# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 03:30:28 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: N-{4-[(3,5-difluorophenyl)sulfonyl]benzyl}imidazo[1,2-a]pyridine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(F)cc(c1)[S](=O)(=O)c2ccc(CNC(=O)c3ccn4ccnc4c3)cc2
#
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
 1XD  1XD  N-{4-[(3,5-difluorophenyl)sulfonyl]benzyl}imidazo[1,2-a]pyridine-7-carboxamide  ligand  45  30  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1XD
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
 1XD  C4   C  CR16  0  -0.216  -1.0008   0.8394  -0.3077
 1XD  C5   C  CR16  0  -0.276   0.1349   0.0729  -0.1042
 1XD  C6   C  CR6   0   0.088   0.2576  -0.7334   1.0236
 1XD  C7   C  CH2   0  -0.275   1.4734  -1.5988   1.2303
 1XD  C13  C  CR16  0   0.062   5.8391   1.6029  -0.3794
 1XD  C15  C  CR15  0  -0.022   8.2672   1.5198  -0.8832
 1XD  C24  C  CR16  0  -0.413  -5.6037   0.0972   0.7614
 1XD  C26  C  CR16  0  -0.412  -6.5428  -1.2717  -1.0067
 1XD  C28  C  CR16  0  -0.414  -4.6600   0.1820  -1.4792
 1XD  C1   C  CR16  0  -0.289  -0.7753  -0.7546   1.9568
 1XD  C2   C  CR16  0  -0.169  -1.9151   0.0085   1.7718
 1XD  C3   C  CR6   0  -0.223  -2.0194   0.7965   0.6335
 1XD  N8   N  NH1   0  -0.655   2.6924  -0.9179   0.8723
 1XD  C9   C  C     0   0.553   3.6406  -1.4507   0.0771
 1XD  O10  O  O     0  -0.494   3.5610  -2.5658  -0.4142
 1XD  C11  C  CR6   0   0.273   4.8273  -0.5781  -0.1727
 1XD  C12  C  CR16  0  -0.484   4.7438   0.8435  -0.1414
 1XD  N14  N  N     0  -0.538   7.0315   0.9948  -0.6361
 1XD  C16  C  CR15  0  -0.197   9.0850   0.4342  -1.0649
 1XD  N17  N  N     0  -0.406   8.4068  -0.7303  -0.9411
 1XD  C18  C  CR56  0   0.551   7.1618  -0.3854  -0.6841
 1XD  C19  C  CR16  0  -0.489   6.0218  -1.1778  -0.4596
 1XD  S20  S  S     0   1.187  -3.4758   1.7724   0.3977
 1XD  O21  O  OS    0  -0.467  -3.9112   2.2711   1.6961
 1XD  O22  O  OS    0  -0.649  -3.2356   2.7002  -0.7004
 1XD  C23  C  CR6   0   0.026  -4.6822   0.5820  -0.1512
 1XD  C25  C  CR6   0   0.425  -6.5207  -0.8299   0.3010
 1XD  C27  C  CR6   0   0.475  -5.5995  -0.7498  -1.8728
 1XD  F29  F  F     0  -0.272  -5.6039  -1.1649  -3.1399
 1XD  F30  F  F     0  -0.288  -7.4268  -1.3111   1.1530
 1XD  H1   H  HCR6  0   0.260  -1.0774   1.4623  -1.1882
 1XD  H2   H  HCR6  0   0.244   0.9319   0.1119  -0.8354
 1XD  H3   H  HCH2  0   0.249   1.5157  -1.9349   2.2689
 1XD  H4   H  HCH2  0   0.253   1.3915  -2.4942   0.6137
 1XD  H6   H  HCR5  0   0.286   8.4515   2.5800  -0.9061
 1XD  H7   H  HCR6  0   0.285  -5.6223   0.4236   1.7920
 1XD  H8   H  HCR6  0   0.293  -7.2718  -1.9974  -1.3432
 1XD  H9   H  HCR6  0   0.288  -3.9456   0.5741  -2.1907
 1XD  H10  H  HCR6  0   0.235  -0.6893  -1.3662   2.8462
 1XD  H11  H  HCR6  0   0.273  -2.7003  -0.0141   2.5156
 1XD  H12  H  HNH1  0   0.370   2.9021  -0.0740   1.3814
 1XD  H13  H  HCR6  0   0.225   3.8081   1.3534   0.0382
 1XD  H14  H  HCR5  0   0.231  10.1427   0.4541  -1.2791
 1XD  H15  H  HCR6  0   0.251   6.1227  -2.2533  -0.5026
 1XD  H5   H  HCR6  0   0.264   5.8277   2.6821  -0.3832

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
