# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 16:45:32 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (3~{S})-3-oxidanyl-2-oxidanylidene-1-phenyl-~{N}-(2-thiophen-2-ylethyl)pyrrolidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@]1(CCN(C1=O)c2ccccc2)C(=O)NCCc3sccc3
#
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
 K4K  K4K  (3~{S})-3-oxidanyl-2-oxidanylidene-1-phenyl-~{N}-(2-thiophen-2-ylethyl)pyrrolidine-3-carboxamide  ligand  41  23  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_K4K
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
 K4K  C1   C  C     0   0.554  -2.0582  -0.3381   0.2848
 K4K  C3   C  CT    0  -0.028  -0.9809   0.7483   0.4109
 K4K  C8   C  CR5   0  -0.148   5.1919   0.5745   0.3955
 K4K  C10  C  CR6   0   0.358  -4.4517  -0.3843  -0.2168
 K4K  C11  C  CR15  0  -0.471   7.3526  -0.6065   0.0738
 K4K  C13  C  CR15  0  -0.237   6.0511   1.2416  -0.4259
 K4K  C14  C  CR15  0  -0.183   7.2905   0.5673  -0.6106
 K4K  C16  C  CH2   0  -0.544   3.8043   0.9601   0.7889
 K4K  C19  C  CR16  0  -0.313  -5.6049   0.2957   0.1703
 K4K  C20  C  CR16  0  -0.249  -6.8456  -0.3154   0.0596
 K4K  C21  C  CR16  0  -0.252  -5.8014  -2.2823  -0.8230
 K4K  C22  C  CR16  0  -0.264  -6.9509  -1.6086  -0.4313
 K4K  N2   N  NT    0  -0.581  -3.2041   0.2590  -0.1216
 K4K  C4   C  C     0   0.544   0.3281   0.2526  -0.1996
 K4K  C5   C  CH2   0  -0.294  -3.0762   1.7071  -0.2393
 K4K  C6   C  CH2   0  -0.466  -1.5725   1.9059  -0.3814
 K4K  S7   S  S2    0   0.200   5.9052  -0.8968   0.9475
 K4K  O9   O  O     0  -0.453  -1.9021  -1.5014   0.5914
 K4K  O12  O  O     0  -0.488   0.3154  -0.2923  -1.2943
 K4K  N15  N  NH1   0  -0.641   1.4268   0.4892   0.5162
 K4K  C17  C  CH2   0  -0.236   2.7534   0.0997   0.0912
 K4K  C18  C  CR16  0  -0.290  -4.5567  -1.6791  -0.7245
 K4K  O23  O  OH1   0  -0.655  -0.8807   1.1230   1.7620
 K4K  H1   H  HCR5  0   0.294   8.1683  -1.3111   0.1189
 K4K  H2   H  HCR5  0   0.261   5.8045   2.1901  -0.8836
 K4K  H3   H  HCR5  0   0.265   8.0972   0.9433  -1.2233
 K4K  H4   H  HCH2  0   0.267   3.6821   0.8838   1.8734
 K4K  H5   H  HCH2  0   0.271   3.6496   2.0081   0.5251
 K4K  H6   H  HCR6  0   0.272  -5.5445   1.3020   0.5639
 K4K  H7   H  HCR6  0   0.261  -7.7321   0.2260   0.3628
 K4K  H8   H  HCR6  0   0.260  -5.8712  -3.2857  -1.2226
 K4K  H9   H  HCR6  0   0.258  -7.9188  -2.0839  -0.5182
 K4K  H10  H  HCH2  0   0.273  -3.6282   2.0669  -1.1066
 K4K  H11  H  HCH2  0   0.261  -3.4670   2.2082   0.6489
 K4K  H12  H  HCH2  0   0.281  -1.2363   2.8735  -0.0122
 K4K  H13  H  HCH2  0   0.278  -1.2895   1.8233  -1.4305
