# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 15:32:14 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: (2~{S})-~{N}-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]-1-[2-[(phenylmethyl)sulfonylamino]ethanoyl]pyrrolidine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1ccc(Cl)cc1CNC(=O)[C@@H]2CCCN2C(=O)CN[S](=O)(=O)Cc3ccccc3
#
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
 KDQ  KDQ  (2~{S})-~{N}-[[5-chloranyl-2-(hydroxymethyl)phenyl]methyl]-1-[2-[(phenylmethyl)sulfonylamino]ethanoyl]pyrrolidine-2-carboxamide  ligand  58  32  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KDQ
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
 KDQ  C3   C   CR16  0  -0.259  -5.8777   1.8270  -0.1396
 KDQ  C5   C   CR16  0  -0.210  -7.8720   0.5478  -0.5542
 KDQ  C6   C   CR16  0  -0.296  -7.2183  -0.5858  -0.0926
 KDQ  C21  C   CR16  0  -0.278   7.6249  -0.7516  -0.4983
 KDQ  C9   C   CH1   0  -0.168  -1.1510  -1.4305  -0.7430
 KDQ  C10  C   CH2   0  -0.485  -1.6904  -2.8600  -0.9123
 KDQ  C11  C   CH2   0  -0.469  -0.4501  -3.6771  -1.2562
 KDQ  C2   C   CR6   0   0.083  -5.2260   0.6900   0.3232
 KDQ  C7   C   CR6   0   0.026  -5.9007  -0.5381   0.3500
 KDQ  C16  C   CR6   0   0.119   6.9132   0.4447  -0.4884
 KDQ  C15  C   CH2   0  -0.717   5.4207   0.4391  -0.5937
 KDQ  C12  C   CH2   0  -0.284   0.6317  -3.0394  -0.3971
 KDQ  N1   N   NT    0  -0.481   0.2404  -1.6341  -0.3858
 KDQ  C20  C   CR16  0  -0.243   9.0075  -0.7443  -0.3825
 KDQ  C19  C   CR16  0  -0.260   9.6888   0.4588  -0.2488
 KDQ  C18  C   CR16  0  -0.242   8.9831   1.6549  -0.2340
 KDQ  C17  C   CR16  0  -0.279   7.6004   1.6474  -0.3492
 KDQ  O4   O   OS    0  -0.665   5.0914  -0.9593   1.6232
 KDQ  S    S   S     0   1.369   4.6944   0.3186   1.0506
 KDQ  O3   O   OS    0  -0.660   4.9902   1.5488   1.7662
 KDQ  N2   N   NC1   0  -0.746   3.0677   0.2677   0.8470
 KDQ  C14  C   CH2   0  -0.392   2.4544  -0.9217   0.2890
 KDQ  O2   O   O     0  -0.494   0.6185   0.5639  -0.1266
 KDQ  C    C   C     0   0.560  -1.9043  -0.7000   0.3611
 KDQ  O    O   O     0  -0.487  -1.6644  -0.9048   1.5398
 KDQ  N    N   NH1   0  -0.629  -2.8915   0.0939  -0.0806
 KDQ  C1   C   CH2   0  -0.387  -3.7965   0.8231   0.7808
 KDQ  O1   O   OH1   0  -0.664  -6.1691  -2.7334   1.2385
 KDQ  C4   C   CR6   0  -0.039  -7.1912   1.7506  -0.5722
 KDQ  CL   CL  CL    0  -0.133  -7.9843   3.1821  -1.1460
 KDQ  H1   H   HCR6  0   0.277  -5.3531   2.7741  -0.1559
 KDQ  H2   H   HCR6  0   0.278  -8.8970   0.4851  -0.8936
 KDQ  H3   H   HCR6  0   0.266  -7.7601  -1.5212  -0.0821
 KDQ  H5   H   HCH1  0   0.284  -1.2187  -0.8777  -1.6850
 KDQ  H6   H   HCH2  0   0.253  -2.1182  -3.2167   0.0275
 KDQ  H7   H   HCH2  0   0.270  -2.4673  -2.9075  -1.6731
 KDQ  H8   H   HCH2  0   0.262  -0.5720  -4.7379  -1.0432
