# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 22:01:59 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 6-diazonio-5-oxo-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)C[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
 02Y  02Y  6-diazonio-5-oxo-L-norleucine  L-peptide  22  12  .  2022-08-09  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_02Y
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
 02Y  N    N  NH2   0  -0.777   2.0502   1.8624  -0.2130
 02Y  CA   C  CH1   0  -0.245   2.0195   0.5561   0.3956
 02Y  C2   C  CH2   0  -0.430   0.7348  -0.1860   0.0014
 02Y  C3   C  CH2   0  -0.567  -0.4894   0.5764   0.4784
 02Y  C4   C  C     0   0.397  -1.7776  -0.0397   0.0573
 02Y  O2   O  O     0  -0.460  -1.9340  -1.0551  -0.5548
 02Y  C6   C  CH2   0  -0.373  -3.0026   0.7949   0.4994
 02Y  H    H  HNH2  0   0.370   2.8336   2.3989   0.1359
 02Y  HA   H  HCH1  0   0.299   2.0184   0.6852   1.4829
 02Y  HB1  H  HCH2  0   0.295   0.7057  -0.3003  -1.0857
 02Y  HB2  H  HCH2  0   0.283   0.7361  -1.1890   0.4278
 02Y  H8   H  HCH2  0   0.321  -0.5033   0.6450   1.5724
 02Y  H9   H  HCH2  0   0.327  -0.4660   1.6125   0.1269
 02Y  N2   N  N     1   0.389  -4.1766   0.1011   0.1040
 02Y  N3   N  N     0   0.064  -5.0271  -0.4893  -0.2279
 02Y  H42  H  HCH2  0   0.410  -3.0699   0.9166   1.5822
 02Y  H2   H  HNH2  0   0.354   2.1822   1.7797  -1.2136
 02Y  H10  H  HCH2  0   0.397  -3.0440   1.7723   0.0142
 02Y  C1   C  C     0   0.488   3.2253  -0.3093   0.0481
 02Y  OXT  O  OH1   0  -0.621   3.3201  -1.3726   0.8377
 02Y  HXT  H  HOH1  0   0.474   4.0761  -1.9186   0.5741
 02Y  O    O  O     0  -0.395   4.0016  -0.0700  -0.8413

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
 02Y  N    CA   single  1.458  0.019  1.458
 02Y  N    H    single  0.860  0.020  0.860
 02Y  N    H2   single  0.890  0.020  1.040
 02Y  CA   C1   single  1.524  0.020  1.524
 02Y  CA   HA   single  0.970  0.020  0.970
 02Y  C2   CA   single  1.535  0.020  1.535
 02Y  C2   HB1  single  0.970  0.020  1.090
 02Y  C2   HB2  single  0.970  0.020  1.090
 02Y  C3   C2   single  1.519  0.020  1.519
 02Y  C3   H8   single  0.970  0.020  1.090
 02Y  C3   H9   single  0.970  0.020  1.090
 02Y  C4   C3   single  1.489  0.020  1.489
 02Y  O    C1   double  1.205  0.020  1.205
 02Y  O2   C4   double  1.196  0.020  1.196
 02Y  C6   C4   single  1.547  0.020  1.547
 02Y  C6   N2   single  1.420  0.020  1.420
 02Y  C6   H42  single  0.970  0.020  1.090
 02Y  N2   N3   triple  1.087  0.020  1.087
 02Y  C6   H10  single  0.970  0.020  1.090
 02Y  C1   OXT  single  1.328  0.020  1.328
 02Y  OXT  HXT  single  0.850  0.020  0.980

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
 02Y  H2   N    H    106.45  3.000
 02Y  H2   N    CA   110.24  3.000
 02Y  H    N    CA   114.00  3.000
 02Y  C1   CA   HA   107.10  3.000
 02Y  HA   CA   C2   108.13  3.000
 02Y  C1   CA   C2   109.21  3.000
 02Y  C2   CA   N    110.34  3.000
 02Y  HA   CA   N    110.00  3.000
 02Y  C1   CA   N    113.66  3.000
 02Y  HB2  C2   HB1  107.03  3.000
 02Y  HB2  C2   C3   109.88  3.000
 02Y  HB1  C2   C3   110.07  3.000
 02Y  C3   C2   CA   110.56  3.000
 02Y  HB2  C2   CA   110.08  3.000
 02Y  HB1  C2   CA   109.15  3.000
 02Y  H9   C3   H8   105.16  3.000
 02Y  H9   C3   C4   108.63  3.000
 02Y  H8   C3   C4   107.29  3.000
 02Y  C4   C3   C2   113.63  3.000
 02Y  H9   C3   C2   110.92  3.000
 02Y  H8   C3   C2   110.79  3.000
 02Y  C6   C4   O2   120.06  3.000
 02Y  C6   C4   C3   112.40  3.000
 02Y  O2   C4   C3   127.54  3.000
 02Y  H10  C6   H42  109.80  3.000
 02Y  H10  C6   N2   106.39  3.000
 02Y  H42  C6   N2   106.24  3.000
 02Y  H10  C6   C4   112.71  3.000
 02Y  H42  C6   C4   113.11  3.000
 02Y  N2   C6   C4   108.15  3.000
 02Y  N3   N2   C6   180.00  3.000
 02Y  OXT  C1   O    123.51  3.000
 02Y  OXT  C1   CA   112.06  3.000
 02Y  O    C1   CA   124.42  3.000
 02Y  HXT  OXT  C1   110.19  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
 02Y  CONST_01  HXT  OXT  C1  CA   180.00   0.0  0
 02Y  Var_01    C4   C3   C2  CA   176.36  30.0  1
 02Y  Var_02    O2   C4   C3  C2     2.59  30.0  1
 02Y  Var_03    N2   C6   C4  C3  -177.56  30.0  1

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
 02Y  chir_01  CA  N  C1  C2  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
 02Y  plan-1  C3   0.020
 02Y  plan-1  C4   0.020
 02Y  plan-1  O2   0.020
 02Y  plan-1  C6   0.020
 02Y  plan-2  CA   0.020
 02Y  plan-2  C1   0.020
 02Y  plan-2  OXT  0.020
 02Y  plan-2  HXT  0.020
 02Y  plan-2  O    0.020

