# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed May 20 04:20:17 2020
#   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  70  35  .  2022-09-22  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_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   1.366   0.9570  -1.6640  -1.7324
 15U  O1   O  OS     0  -0.666   1.9863  -2.1203  -0.8019
 15U  O2   O  OS     0  -0.660   1.0329  -2.0935  -3.1201
 15U  C1   C  CH2    0  -0.242  -0.0923  -3.0914   2.5205
 15U  C2   C  CH1    0  -0.285  -1.3119  -3.9868   2.6538
 15U  C3   C  CH2    0  -0.468  -2.4971  -3.2845   2.0059
 15U  C4   C  CR6    0   0.027  -2.1944  -2.8078   0.6108
 15U  C5   C  CR16   0  -0.294  -3.2146  -2.6120  -0.2938
 15U  C6   C  CR16   0  -0.273  -2.9860  -2.1467  -1.5882
 15U  C7   C  CR16   0  -0.237  -1.6923  -1.8900  -1.9731
 15U  C8   C  CR6    0  -0.319  -0.6308  -2.0849  -1.0846
 15U  C9   C  CR6    0   0.414  -0.8502  -2.5394   0.2384
 15U  C10  C  CH3    0  -0.657  -1.5870  -4.3228   4.1109
 15U  N    N  NH1    0  -0.723   0.1362  -2.7133   1.1459
 15U  N1   N  NC1    0  -0.700   1.0623  -0.0203  -1.7826
 15U  CA   C  CH1    0  -0.263   0.8093   0.7445  -0.5707
 15U  C    C  C      0   0.596  -0.5668   1.4233  -0.6895
 15U  O    O  O      0  -0.483  -1.1093   1.4578  -1.7841
 15U  CB   C  CH2    0  -0.405   1.9145   1.7905  -0.3867
 15U  CG   C  CH2    0  -0.461   3.2787   1.1554  -0.1638
 15U  CD   C  CH2    0  -0.253   4.3854   2.1960  -0.1180
 15U  NE   N  NH1    0  -0.651   5.6706   1.5390   0.0451
 15U  CZ   C  C      0   0.526   6.8636   2.2176   0.0872
 15U  NH1  N  NH2    0  -0.814   6.7733   3.5306   0.4848
 15U  NH2  N  N      0  -0.720   8.0099   1.7258  -0.2168
 15U  N2   N  NT     0  -0.434  -1.0726   2.0199   0.4059
 15U  C11  C  CH1    0  -0.247  -2.4175   2.5929   0.3395
 15U  C21  C  CH2    0  -0.417  -3.4232   1.4826   0.6164
 15U  C31  C  CH1    0  -0.247  -3.1787   0.8385   1.9918
 15U  C41  C  CH2    0  -0.435  -1.7025   0.4614   2.1675
 15U  C51  C  CH2    0  -0.354  -0.7502   1.5816   1.7587
 15U  C61  C  C      0   0.434  -2.6602   3.4734  -0.9094
 15U  O11  O  O      0  -0.601  -3.7694   3.3664  -1.4633
 15U  O21  O  OC    -1  -0.617  -1.7558   4.2822  -1.1850
 15U  C71  C  CH3    0  -0.661  -3.6686   1.7276   3.1337
 15U  H3   H  HCH1   0   0.240  -1.1112  -4.9145   2.1063
 15U  H4   H  HCH2   0   0.256  -3.3634  -3.9498   1.9821
 15U  H5   H  HCH2   0   0.242  -2.7885  -2.4283   2.6286
 15U  H6   H  HCR6   0   0.254  -4.2286  -2.8288   0.0223
 15U  H7   H  HCR6   0   0.254  -3.8053  -2.0000  -2.2775
 15U  H8   H  HCR6   0   0.271  -1.4971  -1.5392  -2.9778
 15U  H9   H  HCH3   0   0.234  -2.4512  -4.9816   4.2042
 15U  H10  H  HCH3   0   0.233  -0.7360  -4.8258   4.5723
 15U  H11  H  HCH3   0   0.219  -1.7940  -3.4187   4.6878
 15U  H12  H  HNH1   0   0.405   1.0858  -2.5638   0.8496
 15U  H13  H  HNC1   0   0.406   0.5526   0.3617  -2.5768
