# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 22:09:39 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: (2~{S})-2-azanyl-6-[(2-azidophenyl)methoxycarbonylamino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)OCc1ccccc1N=[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
 9V0  9V0  '(2~{S})-2-azanyl-6-[(2-azidophenyl)methoxycarbonylamino]hexanoic acid'  peptide  41  23  .  2019-07-05  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_9V0
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
 9V0  C15  C  CR6    0   0.022  263.5171  35.7369  140.2510
 9V0  C20  C  CR16   0  -0.300  263.6989  36.2623  137.8932
 9V0  C21  C  CR16   0  -0.256  263.6407  34.9119  137.5861
 9V0  C22  C  CR16   0  -0.256  263.5254  33.9686  138.5965
 9V0  C    C  C      0   0.387  256.2318  37.5744  146.5063
 9V0  CA   C  CH1    0  -0.194  256.9406  36.2002  146.5534
 9V0  CB   C  CH2    0  -0.420  256.6109  35.3969  145.2923
 9V0  CG   C  CH2    0  -0.432  256.9609  36.0618  143.9638
 9V0  CD   C  CH2    0  -0.430  258.4352  36.4209  143.8190
 9V0  CE   C  CH2    0  -0.277  258.7705  36.8655  142.4013
 9V0  C11  C  C      0   0.748  261.1365  36.3599  142.0421
 9V0  C14  C  CH2    0  -0.255  263.4669  36.1637  141.6905
 9V0  C16  C  CR6    0   0.236  263.6433  36.6770  139.2223
 9V0  C23  C  CR16   0  -0.280  263.4580  34.3904  139.9162
 9V0  N    N  NH2    0  -0.794  256.5853  35.3861  147.7152
 9V0  NZ   N  NH1    0  -0.658  260.1516  37.2557  142.2168
 9V0  N17  N  N      0  -0.388  263.7193  38.0230  139.6186
 9V0  N18  N  N      1   0.369  263.8425  38.8834  138.7611
 9V0  N19  N  N     -1  -0.188  263.9550  39.7540  138.0639
 9V0  O12  O  O      0  -0.509  260.9837  35.1600  141.9360
 9V0  O13  O  O2     0  -0.482  262.3313  36.9700  141.9924
 9V0  H20  H  HCR6   0   0.269  263.7952  36.9827  137.0898
 9V0  H21  H  HCR6   0   0.264  263.6884  34.6014  136.5506
 9V0  H22  H  HCR6   0   0.258  263.4810  32.9141  138.3595
 9V0  HA   H  HCH1   0   0.200  258.0222  36.3616  146.5914
 9V0  HB2  H  HCH2   0   0.208  255.5400  35.1664  145.3009
 9V0  HB3  H  HCH2   0   0.209  257.1300  34.4353  145.3557
 9V0  HG2  H  HCH2   0   0.214  256.3518  36.9579  143.8129
 9V0  HG3  H  HCH2   0   0.215  256.6817  35.3745  143.1584
 9V0  HD2  H  HCH2   0   0.214  259.0517  35.5554  144.0813
 9V0  HD3  H  HCH2   0   0.222  258.6909  37.2195  144.5186
 9V0  HE2  H  HCH2   0   0.244  258.1563  37.7244  142.1262
 9V0  HE3  H  HCH2   0   0.234  258.5273  36.0717  141.6924
 9V0  H13  H  HCH2   0   0.259  263.5038  35.2870  142.3393
 9V0  H14  H  HCH2   0   0.262  264.3214  36.7939  141.9369
 9V0  H23  H  HCR6   0   0.258  263.3600  33.6594  140.7089
 9V0  H    H  HNH2   0   0.331  256.9037  35.8573  148.5545
 9V0  H2   H  HNH2   0   0.320  255.5732  35.3891  147.7876
 9V0  HZ   H  HNH1   0   0.397  260.3974  38.2224  142.3558
 9V0  OXT  O  OC    -1  -0.611  255.0117  37.5697  146.7794
 9V0  O    O  O      0  -0.610  256.9173  38.5656  146.1804

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
 9V0  C21  C22  aromatic  1.387  0.020  1.387
