# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:48:04 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: (2~{S})-2-azanyl-3-(4-azidophenyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1ccc(cc1)N=[N+]=[N-])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
 4II  4II  '(2~{S})-2-azanyl-3-(4-azidophenyl)propanoic acid'  L-peptide  24  15  .  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_4II
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
 4II  N1   N  N      0  -0.396  28.4383   0.6608  50.8696
 4II  N2   N  N      1   0.359  28.4237   0.5413  49.6550
 4II  N3   N  N     -1  -0.194  28.3043   0.4825  48.5410
 4II  C    C  C      0   0.396  32.7246  -3.5157  53.3064
 4II  O    O  O      0  -0.605  31.6767  -4.1557  53.0911
 4II  CA   C  CH1    0  -0.153  32.7062  -2.5351  54.5064
 4II  N    N  NH2    0  -0.808  33.8064  -2.8339  55.4188
 4II  CG   C  CR6    0   0.115  31.7306  -0.6215  53.1655
 4II  CD2  C  CR16   0  -0.305  30.6070  -0.0245  53.7339
 4II  CE2  C  CR16   0  -0.286  29.5364   0.3876  52.9582
 4II  CZ   C  CR6    0   0.233  29.5681   0.2100  51.5787
 4II  CE1  C  CR16   0  -0.282  30.6815  -0.3844  50.9900
 4II  CD1  C  CR16   0  -0.289  31.7432  -0.7918  51.7832
 4II  H2   H  HCH1   0   0.178  31.7237  -2.6137  54.9952
 4II  H3   H  HNH2   0   0.334  33.7093  -2.2600  56.2487
 4II  H4   H  HNH2   0   0.337  33.7277  -3.7895  55.7455
 4II  H8   H  HCR6   0   0.248  30.5685   0.1271  54.8064
 4II  H9   H  HCR6   0   0.262  28.6729   0.8527  53.4163
 4II  H10  H  HCR6   0   0.263  30.7352  -0.5349  49.9183
 4II  H11  H  HCR6   0   0.248  32.6001  -1.2582  51.3127
 4II  CB   C  CH2    0  -0.511  32.8708  -1.0888  54.0221
 4II  OXT  O  OC    -1  -0.606  33.7854  -3.5745  52.6529
 4II  H6   H  HCH2   0   0.232  33.8135  -1.0149  53.4763
 4II  H7   H  HCH2   0   0.232  32.9529  -0.4339  54.8951

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
 4II  N3   N2   double    1.122  0.020  1.122
 4II  N2   N1   double    1.221  0.020  1.221
 4II  N1   CZ   single    1.408  0.020  1.408
 4II  CE1  CZ   aromatic  1.393  0.020  1.393
 4II  CE1  CD1  aromatic  1.386  0.020  1.386
 4II  CZ   CE2  aromatic  1.391  0.020  1.391
 4II  CD1  CG   aromatic  1.393  0.020  1.393
 4II  CE2  CD2  aromatic  1.385  0.020  1.385
 4II  O    C    deloc     1.231  0.020  1.231
 4II  CG   CD2  aromatic  1.394  0.020  1.394
 4II  CG   CB   single    1.501  0.020  1.501
 4II  C    CA   single    1.525  0.021  1.525
 4II  CB   CA   single    1.530  0.020  1.530
 4II  CA   N    single    1.458  0.019  1.458
 4II  C    OXT  deloc     1.247  0.020  1.247
 4II  CA   H2   single    0.970  0.020  1.090
 4II  N    H3   single    0.890  0.020  1.040
 4II  N    H4   single    0.890  0.020  1.040
 4II  CB   H6   single    0.970  0.020  1.090
 4II  CB   H7   single    0.970  0.020  1.090
 4II  CD2  H8   single    0.930  0.020  1.080
 4II  CE2  H9   single    0.930  0.020  1.080
