.000
 PG9  C    CA   CB   110.50  1.500
 PG9  HA   CA   N    110.00  3.000
 PG9  C    CA   N    111.00  2.800
 PG9  CB   CA   N    110.40  1.500
 PG9  CG2  CB   CG1  118.17  3.000
 PG9  CG2  CB   CA   121.50  3.000
 PG9  CG1  CB   CA   120.28  3.000
 PG9  HG1  CG1  CD1  119.43  3.000
 PG9  HG1  CG1  CB   119.50  3.000
 PG9  CD1  CG1  CB   121.07  3.000
 PG9  HD1  CD1  CE   120.01  3.000
 PG9  HD1  CD1  CG1  119.74  3.000
 PG9  CE   CD1  CG1  120.25  3.000
 PG9  HE   CE   CD2  120.41  3.000
 PG9  HE   CE   CD1  120.38  3.000
 PG9  CD2  CE   CD1  119.21  3.000
 PG9  HD2  CD2  CG2  119.64  3.000
 PG9  HD2  CD2  CE   119.99  3.000
 PG9  CG2  CD2  CE   120.38  3.000
 PG9  HG2  CG2  CD2  119.25  3.000
 PG9  HG2  CG2  CB   119.83  3.000
 PG9  CD2  CG2  CB   120.91  3.000
 PG9  OXT  C    O    127.61  3.000
 PG9  OXT  C    CA   120.80  1.700
 PG9  O    C    CA   120.80  1.700

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
 PG9  CONST_01  CE   CD1  CG1  CB     0.00  0.0  0
 PG9  CONST_02  CE   CD2  CG2  CB     0.00  0.0  0
 PG9  CONST_03  CD2  CG2  CB   CG1    0.00  0.0  0
 PG9  CONST_04  CD2  CE   CD1  CG1    0.00  0.0  0
 PG9  CONST_05  CG2  CB   CG1  CD1    0.00  0.0  0
 PG9  CONST_06  CG2  CD2  CE   CD1    0.00  0.0  0
 PG9  CONST_07  CD1  CG1  CB   CA   180.00  0.0  0
 PG9  CONST_08  CD2  CG2  CB   CA   180.00  0.0  0
 PG9  CONST_09  HD1  CD1  CG1  CB   180.00  0.0  0
 PG9  CONST_10  HD2  CD2  CG2  CB   180.00  0.0  0
 PG9  CONST_11  HG2  CG2  CB   CG1  180.00  0.0  0
 PG9  CONST_12  HE   CE   CD1  CG1  180.00  0.0  0
 PG9  CONST_13  HG1  CG1  CD1  CE   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
 PG9  chir_01  CA  N  CB  C  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
 PG9  plan-1  CA   0.020
 PG9  plan-1  CB   0.020
 PG9  plan-1  CG1  0.020
 PG9  plan-1  CD1  0.020
 PG9  plan-1  CE   0.020
 PG9  plan-1  CD2  0.020
 PG9  plan-1  CG2  0.020
 PG9  plan-1  HG1  0.020
 PG9  plan-1  HD1  0.020
 PG9  plan-1  HE   0.020
 PG9  plan-1  HD2  0.020
 PG9  plan-1  HG2  0.020
 PG9  plan-2  CA   0.020
 PG9  plan-2  C    0.020
 PG9  plan-2  O    0.020
 PG9  plan-2  OXT  0.020

