# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jun  5 23:07:35 2020
#   Inital geometry file: a 159 line input string
#   Ligand name: N-[2-(benzoylamino)ethyl]-N-(biphenyl-4-ylsulfonyl)-D-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H](N(CCNC(=O)c1ccccc1)[S](=O)(=O)c2ccc(cc2)c3ccccc3)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
 Y38  Y38  N-[2-(benzoylamino)ethyl]-N-(biphenyl-4-ylsulfonyl)-D-valine  ligand  62  34  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y38
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
 Y38  O15  O  OS    0  -0.640   0.2573  -1.6813  -2.5039
 Y38  S13  S  S     0   1.392  -0.4880  -2.0713  -1.3163
 Y38  O14  O  OS    0  -0.647  -1.2977  -3.2814  -1.3458
 Y38  N16  N  N     0  -0.601   0.5656  -2.2650  -0.0643
 Y38  C17  C  CH1   0  -0.173   0.5195  -3.4744   0.7530
 Y38  C18  C  CH1   0  -0.245   0.9557  -4.7891   0.0770
 Y38  C19  C  CH3   0  -0.659   2.0354  -4.5682  -0.9748
 Y38  C20  C  CH3   0  -0.668   1.4753  -5.7599   1.1380
 Y38  C21  C  C     0   0.562  -0.8178  -3.6019   1.4802
 Y38  O22  O  O     0  -0.422  -1.4103  -4.6305   1.6722
 Y38  O23  O  OH1   0  -0.585  -1.2321  -2.4235   1.9258
 Y38  C24  C  CH2   0  -0.325   1.3628  -1.1193   0.3598
 Y38  C25  C  CH2   0  -0.289   2.6535  -0.9340  -0.4356
 Y38  N26  N  NH1   0  -0.649   3.3891   0.2139   0.0402
 Y38  C27  C  C     0   0.540   3.1018   1.4698  -0.3424
 Y38  O28  O  O     0  -0.484   2.2368   1.7273  -1.1702
 Y38  C29  C  CR6   0  -0.029   3.9114   2.5595   0.2855
 Y38  C34  C  CR16  0  -0.269   4.0290   3.7663  -0.4017
 Y38  C31  C  CR16  0  -0.241   4.7589   4.8137   0.1377
 Y38  C32  C  CR16  0  -0.252   5.3653   4.6739   1.3798
 Y38  C3B  C  CR16  0  -0.295   4.5155   2.4286   1.5346
 Y38  C33  C  CR16  0  -0.240   5.2372   3.4816   2.0788
 Y38  C10  C  CR6   0  -0.207  -1.5468  -0.7049  -0.9299
 Y38  C11  C  CR16  0  -0.214  -2.8026  -0.9451  -0.3885
 Y38  C12  C  CR16  0  -0.305  -3.6409   0.1232  -0.1229
 Y38  C7   C  CR6   0   0.109  -3.2427   1.4362  -0.3826
 Y38  C8   C  CR16  0  -0.312  -1.9773   1.6498  -0.9324
 Y38  C9   C  CR16  0  -0.221  -1.1346   0.5903  -1.2203
 Y38  C1   C  CR6   0   0.089  -4.1418   2.5694  -0.0919
 Y38  C2   C  CR16  0  -0.306  -4.9931   2.5381   1.0145
 Y38  C3   C  CR16  0  -0.240  -5.8350   3.6053   1.2896
 Y38  C4   C  CR16  0  -0.261  -5.8428   4.7211   0.4624
 Y38  C5   C  CR16  0  -0.239  -5.0021   4.7616  -0.6423
 Y38  C6   C  CR16  0  -0.308  -4.1587   3.6956  -0.9169
 Y38  H1   H  HCH1  0   0.309   1.2549  -3.2810   1.5421
 Y38  H2   H  HCH1  0   0.244   0.0917  -5.2431  -0.4098
 Y38  H3   H  HCH3  0   0.221   2.9059  -4.0582  -0.5576
 Y38  H4   H  HCH3  0   0.237   2.3750  -5.5325  -1.3548
 Y38  H5   H  HCH3  0   0.229   1.6859  -3.9891  -1.8279
 Y38  H6   H  HCH3  0   0.239   0.7587  -5.9290   1.9396
 Y38  H7   H  HCH3  0   0.236   1.6968  -6.7274   0.6861
 Y38  H8   H  HCH3  0   0.219   2.3999  -5.3867   1.5861
 Y38  H9   H  HOH1  0   0.484  -2.0651  -2.5249   2.4105