 4II  CE1  H10  single    0.930  0.020  1.080
 4II  CD1  H11  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
 4II  CZ   N1   N2   118.64  3.000
 4II  N3   N2   N1   173.99  3.000
 4II  OXT  C    CA   116.46  3.000
 4II  OXT  C    O    126.88  3.000
 4II  CA   C    O    120.80  1.700
 4II  H2   CA   CB   107.66  3.000
 4II  H2   CA   N    112.37  3.000
 4II  CB   CA   N    110.50  1.700
 4II  H2   CA   C    108.03  3.000
 4II  N    CA   C    111.00  2.800
 4II  CB   CA   C    110.10  1.900
 4II  H4   N    H3   105.23  3.000
 4II  H4   N    CA   109.63  3.000
 4II  H3   N    CA   108.87  3.000
 4II  CD1  CG   CD2  117.67  3.000
 4II  CD2  CG   CB   120.88  3.000
 4II  CD1  CG   CB   121.44  3.000
 4II  H8   CD2  CE2  119.03  3.000
 4II  H8   CD2  CG   119.48  3.000
 4II  CE2  CD2  CG   121.49  3.000
 4II  H9   CE2  CZ   119.51  3.000
 4II  H9   CE2  CD2  120.50  3.000
 4II  CZ   CE2  CD2  119.99  3.000
 4II  CE1  CZ   CE2  119.46  3.000
 4II  CE2  CZ   N1   116.12  3.000
 4II  CE1  CZ   N1   124.42  3.000
 4II  H10  CE1  CD1  119.14  3.000
 4II  H10  CE1  CZ   121.13  3.000
 4II  CD1  CE1  CZ   119.72  3.000
 4II  H11  CD1  CE1  118.94  3.000
 4II  H11  CD1  CG   119.40  3.000
 4II  CE1  CD1  CG   121.66  3.000
 4II  H7   CB   H6   107.07  3.000
 4II  H7   CB   CG   109.03  3.000
 4II  H6   CB   CG   110.46  3.000
 4II  H7   CB   CA   108.68  3.000
 4II  H6   CB   CA   108.32  3.000
 4II  CG   CB   CA   113.09  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
 4II  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 4II  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 4II  CONST_03  CE1  CZ   CE2  CD2    0.00   0.0  0
 4II  CONST_04  CE1  CD1  CG   CD2    0.00   0.0  0
 4II  CONST_05  CD1  CE1  CZ   CE2    0.00   0.0  0
 4II  CONST_06  CD1  CG   CD2  CE2    0.00   0.0  0
 4II  CONST_07  CD1  CE1  CZ   N1   180.00   0.0  0
 4II  CONST_08  CD2  CE2  CZ   N1   180.00   0.0  0
 4II  CONST_09  CE1  CD1  CG   CB   180.00   0.0  0
 4II  CONST_10  CE2  CD2  CG   CB   180.00   0.0  0
 4II  CONST_11  H10  CE1  CD1  CG   180.00   0.0  0
 4II  CONST_12  H9   CE2  CD2  CG   180.00   0.0  0
 4II  CONST_13  H11  CD1  CG   CD2  180.00   0.0  0
 4II  CONST_14  H8   CD2  CE2  CZ   180.00   0.0  0
 4II  CONST_15  CE1  CZ   N1   N2     0.00   0.0  0
 4II  CONST_16  CE2  CZ   N1   N2   180.00   0.0  0
 4II  Var_01    CD1  CG   CB   CA   -89.60  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
 4II  chir_01  CA  C  CB  N  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
 4II  plan-1  C    0.020
 4II  plan-1  O    0.020
 4II  plan-1  CA   0.020
 4II  plan-1  OXT  0.020
 4II  plan-2  N1   0.020
 4II  plan-2  N2   0.020
 4II  plan-2  N3   0.020
 4II  plan-2  CG   0.020
 4II  plan-2  CD2  0.020
 4II  plan-2  CE2  0.020
 4II  plan-2  CZ   0.020
 4II  plan-2  CE1  0.020
 4II  plan-2  CD1  0.020
 4II  plan-2  H8   0.020
 4II  plan-2  H9   0.020
 4II  plan-2  H10  0.020
 4II  plan-2  H11  0.020
 4II  plan-2  CB   0.020

