# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 12:08:11 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 1-(5-chloro-6-methoxypyridin-3-yl)-3-methyl-N-(methylsulfonyl)-1H-indazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(cc1Cl)n2nc(C)c3cc(ccc23)C(=O)N[S](C)(=O)=O
#
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
 6LK  6LK  1-(5-chloro-6-methoxypyridin-3-yl)-3-methyl-N-(methylsulfonyl)-1H-indazole-5-carboxamide  ligand  41  26  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6LK
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
 6LK  C5   C   CR16  0  -0.086  -2.8989   0.9552   1.0166
 6LK  C6   C   CR6   0   0.224  -2.7716  -0.2113   0.2881
 6LK  C7   C   CR16  0  -0.120  -3.8512  -0.6294  -0.4915
 6LK  C8   C   CR6   0  -0.195  -4.9871   0.1400  -0.5037
 6LK  C13  C   CH3   0  -0.740  -0.1643  -4.2463   0.4483
 6LK  C15  C   CR16  0  -0.355   1.8643  -1.6347   0.2339
 6LK  C17  C   CR16  0  -0.287   1.6396   0.7736   0.0526
 6LK  C20  C   C     0   0.591   3.9296  -0.3330   0.0624
 6LK  C26  C   CH3   0  -0.792   6.8244   0.0690  -1.5749
 6LK  C1   C   CH3   0  -0.418  -6.1660   3.2585   0.9611
 6LK  C3   C   CR6   0   0.593  -5.0174   1.3285   0.2476
 6LK  N4   N   N     0  -0.453  -3.9947   1.7059   0.9772
 6LK  CL9  CL  CL    0  -0.089  -6.3577  -0.3183  -1.4367
 6LK  N10  N   NR5   0  -0.527  -1.5960  -0.9736   0.3264
 6LK  N11  N   N     0  -0.259  -1.6749  -2.3213   0.3989
 6LK  C12  C   CR5   0   0.266  -0.4595  -2.7923   0.3830
 6LK  C14  C   CR56  0  -0.102   0.4781  -1.7173   0.2926
 6LK  C16  C   CR6   0  -0.044   2.4483  -0.3849   0.1085
 6LK  C18  C   CR16  0  -0.280   0.2682   0.7136   0.1222
 6LK  C19  C   CR56  0   0.460  -0.3066  -0.5544   0.2497
 6LK  O21  O   O     0  -0.437   4.6301  -1.2642   0.4008
 6LK  N22  N   NC1   0  -0.851   4.4815   0.8365  -0.4052
 6LK  S23  S   S     0   1.358   6.1296   1.1683  -0.3739
 6LK  O24  O   OS    0  -0.640   6.6480   0.8409   0.9383
 6LK  O25  O   OS    0  -0.654   6.2202   2.5328  -0.8607
 6LK  H1   H   HCR6  0   0.292  -2.1007   1.3000   1.6633
 6LK  H2   H   HCR6  0   0.308  -3.7947  -1.5393  -1.0733
 6LK  H3   H   HCH3  0   0.258   0.2882  -4.5921  -0.4822
 6LK  H4   H   HCH3  0   0.256   0.5403  -4.4646   1.2513
 6LK  H5   H   HCH3  0   0.261  -1.0720  -4.8209   0.6199
 6LK  H6   H   HCR6  0   0.271   2.4751  -2.5272   0.2738
 6LK  H7   H   HCR6  0   0.267   2.0875   1.7555  -0.0245
 6LK  H8   H   HCH3  0   0.302   6.3821   0.2835  -2.5443
 6LK  H9   H   HCH3  0   0.314   7.8962   0.2605  -1.5999
 6LK  H10  H   HCH3  0   0.301   6.6362  -0.9597  -1.2812
 6LK  H11  H   HCH3  0   0.236  -5.3929   3.9605   0.6480
 6LK  H12  H   HCH3  0   0.253  -7.1450   3.6898   0.7725
 6LK  H13  H   HCH3  0   0.237  -6.0547   3.0607   2.0274