 9V0  C21  C20  aromatic  1.386  0.020  1.386
 9V0  C22  C23  aromatic  1.387  0.020  1.387
 9V0  C20  C16  aromatic  1.393  0.020  1.393
 9V0  C23  C15  aromatic  1.389  0.020  1.389
 9V0  C16  C15  aromatic  1.399  0.020  1.399
 9V0  C16  N17  single    1.405  0.020  1.405
 9V0  C15  C14  single    1.502  0.020  1.502
 9V0  N19  N18  double    1.121  0.020  1.121
 9V0  N18  N17  double    1.221  0.020  1.221
 9V0  C14  O13  single    1.425  0.020  1.425
 9V0  O12  C11  double    1.214  0.020  1.214
 9V0  NZ   C11  single    1.343  0.020  1.343
 9V0  NZ   CE   single    1.447  0.020  1.447
 9V0  C11  O13  single    1.342  0.020  1.342
 9V0  CE   CD   single    1.523  0.020  1.523
 9V0  CD   CG   single    1.524  0.020  1.524
 9V0  CG   CB   single    1.526  0.020  1.526
 9V0  O    C    deloc     1.231  0.020  1.231
 9V0  CB   CA   single    1.521  0.033  1.521
 9V0  C    CA   single    1.525  0.021  1.525
 9V0  C    OXT  deloc     1.250  0.020  1.250
 9V0  CA   N    single    1.458  0.019  1.458
 9V0  C20  H20  single    0.930  0.020  1.080
 9V0  C21  H21  single    0.930  0.020  1.080
 9V0  C22  H22  single    0.930  0.020  1.080
 9V0  CA   HA   single    0.970  0.020  0.970
 9V0  CB   HB2  single    0.970  0.020  1.090
 9V0  CB   HB3  single    0.970  0.020  1.090
 9V0  CG   HG2  single    0.970  0.020  1.090
 9V0  CG   HG3  single    0.970  0.020  1.090
 9V0  CD   HD2  single    0.970  0.020  1.090
 9V0  CD   HD3  single    0.970  0.020  1.090
 9V0  CE   HE2  single    0.970  0.020  1.090
 9V0  CE   HE3  single    0.970  0.020  1.090
 9V0  C14  H13  single    0.970  0.020  1.090
 9V0  C14  H14  single    0.970  0.020  1.090
 9V0  C23  H23  single    0.930  0.020  1.080
 9V0  N    H    single    0.860  0.020  0.860
 9V0  N    H2   single    0.890  0.020  1.040
 9V0  NZ   HZ   single    0.860  0.020  1.020

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
 9V0  C23  C15  C16  118.55  3.000
 9V0  C16  C15  C14  121.11  3.000
 9V0  C23  C15  C14  120.33  3.000
 9V0  H20  C20  C16  120.86  3.000
 9V0  H20  C20  C21  119.16  3.000
 9V0  C16  C20  C21  119.98  3.000
 9V0  H21  C21  C22  120.37  3.000
 9V0  H21  C21  C20  119.32  3.000
 9V0  C22  C21  C20  120.31  3.000
 9V0  H22  C22  C23  120.19  3.000
 9V0  H22  C22  C21  120.45  3.000
 9V0  C23  C22  C21  119.36  3.000
 9V0  O    C    OXT  126.57  3.000
 9V0  OXT  C    CA   120.80  1.700
 9V0  O    C    CA   120.80  1.700
 9V0  HA   CA   N    110.00  3.000
 9V0  HA   CA   CB   109.00  3.000
 9V0  N    CA   CB   110.40  1.500
 9V0  HA   CA   C    110.00  3.000
 9V0  N    CA   C    111.00  2.800
 9V0  CB   CA   C    110.50  1.500
 9V0  HB3  CB   HB2  106.16  3.000
 9V0  HB3  CB   CG   108.93  3.000
 9V0  HB2  CB   CG   108.83  3.000
 9V0  HB3  CB   CA   108.12  3.000
 9V0  HB2  CB   CA   108.32  3.000
 9V0  CG   CB   CA   116.04  3.000
 9V0  HG3  CG   HG2  105.71  3.000
 9V0  HG3  CG   CD   108.94  3.000
 9V0  HG2  CG   CD   109.42  3.000
 9V0  HG3  CG   CB   107.96  3.000
 9V0  HG2  CG   CB   110.44  3.000
 9V0  CD   CG   CB   114.02  3.000
 9V0  HD3  CD   HD2  107.03  3.000
