# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 08:02:59 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: 4-acetamido-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1ccc(C[C@H](N)C(O)=O)cc1
#
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
 A3U  A3U  "4-acetamido-L-phenylalanine"
  L-peptide  29  16  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A3U
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
 A3U  N    N  NH2    0  -0.808  -28.1692  -12.9400  20.2720
 A3U  CA   C  CH1    0  -0.158  -26.9709  -13.7576  20.1032
 A3U  C    C  C      0   0.397  -26.3207  -13.4870  18.7226
 A3U  O    O  O      0  -0.607  -25.1400  -13.0860  18.7349
 A3U  CB   C  CH2    0  -0.506  -27.3735  -15.2306  20.2298
 A3U  CG   C  CR6    0   0.112  -26.2032  -16.1666  20.1465
 A3U  CD1  C  CR16   0  -0.299  -25.3841  -16.3947  21.2506
 A3U  CD2  C  CR16   0  -0.291  -25.8708  -16.8180  18.9643
 A3U  CE1  C  CR16   0  -0.332  -24.2853  -17.2312  21.1724
 A3U  CE2  C  CR16   0  -0.304  -24.7740  -17.6642  18.8642
 A3U  CZ   C  CR6    0   0.351  -23.9614  -17.8793  19.9774
 A3U  NZ   N  NH1    0  -0.727  -22.8368  -18.7119  19.9932
 A3U  OZ   O  O      0  -0.463  -22.6854  -19.4208  17.8356
 A3U  C1   C  C      0   0.496  -22.2607  -19.4077  18.9768
 A3U  C2   C  CH3    0  -0.785  -21.0201  -20.1613  19.3902
 A3U  OXT  O  OC    -1  -0.606  -27.0268  -13.6990  17.7163
 A3U  H    H  HNH2   0   0.334  -28.5210  -13.0656  21.2142
 A3U  H2   H  HNH2   0   0.336  -27.9235  -11.9593  20.2080
 A3U  HA   H  HCH1   0   0.176  -26.2146  -13.5516  20.8753
 A3U  HB2  H  HCH2   0   0.228  -28.0997  -15.4601  19.4475
 A3U  HB3  H  HCH2   0   0.229  -27.8836  -15.3723  21.1886
 A3U  HD1  H  HCR6   0   0.244  -25.6089  -15.9122  22.1950
 A3U  HD2  H  HCR6   0   0.239  -26.4839  -16.6633  18.0848
 A3U  HE1  H  HCR6   0   0.261  -23.6705  -17.3881  22.0516
 A3U  HE2  H  HCR6   0   0.272  -24.5662  -18.1474  17.9244
 A3U  H11  H  HNH1   0   0.415  -22.3759  -18.7797  20.8887
 A3U  H12  H  HCH3   0   0.264  -20.6918  -20.8094  18.5824
 A3U  H13  H  HCH3   0   0.270  -20.2140  -19.4637  19.6243
 A3U  H14  H  HCH3   0   0.263  -21.1956  -20.7667  20.2800

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
 A3U  OZ   C1   double    1.218  0.020  1.218
 A3U  C1   C2   single    1.509  0.020  1.509
 A3U  C1   NZ   single    1.360  0.020  1.360
 A3U  CE2  CD2  aromatic  1.389  0.020  1.389
 A3U  CE2  CZ   aromatic  1.395  0.020  1.395
 A3U  CD2  CG   aromatic  1.390  0.020  1.390
 A3U  C    O    deloc     1.231  0.020  1.231
 A3U  C    CA   single    1.525  0.021  1.525
 A3U  N    CA   single    1.458  0.019  1.458
 A3U  CZ   NZ   single    1.399  0.020  1.399