 K4K  H14  H  HNH1  0   0.405   1.3215   0.9244   1.4200
 K4K  H15  H  HCH2  0   0.253   2.8357   0.2224  -0.9889
 K4K  H16  H  HCH2  0   0.242   2.9259  -0.9580   0.3112
 K4K  H17  H  HCR6  0   0.269  -3.6799  -2.2120  -1.0610
 K4K  H18  H  HOH1  0   0.464  -0.7910   0.3352   2.3130

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
 K4K  C16  C8   single    1.493  0.020  1.493
 K4K  C16  C17  single    1.527  0.020  1.527
 K4K  C8   C13  aromatic  1.363  0.020  1.363
 K4K  C8   S7   aromatic  1.726  0.020  1.726
 K4K  C13  C14  aromatic  1.423  0.020  1.423
 K4K  S7   C11  aromatic  1.715  0.020  1.715
 K4K  O12  C4   double    1.223  0.020  1.223
 K4K  C17  N15  single    1.446  0.020  1.446
 K4K  C14  C11  aromatic  1.360  0.020  1.360
 K4K  C4   N15  single    1.333  0.020  1.333
 K4K  C4   C3   single    1.527  0.020  1.527
 K4K  O9   C1   double    1.213  0.020  1.213
 K4K  O23  C3   single    1.406  0.020  1.406
 K4K  C3   C1   single    1.535  0.020  1.535
 K4K  C3   C6   single    1.522  0.020  1.522
 K4K  C1   N2   single    1.355  0.020  1.355
 K4K  C6   C5   single    1.523  0.020  1.523
 K4K  N2   C10  single    1.407  0.020  1.407
 K4K  N2   C5   single    1.458  0.020  1.458
 K4K  C19  C10  aromatic  1.394  0.020  1.394
 K4K  C19  C20  aromatic  1.387  0.020  1.387
 K4K  C10  C18  aromatic  1.395  0.020  1.395
 K4K  C20  C22  aromatic  1.387  0.020  1.387
 K4K  C18  C21  aromatic  1.387  0.020  1.387
 K4K  C22  C21  aromatic  1.389  0.020  1.389
 K4K  C11  H1   single    0.930  0.020  1.080
 K4K  C13  H2   single    0.930  0.020  1.080
 K4K  C14  H3   single    0.930  0.020  1.080
 K4K  C16  H4   single    0.970  0.020  1.090
 K4K  C16  H5   single    0.970  0.020  1.090
 K4K  C19  H6   single    0.930  0.020  1.080
 K4K  C20  H7   single    0.930  0.020  1.080
 K4K  C21  H8   single    0.930  0.020  1.080
 K4K  C22  H9   single    0.930  0.020  1.080
 K4K  C5   H10  single    0.970  0.020  1.090
 K4K  C5   H11  single    0.970  0.020  1.090
 K4K  C6   H12  single    0.970  0.020  1.090
 K4K  C6   H13  single    0.970  0.020  1.090
 K4K  N15  H14  single    0.860  0.020  1.020
 K4K  C17  H15  single    0.970  0.020  1.090
 K4K  C17  H16  single    0.970  0.020  1.090
 K4K  C18  H17  single    0.930  0.020  1.080
 K4K  O23  H18  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
 K4K  O9   C1   N2   127.40  3.000
 K4K  N2   C1   C3   107.84  3.000
 K4K  O9   C1   C3   124.58  3.000
 K4K  O23  C3   C6   108.98  3.000
 K4K  C6   C3   C4   111.83  3.000
 K4K  O23  C3   C4   114.19  3.000
 K4K  C6   C3   C1   102.86  3.000
