# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 14:33:03 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (2S)-2-{4-[(1S)-1,5-diaminopentyl]-1H-1,2,3-triazol-1-yl}-4-methylpentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](n1cc(nn1)[C@@H](N)CCCCN)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
 TKL  TKL  '(2S)-2-{4-[(1S)-1,5-diaminopentyl]-1H-1,2,3-triazol-1-yl}-4-methylpentanoic acid'  peptide  44  20  .  2022-03-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TKL
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
 TKL  O    O  O      0  -0.588  -3.0496  -2.1824  -0.3947
 TKL  C    C  C      0   0.428  -3.5234  -1.4240   0.4690
 TKL  CA   C  CH1    0  -0.198  -2.7996  -0.0665   0.6637
 TKL  CB   C  CH2    0  -0.419  -3.1369   0.9131  -0.4626
 TKL  CG   C  CH1    0  -0.239  -4.6257   1.2267  -0.6255
 TKL  CD1  C  CH3    0  -0.666  -5.2445   1.7691   0.6585
 TKL  CD2  C  CH3    0  -0.651  -4.8064   2.2220  -1.7683
 TKL  NT1  N  NR5    0  -0.255  -1.3567  -0.2416   0.7428
 TKL  NT2  N  N      0  -0.119  -0.7190   0.0260   1.8677
 TKL  NT3  N  N      0  -0.341   0.5371  -0.2099   1.6822
 TKL  CT4  C  CR5    0   0.169   0.7266  -0.6404   0.4171
 TKL  CT5  C  CR15   0  -0.083  -0.4990  -0.6667  -0.2011
 TKL  CT6  C  CH1    0  -0.164   2.0703  -1.0103  -0.1323
 TKL  N    N  NH2    0  -0.792   1.9232  -1.3345  -1.5434
 TKL  CI   C  CH2    0  -0.422   3.1043   0.0814   0.1745
 TKL  CJ   C  CH2    0  -0.433   4.5213  -0.2942  -0.2370
 TKL  CK   C  CH2    0  -0.423   5.5346   0.8006   0.0718
 TKL  CL   C  CH2    0  -0.272   6.9473   0.4284  -0.3508
 TKL  NZ   N  NH2    0  -0.801   7.8876   1.4968  -0.0406
 TKL  OXT  O  OC    -1  -0.592  -4.5326  -1.6056   1.1717
 TKL  H2   H  HCH1   0   0.257  -3.0800   0.3658   1.6240
 TKL  H3   H  HCH2   0   0.228  -2.6004   1.8500  -0.2750
 TKL  H4   H  HCH2   0   0.233  -2.7549   0.5175  -1.4087
 TKL  H5   H  HCH1   0   0.223  -5.1493   0.3042  -0.8980
 TKL  H6   H  HCH3   0   0.211  -4.6997   2.6494   1.0084
 TKL  H7   H  HCH3   0   0.225  -6.2817   2.0678   0.4954
 TKL  H8   H  HCH3   0   0.233  -5.2419   1.0255   1.4547
 TKL  H9   H  HCH3   0   0.224  -4.3561   1.8579  -2.6934
 TKL  H10  H  HCH3   0   0.227  -5.8629   2.4093  -1.9660
 TKL  H11  H  HCH3   0   0.213  -4.3395   3.1804  -1.5271
 TKL  H12  H  HCR5   0   0.290  -0.8030  -0.9489  -1.1913
 TKL  H13  H  HCH1   0   0.241   2.3982  -1.9289   0.3700
 TKL  HN1  H  HNH2   0   0.341   1.8082  -0.4795  -2.0767
 TKL  HN2  H  HNH2   0   0.355   2.7739  -1.7618  -1.8857
 TKL  H17  H  HCH2   0   0.215   2.8001   1.0038  -0.3343
 TKL  H18  H  HCH2   0   0.223   3.0834   0.3006   1.2456
 TKL  H19  H  HCH2   0   0.214   4.8150  -1.2181   0.2743
 TKL  H20  H  HCH2   0   0.206   4.5531  -0.5150  -1.3089
 TKL  H21  H  HCH2   0   0.212   5.2420   1.7277  -0.4309
 TKL  H22  H  HCH2   0   0.211   5.5211   1.0145   1.1465
 TKL  H23  H  HCH2   0   0.186   7.2135  -0.5351   0.1086
 TKL  H24  H  HCH2   0   0.210   6.9642   0.2643  -1.4320
 TKL  H25  H  HNH2   0   0.336   7.9874   1.5691   0.9647
 TKL  H26  H  HNH2   0   0.344   8.8060   1.2466  -0.3844

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
