# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:45:37 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: [(1R)-1-amino-2-phenylethyl]carbamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccccc1)NC(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
 APE  APE  '[(1R)-1-amino-2-phenylethyl]carbamic acid'  peptide  25  13  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_APE
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
 APE  N    N  NH2   0  -0.773   0.6500   1.1657   1.0713
 APE  CA   C  CH1   0   0.081   0.8971   0.1445   0.0897
 APE  CB   C  CH2   0  -0.563  -0.1402   0.2100  -1.0329
 APE  CG   C  CR6   0   0.163  -1.5455   0.0227  -0.5384
 APE  CD1  C  CR16  0  -0.309  -2.3666   1.1146  -0.2702
 APE  CD2  C  CR16  0  -0.308  -2.0536  -1.2572  -0.3287
 APE  CE1  C  CR16  0  -0.244  -3.6631   0.9352   0.1927
 APE  CE2  C  CR16  0  -0.241  -3.3477  -1.4430   0.1393
 APE  CZ   C  CR16  0  -0.273  -4.1579  -0.3459   0.4016
 APE  NHO  N  NH1   0  -0.658   2.2176   0.1797  -0.5333
 APE  C    C  C     0   0.678   3.3231  -0.1961   0.1324
 APE  O    O  O     0  -0.523   3.3339  -0.7034   1.2381
 APE  OXT  O  OH1   0  -0.622   4.4328   0.0396  -0.5774
 APE  H    H  HNH2  0   0.354   1.3074   1.0878   1.8366
 APE  H2   H  HNH2  0   0.341   0.7678   2.0865   0.6666
 APE  HA   H  HCH1  0   0.251   0.8072  -0.8211   0.5913
 APE  HB2  H  HCH2  0   0.256  -0.0515   1.1738  -1.5453
 APE  HB3  H  HCH2  0   0.263   0.0995  -0.5609  -1.7685
 APE  HD1  H  HCR6  0   0.243  -1.9892   2.1172  -0.4319
 APE  HD2  H  HCR6  0   0.246  -1.4320  -2.1208  -0.5372
 APE  HE1  H  HCR6  0   0.252  -4.2874   1.7974   0.3902
 APE  HE2  H  HCR6  0   0.253  -3.7249  -2.4457   0.2945
 APE  HZ   H  HCR6  0   0.253  -5.1689  -0.4888   0.7611
 APE  HN   H  HNH1  0   0.400   2.3277   0.7086  -1.3858
 APE  HXT  H  HOH1  0   0.481   5.2008  -0.2404  -0.0626

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
 APE  N    CA   single    1.458  0.019  1.458
 APE  N    H    single    0.860  0.020  0.860
 APE  N    H2   single    0.890  0.020  1.040
 APE  CA   CB   single    1.521  0.033  1.521
 APE  CA   NHO  single    1.461  0.020  1.461
 APE  CA   HA   single    0.970  0.020  0.970
 APE  CB   CG   single    1.501  0.020  1.501
 APE  CB   HB2  single    0.970  0.020  1.090
 APE  CB   HB3  single    0.970  0.020  1.090
 APE  CG   CD1  aromatic  1.392  0.020  1.392
 APE  CG   CD2  aromatic  1.393  0.020  1.393
 APE  CD1  CE1  aromatic  1.388  0.020  1.388
 APE  CD1  HD1  single    0.930  0.020  1.080
 APE  CD2  CE2  aromatic  1.389  0.020  1.389
 APE  CD2  HD2  single    0.930  0.020  1.080
 APE  CE1  CZ   aromatic  1.389  0.020  1.389
 APE  CE1  HE1  single    0.930  0.020  1.080
 APE  CE2  CZ   aromatic  1.389  0.020  1.389
 APE  CE2  HE2  single    0.930  0.020  1.080
 APE  CZ   HZ   single    0.930  0.020  1.080
 APE  NHO  C    single    1.344  0.020  1.344
 APE  NHO  HN   single    0.860  0.020  1.020
 APE  C    O    double    1.231  0.020  1.231
 APE  C    OXT  single    1.338  0.020  1.338
 APE  OXT  HXT  single    0.850  0.020  0.980

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
 APE  H2   N    H    107.26  3.000
 APE  H2   N    CA   110.67  3.000
 APE  H    N    CA   114.00  3.000
 APE  HA   CA   NHO  106.96  3.000
 APE  HA   CA   CB   109.00  3.000
 APE  NHO  CA   CB   107.40  3.000
 APE  HA   CA   N    110.00  3.000
 APE  NHO  CA   N    115.44  3.000
 APE  CB   CA   N    110.40  1.500
 APE  HB3  CB   HB2  106.76  3.000
 APE  HB3  CB   CG   109.83  3.000
 APE  HB2  CB   CG   109.86  3.000
 APE  HB3  CB   CA   108.37  3.000
 APE  HB2  CB   CA   109.03  3.000
 APE  CG   CB   CA   112.80  3.000
 APE  CD2  CG   CD1  118.46  3.000
 APE  CD2  CG   CB   120.37  3.000
 APE  CD1  CG   CB   121.17  3.000
 APE  HD1  CD1  CE1  119.65  3.000
 APE  HD1  CD1  CG   119.45  3.000
 APE  CE1  CD1  CG   120.91  3.000
 APE  HD2  CD2  CE2  119.50  3.000
 APE  HD2  CD2  CG   119.59  3.000
 APE  CE2  CD2  CG   120.90  3.000
 APE  HE1  CE1  CZ   120.11  3.000
 APE  HE1  CE1  CD1  119.76  3.000
 APE  CZ   CE1  CD1  120.13  3.000
 APE  HE2  CE2  CZ   120.09  3.000
 APE  HE2  CE2  CD2  119.80  3.000
 APE  CZ   CE2  CD2  120.11  3.000
 APE  HZ   CZ   CE2  120.22  3.000
 APE  HZ   CZ   CE1  120.29  3.000
 APE  CE2  CZ   CE1  119.49  3.000
 APE  HN   NHO  C    118.37  3.000
 APE  HN   NHO  CA   118.13  3.000
 APE  C    NHO  CA   121.71  3.000
 APE  OXT  C    O    123.24  3.000
 APE  OXT  C    NHO  111.73  3.000
 APE  O    C    NHO  125.03  3.000
 APE  HXT  OXT  C    109.00  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
 APE  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 APE  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 APE  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 APE  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 APE  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 APE  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 APE  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 APE  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 APE  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 APE  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 APE  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 APE  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 APE  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 APE  CONST_14  HXT  OXT  C    NHO  180.00   0.0  0
 APE  Var_01    CD1  CG   CB   CA    96.66  30.0  2
 APE  Var_02    O    C    NHO  CA     6.95  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
 APE  chir_01  CA  N  CB  NHO  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
 APE  plan-1  CB   0.020
 APE  plan-1  CG   0.020
 APE  plan-1  CD1  0.020
 APE  plan-1  CD2  0.020
 APE  plan-1  CE1  0.020
 APE  plan-1  CE2  0.020
 APE  plan-1  CZ   0.020
 APE  plan-1  HD1  0.020
 APE  plan-1  HD2  0.020
 APE  plan-1  HE1  0.020
 APE  plan-1  HE2  0.020
 APE  plan-1  HZ   0.020
 APE  plan-2  NHO  0.020
 APE  plan-2  C    0.020
 APE  plan-2  O    0.020
 APE  plan-2  OXT  0.020
 APE  plan-2  HXT  0.020