 6LK  H14  H   HCR6  0   0.288  -0.3232   1.6174   0.0809
 6LK  H15  H   HNC1  0   0.448   3.9169   1.5488  -0.8495
 6LK  O2   O   O2    0  -0.455  -6.1217   2.0567   0.1984

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
 6LK  C1   O2   single    1.424  0.020  1.424
 6LK  O2   C3   single    1.324  0.020  1.324
 6LK  N4   C3   aromatic  1.312  0.020  1.312
 6LK  N4   C5   aromatic  1.329  0.020  1.329
 6LK  C3   C8   aromatic  1.406  0.020  1.406
 6LK  C5   C6   aromatic  1.381  0.020  1.381
 6LK  O21  C20  double    1.213  0.020  1.213
 6LK  C17  C18  aromatic  1.374  0.020  1.374
 6LK  C17  C16  aromatic  1.414  0.020  1.414
 6LK  C18  C19  aromatic  1.398  0.020  1.398
 6LK  C8   CL9  single    1.720  0.020  1.720
 6LK  C8   C7   aromatic  1.372  0.020  1.372
 6LK  C6   C7   aromatic  1.396  0.020  1.396
 6LK  C6   N10  single    1.402  0.020  1.402
 6LK  C20  C16  single    1.483  0.020  1.483
 6LK  C20  N22  single    1.375  0.020  1.375
 6LK  O24  S23  double    1.448  0.020  1.448
 6LK  C16  C15  aromatic  1.385  0.020  1.385
 6LK  C19  N10  aromatic  1.358  0.020  1.358
 6LK  C19  C14  aromatic  1.404  0.020  1.404
 6LK  C26  S23  single    1.770  0.020  1.770
 6LK  N10  N11  aromatic  1.352  0.020  1.352
 6LK  S23  N22  single    1.681  0.020  1.681
 6LK  S23  O25  double    1.452  0.020  1.452
 6LK  C15  C14  aromatic  1.390  0.020  1.390
 6LK  C14  C12  aromatic  1.429  0.020  1.429
 6LK  N11  C12  aromatic  1.304  0.020  1.304
 6LK  C12  C13  single    1.485  0.020  1.485
 6LK  C5   H1   single    0.930  0.020  1.080
 6LK  C7   H2   single    0.930  0.020  1.080
 6LK  C13  H3   single    0.970  0.020  1.090
 6LK  C13  H4   single    0.970  0.020  1.090
 6LK  C13  H5   single    0.970  0.020  1.090
 6LK  C15  H6   single    0.930  0.020  1.080
 6LK  C17  H7   single    0.930  0.020  1.080
 6LK  C26  H8   single    0.970  0.020  1.090
 6LK  C26  H9   single    0.970  0.020  1.090
 6LK  C26  H10  single    0.970  0.020  1.090
 6LK  C1   H11  single    0.970  0.020  1.090
 6LK  C1   H12  single    0.970  0.020  1.090
 6LK  C1   H13  single    0.970  0.020  1.090
 6LK  C18  H14  single    0.930  0.020  1.080
 6LK  N22  H15  single    0.860  0.020  1.020

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
 6LK  H1   C5   N4   116.44  3.000
 6LK  H1   C5   C6   121.04  3.000
 6LK  N4   C5   C6   122.51  3.000
 6LK  N10  C6   C7   120.08  3.000
 6LK  N10  C6   C5   121.48  3.000
 6LK  C7   C6   C5   118.44  3.000
 6LK  H2   C7   C8   120.68  3.000
 6LK  H2   C7   C6   120.80  3.000
 6LK  C8   C7   C6   118.52  3.000
 6LK  CL9  C8   C3   119.85  3.000
 6LK  CL9  C8   C7   121.00  3.000
 6LK  C3   C8   C7   119.14  3.000
 6LK  H5   C13  H4   108.49  3.000
 6LK  H5   C13  H3   108.25  3.000
 6LK  H4   C13  H3   107.25  3.000
