# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 14:50:02 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-({4-[(5-chloro-1H-indol-2-yl)sulfonyl]piperazin-1-yl}carbonyl)thieno[3,2-b]pyridine 4-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][n+]1cccc2sc(cc12)C(=O)N3CCN(CC3)[S](=O)(=O)c4[nH]c5ccc(Cl)cc5c4
#
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
 D01  D01  '2-({4-[(5-chloro-1H-indol-2-yl)sulfonyl]piperazin-1-yl}carbonyl)thieno[3,2-b]pyridine 4-oxide'  ligand  48  31  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D01
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
 D01  N1    N   NR15   0  -0.712  -2.9194   0.0079  -1.4145
 D01  C1    C   CR56   0   0.369  -3.5614   1.0246  -0.7769
 D01  C2    C   CR16   0  -0.298  -3.7252   2.3590  -1.1503
 D01  C3    C   CR16   0  -0.232  -4.4335   3.1760  -0.2990
 D01  C4    C   CR6    0  -0.047  -4.9692   2.6691   0.8987
 D01  CL1   CL  CL     0  -0.134  -5.8553   3.7562   1.9241
 D01  C5    C   CR16   0  -0.294  -4.8196   1.3573   1.2786
 D01  C6    C   CR56   0   0.059  -4.1011   0.5122   0.4224
 D01  C7    C   CR15   0  -0.363  -3.7638  -0.8700   0.4771
 D01  C8    C   CR5    0   0.089  -3.0586  -1.1264  -0.6641
 D01  S1    S   S      0   1.372  -2.2730  -2.6230  -1.1200
 D01  O1    O   OS     0  -0.635  -2.9737  -3.6973  -0.4459
 D01  O2    O   OS     0  -0.645  -2.1401  -2.6131  -2.5655
 D01  N2    N   N      0  -0.568  -0.7477  -2.5653  -0.4917
 D01  C9    C   CH2    0  -0.311  -0.6358  -2.6110   0.9678
 D01  C10   C   CH2    0  -0.325   0.7926  -2.9758   1.3362
 D01  N3    N   NT     0  -0.456   1.7340  -2.0499   0.7335
 D01  C11   C   C      0   0.542   2.3113  -1.0860   1.4819
 D01  O3    O   O      0  -0.453   2.0890  -0.9172   2.6680
 D01  C12   C   CR5    0  -0.347   3.3191  -0.2209   0.8026
 D01  C13   C   CR15   0  -0.163   3.3055   1.1326   0.7868
 D01  C14   C   CR56   0   0.393   4.4578   1.6481   0.1342
 D01  C15   C   CR56   0  -0.258   5.3455   0.6665  -0.3130
 D01  S2    S   S2     0   0.282   4.7363  -0.9045   0.0651
 D01  C16   C   CR16   0  -0.142   6.5313   0.9948  -0.9585
 D01  C17   C   CR16   0  -0.369   6.7682   2.3424  -1.1346
 D01  C18   C   CR16   0  -0.044   5.8704   3.3023  -0.6874
 D01  N4    N   NR6    1  -0.089   4.7270   2.9727  -0.0601
 D01  O4    O   O     -1  -0.561   3.9075   3.8496   0.3486
 D01  C19   C   CH2    0  -0.327   1.6104  -2.0046  -0.7132
 D01  C20   C   CH2    0  -0.305   0.1908  -1.6287  -1.1106
 D01  HN1   H   HNR5   0   0.425  -2.5126   0.0578  -2.3355
 D01  H2    H   HCR6   0   0.282  -3.3110   2.7450  -2.0717
 D01  H3    H   HCR6   0   0.282  -4.5792   4.2173  -0.5516
 D01  H5    H   HCR6   0   0.280  -5.2406   0.9861   2.2032
