# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 17:46:13 2021
#   Inital geometry file: a 169 line input string
#   Ligand name: (2R,4R)-4-methyl-1-(N~2~-{[(3S)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}-L-arginyl)piperidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCN([C@H](C1)C(O)=O)C(=O)[C@H](CCCNC(N)=N)N[S](=O)(=O)c2cccc3C[C@H](C)CNc23
#
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
 15U  15U  '(2R,4R)-4-methyl-1-(N~2~-{[(3S)-3-methyl-1,2,3,4-tetrahydroquinolin-8-yl]sulfonyl}-L-arginyl)piperidine-2-carboxylic acid'  peptide  71  35  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_15U
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
 15U  S    S  S     0   1.352   2.3617  13.6311   0.1725
 15U  O1   O  OS    0  -0.669   1.5546  12.4530  -0.1314
 15U  O2   O  OS    0  -0.649   2.1801  14.2923   1.4546
 15U  C1   C  CH2   0  -0.224   2.5924  12.7969  -4.2366
 15U  C2   C  CH1   0  -0.304   3.3018  13.8895  -5.0186
 15U  C3   C  CH2   0  -0.465   2.5191  15.1867  -4.8549
 15U  C4   C  CR6   0   0.039   2.3403  15.5330  -3.4037
 15U  C5   C  CR16  0  -0.314   2.2339  16.8419  -2.9832
 15U  C6   C  CR16  0  -0.274   2.0641  17.1825  -1.6417
 15U  C7   C  CR16  0  -0.263   2.0573  16.1777  -0.6999
 15U  C8   C  CR6   0  -0.312   2.1831  14.8439  -1.0933
 15U  C9   C  CR6   0   0.446   2.2824  14.4815  -2.4572
 15U  C10  C  CH3   0  -0.656   3.4513  13.4982  -6.4800
 15U  N    N  NH1   0  -0.724   2.3467  13.1970  -2.8686
 15U  N1   N  NC1   0  -0.708   3.9288  13.1027   0.1229
 15U  CA   C  CH1   0  -0.266   4.9845  14.1053   0.1630
 15U  C    C  C     0   0.596   5.5676  14.2573  -1.2499
 15U  O    O  O     0  -0.484   5.4380  13.3251  -2.0311
 15U  CB   C  CH2   0  -0.402   6.0707  13.7050   1.1670
 15U  CG   C  CH2   0  -0.451   6.8973  12.4920   0.7662
 15U  CD   C  CH2   0  -0.304   7.9700  12.1944   1.8116
 15U  NE   N  NH1   0  -0.644   8.8815  11.1418   1.4415
 15U  CZ   C  C     0   0.541   9.8336  11.2927   0.4736
 15U  NH1  N  NH2   0  -0.827  10.5179  10.1309   0.1809
 15U  NH2  N  N     0  -0.729  10.1802  12.3869  -0.1032
 15U  N2   N  NT    0  -0.439   6.2463  15.3760  -1.5652
 15U  C11  C  CH1   0  -0.281   6.3920  16.5384  -0.7179
 15U  C21  C  CH2   0  -0.404   5.8108  17.7761  -1.4075
 15U  C31  C  CH1   0  -0.257   6.3814  18.0008  -2.8033
 15U  C41  C  CH2   0  -0.418   6.2221  16.7206  -3.6175
 15U  C51  C  CH2   0  -0.334   6.8257  15.5258  -2.8974
 15U  C61  C  C     0   0.572   7.8462  16.6667  -0.2674
 15U  O11  O  O     0  -0.424   8.6376  15.7598  -0.2746
 15U  O21  O  OH1   0  -0.582   8.1171  17.8775   0.1915
 15U  C71  C  CH3   0  -0.651   5.7151  19.1888  -3.4813
 15U  H2   H  HCH2  0   0.246   3.2000  11.8901  -4.2189
 15U  H3   H  HCH1  0   0.250   4.2976  14.0278  -4.5835
 15U  H4   H  HCH2  0   0.250   3.0288  16.0065  -5.3667
 15U  H5   H  HCH2  0   0.247   1.5423  15.0779  -5.3413
 15U  H6   H  HCR6  0   0.254   2.2761  17.6268  -3.7300
 15U  H7   H  HCR6  0   0.258   1.9632  18.2161  -1.3420
 15U  H8   H  HCR6  0   0.278   1.9618  16.4217   0.3488
 15U  H9   H  HCH3  0   0.233   4.0280  12.5785  -6.5888