 KDQ  H9   H   HCH2  0   0.249  -0.2007  -3.5700  -2.3132
 KDQ  H12  H   HCH2  0   0.324   5.0317   1.3567  -1.0373
 KDQ  H13  H   HCH2  0   0.320   5.0515  -0.4109  -1.1696
 KDQ  H14  H   HCH2  0   0.254   0.6311  -3.4488   0.6170
 KDQ  H15  H   HCH2  0   0.267   1.6276  -3.1733  -0.8187
 KDQ  H16  H   HCR6  0   0.260   9.5542  -1.6782  -0.3978
 KDQ  H17  H   HCR6  0   0.260  10.7674   0.4643  -0.1625
 KDQ  H18  H   HCR6  0   0.260   9.5100   2.5947  -0.1323
 KDQ  H19  H   HCR6  0   0.258   7.0530   2.5820  -0.3440
 KDQ  H20  H   HNC1  0   0.416   2.6680   1.1395   0.5115
 KDQ  H21  H   HCH2  0   0.297   2.4770  -1.7300   1.0205
 KDQ  H22  H   HCH2  0   0.282   2.9607  -1.2863  -0.6141
 KDQ  H23  H   HNH1  0   0.405  -2.9670   0.2623  -1.0719
 KDQ  H24  H   HCH2  0   0.277  -3.5202   1.8798   0.8044
 KDQ  H25  H   HCH2  0   0.277  -3.6761   0.4463   1.7969
 KDQ  H26  H   HOH1  0   0.462  -5.7272  -3.5812   1.3388
 KDQ  C8   C   CH2   0  -0.201  -5.2135  -1.7931   0.8179
 KDQ  C13  C   C     0   0.556   1.0191  -0.5923  -0.0855
 KDQ  H4   H   HCR6  0   0.257   7.0973  -1.6907  -0.6108
 KDQ  H10  H   HCH2  0   0.225  -4.6093  -2.1870  -0.0106
 KDQ  H11  H   HCH2  0   0.214  -4.5111  -1.5549   1.6266

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
 KDQ  C10  C11  single    1.525  0.020  1.525
 KDQ  C10  C9   single    1.537  0.020  1.537
 KDQ  C11  C12  single    1.521  0.020  1.521
 KDQ  O    C    double    1.220  0.020  1.220
 KDQ  C1   N    single    1.447  0.020  1.447
 KDQ  C1   C2   single    1.507  0.020  1.507
 KDQ  C    N    single    1.342  0.020  1.342
 KDQ  C    C9   single    1.523  0.020  1.523
 KDQ  C12  N1   single    1.459  0.020  1.459
 KDQ  C9   N1   single    1.451  0.020  1.451
 KDQ  C8   O1   single    1.405  0.020  1.405
 KDQ  C8   C7   single    1.505  0.020  1.505
 KDQ  N1   C13  single    1.335  0.020  1.335
 KDQ  C2   C7   aromatic  1.401  0.020  1.401
 KDQ  C2   C3   aromatic  1.390  0.020  1.390
 KDQ  C7   C6   aromatic  1.391  0.020  1.391
 KDQ  C13  O2   double    1.224  0.020  1.224
 KDQ  C13  C14  single    1.519  0.020  1.519
 KDQ  C3   C4   aromatic  1.385  0.020  1.385
 KDQ  C14  N2   single    1.450  0.020  1.450
 KDQ  C6   C5   aromatic  1.388  0.020  1.388
 KDQ  C4   C5   aromatic  1.382  0.020  1.382
 KDQ  C4   CL   single    1.734  0.020  1.734
 KDQ  O4   S    double    1.455  0.020  1.455
 KDQ  N2   S    single    1.640  0.020  1.640
 KDQ  S    O3   double    1.454  0.020  1.454
 KDQ  S    C15  single    1.802  0.020  1.802
 KDQ  C20  C19  aromatic  1.389  0.020  1.389
 KDQ  C20  C21  aromatic  1.387  0.020  1.387
 KDQ  C19  C18  aromatic  1.389  0.020  1.389
 KDQ  C21  C16  aromatic  1.392  0.020  1.392
 KDQ  C18  C17  aromatic  1.388  0.020  1.388
 KDQ  C16  C17  aromatic  1.392  0.020  1.392
 KDQ  C16  C15  single    1.496  0.020  1.496