 A3U  CZ   CE1  aromatic  1.397  0.020  1.397
 A3U  CG   CB   single    1.501  0.020  1.501
 A3U  CG   CD1  aromatic  1.394  0.020  1.394
 A3U  CB   CA   single    1.530  0.020  1.530
 A3U  CE1  CD1  aromatic  1.383  0.020  1.383
 A3U  C    OXT  deloc     1.247  0.020  1.247
 A3U  N    H    single    0.860  0.020  0.860
 A3U  N    H2   single    0.890  0.020  1.040
 A3U  CA   HA   single    0.970  0.020  0.970
 A3U  CB   HB2  single    0.970  0.020  1.090
 A3U  CB   HB3  single    0.970  0.020  1.090
 A3U  CD1  HD1  single    0.930  0.020  1.080
 A3U  CD2  HD2  single    0.930  0.020  1.080
 A3U  CE1  HE1  single    0.930  0.020  1.080
 A3U  CE2  HE2  single    0.930  0.020  1.080
 A3U  NZ   H11  single    0.860  0.020  1.020
 A3U  C2   H12  single    0.970  0.020  1.090
 A3U  C2   H13  single    0.970  0.020  1.090
 A3U  C2   H14  single    0.970  0.020  1.090

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
 A3U  H2   N    H    105.24  3.000
 A3U  H2   N    CA   109.61  3.000
 A3U  H    N    CA   114.00  3.000
 A3U  HA   CA   CB   109.00  3.000
 A3U  HA   CA   C    109.00  3.000
 A3U  CB   CA   C    110.10  1.900
 A3U  HA   CA   N    110.00  3.000
 A3U  CB   CA   N    110.50  1.700
 A3U  C    CA   N    111.00  2.800
 A3U  OXT  C    O    126.76  3.000
 A3U  OXT  C    CA   116.84  3.000
 A3U  O    C    CA   120.80  1.700
 A3U  HB3  CB   HB2  106.87  3.000
 A3U  HB3  CB   CG   109.33  3.000
 A3U  HB2  CB   CG   110.35  3.000
 A3U  HB3  CB   CA   108.61  3.000
 A3U  HB2  CB   CA   108.52  3.000
 A3U  CG   CB   CA   112.96  3.000
 A3U  CD2  CG   CD1  117.16  3.000
 A3U  CD1  CG   CB   121.09  3.000
 A3U  CD2  CG   CB   121.73  3.000
 A3U  HD1  CD1  CE1  118.89  3.000
 A3U  HD1  CD1  CG   119.70  3.000
 A3U  CE1  CD1  CG   121.41  3.000
 A3U  HD2  CD2  CE2  118.39  3.000
 A3U  HD2  CD2  CG   119.22  3.000
 A3U  CE2  CD2  CG   122.39  3.000
 A3U  HE1  CE1  CZ   119.66  3.000
 A3U  HE1  CE1  CD1  119.48  3.000
 A3U  CZ   CE1  CD1  120.86  3.000
 A3U  HE2  CE2  CZ   120.99  3.000
 A3U  HE2  CE2  CD2  119.24  3.000
 A3U  CZ   CE2  CD2  119.77  3.000
 A3U  NZ   CZ   CE2  124.67  3.000
 A3U  NZ   CZ   CE1  116.91  3.000
 A3U  CE2  CZ   CE1  118.41  3.000
 A3U  H11  NZ   C1   115.81  3.000
 A3U  H11  NZ   CZ   114.64  3.000
 A3U  C1   NZ   CZ   129.53  3.000
 A3U  C2   C1   OZ   122.55  3.000
 A3U  C2   C1   NZ   113.51  3.000
 A3U  OZ   C1   NZ   123.94  3.000
 A3U  H14  C2   H13  107.38  3.000
 A3U  H14  C2   H12  108.92  3.000
 A3U  H13  C2   H12  108.51  3.000
 A3U  H14  C2   C1   111.62  3.000
 A3U  H13  C2   C1   110.28  3.000
 A3U  H12  C2   C1   110.03  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
