# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 01:05:29 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 2-(5-chlorothiophen-2-yl)-N-[(3S)-1-(4-{2-[(dimethylamino)methyl]-1H-imidazol-1-yl}-2-fluorophenyl)-2-oxopyrrolidin-3-yl]ethanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)Cc1nccn1c2ccc(N3CC[C@H](N[S](=O)(=O)CCc4sc(Cl)cc4)C3=O)c(F)c2
#
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
 GSI  GSI  2-(5-chlorothiophen-2-yl)-N-[(3S)-1-(4-{2-[(dimethylamino)methyl]-1H-imidazol-1-yl}-2-fluorophenyl)-2-oxopyrrolidin-3-yl]ethanesulfonamide  ligand  59  34  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GSI
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
 GSI  CL1   CL  CL    0  -0.082  13.8047   8.0639  26.0718
 GSI  C1    C   CR5   0  -0.257  12.2490   7.6943  25.4690
 GSI  C2    C   CR15  0  -0.130  11.9356   6.7893  24.5074
 GSI  C3    C   CR15  0  -0.221  10.5349   6.7459  24.2664
 GSI  S2    S   S2    0   0.269  10.8612   8.4950  26.0961
 GSI  C4    C   CR5   0  -0.157   9.8193   7.6024  25.0454
 GSI  C5    C   CH2   0  -0.514   8.3454   7.8449  25.0336
 GSI  C6    C   CH2   0  -0.612   8.0118   9.1036  24.2370
 GSI  S1    S   S     0   1.368   6.2461   9.3785  24.0274
 GSI  O2    O   OS    0  -0.664   6.0694  10.7733  23.6557
 GSI  O1    O   OS    0  -0.662   5.5601   8.8419  25.1947
 GSI  N1    N   NC1   0  -0.739   5.7275   8.5124  22.7308
 GSI  C12   C   CH1   0  -0.238   5.5431   7.0841  22.7447
 GSI  C13   C   CH2   0  -0.462   4.2522   6.6067  22.0883
 GSI  C14   C   CH2   0  -0.283   4.5974   5.1860  21.6522
 GSI  C50   C   C     0   0.576   6.6283   6.3268  21.9848
 GSI  O3    O   O     0  -0.450   7.8090   6.6020  21.9541
 GSI  N2    N   NT    0  -0.577   6.0284   5.2801  21.3731
 GSI  C15   C   CR6   0   0.170   6.7346   4.2885  20.6784
 GSI  C21   C   CR16  0  -0.280   6.6747   2.9542  21.0617
 GSI  C24   C   CR16  0  -0.291   7.3563   1.9777  20.3553
 GSI  C27   C   CR6   0   0.330   8.1391   2.3382  19.2663
 GSI  C26   C   CR16  0  -0.450   8.2256   3.6671  18.8731
 GSI  C22   C   CR6   0   0.545   7.5023   4.6139  19.5673
 GSI  F1    F   F     0  -0.293   7.5404   5.8802  19.1521
 GSI  N4    N   NR5   0  -0.557   8.8672   1.3515  18.5693
 GSI  C9    C   CR15  0  -0.118   9.7246   0.4472  19.1520
 GSI  C7    C   CR15  0  -0.221  10.2104  -0.2990  18.1253
 GSI  N3    N   N     0  -0.443   9.6740   0.1177  16.9382
 GSI  C8    C   CR5   0   0.440   8.8707   1.1053  17.2257
 GSI  C10   C   CH2   0  -0.364   8.0354   1.8775  16.2515
 GSI  N5    N   NT    0  -0.397   7.7315   1.1136  15.0645
 GSI  C11   C   CH3   0  -0.527   6.8315   0.0119  15.3367
 GSI  C16   C   CH3   0  -0.524   7.1987   1.9748  14.0296
 GSI  H2    H   HCR5  0   0.287  12.6631   6.1783  23.9941
 GSI  H3    H   HCR5  0   0.270  10.0724   6.0997  23.5332
 GSI  H5C1  H   HCH2  0   0.279   7.8750   6.9671  24.5945
 GSI  H5C2  H   HCH2  0   0.285   7.9619   7.9399  26.0495
 GSI  H6C1  H   HCH2  0   0.308   8.3826   9.9960  24.7448
 GSI  H6C2  H   HCH2  0   0.315   8.4421   9.0765  23.2365
