# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 03:10:13 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: ~{N}-[2-chloranyl-5-(3,6-dihydro-2~{H}-pyran-4-yl)pyridin-3-yl]methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)Nc1cc(cnc1Cl)C2=CCOCC2
#
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
 HKK  HKK  ~{N}-[2-chloranyl-5-(3,6-dihydro-2~{H}-pyran-4-yl)pyridin-3-yl]methanesulfonamide  ligand  31  18  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HKK
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
 HKK  N1   N   N     0  -0.377   0.2991  -2.3299   0.2470
 HKK  C4   C   CR16  0  -0.109  -0.9613  -1.9191   0.2006
 HKK  C5   C   CR6   0   0.109   1.2510  -1.4667   0.0149
 HKK  C6   C   C     0   0.080  -2.7399  -0.1804  -0.1272
 HKK  C7   C   C1    0  -0.336  -3.0924   1.0555   0.2349
 HKK  C8   C   CH2   0  -0.193  -4.4971   1.5563   0.1481
 HKK  C10  C   CH2   0  -0.523  -3.7953  -1.1527  -0.5812
 HKK  CL   CL  CL    0  -0.082   2.8794  -2.0565   0.0997
 HKK  C1   C   CR6   0   0.290   1.0249  -0.1287  -0.3138
 HKK  N    N   NC1   0  -0.824   2.0648   0.7670  -0.6110
 HKK  S    S   S     0   1.319   2.4596   1.9766   0.4704
 HKK  O    O   OS    0  -0.655   3.4873   2.7612  -0.1877
 HKK  O1   O   OS    0  -0.647   1.2141   2.5997   0.8795
 HKK  C    C   CH3   0  -0.795   3.1697   1.1631   1.8799
 HKK  C3   C   CR6   0   0.021  -1.3313  -0.6086  -0.0957
 HKK  C2   C   CR16  0  -0.191  -0.2970   0.2812  -0.3799
 HKK  C9   C   CH2   0  -0.188  -5.1761  -0.6506  -0.1975
 HKK  O2   O   O2    0  -0.482  -5.3473   0.7000  -0.5689
 HKK  H1   H   HCR6  0   0.277  -1.7056  -2.6739   0.4210
 HKK  H2   H   H     0   0.256  -2.3613   1.7574   0.6226
 HKK  H3   H   HCH2  0   0.222  -4.8802   1.7405   1.1642
 HKK  H4   H   HCH2  0   0.249  -4.5066   2.5230  -0.3635
 HKK  H5   H   HCH2  0   0.258  -3.7191  -1.3027  -1.6631
 HKK  H6   H   HCH2  0   0.253  -3.6480  -2.1367  -0.1296
 HKK  H7   H   HNC1  0   0.421   2.8829   0.3674  -1.0592
 HKK  H8   H   HCH3  0   0.298   4.0733   0.6425   1.5728
 HKK  H9   H   HCH3  0   0.313   3.4103   1.9297   2.6150
 HKK  H10  H   HCH3  0   0.294   2.4493   0.4652   2.3013
 HKK  H11  H   HCR6  0   0.287  -0.5167   1.2925  -0.6920
 HKK  H12  H   HCH2  0   0.243  -5.9510  -1.2243  -0.7063
 HKK  H13  H   HCH2  0   0.210  -5.3245  -0.7768   0.8834

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
 HKK  O1   S    double    1.452  0.020  1.452
 HKK  O    S    double    1.451  0.020  1.451
 HKK  S    C    single    1.776  0.020  1.776
 HKK  S    N    single    1.670  0.020  1.670
 HKK  N    C1   single    1.404  0.020  1.404
 HKK  CL   C5   single    1.734  0.020  1.734
 HKK  C1   C2   aromatic  1.385  0.020  1.385
 HKK  C1   C5   aromatic  1.396  0.020  1.396
 HKK  C2   C3   aromatic  1.394  0.020  1.394
 HKK  C5   N1   aromatic  1.306  0.020  1.306
 HKK  N1   C4   aromatic  1.326  0.020  1.326
 HKK  C3   C4   aromatic  1.394  0.020  1.394
 HKK  C3   C6   single    1.473  0.020  1.473
 HKK  C7   C6   double    1.335  0.020  1.335
 HKK  C7   C8   single    1.494  0.020  1.494
 HKK  C6   C10  single    1.505  0.020  1.505
 HKK  C8   O2   single    1.404  0.020  1.404
 HKK  C10  C9   single    1.519  0.020  1.519
 HKK  O2   C9   single    1.411  0.020  1.411
 HKK  C4   H1   single    0.930  0.020  1.080
 HKK  C7   H2   single    0.930  0.020  1.080
 HKK  C8   H3   single    0.970  0.020  1.090
 HKK  C8   H4   single    0.970  0.020  1.090
 HKK  C10  H5   single    0.970  0.020  1.090
 HKK  C10  H6   single    0.970  0.020  1.090
 HKK  N    H7   single    0.890  0.020  1.040
 HKK  C    H8   single    0.970  0.020  1.090
 HKK  C    H9   single    0.970  0.020  1.090
 HKK  C    H10  single    0.970  0.020  1.090