 1XD  F30  C25  single    1.334  0.020  1.334
 1XD  C25  C24  aromatic  1.383  0.020  1.383
 1XD  C25  C26  aromatic  1.380  0.020  1.380
 1XD  C24  C23  aromatic  1.385  0.020  1.385
 1XD  C26  C27  aromatic  1.383  0.020  1.383
 1XD  O22  S20  double    1.457  0.020  1.457
 1XD  C23  C28  aromatic  1.387  0.020  1.387
 1XD  C23  S20  single    1.782  0.020  1.782
 1XD  C27  C28  aromatic  1.380  0.020  1.380
 1XD  C27  F29  single    1.333  0.020  1.333
 1XD  S20  O21  double    1.457  0.020  1.457
 1XD  S20  C3   single    1.769  0.020  1.769
 1XD  C4   C3   aromatic  1.388  0.020  1.388
 1XD  C4   C5   aromatic  1.385  0.020  1.385
 1XD  C3   C2   aromatic  1.388  0.020  1.388
 1XD  C5   C6   aromatic  1.392  0.020  1.392
 1XD  C2   C1   aromatic  1.384  0.020  1.384
 1XD  C6   C1   aromatic  1.392  0.020  1.392
 1XD  C6   C7   single    1.507  0.020  1.507
 1XD  C7   N8   single    1.441  0.020  1.441
 1XD  O10  C9   double    1.221  0.020  1.221
 1XD  N8   C9   single    1.347  0.020  1.347
 1XD  C9   C11  single    1.494  0.020  1.494
 1XD  C11  C19  aromatic  1.367  0.020  1.367
 1XD  C11  C12  aromatic  1.424  0.020  1.424
 1XD  C19  C18  aromatic  1.406  0.020  1.406
 1XD  C12  C13  aromatic  1.354  0.020  1.354
 1XD  C18  N17  aromatic  1.317  0.020  1.317
 1XD  C18  N14  aromatic  1.387  0.020  1.387
 1XD  C13  N14  aromatic  1.363  0.020  1.363
 1XD  N17  C16  aromatic  1.353  0.020  1.353
 1XD  N14  C15  aromatic  1.365  0.020  1.365
 1XD  C16  C15  aromatic  1.371  0.020  1.371
 1XD  C4   H1   single    0.930  0.020  1.080
 1XD  C5   H2   single    0.930  0.020  1.080
 1XD  C7   H3   single    0.970  0.020  1.090
 1XD  C7   H4   single    0.970  0.020  1.090
 1XD  C13  H5   single    0.930  0.020  1.080
 1XD  C15  H6   single    0.930  0.020  1.080
 1XD  C24  H7   single    0.930  0.020  1.080
 1XD  C26  H8   single    0.930  0.020  1.080
 1XD  C28  H9   single    0.930  0.020  1.080
 1XD  C1   H10  single    0.930  0.020  1.080
 1XD  C2   H11  single    0.930  0.020  1.080
 1XD  N8   H12  single    0.860  0.020  1.020
 1XD  C12  H13  single    0.930  0.020  1.080
 1XD  C16  H14  single    0.930  0.020  1.080
 1XD  C19  H15  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
 1XD  H1   C4   C3   121.21  3.000
 1XD  H1   C4   C5   119.77  3.000
 1XD  C3   C4   C5   119.02  3.000
 1XD  H2   C5   C6   120.23  3.000
 1XD  H2   C5   C4   118.98  3.000
 1XD  C6   C5   C4   120.79  3.000
 1XD  C1   C6   C7   119.87  3.000
 1XD  C7   C6   C5   121.00  3.000
 1XD  C1   C6   C5   119.12  3.000
 1XD  H4   C7   H3   106.73  3.000
 1XD  H4   C7   N8   108.13  3.000
 1XD  H3   C7   N8   110.41  3.000
 1XD  H4   C7   C6   109.48  3.000
 1XD  H3   C7   C6   109.78  3.000
 1XD  N8   C7   C6   112.15  3.000
 1XD  H5   C13  N14  117.05  3.000
 1XD  H5   C13  C12  123.57  3.000
 1XD  N14  C13  C12  119.38  3.000
 1XD  H6   C15  C16  132.44  3.000
 1XD  H6   C15  N14  122.52  3.000
 1XD  C16  C15  N14  105.03  3.000
 1XD  H7   C24  C25  120.55  3.000
 1XD  H7   C24  C23  122.28  3.000
 1XD  C25  C24  C23  117.17  3.000
 1XD  H8   C26  C27  121.19  3.000
 1XD  H8   C26  C25  121.32  3.000
