# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 01:02:01 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: N-(benzylsulfonyl)glycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(CNC(=O)[C@@H]2CCCN2C(=O)CN[S](=O)(=O)Cc3ccccc3)cc1
#
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
 S28  S28  N-(benzylsulfonyl)glycyl-N-(4-carbamimidoylbenzyl)-L-prolinamide  peptide  59  32  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S28
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
 S28  C7    C  CH2   0  -0.706   -5.3144   0.1769   1.1094
 S28  S8    S  S     0   1.377   -4.2337   0.8221  -0.1727
 S28  C6    C  CR6   0   0.110   -6.7339   0.5286   0.7923
 S28  C1    C  CR16  0  -0.278   -7.5193  -0.3214   0.0188
 S28  C2    C  CR16  0  -0.243   -8.8280   0.0209  -0.2895
 S28  C3    C  CR16  0  -0.260   -9.3608   1.2199   0.1666
 S28  C4    C  CR16  0  -0.243   -8.5807   2.0736   0.9355
 S28  C5    C  CR16  0  -0.278   -7.2715   1.7313   1.2426
 S28  O13   O  OS    0  -0.660   -4.5821   0.1555  -1.4212
 S28  O14   O  OS    0  -0.666   -4.2622   2.2764  -0.1167
 S28  N9    N  NC1   0  -0.765   -2.7414   0.3624   0.3455
 S28  C10   C  CH2   0  -0.381   -2.2075  -0.9291  -0.0312
 S28  C11   C  C     0   0.551   -0.7091  -0.9145   0.2193
 S28  O15   O  O     0  -0.494   -0.1121   0.1294   0.4490
 S28  N12   N  NT    0  -0.463   -0.0942  -2.0980   0.1532
 S28  C16   C  CH1   0  -0.217    1.3418  -2.1845   0.3161
 S28  C17   C  C     0   0.579    2.0536  -1.4931  -0.8433
 S28  O18   O  O     0  -0.492    1.5685  -1.4348  -1.9624
 S28  C21   C  CH2   0  -0.472    1.6018  -3.6980   0.3063
 S28  C22   C  CH2   0  -0.473    0.4765  -4.2531  -0.5604
 S28  C23   C  CH2   0  -0.281   -0.7136  -3.3729  -0.1995
 S28  N19   N  NH1   0  -0.636    3.2652  -1.0104  -0.5428
 S28  C20   C  CH2   0  -0.314    4.1249  -0.3925  -1.5366
 S28  C24   C  CR6   0   0.043    5.3494   0.1696  -0.8721
 S28  C31   C  CR16  0  -0.267    5.3053   1.4152  -0.2546
 S28  C29   C  CR16  0  -0.277    6.4241   1.9309   0.3812
 S28  C28   C  CR6   0   0.038    7.6134   1.2050   0.4204
 S28  C26   C  C     0   0.331    8.8267   1.7294   1.1065
 S28  N30   N  N     0  -0.650    9.6648   0.8946   1.5888
 S28  N32   N  NH2   0  -0.820    8.8976   3.0897   1.1990
 S28  C27   C  CR16  0  -0.260    7.6540  -0.0477  -0.1864
 S28  C25   C  CR16  0  -0.277    6.5363  -0.5557  -0.8286
 S28  H7    H  HCH2  0   0.324   -4.9752   0.6179   2.0466
 S28  H7A   H  HCH2  0   0.321   -5.1537  -0.9016   1.1532
 S28  H1    H  HCR6  0   0.257   -7.1117  -1.2601  -0.3350
 S28  H2    H  HCR6  0   0.260   -9.4319  -0.6484  -0.8880
 S28  H3    H  HCR6  0   0.260  -10.3822   1.4851  -0.0730
 S28  H4    H  HCR6  0   0.260   -8.9910   3.0072   1.2974
 S28  H5    H  HCR6  0   0.258   -6.6684   2.3977   1.8466
 S28  HN9   H  HNC1  0   0.418   -2.0618   1.1167   0.3125
 S28  H10   H  HCH2  0   0.284   -2.6802  -1.7223   0.5528
