# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 05:42:46 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 DPN  DPN  'D-phenylalanine          '  D-peptide  22  12  .  2022-07-24  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_DPN
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
 DPN  N    N  NH2    0  -0.774  -1.1025   1.4779   0.8830
 DPN  CA   C  CH1    0  -0.205  -1.3452   0.1178   0.4365
 DPN  C    C  C      0   0.382  -2.8164  -0.2253   0.0798
 DPN  O    O  O      0  -0.604  -3.6520   0.6982   0.1144
 DPN  OXT  O  OC    -1  -0.622  -3.0401  -1.4190  -0.2125
 DPN  CB   C  CH2    0  -0.526  -0.4364  -0.2070  -0.7581
 DPN  CG   C  CR6    0   0.166   1.0253  -0.1566  -0.4213
 DPN  CD1  C  CR16   0  -0.314   1.6637  -1.2808   0.1001
 DPN  CD2  C  CR16   0  -0.309   1.7755   1.0042  -0.5955
 DPN  CE1  C  CR16   0  -0.242   3.0105  -1.2507   0.4372
 DPN  CE2  C  CR16   0  -0.245   3.1241   1.0401  -0.2659
 DPN  CZ   C  CR16   0  -0.278   3.7474  -0.0876   0.2541
 DPN  H    H  HNH2   0   0.323  -1.4071   2.1126   0.1529
 DPN  H2   H  HNH2   0   0.333  -1.7225   1.6769   1.6589
 DPN  HA   H  HCH1   0   0.220  -1.0557  -0.5544   1.2546
 DPN  HB2  H  HCH2   0   0.243  -0.6934  -1.2016  -1.1234
 DPN  HB3  H  HCH2   0   0.232  -0.6553   0.4970  -1.5685
 DPN  HD1  H  HCR6   0   0.240   1.0976  -2.1956   0.2390
 DPN  HD2  H  HCR6   0   0.236   1.2999   1.8883  -1.0022
 DPN  HE1  H  HCR6   0   0.248   3.4852  -2.1380   0.8369
 DPN  HE2  H  HCR6   0   0.248   3.6912   1.9504  -0.4159
 DPN  HZ   H  HCR6   0   0.249   4.7991  -0.0608   0.5093

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
 DPN  N    CA   single    1.458  0.019  1.458
 DPN  N    H    single    0.860  0.020  0.860
 DPN  N    H2   single    0.890  0.020  1.040
 DPN  CA   C    single    1.525  0.021  1.525
 DPN  CA   CB   single    1.521  0.033  1.521
 DPN  CA   HA   single    0.970  0.020  0.970
 DPN  C    O    deloc     1.231  0.020  1.231
 DPN  C    OXT  deloc     1.249  0.020  1.249
 DPN  CB   CG   single    1.501  0.020  1.501
 DPN  CB   HB2  single    0.970  0.020  1.090
 DPN  CB   HB3  single    0.970  0.020  1.090
 DPN  CG   CD1  aromatic  1.394  0.020  1.394
 DPN  CG   CD2  aromatic  1.393  0.020  1.393
 DPN  CD1  CE1  aromatic  1.389  0.020  1.389
 DPN  CD1  HD1  single    0.930  0.020  1.080
 DPN  CD2  CE2  aromatic  1.389  0.020  1.389
 DPN  CD2  HD2  single    0.930  0.020  1.080
 DPN  CE1  CZ   aromatic  1.389  0.020  1.389
 DPN  CE1  HE1  single    0.930  0.020  1.080
 DPN  CE2  CZ   aromatic  1.390  0.020  1.390
 DPN  CE2  HE2  single    0.930  0.020  1.080
 DPN  CZ   HZ   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
 DPN  H2   N    H    104.16  3.000
 DPN  H2   N    CA   108.50  3.000
 DPN  H    N    CA   114.00  3.000
 DPN  HA   CA   CB   109.00  3.000
 DPN  HA   CA   C    110.00  3.000
 DPN  CB   CA   C    110.50  1.500
 DPN  HA   CA   N    110.00  3.000
 DPN  CB   CA   N    110.40  1.500
 DPN  C    CA   N    111.00  2.800
 DPN  OXT  C    O    126.49  3.000
 DPN  OXT  C    CA   120.80  1.700
 DPN  O    C    CA   120.80  1.700
 DPN  HB3  CB   HB2  106.94  3.000
 DPN  HB3  CB   CG   109.82  3.000
 DPN  HB2  CB   CG   109.60  3.000
 DPN  HB3  CB   CA   108.74  3.000
 DPN  HB2  CB   CA   108.30  3.000
 DPN  CG   CB   CA   113.24  3.000
 DPN  CD2  CG   CD1  118.18  3.000
 DPN  CD2  CG   CB   121.63  3.000
 DPN  CD1  CG   CB   120.19  3.000
 DPN  HD1  CD1  CE1  119.56  3.000
 DPN  HD1  CD1  CG   119.28  3.000
 DPN  CE1  CD1  CG   121.16  3.000
 DPN  HD2  CD2  CE2  119.63  3.000
 DPN  HD2  CD2  CG   119.38  3.000
 DPN  CE2  CD2  CG   120.99  3.000
 DPN  HE1  CE1  CZ   120.15  3.000
 DPN  HE1  CE1  CD1  119.80  3.000
 DPN  CZ   CE1  CD1  120.05  3.000
 DPN  HE2  CE2  CZ   119.94  3.000
 DPN  HE2  CE2  CD2  119.83  3.000
 DPN  CZ   CE2  CD2  120.23  3.000
 DPN  HZ   CZ   CE2  120.26  3.000
 DPN  HZ   CZ   CE1  120.34  3.000
 DPN  CE2  CZ   CE1  119.40  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
 DPN  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 DPN  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 DPN  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 DPN  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 DPN  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 DPN  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 DPN  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 DPN  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 DPN  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 DPN  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 DPN  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 DPN  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 DPN  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 DPN  Var_01    CD1  CG   CB   CA    86.55  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
 DPN  chir_01  CA  N  C  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
 DPN  plan-1  CB   0.020
 DPN  plan-1  CG   0.020
 DPN  plan-1  CD1  0.020
 DPN  plan-1  CD2  0.020
 DPN  plan-1  CE1  0.020
 DPN  plan-1  CE2  0.020
 DPN  plan-1  CZ   0.020
 DPN  plan-1  HD1  0.020
 DPN  plan-1  HD2  0.020
 DPN  plan-1  HE1  0.020
 DPN  plan-1  HE2  0.020
 DPN  plan-1  HZ   0.020
 DPN  plan-2  CA   0.020
 DPN  plan-2  C    0.020
 DPN  plan-2  O    0.020
 DPN  plan-2  OXT  0.020