 1XD  C27  C26  C25  117.49  3.000
 1XD  H9   C28  C27  120.44  3.000
 1XD  H9   C28  C23  122.39  3.000
 1XD  C27  C28  C23  117.18  3.000
 1XD  H10  C1   C2   119.12  3.000
 1XD  H10  C1   C6   120.02  3.000
 1XD  C2   C1   C6   120.86  3.000
 1XD  H11  C2   C3   121.41  3.000
 1XD  H11  C2   C1   119.62  3.000
 1XD  C3   C2   C1   118.97  3.000
 1XD  S20  C3   C2   118.97  3.000
 1XD  C2   C3   C4   121.24  3.000
 1XD  S20  C3   C4   119.79  3.000
 1XD  H12  N8   C9   118.88  3.000
 1XD  H12  N8   C7   116.50  3.000
 1XD  C9   N8   C7   123.71  3.000
 1XD  C11  C9   O10  121.19  3.000
 1XD  C11  C9   N8   115.26  3.000
 1XD  O10  C9   N8   123.55  3.000
 1XD  C19  C11  C12  119.58  3.000
 1XD  C12  C11  C9   122.19  3.000
 1XD  C19  C11  C9   118.23  3.000
 1XD  H13  C12  C11  121.69  3.000
 1XD  H13  C12  C13  117.71  3.000
 1XD  C11  C12  C13  120.56  3.000
 1XD  C18  N14  C15  106.93  3.000
 1XD  C15  N14  C13  130.88  3.000
 1XD  C18  N14  C13  122.19  3.000
 1XD  H14  C16  N17  121.68  3.000
 1XD  H14  C16  C15  126.59  3.000
 1XD  N17  C16  C15  111.73  3.000
 1XD  C18  N17  C16  105.44  3.000
 1XD  C19  C18  N17  130.53  3.000
 1XD  N17  C18  N14  110.86  3.000
 1XD  C19  C18  N14  118.61  3.000
 1XD  H15  C19  C18  118.58  3.000
 1XD  H15  C19  C11  121.76  3.000
 1XD  C18  C19  C11  119.65  3.000
 1XD  C23  S20  O22  107.75  3.000
 1XD  C23  S20  O21  107.51  3.000
 1XD  O22  S20  O21  120.17  3.000
 1XD  O21  S20  C3   108.42  3.000
 1XD  C23  S20  C3   103.29  3.000
 1XD  O22  S20  C3   108.42  3.000
 1XD  S20  C23  C28  118.48  3.000
 1XD  S20  C23  C24  118.79  3.000
 1XD  C28  C23  C24  122.73  3.000
 1XD  F30  C25  C26  118.61  3.000
 1XD  C26  C25  C24  122.72  3.000
 1XD  F30  C25  C24  118.67  3.000
 1XD  F29  C27  C28  118.90  3.000
 1XD  F29  C27  C26  118.39  3.000
 1XD  C28  C27  C26  122.71  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
 1XD  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 1XD  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 1XD  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 1XD  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 1XD  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 1XD  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 1XD  CONST_07  C19  C11  C12  C13     0.00   0.0  0
 1XD  CONST_08  C19  C18  N14  C13     0.00   0.0  0
 1XD  CONST_09  N17  C18  N14  C13   180.00   0.0  0
 1XD  CONST_10  C16  C15  N14  C13   180.00   0.0  0
 1XD  CONST_11  C19  C18  N14  C15   180.00   0.0  0
 1XD  CONST_12  N17  C18  N14  C15     0.00   0.0  0
 1XD  CONST_13  C12  C13  N14  C15   180.00   0.0  0
 1XD  CONST_14  C18  N17  C16  C15     0.00   0.0  0
 1XD  CONST_15  C27  C26  C25  C24     0.00   0.0  0
 1XD  CONST_16  C27  C28  C23  C24     0.00   0.0  0
 1XD  CONST_17  C23  C24  C25  C26     0.00   0.0  0
 1XD  CONST_18  C23  C28  C27  C26     0.00   0.0  0
 1XD  CONST_19  C25  C24  C23  C28     0.00   0.0  0
 1XD  CONST_20  C25  C26  C27  C28     0.00   0.0  0
 1XD  CONST_21  N17  C18  C19  C11   180.00   0.0  0
 1XD  CONST_22  N14  C18  C19  C11     0.00   0.0  0
 1XD  CONST_23  N14  C13  C12  C11     0.00   0.0  0
