# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 12:35:09 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: (2S)-2-amino-6-azidohexan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CO)CCCCN=[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
 AZK  AZK  (2S)-2-amino-6-azidohexan-1-ol  L-peptide  25  11  .  2019-03-22  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AZK
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
 AZK  N    N  NH2    0  -0.795  23.2675  -7.6916  4.9633
 AZK  CA   C  CH1    0  -0.148  23.1157  -7.8255  3.5198
 AZK  CB   C  CH2    0  -0.407  24.4290  -7.9165  2.7395
 AZK  CG   C  CH2    0  -0.416  25.3335  -6.7025  2.9094
 AZK  CD   C  CH2    0  -0.441  26.5706  -6.7800  2.0236
 AZK  CE   C  CH2    0  -0.321  27.5135  -5.5957  2.1740
 AZK  NZ   N  N      0  -0.361  28.0590  -5.4517  3.5341
 AZK  NZ2  N  N      1   0.354  28.8645  -6.2923  3.8829
 AZK  NZ3  N  N     -1  -0.229  29.6179  -7.0205  4.2942
 AZK  C    C  CH2    0  -0.145  22.2242  -9.0423  3.2715
 AZK  O    O  OH1    0  -0.660  21.9411  -9.2850  1.9128
 AZK  H    H  HNH2   0   0.350  23.6947  -6.8029  5.1903
 AZK  H2   H  HNH2   0   0.336  23.9069  -8.4014  5.3040
 AZK  HA   H  HCH1   0   0.216  22.5733  -6.9353  3.1752
 AZK  HB2  H  HCH2   0   0.213  24.2074  -8.0500  1.6768
 AZK  HB3  H  HCH2   0   0.206  24.9659  -8.8189  3.0579
 AZK  HG2  H  HCH2   0   0.213  25.6384  -6.6068  3.9548
 AZK  HG3  H  HCH2   0   0.214  24.7748  -5.7920  2.6653
 AZK  HD2  H  HCH2   0   0.236  26.2669  -6.8220  0.9735
 AZK  HD3  H  HCH2   0   0.227  27.1141  -7.7108  2.2175
 AZK  HE2  H  HCH2   0   0.253  26.9848  -4.6641  1.9793
 AZK  HE3  H  HCH2   0   0.258  28.3298  -5.6652  1.4495
 AZK  HC1  H  HCH2   0   0.202  21.3068  -8.9256  3.8623
 AZK  HC2  H  HCH2   0   0.204  22.7321  -9.9372  3.6455
 AZK  HO   H  HOH1   0   0.443  21.4407  -8.5359  1.5751

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
 AZK  N    CA   single  1.458  0.019  1.458
 AZK  N    H    single  0.860  0.020  0.860
 AZK  N    H2   single  0.890  0.020  1.040
 AZK  CA   CB   single  1.530  0.020  1.530
 AZK  CA   C    single  1.525  0.021  1.525
 AZK  CA   HA   single  0.970  0.020  0.970
 AZK  CB   CG   single  1.523  0.020  1.523
 AZK  CB   HB2  single  0.970  0.020  1.090
 AZK  CB   HB3  single  0.970  0.020  1.090
 AZK  CG   CD   single  1.523  0.020  1.523
 AZK  CG   HG2  single  0.970  0.020  1.090
 AZK  CG   HG3  single  0.970  0.020  1.090
 AZK  CD   CE   single  1.521  0.020  1.521
 AZK  CD   HD2  single  0.970  0.020  1.090
 AZK  CD   HD3  single  0.970  0.020  1.090
 AZK  CE   NZ   single  1.472  0.020  1.472
 AZK  CE   HE2  single  0.970  0.020  1.090
 AZK  CE   HE3  single  0.970  0.020  1.090
 AZK  NZ   NZ2  double  1.215  0.020  1.215
 AZK  NZ2  NZ3  double  1.126  0.020  1.126
 AZK  C    O    single  1.231  0.020  1.231
 AZK  C    HC1  single  0.970  0.020  1.090
 AZK  C    HC2  single  0.970  0.020  1.090
 AZK  O    HO   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
 AZK  H2   N    H    105.86  3.000
 AZK  H2   N    CA   109.51  3.000
 AZK  H    N    CA   114.00  3.000
 AZK  HA   CA   C    109.00  3.000
 AZK  HA   CA   CB   109.00  3.000
 AZK  C    CA   CB   110.10  1.900
 AZK  HA   CA   N    110.00  3.000
 AZK  C    CA   N    111.00  2.800
 AZK  CB   CA   N    110.50  1.700
 AZK  HB3  CB   HB2  106.30  3.000
 AZK  HB3  CB   CG   109.42  3.000
 AZK  HB2  CB   CG   109.02  3.000
 AZK  HB3  CB   CA   108.72  3.000
 AZK  HB2  CB   CA   109.20  3.000
 AZK  CG   CB   CA   113.91  3.000
 AZK  HG3  CG   HG2  106.41  3.000
 AZK  HG3  CG   CD   109.08  3.000
 AZK  HG2  CG   CD   109.51  3.000
 AZK  HG3  CG   CB   109.54  3.000
 AZK  HG2  CG   CB   110.00  3.000
 AZK  CD   CG   CB   112.13  3.000
 AZK  HD3  CD   HD2  105.96  3.000
 AZK  HD3  CD   CE   109.67  3.000
 AZK  HD2  CD   CE   107.27  3.000
 AZK  HD3  CD   CG   110.08  3.000
 AZK  HD2  CD   CG   109.55  3.000
 AZK  CE   CD   CG   113.96  3.000
 AZK  HE3  CE   HE2  107.36  3.000
 AZK  HE3  CE   NZ   109.97  3.000
 AZK  HE2  CE   NZ   105.16  3.000
 AZK  HE3  CE   CD   110.34  3.000
 AZK  HE2  CE   CD   110.33  3.000
 AZK  NZ   CE   CD   113.40  3.000
 AZK  NZ2  NZ   CE   116.30  3.000
 AZK  NZ3  NZ2  NZ   174.82  3.000
 AZK  HC2  C    HC1  106.91  3.000
 AZK  HC2  C    O    106.37  3.000
 AZK  HC1  C    O    111.68  3.000
 AZK  HC2  C    CA   108.94  3.000
 AZK  HC1  C    CA   108.39  3.000
 AZK  O    C    CA   120.80  1.700
 AZK  HO   O    C    108.00  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
 AZK  Var_01  CD  CG  CB  CA  -175.03  30.0  3
 AZK  Var_02  CE  CD  CG  CB  -179.23  30.0  3
 AZK  Var_03  NZ  CE  CD  CG    61.32  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
 AZK  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
 AZK  plan-1  CE   0.020
 AZK  plan-1  NZ   0.020
 AZK  plan-1  NZ2  0.020
 AZK  plan-1  NZ3  0.020