 15U  H10  H  HCH3  0   0.220   2.4766  13.3398  -6.9467
 15U  H11  H  HCH3  0   0.234   3.9646  14.2793  -7.0420
 15U  H12  H  HNH1  0   0.392   2.0672  12.4702  -2.2324
 15U  H13  H  HNC1  0   0.406   4.0788  12.4276  -0.6241
 15U  H14  H  HCH1  0   0.291   4.5465  15.0425   0.5110
 15U  H15  H  HCH2  0   0.240   6.7400  14.5544   1.3214
 15U  H16  H  HCH2  0   0.255   5.5756  13.5300   2.1250
 15U  H17  H  HCH2  0   0.234   6.2603  11.6124   0.6399
 15U  H18  H  HCH2  0   0.234   7.3870  12.6722  -0.1933
 15U  H19  H  HCH2  0   0.229   8.5375  13.1055   2.0278
 15U  H20  H  HCH2  0   0.260   7.5052  11.9055   2.7549
 15U  H21  H  HNH1  0   0.387   8.6210  10.2062   1.7040
 15U  H22  H  HNH2  0   0.378   9.9962   9.2708   0.2462
 15U  H23  H  HNH2  0   0.376  11.0392  10.1876  -0.6790
 15U  H24  H  H     0   0.323   9.6432  13.1796   0.2250
 15U  H26  H  HCH1  0   0.320   5.8322  16.4070   0.2111
 15U  H27  H  HCH2  0   0.255   5.9494  18.6541  -0.7762
 15U  H28  H  HCH2  0   0.259   4.7315  17.6129  -1.4826
 15U  H29  H  HCH1  0   0.227   7.4539  18.2171  -2.7141
 15U  H30  H  HCH2  0   0.241   6.7028  16.8264  -4.5930
 15U  H31  H  HCH2  0   0.230   5.1585  16.5300  -3.8000
 15U  H32  H  HCH2  0   0.276   6.6600  14.6109  -3.4577
 15U  H33  H  HCH2  0   0.250   7.9076  15.6496  -2.8018
 15U  H34  H  HOH1  0   0.487   9.0259  17.9099   0.5279
 15U  H35  H  HCH3  0   0.230   5.8517  20.1044  -2.9037
 15U  H36  H  HCH3  0   0.231   6.1308  19.3582  -4.4758
 15U  H37  H  HCH3  0   0.215   4.6410  19.0240  -3.5938
 15U  H1   H  HCH2  0   0.221   1.6513  12.5432  -4.7406

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
 15U  C10  C2   single    1.520  0.020  1.520
 15U  C2   C3   single    1.524  0.020  1.524
 15U  C2   C1   single    1.519  0.020  1.519
 15U  C3   C4   single    1.503  0.020  1.503
 15U  C1   N    single    1.446  0.020  1.446
 15U  C4   C5   aromatic  1.379  0.020  1.379
 15U  C4   C9   aromatic  1.416  0.020  1.416
 15U  C41  C51  single    1.520  0.020  1.520
 15U  C41  C31  single    1.526  0.020  1.526
 15U  C5   C6   aromatic  1.394  0.020  1.394
 15U  C71  C31  single    1.521  0.020  1.521
 15U  C51  N2   single    1.460  0.020  1.460
 15U  N    C9   single    1.350  0.020  1.350
 15U  C9   C8   aromatic  1.415  0.020  1.415
 15U  C31  C21  single    1.525  0.020  1.525
 15U  O    C    double    1.231  0.020  1.231
 15U  C6   C7   aromatic  1.377  0.020  1.377
 15U  N2   C    single    1.346  0.020  1.346
 15U  N2   C11  single    1.446  0.020  1.446
 15U  C    CA   single    1.525  0.021  1.525
 15U  C8   C7   aromatic  1.396  0.020  1.396
 15U  C8   S    single    1.762  0.020  1.762
 15U  C21  C11  single    1.531  0.020  1.531
 15U  C11  C61  single    1.528  0.020  1.528
 15U  NH2  CZ   double    1.285  0.020  1.285
 15U  O11  C61  double    1.204  0.020  1.204
 15U  N1   CA   single    1.456  0.020  1.456
 15U  N1   S    single    1.655  0.020  1.655
 15U  C61  O21  single    1.323  0.020  1.323
 15U  CA   CB   single    1.521  0.033  1.521
 15U  S    O1   double    1.460  0.020  1.460
 15U  S    O2   double    1.454  0.020  1.454
 15U  CG   CB   single    1.522  0.020  1.522