 KDQ  C3   H1   single    0.930  0.020  1.080
 KDQ  C5   H2   single    0.930  0.020  1.080
 KDQ  C6   H3   single    0.930  0.020  1.080
 KDQ  C21  H4   single    0.930  0.020  1.080
 KDQ  C9   H5   single    0.970  0.020  1.090
 KDQ  C10  H6   single    0.970  0.020  1.090
 KDQ  C10  H7   single    0.970  0.020  1.090
 KDQ  C11  H8   single    0.970  0.020  1.090
 KDQ  C11  H9   single    0.970  0.020  1.090
 KDQ  C8   H10  single    0.970  0.020  1.090
 KDQ  C8   H11  single    0.970  0.020  1.090
 KDQ  C15  H12  single    0.970  0.020  1.090
 KDQ  C15  H13  single    0.970  0.020  1.090
 KDQ  C12  H14  single    0.970  0.020  1.090
 KDQ  C12  H15  single    0.970  0.020  1.090
 KDQ  C20  H16  single    0.930  0.020  1.080
 KDQ  C19  H17  single    0.930  0.020  1.080
 KDQ  C18  H18  single    0.930  0.020  1.080
 KDQ  C17  H19  single    0.930  0.020  1.080
 KDQ  N2   H20  single    0.890  0.020  1.040
 KDQ  C14  H21  single    0.970  0.020  1.090
 KDQ  C14  H22  single    0.970  0.020  1.090
 KDQ  N    H23  single    0.860  0.020  1.020
 KDQ  C1   H24  single    0.970  0.020  1.090
 KDQ  C1   H25  single    0.970  0.020  1.090
 KDQ  O1   H26  single    0.850  0.020  0.980

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
 KDQ  H1   C3   C4   120.21  3.000
 KDQ  H1   C3   C2   119.56  3.000
 KDQ  C4   C3   C2   120.23  3.000
 KDQ  H2   C5   C4   120.87  3.000
 KDQ  H2   C5   C6   120.24  3.000
 KDQ  C4   C5   C6   118.89  3.000
 KDQ  H3   C6   C7   120.10  3.000
 KDQ  H3   C6   C5   118.29  3.000
 KDQ  C7   C6   C5   121.61  3.000
 KDQ  H4   C21  C20  119.91  3.000
 KDQ  H4   C21  C16  119.79  3.000
 KDQ  C20  C21  C16  120.29  3.000
 KDQ  H5   C9   C    110.55  3.000
 KDQ  H5   C9   N1   110.01  3.000
 KDQ  C    C9   N1   111.29  3.000
 KDQ  H5   C9   C10  110.69  3.000
 KDQ  N1   C9   C10  103.48  3.000
 KDQ  C    C9   C10  110.62  3.000
 KDQ  H7   C10  H6   107.91  3.000
 KDQ  H7   C10  C11  113.55  3.000
 KDQ  H6   C10  C11  109.73  3.000
 KDQ  H7   C10  C9   111.60  3.000
 KDQ  H6   C10  C9   110.26  3.000
 KDQ  C11  C10  C9   103.75  3.000
 KDQ  H9   C11  H8   108.10  3.000
 KDQ  H9   C11  C12  110.08  3.000
 KDQ  H8   C11  C12  112.18  3.000
 KDQ  H9   C11  C10  110.59  3.000
 KDQ  H8   C11  C10  112.77  3.000
 KDQ  C12  C11  C10  103.09  3.000
 KDQ  C1   C2   C7   121.89  3.000
 KDQ  C7   C2   C3   119.84  3.000
 KDQ  C1   C2   C3   118.27  3.000
 KDQ  C2   C7   C8   121.11  3.000
 KDQ  C2   C7   C6   118.69  3.000
 KDQ  C8   C7   C6   120.18  3.000
 KDQ  C17  C16  C15  120.18  3.000
 KDQ  C15  C16  C21  120.42  3.000
 KDQ  C17  C16  C21  119.39  3.000
 KDQ  H13  C15  H12  108.66  3.000
 KDQ  H13  C15  S    107.04  3.000
 KDQ  H12  C15  S    106.48  3.000
 KDQ  H13  C15  C16  112.19  3.000
 KDQ  H12  C15  C16  112.41  3.000
 KDQ  S    C15  C16  109.77  3.000
