# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:04:12 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: N~6~-[({3-[3-(trifluoromethyl)-3H-diaziren-3-yl]phenyl}methoxy)carbonyl]-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)OCc1cccc(c1)C2(N=N2)C(F)(F)F)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
 9TU  9TU  N~6~-[({3-[3-(trifluoromethyl)-3H-diaziren-3-yl]phenyl}methoxy)carbonyl]-L-lysine  peptide  45  27  .  2019-07-05  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_9TU
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
 9TU  C10  C  CR6    0   0.081  260.7639  48.0462  138.5720
 9TU  C13  C  C      0   0.752  258.6437  48.7778  140.5981
 9TU  CD   C  CH2    0  -0.425  256.0561  48.9133  142.5110
 9TU  CA   C  CH1    0  -0.202  253.9280  48.6559  145.1655
 9TU  C    C  C      0   0.378  253.1573  47.6807  146.0949
 9TU  C26  C  CR16   0  -0.221  260.7932  46.8821  136.4648
 9TU  N1   N  N      0  -0.055  259.4909  50.8556  134.9331
 9TU  N2   N  N      0  -0.068  260.4719  50.5272  134.3090
 9TU  C3   C  CT     0  -0.186  260.6627  50.5692  135.7523
 9TU  C4   C  CT     0   1.061  261.4197  51.7699  136.2627
 9TU  F5   F  F      0  -0.291  262.6301  51.4191  136.6952
 9TU  F6   F  F      0  -0.307  260.7894  52.3710  137.2787
 9TU  F7   F  F      0  -0.296  261.5725  52.6788  135.2997
 9TU  C8   C  CR6    0   0.164  260.7218  49.2878  136.4984
 9TU  C9   C  CR16   0  -0.339  260.7300  49.2569  137.8902
 9TU  C11  C  CH2    0  -0.234  260.8096  48.0161  140.0756
 9TU  O12  O  O2     0  -0.487  259.9710  48.9909  140.6776
 9TU  O14  O  O      0  -0.505  258.1515  47.8045  140.0667
 9TU  NZ   N  NH1    0  -0.658  257.9640  49.7842  141.1673
 9TU  CE   C  CH2    0  -0.280  256.5253  49.7505  141.3275
 9TU  CG   C  CH2    0  -0.421  254.5390  48.9438  142.6560
 9TU  CB   C  CH2    0  -0.427  253.9724  48.0476  143.7600
 9TU  N    N  NH2    0  -0.776  255.2622  49.0162  145.6251
 9TU  OXT  O  OC    -1  -0.604  253.8377  46.9796  146.8709
 9TU  O    O  O      0  -0.618  251.9157  47.6569  145.9591
 9TU  C25  C  CR16   0  -0.300  260.7951  46.8589  137.8510
 9TU  C27  C  CR16   0  -0.309  260.7505  48.0900  135.7878
 9TU  HD2  H  HCH2   0   0.211  256.3857  47.8792  142.3713
 9TU  HD3  H  HCH2   0   0.227  256.5232  49.2742  143.4276
 9TU  HA   H  HCH1   0   0.198  253.3458  49.5829  145.0979
 9TU  H4   H  HCR6   0   0.265  260.8148  45.9553  135.9069
 9TU  H7   H  HCR6   0   0.258  260.6916  50.1745  138.4627
 9TU  H8   H  HCH2   0   0.253  260.5768  47.0146  140.4432
 9TU  H9   H  HCH2   0   0.268  261.8131  48.2664  140.4223
 9TU  HZ   H  HNH1   0   0.398  258.4795  50.5011  141.6522
 9TU  HE2  H  HCH2   0   0.243  256.1936  50.7831  141.4470
 9TU  HE3  H  HCH2   0   0.234  256.0726  49.3853  140.4036
 9TU  HG2  H  HCH2   0   0.207  254.2044  49.9746  142.8173
 9TU  HG3  H  HCH2   0   0.213  254.0993  48.6370  141.7009
 9TU  HB2  H  HCH2   0   0.222  252.9492  47.7721  143.4962
 9TU  HB3  H  HCH2   0   0.204  254.5368  47.1071  143.7910
 9TU  H    H  HNH2   0   0.331  255.1795  49.4681  146.5286
 9TU  H2   H  HNH2   0   0.320  255.7616  48.1555  145.8216
 9TU  H21  H  HCR6   0   0.261  260.8121  45.9111  138.3752
 9TU  H22  H  HCR6   0   0.263  260.7411  48.0871  134.7047

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
 9TU  N2   N1   double    1.208  0.020  1.208
 9TU  N2   C3   single    1.456  0.020  1.456
 9TU  N1   C3   single    1.458  0.020  1.458
