# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 07:17:59 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  38  18  .  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_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   8.7428  -0.0301   0.3872
 5LF  C20  C  CH2    0  -0.273   7.4625  -0.7179   0.2910
 5LF  C21  C  CH2    0  -0.425   6.3145   0.2762   0.2120
 5LF  C22  C  CH2    0  -0.419   4.9514  -0.3987   0.1284
 5LF  C23  C  CH2    0  -0.424   3.8121   0.5945  -0.0615
 5LF  C24  C  CH2    0  -0.432   2.4427  -0.0714  -0.1056
 5LF  C25  C  CH2    0  -0.281   1.3538   0.9322  -0.4559
 5LF  N26  N  NR5    0  -0.254   0.0299   0.3392  -0.4590
 5LF  C27  C  CR15   0  -0.104  -0.9571   0.4863   0.4417
 5LF  C28  C  CR5    0   0.195  -1.9619  -0.3301  -0.0120
 5LF  C29  C  CH2    0  -0.522  -3.3203  -0.5694   0.5425
 5LF  C30  C  CH1    0  -0.211  -4.4219   0.2017  -0.1989
 5LF  N31  N  NH2    0  -0.778  -4.1431   1.6252  -0.1519
 5LF  C42  C  C      0   0.384  -5.8061  -0.2379   0.3446
 5LF  O43  O  O      0  -0.604  -6.5197   0.6303   0.8826
 5LF  N44  N  N      0  -0.330  -1.5213  -0.9153  -1.1474
 5LF  N45  N  N      0  -0.121  -0.3233  -0.5068  -1.4064
 5LF  H25  H  HNH2   0   0.336   8.8041   0.4300   1.2876
 5LF  H26  H  HCH2   0   0.211   7.4680  -1.3256  -0.6182
 5LF  H27  H  HCH2   0   0.186   7.2768  -1.4142   1.1225
 5LF  H28  H  HCH2   0   0.212   6.3408   0.9323   1.0895
 5LF  H29  H  HCH2   0   0.212   6.4622   0.9222  -0.6595
 5LF  H30  H  HCH2   0   0.213   4.9472  -1.1118  -0.7034
 5LF  H31  H  HCH2   0   0.213   4.7793  -0.9887   1.0349
 5LF  H32  H  HCH2   0   0.220   3.8314   1.3355   0.7444
 5LF  H33  H  HCH2   0   0.218   3.9759   1.1513  -0.9904
 5LF  H34  H  HCH2   0   0.233   2.4440  -0.8752  -0.8469
 5LF  H35  H  HCH2   0   0.234   2.2176  -0.5302   0.8612
 5LF  H36  H  HCH2   0   0.263   1.3353   1.7515   0.2625
 5LF  H37  H  HCH2   0   0.268   1.5323   1.3653  -1.4406
 5LF  H38  H  HCR5   0   0.297  -0.8790   1.1365   1.2962
 5LF  H39  H  HCH2   0   0.248  -3.5491  -1.6346   0.4984
 5LF  H40  H  HCH2   0   0.237  -3.3325  -0.2881   1.6002
 5LF  H41  H  HCH1   0   0.220  -4.3770  -0.1063  -1.2505
 5LF  H42  H  HNH2   0   0.334  -4.8616   2.1099  -0.6760
 5LF  OXT  O  OC    -1  -0.622  -6.0875  -1.4460   0.1979
 5LF  H2   H  HNH2   0   0.345   9.4935  -0.7087   0.3792
 5LF  H1   H  HNH2   0   0.322  -4.2717   1.9458   0.8016

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    1.522  0.020  1.522
 5LF  C25  N26  single    1.451  0.020  1.451
 5LF  N26  C27  aromatic  1.344  0.020  1.344
 5LF  N26  N45  aromatic  1.318  0.020  1.318
 5LF  C27  C28  aromatic  1.372  0.020  1.372
 5LF  C28  N44  aromatic  1.351  0.020  1.351
 5LF  C28  C29  single    1.487  0.020  1.487
 5LF  C29  C30  single    1.535  0.020  1.535
 5LF  C30  C42  single    1.551  0.020  1.551
 5LF  C30  N31  single    1.451  0.020  1.451
 5LF  C42  O43  deloc     1.246  0.020  1.246
 5LF  N44  N45  aromatic  1.292  0.020  1.292