 D01  H7    H   HCR5   0   0.286  -4.0091  -1.5760   1.2536
 D01  H91   H   HCH2   0   0.289  -1.3035  -3.3710   1.3677
 D01  H92   H   HCH2   0   0.254  -0.9049  -1.6459   1.4148
 D01  H101  H   HCH2   0   0.274   1.0214  -3.9798   0.9720
 D01  H102  H   HCH2   0   0.287   0.9027  -2.9747   2.4169
 D01  H13   H   HCR5   0   0.299   2.5142   1.7347   1.2063
 D01  H16   H   HCR6   0   0.293   7.2261   0.2432  -1.3046
 D01  H17   H   HCR6   0   0.297   7.6654   2.6848  -1.6298
 D01  H18   H   HCR6   0   0.315   6.0386   4.3607  -0.8164
 D01  H191  H   HCH2   0   0.291   2.2870  -1.2723  -1.1449
 D01  H192  H   HCH2   0   0.274   1.8679  -2.9823  -1.1245
 D01  H201  H   HCH2   0   0.293   0.1123  -1.6848  -2.1937
 D01  H202  H   HCH2   0   0.250  -0.0136  -0.5961  -0.8006

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
 D01  N1   C1    aromatic  1.361  0.020  1.361
 D01  N1   C8    aromatic  1.367  0.020  1.367
 D01  N1   HN1   single    0.860  0.020  1.020
 D01  C1   C2    aromatic  1.395  0.020  1.395
 D01  C1   C6    aromatic  1.411  0.020  1.411
 D01  C2   C3    aromatic  1.376  0.020  1.376
 D01  C2   H2    single    0.930  0.020  1.080
 D01  C3   C4    aromatic  1.407  0.020  1.407
 D01  C3   H3    single    0.930  0.020  1.080
 D01  C4   CL1   single    1.737  0.020  1.737
 D01  C4   C5    aromatic  1.374  0.020  1.374
 D01  C5   C6    aromatic  1.401  0.020  1.401
 D01  C5   H5    single    0.930  0.020  1.080
 D01  C6   C7    aromatic  1.424  0.020  1.424
 D01  C7   C8    aromatic  1.366  0.020  1.366
 D01  C7   H7    single    0.930  0.020  1.080
 D01  C8   S1    single    1.751  0.020  1.751
 D01  S1   O1    double    1.449  0.020  1.449
 D01  S1   O2    double    1.452  0.020  1.452
 D01  S1   N2    single    1.651  0.020  1.651
 D01  N2   C9    single    1.464  0.020  1.464
 D01  N2   C20   single    1.463  0.020  1.463
 D01  C9   C10   single    1.520  0.020  1.520
 D01  C9   H91   single    0.970  0.020  1.090
 D01  C9   H92   single    0.970  0.020  1.090
 D01  C10  N3    single    1.451  0.020  1.451
 D01  C10  H101  single    0.970  0.020  1.090
 D01  C10  H102  single    0.970  0.020  1.090
 D01  N3   C11   single    1.350  0.020  1.350
 D01  N3   C19   single    1.453  0.020  1.453
 D01  C11  O3    double    1.219  0.020  1.219
 D01  C11  C12   single    1.492  0.020  1.492
 D01  C12  C13   aromatic  1.354  0.020  1.354
 D01  C12  S2    aromatic  1.738  0.020  1.738
 D01  C13  C14   aromatic  1.421  0.020  1.421
 D01  C13  H13   single    0.930  0.020  1.080
 D01  C14  C15   aromatic  1.397  0.020  1.397
 D01  C14  N4    aromatic  1.366  0.020  1.366
 D01  C15  S2    aromatic  1.727  0.020  1.727
 D01  C15  C16   aromatic  1.389  0.020  1.389
 D01  C16  C17   aromatic  1.380  0.020  1.380