 Y38  H10  H  HCH2  0   0.275   0.7647  -0.2068   0.3223
 Y38  H11  H  HCH2  0   0.281   1.6045  -1.2602   1.4126
 Y38  H12  H  HCH2  0   0.262   3.2919  -1.8094  -0.3227
 Y38  H13  H  HCH2  0   0.257   2.4404  -0.8209  -1.4968
 Y38  H14  H  HNH1  0   0.413   4.1474   0.0492   0.6806
 Y38  H15  H  HCR6  0   0.260   3.5536   3.8846  -1.3663
 Y38  H16  H  HCR6  0   0.263   4.8510   5.7423  -0.4103
 Y38  H17  H  HCR6  0   0.265   5.9319   5.4927   1.8035
 Y38  H18  H  HCR6  0   0.259   4.4144   1.5191   2.1134
 Y38  H19  H  HCR6  0   0.265   5.6947   3.3694   3.0528
 Y38  H20  H  HCR6  0   0.284  -3.1491  -1.9508  -0.1976
 Y38  H21  H  HCR6  0   0.270  -4.6293  -0.0775   0.2686
 Y38  H22  H  HCR6  0   0.269  -1.6330   2.6558  -1.1319
 Y38  H23  H  HCR6  0   0.296  -0.1626   0.7891  -1.6519
 Y38  H24  H  HCR6  0   0.259  -4.9838   1.6835   1.6791
 Y38  H25  H  HCR6  0   0.261  -6.4815   3.5674   2.1566
 Y38  H26  H  HCR6  0   0.261  -6.5001   5.5535   0.6775
 Y38  H27  H  HCR6  0   0.261  -5.0060   5.6230  -1.2972
 Y38  H28  H  HCR6  0   0.259  -3.5247   3.7339  -1.7938

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
 Y38  C32  C33  aromatic  1.388  0.020  1.388
 Y38  C32  C31  aromatic  1.389  0.020  1.389
 Y38  C33  C3B  aromatic  1.388  0.020  1.388
 Y38  C31  C34  aromatic  1.386  0.020  1.386
 Y38  C3B  C29  aromatic  1.394  0.020  1.394
 Y38  C34  C29  aromatic  1.394  0.020  1.394
 Y38  C29  C27  single    1.496  0.020  1.496
 Y38  O28  C27  double    1.225  0.020  1.225
 Y38  C27  N26  single    1.344  0.020  1.344
 Y38  N26  C25  single    1.444  0.020  1.444
 Y38  C25  C24  single    1.527  0.020  1.527
 Y38  C20  C18  single    1.529  0.020  1.529
 Y38  C18  C19  single    1.523  0.020  1.523
 Y38  C18  C17  single    1.541  0.020  1.541
 Y38  C24  N16  single    1.459  0.020  1.459
 Y38  N16  C17  single    1.460  0.020  1.460
 Y38  N16  S13  single    1.648  0.020  1.648
 Y38  C17  C21  single    1.528  0.020  1.528
 Y38  O22  C21  double    1.202  0.020  1.202
 Y38  C21  O23  single    1.326  0.020  1.326
 Y38  S13  O14  double    1.456  0.020  1.456
 Y38  S13  O15  double    1.455  0.020  1.455
 Y38  S13  C10  single    1.771  0.020  1.771
 Y38  C10  C9   aromatic  1.390  0.020  1.390
 Y38  C10  C11  aromatic  1.388  0.020  1.388
 Y38  C9   C8   aromatic  1.384  0.020  1.384
 Y38  C11  C12  aromatic  1.384  0.020  1.384
 Y38  C8   C7   aromatic  1.396  0.020  1.396
 Y38  C12  C7   aromatic  1.396  0.020  1.396
 Y38  C7   C1   single    1.476  0.020  1.476
 Y38  C2   C1   aromatic  1.396  0.020  1.396
 Y38  C2   C3   aromatic  1.387  0.020  1.387
 Y38  C1   C6   aromatic  1.396  0.020  1.396
 Y38  C3   C4   aromatic  1.389  0.020  1.389
 Y38  C6   C5   aromatic  1.387  0.020  1.387
 Y38  C4   C5   aromatic  1.389  0.020  1.389
 Y38  C17  H1   single    0.970  0.020  1.090
 Y38  C18  H2   single    0.970  0.020  1.090
 Y38  C19  H3   single    0.970  0.020  1.090
 Y38  C19  H4   single    0.970  0.020  1.090
 Y38  C19  H5   single    0.970  0.020  1.090
