# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 07:49:22 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2~{S})-2-azanyl-3-[1-(3-azanylpropyl)-1,2,3-triazol-4-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCn1cc(C[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
 5LE  5LE  '(2~{S})-2-azanyl-3-[1-(3-azanylpropyl)-1,2,3-triazol-4-yl]propanoic acid'  peptide  29  15  .  2022-07-23  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_5LE
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
 5LE  N16  N  NH2    0  -0.799   6.2401   0.1276  -1.0029
 5LE  C17  C  CH2    0  -0.278   5.2754  -0.5627  -0.1607
 5LE  C18  C  CH2    0  -0.442   3.9156   0.1143  -0.2480
 5LE  C19  C  CH2    0  -0.289   2.8957  -0.5737   0.6471
 5LE  N20  N  NR5    0  -0.251   1.5820   0.0320   0.5451
 5LE  C21  C  CR15   0  -0.081   0.5123  -0.4045  -0.1406
 5LE  C22  C  CR5    0   0.176  -0.4356   0.5735   0.0421
 5LE  C23  C  CH2    0  -0.527  -1.8367   0.6658  -0.4520
 5LE  C24  C  CH1    0  -0.229  -2.7770  -0.3719   0.1659
 5LE  N25  N  NH2    0  -0.774  -2.3439  -1.7079  -0.2103
 5LE  C36  C  C      0   0.396  -4.2645  -0.0467  -0.1468
 5LE  O37  O  O      0  -0.608  -5.0109  -1.0108  -0.4068
 5LE  N38  N  N      0  -0.327   0.1213   1.5283   0.8203
 5LE  N39  N  N      0  -0.124   1.3335   1.1942   1.1170
 5LE  H21  H  HNH2   0   0.340   6.4390   1.0368  -0.6036
 5LE  H22  H  HCH2   0   0.221   5.1838  -1.5925  -0.5158
 5LE  H23  H  HCH2   0   0.196   5.5790  -0.6265   0.8943
 5LE  H24  H  HCH2   0   0.235   4.0069   1.1629   0.0492
 5LE  H25  H  HCH2   0   0.236   3.5683   0.0996  -1.2841
 5LE  H26  H  HCH2   0   0.264   2.7859  -1.6230   0.3753
 5LE  H27  H  HCH2   0   0.269   3.2023  -0.5362   1.6926
 5LE  H28  H  HCR5   0   0.293   0.5019  -1.3363  -0.6779
 5LE  H29  H  HCH2   0   0.247  -2.2139   1.6625  -0.2308
 5LE  H30  H  HCH2   0   0.234  -1.8587   0.5570  -1.5422
 5LE  H31  H  HCH1   0   0.227  -2.6742  -0.2932   1.2574
 5LE  H32  H  HNH2   0   0.335  -3.0015  -2.3743   0.1758
 5LE  OXT  O  OC    -1  -0.614  -4.6024   1.1523  -0.0766
 5LE  H2   H  HNH2   0   0.348   7.1192  -0.3732  -0.9886
 5LE  H1   H  HNH2   0   0.324  -2.4509  -1.8055  -1.2147

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
 5LE  N16  C17  single    1.455  0.020  1.455
 5LE  C17  C18  single    1.522  0.020  1.522
 5LE  C18  C19  single    1.521  0.020  1.521
 5LE  C19  N20  single    1.450  0.020  1.450
 5LE  N20  N39  aromatic  1.319  0.020  1.319
 5LE  N20  C21  aromatic  1.344  0.020  1.344
 5LE  C21  C22  aromatic  1.374  0.020  1.374
 5LE  C22  N38  aromatic  1.352  0.020  1.352
 5LE  C22  C23  single    1.489  0.020  1.489
 5LE  C23  C24  single    1.531  0.020  1.531
 5LE  C24  N25  single    1.454  0.020  1.454
 5LE  C24  C36  single    1.554  0.020  1.554
 5LE  C36  O37  deloc     1.247  0.020  1.247
 5LE  N38  N39  aromatic  1.292  0.020  1.292
 5LE  N16  H21  single    0.890  0.020  1.040
 5LE  C17  H22  single    0.970  0.020  1.090
 5LE  C17  H23  single    0.970  0.020  1.090
 5LE  C18  H24  single    0.970  0.020  1.090
 5LE  C18  H25  single    0.970  0.020  1.090
 5LE  C19  H26  single    0.970  0.020  1.090
 5LE  C19  H27  single    0.970  0.020  1.090
 5LE  C21  H28  single    0.930  0.020  1.080
 5LE  C23  H29  single    0.970  0.020  1.090
 5LE  C23  H30  single    0.970  0.020  1.090
