# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 26 01:51:57 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: N~6~-[(1-methyl-1H-imidazol-5-yl)methyl]-N~6~-propan-2-yl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)N(CCCC[C@H](N)C(O)=O)Cc1cncn1C
#
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
 ZT1  ZT1  N~6~-[(1-methyl-1H-imidazol-5-yl)methyl]-N~6~-propan-2-yl-L-lysine  ligand  45  20  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ZT1
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
 ZT1  O    O  O      0  -0.612  15.4088  26.8133  25.7416
 ZT1  C    C  C      0   0.384  14.4179  26.6378  24.9999
 ZT1  CA   C  CH1    0  -0.189  14.3117  27.5865  23.7822
 ZT1  N    N  NH2    0  -0.794  14.5932  28.9876  24.0932
 ZT1  CB   C  CH2    0  -0.412  15.2803  27.1343  22.6880
 ZT1  CG   C  CH2    0  -0.420  15.0651  25.7158  22.1747
 ZT1  CD   C  CH2    0  -0.436  16.0414  25.3544  21.0599
 ZT1  CE   C  CH2    0  -0.270  15.8006  23.9433  20.5418
 ZT1  NZ   N  NT     0  -0.419  16.8585  23.3738  19.7188
 ZT1  CAB  C  CH1    0  -0.086  17.1537  24.0616  18.4534
 ZT1  CAC  C  CH3    0  -0.650  18.1148  25.2353  18.6260
 ZT1  CAA  C  CH3    0  -0.680  15.9260  24.4660  17.6363
 ZT1  CAQ  C  CH2    0  -0.368  16.6093  21.9544  19.4833
 ZT1  CAP  C  CR5    0   0.272  16.5956  21.1484  20.7393
 ZT1  CAR  C  CR15   0  -0.249  17.6051  20.8384  21.6106
 ZT1  NAS  N  N      0  -0.445  17.1385  20.0811  22.6440
 ZT1  CAT  C  CR15   0   0.073  15.8607  19.9307  22.4054
 ZT1  NAN  N  NR5    0  -0.432  15.4792  20.5534  21.2702
 ZT1  CAO  C  CH3    0  -0.536  14.1359  20.5828  20.7364
 ZT1  HA   H  HCH1   0   0.191  13.2939  27.5354  23.3808
 ZT1  H    H  HNH2   0   0.331  13.8930  29.3245  24.7445
 ZT1  H2   H  HNH2   0   0.321  15.4613  29.0096  24.6183
 ZT1  HB2  H  HCH2   0   0.199  16.3046  27.2277  23.0678
 ZT1  HB3  H  HCH2   0   0.208  15.2017  27.8335  21.8491
 ZT1  HG2  H  HCH2   0   0.205  14.0368  25.6102  21.8116
 ZT1  HG3  H  HCH2   0   0.216  15.1745  24.9948  22.9894
 ZT1  HD2  H  HCH2   0   0.212  17.0666  25.4319  21.4343
 ZT1  HD3  H  HCH2   0   0.217  15.9433  26.0874  20.2558
 ZT1  HE2  H  HCH2   0   0.190  14.8199  23.9102  20.0371
 ZT1  HE3  H  HCH2   0   0.236  15.7045  23.2970  21.4187
 ZT1  H15  H  HCH1   0   0.222  17.7012  23.3268  17.8556
 ZT1  H16  H  HCH3   0   0.223  18.9719  24.9453  19.2343
 ZT1  H17  H  HCH3   0   0.222  18.4879  25.5473  17.6490
 ZT1  H18  H  HCH3   0   0.222  17.6496  26.1053  19.0859
 ZT1  H19  H  HCH3   0   0.231  15.2393  23.6308  17.4856
 ZT1  H20  H  HCH3   0   0.221  15.3672  25.2774  18.1061
 ZT1  H21  H  HCH3   0   0.232  16.2344  24.8147  16.6498
 ZT1  H22  H  HCH2   0   0.221  15.6776  21.7777  18.9223
 ZT1  H23  H  HCH2   0   0.258  17.4138  21.5759  18.8491
 ZT1  H24  H  HCR5   0   0.245  18.6429  21.1282  21.5360
 ZT1  H25  H  HCR5   0   0.273  15.1604  19.3772  23.0140
 ZT1  H26  H  HCH3   0   0.269  13.4835  20.0228  21.4010
 ZT1  H27  H  HCH3   0   0.260  13.7671  21.6047  20.6683
 ZT1  H28  H  HCH3   0   0.259  14.0980  20.1276  19.7485
 ZT1  OXT  O  OC    -1  -0.613  13.5342  25.7661  25.1257

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
 ZT1  CAA  CAB  single    1.529  0.020  1.529
 ZT1  CAC  CAB  single    1.527  0.020  1.527