 KDQ  H15  C12  H14  108.26  3.000
 KDQ  H15  C12  N1   111.50  3.000
 KDQ  H14  C12  N1   110.69  3.000
 KDQ  H15  C12  C11  112.33  3.000
 KDQ  H14  C12  C11  111.48  3.000
 KDQ  N1   C12  C11  102.55  3.000
 KDQ  C12  N1   C13  126.66  3.000
 KDQ  C13  N1   C9   120.35  3.000
 KDQ  C12  N1   C9   112.99  3.000
 KDQ  H16  C20  C19  120.06  3.000
 KDQ  H16  C20  C21  119.85  3.000
 KDQ  C19  C20  C21  120.09  3.000
 KDQ  H17  C19  C18  120.08  3.000
 KDQ  H17  C19  C20  120.06  3.000
 KDQ  C18  C19  C20  119.85  3.000
 KDQ  H18  C18  C17  119.85  3.000
 KDQ  H18  C18  C19  120.10  3.000
 KDQ  C17  C18  C19  120.05  3.000
 KDQ  H19  C17  C18  119.90  3.000
 KDQ  H19  C17  C16  119.77  3.000
 KDQ  C18  C17  C16  120.32  3.000
 KDQ  N2   S    O3   106.81  3.000
 KDQ  O3   S    O4   119.59  3.000
 KDQ  N2   S    O4   106.98  3.000
 KDQ  O3   S    C15  108.10  3.000
 KDQ  N2   S    C15  106.78  3.000
 KDQ  O4   S    C15  107.93  3.000
 KDQ  H20  N2   C14  114.23  3.000
 KDQ  H20  N2   S    113.86  3.000
 KDQ  C14  N2   S    119.52  3.000
 KDQ  H22  C14  H21  107.23  3.000
 KDQ  H22  C14  N2   113.21  3.000
 KDQ  H21  C14  N2   109.94  3.000
 KDQ  H22  C14  C13  107.76  3.000
 KDQ  H21  C14  C13  110.22  3.000
 KDQ  N2   C14  C13  108.46  3.000
 KDQ  N    C    O    124.19  3.000
 KDQ  N    C    C9   114.15  3.000
 KDQ  O    C    C9   121.50  3.000
 KDQ  H23  N    C1   117.02  3.000
 KDQ  H23  N    C    118.53  3.000
 KDQ  C1   N    C    124.24  3.000
 KDQ  H25  C1   H24  106.64  3.000
 KDQ  H25  C1   N    108.15  3.000
 KDQ  H24  C1   N    110.01  3.000
 KDQ  H25  C1   C2   110.93  3.000
 KDQ  H24  C1   C2   109.39  3.000
 KDQ  N    C1   C2   111.60  3.000
 KDQ  H26  O1   C8   107.99  3.000
 KDQ  CL   C4   C5   119.82  3.000
 KDQ  CL   C4   C3   119.44  3.000
 KDQ  C5   C4   C3   120.74  3.000
 KDQ  H11  C8   H10  106.36  3.000
 KDQ  H11  C8   O1   111.10  3.000
 KDQ  H10  C8   O1   111.10  3.000
 KDQ  H11  C8   C7   109.90  3.000
 KDQ  H10  C8   C7   108.40  3.000
 KDQ  O1   C8   C7   109.90  3.000
 KDQ  O2   C13  C14  121.47  3.000
 KDQ  C14  C13  N1   115.93  3.000
 KDQ  O2   C13  N1   122.58  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
 KDQ  CONST_01  C6   C7   C2   C3      0.00   0.0  0
 KDQ  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 KDQ  CONST_03  C2   C7   C6   C5      0.00   0.0  0
 KDQ  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 KDQ  CONST_05  C18  C19  C20  C21     0.00   0.0  0
 KDQ  CONST_06  C18  C17  C16  C21     0.00   0.0  0
 KDQ  CONST_07  C4   C3   C2   C7      0.00   0.0  0
 KDQ  CONST_08  C4   C5   C6   C7      0.00   0.0  0
 KDQ  CONST_09  C19  C20  C21  C16     0.00   0.0  0
 KDQ  CONST_10  C19  C18  C17  C16     0.00   0.0  0
 KDQ  CONST_11  C17  C18  C19  C20     0.00   0.0  0
 KDQ  CONST_12  C17  C16  C21  C20     0.00   0.0  0