 15U  H14  H  HCH1   0   0.263   0.8240   0.0640   0.2859
 15U  H15  H  HCH2   0   0.244   1.9319   2.4304  -1.2744
 15U  H16  H  HCH2   0   0.252   1.6684   2.4404   0.4564
 15U  H17  H  HCH2   0   0.235   3.2747   0.5868   0.7710
 15U  H18  H  HCH2   0   0.239   3.4829   0.4419  -0.9664
 15U  H19  H  HCH2   0   0.223   4.3531   2.8067  -1.0286
 15U  H20  H  HCH2   0   0.227   4.2027   2.8702   0.7223
 15U  H21  H  HNH1   0   0.380   5.7331   0.6498  -0.4276
 15U  H22  H  HNH2   0   0.383   6.0674   3.7576   1.1667
 15U  H23  H  HNH2   0   0.381   7.6656   3.9397   0.7116
 15U  H24  H  H      0   0.311   7.9121   0.7896  -0.5931
 15U  H26  H  HCH1   0   0.243  -2.4594   3.3092   1.1712
 15U  H27  H  HCH2   0   0.223  -4.4389   1.8790   0.5751
 15U  H28  H  HCH2   0   0.235  -3.3449   0.7269  -0.1707
 15U  H29  H  HCH1   0   0.230  -3.7631  -0.0870   2.0324
 15U  H30  H  HCH2   0   0.231  -1.5014   0.1678   3.2018
 15U  H31  H  HCH2   0   0.247  -1.4800  -0.4095   1.5465
 15U  H32  H  HCH2   0   0.263   0.2860   1.2563   1.8385
 15U  H33  H  HCH2   0   0.257  -0.8410   2.4469   2.4187
 15U  H35  H  HCH3   0   0.226  -4.7216   1.9848   3.0052
 15U  H36  H  HCH3   0   0.227  -3.5688   1.2173   4.0933
 15U  H37  H  HCH3   0   0.217  -3.1120   2.6635   3.2061
 15U  H1   H  HCH2   0   0.219  -0.2184  -2.2050   3.1567
 15U  H2   H  HCH2   0   0.252   0.8010  -3.6073   2.8744

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    1.522  0.020  1.522
 15U  C2   C1   single    1.519  0.020  1.519
 15U  C3   C4   single    1.505  0.020  1.505
 15U  C1   N    single    1.444  0.020  1.444
 15U  C4   C5   aromatic  1.378  0.020  1.378
 15U  C4   C9   aromatic  1.420  0.020  1.420
 15U  C41  C51  single    1.526  0.020  1.526
 15U  C41  C31  single    1.534  0.020  1.534
 15U  C5   C6   aromatic  1.394  0.020  1.394
 15U  C71  C31  single    1.528  0.020  1.528
 15U  C51  N2   single    1.458  0.020  1.458
 15U  N    C9   single    1.352  0.020  1.352
 15U  C9   C8   aromatic  1.416  0.020  1.416
 15U  C31  C21  single    1.538  0.020  1.538
 15U  O    C    double    1.231  0.020  1.231
 15U  C6   C7   aromatic  1.374  0.020  1.374
 15U  N2   C    single    1.346  0.020  1.346
 15U  N2   C11  single    1.463  0.020  1.463
 15U  C    CA   single    1.525  0.021  1.525
 15U  C8   C7   aromatic  1.398  0.020  1.398
 15U  C8   S    single    1.766  0.020  1.766
 15U  C21  C11  single    1.523  0.020  1.523
 15U  C11  C61  single    1.547  0.020  1.547
 15U  NH2  CZ   double    1.284  0.020  1.284
 15U  O11  C61  deloc     1.244  0.020  1.244
 15U  N1   CA   single    1.455  0.020  1.455
 15U  N1   S    single    1.648  0.020  1.648
 15U  C61  O21  deloc     1.244  0.020  1.244
 15U  CA   CB   single    1.521  0.033  1.521
 15U  S    O1   double    1.461  0.020  1.461
 15U  S    O2   double    1.455  0.020  1.455
 15U  CG   CB   single    1.521  0.020  1.521
 15U  CG   CD   single    1.520  0.020  1.520