 D01  C16  H16   single    0.930  0.020  1.080
 D01  C17  C18   aromatic  1.388  0.020  1.388
 D01  C17  H17   single    0.930  0.020  1.080
 D01  C18  N4    aromatic  1.345  0.020  1.345
 D01  C18  H18   single    0.930  0.020  1.080
 D01  N4   O4    single    1.268  0.020  1.268
 D01  C19  C20   single    1.521  0.020  1.521
 D01  C19  H191  single    0.970  0.020  1.090
 D01  C19  H192  single    0.970  0.020  1.090
 D01  C20  H201  single    0.970  0.020  1.090
 D01  C20  H202  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
 D01  HN1   N1   C8    125.71  3.000
 D01  HN1   N1   C1    125.55  3.000
 D01  C8    N1   C1    108.33  3.000
 D01  C6    C1   C2    121.99  3.000
 D01  C6    C1   N1    107.89  3.000
 D01  C2    C1   N1    130.12  3.000
 D01  H2    C2   C3    120.81  3.000
 D01  H2    C2   C1    121.63  3.000
 D01  C3    C2   C1    117.56  3.000
 D01  H3    C3   C4    119.65  3.000
 D01  H3    C3   C2    119.77  3.000
 D01  C4    C3   C2    120.58  3.000
 D01  C5    C4   CL1   119.33  3.000
 D01  C5    C4   C3    122.55  3.000
 D01  CL1   C4   C3    118.12  3.000
 D01  H5    C5   C6    120.99  3.000
 D01  H5    C5   C4    121.45  3.000
 D01  C6    C5   C4    117.56  3.000
 D01  C7    C6   C5    133.12  3.000
 D01  C7    C6   C1    107.13  3.000
 D01  C5    C6   C1    119.76  3.000
 D01  H7    C7   C8    126.62  3.000
 D01  H7    C7   C6    127.57  3.000
 D01  C8    C7   C6    105.81  3.000
 D01  S1    C8   C7    127.58  3.000
 D01  S1    C8   N1    121.37  3.000
 D01  C7    C8   N1    110.82  3.000
 D01  N2    S1   O2    107.11  3.000
 D01  N2    S1   O1    107.20  3.000
 D01  O2    S1   O1    120.83  3.000
 D01  N2    S1   C8    106.60  3.000
 D01  O2    S1   C8    107.13  3.000
 D01  O1    S1   C8    107.20  3.000
 D01  C20   N2   C9    113.11  3.000
 D01  C20   N2   S1    117.00  3.000
 D01  C9    N2   S1    116.67  3.000
 D01  H92   C9   H91   108.32  3.000
 D01  H92   C9   C10   110.06  3.000
 D01  H91   C9   C10   108.67  3.000
 D01  H92   C9   N2    111.09  3.000
 D01  H91   C9   N2    109.95  3.000
 D01  C10   C9   N2    108.72  3.000
 D01  H102  C10  H101  108.14  3.000
 D01  H102  C10  N3    110.29  3.000
 D01  H101  C10  N3    108.18  3.000
 D01  H102  C10  C9    109.65  3.000
 D01  H101  C10  C9    109.68  3.000
 D01  N3    C10  C9    110.85  3.000
 D01  C19   N3   C11   124.49  3.000
 D01  C19   N3   C10   112.23  3.000
 D01  C11   N3   C10   120.17  3.000
 D01  C12   C11  O3    119.09  3.000
 D01  C12   C11  N3    116.78  3.000
 D01  O3    C11  N3    124.09  3.000
 D01  S2    C12  C13   113.37  3.000
 D01  S2    C12  C11   121.07  3.000
 D01  C13   C12  C11   125.33  3.000
 D01  H13   C13  C14   124.79  3.000
 D01  H13   C13  C12   124.11  3.000