 S28  H10A  H  HCH2  0   0.288   -2.3714  -1.1649  -1.0888
 S28  H16   H  HCH1  0   0.291    1.6533  -1.7381   1.2637
 S28  H21   H  HCH2  0   0.268    2.5962  -3.9465  -0.0630
 S28  H21A  H  HCH2  0   0.262    1.5231  -4.0785   1.3259
 S28  H22   H  HCH2  0   0.249    0.7164  -4.1483  -1.6186
 S28  H22A  H  HCH2  0   0.260    0.2756  -5.3051  -0.3646
 S28  H23   H  HCH2  0   0.253   -1.2639  -3.7796   0.6532
 S28  H23A  H  HCH2  0   0.264   -1.4110  -3.2617  -1.0303
 S28  HN19  H  HNH1  0   0.407    3.6042  -1.0826   0.4032
 S28  H20   H  HCH2  0   0.257    4.4081  -1.1236  -2.2977
 S28  H20A  H  HCH2  0   0.258    3.5766   0.4034  -2.0454
 S28  H31   H  HCR6  0   0.259    4.3890   1.9930  -0.2699
 S28  H29   H  HCR6  0   0.260    6.3544   2.8984   0.8617
 S28  HN30  H  H     0   0.324   10.4602   1.3722   2.0042
 S28  HN32  H  HNH2  0   0.395    8.4566   3.6404   0.4807
 S28  HN3A  H  HNH2  0   0.391    9.7595   3.4866   1.5379
 S28  H27   H  HCR6  0   0.257    8.5708  -0.6212  -0.1643
 S28  H25   H  HCR6  0   0.257    6.5906  -1.5257  -1.3081

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
 S28  C1   C2    aromatic  1.387  0.020  1.387
 S28  C1   C6    aromatic  1.392  0.020  1.392
 S28  C2   C3    aromatic  1.389  0.020  1.389
 S28  C3   C4    aromatic  1.389  0.020  1.389
 S28  C4   C5    aromatic  1.388  0.020  1.388
 S28  C5   C6    aromatic  1.392  0.020  1.392
 S28  C6   C7    single    1.496  0.020  1.496
 S28  C7   S8    single    1.797  0.020  1.797
 S28  S8   N9    single    1.645  0.020  1.645
 S28  S8   O13   double    1.458  0.020  1.458
 S28  S8   O14   double    1.456  0.020  1.456
 S28  N9   C10   single    1.447  0.020  1.447
 S28  C10  C11   single    1.519  0.020  1.519
 S28  C11  N12   single    1.335  0.020  1.335
 S28  C11  O15   double    1.224  0.020  1.224
 S28  N12  C16   single    1.448  0.020  1.448
 S28  N12  C23   single    1.461  0.020  1.461
 S28  C16  C17   single    1.526  0.020  1.526
 S28  C16  C21   single    1.536  0.020  1.536
 S28  C17  O18   double    1.221  0.020  1.221
 S28  C17  N19   single    1.338  0.020  1.338
 S28  N19  C20   single    1.452  0.020  1.452
 S28  C20  C24   single    1.502  0.020  1.502
 S28  C21  C22   single    1.525  0.020  1.525
 S28  C22  C23   single    1.524  0.020  1.524
 S28  C24  C25   aromatic  1.392  0.020  1.392
 S28  C24  C31   aromatic  1.391  0.020  1.391
 S28  C25  C27   aromatic  1.386  0.020  1.386
 S28  C26  C28   single    1.489  0.020  1.489
 S28  C26  N30   double    1.277  0.020  1.277
 S28  C26  N32   single    1.365  0.020  1.365
 S28  C27  C28   aromatic  1.393  0.020  1.393
 S28  C28  C29   aromatic  1.394  0.020  1.394
 S28  C29  C31   aromatic  1.386  0.020  1.386
 S28  C1   H1    single    0.930  0.020  1.080
 S28  C2   H2    single    0.930  0.020  1.080
 S28  C3   H3    single    0.930  0.020  1.080
 S28  C4   H4    single    0.930  0.020  1.080
 S28  C5   H5    single    0.930  0.020  1.080