 15U  CZ   NH1  single    1.375  0.020  1.375
 15U  CZ   NE   single    1.373  0.020  1.373
 15U  CD   NE   single    1.453  0.020  1.453
 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    0.890  0.020  1.040
 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  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   107.84  3.000
 15U  N1   S    O2   105.20  3.000
 15U  C8   S    O2   109.06  3.000
 15U  O2   S    O1   118.60  3.000
 15U  N1   S    O1   106.62  3.000
 15U  C8   S    O1   108.99  3.000
 15U  H2   C1   H1   106.72  3.000
 15U  H2   C1   N    107.65  3.000
 15U  H1   C1   N    110.99  3.000
 15U  H2   C1   C2   110.51  3.000
 15U  H1   C1   C2   109.44  3.000
 15U  N    C1   C2   111.41  3.000
 15U  H3   C2   C10  108.96  3.000
 15U  H3   C2   C3   108.69  3.000
 15U  C10  C2   C3   111.65  3.000
 15U  H3   C2   C1   107.94  3.000
 15U  C3   C2   C1   108.41  3.000
 15U  C10  C2   C1   111.08  3.000
 15U  H5   C3   H4   106.07  3.000
 15U  H5   C3   C4   109.39  3.000
 15U  H4   C3   C4   109.41  3.000
 15U  H5   C3   C2   108.96  3.000
 15U  H4   C3   C2   110.22  3.000
 15U  C4   C3   C2   112.58  3.000
 15U  C9   C4   C5   120.12  3.000
 15U  C9   C4   C3   119.56  3.000
 15U  C5   C4   C3   120.31  3.000
 15U  H6   C5   C6   119.39  3.000
 15U  H6   C5   C4   118.22  3.000
 15U  C6   C5   C4   122.39  3.000
 15U  H7   C6   C7   120.65  3.000
 15U  H7   C6   C5   120.87  3.000
 15U  C7   C6   C5   118.48  3.000
 15U  H8   C7   C8   119.90  3.000
 15U  H8   C7   C6   119.38  3.000
 15U  C8   C7   C6   120.72  3.000
 15U  C9   C8   C7   121.40  3.000
 15U  C7   C8   S    114.60  3.000
 15U  C9   C8   S    123.96  3.000
 15U  N    C9   C8   123.75  3.000
 15U  C8   C9   C4   116.89  3.000
 15U  N    C9   C4   119.36  3.000
 15U  H11  C10  H10  107.83  3.000
 15U  H11  C10  H9   107.74  3.000
 15U  H10  C10  H9   107.66  3.000
 15U  H11  C10  C2   110.95  3.000
 15U  H10  C10  C2   111.47  3.000
 15U  H9   C10  C2   111.03  3.000
 15U  H12  N    C9   118.17  3.000
 15U  H12  N    C1   117.96  3.000
 15U  C9   N    C1   123.87  3.000
 15U  H13  N1   CA   111.44  3.000
 15U  H13  N1   S    111.47  3.000
 15U  CA   N1   S    119.19  3.000
 15U  H14  CA   CB   108.71  3.000
 15U  H14  CA   C    110.30  3.000
 15U  CB   CA   C    110.50  1.500
 15U  H14  CA   N1   108.84  3.000
 15U  CB   CA   N1   109.46  3.000
 15U  C    CA   N1   108.84  3.000
 15U  N2   C    O    123.34  3.000
 15U  N2   C    CA   117.95  3.000
 15U  O    C    CA   120.80  1.700
 15U  H16  CB   H15  106.36  3.000
 15U  H16  CB   CG   109.71  3.000
 15U  H15  CB   CG   110.41  3.000
 15U  H16  CB   CA   109.64  3.000
 15U  H15  CB   CA   108.25  3.000
 15U  CG   CB   CA   112.29  3.000
 15U  H18  CG   H17  106.79  3.000
 15U  H18  CG   CD   109.45  3.000
 15U  H17  CG   CD   109.44  3.000
 15U  H18  CG   CB   109.42  3.000
 15U  H17  CG   CB   109.81  3.000
 15U  CD   CG   CB   111.81  3.000