 KDQ  CONST_13  C8   C7   C2   C3    180.00   0.0  0
 KDQ  CONST_14  C8   C7   C6   C5    180.00   0.0  0
 KDQ  CONST_15  C1   C2   C7   C6    180.00   0.0  0
 KDQ  CONST_16  CL   C4   C5   C6    180.00   0.0  0
 KDQ  CONST_17  CL   C4   C3   C2    180.00   0.0  0
 KDQ  CONST_18  C20  C21  C16  C15   180.00   0.0  0
 KDQ  CONST_19  C18  C17  C16  C15   180.00   0.0  0
 KDQ  CONST_20  C4   C3   C2   C1    180.00   0.0  0
 KDQ  CONST_21  H2   C5   C4   C3    180.00   0.0  0
 KDQ  CONST_22  H1   C3   C4   C5    180.00   0.0  0
 KDQ  CONST_23  H17  C19  C20  C21   180.00   0.0  0
 KDQ  CONST_24  H19  C17  C16  C21   180.00   0.0  0
 KDQ  CONST_25  H3   C6   C7   C2    180.00   0.0  0
 KDQ  CONST_26  H16  C20  C21  C16   180.00   0.0  0
 KDQ  CONST_27  H18  C18  C17  C16   180.00   0.0  0
 KDQ  CONST_28  H4   C21  C20  C19   180.00   0.0  0
 KDQ  CONST_29  O2   C13  N1   C9      0.00   0.0  0
 KDQ  CONST_30  C14  C13  N1   C9    180.00   0.0  0
 KDQ  CONST_31  O2   C13  N1   C12   180.00   0.0  0
 KDQ  CONST_32  C14  C13  N1   C12     0.00   0.0  0
 KDQ  CONST_33  C1   N    C    C9    180.00   0.0  0
 KDQ  CONST_34  H23  N    C    C9      0.00   0.0  0
 KDQ  CONST_35  C1   N    C    O       0.00   0.0  0
 KDQ  Var_01    C12  C11  C10  C9     37.03  30.0  1
 KDQ  Var_02    C11  C12  N1   C9     19.51  30.0  1
 KDQ  Var_03    N1   C12  C11  C10   -34.28  30.0  1
 KDQ  Var_04    N    C1   C2   C3   -114.00  30.0  2
 KDQ  Var_05    O1   C8   C7   C6    -23.88  30.0  1
 KDQ  Var_06    S    C15  C16  C21    88.86  30.0  2
 KDQ  Var_07    C    N    C1   C2   -134.49  30.0  3
 KDQ  Var_08    O4   S    C15  C16   -63.42  30.0  2
 KDQ  Var_09    N2   C14  C13  N1   -168.23  30.0  3
 KDQ  Var_10    C14  N2   S    C15    71.23  30.0  1
 KDQ  Var_11    S    N2   C14  C13  -167.14  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
 KDQ  chir_01  C9  C10  C  N1  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
 KDQ  plan-1  C3   0.020
 KDQ  plan-1  C5   0.020
 KDQ  plan-1  C6   0.020
 KDQ  plan-1  C2   0.020
 KDQ  plan-1  C7   0.020
 KDQ  plan-1  C1   0.020
 KDQ  plan-1  C4   0.020
 KDQ  plan-1  CL   0.020
 KDQ  plan-1  H1   0.020
 KDQ  plan-1  H2   0.020
 KDQ  plan-1  H3   0.020
 KDQ  plan-1  C8   0.020
 KDQ  plan-2  C21  0.020
 KDQ  plan-2  C16  0.020
 KDQ  plan-2  C15  0.020
 KDQ  plan-2  C20  0.020
 KDQ  plan-2  C19  0.020
 KDQ  plan-2  C18  0.020
 KDQ  plan-2  C17  0.020
 KDQ  plan-2  H16  0.020
 KDQ  plan-2  H17  0.020
 KDQ  plan-2  H18  0.020
 KDQ  plan-2  H19  0.020
 KDQ  plan-2  H4   0.020
 KDQ  plan-3  C9   0.020
 KDQ  plan-3  C12  0.020
 KDQ  plan-3  N1   0.020
 KDQ  plan-3  C14  0.020
 KDQ  plan-3  O2   0.020
 KDQ  plan-3  C13  0.020
 KDQ  plan-4  C9   0.020
 KDQ  plan-4  C    0.020
 KDQ  plan-4  O    0.020
 KDQ  plan-4  N    0.020
 KDQ  plan-4  C1   0.020
 KDQ  plan-4  H23  0.020

