# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 21:03:47 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: (2~{S})-2-azanyl-5-(4-methyl-1,2,3-triazol-1-yl)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cn(CCC[C@H](N)C(O)=O)nn1
#
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
 9FZ  9FZ  '(2~{S})-2-azanyl-5-(4-methyl-1,2,3-triazol-1-yl)pentanoic acid'  ligand  28  14  .  2022-07-24  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9FZ
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
 9FZ  C7   C  CR5   0   0.146  -4.1375   0.1400  -0.0785
 9FZ  C2   C  CH2   0  -0.292  -0.7863  -0.7487  -0.9431
 9FZ  N    N  NH2   0  -0.776   2.4393   1.7647   0.6253
 9FZ  CA   C  CH1   0  -0.206   2.6397   0.3406   0.5216
 9FZ  C    C  C     0   0.522   4.0482  -0.0462   0.0862
 9FZ  O    O  O     0  -0.439   4.8554   0.7196  -0.3779
 9FZ  CB   C  CH2   0  -0.444   1.6231  -0.2866  -0.4417
 9FZ  C1   C  CH2   0  -0.426   0.1842  -0.0276  -0.0183
 9FZ  C8   C  CR15  0  -0.096  -2.9901   0.4547  -0.7624
 9FZ  C9   C  CH3   0  -0.727  -5.4094   0.9017   0.0407
 9FZ  N4   N  NR5   0  -0.245  -2.1644  -0.5802  -0.5264
 9FZ  N5   N  N     0  -0.111  -2.7438  -1.4725   0.2522
 9FZ  N6   N  N     0  -0.326  -3.9327  -1.0524   0.5253
 9FZ  H1   H  HCH2  0   0.269  -0.6967  -0.3837  -1.9663
 9FZ  H2   H  HCH2  0   0.271  -0.5885  -1.8200  -0.9583
 9FZ  H4   H  HNH2  0   0.344   2.6649   2.2168  -0.2524
 9FZ  H6   H  HCH1  0   0.271   2.4771  -0.0987   1.5117
 9FZ  H8   H  HCH2  0   0.239   1.7915   0.1066  -1.4502
 9FZ  H9   H  HCH2  0   0.249   1.7930  -1.3642  -0.4977
 9FZ  H10  H  HCH2  0   0.246  -0.0237   1.0432  -0.0227
 9FZ  H11  H  HCH2  0   0.236   0.0315  -0.3805   1.0055
 9FZ  H12  H  HCR5  0   0.303  -2.7173   1.2975  -1.3751
 9FZ  H13  H  HCH3  0   0.250  -5.5419   1.2997   1.0478
 9FZ  H14  H  HCH3  0   0.249  -5.4254   1.7410  -0.6519
 9FZ  H15  H  HCH3  0   0.249  -6.2708   0.2697  -0.1758
 9FZ  OXT  O  OH1   0  -0.594   4.2907  -1.3395   0.2673
 9FZ  HXT  H  HOH1  0   0.481   5.1822  -1.5603  -0.0423
 9FZ  H3   H  HNH2  0   0.355   3.0633   2.1593   1.3170

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
 9FZ  C9   C7   single    1.487  0.020  1.487
 9FZ  C    O    double    1.206  0.020  1.206
 9FZ  C    CA   single    1.524  0.020  1.524
 9FZ  C7   N6   aromatic  1.352  0.020  1.352
 9FZ  C7   C8   aromatic  1.372  0.020  1.372
 9FZ  N6   N5   aromatic  1.290  0.020  1.290
 9FZ  C8   N4   aromatic  1.345  0.020  1.345
 9FZ  CA   N    single    1.442  0.020  1.442
 9FZ  CA   CB   single    1.535  0.020  1.535
 9FZ  C1   CB   single    1.522  0.020  1.522
 9FZ  C1   C2   single    1.522  0.020  1.522
 9FZ  N5   N4   aromatic  1.318  0.020  1.318
 9FZ  N4   C2   single    1.450  0.020  1.450
 9FZ  C2   H1   single    0.970  0.020  1.090
 9FZ  C2   H2   single    0.970  0.020  1.090
 9FZ  N    H3   single    0.890  0.020  1.040
 9FZ  N    H4   single    0.890  0.020  1.040
 9FZ  CA   H6   single    0.970  0.020  1.090
 9FZ  CB   H8   single    0.970  0.020  1.090
 9FZ  CB   H9   single    0.970  0.020  1.090
 9FZ  C1   H10  single    0.970  0.020  1.090
 9FZ  C1   H11  single    0.970  0.020  1.090
 9FZ  C8   H12  single    0.930  0.020  1.080