 15U  H20  CD   H19  106.85  3.000
 15U  H20  CD   NE   109.92  3.000
 15U  H19  CD   NE   111.78  3.000
 15U  H20  CD   CG   108.90  3.000
 15U  H19  CD   CG   109.56  3.000
 15U  NE   CD   CG   109.76  3.000
 15U  H21  NE   CZ   113.33  3.000
 15U  H21  NE   CD   113.63  3.000
 15U  CZ   NE   CD   123.27  3.000
 15U  NH2  CZ   NH1  119.54  3.000
 15U  NH1  CZ   NE   115.07  3.000
 15U  NH2  CZ   NE   125.39  3.000
 15U  H23  NH1  H22  112.13  3.000
 15U  H23  NH1  CZ   113.25  3.000
 15U  H22  NH1  CZ   117.19  3.000
 15U  H24  NH2  CZ   110.82  3.000
 15U  C51  N2   C11  111.29  3.000
 15U  C11  N2   C    118.82  3.000
 15U  C51  N2   C    122.60  3.000
 15U  H26  C11  C61  103.54  3.000
 15U  H26  C11  C21  108.20  3.000
 15U  C61  C11  C21  117.25  3.000
 15U  H26  C11  N2   104.84  3.000
 15U  C61  C11  N2   113.81  3.000
 15U  C21  C11  N2   108.24  3.000
 15U  H28  C21  H27  106.87  3.000
 15U  H28  C21  C31  110.04  3.000
 15U  H27  C21  C31  109.51  3.000
 15U  H28  C21  C11  108.99  3.000
 15U  H27  C21  C11  110.05  3.000
 15U  C31  C21  C11  111.27  3.000
 15U  H29  C31  C71  107.03  3.000
 15U  H29  C31  C41  107.55  3.000
 15U  C71  C31  C41  111.47  3.000
 15U  H29  C31  C21  107.59  3.000
 15U  C71  C31  C21  111.94  3.000
 15U  C41  C31  C21  111.00  3.000
 15U  H31  C41  H30  106.62  3.000
 15U  H31  C41  C51  107.81  3.000
 15U  H30  C41  C51  109.61  3.000
 15U  H31  C41  C31  109.07  3.000
 15U  H30  C41  C31  110.57  3.000
 15U  C51  C41  C31  112.92  3.000
 15U  H33  C51  H32  105.75  3.000
 15U  H33  C51  C41  111.58  3.000
 15U  H32  C51  C41  110.78  3.000
 15U  H33  C51  N2   107.71  3.000
 15U  H32  C51  N2   111.61  3.000
 15U  C41  C51  N2   109.34  3.000
 15U  O21  C61  O11  127.25  3.000
 15U  O21  C61  C11  115.76  3.000
 15U  O11  C61  C11  116.75  3.000
 15U  H37  C71  H36  107.21  3.000
 15U  H37  C71  H35  107.32  3.000
 15U  H36  C71  H35  107.57  3.000
 15U  H37  C71  C31  112.65  3.000
 15U  H36  C71  C31  110.84  3.000
 15U  H35  C71  C31  111.01  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_14  C11  N2   C    CA    180.00   0.0  0
 15U  CONST_16  C11  N2   C    O       0.00   0.0  0
 15U  CONST_19  H24  NH2  CZ   NE      0.00   0.0  0
 15U  CONST_21  H23  NH1  CZ   NE    180.00   0.0  0
 15U  CONST_22  H21  NE   CZ   NH1   180.00   0.0  0
 15U  Var_01    C4   C9   N    C1     -3.59  30.0  1
 15U  Var_02    C5   C4   C3   C2    155.94  30.0  1
 15U  Var_03    C9   N    C1   C2     32.10  30.0  1
 15U  Var_04    C31  C41  C51  N2    -53.08  30.0  1
 15U  Var_05    C41  C51  N2   C11    63.37  30.0  1
 15U  Var_06    C9   C8   S    O1     11.65  30.0  2
 15U  Var_07    CA   N1   S    C8     54.20  30.0  1
 15U  Var_08    CD   CG   CB   CA    174.45  30.0  2
 15U  Var_09    NE   CD   CG   CB   -177.84  30.0  3
 15U  Var_10    CZ   NE   CD   CG    178.35  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