 S28  C7   H7    single    0.970  0.020  1.090
 S28  C7   H7A   single    0.970  0.020  1.090
 S28  N9   HN9   single    0.890  0.020  1.040
 S28  C10  H10   single    0.970  0.020  1.090
 S28  C10  H10A  single    0.970  0.020  1.090
 S28  C16  H16   single    0.970  0.020  1.090
 S28  N19  HN19  single    0.860  0.020  1.020
 S28  C20  H20   single    0.970  0.020  1.090
 S28  C20  H20A  single    0.970  0.020  1.090
 S28  C21  H21   single    0.970  0.020  1.090
 S28  C21  H21A  single    0.970  0.020  1.090
 S28  C22  H22   single    0.970  0.020  1.090
 S28  C22  H22A  single    0.970  0.020  1.090
 S28  C23  H23   single    0.970  0.020  1.090
 S28  C23  H23A  single    0.970  0.020  1.090
 S28  C25  H25   single    0.930  0.020  1.080
 S28  C27  H27   single    0.930  0.020  1.080
 S28  C29  H29   single    0.930  0.020  1.080
 S28  N30  HN30  single    0.890  0.020  1.040
 S28  C31  H31   single    0.930  0.020  1.080
 S28  N32  HN32  single    0.890  0.020  1.040
 S28  N32  HN3A  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
 S28  H7A   C7   H7    108.64  3.000
 S28  H7A   C7   C6    112.37  3.000
 S28  H7    C7   C6    112.47  3.000
 S28  H7A   C7   S8    107.16  3.000
 S28  H7    C7   S8    106.33  3.000
 S28  C6    C7   S8    109.57  3.000
 S28  N9    S8   O14   106.55  3.000
 S28  O14   S8   O13   119.03  3.000
 S28  N9    S8   O13   111.03  3.000
 S28  O14   S8   C7    108.64  3.000
 S28  O13   S8   C7    107.65  3.000
 S28  N9    S8   C7    102.74  3.000
 S28  C5    C6   C1    119.30  3.000
 S28  C5    C6   C7    120.06  3.000
 S28  C1    C6   C7    120.62  3.000
 S28  H1    C1   C2    119.76  3.000
 S28  H1    C1   C6    119.90  3.000
 S28  C2    C1   C6    120.33  3.000
 S28  H2    C2   C3    120.10  3.000
 S28  H2    C2   C1    119.78  3.000
 S28  C3    C2   C1    120.12  3.000
 S28  H3    C3   C4    120.14  3.000
 S28  H3    C3   C2    120.05  3.000
 S28  C4    C3   C2    119.80  3.000
 S28  H4    C4   C5    119.77  3.000
 S28  H4    C4   C3    120.17  3.000
 S28  C5    C4   C3    120.06  3.000
 S28  H5    C5   C4    119.81  3.000
 S28  H5    C5   C6    119.80  3.000
 S28  C4    C5   C6    120.39  3.000
 S28  HN9   N9   C10   114.03  3.000
 S28  HN9   N9   S8    112.90  3.000
 S28  C10   N9   S8    120.13  3.000
 S28  H10A  C10  H10   107.15  3.000
 S28  H10A  C10  C11   107.98  3.000
 S28  H10   C10  C11   110.22  3.000
 S28  H10A  C10  N9    112.83  3.000
 S28  H10   C10  N9    110.44  3.000
 S28  C11   C10  N9    108.20  3.000
 S28  N12   C11  O15   122.71  3.000
 S28  O15   C11  C10   121.34  3.000
 S28  N12   C11  C10   115.94  3.000
 S28  C23   N12  C16   113.30  3.000
 S28  C23   N12  C11   126.18  3.000
 S28  C16   N12  C11   120.27  3.000
 S28  H16   C16  C21   111.09  3.000
 S28  H16   C16  C17   109.93  3.000
 S28  C21   C16  C17   111.27  3.000
 S28  H16   C16  N12   110.84  3.000
 S28  C21   C16  N12   103.07  3.000