 HKK  C2   H11  single    0.930  0.020  1.080
 HKK  C9   H12  single    0.970  0.020  1.090
 HKK  C9   H13  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
 HKK  C5   N1   C4   118.80  3.000
 HKK  H1   C4   C3   121.09  3.000
 HKK  H1   C4   N1   115.48  3.000
 HKK  C3   C4   N1   123.43  3.000
 HKK  C1   C5   CL   119.32  3.000
 HKK  C1   C5   N1   123.86  3.000
 HKK  CL   C5   N1   116.81  3.000
 HKK  C3   C6   C10  119.30  3.000
 HKK  C10  C6   C7   119.65  3.000
 HKK  C3   C6   C7   121.05  3.000
 HKK  H2   C7   C8   115.95  3.000
 HKK  H2   C7   C6   121.18  3.000
 HKK  C8   C7   C6   122.87  3.000
 HKK  H4   C8   H3   106.30  3.000
 HKK  H4   C8   O2   107.16  3.000
 HKK  H3   C8   O2   111.26  3.000
 HKK  H4   C8   C7   109.37  3.000
 HKK  H3   C8   C7   109.24  3.000
 HKK  O2   C8   C7   113.25  3.000
 HKK  H6   C10  H5   106.00  3.000
 HKK  H6   C10  C9   108.41  3.000
 HKK  H5   C10  C9   110.99  3.000
 HKK  H6   C10  C6   111.26  3.000
 HKK  H5   C10  C6   109.74  3.000
 HKK  C9   C10  C6   110.35  3.000
 HKK  C2   C1   N    120.51  3.000
 HKK  C2   C1   C5   116.70  3.000
 HKK  N    C1   C5   122.76  3.000
 HKK  H7   N    S    112.38  3.000
 HKK  H7   N    C1   116.06  3.000
 HKK  S    N    C1   120.00  3.000
 HKK  C    S    O1   108.43  3.000
 HKK  C    S    O    108.94  3.000
 HKK  O1   S    O    120.23  3.000
 HKK  C    S    N    106.07  3.000
 HKK  O    S    N    105.39  3.000
 HKK  O1   S    N    106.90  3.000
 HKK  H10  C    H9   109.66  3.000
 HKK  H10  C    H8   110.64  3.000
 HKK  H9   C    H8   110.13  3.000
 HKK  H10  C    S    109.66  3.000
 HKK  H9   C    S    107.56  3.000
 HKK  H8   C    S    109.12  3.000
 HKK  C2   C3   C6   121.33  3.000
 HKK  C6   C3   C4   122.14  3.000
 HKK  C2   C3   C4   116.53  3.000
 HKK  H11  C2   C3   120.35  3.000
 HKK  H11  C2   C1   118.98  3.000
 HKK  C3   C2   C1   120.63  3.000
 HKK  H13  C9   H12  107.62  3.000
 HKK  H13  C9   O2   110.65  3.000
 HKK  H12  C9   O2   107.13  3.000
 HKK  H13  C9   C10  109.49  3.000
 HKK  H12  C9   C10  110.76  3.000
 HKK  O2   C9   C10  111.12  3.000
 HKK  C9   O2   C8   112.08  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
 HKK  CONST_01  C2   C1   C5   N1    0.00   0.0  0
 HKK  CONST_02  C2   C3   C4   N1    0.00   0.0  0
 HKK  CONST_03  C1   C5   N1   C4    0.00   0.0  0
 HKK  CONST_04  C1   C2   C3   C4    0.00   0.0  0
 HKK  CONST_05  C3   C2   C1   C5    0.00   0.0  0
 HKK  CONST_06  C3   C4   N1   C5    0.00   0.0  0
 HKK  CONST_07  C6   C3   C4   N1  180.00   0.0  0
 HKK  CONST_08  C1   C2   C3   C6  180.00   0.0  0
 HKK  CONST_09  N    C1   C5   N1  180.00   0.0  0
 HKK  CONST_10  CL   C5   N1   C4  180.00   0.0  0
 HKK  CONST_11  C2   C1   C5   CL  180.00   0.0  0
 HKK  CONST_12  C3   C2   C1   N   180.00   0.0  0
 HKK  CONST_13  H11  C2   C3   C4  180.00   0.0  0
 HKK  CONST_14  H1   C4   N1   C5  180.00   0.0  0
 HKK  Var_01    C7   C6   C3   C4  147.01  30.0  2
 HKK  Var_02    O2   C8   C7   C6  -10.97  30.0  1
 HKK  Var_03    O2   C9   C10  C6   48.54  30.0  1
 HKK  Var_04    C9   C10  C6   C7  -15.12  30.0  1
 HKK  Var_05    C3   C6   C7   C8  176.57  30.0  1
 HKK  Var_06    C10  C9   O2   C8  -65.72  30.0  1
 HKK  Var_07    O1   S    N    C1  -46.86  30.0  1
 HKK  Var_08    H8   C    S    N    62.16  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
 HKK  plan-1  N1   0.020
 HKK  plan-1  C4   0.020
 HKK  plan-1  C5   0.020
 HKK  plan-1  C6   0.020
 HKK  plan-1  CL   0.020
 HKK  plan-1  C1   0.020
 HKK  plan-1  N    0.020
 HKK  plan-1  C3   0.020
 HKK  plan-1  C2   0.020
 HKK  plan-1  H1   0.020
 HKK  plan-1  H11  0.020
 HKK  plan-2  C1   0.020
 HKK  plan-2  N    0.020
 HKK  plan-2  S    0.020
 HKK  plan-2  H7   0.020

