# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 01:43:41 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 6-azido-L-norleucine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCN=[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
 NOT  NOT  '6-azido-L-norleucine     '  L-peptide  23  12  .  2012-08-28  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_NOT
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
 NOT  N    N  NH2    0  -0.819  14.3570  -0.0150  19.4818
 NOT  CA   C  CH1    0  -0.218  14.2807   1.4409  19.4602
 NOT  C    C  C      0   0.410  15.3761   2.0722  20.3626
 NOT  OXT  O  OC     0  -0.600  16.2777   1.3146  20.7761
 NOT  CB   C  CH2    0  -0.387  12.8826   1.9058  19.8636
 NOT  CG   C  CH2    0  -0.425  11.7859   1.4025  18.9341
 NOT  C1   C  CH2    0  -0.430  10.3978   1.8492  19.3758
 NOT  C2   C  CH2    0  -0.300   9.3203   1.3532  18.4239
 NOT  O    O  O     -1  -0.606  15.2796   3.2968  20.5741
 NOT  N1   N  N      0  -0.362   7.9697   1.7928  18.8052
 NOT  N2   N  N      1   0.352   7.4692   1.2349  19.7617
 NOT  N3   N  N     -1  -0.233   6.9213   0.7758  20.6313
 NOT  HN   H  HNH2   0   0.329  14.1471  -0.3944  18.5689
 NOT  HNA  H  HNH2   0   0.333  15.3138  -0.2668  19.6952
 NOT  HA   H  HCH1   0   0.192  14.4725   1.8393  18.4485
 NOT  HB   H  HCH2   0   0.195  12.6778   1.5616  20.8839
 NOT  HBA  H  HCH2   0   0.204  12.8545   2.9968  19.8871
 NOT  HG   H  HCH2   0   0.208  11.9775   1.7622  17.9166
 NOT  HGA  H  HCH2   0   0.213  11.8118   0.3097  18.8850
 NOT  H1   H  HCH2   0   0.224  10.2014   1.4734  20.3850
 NOT  H1A  H  HCH2   0   0.226  10.3549   2.9405  19.4315
 NOT  H2   H  HCH2   0   0.251   9.4832   1.7592  17.4268
 NOT  H2A  H  HCH2   0   0.243   9.3565   0.2625  18.3402

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
 NOT  N   CA   single  1.458  0.019  1.458
 NOT  N   HN   single  0.890  0.020  1.040
 NOT  N   HNA  single  0.890  0.020  1.040
 NOT  CA  CB   single  1.530  0.020  1.530
 NOT  CA  C    single  1.525  0.021  1.525
 NOT  CA  HA   single  0.970  0.020  0.970
 NOT  C   O    deloc   1.231  0.020  1.231
 NOT  C   OXT  deloc   1.248  0.020  1.248
 NOT  CB  HB   single  0.970  0.020  1.090
 NOT  CB  HBA  single  0.970  0.020  1.090
 NOT  CG  CB   single  1.523  0.020  1.523
 NOT  CG  C1   single  1.524  0.020  1.524
 NOT  CG  HG   single  0.970  0.020  1.090
 NOT  CG  HGA  single  0.970  0.020  1.090
 NOT  C1  H1   single  0.970  0.020  1.090
 NOT  C1  H1A  single  0.970  0.020  1.090
 NOT  C2  C1   single  1.521  0.020  1.521
 NOT  C2  N1   single  1.471  0.020  1.471
 NOT  C2  H2   single  0.970  0.020  1.090
 NOT  C2  H2A  single  0.970  0.020  1.090
 NOT  N1  N2   double  1.215  0.020  1.215
 NOT  N2  N3   double  1.126  0.020  1.126

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
 NOT  HNA  N   HN   107.06  3.000
 NOT  HNA  N   CA   107.52  3.000
 NOT  HN   N   CA   110.53  3.000
 NOT  HA   CA  CB   109.00  3.000
 NOT  HA   CA  C    109.00  3.000
 NOT  CB   CA  C    110.10  1.900
 NOT  HA   CA  N    110.00  3.000
 NOT  C    CA  N    111.00  2.800
 NOT  CB   CA  N    110.50  1.700
 NOT  O    C   OXT  126.58  3.000
 NOT  OXT  C   CA   117.08  3.000
 NOT  O    C   CA   120.80  1.700
 NOT  HBA  CB  HB   106.80  3.000
 NOT  HBA  CB  CG   108.96  3.000
 NOT  HB   CB  CG   109.26  3.000
 NOT  CG   CB  CA   113.40  3.000
 NOT  HBA  CB  CA   109.47  3.000
 NOT  HB   CB  CA   108.74  3.000
 NOT  HGA  CG  HG   106.38  3.000
 NOT  HGA  CG  C1   109.11  3.000
 NOT  HG   CG  C1   109.40  3.000
 NOT  HGA  CG  CB   109.90  3.000
 NOT  HG   CG  CB   109.40  3.000
 NOT  C1   CG  CB   112.46  3.000
 NOT  H1A  C1  H1   106.78  3.000
 NOT  H1A  C1  C2   109.24  3.000
 NOT  H1   C1  C2   109.75  3.000
 NOT  C2   C1  CG   111.62  3.000
 NOT  H1A  C1  CG   110.07  3.000
 NOT  H1   C1  CG   109.27  3.000
 NOT  H2A  C2  H2   107.25  3.000
 NOT  H2A  C2  N1   110.37  3.000
 NOT  H2   C2  N1   105.28  3.000
 NOT  H2A  C2  C1   110.45  3.000
 NOT  H2   C2  C1   110.21  3.000
 NOT  N1   C2  C1   113.01  3.000
 NOT  N2   N1  C2   116.43  3.000
 NOT  N3   N2  N1   174.73  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
 NOT  Var_01  C1  CG  CB  CA   178.56  30.0  1
 NOT  Var_02  C2  C1  CG  CB   179.18  30.0  3
 NOT  Var_03  N1  C2  C1  CG  -178.71  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
 NOT  chir_01  CA  N  CB  C  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
 NOT  plan-1  CA   0.020
 NOT  plan-1  C    0.020
 NOT  plan-1  OXT  0.020
 NOT  plan-1  O    0.020
 NOT  plan-2  C2   0.020
 NOT  plan-2  N1   0.020
 NOT  plan-2  N2   0.020
 NOT  plan-2  N3   0.020