 1XD  CONST_24  C18  C19  C11  C12     0.00   0.0  0
 1XD  CONST_25  C18  N14  C13  C12     0.00   0.0  0
 1XD  CONST_26  C16  N17  C18  N14     0.00   0.0  0
 1XD  CONST_27  N17  C16  C15  N14     0.00   0.0  0
 1XD  CONST_28  C19  C18  N17  C16   180.00   0.0  0
 1XD  CONST_29  C18  N14  C15  C16     0.00   0.0  0
 1XD  CONST_30  C7   C6   C5   C4    180.00   0.0  0
 1XD  CONST_31  S20  C3   C4   C5    180.00   0.0  0
 1XD  CONST_32  C2   C1   C6   C7    180.00   0.0  0
 1XD  CONST_33  C9   C11  C12  C13   180.00   0.0  0
 1XD  CONST_34  S20  C3   C2   C1    180.00   0.0  0
 1XD  CONST_35  C18  C19  C11  C9    180.00   0.0  0
 1XD  CONST_36  C25  C24  C23  S20   180.00   0.0  0
 1XD  CONST_37  C27  C28  C23  S20   180.00   0.0  0
 1XD  CONST_38  F30  C25  C24  C23   180.00   0.0  0
 1XD  CONST_39  F29  C27  C28  C23   180.00   0.0  0
 1XD  CONST_40  F29  C27  C26  C25   180.00   0.0  0
 1XD  CONST_41  F30  C25  C26  C27   180.00   0.0  0
 1XD  CONST_42  H11  C2   C3   C4    180.00   0.0  0
 1XD  CONST_43  H10  C1   C6   C5    180.00   0.0  0
 1XD  CONST_44  H1   C4   C5   C6    180.00   0.0  0
 1XD  CONST_45  H6   C15  N14  C13     0.00   0.0  0
 1XD  CONST_46  H5   C13  N14  C15     0.00   0.0  0
 1XD  CONST_47  H8   C26  C25  C24   180.00   0.0  0
 1XD  CONST_48  H9   C28  C23  C24   180.00   0.0  0
 1XD  CONST_49  H7   C24  C25  C26   180.00   0.0  0
 1XD  CONST_50  H2   C5   C6   C1    180.00   0.0  0
 1XD  CONST_51  H15  C19  C11  C12   180.00   0.0  0
 1XD  CONST_52  H13  C12  C13  N14   180.00   0.0  0
 1XD  CONST_53  H14  C16  C15  N14   180.00   0.0  0
 1XD  CONST_54  C11  C9   N8   C7    180.00   0.0  0
 1XD  CONST_55  H12  N8   C9   C11     0.00   0.0  0
 1XD  CONST_56  O10  C9   N8   C7      0.00   0.0  0
 1XD  Var_01    C23  S20  C3   C4    103.31  30.0  1
 1XD  Var_02    C3   S20  C23  C24   100.55  30.0  2
 1XD  Var_03    N8   C7   C6   C5     41.50  30.0  2
 1XD  Var_04    C19  C11  C9   N8    153.08  30.0  2
 1XD  Var_05    C9   N8   C7   C6   -130.94  30.0  3

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
 1XD  plan-1  C4   0.020
 1XD  plan-1  C5   0.020
 1XD  plan-1  C6   0.020
 1XD  plan-1  C7   0.020
 1XD  plan-1  C1   0.020
 1XD  plan-1  C2   0.020
 1XD  plan-1  C3   0.020
 1XD  plan-1  S20  0.020
 1XD  plan-1  H1   0.020
 1XD  plan-1  H2   0.020
 1XD  plan-1  H10  0.020
 1XD  plan-1  H11  0.020
 1XD  plan-2  C24  0.020
 1XD  plan-2  C26  0.020
 1XD  plan-2  C28  0.020
 1XD  plan-2  S20  0.020
 1XD  plan-2  C23  0.020
 1XD  plan-2  C25  0.020
 1XD  plan-2  C27  0.020
 1XD  plan-2  F29  0.020
 1XD  plan-2  F30  0.020
 1XD  plan-2  H7   0.020
 1XD  plan-2  H8   0.020
 1XD  plan-2  H9   0.020
 1XD  plan-3  C13  0.020
 1XD  plan-3  C15  0.020
 1XD  plan-3  C9   0.020
 1XD  plan-3  C11  0.020
 1XD  plan-3  C12  0.020
 1XD  plan-3  N14  0.020
 1XD  plan-3  C16  0.020
 1XD  plan-3  N17  0.020
 1XD  plan-3  C18  0.020
 1XD  plan-3  C19  0.020
 1XD  plan-3  H6   0.020
 1XD  plan-3  H13  0.020
 1XD  plan-3  H14  0.020
 1XD  plan-3  H15  0.020
 1XD  plan-3  H5   0.020
 1XD  plan-4  C7   0.020
 1XD  plan-4  N8   0.020
 1XD  plan-4  C9   0.020
 1XD  plan-4  O10  0.020
 1XD  plan-4  C11  0.020
 1XD  plan-4  H12  0.020