 D01  C14   C13  C12   111.10  3.000
 D01  N4    C14  C15   120.71  3.000
 D01  N4    C14  C13   125.25  3.000
 D01  C15   C14  C13   114.04  3.000
 D01  C16   C15  S2    128.15  3.000
 D01  C16   C15  C14   121.67  3.000
 D01  S2    C15  C14   110.18  3.000
 D01  C15   S2   C12    91.30  3.000
 D01  H16   C16  C17   121.88  3.000
 D01  H16   C16  C15   122.23  3.000
 D01  C17   C16  C15   115.89  3.000
 D01  H17   C17  C18   117.74  3.000
 D01  H17   C17  C16   120.71  3.000
 D01  C18   C17  C16   121.55  3.000
 D01  H18   C18  N4    115.37  3.000
 D01  H18   C18  C17   122.59  3.000
 D01  N4    C18  C17   122.04  3.000
 D01  O4    N4   C18   122.02  3.000
 D01  O4    N4   C14   119.83  3.000
 D01  C18   N4   C14   118.14  3.000
 D01  H192  C19  H191  107.88  3.000
 D01  H192  C19  C20   110.06  3.000
 D01  H191  C19  C20   108.11  3.000
 D01  H192  C19  N3    109.11  3.000
 D01  H191  C19  N3    111.33  3.000
 D01  C20   C19  N3    110.32  3.000
 D01  H202  C20  H201  108.45  3.000
 D01  H202  C20  C19   109.42  3.000
 D01  H201  C20  C19   108.35  3.000
 D01  H202  C20  N2    111.31  3.000
 D01  H201  C20  N2    110.00  3.000
 D01  C19   C20  N2    109.26  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
 D01  CONST_01  C3   C2   C1   N1   180.00   0.0  0
 D01  CONST_02  C5   C6   C1   N1   180.00   0.0  0
 D01  CONST_03  C7   C6   C1   N1     0.00   0.0  0
 D01  CONST_04  C6   C7   C8   N1     0.00   0.0  0
 D01  CONST_05  C7   C8   N1   C1     0.00   0.0  0
 D01  CONST_06  C4   C3   C2   C1     0.00   0.0  0
 D01  CONST_07  C4   C5   C6   C1     0.00   0.0  0
 D01  CONST_08  C8   C7   C6   C1     0.00   0.0  0
 D01  CONST_09  C8   N1   C1   C2   180.00   0.0  0
 D01  CONST_10  C5   C6   C1   C2     0.00   0.0  0
 D01  CONST_11  C7   C6   C1   C2   180.00   0.0  0
 D01  CONST_12  C5   C4   C3   C2     0.00   0.0  0
 D01  CONST_13  C6   C1   C2   C3     0.00   0.0  0
 D01  CONST_14  C6   C5   C4   C3     0.00   0.0  0
 D01  CONST_15  C7   C6   C5   C4   180.00   0.0  0
 D01  CONST_16  C8   C7   C6   C5   180.00   0.0  0
 D01  CONST_17  C8   N1   C1   C6     0.00   0.0  0
 D01  CONST_18  C15  C14  C13  C12    0.00   0.0  0
 D01  CONST_19  N4   C14  C13  C12  180.00   0.0  0
 D01  CONST_20  C14  C15  S2   C12    0.00   0.0  0
 D01  CONST_21  C16  C15  S2   C12  180.00   0.0  0
 D01  CONST_22  C15  S2   C12  C13    0.00   0.0  0
 D01  CONST_23  S2   C15  C14  C13    0.00   0.0  0
 D01  CONST_24  C16  C15  C14  C13  180.00   0.0  0
 D01  CONST_25  C18  N4   C14  C13  180.00   0.0  0
 D01  CONST_26  S2   C12  C13  C14    0.00   0.0  0
 D01  CONST_27  C17  C16  C15  C14    0.00   0.0  0
 D01  CONST_28  C17  C18  N4   C14    0.00   0.0  0
 D01  CONST_29  C18  N4   C14  C15    0.00   0.0  0