 9FZ  C9   H13  single    0.970  0.020  1.090
 9FZ  C9   H14  single    0.970  0.020  1.090
 9FZ  C9   H15  single    0.970  0.020  1.090
 9FZ  C    OXT  single    1.328  0.020  1.328
 9FZ  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
 9FZ  N6   C7   C9   123.05  3.000
 9FZ  N6   C7   C8   107.35  3.000
 9FZ  C9   C7   C8   129.60  3.000
 9FZ  H2   C2   H1   107.53  3.000
 9FZ  H2   C2   N4   106.92  3.000
 9FZ  H1   C2   N4   108.00  3.000
 9FZ  H2   C2   C1   111.01  3.000
 9FZ  H1   C2   C1   111.05  3.000
 9FZ  N4   C2   C1   112.11  3.000
 9FZ  H4   N    H3   106.33  3.000
 9FZ  H4   N    CA   110.34  3.000
 9FZ  H3   N    CA   110.41  3.000
 9FZ  H6   CA   CB   107.77  3.000
 9FZ  H6   CA   C    107.07  3.000
 9FZ  CB   CA   C    109.22  3.000
 9FZ  H6   CA   N    108.09  3.000
 9FZ  CB   CA   N    110.90  3.000
 9FZ  C    CA   N    113.56  3.000
 9FZ  OXT  C    O    123.28  3.000
 9FZ  OXT  C    CA   112.14  3.000
 9FZ  O    C    CA   124.58  3.000
 9FZ  H9   CB   H8   106.45  3.000
 9FZ  H9   CB   C1   109.22  3.000
 9FZ  H8   CB   C1   109.90  3.000
 9FZ  H9   CB   CA   109.41  3.000
 9FZ  H8   CB   CA   109.23  3.000
 9FZ  C1   CB   CA   112.46  3.000
 9FZ  H11  C1   H10  107.10  3.000
 9FZ  H11  C1   CB   109.73  3.000
 9FZ  H10  C1   CB   110.25  3.000
 9FZ  H11  C1   C2   109.08  3.000
 9FZ  H10  C1   C2   109.94  3.000
 9FZ  CB   C1   C2   110.67  3.000
 9FZ  H12  C8   N4   123.13  3.000
 9FZ  H12  C8   C7   132.43  3.000
 9FZ  N4   C8   C7   104.44  3.000
 9FZ  H15  C9   H14  108.01  3.000
 9FZ  H15  C9   H13  107.39  3.000
 9FZ  H14  C9   H13  107.72  3.000
 9FZ  H15  C9   C7   111.28  3.000
 9FZ  H14  C9   C7   110.88  3.000
 9FZ  H13  C9   C7   111.39  3.000
 9FZ  N5   N4   C8   110.77  3.000
 9FZ  N5   N4   C2   120.59  3.000
 9FZ  C8   N4   C2   128.52  3.000
 9FZ  N6   N5   N4   108.03  3.000
 9FZ  N5   N6   C7   109.40  3.000
 9FZ  HXT  OXT  C    110.26  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
 9FZ  CONST_01  N4   N5   N6  C7     0.00   0.0  0
 9FZ  CONST_02  N5   N4   C8  C7     0.00   0.0  0
 9FZ  CONST_03  N5   N6   C7  C8     0.00   0.0  0
 9FZ  CONST_04  N6   N5   N4  C8     0.00   0.0  0
 9FZ  CONST_05  N6   C7   C8  N4     0.00   0.0  0
 9FZ  CONST_06  C2   N4   C8  C7   180.00   0.0  0
 9FZ  CONST_07  N6   N5   N4  C2   180.00   0.0  0
 9FZ  CONST_08  N5   N6   C7  C9   180.00   0.0  0
 9FZ  CONST_09  N4   C8   C7  C9   180.00   0.0  0
 9FZ  CONST_10  H12  C8   N4  N5   180.00   0.0  0
 9FZ  CONST_11  HXT  OXT  C   CA   180.00   0.0  0
 9FZ  Var_01    C8   N4   C2  C1    81.99  30.0  2
 9FZ  Var_02    H13  C9   C7  C8  -110.00  30.0  2
 9FZ  Var_03    N4   C2   C1  CB   176.99  30.0  3
 9FZ  Var_04    CA   CB   C1  C2  -175.97  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
 9FZ  chir_01  CA  C  N  CB  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
 9FZ  plan-1  C7   0.020
 9FZ  plan-1  C2   0.020
 9FZ  plan-1  C8   0.020
 9FZ  plan-1  C9   0.020
 9FZ  plan-1  N4   0.020
 9FZ  plan-1  N5   0.020
 9FZ  plan-1  N6   0.020
 9FZ  plan-1  H12  0.020
 9FZ  plan-2  CA   0.020
 9FZ  plan-2  C    0.020
 9FZ  plan-2  O    0.020
 9FZ  plan-2  OXT  0.020
 9FZ  plan-2  HXT  0.020

