# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 20:11:12 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: N-[(2S)-4-diazo-3-oxo-1-phenylbutan-2-yl]glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC(=O)N[C@@H](Cc1ccccc1)C(=O)C=[N+]=[N-]
#
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
 1ZB  1ZB  N-[(2S)-4-diazo-3-oxo-1-phenylbutan-2-yl]glycinamide  peptide  32  18  .  2019-03-22  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_1ZB
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
 1ZB  N    N  NH2    0  -0.790  31.7762  24.8588  19.0683
 1ZB  CA   C  CH2    0  -0.409  30.8407  25.9323  19.3293
 1ZB  C    C  C      0   0.546  30.0556  25.6663  20.5980
 1ZB  O    O  O      0  -0.474  30.5088  25.0086  21.5184
 1ZB  N1   N  NH1    0  -0.638  28.8250  26.2272  20.6252
 1ZB  CA1  C  CH1    0  -0.219  28.0074  26.3102  21.8116
 1ZB  C1   C  C      0   0.383  26.5977  25.7979  21.5023
 1ZB  O1   O  O      0  -0.417  25.6082  26.4696  21.7208
 1ZB  CB   C  CH2    0  -0.509  27.9990  27.7261  22.3961
 1ZB  CG   C  CR6    0   0.130  29.3893  28.1464  22.7808
 1ZB  CD1  C  CR16   0  -0.307  30.2049  28.8389  21.8899
 1ZB  CD2  C  CR16   0  -0.300  29.9085  27.8000  24.0264
 1ZB  CE1  C  CR16   0  -0.241  31.5103  29.1702  22.2307
 1ZB  CE2  C  CR16   0  -0.239  31.2105  28.1312  24.3727
 1ZB  CZ   C  CR16   0  -0.269  32.0179  28.8155  23.4730
 1ZB  C2   C  C1     0  -0.288  26.4684  24.4704  20.9471
 1ZB  N3   N  N      1   0.142  27.5006  23.6982  20.7593
 1ZB  N4   N  N     -1  -0.104  28.3832  23.0308  20.6011
 1ZB  H    H  HNH2   0   0.354  32.2636  25.0551  18.2041
 1ZB  H2   H  HNH2   0   0.345  32.4854  24.8412  19.7894
 1ZB  HA2  H  HCH2   0   0.241  31.3009  26.9252  19.4535
 1ZB  HA3  H  HCH2   0   0.252  30.1558  26.0231  18.4837
 1ZB  H1   H  HNH1   0   0.406  28.5490  26.8024  19.8424
 1ZB  HA   H  HCH1   0   0.301  28.4439  25.6305  22.5507
 1ZB  HB2  H  HCH2   0   0.259  27.5783  28.4204  21.6652
 1ZB  HB3  H  HCH2   0   0.263  27.3477  27.7444  23.2711
 1ZB  HD1  H  HCR6   0   0.248  29.8150  29.1231  20.9194
 1ZB  HD2  H  HCR6   0   0.246  29.2852  27.2630  24.7325
 1ZB  HE1  H  HCR6   0   0.252  32.1303  29.7074  21.5242
 1ZB  HE2  H  HCR6   0   0.252  31.5956  27.8554  25.3461
 1ZB  HZ   H  HCR6   0   0.252  33.0345  29.0739  23.7396
 1ZB  H11  H  H      0   0.333  25.5098  24.0400  20.6970

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
 1ZB  N    CA   single    1.458  0.019  1.458
 1ZB  N    H    single    0.860  0.020  0.860
 1ZB  N    H2   single    0.890  0.020  1.040
 1ZB  CA   C    single    1.525  0.021  1.525
 1ZB  CA   HA2  single    0.970  0.020  1.090
 1ZB  CA   HA3  single    0.970  0.020  1.090
 1ZB  C    O    double    1.231  0.020  1.231
 1ZB  C    N1   single    1.353  0.020  1.353
 1ZB  N1   CA1  single    1.443  0.020  1.443
 1ZB  N1   H1   single    0.860  0.020  1.020
 1ZB  CA1  C1   single    1.531  0.020  1.531
 1ZB  CA1  CB   single    1.532  0.020  1.532
 1ZB  CA1  HA   single    0.970  0.020  1.090
 1ZB  C1   O1   double    1.216  0.020  1.216
 1ZB  C1   C2   single    1.445  0.020  1.445
 1ZB  CB   CG   single    1.503  0.020  1.503
 1ZB  CB   HB2  single    0.970  0.020  1.090
 1ZB  CB   HB3  single    0.970  0.020  1.090
 1ZB  CG   CD1  aromatic  1.392  0.020  1.392
 1ZB  CG   CD2  aromatic  1.393  0.020  1.393
 1ZB  CD1  CE1  aromatic  1.389  0.020  1.389
 1ZB  CD1  HD1  single    0.930  0.020  1.080
 1ZB  CD2  CE2  aromatic  1.387  0.020  1.387
 1ZB  CD2  HD2  single    0.930  0.020  1.080
 1ZB  CE1  CZ   aromatic  1.388  0.020  1.388
 1ZB  CE1  HE1  single    0.930  0.020  1.080
 1ZB  CE2  CZ   aromatic  1.389  0.020  1.389
 1ZB  CE2  HE2  single    0.930  0.020  1.080
 1ZB  CZ   HZ   single    0.930  0.020  1.080
 1ZB  C2   H11  single    0.930  0.020  1.080
 1ZB  C2   N3   double    1.303  0.020  1.303
 1ZB  N3   N4   double    1.118  0.020  1.118