 D01  CONST_30  C18  C17  C16  C15    0.00   0.0  0
 D01  CONST_31  N4   C14  C15  S2   180.00   0.0  0
 D01  CONST_32  C17  C16  C15  S2   180.00   0.0  0
 D01  CONST_33  N4   C14  C15  C16    0.00   0.0  0
 D01  CONST_34  N4   C18  C17  C16    0.00   0.0  0
 D01  CONST_35  S1   C8   N1   C1   180.00   0.0  0
 D01  CONST_36  CL1  C4   C3   C2   180.00   0.0  0
 D01  CONST_37  C6   C5   C4   CL1  180.00   0.0  0
 D01  CONST_38  S1   C8   C7   C6   180.00   0.0  0
 D01  CONST_39  C14  C13  C12  C11  180.00   0.0  0
 D01  CONST_40  C15  S2   C12  C11  180.00   0.0  0
 D01  CONST_41  O4   N4   C14  C13    0.00   0.0  0
 D01  CONST_42  O4   N4   C14  C15  180.00   0.0  0
 D01  CONST_43  O4   N4   C18  C17  180.00   0.0  0
 D01  CONST_44  C12  C11  N3   C10  180.00   0.0  0
 D01  CONST_46  H2   C2   C1   N1     0.00   0.0  0
 D01  CONST_47  H7   C7   C8   N1   180.00   0.0  0
 D01  CONST_48  H3   C3   C2   C1   180.00   0.0  0
 D01  CONST_49  H5   C5   C6   C1   180.00   0.0  0
 D01  CONST_50  HN1  N1   C1   C2     0.00   0.0  0
 D01  CONST_51  H16  C16  C15  C14  180.00   0.0  0
 D01  CONST_52  H18  C18  N4   C14  180.00   0.0  0
 D01  CONST_53  H13  C13  C14  C15  180.00   0.0  0
 D01  CONST_54  H17  C17  C16  C15  180.00   0.0  0
 D01  CONST_55  O3   C11  N3   C10    0.00   0.0  0
 D01  Var_01    N3   C10  C9   N2    55.73  30.0  1
 D01  Var_02    N3   C19  C20  N2   -55.52  30.0  1
 D01  Var_03    C19  C20  N2   C9    57.32  30.0  1
 D01  Var_04    C19  N3   C10  C9   -57.61  30.0  1
 D01  Var_05    C20  N2   C9   C10  -57.14  30.0  1
 D01  Var_06    C20  C19  N3   C10   57.18  30.0  1
 D01  Var_07    N2   S1   C8   N1    85.59  30.0  2
 D01  Var_08    C9   N2   S1   C8    67.57  30.0  3
 D01  Var_09    C13  C12  C11  N3   127.42  30.0  2

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
 D01  plan-1  N1   0.020
 D01  plan-1  C1   0.020
 D01  plan-1  C2   0.020
 D01  plan-1  C3   0.020
 D01  plan-1  C4   0.020
 D01  plan-1  CL1  0.020
 D01  plan-1  C5   0.020
 D01  plan-1  C6   0.020
 D01  plan-1  C7   0.020
 D01  plan-1  C8   0.020
 D01  plan-1  S1   0.020
 D01  plan-1  HN1  0.020
 D01  plan-1  H2   0.020
 D01  plan-1  H3   0.020
 D01  plan-1  H5   0.020
 D01  plan-1  H7   0.020
 D01  plan-2  C11  0.020
 D01  plan-2  C12  0.020
 D01  plan-2  C13  0.020
 D01  plan-2  C14  0.020
 D01  plan-2  C15  0.020
 D01  plan-2  S2   0.020
 D01  plan-2  C16  0.020
 D01  plan-2  C17  0.020
 D01  plan-2  C18  0.020
 D01  plan-2  N4   0.020
 D01  plan-2  O4   0.020
 D01  plan-2  H13  0.020
 D01  plan-2  H16  0.020
 D01  plan-2  H17  0.020
 D01  plan-2  H18  0.020
 D01  plan-3  C10  0.020
 D01  plan-3  N3   0.020
 D01  plan-3  C11  0.020
 D01  plan-3  O3   0.020
 D01  plan-3  C12  0.020
 D01  plan-3  C19  0.020