 Y38  C20  H6   single    0.970  0.020  1.090
 Y38  C20  H7   single    0.970  0.020  1.090
 Y38  C20  H8   single    0.970  0.020  1.090
 Y38  O23  H9   single    0.850  0.020  0.980
 Y38  C24  H10  single    0.970  0.020  1.090
 Y38  C24  H11  single    0.970  0.020  1.090
 Y38  C25  H12  single    0.970  0.020  1.090
 Y38  C25  H13  single    0.970  0.020  1.090
 Y38  N26  H14  single    0.860  0.020  1.020
 Y38  C34  H15  single    0.930  0.020  1.080
 Y38  C31  H16  single    0.930  0.020  1.080
 Y38  C32  H17  single    0.930  0.020  1.080
 Y38  C3B  H18  single    0.930  0.020  1.080
 Y38  C33  H19  single    0.930  0.020  1.080
 Y38  C11  H20  single    0.930  0.020  1.080
 Y38  C12  H21  single    0.930  0.020  1.080
 Y38  C8   H22  single    0.930  0.020  1.080
 Y38  C9   H23  single    0.930  0.020  1.080
 Y38  C2   H24  single    0.930  0.020  1.080
 Y38  C3   H25  single    0.930  0.020  1.080
 Y38  C4   H26  single    0.930  0.020  1.080
 Y38  C5   H27  single    0.930  0.020  1.080
 Y38  C6   H28  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
 Y38  C10  S13  N16  107.88  3.000
 Y38  C10  S13  O14  108.24  3.000
 Y38  N16  S13  O14  105.86  3.000
 Y38  C10  S13  O15  106.11  3.000
 Y38  O14  S13  O15  119.40  3.000
 Y38  N16  S13  O15  108.91  3.000
 Y38  C24  N16  C17  120.32  3.000
 Y38  C17  N16  S13  120.16  3.000
 Y38  C24  N16  S13  118.56  3.000
 Y38  H1   C17  C21  105.03  3.000
 Y38  H1   C17  C18  106.05  3.000
 Y38  C21  C17  C18  112.66  3.000
 Y38  H1   C17  N16  103.63  3.000
 Y38  C21  C17  N16  111.29  3.000
 Y38  C18  C17  N16  116.87  3.000
 Y38  H2   C18  C20  108.34  3.000
 Y38  H2   C18  C19  108.28  3.000
 Y38  C20  C18  C19  109.28  3.000
 Y38  H2   C18  C17  109.07  3.000
 Y38  C19  C18  C17  112.31  3.000
 Y38  C20  C18  C17  109.47  3.000
 Y38  H5   C19  H4   107.29  3.000
 Y38  H5   C19  H3   107.87  3.000
 Y38  H4   C19  H3   107.33  3.000
 Y38  H5   C19  C18  112.99  3.000
 Y38  H4   C19  C18  109.45  3.000
 Y38  H3   C19  C18  111.65  3.000
 Y38  H8   C20  H7   107.51  3.000
 Y38  H8   C20  H6   107.94  3.000
 Y38  H7   C20  H6   107.52  3.000
 Y38  H8   C20  C18  110.80  3.000
 Y38  H7   C20  C18  110.17  3.000
 Y38  H6   C20  C18  112.70  3.000
 Y38  O23  C21  O22  123.54  3.000
 Y38  O23  C21  C17  111.06  3.000
 Y38  O22  C21  C17  125.36  3.000
 Y38  H9   O23  C21  110.10  3.000
 Y38  H11  C24  H10  105.24  3.000
 Y38  H11  C24  C25  109.36  3.000
 Y38  H10  C24  C25  110.10  3.000
 Y38  H11  C24  N16  107.50  3.000
 Y38  H10  C24  N16  110.31  3.000
 Y38  C25  C24  N16  113.93  3.000
 Y38  H13  C25  H12  107.42  3.000
 Y38  H13  C25  N26  109.78  3.000
 Y38  H12  C25  N26  107.83  3.000
 Y38  H13  C25  C24  110.79  3.000
 Y38  H12  C25  C24  110.11  3.000
 Y38  N26  C25  C24  110.81  3.000
 Y38  H14  N26  C27  119.69  3.000
 Y38  H14  N26  C25  117.62  3.000
 Y38  C27  N26  C25  122.70  3.000
 Y38  C29  C27  O28  120.85  3.000
 Y38  O28  C27  N26  122.68  3.000
 Y38  C29  C27  N26  116.46  3.000