 GSI  H1    H   HNC1  0   0.420   5.9676   8.9318  21.8399
 GSI  H12   H   HCH1  0   0.316   5.5663   6.7325  23.7811
 GSI  H131  H   HCH2  0   0.277   3.3997   6.6404  22.7627
 GSI  H132  H   HCH2  0   0.265   4.0271   7.2223  21.2152
 GSI  H141  H   HCH2  0   0.259   4.4019   4.4619  22.4473
 GSI  H142  H   HCH2  0   0.275   4.0585   4.8717  20.7601
 GSI  H21   H   HCR6  0   0.288   6.0820   2.6724  21.9220
 GSI  H24   H   HCR6  0   0.288   7.2780   0.9414  20.6544
 GSI  H26   H   HCR6  0   0.301   8.8436   3.9712  18.0384
 GSI  H9    H   HCR5  0   0.298   9.9169   0.4424  20.2116
 GSI  H7    H   HCR5  0   0.254  10.9178  -1.1117  18.1767
 GSI  H101  H   HCH2  0   0.227   7.1242   2.2410  16.7572
 GSI  H102  H   HCH2  0   0.269   8.5840   2.7750  15.9463
 GSI  H111  H   HCH3  0   0.235   6.6414  -0.5393  14.4149
 GSI  H112  H   HCH3  0   0.241   7.2760  -0.6820  16.0489
 GSI  H113  H   HCH3  0   0.193   5.8596   0.3396  15.7378
 GSI  H161  H   HCH3  0   0.194   6.2416   2.4457  14.3033
 GSI  H162  H   HCH3  0   0.236   7.9081   2.7713  13.8004
 GSI  H163  H   HCH3  0   0.237   7.0361   1.3987  13.1180

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
 GSI  CL1  C1    single    1.709  0.020  1.709
 GSI  C1   C2    aromatic  1.357  0.020  1.357
 GSI  C1   S2    aromatic  1.721  0.020  1.721
 GSI  C2   C3    aromatic  1.422  0.020  1.422
 GSI  C3   C4    aromatic  1.361  0.020  1.361
 GSI  S2   C4    aromatic  1.728  0.020  1.728
 GSI  C4   C5    single    1.494  0.020  1.494
 GSI  C5   C6    single    1.526  0.020  1.526
 GSI  C6   S1    single    1.799  0.020  1.799
 GSI  S1   O2    double    1.454  0.020  1.454
 GSI  S1   O1    double    1.456  0.020  1.456
 GSI  S1   N1    single    1.643  0.020  1.643
 GSI  N1   C12   single    1.440  0.020  1.440
 GSI  C12  C13   single    1.525  0.020  1.525
 GSI  C12  C50   single    1.526  0.020  1.526
 GSI  C13  C14   single    1.526  0.020  1.526
 GSI  C14  N2    single    1.461  0.020  1.461
 GSI  C50  O3    double    1.213  0.020  1.213
 GSI  C50  N2    single    1.353  0.020  1.353
 GSI  N2   C15   single    1.402  0.020  1.402
 GSI  C15  C21   aromatic  1.390  0.020  1.390
 GSI  C15  C22   aromatic  1.389  0.020  1.389
 GSI  C21  C24   aromatic  1.385  0.020  1.385
 GSI  C24  C27   aromatic  1.389  0.020  1.389
 GSI  C27  C26   aromatic  1.389  0.020  1.389
 GSI  C27  N4    single    1.411  0.020  1.411
 GSI  C26  C22   aromatic  1.379  0.020  1.379
 GSI  C22  F1    single    1.333  0.020  1.333
 GSI  N4   C9    aromatic  1.376  0.020  1.376
 GSI  N4   C8    aromatic  1.366  0.020  1.366
 GSI  C9   C7    aromatic  1.359  0.020  1.359
 GSI  C7   N3    aromatic  1.368  0.020  1.368
 GSI  N3   C8    aromatic  1.305  0.020  1.305
 GSI  C8   C10   single    1.498  0.020  1.498
 GSI  C10  N5    single    1.444  0.020  1.444
 GSI  N5   C11   single    1.448  0.020  1.448
 GSI  N5   C16   single    1.448  0.020  1.448
 GSI  C2   H2    single    0.930  0.020  1.080
 GSI  C3   H3    single    0.930  0.020  1.080
 GSI  C5   H5C1  single    0.970  0.020  1.090