 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  deloc     1.249  0.020  1.249
 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  105.47  3.000
 5LF  H2   N19  C20  109.56  3.000
 5LF  H25  N19  C20  109.05  3.000
 5LF  H27  C20  H26  106.11  3.000
 5LF  H27  C20  C21  108.99  3.000
 5LF  H26  C20  C21  108.90  3.000
 5LF  H27  C20  N19  113.41  3.000
 5LF  H26  C20  N19  108.24  3.000
 5LF  C21  C20  N19  111.00  3.000
 5LF  H29  C21  H28  106.31  3.000
 5LF  H29  C21  C22  109.78  3.000
 5LF  H28  C21  C22  109.32  3.000
 5LF  H29  C21  C20  108.98  3.000
 5LF  H28  C21  C20  109.37  3.000
 5LF  C22  C21  C20  112.88  3.000
 5LF  H31  C22  H30  106.09  3.000
 5LF  H31  C22  C23  109.69  3.000
 5LF  H30  C22  C23  109.08  3.000
 5LF  H31  C22  C21  109.50  3.000
 5LF  H30  C22  C21  109.48  3.000
 5LF  C23  C22  C21  112.78  3.000
 5LF  H33  C23  H32  106.12  3.000
 5LF  H33  C23  C24  109.40  3.000
 5LF  H32  C23  C24  109.45  3.000
 5LF  H33  C23  C22  108.98  3.000
 5LF  H32  C23  C22  109.65  3.000
 5LF  C24  C23  C22  113.01  3.000
 5LF  H35  C24  H34  106.93  3.000
 5LF  H35  C24  C25  109.44  3.000
 5LF  H34  C24  C25  109.25  3.000
 5LF  H35  C24  C23  110.05  3.000
 5LF  H34  C24  C23  109.87  3.000
 5LF  C25  C24  C23  111.20  3.000
 5LF  H37  C25  H36  107.42  3.000
 5LF  H37  C25  N26  108.05  3.000
 5LF  H36  C25  N26  107.05  3.000
 5LF  H37  C25  C24  110.65  3.000
 5LF  H36  C25  C24  110.87  3.000
 5LF  N26  C25  C24  112.58  3.000
 5LF  N45  N26  C27  110.80  3.000
 5LF  N45  N26  C25  120.55  3.000
 5LF  C27  N26  C25  128.60  3.000
 5LF  H38  C27  C28  132.46  3.000
 5LF  H38  C27  N26  123.00  3.000
 5LF  C28  C27  N26  104.54  3.000
 5LF  N44  C28  C29  122.80  3.000
 5LF  C29  C28  C27  129.91  3.000
 5LF  N44  C28  C27  107.27  3.000
 5LF  H40  C29  H39  106.73  3.000
 5LF  H40  C29  C30  109.24  3.000
 5LF  H39  C29  C30  108.69  3.000
 5LF  H40  C29  C28  109.22  3.000
 5LF  H39  C29  C28  109.50  3.000
 5LF  C30  C29  C28  113.24  3.000
 5LF  H41  C30  C42  107.04  3.000
 5LF  H41  C30  N31  107.37  3.000
 5LF  C42  C30  N31  115.99  3.000
 5LF  H41  C30  C29  107.01  3.000
 5LF  N31  C30  C29  109.82  3.000
 5LF  C42  C30  C29  109.20  3.000
 5LF  H1   N31  H42  104.20  3.000
 5LF  H1   N31  C30  108.43  3.000
 5LF  H42  N31  C30  108.44  3.000
 5LF  OXT  C42  O43  126.55  3.000
 5LF  OXT  C42  C30  115.73  3.000
 5LF  O43  C42  C30  117.71  3.000
 5LF  N45  N44  C28  109.50  3.000
 5LF  N44  N45  N26  107.90  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  Var_01    C27  N26  C25  C24   106.40  30.0  2
 5LF  Var_02    C30  C29  C28  C27   100.89  30.0  2
 5LF  Var_03    N26  C25  C24  C23  -177.92  30.0  3
 5LF  Var_04    C22  C21  C20  N19  -179.25  30.0  3
 5LF  Var_05    C23  C22  C21  C20  -175.46  30.0  3
 5LF  Var_06    C24  C23  C22  C21  -178.34  30.0  3
 5LF  Var_07    C25  C24  C23  C22  -173.44  30.0  3
 5LF  Var_08    H25  N19  C20  C21    68.60  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