 TKL  O    C    deloc     1.231  0.020  1.231
 TKL  NT2  NT3  aromatic  1.291  0.020  1.291
 TKL  NT2  NT1  aromatic  1.321  0.020  1.321
 TKL  NT3  CT4  aromatic  1.350  0.020  1.350
 TKL  C    CA   single    1.525  0.021  1.525
 TKL  NZ   CL   single    1.457  0.020  1.457
 TKL  CA   NT1  single    1.456  0.020  1.456
 TKL  CA   CB   single    1.521  0.033  1.521
 TKL  NT1  CT5  aromatic  1.344  0.020  1.344
 TKL  CT4  CT6  single    1.498  0.020  1.498
 TKL  CT4  CT5  aromatic  1.373  0.020  1.373
 TKL  CK   CL   single    1.521  0.020  1.521
 TKL  CK   CJ   single    1.523  0.020  1.523
 TKL  CT6  CI   single    1.535  0.020  1.535
 TKL  CT6  N    single    1.455  0.020  1.455
 TKL  CD1  CG   single    1.525  0.020  1.525
 TKL  CI   CJ   single    1.523  0.020  1.523
 TKL  CB   CG   single    1.530  0.020  1.530
 TKL  CG   CD2  single    1.526  0.020  1.526
 TKL  C    OXT  deloc     1.243  0.020  1.243
 TKL  CA   H2   single    0.970  0.020  1.090
 TKL  CB   H3   single    0.970  0.020  1.090
 TKL  CB   H4   single    0.970  0.020  1.090
 TKL  CG   H5   single    0.970  0.020  1.090
 TKL  CD1  H6   single    0.970  0.020  1.090
 TKL  CD1  H7   single    0.970  0.020  1.090
 TKL  CD1  H8   single    0.970  0.020  1.090
 TKL  CD2  H9   single    0.970  0.020  1.090
 TKL  CD2  H10  single    0.970  0.020  1.090
 TKL  CD2  H11  single    0.970  0.020  1.090
 TKL  CT5  H12  single    0.930  0.020  1.080
 TKL  CT6  H13  single    0.970  0.020  1.090
 TKL  N    HN1  single    0.890  0.020  1.040
 TKL  N    HN2  single    0.890  0.020  1.040
 TKL  CI   H17  single    0.970  0.020  1.090
 TKL  CI   H18  single    0.970  0.020  1.090
 TKL  CJ   H19  single    0.970  0.020  1.090
 TKL  CJ   H20  single    0.970  0.020  1.090
 TKL  CK   H21  single    0.970  0.020  1.090
 TKL  CK   H22  single    0.970  0.020  1.090
 TKL  CL   H23  single    0.970  0.020  1.090
 TKL  CL   H24  single    0.970  0.020  1.090
 TKL  NZ   H25  single    0.890  0.020  1.040
 TKL  NZ   H26  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
 TKL  OXT  C    CA   120.80  1.700
 TKL  OXT  C    O    127.81  3.000
 TKL  CA   C    O    120.80  1.700
 TKL  H2   CA   NT1  104.77  3.000
 TKL  H2   CA   CB   109.75  3.000
 TKL  NT1  CA   CB   109.60  3.000
 TKL  H2   CA   C    109.74  3.000
 TKL  CB   CA   C    110.50  1.500
 TKL  NT1  CA   C    111.36  3.000
 TKL  H4   CB   H3   106.63  3.000
 TKL  H4   CB   CG   108.77  3.000
 TKL  H3   CB   CG   108.62  3.000
 TKL  H4   CB   CA   109.14  3.000
 TKL  H3   CB   CA   108.26  3.000
 TKL  CG   CB   CA   115.09  3.000
 TKL  H5   CG   CD2  107.84  3.000
 TKL  H5   CG   CD1  108.36  3.000
 TKL  CD2  CG   CD1  110.52  3.000
 TKL  H5   CG   CB   108.60  3.000
 TKL  CD2  CG   CB   109.18  3.000
 TKL  CD1  CG   CB   112.21  3.000
 TKL  H8   CD1  H7   107.35  3.000
 TKL  H8   CD1  H6   108.33  3.000
 TKL  H7   CD1  H6   107.52  3.000
 TKL  H8   CD1  CG   111.82  3.000
 TKL  H7   CD1  CG   110.92  3.000
 TKL  H6   CD1  CG   110.72  3.000
 TKL  H11  CD2  H10  107.64  3.000
 TKL  H11  CD2  H9   107.65  3.000
 TKL  H10  CD2  H9   107.65  3.000
 TKL  H11  CD2  CG   110.86  3.000