 GSI  C5   H5C2  single    0.970  0.020  1.090
 GSI  C6   H6C1  single    0.970  0.020  1.090
 GSI  C6   H6C2  single    0.970  0.020  1.090
 GSI  N1   H1    single    0.890  0.020  1.040
 GSI  C12  H12   single    0.970  0.020  1.090
 GSI  C13  H131  single    0.970  0.020  1.090
 GSI  C13  H132  single    0.970  0.020  1.090
 GSI  C14  H141  single    0.970  0.020  1.090
 GSI  C14  H142  single    0.970  0.020  1.090
 GSI  C21  H21   single    0.930  0.020  1.080
 GSI  C24  H24   single    0.930  0.020  1.080
 GSI  C26  H26   single    0.930  0.020  1.080
 GSI  C9   H9    single    0.930  0.020  1.080
 GSI  C7   H7    single    0.930  0.020  1.080
 GSI  C10  H101  single    0.970  0.020  1.090
 GSI  C10  H102  single    0.970  0.020  1.090
 GSI  C11  H111  single    0.970  0.020  1.090
 GSI  C11  H112  single    0.970  0.020  1.090
 GSI  C11  H113  single    0.970  0.020  1.090
 GSI  C16  H161  single    0.970  0.020  1.090
 GSI  C16  H162  single    0.970  0.020  1.090
 GSI  C16  H163  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
 GSI  S2    C1   C2    112.47  3.000
 GSI  S2    C1   CL1   120.34  3.000
 GSI  C2    C1   CL1   127.19  3.000
 GSI  H2    C2   C3    124.46  3.000
 GSI  H2    C2   C1    123.95  3.000
 GSI  C3    C2   C1    111.59  3.000
 GSI  H3    C3   C4    122.64  3.000
 GSI  H3    C3   C2    123.68  3.000
 GSI  C4    C3   C2    113.68  3.000
 GSI  C4    S2   C1     91.39  3.000
 GSI  C5    C4   S2    121.05  3.000
 GSI  C5    C4   C3    128.05  3.000
 GSI  S2    C4   C3    110.86  3.000
 GSI  H5C2  C5   H5C1  107.11  3.000
 GSI  H5C2  C5   C6    109.73  3.000
 GSI  H5C1  C5   C6    111.10  3.000
 GSI  H5C2  C5   C4    110.73  3.000
 GSI  H5C1  C5   C4    107.37  3.000
 GSI  C6    C5   C4    110.71  3.000
 GSI  H6C2  C6   H6C1  108.26  3.000
 GSI  H6C2  C6   S1    106.52  3.000
 GSI  H6C1  C6   S1    105.22  3.000
 GSI  H6C2  C6   C5    111.86  3.000
 GSI  H6C1  C6   C5    110.92  3.000
 GSI  S1    C6   C5    113.66  3.000
 GSI  N1    S1   O1    106.83  3.000
 GSI  N1    S1   O2    105.39  3.000
 GSI  O1    S1   O2    120.06  3.000
 GSI  N1    S1   C6    108.73  3.000
 GSI  O1    S1   C6    108.22  3.000
 GSI  O2    S1   C6    107.19  3.000
 GSI  H1    N1   C12   116.69  3.000
 GSI  H1    N1   S1    113.63  3.000
 GSI  C12   N1   S1    123.74  3.000
 GSI  H12   C12  C50   107.27  3.000
 GSI  H12   C12  C13   108.96  3.000
 GSI  C50   C12  C13   103.43  3.000
 GSI  H12   C12  N1    108.97  3.000
 GSI  C50   C12  N1    113.35  3.000
 GSI  C13   C12  N1    114.50  3.000
 GSI  H132  C13  H131  108.47  3.000
 GSI  H132  C13  C14   110.07  3.000
 GSI  H131  C13  C14   112.55  3.000
 GSI  H132  C13  C12   110.02  3.000
 GSI  H131  C13  C12   112.76  3.000
 GSI  C14   C13  C12   102.89  3.000
 GSI  H142  C14  H141  108.43  3.000
 GSI  H142  C14  N2    110.30  3.000
 GSI  H141  C14  N2    110.91  3.000
 GSI  H142  C14  C13   113.02  3.000
 GSI  H141  C14  C13   111.62  3.000
 GSI  N2    C14  C13   102.49  3.000
 GSI  N2    C50  O3    126.58  3.000