 K4K  O23  C3   C1   108.51  3.000
 K4K  C4   C3   C1   109.81  3.000
 K4K  S7   C8   C16  121.34  3.000
 K4K  S7   C8   C13  110.45  3.000
 K4K  C16  C8   C13  128.19  3.000
 K4K  C18  C10  N2   121.05  3.000
 K4K  C18  C10  C19  119.46  3.000
 K4K  N2   C10  C19  119.46  3.000
 K4K  H1   C11  S7   120.41  3.000
 K4K  H1   C11  C14  128.26  3.000
 K4K  S7   C11  C14  111.33  3.000
 K4K  H2   C13  C14  124.00  3.000
 K4K  H2   C13  C8   122.71  3.000
 K4K  C14  C13  C8   113.29  3.000
 K4K  H3   C14  C13  123.99  3.000
 K4K  H3   C14  C11  123.47  3.000
 K4K  C13  C14  C11  112.54  3.000
 K4K  H5   C16  H4   106.90  3.000
 K4K  H5   C16  C17  109.45  3.000
 K4K  H4   C16  C17  109.68  3.000
 K4K  H5   C16  C8   108.42  3.000
 K4K  H4   C16  C8   110.30  3.000
 K4K  C17  C16  C8   111.95  3.000
 K4K  H6   C19  C20  119.24  3.000
 K4K  H6   C19  C10  120.57  3.000
 K4K  C20  C19  C10  120.19  3.000
 K4K  H7   C20  C22  120.22  3.000
 K4K  H7   C20  C19  119.33  3.000
 K4K  C22  C20  C19  120.45  3.000
 K4K  H8   C21  C18  119.17  3.000
 K4K  H8   C21  C22  120.03  3.000
 K4K  C18  C21  C22  120.79  3.000
 K4K  H9   C22  C21  120.32  3.000
 K4K  H9   C22  C20  120.39  3.000
 K4K  C21  C22  C20  119.29  3.000
 K4K  C5   N2   C10  121.76  3.000
 K4K  C5   N2   C1   112.81  3.000
 K4K  C10  N2   C1   124.67  3.000
 K4K  N15  C4   O12  124.65  3.000
 K4K  N15  C4   C3   115.74  3.000
 K4K  O12  C4   C3   119.58  3.000
 K4K  H11  C5   H10  108.34  3.000
 K4K  H11  C5   C6   111.67  3.000
 K4K  H10  C5   C6   112.51  3.000
 K4K  H11  C5   N2   111.02  3.000
 K4K  H10  C5   N2   110.35  3.000
 K4K  C6   C5   N2   102.93  3.000
 K4K  H13  C6   H12  108.28  3.000
 K4K  H13  C6   C5   109.65  3.000
 K4K  H12  C6   C5   112.90  3.000
 K4K  H13  C6   C3   110.02  3.000
 K4K  H12  C6   C3   112.29  3.000
 K4K  C5   C6   C3   103.64  3.000
 K4K  C11  S7   C8    92.38  3.000
 K4K  H14  N15  C17  118.37  3.000
 K4K  H14  N15  C4   118.16  3.000
 K4K  C17  N15  C4   123.41  3.000
 K4K  H16  C17  H15  107.23  3.000
 K4K  H16  C17  N15  110.23  3.000
 K4K  H15  C17  N15  109.27  3.000
 K4K  H16  C17  C16  110.14  3.000
 K4K  H15  C17  C16  109.72  3.000
 K4K  N15  C17  C16  110.20  3.000
 K4K  H17  C18  C21  119.48  3.000
 K4K  H17  C18  C10  120.70  3.000
 K4K  C21  C18  C10  119.82  3.000
 K4K  H18  O23  C3   109.74  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
 K4K  CONST_01  C11  C14  C13  C8     0.00   0.0  0
 K4K  CONST_02  C14  C11  S7   C8     0.00   0.0  0
 K4K  CONST_03  C22  C20  C19  C10    0.00   0.0  0
 K4K  CONST_04  C22  C21  C18  C10    0.00   0.0  0