 6LK  H5   C13  C12  110.99  3.000
 6LK  H4   C13  C12  110.91  3.000
 6LK  H3   C13  C12  110.81  3.000
 6LK  H6   C15  C16  120.63  3.000
 6LK  H6   C15  C14  120.82  3.000
 6LK  C16  C15  C14  118.55  3.000
 6LK  H7   C17  C18  117.14  3.000
 6LK  H7   C17  C16  120.64  3.000
 6LK  C18  C17  C16  122.20  3.000
 6LK  N22  C20  O21  121.05  3.000
 6LK  N22  C20  C16  116.18  3.000
 6LK  O21  C20  C16  122.76  3.000
 6LK  H10  C26  H9   110.07  3.000
 6LK  H10  C26  H8   110.95  3.000
 6LK  H9   C26  H8   110.20  3.000
 6LK  H10  C26  S23  109.67  3.000
 6LK  H9   C26  S23  107.02  3.000
 6LK  H8   C26  S23  108.83  3.000
 6LK  H13  C1   H12  109.50  3.000
 6LK  H13  C1   H11  108.98  3.000
 6LK  H12  C1   H11  109.48  3.000
 6LK  H13  C1   O2   111.56  3.000
 6LK  H12  C1   O2   105.68  3.000
 6LK  H11  C1   O2   111.56  3.000
 6LK  N4   C3   O2   120.85  3.000
 6LK  N4   C3   C8   121.56  3.000
 6LK  O2   C3   C8   117.58  3.000
 6LK  C3   N4   C5   119.79  3.000
 6LK  C19  N10  N11  111.48  3.000
 6LK  N11  N10  C6   119.65  3.000
 6LK  C19  N10  C6   128.82  3.000
 6LK  C12  N11  N10  107.77  3.000
 6LK  C14  C12  N11  109.92  3.000
 6LK  N11  C12  C13  122.58  3.000
 6LK  C14  C12  C13  127.50  3.000
 6LK  C19  C14  C12  104.97  3.000
 6LK  C12  C14  C15  134.56  3.000
 6LK  C19  C14  C15  120.46  3.000
 6LK  C20  C16  C17  122.78  3.000
 6LK  C20  C16  C15  117.10  3.000
 6LK  C17  C16  C15  120.11  3.000
 6LK  H14  C18  C19  122.48  3.000
 6LK  H14  C18  C17  120.50  3.000
 6LK  C19  C18  C17  117.03  3.000
 6LK  C18  C19  C14  121.63  3.000
 6LK  C14  C19  N10  105.86  3.000
 6LK  C18  C19  N10  132.49  3.000
 6LK  H15  N22  S23  114.60  3.000
 6LK  H15  N22  C20  121.61  3.000
 6LK  S23  N22  C20  123.70  3.000
 6LK  O25  S23  O24  119.60  3.000
 6LK  O25  S23  N22  103.91  3.000
 6LK  O24  S23  N22  108.85  3.000
 6LK  O25  S23  C26  109.37  3.000
 6LK  N22  S23  C26  104.45  3.000
 6LK  O24  S23  C26  109.50  3.000
 6LK  C3   O2   C1   118.06  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
 6LK  CONST_01  C8   C3   N4   C5     0.00   0.0  0
 6LK  CONST_02  C8   C7   C6   C5     0.00   0.0  0
 6LK  CONST_05  C3   N4   C5   C6     0.00   0.0  0
 6LK  CONST_06  C3   C8   C7   C6     0.00   0.0  0
 6LK  CONST_07  C18  C19  N10  C6     0.00   0.0  0
 6LK  CONST_08  C14  C19  N10  C6   180.00   0.0  0
 6LK  CONST_09  C12  N11  N10  C6   180.00   0.0  0
 6LK  CONST_10  N4   C3   C8   C7     0.00   0.0  0
 6LK  CONST_11  N4   C5   C6   C7     0.00   0.0  0
 6LK  CONST_14  N10  C6   C7   C8   180.00   0.0  0
 6LK  CONST_15  C18  C17  C16  C15    0.00   0.0  0
 6LK  CONST_16  C18  C19  C14  C15    0.00   0.0  0
 6LK  CONST_17  N10  C19  C14  C15  180.00   0.0  0
 6LK  CONST_18  N11  C12  C14  C15  180.00   0.0  0