 9TU  C26  C27  aromatic  1.385  0.020  1.385
 9TU  C26  C25  aromatic  1.386  0.020  1.386
 9TU  C27  C8   aromatic  1.393  0.020  1.393
 9TU  C3   C8   single    1.484  0.020  1.484
 9TU  C3   C4   single    1.508  0.020  1.508
 9TU  C25  C10  aromatic  1.389  0.020  1.389
 9TU  C8   C9   aromatic  1.392  0.020  1.392
 9TU  F7   C4   single    1.333  0.020  1.333
 9TU  C4   F6   single    1.338  0.020  1.338
 9TU  C4   F5   single    1.332  0.020  1.332
 9TU  C10  C9   aromatic  1.390  0.020  1.390
 9TU  C10  C11  single    1.505  0.020  1.505
 9TU  C11  O12  single    1.420  0.020  1.420
 9TU  NZ   CE   single    1.448  0.020  1.448
 9TU  NZ   C13  single    1.341  0.020  1.341
 9TU  CE   CD   single    1.524  0.020  1.524
 9TU  C13  O14  double    1.213  0.020  1.213
 9TU  C13  O12  single    1.347  0.020  1.347
 9TU  CD   CG   single    1.524  0.020  1.524
 9TU  CG   CB   single    1.531  0.020  1.531
 9TU  CA   N    single    1.458  0.019  1.458
 9TU  CA   CB   single    1.530  0.020  1.530
 9TU  CA   C    single    1.525  0.021  1.525
 9TU  O    C    deloc     1.231  0.020  1.231
 9TU  C    OXT  deloc     1.248  0.020  1.248
 9TU  CD   HD2  single    0.970  0.020  1.090
 9TU  CD   HD3  single    0.970  0.020  1.090
 9TU  CA   HA   single    0.970  0.020  0.970
 9TU  C26  H4   single    0.930  0.020  1.080
 9TU  C9   H7   single    0.930  0.020  1.080
 9TU  C11  H8   single    0.970  0.020  1.090
 9TU  C11  H9   single    0.970  0.020  1.090
 9TU  NZ   HZ   single    0.860  0.020  1.020
 9TU  CE   HE2  single    0.970  0.020  1.090
 9TU  CE   HE3  single    0.970  0.020  1.090
 9TU  CG   HG2  single    0.970  0.020  1.090
 9TU  CG   HG3  single    0.970  0.020  1.090
 9TU  CB   HB2  single    0.970  0.020  1.090
 9TU  CB   HB3  single    0.970  0.020  1.090
 9TU  N    H    single    0.860  0.020  0.860
 9TU  N    H2   single    0.890  0.020  1.040
 9TU  C25  H21  single    0.930  0.020  1.080
 9TU  C27  H22  single    0.930  0.020  1.080

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
 9TU  C25  C10  C11  120.06  3.000
 9TU  C11  C10  C9   120.55  3.000
 9TU  C25  C10  C9   119.37  3.000
 9TU  NZ   C13  O14  125.61  3.000
 9TU  O14  C13  O12  123.55  3.000
 9TU  NZ   C13  O12  110.84  3.000
 9TU  HD3  CD   HD2  106.93  3.000
 9TU  HD3  CD   CG   109.86  3.000
 9TU  HD2  CD   CG   109.32  3.000
 9TU  HD3  CD   CE   109.83  3.000
 9TU  HD2  CD   CE   109.10  3.000
 9TU  CG   CD   CE   111.67  3.000
 9TU  HA   CA   N    110.00  3.000
 9TU  HA   CA   CB   109.00  3.000
 9TU  N    CA   CB   110.50  1.700
 9TU  HA   CA   C    109.00  3.000
 9TU  CB   CA   C    110.10  1.900
 9TU  N    CA   C    111.00  2.800
 9TU  O    C    OXT  126.80  3.000
 9TU  OXT  C    CA   117.05  3.000
 9TU  O    C    CA   120.80  1.700
 9TU  H4   C26  C27  119.70  3.000
 9TU  H4   C26  C25  120.08  3.000
 9TU  C27  C26  C25  120.21  3.000
 9TU  C3   N1   N2    65.44  3.000
 9TU  C3   N2   N1    65.58  3.000
 9TU  C8   C3   C4   119.82  3.000
 9TU  C4   C3   N2   115.09  3.000
 9TU  C8   C3   N2   118.59  3.000
 9TU  C4   C3   N1   115.92  3.000
 9TU  C8   C3   N1   118.95  3.000
 9TU  N2   C3   N1    48.98  3.000
 9TU  F7   C4   F6   107.23  3.000
 9TU  F6   C4   F5   107.44  3.000
 9TU  F7   C4   F5   108.06  3.000
 9TU  F5   C4   C3   110.87  3.000
 9TU  F6   C4   C3   112.22  3.000
 9TU  F7   C4   C3   110.85  3.000
 9TU  C27  C8   C9   119.39  3.000
 9TU  C9   C8   C3   121.47  3.000