 K4K  CONST_05  C13  C8   S7   C11    0.00   0.0  0
 K4K  CONST_06  S7   C11  C14  C13    0.00   0.0  0
 K4K  CONST_07  S7   C8   C13  C14    0.00   0.0  0
 K4K  CONST_08  C21  C18  C10  C19    0.00   0.0  0
 K4K  CONST_09  C21  C22  C20  C19    0.00   0.0  0
 K4K  CONST_10  C18  C10  C19  C20    0.00   0.0  0
 K4K  CONST_11  C18  C21  C22  C20    0.00   0.0  0
 K4K  CONST_12  N2   C10  C19  C20  180.00   0.0  0
 K4K  CONST_13  N2   C10  C18  C21  180.00   0.0  0
 K4K  CONST_14  C10  N2   C1   C3   180.00   0.0  0
 K4K  CONST_15  C5   N2   C1   C3     0.00   0.0  0
 K4K  CONST_16  C16  C8   S7   C11  180.00   0.0  0
 K4K  CONST_17  C16  C8   C13  C14  180.00   0.0  0
 K4K  CONST_18  O9   C1   N2   C10    0.00   0.0  0
 K4K  CONST_19  O9   C1   N2   C5   180.00   0.0  0
 K4K  CONST_20  H3   C14  C13  C8   180.00   0.0  0
 K4K  CONST_21  H1   C11  S7   C8   180.00   0.0  0
 K4K  CONST_22  H7   C20  C19  C10  180.00   0.0  0
 K4K  CONST_23  H8   C21  C18  C10  180.00   0.0  0
 K4K  CONST_24  H2   C13  C14  C11  180.00   0.0  0
 K4K  CONST_25  H17  C18  C10  C19  180.00   0.0  0
 K4K  CONST_26  H9   C22  C20  C19  180.00   0.0  0
 K4K  CONST_27  H6   C19  C20  C22  180.00   0.0  0
 K4K  CONST_28  C17  N15  C4   C3   180.00   0.0  0
 K4K  CONST_29  H14  N15  C4   C3     0.00   0.0  0
 K4K  CONST_30  C17  N15  C4   O12    0.00   0.0  0
 K4K  Var_01    C19  C10  N2   C1   140.43  30.0  2
 K4K  Var_02    C6   C5   N2   C1    21.45  30.0  1
 K4K  Var_03    N2   C5   C6   C3   -30.56  30.0  1
 K4K  Var_04    C17  C16  C8   C13  106.18  30.0  1
 K4K  Var_05    N15  C17  C16  C8   179.01  30.0  3
 K4K  Var_06    C4   N15  C17  C16  157.33  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
 K4K  chir_01  C3  O23  C1  C6  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
 K4K  plan-1  C8   0.020
 K4K  plan-1  C11  0.020
 K4K  plan-1  C13  0.020
 K4K  plan-1  C14  0.020
 K4K  plan-1  C16  0.020
 K4K  plan-1  S7   0.020
 K4K  plan-1  H1   0.020
 K4K  plan-1  H2   0.020
 K4K  plan-1  H3   0.020
 K4K  plan-2  C10  0.020
 K4K  plan-2  C19  0.020
 K4K  plan-2  C20  0.020
 K4K  plan-2  C21  0.020
 K4K  plan-2  C22  0.020
 K4K  plan-2  N2   0.020
 K4K  plan-2  C18  0.020
 K4K  plan-2  H6   0.020
 K4K  plan-2  H7   0.020
 K4K  plan-2  H8   0.020
 K4K  plan-2  H9   0.020
 K4K  plan-2  H17  0.020
 K4K  plan-3  C3   0.020
 K4K  plan-3  C4   0.020
 K4K  plan-3  O12  0.020
 K4K  plan-3  N15  0.020
 K4K  plan-3  C17  0.020
 K4K  plan-3  H14  0.020
 K4K  plan-4  C1   0.020
 K4K  plan-4  C3   0.020
 K4K  plan-4  C10  0.020
 K4K  plan-4  N2   0.020
 K4K  plan-4  C5   0.020
 K4K  plan-4  O9   0.020

