# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 09:44:46 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: ~{N}-[5-(3,6-dihydro-2~{H}-pyran-4-yl)-2-methoxy-pyridin-3-yl]-2-methyl-1-(phenylmethyl)imidazole-4-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(cc1N[S](=O)(=O)c2cn(Cc3ccccc3)c(C)n2)C4=CCOCC4
#
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
 HKN  HKN  ~{N}-[5-(3,6-dihydro-2~{H}-pyran-4-yl)-2-methoxy-pyridin-3-yl]-2-methyl-1-(phenylmethyl)imidazole-4-sulfonamide  ligand  55  31  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HKN
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
 HKN  N1   N  NC1   0  -0.787  -1.5298   1.8469   1.6655
 HKN  N3   N  N     0  -0.425   1.7509   2.2871   0.7991
 HKN  C4   C  CR16  0  -0.203  -2.8646   0.0215   0.7961
 HKN  C5   C  CR6   0   0.118  -2.0366   1.0975   0.5781
 HKN  C6   C  CR5   0  -0.135   1.0696   1.1804   1.1962
 HKN  C7   C  CR15  0  -0.046   1.3610   0.1037   0.4097
 HKN  C10  C  CR16  0  -0.282   4.7933  -0.6971   0.1330
 HKN  C13  C  CR16  0  -0.241   6.6166  -0.9532  -1.9425
 HKN  C15  C  CR5   0   0.441   2.4717   1.8979  -0.2186
 HKN  C17  C  C     0   0.109  -4.2145  -1.9137  -0.0999
 HKN  C20  C  CH2   0  -0.190  -4.8711  -4.2366  -0.6825
 HKN  C21  C  CH2   0  -0.531  -4.2782  -2.9389  -1.2023
 HKN  S    S  S     0   1.331  -0.1625   1.2484   2.4186
 HKN  O1   O  OS    0  -0.647  -0.4672  -0.1188   2.7983
 HKN  C3   C  CR6   0   0.005  -3.3270  -0.7514  -0.2769
 HKN  O3   O  O2    0  -0.482  -6.0801  -4.0020   0.0058
 HKN  C19  C  CH2   0  -0.188  -5.8825  -3.2526   1.1766
 HKN  C18  C  C1    0  -0.369  -4.9568  -2.0931   0.9955
 HKN  C2   C  CR16  0  -0.111  -2.8940  -0.3629  -1.5370
 HKN  N    N  N     0  -0.452  -2.1066   0.6859  -1.7688
 HKN  C1   C  CR6   0   0.532  -1.6815   1.3963  -0.7526
 HKN  O    O  O2    0  -0.465  -0.8921   2.4471  -0.9453
 HKN  C    C  CH3   0  -0.423  -0.4306   2.7118  -2.2626
 HKN  C16  C  CH3   0  -0.751   3.3921   2.7482  -1.0118
 HKN  N2   N  NR5   0  -0.438   2.2600   0.5768  -0.4912
 HKN  C9   C  CR6   0   0.087   4.3707  -0.5066  -1.1789
 HKN  C14  C  CR16  0  -0.296   5.2936  -0.6325  -2.2124
 HKN  C12  C  CR16  0  -0.264   7.0336  -1.1411  -0.6315
 HKN  C11  C  CR16  0  -0.239   6.1184  -1.0099   0.4045
 HKN  H1   H  HNC1  0   0.416  -1.4512   2.8460   1.5001
 HKN  H2   H  HCR6  0   0.271  -3.1389  -0.2184   1.8149
 HKN  H3   H  HCR5  0   0.326   1.0215  -0.9185   0.4162
 HKN  H4   H  HCH2  0   0.304   2.3673  -1.1274  -1.6361
 HKN  H5   H  HCH2  0   0.289   2.8673   0.3302  -2.4625
 HKN  H7   H  HCR6  0   0.259   7.3233  -1.0463  -2.7568
 HKN  H8   H  HCH2  0   0.241  -5.0959  -4.9167  -1.5048
 HKN  H9   H  HCH2  0   0.208  -4.1443  -4.7356  -0.0267
 HKN  H10  H  HCH2  0   0.253  -4.8648  -2.5640  -2.0476
 HKN  H11  H  HCH2  0   0.249  -3.2774  -3.1422  -1.5928
 HKN  H12  H  HCH2  0   0.246  -6.8635  -2.8906   1.4967
 HKN  H13  H  HCH2  0   0.218  -5.5062  -3.8873   1.9951
 HKN  H14  H  H     0   0.254  -4.9332  -1.3901   1.8207
 HKN  H15  H  HCR6  0   0.268  -3.1995  -0.9131  -2.4191
 HKN  H16  H  HCH3  0   0.251   0.2666   3.5402  -2.1711
 HKN  H17  H  HCH3  0   0.229   0.0813   1.8489  -2.6905
 HKN  H18  H  HCH3  0   0.242  -1.2480   2.9965  -2.9260
 HKN  H19  H  HCH3  0   0.265   4.3899   2.3142  -1.0809
 HKN  H20  H  HCH3  0   0.264   3.0268   2.8928  -2.0302
 HKN  H21  H  HCH3  0   0.277   3.4772   3.7249  -0.5424
 HKN  H22  H  HCR6  0   0.257   4.9772  -0.4744  -3.2368
