# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 10:36:22 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  21  12  .  2022-08-09  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_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  -0.788   2.0171   1.8384  -0.2907
 02Y  CA   C  CH1    0  -0.220   2.0054   0.5440   0.3713
 02Y  C2   C  CH2    0  -0.419   0.7160  -0.2074   0.0238
 02Y  C3   C  CH2    0  -0.571  -0.5144   0.5905   0.4190
 02Y  C4   C  C      0   0.393  -1.8044  -0.0279   0.0117
 02Y  O2   O  O      0  -0.342  -1.9714  -1.0298  -0.6204
 02Y  C6   C  CH2    0  -0.387  -3.0270   0.7887   0.5018
 02Y  H    H  HNH2   0   0.340   2.7441   2.4109   0.1203
 02Y  HA   H  HCH1   0   0.219   1.9992   0.7261   1.4521
 02Y  HB1  H  HCH2   0   0.230   0.6954  -0.4103  -1.0515
 02Y  HB2  H  HCH2   0   0.243   0.7171  -1.1719   0.5313
 02Y  H8   H  HCH2   0   0.292  -0.5480   0.7497   1.5030
 02Y  H9   H  HCH2   0   0.304  -0.4679   1.5965  -0.0128
 02Y  N2   N  N      1   0.283  -4.2059   0.1358   0.0578
 02Y  N3   N  N      0   0.117  -5.0596  -0.4260  -0.3148
 02Y  H42  H  HCH2   0   0.406  -3.0949   0.8336   1.5904
 02Y  H2   H  HNH2   0   0.327   2.3175   1.6946  -1.2485
 02Y  H10  H  HCH2   0   0.406  -3.0576   1.7982   0.0872
 02Y  C1   C  C      0   0.390   3.2160  -0.3736   0.0610
 02Y  OXT  O  OC    -1  -0.620   3.3321  -1.3853   0.7829
 02Y  O    O  O      0  -0.603   3.9556  -0.0468  -0.8871

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  1.550  0.020  1.550
 02Y  CA  HA   single  0.970  0.020  0.970
 02Y  C2  CA   single  1.532  0.020  1.532
 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  1.487  0.020  1.487
 02Y  O   C1   deloc   1.246  0.020  1.246
 02Y  O2  C4   double  1.196  0.020  1.196
 02Y  C6  C4   single  1.550  0.020  1.550
 02Y  C6  N2   single  1.419  0.020  1.419
 02Y  C6  H42  single  0.970  0.020  1.090
 02Y  N2  N3   triple  1.088  0.020  1.088
 02Y  C6  H10  single  0.970  0.020  1.090
 02Y  C1  OXT  deloc   1.248  0.020  1.248

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    104.53  3.000
 02Y  H2   N   CA   107.83  3.000
 02Y  H    N   CA   114.00  3.000
 02Y  C1   CA  HA   107.47  3.000
 02Y  HA   CA  C2   107.48  3.000
 02Y  C1   CA  C2   108.75  3.000
 02Y  C2   CA  N    109.88  3.000
 02Y  HA   CA  N    110.00  3.000
 02Y  C1   CA  N    115.44  3.000
 02Y  HB2  C2  HB1  107.07  3.000
 02Y  HB2  C2  C3   110.16  3.000
 02Y  HB1  C2  C3   109.74  3.000
 02Y  C3   C2  CA   111.41  3.000
 02Y  HB2  C2  CA   109.11  3.000
 02Y  HB1  C2  CA   109.24  3.000
 02Y  H9   C3  H8   104.93  3.000
 02Y  H9   C3  C4   108.10  3.000
 02Y  H8   C3  C4   107.73  3.000
 02Y  C4   C3  C2   114.39  3.000
 02Y  H9   C3  C2   110.21  3.000
 02Y  H8   C3  C2   111.01  3.000
 02Y  C6   C4  O2   119.88  3.000
 02Y  C6   C4  C3   112.24  3.000
 02Y  O2   C4  C3   127.88  3.000
 02Y  H10  C6  H42  109.81  3.000
 02Y  H10  C6  N2   106.46  3.000
 02Y  H42  C6  N2   106.22  3.000
 02Y  H10  C6  C4   112.91  3.000
 02Y  H42  C6  C4   112.71  3.000
 02Y  N2   C6  C4   108.30  3.000
 02Y  N3   N2  C6   180.00  3.000
 02Y  OXT  C1  O    126.68  3.000
 02Y  OXT  C1  CA   115.89  3.000
 02Y  O    C1  CA   117.42  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  Var_01  C4  C3  C2  CA  175.28  30.0  1
 02Y  Var_02  O2  C4  C3  C2   -3.11  30.0  1
 02Y  Var_03  N2  C6  C4  C3  179.39  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  O    0.020