 ZT1  CAB  NZ   single    1.470  0.020  1.470
 ZT1  CAO  NAN  single    1.446  0.020  1.446
 ZT1  CAQ  NZ   single    1.460  0.020  1.460
 ZT1  CAQ  CAP  single    1.492  0.020  1.492
 ZT1  NZ   CE   single    1.456  0.020  1.456
 ZT1  CE   CD   single    1.522  0.020  1.522
 ZT1  NAN  CAP  aromatic  1.372  0.020  1.372
 ZT1  NAN  CAT  aromatic  1.350  0.020  1.350
 ZT1  CAP  CAR  aromatic  1.369  0.020  1.369
 ZT1  CD   CG   single    1.525  0.020  1.525
 ZT1  CAT  NAS  aromatic  1.309  0.020  1.309
 ZT1  CAR  NAS  aromatic  1.364  0.020  1.364
 ZT1  CG   CB   single    1.524  0.020  1.524
 ZT1  CB   CA   single    1.530  0.020  1.530
 ZT1  CA   N    single    1.463  0.020  1.463
 ZT1  CA   C    single    1.547  0.020  1.547
 ZT1  C    O    deloc     1.250  0.020  1.250
 ZT1  CA   HA   single    0.970  0.020  1.090
 ZT1  N    H    single    0.860  0.020  1.020
 ZT1  N    H2   single    0.890  0.020  1.040
 ZT1  CB   HB2  single    0.970  0.020  1.090
 ZT1  CB   HB3  single    0.970  0.020  1.090
 ZT1  CG   HG2  single    0.970  0.020  1.090
 ZT1  CG   HG3  single    0.970  0.020  1.090
 ZT1  CD   HD2  single    0.970  0.020  1.090
 ZT1  CD   HD3  single    0.970  0.020  1.090
 ZT1  CE   HE2  single    0.970  0.020  1.090
 ZT1  CE   HE3  single    0.970  0.020  1.090
 ZT1  CAB  H15  single    0.970  0.020  1.090
 ZT1  CAC  H16  single    0.970  0.020  1.090
 ZT1  CAC  H17  single    0.970  0.020  1.090
 ZT1  CAC  H18  single    0.970  0.020  1.090
 ZT1  CAA  H19  single    0.970  0.020  1.090
 ZT1  CAA  H20  single    0.970  0.020  1.090
 ZT1  CAA  H21  single    0.970  0.020  1.090
 ZT1  CAQ  H22  single    0.970  0.020  1.090
 ZT1  CAQ  H23  single    0.970  0.020  1.090
 ZT1  CAR  H24  single    0.930  0.020  1.080
 ZT1  CAT  H25  single    0.930  0.020  1.080
 ZT1  CAO  H26  single    0.970  0.020  1.090
 ZT1  CAO  H27  single    0.970  0.020  1.090
 ZT1  CAO  H28  single    0.970  0.020  1.090
 ZT1  C    OXT  deloc     1.248  0.020  1.248

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
 ZT1  OXT  C    CA   117.33  3.000
 ZT1  OXT  C    O    126.85  3.000
 ZT1  CA   C    O    115.80  3.000
 ZT1  HA   CA   CB   108.21  3.000
 ZT1  HA   CA   N    107.55  3.000
 ZT1  CB   CA   N    108.27  3.000
 ZT1  HA   CA   C    108.88  3.000
 ZT1  N    CA   C    114.01  3.000
 ZT1  CB   CA   C    109.77  3.000
 ZT1  H2   N    H    104.55  3.000
 ZT1  H2   N    CA   107.18  3.000
 ZT1  H    N    CA   108.78  3.000
 ZT1  HB3  CB   HB2  106.15  3.000
 ZT1  HB3  CB   CG   109.04  3.000
 ZT1  HB2  CB   CG   109.14  3.000
 ZT1  HB3  CB   CA   108.29  3.000
 ZT1  HB2  CB   CA   108.57  3.000
 ZT1  CG   CB   CA   115.26  3.000
 ZT1  HG3  CG   HG2  106.10  3.000
 ZT1  HG3  CG   CD   108.92  3.000
 ZT1  HG2  CG   CD   109.61  3.000
 ZT1  HG3  CG   CB   110.41  3.000
 ZT1  HG2  CG   CB   109.51  3.000
 ZT1  CD   CG   CB   112.11  3.000
 ZT1  HD3  CD   HD2  106.77  3.000
 ZT1  HD3  CD   CE   110.93  3.000
 ZT1  HD2  CD   CE   109.29  3.000
 ZT1  HD3  CD   CG   108.75  3.000
 ZT1  HD2  CD   CG   109.44  3.000
 ZT1  CE   CD   CG   111.54  3.000
 ZT1  HE3  CE   HE2  105.72  3.000
 ZT1  HE3  CE   NZ   106.62  3.000
 ZT1  HE2  CE   NZ   112.05  3.000
 ZT1  HE3  CE   CD   106.79  3.000
 ZT1  HE2  CE   CD   108.91  3.000
