# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 13:18:17 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 4-chloro-D-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1ccc(Cl)cc1)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
 D0C  D0C  "4-chloro-D-phenylalanine"  D-peptide  22  13  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT (side chain)
;

data_comp_D0C
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
 D0C  N    N   NH2    0  -0.795  29.9832  -22.0150   -9.7518
 D0C  CA   C   CH1    0  -0.175  29.5591  -20.8359   -9.0102
 D0C  C    C   C      0   0.410  29.7766  -19.5766   -9.8784
 D0C  O    O   O      0  -0.601  30.3822  -18.6200   -9.3616
 D0C  CB   C   CH2    0  -0.528  28.0816  -20.9129   -8.5667
 D0C  CG   C   CR6    0   0.145  27.6334  -19.7101   -7.7915
 D0C  CD1  C   CR16   0  -0.307  26.9086  -18.6876   -8.3987
 D0C  CD2  C   CR16   0  -0.319  27.9718  -19.5620   -6.4477
 D0C  CE1  C   CR16   0  -0.198  26.5327  -17.5501   -7.6981
 D0C  CE2  C   CR16   0  -0.197  27.6092  -18.4328   -5.7291
 D0C  CZ   C   CR6    0  -0.059  26.8903  -17.4325   -6.3651
 D0C  CL   CL  CL     0  -0.140  26.4299  -16.0133   -5.4768
 D0C  OXT  O   OC    -1  -0.610  29.2945  -19.6303  -11.0301
 D0C  H    H   HNH2   0   0.332  29.6998  -22.8536   -9.2584
 D0C  H2   H   HNH2   0   0.327  29.4878  -22.0237  -10.6356
 D0C  HA   H   HCH1   0   0.200  30.1764  -20.7589   -8.1096
 D0C  HB2  H   HCH2   0   0.231  27.4601  -21.0371   -9.4569
 D0C  HB3  H   HCH2   0   0.236  27.9533  -21.8130   -7.9574
 D0C  HD1  H   HCR6   0   0.252  26.6332  -18.7746   -9.4426
 D0C  HD2  H   HCR6   0   0.254  28.5316  -20.3435   -5.9471
 D0C  HE1  H   HCR6   0   0.272  25.9675  -16.7687   -8.1883
 D0C  HE2  H   HCR6   0   0.272  27.8830  -18.3357   -4.6870

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
 D0C  C    O    deloc     1.231  0.020  1.231
 D0C  C    CA   single    1.525  0.021  1.525
 D0C  N    CA   single    1.458  0.019  1.458
 D0C  CA   CB   single    1.521  0.033  1.521
 D0C  CB   CG   single    1.500  0.020  1.500
 D0C  CD1  CG   aromatic  1.393  0.020  1.393
 D0C  CD1  CE1  aromatic  1.388  0.020  1.388
 D0C  CG   CD2  aromatic  1.394  0.020  1.394
 D0C  CE1  CZ   aromatic  1.385  0.020  1.385
 D0C  CD2  CE2  aromatic  1.387  0.020  1.387
 D0C  CZ   CE2  aromatic  1.386  0.020  1.386
 D0C  CZ   CL   single    1.736  0.020  1.736
 D0C  C    OXT  deloc     1.250  0.020  1.250
 D0C  N    H    single    0.860  0.020  0.860
 D0C  N    H2   single    0.890  0.020  1.040
 D0C  CA   HA   single    0.970  0.020  0.970
 D0C  CB   HB2  single    0.970  0.020  1.090
 D0C  CB   HB3  single    0.970  0.020  1.090
 D0C  CD1  HD1  single    0.930  0.020  1.080
 D0C  CD2  HD2  single    0.930  0.020  1.080
 D0C  CE1  HE1  single    0.930  0.020  1.080
 D0C  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
 D0C  H2   N    H    106.31  3.000
 D0C  H2   N    CA   107.99  3.000
 D0C  H    N    CA   114.00  3.000
 D0C  HA   CA   CB   109.00  3.000
