# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 17:16:53 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2~{S})-2-azanyl-3-[1-(6-azanylhexyl)-1,2,3-triazol-4-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCCCn1cc(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
 5LF  5LF  '(2~{S})-2-azanyl-3-[1-(6-azanylhexyl)-1,2,3-triazol-4-yl]propanoic acid'  peptide  39  18  .  2022-07-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5LF
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
 5LF  N19  N  NH2   0  -0.801   8.7723  -0.0794   0.2702
 5LF  C20  C  CH2   0  -0.273   7.4826  -0.7502   0.1794
 5LF  C21  C  CH2   0  -0.425   6.3447   0.2581   0.1445
 5LF  C22  C  CH2   0  -0.419   4.9740  -0.3998   0.0548
 5LF  C23  C  CH2   0  -0.424   3.8360   0.6111  -0.0027
 5LF  C24  C  CH2   0  -0.437   2.4645  -0.0480  -0.0761
 5LF  C25  C  CH2   0  -0.272   1.3618   0.9926  -0.1974
 5LF  N26  N  NR5   0  -0.257   0.0357   0.4007  -0.2224
 5LF  C27  C  CR15  0  -0.103  -0.9749   0.5738   0.6465
 5LF  C28  C  CR5   0   0.201  -1.9817  -0.2193   0.1600
 5LF  C29  C  CH2   0  -0.529  -3.3551  -0.4441   0.6830
 5LF  C30  C  CH1   0  -0.206  -4.4287   0.1367  -0.2555
 5LF  N31  N  NH2   0  -0.771  -4.2266   1.5494  -0.4423
 5LF  C42  C  C     0   0.520  -5.8098  -0.2239   0.2775
 5LF  O43  O  O     0  -0.436  -6.6007   0.5705   0.7204
 5LF  N44  N  N     0  -0.325  -1.5230  -0.8160  -0.9605
 5LF  N45  N  N     0  -0.113  -0.3098  -0.4338  -1.1825
 5LF  H25  H  HNH2  0   0.336   8.8530   0.3608   1.1790
 5LF  H26  H  HCH2  0   0.211   7.4664  -1.3373  -0.7432
 5LF  H27  H  HCH2  0   0.186   7.3018  -1.4627   0.9979
 5LF  H28  H  HCH2  0   0.211   6.3884   0.8842   1.0431
 5LF  H29  H  HCH2  0   0.212   6.4888   0.9309  -0.7070
 5LF  H30  H  HCH2  0   0.213   4.9327  -1.0409  -0.8326
 5LF  H31  H  HCH2  0   0.213   4.8296  -1.0629   0.9146
 5LF  H32  H  HCH2  0   0.220   3.8825   1.2624   0.8765
 5LF  H33  H  HCH2  0   0.219   3.9747   1.2629  -0.8719
 5LF  H34  H  HCH2  0   0.236   2.4231  -0.7240  -0.9336
 5LF  H35  H  HCH2  0   0.233   2.2963  -0.6561   0.8173
 5LF  H36  H  HCH2  0   0.263   1.3847   1.6782   0.6485
 5LF  H37  H  HCH2  0   0.268   1.4889   1.5872  -1.1033
 5LF  H38  H  HCR5  0   0.303  -0.9087   1.2221   1.5035
 5LF  H39  H  HCH2  0   0.272  -3.5241  -1.5140   0.8155
 5LF  H40  H  HCH2  0   0.263  -3.4487   0.0125   1.6715
 5LF  H41  H  HCH1  0   0.279  -4.3195  -0.3561  -1.2267
 5LF  H42  H  HNH2  0   0.355  -4.8791   1.9105  -1.1256
 5LF  OXT  O  OH1   0  -0.593  -6.0469  -1.5284   0.2051
 5LF  HXT  H  HOH1  0   0.482  -6.9206  -1.7327   0.5716
 5LF  H2   H  HNH2  0   0.345   9.5143  -0.7666   0.2362
 5LF  H1   H  HNH2  0   0.343  -4.4085   2.0510   0.4182

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
 5LF  N19  C20  single    1.457  0.020  1.457