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
 1ZB  H2   N    H    105.94  3.000
 1ZB  H2   N    CA   109.72  3.000
 1ZB  H    N    CA   114.00  3.000
 1ZB  HA3  CA   HA2  105.93  3.000
 1ZB  HA3  CA   C    109.75  3.000
 1ZB  HA2  CA   C    106.28  3.000
 1ZB  HA3  CA   N    109.11  3.000
 1ZB  HA2  CA   N    114.76  3.000
 1ZB  C    CA   N    111.00  2.800
 1ZB  N1   C    O    123.15  3.000
 1ZB  N1   C    CA   114.55  3.000
 1ZB  O    C    CA   120.80  1.700
 1ZB  H1   N1   CA1  116.73  3.000
 1ZB  H1   N1   C    117.97  3.000
 1ZB  CA1  N1   C    123.77  3.000
 1ZB  HA   CA1  CB   108.57  3.000
 1ZB  HA   CA1  C1   107.20  3.000
 1ZB  CB   CA1  C1   112.41  3.000
 1ZB  HA   CA1  N1   107.06  3.000
 1ZB  CB   CA1  N1   111.71  3.000
 1ZB  C1   CA1  N1   109.64  3.000
 1ZB  C2   C1   O1   120.25  3.000
 1ZB  C2   C1   CA1  117.87  3.000
 1ZB  O1   C1   CA1  121.88  3.000
 1ZB  HB3  CB   HB2  107.22  3.000
 1ZB  HB3  CB   CG   110.02  3.000
 1ZB  HB2  CB   CG   110.48  3.000
 1ZB  HB3  CB   CA1  108.96  3.000
 1ZB  HB2  CB   CA1  109.53  3.000
 1ZB  CG   CB   CA1  110.56  3.000
 1ZB  CD2  CG   CD1  118.52  3.000
 1ZB  CD2  CG   CB   120.28  3.000
 1ZB  CD1  CG   CB   121.15  3.000
 1ZB  HD1  CD1  CE1  119.68  3.000
 1ZB  HD1  CD1  CG   119.52  3.000
 1ZB  CE1  CD1  CG   120.80  3.000
 1ZB  HD2  CD2  CE2  119.68  3.000
 1ZB  HD2  CD2  CG   119.42  3.000
 1ZB  CE2  CD2  CG   120.90  3.000
 1ZB  HE1  CE1  CZ   120.09  3.000
 1ZB  HE1  CE1  CD1  119.76  3.000
 1ZB  CZ   CE1  CD1  120.15  3.000
 1ZB  HE2  CE2  CZ   120.07  3.000
 1ZB  HE2  CE2  CD2  119.84  3.000
 1ZB  CZ   CE2  CD2  120.09  3.000
 1ZB  HZ   CZ   CE2  120.27  3.000
 1ZB  HZ   CZ   CE1  120.19  3.000
 1ZB  CE2  CZ   CE1  119.53  3.000
 1ZB  H11  C2   N3   115.69  3.000
 1ZB  N3   C2   C1   121.95  3.000
 1ZB  H11  C2   C1   122.32  3.000
 1ZB  N4   N3   C2   180.00  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
 1ZB  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 1ZB  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 1ZB  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 1ZB  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 1ZB  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 1ZB  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 1ZB  CONST_07  CE1  CD1  CG   CB   180.00   0.0  0
 1ZB  CONST_08  CE2  CD2  CG   CB   180.00   0.0  0
 1ZB  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 1ZB  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 1ZB  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 1ZB  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 1ZB  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 1ZB  CONST_14  CA1  N1   C    CA   180.00   0.0  0
 1ZB  CONST_15  CA1  N1   C    O      0.00   0.0  0
 1ZB  CONST_16  H1   N1   C    CA     0.00   0.0  0
 1ZB  Var_01    CD1  CG   CB   CA1   92.20  30.0  2
 1ZB  Var_02    O    C    CA   N     28.49  30.0  3
 1ZB  Var_03    N3   C2   C1   CA1    2.76  30.0  2
 1ZB  Var_04    H11  C2   N3   N4   -46.81   0.0  2
 1ZB  Var_05    H    N    CA   C    178.45  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
 1ZB  chir_01  CA1  N1  C1  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
 1ZB  plan-1  CB   0.020
 1ZB  plan-1  CG   0.020
 1ZB  plan-1  CD1  0.020
 1ZB  plan-1  CD2  0.020
 1ZB  plan-1  CE1  0.020
 1ZB  plan-1  CE2  0.020
 1ZB  plan-1  CZ   0.020
 1ZB  plan-1  HD1  0.020
 1ZB  plan-1  HD2  0.020
 1ZB  plan-1  HE1  0.020
 1ZB  plan-1  HE2  0.020
 1ZB  plan-1  HZ   0.020
 1ZB  plan-2  CA   0.020
 1ZB  plan-2  C    0.020
 1ZB  plan-2  O    0.020
 1ZB  plan-2  N1   0.020
 1ZB  plan-2  CA1  0.020
 1ZB  plan-2  H1   0.020
 1ZB  plan-3  CA1  0.020
 1ZB  plan-3  C1   0.020
 1ZB  plan-3  O1   0.020
 1ZB  plan-3  C2   0.020
 1ZB  plan-4  C1   0.020
 1ZB  plan-4  C2   0.020
 1ZB  plan-4  N3   0.020
 1ZB  plan-4  N4   0.020
 1ZB  plan-4  H11  0.020