 9V0  HD3  CD   CE   109.34  3.000
 9V0  HD2  CD   CE   109.26  3.000
 9V0  HD3  CD   CG   109.75  3.000
 9V0  HD2  CD   CG   109.62  3.000
 9V0  CE   CD   CG   111.72  3.000
 9V0  HE3  CE   HE2  106.46  3.000
 9V0  HE3  CE   NZ   109.02  3.000
 9V0  HE2  CE   NZ   107.03  3.000
 9V0  HE3  CE   CD   110.06  3.000
 9V0  HE2  CE   CD   109.91  3.000
 9V0  NZ   CE   CD   114.05  3.000
 9V0  O13  C11  O12  123.91  3.000
 9V0  O13  C11  NZ   110.76  3.000
 9V0  O12  C11  NZ   125.33  3.000
 9V0  H14  C14  H13  107.68  3.000
 9V0  H14  C14  O13  104.46  3.000
 9V0  H13  C14  O13  110.82  3.000
 9V0  H14  C14  C15  110.78  3.000
 9V0  H13  C14  C15  109.90  3.000
 9V0  O13  C14  C15  112.98  3.000
 9V0  N17  C16  C20  123.50  3.000
 9V0  N17  C16  C15  116.17  3.000
 9V0  C20  C16  C15  120.32  3.000
 9V0  H23  C23  C22  119.72  3.000
 9V0  H23  C23  C15  118.81  3.000
 9V0  C22  C23  C15  121.48  3.000
 9V0  H2   N    H    104.64  3.000
 9V0  H2   N    CA   107.30  3.000
 9V0  H    N    CA   114.00  3.000
 9V0  HZ   NZ   C11  118.64  3.000
 9V0  HZ   NZ   CE   118.31  3.000
 9V0  C11  NZ   CE   122.47  3.000
 9V0  N18  N17  C16  118.84  3.000
 9V0  N19  N18  N17  173.81  3.000
 9V0  C14  O13  C11  117.38  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
 9V0  CONST_01  C21  C22  C23  C15    0.00   0.0  0
 9V0  CONST_02  C21  C20  C16  C15    0.00   0.0  0
 9V0  CONST_03  C23  C22  C21  C20    0.00   0.0  0
 9V0  CONST_04  C23  C15  C16  C20    0.00   0.0  0
 9V0  CONST_05  C16  C20  C21  C22    0.00   0.0  0
 9V0  CONST_06  C16  C15  C23  C22    0.00   0.0  0
 9V0  CONST_07  C14  C15  C16  C20  180.00   0.0  0
 9V0  CONST_08  N17  C16  C20  C21  180.00   0.0  0
 9V0  CONST_09  C14  C15  C23  C22  180.00   0.0  0
 9V0  CONST_10  N17  C16  C15  C23  180.00   0.0  0
 9V0  CONST_11  H22  C22  C23  C15  180.00   0.0  0
 9V0  CONST_12  H20  C20  C16  C15  180.00   0.0  0
 9V0  CONST_13  H23  C23  C22  C21  180.00   0.0  0
 9V0  CONST_14  H21  C21  C20  C16  180.00   0.0  0
 9V0  CONST_15  N18  N17  C16  C15  180.00   0.0  0
 9V0  CONST_16  N18  N17  C16  C20    0.00   0.0  0
 9V0  Var_01    O13  C14  C15  C16   63.30  30.0  2
 9V0  Var_02    CD   CG   CB   CA    58.21  30.0  1
 9V0  Var_03    CE   CD   CG   CB   170.60  30.0  2
 9V0  Var_04    NZ   CE   CD   CG   178.32  30.0  1
 9V0  Var_05    C11  NZ   CE   CD    80.22  30.0  1
 9V0  Var_06    O12  C11  NZ   CE     4.81  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
 9V0  chir_01  CA  CB  C  N  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
 9V0  plan-1  C    0.020
 9V0  plan-1  CA   0.020
 9V0  plan-1  OXT  0.020
 9V0  plan-1  O    0.020
 9V0  plan-2  C15  0.020
 9V0  plan-2  C20  0.020
 9V0  plan-2  C21  0.020
 9V0  plan-2  C22  0.020
 9V0  plan-2  C14  0.020
 9V0  plan-2  C16  0.020
 9V0  plan-2  C23  0.020
 9V0  plan-2  N17  0.020
 9V0  plan-2  N18  0.020
 9V0  plan-2  N19  0.020
 9V0  plan-2  H20  0.020
 9V0  plan-2  H21  0.020
 9V0  plan-2  H22  0.020
 9V0  plan-2  H23  0.020
 9V0  plan-3  C11  0.020
 9V0  plan-3  NZ   0.020
 9V0  plan-3  O12  0.020
 9V0  plan-3  O13  0.020