 5LF  C20  C21  single    1.521  0.020  1.521
 5LF  C21  C22  single    1.523  0.020  1.523
 5LF  C22  C23  single    1.523  0.020  1.523
 5LF  C23  C24  single    1.523  0.020  1.523
 5LF  C24  C25  single    1.521  0.020  1.521
 5LF  C25  N26  single    1.452  0.020  1.452
 5LF  N26  C27  aromatic  1.344  0.020  1.344
 5LF  N26  N45  aromatic  1.318  0.020  1.318
 5LF  C27  C28  aromatic  1.371  0.020  1.371
 5LF  C28  N44  aromatic  1.350  0.020  1.350
 5LF  C28  C29  single    1.487  0.020  1.487
 5LF  C29  C30  single    1.540  0.020  1.540
 5LF  C30  C42  single    1.524  0.020  1.524
 5LF  C30  N31  single    1.439  0.020  1.439
 5LF  C42  O43  double    1.205  0.020  1.205
 5LF  N44  N45  aromatic  1.291  0.020  1.291
 5LF  N19  H25  single    0.890  0.020  1.040
 5LF  C20  H26  single    0.970  0.020  1.090
 5LF  C20  H27  single    0.970  0.020  1.090
 5LF  C21  H28  single    0.970  0.020  1.090
 5LF  C21  H29  single    0.970  0.020  1.090
 5LF  C22  H30  single    0.970  0.020  1.090
 5LF  C22  H31  single    0.970  0.020  1.090
 5LF  C23  H32  single    0.970  0.020  1.090
 5LF  C23  H33  single    0.970  0.020  1.090
 5LF  C24  H34  single    0.970  0.020  1.090
 5LF  C24  H35  single    0.970  0.020  1.090
 5LF  C25  H36  single    0.970  0.020  1.090
 5LF  C25  H37  single    0.970  0.020  1.090
 5LF  C27  H38  single    0.930  0.020  1.080
 5LF  C29  H39  single    0.970  0.020  1.090
 5LF  C29  H40  single    0.970  0.020  1.090
 5LF  C30  H41  single    0.970  0.020  1.090
 5LF  N31  H42  single    0.890  0.020  1.040
 5LF  C42  OXT  single    1.328  0.020  1.328
 5LF  OXT  HXT  single    0.850  0.020  0.980
 5LF  N19  H2   single    0.890  0.020  1.040
 5LF  N31  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
 5LF  H2   N19  H25  105.48  3.000
 5LF  H2   N19  C20  109.54  3.000
 5LF  H25  N19  C20  109.06  3.000
 5LF  H27  C20  H26  106.11  3.000
 5LF  H27  C20  C21  108.87  3.000
 5LF  H26  C20  C21  108.99  3.000
 5LF  H27  C20  N19  113.42  3.000
 5LF  H26  C20  N19  108.23  3.000
 5LF  C21  C20  N19  111.02  3.000
 5LF  H29  C21  H28  106.34  3.000
 5LF  H29  C21  C22  109.77  3.000
 5LF  H28  C21  C22  109.32  3.000
 5LF  H29  C21  C20  109.08  3.000
 5LF  H28  C21  C20  109.28  3.000
 5LF  C22  C21  C20  112.85  3.000
 5LF  H31  C22  H30  106.06  3.000
 5LF  H31  C22  C23  109.44  3.000
 5LF  H30  C22  C23  109.24  3.000
 5LF  H31  C22  C21  109.51  3.000
 5LF  H30  C22  C21  109.53  3.000
 5LF  C23  C22  C21  112.82  3.000
 5LF  H33  C23  H32  106.12  3.000
 5LF  H33  C23  C24  109.46  3.000
 5LF  H32  C23  C24  109.53  3.000
 5LF  H33  C23  C22  109.29  3.000
 5LF  H32  C23  C22  109.43  3.000
 5LF  C24  C23  C22  112.79  3.000
 5LF  H35  C24  H34  106.93  3.000
 5LF  H35  C24  C25  109.52  3.000
 5LF  H34  C24  C25  109.46  3.000
 5LF  H35  C24  C23  109.85  3.000