 S28  C17   C16  N12   110.49  3.000
 S28  N19   C17  O18   123.25  3.000
 S28  N19   C17  C16   114.52  3.000
 S28  O18   C17  C16   122.18  3.000
 S28  H21A  C21  H21   107.64  3.000
 S28  H21A  C21  C22   110.54  3.000
 S28  H21   C21  C22   113.44  3.000
 S28  H21A  C21  C16   109.00  3.000
 S28  H21   C21  C16   112.42  3.000
 S28  C22   C21  C16   103.73  3.000
 S28  H22A  C22  H22   107.95  3.000
 S28  H22A  C22  C23   111.81  3.000
 S28  H22   C22  C23   110.26  3.000
 S28  H22A  C22  C21   112.68  3.000
 S28  H22   C22  C21   110.75  3.000
 S28  C23   C22  C21   103.38  3.000
 S28  H23A  C23  H23   108.07  3.000
 S28  H23A  C23  C22   112.22  3.000
 S28  H23   C23  C22   111.28  3.000
 S28  H23A  C23  N12   111.48  3.000
 S28  H23   C23  N12   110.47  3.000
 S28  C22   C23  N12   103.31  3.000
 S28  HN19  N19  C20   118.29  3.000
 S28  HN19  N19  C17   119.31  3.000
 S28  C20   N19  C17   122.40  3.000
 S28  H20A  C20  H20   107.05  3.000
 S28  H20A  C20  C24   110.04  3.000
 S28  H20   C20  C24   110.32  3.000
 S28  H20A  C20  N19   109.37  3.000
 S28  H20   C20  N19   110.20  3.000
 S28  C24   C20  N19   109.82  3.000
 S28  C25   C24  C31   118.68  3.000
 S28  C31   C24  C20   120.37  3.000
 S28  C25   C24  C20   120.93  3.000
 S28  H31   C31  C29   119.38  3.000
 S28  H31   C31  C24   119.88  3.000
 S28  C29   C31  C24   120.74  3.000
 S28  H29   C29  C28   120.52  3.000
 S28  H29   C29  C31   118.95  3.000
 S28  C28   C29  C31   120.51  3.000
 S28  C27   C28  C26   119.59  3.000
 S28  C27   C28  C29   118.76  3.000
 S28  C26   C28  C29   121.65  3.000
 S28  N32   C26  N30   126.26  3.000
 S28  N32   C26  C28   115.11  3.000
 S28  N30   C26  C28   118.58  3.000
 S28  HN30  N30  C26   111.14  3.000
 S28  HN3A  N32  HN32  113.53  3.000
 S28  HN3A  N32  C26   117.36  3.000
 S28  HN32  N32  C26   118.28  3.000
 S28  H27   C27  C25   119.92  3.000
 S28  H27   C27  C28   119.53  3.000
 S28  C25   C27  C28   120.55  3.000
 S28  H25   C25  C27   119.54  3.000
 S28  H25   C25  C24   119.71  3.000
 S28  C27   C25  C24   120.76  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
 S28  CONST_01  C3    C2   C1   C6     0.00   0.0  0
 S28  CONST_02  C3    C4   C5   C6     0.00   0.0  0
 S28  CONST_03  C4    C3   C2   C1     0.00   0.0  0
 S28  CONST_04  C4    C5   C6   C1     0.00   0.0  0
 S28  CONST_05  C5    C6   C1   C2     0.00   0.0  0
 S28  CONST_06  C5    C4   C3   C2     0.00   0.0  0
 S28  CONST_07  C28   C27  C25  C24    0.00   0.0  0
 S28  CONST_08  C28   C29  C31  C24    0.00   0.0  0
 S28  CONST_09  C27   C25  C24  C31    0.00   0.0  0
 S28  CONST_10  C27   C28  C29  C31    0.00   0.0  0
 S28  CONST_11  C25   C27  C28  C29    0.00   0.0  0
 S28  CONST_12  C25   C24  C31  C29    0.00   0.0  0
 S28  CONST_13  C2    C1   C6   C7   180.00   0.0  0
 S28  CONST_14  C4    C5   C6   C7   180.00   0.0  0
 S28  CONST_15  C27   C25  C24  C20  180.00   0.0  0