 D0C  HA   CA   C    110.00  3.000
 D0C  CB   CA   C    110.50  1.500
 D0C  HA   CA   N    110.00  3.000
 D0C  CB   CA   N    110.40  1.500
 D0C  C    CA   N    111.00  2.800
 D0C  OXT  C    O    127.12  3.000
 D0C  OXT  C    CA   120.80  1.700
 D0C  O    C    CA   120.80  1.700
 D0C  HB3  CB   HB2  107.06  3.000
 D0C  HB3  CB   CG   109.68  3.000
 D0C  HB2  CB   CG   110.01  3.000
 D0C  HB3  CB   CA   108.24  3.000
 D0C  HB2  CB   CA   108.41  3.000
 D0C  CG   CB   CA   113.23  3.000
 D0C  CD2  CG   CD1  117.95  3.000
 D0C  CD2  CG   CB   120.74  3.000
 D0C  CD1  CG   CB   121.28  3.000
 D0C  HD1  CD1  CE1  118.92  3.000
 D0C  HD1  CD1  CG   119.57  3.000
 D0C  CE1  CD1  CG   121.51  3.000
 D0C  HD2  CD2  CE2  118.87  3.000
 D0C  HD2  CD2  CG   119.62  3.000
 D0C  CE2  CD2  CG   121.51  3.000
 D0C  HE1  CE1  CZ   120.63  3.000
 D0C  HE1  CE1  CD1  120.32  3.000
 D0C  CZ   CE1  CD1  119.05  3.000
 D0C  HE2  CE2  CZ   120.56  3.000
 D0C  HE2  CE2  CD2  120.40  3.000
 D0C  CZ   CE2  CD2  119.04  3.000
 D0C  CL   CZ   CE2  119.51  3.000
 D0C  CL   CZ   CE1  119.56  3.000
 D0C  CE2  CZ   CE1  120.93  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
 D0C  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 D0C  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 D0C  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 D0C  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 D0C  CONST_05  CE1  CD1  CG   CD2     0.00   0.0  0
 D0C  CONST_06  CE1  CZ   CE2  CD2     0.00   0.0  0
 D0C  CONST_07  CE1  CD1  CG   CB    180.00   0.0  0
 D0C  CONST_08  CE2  CD2  CG   CB    180.00   0.0  0
 D0C  CONST_09  CL   CZ   CE1  CD1   180.00   0.0  0
 D0C  CONST_10  CL   CZ   CE2  CD2   180.00   0.0  0
 D0C  CONST_11  HE1  CE1  CD1  CG    180.00   0.0  0
 D0C  CONST_12  HE2  CE2  CD2  CG    180.00   0.0  0
 D0C  CONST_13  HD2  CD2  CG   CD1   180.00   0.0  0
 D0C  CONST_14  HD1  CD1  CG   CD2   180.00   0.0  0
 D0C  CONST_15  HE2  CE2  CZ   CE1   180.00   0.0  0
 D0C  CONST_16  HE1  CE1  CZ   CE2   180.00   0.0  0
 D0C  CONST_17  HD1  CD1  CE1  CZ    180.00   0.0  0
 D0C  CONST_18  HD2  CD2  CE2  CZ    180.00   0.0  0
 D0C  Var_01    CD1  CG   CB   CA     99.62  30.0  2
 D0C  Var_02    CD2  CG   CB   CA    -78.14  30.0  2
 D0C  Var_03    HB2  CB   CG   CD1   -21.85  30.0  2
 D0C  Var_04    HB3  CB   CG   CD1  -139.36  30.0  2
 D0C  Var_05    HB2  CB   CG   CD2   160.39  30.0  2
 D0C  Var_06    HB3  CB   CG   CD2    42.88  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
 D0C  chir_01  CA  C  N  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
 D0C  plan-1  CB   0.020
 D0C  plan-1  CG   0.020
 D0C  plan-1  CD1  0.020
 D0C  plan-1  CD2  0.020
 D0C  plan-1  CE1  0.020
 D0C  plan-1  CE2  0.020
 D0C  plan-1  CZ   0.020
 D0C  plan-1  CL   0.020
 D0C  plan-1  HD1  0.020
 D0C  plan-1  HD2  0.020
 D0C  plan-1  HE1  0.020
 D0C  plan-1  HE2  0.020
 D0C  plan-2  CA   0.020
 D0C  plan-2  C    0.020
 D0C  plan-2  O    0.020
 D0C  plan-2  OXT  0.020