 5LF  H34  C24  C23  109.85  3.000
 5LF  C25  C24  C23  111.14  3.000
 5LF  H37  C25  H36  107.42  3.000
 5LF  H37  C25  N26  108.31  3.000
 5LF  H36  C25  N26  106.81  3.000
 5LF  H37  C25  C24  110.77  3.000
 5LF  H36  C25  C24  110.70  3.000
 5LF  N26  C25  C24  112.62  3.000
 5LF  N45  N26  C27  110.82  3.000
 5LF  N45  N26  C25  120.65  3.000
 5LF  C27  N26  C25  128.53  3.000
 5LF  H38  C27  C28  132.53  3.000
 5LF  H38  C27  N26  123.09  3.000
 5LF  C28  C27  N26  104.38  3.000
 5LF  N44  C28  C29  122.63  3.000
 5LF  C29  C28  C27  129.87  3.000
 5LF  N44  C28  C27  107.50  3.000
 5LF  H40  C29  H39  106.66  3.000
 5LF  H40  C29  C30  109.51  3.000
 5LF  H39  C29  C30  109.62  3.000
 5LF  H40  C29  C28  109.52  3.000
 5LF  H39  C29  C28  109.51  3.000
 5LF  C30  C29  C28  111.88  3.000
 5LF  H41  C30  C42  107.11  3.000
 5LF  H41  C30  N31  108.22  3.000
 5LF  C42  C30  N31  113.89  3.000
 5LF  H41  C30  C29  107.55  3.000
 5LF  N31  C30  C29  110.58  3.000
 5LF  C42  C30  C29  109.24  3.000
 5LF  H1   N31  H42  106.34  3.000
 5LF  H1   N31  C30  110.53  3.000
 5LF  H42  N31  C30  110.34  3.000
 5LF  OXT  C42  O43  123.39  3.000
 5LF  OXT  C42  C30  112.04  3.000
 5LF  O43  C42  C30  124.57  3.000
 5LF  N45  N44  C28  109.34  3.000
 5LF  N44  N45  N26  107.96  3.000
 5LF  HXT  OXT  C42  110.33  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
 5LF  CONST_01  N44  C28  C27  N26     0.00   0.0  0
 5LF  CONST_02  C28  N44  N45  N26     0.00   0.0  0
 5LF  CONST_03  N44  N45  N26  C27     0.00   0.0  0
 5LF  CONST_04  N45  N44  C28  C27     0.00   0.0  0
 5LF  CONST_05  N45  N26  C27  C28     0.00   0.0  0
 5LF  CONST_06  C28  C27  N26  C25   180.00   0.0  0
 5LF  CONST_07  N44  N45  N26  C25   180.00   0.0  0
 5LF  CONST_08  C29  C28  C27  N26   180.00   0.0  0
 5LF  CONST_09  N45  N44  C28  C29   180.00   0.0  0
 5LF  CONST_10  H38  C27  C28  N44   180.00   0.0  0
 5LF  CONST_11  HXT  OXT  C42  C30   180.00   0.0  0
 5LF  Var_01    C27  N26  C25  C24   118.27  30.0  2
 5LF  Var_02    C30  C29  C28  C27   112.39  30.0  2
 5LF  Var_03    N26  C25  C24  C23  -177.96  30.0  3
 5LF  Var_04    C22  C21  C20  N19  -179.78  30.0  3
 5LF  Var_05    C23  C22  C21  C20  -179.08  30.0  3
 5LF  Var_06    C24  C23  C22  C21  -179.34  30.0  3
 5LF  Var_07    C25  C24  C23  C22  -177.35  30.0  3
 5LF  Var_08    H25  N19  C20  C21    68.38  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
 5LF  chir_01  C30  C29  C42  N31  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
 5LF  plan-1  C25  0.020
 5LF  plan-1  N26  0.020
 5LF  plan-1  C27  0.020
 5LF  plan-1  C28  0.020
 5LF  plan-1  C29  0.020
 5LF  plan-1  N44  0.020
 5LF  plan-1  N45  0.020
 5LF  plan-1  H38  0.020
 5LF  plan-2  C30  0.020
 5LF  plan-2  C42  0.020
 5LF  plan-2  O43  0.020
 5LF  plan-2  OXT  0.020
 5LF  plan-2  HXT  0.020