 ZT1  NZ   CE   CD   116.10  3.000
 ZT1  CAQ  NZ   CAB  110.50  3.000
 ZT1  CAQ  NZ   CE   110.32  3.000
 ZT1  CAB  NZ   CE   116.70  3.000
 ZT1  H15  CAB  CAA  106.70  3.000
 ZT1  H15  CAB  CAC  105.25  3.000
 ZT1  CAA  CAB  CAC  111.25  3.000
 ZT1  H15  CAB  NZ   104.87  3.000
 ZT1  CAC  CAB  NZ   112.88  3.000
 ZT1  CAA  CAB  NZ   114.99  3.000
 ZT1  H18  CAC  H17  107.21  3.000
 ZT1  H18  CAC  H16  108.23  3.000
 ZT1  H17  CAC  H16  107.86  3.000
 ZT1  H18  CAC  CAB  113.15  3.000
 ZT1  H17  CAC  CAB  109.50  3.000
 ZT1  H16  CAC  CAB  110.70  3.000
 ZT1  H21  CAA  H20  107.24  3.000
 ZT1  H21  CAA  H19  107.32  3.000
 ZT1  H20  CAA  H19  107.82  3.000
 ZT1  H21  CAA  CAB  109.93  3.000
 ZT1  H20  CAA  CAB  112.18  3.000
 ZT1  H19  CAA  CAB  112.11  3.000
 ZT1  H23  CAQ  H22  105.76  3.000
 ZT1  H23  CAQ  CAP  107.96  3.000
 ZT1  H22  CAQ  CAP  109.52  3.000
 ZT1  H23  CAQ  NZ   107.75  3.000
 ZT1  H22  CAQ  NZ   112.48  3.000
 ZT1  CAP  CAQ  NZ   113.01  3.000
 ZT1  NAN  CAP  CAR  104.80  3.000
 ZT1  CAR  CAP  CAQ  130.63  3.000
 ZT1  NAN  CAP  CAQ  124.57  3.000
 ZT1  H24  CAR  NAS  122.02  3.000
 ZT1  H24  CAR  CAP  127.14  3.000
 ZT1  NAS  CAR  CAP  110.85  3.000
 ZT1  CAT  NAS  CAR  105.05  3.000
 ZT1  H25  CAT  NAN  121.80  3.000
 ZT1  H25  CAT  NAS  126.09  3.000
 ZT1  NAN  CAT  NAS  112.10  3.000
 ZT1  CAO  NAN  CAT  125.62  3.000
 ZT1  CAT  NAN  CAP  107.19  3.000
 ZT1  CAO  NAN  CAP  127.18  3.000
 ZT1  H28  CAO  H27  108.91  3.000
 ZT1  H28  CAO  H26  108.59  3.000
 ZT1  H27  CAO  H26  108.58  3.000
 ZT1  H28  CAO  NAN  111.03  3.000
 ZT1  H27  CAO  NAN  110.91  3.000
 ZT1  H26  CAO  NAN  108.75  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
 ZT1  CONST_01  NAS  CAT  NAN  CAP     0.00   0.0  0
 ZT1  CONST_02  CAT  NAS  CAR  CAP     0.00   0.0  0
 ZT1  CONST_03  CAT  NAN  CAP  CAR     0.00   0.0  0
 ZT1  CONST_04  NAN  CAT  NAS  CAR     0.00   0.0  0
 ZT1  CONST_05  NAN  CAP  CAR  NAS     0.00   0.0  0
 ZT1  CONST_06  CAT  NAN  CAP  CAQ   180.00   0.0  0
 ZT1  CONST_07  NAS  CAR  CAP  CAQ   180.00   0.0  0
 ZT1  CONST_08  CAO  NAN  CAP  CAR   180.00   0.0  0
 ZT1  CONST_09  CAO  NAN  CAT  NAS   180.00   0.0  0
 ZT1  CONST_10  H25  CAT  NAN  CAP   180.00   0.0  0
 ZT1  CONST_11  H24  CAR  NAS  CAT   180.00   0.0  0
 ZT1  Var_01    NAN  CAP  CAQ  NZ    111.37  30.0  2
 ZT1  Var_02    H26  CAO  NAN  CAP  -179.40  30.0  2
 ZT1  Var_03    CAP  CAQ  NZ   CE    -61.88  30.0  2
 ZT1  Var_04    CD   CG   CB   CA    178.33  30.0  1
 ZT1  Var_05    CE   CD   CG   CB   -179.09  30.0  1
 ZT1  Var_06    NZ   CE   CD   CG   -165.62  30.0  2
 ZT1  Var_07    CAB  NZ   CE   CD    -62.52  30.0  2
 ZT1  Var_08    CAA  CAB  NZ   CE    -44.82  30.0  2
 ZT1  Var_09    H19  CAA  CAB  NZ    -51.35  30.0  3
 ZT1  Var_10    H16  CAC  CAB  NZ     47.32  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
 ZT1  chir_01  CA  CB  N  C  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
 ZT1  plan-1  CAQ  0.020
 ZT1  plan-1  CAP  0.020
 ZT1  plan-1  CAR  0.020
 ZT1  plan-1  NAS  0.020
 ZT1  plan-1  CAT  0.020
 ZT1  plan-1  NAN  0.020
 ZT1  plan-1  CAO  0.020
 ZT1  plan-1  H24  0.020
 ZT1  plan-1  H25  0.020
 ZT1  plan-2  O    0.020
 ZT1  plan-2  C    0.020
 ZT1  plan-2  CA   0.020
 ZT1  plan-2  OXT  0.020