 6LK  CONST_19  N10  C19  C18  C17  180.00   0.0  0
 6LK  CONST_20  C14  C19  C18  C17    0.00   0.0  0
 6LK  CONST_21  C14  C15  C16  C17    0.00   0.0  0
 6LK  CONST_22  N10  C6   C5   N4   180.00   0.0  0
 6LK  CONST_23  C12  C14  C19  N10    0.00   0.0  0
 6LK  CONST_24  C14  C12  N11  N10    0.00   0.0  0
 6LK  CONST_25  C18  C19  N10  N11  180.00   0.0  0
 6LK  CONST_26  C14  C19  N10  N11    0.00   0.0  0
 6LK  CONST_27  C19  C14  C12  N11    0.00   0.0  0
 6LK  CONST_28  C18  C19  C14  C12  180.00   0.0  0
 6LK  CONST_29  C16  C15  C14  C12  180.00   0.0  0
 6LK  CONST_30  C19  N10  N11  C12    0.00   0.0  0
 6LK  CONST_31  C19  C18  C17  C16    0.00   0.0  0
 6LK  CONST_32  C19  C14  C15  C16    0.00   0.0  0
 6LK  CONST_33  O2   C3   N4   C5   180.00   0.0  0
 6LK  CONST_34  CL9  C8   C7   C6   180.00   0.0  0
 6LK  CONST_35  O2   C3   C8   C7   180.00   0.0  0
 6LK  CONST_36  C19  C14  C12  C13  180.00   0.0  0
 6LK  CONST_37  C15  C14  C12  C13    0.00   0.0  0
 6LK  CONST_38  N10  N11  C12  C13  180.00   0.0  0
 6LK  CONST_39  C18  C17  C16  C20  180.00   0.0  0
 6LK  CONST_40  C14  C15  C16  C20  180.00   0.0  0
 6LK  CONST_41  CL9  C8   C3   N4   180.00   0.0  0
 6LK  CONST_42  H2   C7   C6   C5   180.00   0.0  0
 6LK  CONST_43  H1   C5   C6   C7   180.00   0.0  0
 6LK  CONST_44  H7   C17  C16  C15  180.00   0.0  0
 6LK  CONST_45  H6   C15  C16  C17  180.00   0.0  0
 6LK  CONST_46  H14  C18  C19  N10    0.00   0.0  0
 6LK  CONST_47  S23  N22  C20  C16  180.00   0.0  0
 6LK  CONST_48  H15  N22  C20  C16    0.00   0.0  0
 6LK  CONST_49  S23  N22  C20  O21    0.00   0.0  0
 6LK  Var_01    O21  C20  C16  C15  -15.69  30.0  2
 6LK  Var_02    N4   C3   O2   C1    -0.08  30.0  2
 6LK  Var_03    H3   C13  C12  N11  114.00  30.0  2
 6LK  Var_04    H11  C1   O2   C3    60.87  30.0  3
 6LK  Var_05    O24  S23  N22  C20  -47.10  30.0  2
 6LK  Var_06    H8   C26  S23  N22   60.08  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
 6LK  plan-1  C5   0.020
 6LK  plan-1  C6   0.020
 6LK  plan-1  C7   0.020
 6LK  plan-1  C8   0.020
 6LK  plan-1  C3   0.020
 6LK  plan-1  N4   0.020
 6LK  plan-1  CL9  0.020
 6LK  plan-1  N10  0.020
 6LK  plan-1  H1   0.020
 6LK  plan-1  H2   0.020
 6LK  plan-1  O2   0.020
 6LK  plan-2  C6   0.020
 6LK  plan-2  C13  0.020
 6LK  plan-2  C15  0.020
 6LK  plan-2  C17  0.020
 6LK  plan-2  C20  0.020
 6LK  plan-2  N10  0.020
 6LK  plan-2  N11  0.020
 6LK  plan-2  C12  0.020
 6LK  plan-2  C14  0.020
 6LK  plan-2  C16  0.020
 6LK  plan-2  C18  0.020
 6LK  plan-2  C19  0.020
 6LK  plan-2  H6   0.020
 6LK  plan-2  H7   0.020
 6LK  plan-2  H14  0.020
 6LK  plan-3  C20  0.020
 6LK  plan-3  C16  0.020
 6LK  plan-3  O21  0.020
 6LK  plan-3  N22  0.020
 6LK  plan-3  S23  0.020
 6LK  plan-3  H15  0.020