 A3U  CONST_01  CZ   CE2  CD2  CG      0.00   0.0  0
 A3U  CONST_02  CZ   CE1  CD1  CG      0.00   0.0  0
 A3U  CONST_03  CE2  CD2  CG   CD1     0.00   0.0  0
 A3U  CONST_04  CE2  CZ   CE1  CD1     0.00   0.0  0
 A3U  CONST_05  CE1  CZ   CE2  CD2     0.00   0.0  0
 A3U  CONST_06  CE1  CD1  CG   CD2     0.00   0.0  0
 A3U  CONST_07  CE2  CD2  CG   CB    180.00   0.0  0
 A3U  CONST_08  CE1  CD1  CG   CB    180.00   0.0  0
 A3U  CONST_09  NZ   CZ   CE1  CD1   180.00   0.0  0
 A3U  CONST_10  NZ   CZ   CE2  CD2   180.00   0.0  0
 A3U  CONST_11  HE2  CE2  CD2  CG    180.00   0.0  0
 A3U  CONST_12  HE1  CE1  CD1  CG    180.00   0.0  0
 A3U  CONST_13  HD2  CD2  CG   CD1   180.00   0.0  0
 A3U  CONST_14  HD1  CD1  CG   CD2   180.00   0.0  0
 A3U  CONST_15  HE2  CE2  CZ   CE1   180.00   0.0  0
 A3U  CONST_16  HE1  CE1  CZ   CE2   180.00   0.0  0
 A3U  CONST_17  HD2  CD2  CE2  CZ    180.00   0.0  0
 A3U  CONST_18  HD1  CD1  CE1  CZ    180.00   0.0  0
 A3U  CONST_19  C1   NZ   CZ   CE1   180.00   0.0  0
 A3U  CONST_20  C1   NZ   CZ   CE2     0.00   0.0  0
 A3U  CONST_21  H11  NZ   CZ   CE1     0.00   0.0  0
 A3U  CONST_22  H11  NZ   CZ   CE2   180.00   0.0  0
 A3U  CONST_23  OZ   C1   NZ   CZ      0.00   0.0  0
 A3U  CONST_24  C2   C1   NZ   CZ    180.00   0.0  0
 A3U  CONST_25  H11  NZ   C1   OZ    180.00   0.0  0
 A3U  CONST_26  H11  NZ   C1   C2      0.00   0.0  0
 A3U  Var_01    CD2  CG   CB   CA    -98.24  30.0  2
 A3U  Var_02    CD1  CG   CB   CA     80.28  30.0  2
 A3U  Var_03    HB2  CB   CG   CD1  -158.04  30.0  2
 A3U  Var_04    HB3  CB   CG   CD1   -40.77  30.0  2
 A3U  Var_05    HB2  CB   CG   CD2    23.44  30.0  2
 A3U  Var_06    HB3  CB   CG   CD2   140.71  30.0  2
 A3U  Var_07    H12  C2   C1   NZ    171.65  30.0  3
 A3U  Var_08    H13  C2   C1   NZ    -68.67  30.0  3
 A3U  Var_09    H14  C2   C1   NZ     50.60  30.0  3
 A3U  Var_10    H12  C2   C1   OZ     -9.01  30.0  3
 A3U  Var_11    H13  C2   C1   OZ    110.66  30.0  3
 A3U  Var_12    H14  C2   C1   OZ   -130.06  30.0  3

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
 A3U  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
 A3U  plan-1  CB   0.020
 A3U  plan-1  CG   0.020
 A3U  plan-1  CD1  0.020
 A3U  plan-1  CD2  0.020
 A3U  plan-1  CE1  0.020
 A3U  plan-1  CE2  0.020
 A3U  plan-1  CZ   0.020
 A3U  plan-1  NZ   0.020
 A3U  plan-1  HD1  0.020
 A3U  plan-1  HD2  0.020
 A3U  plan-1  HE1  0.020
 A3U  plan-1  HE2  0.020
 A3U  plan-2  CZ   0.020
 A3U  plan-2  NZ   0.020
 A3U  plan-2  OZ   0.020
 A3U  plan-2  C1   0.020
 A3U  plan-2  C2   0.020
 A3U  plan-2  H11  0.020
 A3U  plan-3  CA   0.020
 A3U  plan-3  C    0.020
 A3U  plan-3  O    0.020
 A3U  plan-3  OXT  0.020