 GSI  N2    C50  C12   107.09  3.000
 GSI  O3    C50  C12   126.32  3.000
 GSI  C15   N2   C50   123.23  3.000
 GSI  C15   N2   C14   122.87  3.000
 GSI  C50   N2   C14   113.44  3.000
 GSI  C22   C15  C21   117.99  3.000
 GSI  C22   C15  N2    120.61  3.000
 GSI  C21   C15  N2    121.39  3.000
 GSI  H21   C21  C24   119.45  3.000
 GSI  H21   C21  C15   119.54  3.000
 GSI  C24   C21  C15   121.01  3.000
 GSI  H24   C24  C27   120.42  3.000
 GSI  H24   C24  C21   119.94  3.000
 GSI  C27   C24  C21   119.64  3.000
 GSI  N4    C27  C26   119.83  3.000
 GSI  N4    C27  C24   119.80  3.000
 GSI  C26   C27  C24   120.37  3.000
 GSI  H26   C26  C22   119.66  3.000
 GSI  H26   C26  C27   121.53  3.000
 GSI  C22   C26  C27   118.81  3.000
 GSI  F1    C22  C26   118.71  3.000
 GSI  F1    C22  C15   119.17  3.000
 GSI  C26   C22  C15   122.12  3.000
 GSI  C8    N4   C9    107.25  3.000
 GSI  C8    N4   C27   127.84  3.000
 GSI  C9    N4   C27   124.91  3.000
 GSI  H9    C9   C7    132.61  3.000
 GSI  H9    C9   N4    122.07  3.000
 GSI  C7    C9   N4    105.29  3.000
 GSI  H7    C7   N3    121.88  3.000
 GSI  H7    C7   C9    127.74  3.000
 GSI  N3    C7   C9    110.38  3.000
 GSI  C8    N3   C7    106.30  3.000
 GSI  C10   C8   N3    126.17  3.000
 GSI  C10   C8   N4    123.05  3.000
 GSI  N3    C8   N4    110.77  3.000
 GSI  H102  C10  H101  105.74  3.000
 GSI  H102  C10  N5    108.05  3.000
 GSI  H101  C10  N5    112.16  3.000
 GSI  H102  C10  C8    108.93  3.000
 GSI  H101  C10  C8    109.41  3.000
 GSI  N5    C10  C8    112.29  3.000
 GSI  C16   N5   C11   110.98  3.000
 GSI  C16   N5   C10   110.51  3.000
 GSI  C11   N5   C10   112.25  3.000
 GSI  H113  C11  H112  108.15  3.000
 GSI  H113  C11  H111  107.72  3.000
 GSI  H112  C11  H111  107.57  3.000
 GSI  H113  C11  N5    112.99  3.000
 GSI  H112  C11  N5    110.72  3.000
 GSI  H111  C11  N5    109.51  3.000
 GSI  H163  C16  H162  107.88  3.000
 GSI  H163  C16  H161  107.71  3.000
 GSI  H162  C16  H161  107.76  3.000
 GSI  H163  C16  N5    109.76  3.000
 GSI  H162  C16  N5    110.19  3.000
 GSI  H161  C16  N5    113.36  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
 GSI  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 GSI  CONST_02  C3    C4   S2   C1      0.00   0.0  0
 GSI  CONST_03  C4    S2   C1   C2      0.00   0.0  0
 GSI  CONST_04  S2    C4   C3   C2      0.00   0.0  0
 GSI  CONST_05  S2    C1   C2   C3      0.00   0.0  0
 GSI  CONST_06  C27   C24  C21  C15     0.00   0.0  0
 GSI  CONST_07  C27   C26  C22  C15     0.00   0.0  0
 GSI  CONST_08  C26   C22  C15  C21     0.00   0.0  0
 GSI  CONST_09  C26   C27  C24  C21     0.00   0.0  0
 GSI  CONST_10  N4    C27  C24  C21   180.00   0.0  0
 GSI  CONST_11  C22   C15  C21  C24     0.00   0.0  0
 GSI  CONST_12  C22   C26  C27  C24     0.00   0.0  0
 GSI  CONST_15  C7    C9   N4   C27   180.00   0.0  0
 GSI  CONST_16  N3    C8   N4   C27   180.00   0.0  0
 GSI  CONST_19  N4    C27  C26  C22   180.00   0.0  0
 GSI  CONST_20  N3    C7   C9   N4      0.00   0.0  0
 GSI  CONST_21  C7    N3   C8   N4      0.00   0.0  0