 5LE  C24  H31  single    0.970  0.020  1.090
 5LE  N25  H32  single    0.890  0.020  1.040
 5LE  C36  OXT  deloc     1.248  0.020  1.248
 5LE  N16  H2   single    0.890  0.020  1.040
 5LE  N25  H1   single    0.890  0.020  1.040

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
 5LE  H2   N16  H21  105.55  3.000
 5LE  H2   N16  C17  109.46  3.000
 5LE  H21  N16  C17  109.15  3.000
 5LE  H23  C17  H22  106.27  3.000
 5LE  H23  C17  C18  109.12  3.000
 5LE  H22  C17  C18  109.00  3.000
 5LE  H23  C17  N16  113.57  3.000
 5LE  H22  C17  N16  108.33  3.000
 5LE  C18  C17  N16  110.38  3.000
 5LE  H25  C18  H24  107.28  3.000
 5LE  H25  C18  C19  109.79  3.000
 5LE  H24  C18  C19  109.25  3.000
 5LE  H25  C18  C17  109.42  3.000
 5LE  H24  C18  C17  109.65  3.000
 5LE  C19  C18  C17  111.36  3.000
 5LE  H27  C19  H26  107.50  3.000
 5LE  H27  C19  N20  107.93  3.000
 5LE  H26  C19  N20  107.07  3.000
 5LE  H27  C19  C18  111.11  3.000
 5LE  H26  C19  C18  110.87  3.000
 5LE  N20  C19  C18  112.15  3.000
 5LE  N39  N20  C21  110.96  3.000
 5LE  C21  N20  C19  128.42  3.000
 5LE  N39  N20  C19  120.55  3.000
 5LE  H28  C21  C22  132.56  3.000
 5LE  H28  C21  N20  122.96  3.000
 5LE  C22  C21  N20  104.48  3.000
 5LE  N38  C22  C23  122.34  3.000
 5LE  C23  C22  C21  130.49  3.000
 5LE  N38  C22  C21  107.16  3.000
 5LE  H30  C23  H29  106.63  3.000
 5LE  H30  C23  C24  108.78  3.000
 5LE  H29  C23  C24  109.03  3.000
 5LE  H30  C23  C22  110.06  3.000
 5LE  H29  C23  C22  108.39  3.000
 5LE  C24  C23  C22  113.71  3.000
 5LE  H31  C24  C36  105.92  3.000
 5LE  H31  C24  N25  107.15  3.000
 5LE  C36  C24  N25  115.17  3.000
 5LE  H31  C24  C23  107.15  3.000
 5LE  C36  C24  C23  111.40  3.000
 5LE  N25  C24  C23  109.61  3.000
 5LE  H1   N25  H32  104.22  3.000
 5LE  H1   N25  C24  108.24  3.000
 5LE  H32  N25  C24  108.21  3.000
 5LE  OXT  C36  O37  126.36  3.000
 5LE  OXT  C36  C24  116.67  3.000
 5LE  O37  C36  C24  116.94  3.000
 5LE  N39  N38  C22  109.63  3.000
 5LE  N38  N39  N20  107.77  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
 5LE  CONST_01  C22  N38  N39  N20     0.00   0.0  0
 5LE  CONST_02  N38  C22  C21  N20     0.00   0.0  0
 5LE  CONST_03  N38  N39  N20  C21     0.00   0.0  0
 5LE  CONST_04  N39  N38  C22  C21     0.00   0.0  0
 5LE  CONST_05  N39  N20  C21  C22     0.00   0.0  0
 5LE  CONST_06  N38  N39  N20  C19   180.00   0.0  0
 5LE  CONST_07  C22  C21  N20  C19   180.00   0.0  0
 5LE  CONST_08  C23  C22  C21  N20   180.00   0.0  0
 5LE  CONST_09  N39  N38  C22  C23   180.00   0.0  0
 5LE  CONST_10  H28  C21  C22  N38   180.00   0.0  0
 5LE  Var_01    N39  N20  C19  C18   -74.83  30.0  2
 5LE  Var_02    C24  C23  C22  C21    67.52  30.0  2
 5LE  Var_03    N20  C19  C18  C17  -178.19  30.0  3
 5LE  Var_04    C19  C18  C17  N16  -178.85  30.0  3
 5LE  Var_05    H21  N16  C17  C18    69.13  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
 5LE  chir_01  C24  C23  N25  C36  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
 5LE  plan-1  C19  0.020
 5LE  plan-1  N20  0.020
 5LE  plan-1  C21  0.020
 5LE  plan-1  C22  0.020
 5LE  plan-1  C23  0.020
 5LE  plan-1  N38  0.020
 5LE  plan-1  N39  0.020
 5LE  plan-1  H28  0.020
 5LE  plan-2  C24  0.020
 5LE  plan-2  C36  0.020
 5LE  plan-2  O37  0.020
 5LE  plan-2  OXT  0.020