 TKL  H10  CD2  CG   111.24  3.000
 TKL  H9   CD2  CG   111.61  3.000
 TKL  CT5  NT1  NT2  110.74  3.000
 TKL  CT5  NT1  CA   129.22  3.000
 TKL  NT2  NT1  CA   120.04  3.000
 TKL  NT3  NT2  NT1  108.08  3.000
 TKL  CT4  NT3  NT2  109.23  3.000
 TKL  CT6  CT4  CT5  129.11  3.000
 TKL  CT5  CT4  NT3  107.63  3.000
 TKL  CT6  CT4  NT3  123.26  3.000
 TKL  H12  CT5  CT4  132.31  3.000
 TKL  H12  CT5  NT1  123.37  3.000
 TKL  CT4  CT5  NT1  104.32  3.000
 TKL  H13  CT6  CI   107.62  3.000
 TKL  H13  CT6  N    106.72  3.000
 TKL  CI   CT6  N    114.86  3.000
 TKL  H13  CT6  CT4  107.88  3.000
 TKL  N    CT6  CT4  108.66  3.000
 TKL  CI   CT6  CT4  110.82  3.000
 TKL  HN2  N    HN1  105.88  3.000
 TKL  HN2  N    CT6  109.70  3.000
 TKL  HN1  N    CT6  109.48  3.000
 TKL  H18  CI   H17  106.30  3.000
 TKL  H18  CI   CJ   109.39  3.000
 TKL  H17  CI   CJ   109.89  3.000
 TKL  H18  CI   CT6  109.00  3.000
 TKL  H17  CI   CT6  108.58  3.000
 TKL  CJ   CI   CT6  113.43  3.000
 TKL  H20  CJ   H19  106.19  3.000
 TKL  H20  CJ   CK   108.91  3.000
 TKL  H19  CJ   CK   109.45  3.000
 TKL  H20  CJ   CI   109.96  3.000
 TKL  H19  CJ   CI   109.35  3.000
 TKL  CK   CJ   CI   112.77  3.000
 TKL  H22  CK   H21  106.37  3.000
 TKL  H22  CK   CL   109.37  3.000
 TKL  H21  CK   CL   109.15  3.000
 TKL  H22  CK   CJ   109.32  3.000
 TKL  H21  CK   CJ   109.75  3.000
 TKL  CL   CK   CJ   112.69  3.000
 TKL  H24  CL   H23  106.12  3.000
 TKL  H24  CL   NZ   108.10  3.000
 TKL  H23  CL   NZ   113.41  3.000
 TKL  H24  CL   CK   109.01  3.000
 TKL  H23  CL   CK   108.85  3.000
 TKL  NZ   CL   CK   111.16  3.000
 TKL  H26  NZ   H25  105.39  3.000
 TKL  H26  NZ   CL   109.40  3.000
 TKL  H25  NZ   CL   109.11  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
 TKL  CONST_01  CT4  NT3  NT2  NT1     0.00   0.0  0
 TKL  CONST_02  NT3  CT4  CT5  NT1     0.00   0.0  0
 TKL  CONST_03  CT5  CT4  NT3  NT2     0.00   0.0  0
 TKL  CONST_04  CT4  CT5  NT1  NT2     0.00   0.0  0
 TKL  CONST_05  CT5  NT1  NT2  NT3     0.00   0.0  0
 TKL  CONST_06  NT3  NT2  NT1  CA    180.00   0.0  0
 TKL  CONST_07  CT4  CT5  NT1  CA    180.00   0.0  0
 TKL  CONST_08  CT6  CT4  CT5  NT1   180.00   0.0  0
 TKL  CONST_09  CT6  CT4  NT3  NT2   180.00   0.0  0
 TKL  CONST_10  H12  CT5  NT1  NT2   180.00   0.0  0
 TKL  Var_01    CD1  CG   CB   CA     56.49  30.0  3
 TKL  Var_02    CK   CJ   CI   CT6   179.89  30.0  3
 TKL  Var_03    CL   CK   CJ   CI   -179.51  30.0  1
 TKL  Var_04    NZ   CL   CK   CJ   -180.00  30.0  3
 TKL  Var_05    H6   CD1  CG   CB     55.71  30.0  3
 TKL  Var_06    H9   CD2  CG   CB     55.24  30.0  3
 TKL  Var_07    H25  NZ   CL   CK     68.71  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
 TKL  chir_01  CA   C  NT1  CB  negativ
 TKL  chir_02  CT6  N  CT4  CI  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
 TKL  plan-1  CA   0.020
 TKL  plan-1  NT1  0.020
 TKL  plan-1  NT2  0.020
 TKL  plan-1  NT3  0.020
 TKL  plan-1  CT4  0.020
 TKL  plan-1  CT5  0.020
 TKL  plan-1  CT6  0.020
 TKL  plan-1  H12  0.020
 TKL  plan-2  O    0.020
 TKL  plan-2  C    0.020
 TKL  plan-2  CA   0.020
 TKL  plan-2  OXT  0.020