 Y38  C3B  C29  C34  119.12  3.000
 Y38  C34  C29  C27  118.00  3.000
 Y38  C3B  C29  C27  122.85  3.000
 Y38  H15  C34  C31  119.72  3.000
 Y38  H15  C34  C29  119.82  3.000
 Y38  C31  C34  C29  120.46  3.000
 Y38  H16  C31  C32  120.13  3.000
 Y38  H16  C31  C34  119.75  3.000
 Y38  C32  C31  C34  120.12  3.000
 Y38  H17  C32  C33  120.07  3.000
 Y38  H17  C32  C31  120.16  3.000
 Y38  C33  C32  C31  119.76  3.000
 Y38  H18  C3B  C33  118.44  3.000
 Y38  H18  C3B  C29  121.17  3.000
 Y38  C33  C3B  C29  120.37  3.000
 Y38  H19  C33  C3B  119.62  3.000
 Y38  H19  C33  C32  120.23  3.000
 Y38  C3B  C33  C32  120.15  3.000
 Y38  C9   C10  C11  120.72  3.000
 Y38  C11  C10  S13  119.49  3.000
 Y38  C9   C10  S13  119.74  3.000
 Y38  H20  C11  C12  119.36  3.000
 Y38  H20  C11  C10  121.32  3.000
 Y38  C12  C11  C10  119.30  3.000
 Y38  H21  C12  C7   120.15  3.000
 Y38  H21  C12  C11  118.67  3.000
 Y38  C7   C12  C11  121.16  3.000
 Y38  C1   C7   C8   120.82  3.000
 Y38  C1   C7   C12  120.78  3.000
 Y38  C8   C7   C12  118.40  3.000
 Y38  H22  C8   C9   118.67  3.000
 Y38  H22  C8   C7   120.22  3.000
 Y38  C9   C8   C7   121.11  3.000
 Y38  H23  C9   C8   119.30  3.000
 Y38  H23  C9   C10  121.40  3.000
 Y38  C8   C9   C10  119.30  3.000
 Y38  C6   C1   C2   118.61  3.000
 Y38  C6   C1   C7   120.69  3.000
 Y38  C2   C1   C7   120.69  3.000
 Y38  H24  C2   C3   119.40  3.000
 Y38  H24  C2   C1   119.92  3.000
 Y38  C3   C2   C1   120.67  3.000
 Y38  H25  C3   C4   120.13  3.000
 Y38  H25  C3   C2   119.64  3.000
 Y38  C4   C3   C2   120.22  3.000
 Y38  H26  C4   C5   120.22  3.000
 Y38  H26  C4   C3   120.19  3.000
 Y38  C5   C4   C3   119.59  3.000
 Y38  H27  C5   C6   119.62  3.000
 Y38  H27  C5   C4   120.17  3.000
 Y38  C6   C5   C4   120.22  3.000
 Y38  H28  C6   C5   119.29  3.000
 Y38  H28  C6   C1   120.00  3.000
 Y38  C5   C6   C1   120.69  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
 Y38  CONST_01  C32  C33  C3B  C29     0.00   0.0  0
 Y38  CONST_02  C32  C31  C34  C29     0.00   0.0  0
 Y38  CONST_03  C33  C32  C31  C34     0.00   0.0  0
 Y38  CONST_04  C33  C3B  C29  C34     0.00   0.0  0
 Y38  CONST_05  C3B  C33  C32  C31     0.00   0.0  0
 Y38  CONST_06  C3B  C29  C34  C31     0.00   0.0  0
 Y38  CONST_07  C7   C8   C9   C10     0.00   0.0  0
 Y38  CONST_08  C7   C12  C11  C10     0.00   0.0  0
 Y38  CONST_09  C8   C9   C10  C11     0.00   0.0  0
 Y38  CONST_10  C8   C7   C12  C11     0.00   0.0  0
 Y38  CONST_11  C1   C7   C12  C11   180.00   0.0  0
 Y38  CONST_12  C9   C10  C11  C12     0.00   0.0  0
 Y38  CONST_13  C9   C8   C7   C12     0.00   0.0  0
 Y38  CONST_16  C3   C2   C1   C7    180.00   0.0  0
 Y38  CONST_17  C5   C6   C1   C7    180.00   0.0  0
 Y38  CONST_20  C1   C7   C8   C9    180.00   0.0  0
 Y38  CONST_21  C4   C3   C2   C1      0.00   0.0  0
 Y38  CONST_22  C4   C5   C6   C1      0.00   0.0  0
 Y38  CONST_23  C5   C6   C1   C2      0.00   0.0  0
 Y38  CONST_24  C5   C4   C3   C2      0.00   0.0  0