 9TU  C27  C8   C3   119.13  3.000
 9TU  H7   C9   C8   120.65  3.000
 9TU  H7   C9   C10  118.68  3.000
 9TU  C8   C9   C10  120.65  3.000
 9TU  H9   C11  H8   107.43  3.000
 9TU  H9   C11  O12  104.54  3.000
 9TU  H8   C11  O12  111.16  3.000
 9TU  H9   C11  C10  109.94  3.000
 9TU  H8   C11  C10  110.38  3.000
 9TU  O12  C11  C10  113.09  3.000
 9TU  C11  O12  C13  116.65  3.000
 9TU  HZ   NZ   CE   118.15  3.000
 9TU  HZ   NZ   C13  118.61  3.000
 9TU  CE   NZ   C13  122.21  3.000
 9TU  HE3  CE   HE2  106.46  3.000
 9TU  HE3  CE   NZ   109.03  3.000
 9TU  HE2  CE   NZ   106.99  3.000
 9TU  HE3  CE   CD   110.23  3.000
 9TU  HE2  CE   CD   109.96  3.000
 9TU  NZ   CE   CD   113.87  3.000
 9TU  HG3  CG   HG2  105.62  3.000
 9TU  HG3  CG   CB   108.44  3.000
 9TU  HG2  CG   CB   109.36  3.000
 9TU  HG3  CG   CD   108.12  3.000
 9TU  HG2  CG   CD   109.68  3.000
 9TU  CB   CG   CD   115.17  3.000
 9TU  HB3  CB   HB2  105.81  3.000
 9TU  HB3  CB   CG   109.37  3.000
 9TU  HB2  CB   CG   108.68  3.000
 9TU  HB3  CB   CA   109.23  3.000
 9TU  HB2  CB   CA   107.14  3.000
 9TU  CG   CB   CA   116.10  3.000
 9TU  H2   N    H    104.22  3.000
 9TU  H2   N    CA   107.60  3.000
 9TU  H    N    CA   114.00  3.000
 9TU  H21  C25  C26  119.89  3.000
 9TU  H21  C25  C10  119.80  3.000
 9TU  C26  C25  C10  120.30  3.000
 9TU  H22  C27  C8   120.81  3.000
 9TU  H22  C27  C26  119.12  3.000
 9TU  C8   C27  C26  120.07  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
 9TU  CONST_01  C27  C26  C25  C10     0.00   0.0  0
 9TU  CONST_02  C27  C8   C9   C10     0.00   0.0  0
 9TU  CONST_03  C9   C8   C27  C26     0.00   0.0  0
 9TU  CONST_04  C9   C10  C25  C26     0.00   0.0  0
 9TU  CONST_05  C25  C26  C27  C8      0.00   0.0  0
 9TU  CONST_06  C25  C10  C9   C8      0.00   0.0  0
 9TU  CONST_07  C3   C8   C9   C10   180.00   0.0  0
 9TU  CONST_08  C3   C8   C27  C26   180.00   0.0  0
 9TU  CONST_09  C11  C10  C25  C26   180.00   0.0  0
 9TU  CONST_10  C11  C10  C9   C8    180.00   0.0  0
 9TU  CONST_11  H4   C26  C25  C10   180.00   0.0  0
 9TU  CONST_12  H22  C27  C8   C3      0.00   0.0  0
 9TU  CONST_13  H7   C9   C8   C3      0.00   0.0  0
 9TU  CONST_14  H21  C25  C10  C9    180.00   0.0  0
 9TU  Var_01    C8   C3   N2   N1    104.87  30.0  1
 9TU  Var_02    C27  C8   C3   N1     63.86  30.0  2
 9TU  Var_03    F7   C4   C3   N1    -44.14  30.0  3
 9TU  Var_04    O12  C11  C10  C9     40.34  30.0  2
 9TU  Var_05    CD   CE   NZ   C13    79.40  30.0  3
 9TU  Var_06    CA   CB   CG   CD     85.55  30.0  3
 9TU  Var_07    NZ   C13  O12  C11  -178.19  30.0  2
 9TU  Var_08    CE   NZ   C13  O12  -174.31  30.0  1
 9TU  Var_09    CG   CD   CE   NZ    178.42  30.0  3
 9TU  Var_10    CB   CG   CD   CE    175.80  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
 9TU  chir_01  CA  N   CB  C   negativ
 9TU  chir_02  C3  N1  C8  C4  both

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
 9TU  plan-1  C10  0.020
 9TU  plan-1  C26  0.020
 9TU  plan-1  C3   0.020
 9TU  plan-1  C8   0.020
 9TU  plan-1  C9   0.020
 9TU  plan-1  C11  0.020
 9TU  plan-1  C25  0.020
 9TU  plan-1  C27  0.020
 9TU  plan-1  H4   0.020
 9TU  plan-1  H7   0.020
 9TU  plan-1  H21  0.020
 9TU  plan-1  H22  0.020
 9TU  plan-2  C13  0.020
 9TU  plan-2  O12  0.020
 9TU  plan-2  O14  0.020
 9TU  plan-2  NZ   0.020
 9TU  plan-3  CA   0.020
 9TU  plan-3  C    0.020
 9TU  plan-3  OXT  0.020
 9TU  plan-3  O    0.020