 S28  CONST_16  C29   C31  C24  C20  180.00   0.0  0
 S28  CONST_17  C26   C28  C29  C31  180.00   0.0  0
 S28  CONST_18  C25   C27  C28  C26  180.00   0.0  0
 S28  CONST_19  H2    C2   C1   C6   180.00   0.0  0
 S28  CONST_20  H4    C4   C5   C6   180.00   0.0  0
 S28  CONST_21  H3    C3   C2   C1   180.00   0.0  0
 S28  CONST_22  H5    C5   C6   C1   180.00   0.0  0
 S28  CONST_23  H1    C1   C2   C3   180.00   0.0  0
 S28  CONST_24  H27   C27  C25  C24  180.00   0.0  0
 S28  CONST_25  H29   C29  C31  C24  180.00   0.0  0
 S28  CONST_26  H25   C25  C24  C31  180.00   0.0  0
 S28  CONST_27  H31   C31  C29  C28  180.00   0.0  0
 S28  CONST_28  C16   N12  C11  C10  180.00   0.0  0
 S28  CONST_29  C23   N12  C11  C10    0.00   0.0  0
 S28  CONST_30  C16   N12  C11  O15    0.00   0.0  0
 S28  CONST_31  C23   N12  C11  O15  180.00   0.0  0
 S28  CONST_32  C20   N19  C17  C16  180.00   0.0  0
 S28  CONST_33  HN19  N19  C17  C16    0.00   0.0  0
 S28  CONST_34  HN30  N30  C26  C28  180.00   0.0  0
 S28  CONST_36  HN3A  N32  C26  C28  180.00   0.0  0
 S28  CONST_37  C20   N19  C17  O18    0.00   0.0  0
 S28  Var_01    C21   C22  C23  N12   29.84  30.0  1
 S28  Var_02    C22   C23  N12  C16  -12.15  30.0  1
 S28  Var_03    C23   C22  C21  C16  -36.66  30.0  1
 S28  Var_04    C1    C6   C7   S8    89.40  30.0  3
 S28  Var_05    C25   C24  C20  N19   96.22  30.0  2
 S28  Var_06    N30   C26  C28  C29  151.94  30.0  3
 S28  Var_07    N9    S8   C7   C6   179.36  30.0  3
 S28  Var_08    N12   C11  C10  N9   168.45  30.0  3
 S28  Var_09    C24   C20  N19  C17  174.33  30.0  3
 S28  Var_10    C10   N9   S8   C7    88.40  30.0  3
 S28  Var_11    C11   C10  N9   S8   163.32  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
 S28  chir_01  C16  N12  C17  C21  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
 S28  plan-1  C7    0.020
 S28  plan-1  C6    0.020
 S28  plan-1  C1    0.020
 S28  plan-1  C2    0.020
 S28  plan-1  C3    0.020
 S28  plan-1  C4    0.020
 S28  plan-1  C5    0.020
 S28  plan-1  H1    0.020
 S28  plan-1  H2    0.020
 S28  plan-1  H3    0.020
 S28  plan-1  H4    0.020
 S28  plan-1  H5    0.020
 S28  plan-2  C20   0.020
 S28  plan-2  C24   0.020
 S28  plan-2  C31   0.020
 S28  plan-2  C29   0.020
 S28  plan-2  C28   0.020
 S28  plan-2  C26   0.020
 S28  plan-2  C27   0.020
 S28  plan-2  C25   0.020
 S28  plan-2  H31   0.020
 S28  plan-2  H29   0.020
 S28  plan-2  H27   0.020
 S28  plan-2  H25   0.020
 S28  plan-3  C16   0.020
 S28  plan-3  C17   0.020
 S28  plan-3  O18   0.020
 S28  plan-3  N19   0.020
 S28  plan-3  C20   0.020
 S28  plan-3  HN19  0.020
 S28  plan-4  C10   0.020
 S28  plan-4  C11   0.020
 S28  plan-4  O15   0.020
 S28  plan-4  N12   0.020
 S28  plan-4  C16   0.020
 S28  plan-4  C23   0.020
 S28  plan-5  C28   0.020
 S28  plan-5  C26   0.020
 S28  plan-5  N30   0.020
 S28  plan-5  N32   0.020
 S28  plan-5  HN30  0.020
 S28  plan-5  HN32  0.020
 S28  plan-5  HN3A  0.020