 Y38  CONST_25  C6   C1   C2   C3      0.00   0.0  0
 Y38  CONST_26  C6   C5   C4   C3      0.00   0.0  0
 Y38  CONST_27  C8   C9   C10  S13   180.00   0.0  0
 Y38  CONST_28  C12  C11  C10  S13   180.00   0.0  0
 Y38  CONST_29  C33  C3B  C29  C27   180.00   0.0  0
 Y38  CONST_30  C31  C34  C29  C27   180.00   0.0  0
 Y38  CONST_31  H19  C33  C3B  C29   180.00   0.0  0
 Y38  CONST_32  H16  C31  C34  C29   180.00   0.0  0
 Y38  CONST_33  H17  C32  C31  C34   180.00   0.0  0
 Y38  CONST_34  H18  C3B  C29  C34   180.00   0.0  0
 Y38  CONST_35  H15  C34  C31  C32   180.00   0.0  0
 Y38  CONST_36  H22  C8   C9   C10   180.00   0.0  0
 Y38  CONST_37  H21  C12  C11  C10   180.00   0.0  0
 Y38  CONST_38  H23  C9   C10  C11   180.00   0.0  0
 Y38  CONST_39  H20  C11  C12  C7    180.00   0.0  0
 Y38  CONST_40  H24  C2   C1   C7      0.00   0.0  0
 Y38  CONST_41  H28  C6   C1   C7      0.00   0.0  0
 Y38  CONST_42  H25  C3   C2   C1    180.00   0.0  0
 Y38  CONST_43  H27  C5   C6   C1    180.00   0.0  0
 Y38  CONST_44  H26  C4   C3   C2    180.00   0.0  0
 Y38  CONST_45  C29  C27  N26  C25   180.00   0.0  0
 Y38  CONST_46  H14  N26  C27  C29     0.00   0.0  0
 Y38  CONST_47  O28  C27  N26  C25     0.00   0.0  0
 Y38  CONST_48  H9   O23  C21  C17   180.00   0.0  0
 Y38  Var_01    C9   C10  S13  O15   -31.71  30.0  2
 Y38  Var_02    C3B  C29  C27  N26   -25.76  30.0  2
 Y38  Var_03    C10  S13  N16  C17   114.68  30.0  3
 Y38  Var_04    C25  C24  N16  S13   -85.46  30.0  1
 Y38  Var_05    N26  C25  C24  N16  -179.89  30.0  2
 Y38  Var_06    C27  N26  C25  C24   -81.89  30.0  1
 Y38  Var_07    H6   C20  C18  C17    54.47  30.0  3
 Y38  Var_08    H3   C19  C18  C17    56.02  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
 Y38  chir_01  C17  C18  N16  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
 Y38  plan-1  C27  0.020
 Y38  plan-1  C29  0.020
 Y38  plan-1  C34  0.020
 Y38  plan-1  C31  0.020
 Y38  plan-1  C32  0.020
 Y38  plan-1  C3B  0.020
 Y38  plan-1  C33  0.020
 Y38  plan-1  H15  0.020
 Y38  plan-1  H16  0.020
 Y38  plan-1  H17  0.020
 Y38  plan-1  H18  0.020
 Y38  plan-1  H19  0.020
 Y38  plan-2  S13  0.020
 Y38  plan-2  C10  0.020
 Y38  plan-2  C11  0.020
 Y38  plan-2  C12  0.020
 Y38  plan-2  C7   0.020
 Y38  plan-2  C8   0.020
 Y38  plan-2  C9   0.020
 Y38  plan-2  C1   0.020
 Y38  plan-2  H20  0.020
 Y38  plan-2  H21  0.020
 Y38  plan-2  H22  0.020
 Y38  plan-2  H23  0.020
 Y38  plan-3  C7   0.020
 Y38  plan-3  C1   0.020
 Y38  plan-3  C2   0.020
 Y38  plan-3  C3   0.020
 Y38  plan-3  C4   0.020
 Y38  plan-3  C5   0.020
 Y38  plan-3  C6   0.020
 Y38  plan-3  H24  0.020
 Y38  plan-3  H25  0.020
 Y38  plan-3  H26  0.020
 Y38  plan-3  H27  0.020
 Y38  plan-3  H28  0.020
 Y38  plan-4  C25  0.020
 Y38  plan-4  N26  0.020
 Y38  plan-4  C27  0.020
 Y38  plan-4  O28  0.020
 Y38  plan-4  C29  0.020
 Y38  plan-4  H14  0.020
 Y38  plan-5  C17  0.020
 Y38  plan-5  C21  0.020
 Y38  plan-5  O22  0.020
 Y38  plan-5  O23  0.020
 Y38  plan-5  H9   0.020