 15U  CG   CD   single    1.527  0.020  1.527
 15U  CZ   NH1  single    1.380  0.020  1.380
 15U  CZ   NE   single    1.366  0.020  1.366
 15U  CD   NE   single    1.441  0.020  1.441
 15U  C1   H1   single    0.970  0.020  1.090
 15U  C1   H2   single    0.970  0.020  1.090
 15U  C2   H3   single    0.970  0.020  1.090
 15U  C3   H4   single    0.970  0.020  1.090
 15U  C3   H5   single    0.970  0.020  1.090
 15U  C5   H6   single    0.930  0.020  1.080
 15U  C6   H7   single    0.930  0.020  1.080
 15U  C7   H8   single    0.930  0.020  1.080
 15U  C10  H9   single    0.970  0.020  1.090
 15U  C10  H10  single    0.970  0.020  1.090
 15U  C10  H11  single    0.970  0.020  1.090
 15U  N    H12  single    0.860  0.020  1.020
 15U  N1   H13  single    0.890  0.020  1.040
 15U  CA   H14  single    0.970  0.020  1.090
 15U  CB   H15  single    0.970  0.020  1.090
 15U  CB   H16  single    0.970  0.020  1.090
 15U  CG   H17  single    0.970  0.020  1.090
 15U  CG   H18  single    0.970  0.020  1.090
 15U  CD   H19  single    0.970  0.020  1.090
 15U  CD   H20  single    0.970  0.020  1.090
 15U  NE   H21  single    0.860  0.020  1.020
 15U  NH1  H22  single    0.890  0.020  1.040
 15U  NH1  H23  single    0.890  0.020  1.040
 15U  NH2  H24  single    0.890  0.020  1.040
 15U  C11  H26  single    0.970  0.020  1.090
 15U  C21  H27  single    0.970  0.020  1.090
 15U  C21  H28  single    0.970  0.020  1.090
 15U  C31  H29  single    0.970  0.020  1.090
 15U  C41  H30  single    0.970  0.020  1.090
 15U  C41  H31  single    0.970  0.020  1.090
 15U  C51  H32  single    0.970  0.020  1.090
 15U  C51  H33  single    0.970  0.020  1.090
 15U  O21  H34  single    0.850  0.020  0.980
 15U  C71  H35  single    0.970  0.020  1.090
 15U  C71  H36  single    0.970  0.020  1.090
 15U  C71  H37  single    0.970  0.020  1.090

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
 15U  N1   S    C8   107.12  3.000
 15U  N1   S    O2   106.85  3.000
 15U  C8   S    O2   107.92  3.000
 15U  O2   S    O1   118.78  3.000
 15U  N1   S    O1   105.05  3.000
 15U  C8   S    O1   110.48  3.000
 15U  H2   C1   H1   107.02  3.000
 15U  H2   C1   N    108.00  3.000
 15U  H1   C1   N    110.66  3.000
 15U  H2   C1   C2   110.23  3.000
 15U  H1   C1   C2   109.29  3.000
 15U  N    C1   C2   111.54  3.000
 15U  H3   C2   C10  108.96  3.000
 15U  H3   C2   C3   108.46  3.000
 15U  C10  C2   C3   111.89  3.000
 15U  H3   C2   C1   108.11  3.000
 15U  C3   C2   C1   108.48  3.000
 15U  C10  C2   C1   110.83  3.000
 15U  H5   C3   H4   106.40  3.000
 15U  H5   C3   C4   110.20  3.000
 15U  H4   C3   C4   109.57  3.000
 15U  H5   C3   C2   108.99  3.000
 15U  H4   C3   C2   110.41  3.000
 15U  C4   C3   C2   111.17  3.000
 15U  C9   C4   C5   119.87  3.000
 15U  C9   C4   C3   118.64  3.000
 15U  C5   C4   C3   121.50  3.000
 15U  H6   C5   C6   119.38  3.000
 15U  H6   C5   C4   118.31  3.000
 15U  C6   C5   C4   122.32  3.000
 15U  H7   C6   C7   120.50  3.000
 15U  H7   C6   C5   120.78  3.000
 15U  C7   C6   C5   118.70  3.000
 15U  H8   C7   C8   119.80  3.000
 15U  H8   C7   C6   119.95  3.000