 GSI  CONST_22  N3    C8   N4   C9      0.00   0.0  0
 GSI  CONST_23  C8    N3   C7   C9      0.00   0.0  0
 GSI  CONST_24  C8    N4   C9   C7      0.00   0.0  0
 GSI  CONST_25  C24   C21  C15  N2    180.00   0.0  0
 GSI  CONST_26  C26   C22  C15  N2    180.00   0.0  0
 GSI  CONST_27  C14   N2   C50  C12     0.00   0.0  0
 GSI  CONST_28  C15   N2   C50  C12   180.00   0.0  0
 GSI  CONST_29  C3    C2   C1   CL1   180.00   0.0  0
 GSI  CONST_30  C4    S2   C1   CL1   180.00   0.0  0
 GSI  CONST_31  C5    C4   S2   C1    180.00   0.0  0
 GSI  CONST_32  C5    C4   C3   C2    180.00   0.0  0
 GSI  CONST_33  F1    C22  C15  N2      0.00   0.0  0
 GSI  CONST_34  F1    C22  C15  C21   180.00   0.0  0
 GSI  CONST_35  F1    C22  C26  C27   180.00   0.0  0
 GSI  CONST_36  C10   C8   N4   C27     0.00   0.0  0
 GSI  CONST_37  C10   C8   N4   C9    180.00   0.0  0
 GSI  CONST_38  C10   C8   N3   C7    180.00   0.0  0
 GSI  CONST_39  O3    C50  N2   C14   180.00   0.0  0
 GSI  CONST_40  C15   N2   C50  O3      0.00   0.0  0
 GSI  CONST_41  H3    C3   C2   C1    180.00   0.0  0
 GSI  CONST_42  H2    C2   C1   S2    180.00   0.0  0
 GSI  CONST_43  H21   C21  C15  N2      0.00   0.0  0
 GSI  CONST_44  H24   C24  C21  C15   180.00   0.0  0
 GSI  CONST_45  H26   C26  C22  C15   180.00   0.0  0
 GSI  CONST_46  H9    C9   N4   C27     0.00   0.0  0
 GSI  CONST_47  H7    C7   C9   N4    180.00   0.0  0
 GSI  Var_01    N2    C14  C13  C12   -31.05  30.0  1
 GSI  Var_02    C50   N2   C14  C13    21.13  30.0  1
 GSI  Var_03    C21   C15  N2   C14   -52.20  30.0  2
 GSI  Var_04    C6    C5   C4   C3    -99.15  30.0  2
 GSI  Var_05    N5    C10  C8   N4   -153.92  30.0  2
 GSI  Var_06    S1    C6   C5   C4    174.04  30.0  3
 GSI  Var_07    C12   N1   S1   C6     74.88  30.0  3
 GSI  Var_08    C11   N5   C10  C8     68.67  30.0  3
 GSI  Var_09    O2    S1   C6   C5    162.00  30.0  3
 GSI  Var_10    H111  C11  N5   C10  -179.39  30.0  3
 GSI  Var_11    H161  C16  N5   C10   -63.28  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
 GSI  chir_01  C12  N1  C13  C50  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
 GSI  plan-1  CL1  0.020
 GSI  plan-1  C1   0.020
 GSI  plan-1  C2   0.020
 GSI  plan-1  C3   0.020
 GSI  plan-1  S2   0.020
 GSI  plan-1  C4   0.020
 GSI  plan-1  C5   0.020
 GSI  plan-1  H2   0.020
 GSI  plan-1  H3   0.020
 GSI  plan-2  C27  0.020
 GSI  plan-2  N4   0.020
 GSI  plan-2  C9   0.020
 GSI  plan-2  C7   0.020
 GSI  plan-2  N3   0.020
 GSI  plan-2  C8   0.020
 GSI  plan-2  C10  0.020
 GSI  plan-2  H9   0.020
 GSI  plan-2  H7   0.020
 GSI  plan-3  N2   0.020
 GSI  plan-3  C15  0.020
 GSI  plan-3  C21  0.020
 GSI  plan-3  C24  0.020
 GSI  plan-3  C27  0.020
 GSI  plan-3  C26  0.020
 GSI  plan-3  C22  0.020
 GSI  plan-3  F1   0.020
 GSI  plan-3  N4   0.020
 GSI  plan-3  H21  0.020
 GSI  plan-3  H24  0.020
 GSI  plan-3  H26  0.020
 GSI  plan-4  C12  0.020
 GSI  plan-4  C14  0.020
 GSI  plan-4  C50  0.020
 GSI  plan-4  O3   0.020
 GSI  plan-4  N2   0.020
 GSI  plan-4  C15  0.020