 15U  C8   C7   C6   120.25  3.000
 15U  C9   C8   C7   121.51  3.000
 15U  C7   C8   S    117.66  3.000
 15U  C9   C8   S    120.60  3.000
 15U  N    C9   C8   122.74  3.000
 15U  C8   C9   C4   117.20  3.000
 15U  N    C9   C4   120.06  3.000
 15U  H11  C10  H10  107.68  3.000
 15U  H11  C10  H9   107.67  3.000
 15U  H10  C10  H9   107.87  3.000
 15U  H11  C10  C2   110.94  3.000
 15U  H10  C10  C2   111.12  3.000
 15U  H9   C10  C2   111.40  3.000
 15U  H12  N    C9   118.79  3.000
 15U  H12  N    C1   116.47  3.000
 15U  C9   N    C1   124.02  3.000
 15U  H13  N1   CA   111.71  3.000
 15U  H13  N1   S    111.92  3.000
 15U  CA   N1   S    117.77  3.000
 15U  H14  CA   CB   107.45  3.000
 15U  H14  CA   C    111.14  3.000
 15U  CB   CA   C    110.50  1.500
 15U  H14  CA   N1   108.00  3.000
 15U  CB   CA   N1   110.61  3.000
 15U  C    CA   N1   108.54  3.000
 15U  N2   C    O    122.50  3.000
 15U  N2   C    CA   119.28  3.000
 15U  O    C    CA   120.80  1.700
 15U  H16  CB   H15  106.15  3.000
 15U  H16  CB   CG   110.45  3.000
 15U  H15  CB   CG   108.93  3.000
 15U  H16  CB   CA   107.17  3.000
 15U  H15  CB   CA   108.89  3.000
 15U  CG   CB   CA   114.88  3.000
 15U  H18  CG   H17  107.01  3.000
 15U  H18  CG   CD   108.58  3.000
 15U  H17  CG   CD   109.36  3.000
 15U  H18  CG   CB   110.08  3.000
 15U  H17  CG   CB   110.81  3.000
 15U  CD   CG   CB   110.89  3.000
 15U  H20  CD   H19  105.69  3.000
 15U  H20  CD   NE   107.35  3.000
 15U  H19  CD   NE   109.31  3.000
 15U  H20  CD   CG   110.14  3.000
 15U  H19  CD   CG   109.71  3.000
 15U  NE   CD   CG   114.26  3.000
 15U  H21  NE   CZ   117.92  3.000
 15U  H21  NE   CD   116.65  3.000
 15U  CZ   NE   CD   122.83  3.000
 15U  NH2  CZ   NH1  119.22  3.000
 15U  NH1  CZ   NE   113.76  3.000
 15U  NH2  CZ   NE   126.89  3.000
 15U  H23  NH1  H22  111.79  3.000
 15U  H23  NH1  CZ   112.98  3.000
 15U  H22  NH1  CZ   116.62  3.000
 15U  H24  NH2  CZ   112.23  3.000
 15U  C51  N2   C11  114.34  3.000
 15U  C11  N2   C    125.58  3.000
 15U  C51  N2   C    119.93  3.000
 15U  H26  C11  C61  104.31  3.000
 15U  H26  C11  C21  106.60  3.000
 15U  C61  C11  C21  115.22  3.000
 15U  H26  C11  N2   110.48  3.000
 15U  C61  C11  N2   109.65  3.000
 15U  C21  C11  N2   110.34  3.000
 15U  H28  C21  H27  106.57  3.000
 15U  H28  C21  C31  109.17  3.000
 15U  H27  C21  C31  111.34  3.000
 15U  H28  C21  C11  106.54  3.000
 15U  H27  C21  C11  109.99  3.000
 15U  C31  C21  C11  112.92  3.000
 15U  H29  C31  C71  108.07  3.000
 15U  H29  C31  C41  108.10  3.000
 15U  C71  C31  C41  111.82  3.000
 15U  H29  C31  C21  108.68  3.000
 15U  C71  C31  C21  111.06  3.000
 15U  C41  C31  C21  109.02  3.000
 15U  H31  C41  H30  107.17  3.000
 15U  H31  C41  C51  109.12  3.000
 15U  H30  C41  C51  108.92  3.000
 15U  H31  C41  C31  109.65  3.000
 15U  H30  C41  C31  110.45  3.000
 15U  C51  C41  C31  111.43  3.000
 15U  H33  C51  H32  106.96  3.000
 15U  H33  C51  C41  110.20  3.000
 15U  H32  C51  C41  110.94  3.000
 15U  H33  C51  N2   108.94  3.000
 15U  H32  C51  N2   108.90  3.000
 15U  C41  C51  N2   110.81  3.000
 15U  O21  C61  O11  123.85  3.000
 15U  O21  C61  C11  111.97  3.000
 15U  O11  C61  C11  124.11  3.000
 15U  H34  O21  C61  110.05  3.000
 15U  H37  C71  H36  107.71  3.000
 15U  H37  C71  H35  107.70  3.000
 15U  H36  C71  H35  107.73  3.000
 15U  H37  C71  C31  111.02  3.000
 15U  H36  C71  C31  111.14  3.000
 15U  H35  C71  C31  111.37  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
 15U  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 15U  CONST_02  C7   C8   C9   C4      0.00   0.0  0
 15U  CONST_03  C8   C9   C4   C5      0.00   0.0  0
 15U  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 15U  CONST_05  C9   C4   C5   C6      0.00   0.0  0
 15U  CONST_06  C9   C8   C7   C6      0.00   0.0  0
 15U  CONST_07  C4   C9   C8   S     180.00   0.0  0
 15U  CONST_08  N    C9   C8   S       0.00   0.0  0
 15U  CONST_09  C6   C7   C8   S     180.00   0.0  0
 15U  CONST_10  H6   C5   C4   C3      0.00   0.0  0
 15U  CONST_11  H7   C6   C5   C4    180.00   0.0  0
 15U  CONST_12  H8   C7   C6   C5    180.00   0.0  0
 15U  CONST_13  C51  N2   C    CA    180.00   0.0  0
 15U  CONST_14  C11  N2   C    CA      0.00   0.0  0
 15U  CONST_15  C51  N2   C    O       0.00   0.0  0
 15U  CONST_16  C11  N2   C    O     180.00   0.0  0
 15U  CONST_17  H34  O21  C61  C11   180.00   0.0  0
 15U  CONST_18  NH2  CZ   NE   CD      0.00   0.0  0
 15U  CONST_19  NH1  CZ   NE   CD    180.00   0.0  0
 15U  CONST_20  H24  NH2  CZ   NE      0.00   0.0  0
 15U  CONST_22  H23  NH1  CZ   NE    180.00   0.0  0
 15U  CONST_23  H21  NE   CZ   NH1     0.00   0.0  0
 15U  Var_01    C4   C9   N    C1      5.66  30.0  1
 15U  Var_02    C5   C4   C3   C2    150.46  30.0  1
 15U  Var_03    C9   N    C1   C2     22.87  30.0  1
 15U  Var_04    C31  C41  C51  N2     55.80  30.0  1
 15U  Var_05    C41  C51  N2   C11   -57.25  30.0  1
 15U  Var_06    C9   C8   S    O1    -47.32  30.0  1
 15U  Var_07    CA   N1   S    C8     52.26  30.0  1
 15U  Var_08    CD   CG   CB   CA    178.66  30.0  1
 15U  Var_09    NE   CD   CG   CB   -174.10  30.0  3
 15U  Var_10    CZ   NE   CD   CG     71.76  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
 15U  chir_01  C2   C10  C3   C1   negativ
 15U  chir_02  CA   C    N1   CB   negativ
 15U  chir_03  C11  N2   C21  C61  positiv
 15U  chir_04  C31  C41  C71  C21  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
 15U  plan-1  CA   0.020
 15U  plan-1  C    0.020
 15U  plan-1  O    0.020
 15U  plan-1  N2   0.020
 15U  plan-1  C11  0.020
 15U  plan-1  C51  0.020
 15U  plan-2  S    0.020
 15U  plan-2  C3   0.020
 15U  plan-2  C4   0.020
 15U  plan-2  C5   0.020
 15U  plan-2  C6   0.020
 15U  plan-2  C7   0.020
 15U  plan-2  C8   0.020
 15U  plan-2  C9   0.020
 15U  plan-2  N    0.020
 15U  plan-2  H6   0.020
 15U  plan-2  H7   0.020
 15U  plan-2  H8   0.020
 15U  plan-3  CD   0.020
 15U  plan-3  NE   0.020
 15U  plan-3  CZ   0.020
 15U  plan-3  NH1  0.020
 15U  plan-3  NH2  0.020
 15U  plan-3  H21  0.020
 15U  plan-3  H22  0.020
 15U  plan-3  H23  0.020
 15U  plan-3  H24  0.020
 15U  plan-4  C11  0.020
 15U  plan-4  C61  0.020
 15U  plan-4  O11  0.020
 15U  plan-4  O21  0.020
 15U  plan-4  H34  0.020