 HKN  H23  H  HCR6  0   0.259   8.0664  -1.3829  -0.4171
 HKN  H24  H  HCR6  0   0.260   6.4345  -1.1538   1.4295
 HKN  C8   C  CH2   0  -0.366   2.9310  -0.2021  -1.5125
 HKN  O2   O  OS    0  -0.651   0.1979   2.2395   3.4135
 HKN  H6   H  HCR6  0   0.255   4.0949  -0.6013   0.9556

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
 HKN  O1   S    double    1.451  0.020  1.451
 HKN  O2   S    double    1.450  0.020  1.450
 HKN  S    N1   single    1.672  0.020  1.672
 HKN  S    C6   single    1.737  0.020  1.737
 HKN  N1   C5   single    1.415  0.020  1.415
 HKN  C6   N3   aromatic  1.359  0.020  1.359
 HKN  C6   C7   aromatic  1.365  0.020  1.365
 HKN  N3   C15  aromatic  1.306  0.020  1.306
 HKN  C7   N2   aromatic  1.358  0.020  1.358
 HKN  C5   C4   aromatic  1.375  0.020  1.375
 HKN  C5   C1   aromatic  1.409  0.020  1.409
 HKN  O    C    single    1.421  0.020  1.421
 HKN  O    C1   single    1.328  0.020  1.328
 HKN  C15  N2   aromatic  1.365  0.020  1.365
 HKN  C15  C16  single    1.483  0.020  1.483
 HKN  N2   C8   single    1.449  0.020  1.449
 HKN  C10  C11  aromatic  1.388  0.020  1.388
 HKN  C10  C9   aromatic  1.391  0.020  1.391
 HKN  C11  C12  aromatic  1.389  0.020  1.389
 HKN  C4   C3   aromatic  1.401  0.020  1.401
 HKN  C1   N    aromatic  1.311  0.020  1.311
 HKN  C8   C9   single    1.509  0.020  1.509
 HKN  C9   C14  aromatic  1.391  0.020  1.391
 HKN  C12  C13  aromatic  1.389  0.020  1.389
 HKN  N    C2   aromatic  1.332  0.020  1.332
 HKN  C3   C2   aromatic  1.388  0.020  1.388
 HKN  C3   C17  single    1.473  0.020  1.473
 HKN  C14  C13  aromatic  1.388  0.020  1.388
 HKN  C18  C17  double    1.335  0.020  1.335
 HKN  C18  C19  single    1.495  0.020  1.495
 HKN  C17  C21  single    1.507  0.020  1.507
 HKN  C19  O3   single    1.404  0.020  1.404
 HKN  C21  C20  single    1.518  0.020  1.518
 HKN  O3   C20  single    1.411  0.020  1.411
 HKN  N1   H1   single    0.890  0.020  1.040
 HKN  C4   H2   single    0.930  0.020  1.080
 HKN  C7   H3   single    0.930  0.020  1.080
 HKN  C8   H4   single    0.970  0.020  1.090
 HKN  C8   H5   single    0.970  0.020  1.090
 HKN  C10  H6   single    0.930  0.020  1.080
 HKN  C13  H7   single    0.930  0.020  1.080
 HKN  C20  H8   single    0.970  0.020  1.090
 HKN  C20  H9   single    0.970  0.020  1.090
 HKN  C21  H10  single    0.970  0.020  1.090
 HKN  C21  H11  single    0.970  0.020  1.090
 HKN  C19  H12  single    0.970  0.020  1.090
 HKN  C19  H13  single    0.970  0.020  1.090
 HKN  C18  H14  single    0.930  0.020  1.080
 HKN  C2   H15  single    0.930  0.020  1.080
 HKN  C    H16  single    0.970  0.020  1.090
 HKN  C    H17  single    0.970  0.020  1.090
 HKN  C    H18  single    0.970  0.020  1.090
 HKN  C16  H19  single    0.970  0.020  1.090
 HKN  C16  H20  single    0.970  0.020  1.090
 HKN  C16  H21  single    0.970  0.020  1.090
 HKN  C14  H22  single    0.930  0.020  1.080
 HKN  C12  H23  single    0.930  0.020  1.080
 HKN  C11  H24  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
 HKN  H1   N1   S    111.24  3.000
 HKN  H1   N1   C5   115.06  3.000
 HKN  S    N1   C5   116.72  3.000
 HKN  C15  N3   C6   105.17  3.000
 HKN  H2   C4   C3   121.01  3.000
 HKN  H2   C4   C5   118.39  3.000
 HKN  C3   C4   C5   120.60  3.000
 HKN  C1   C5   C4   117.86  3.000
 HKN  C1   C5   N1   121.55  3.000
 HKN  C4   C5   N1   120.56  3.000
 HKN  S    C6   C7   126.00  3.000
 HKN  C7   C6   N3   111.54  3.000
 HKN  S    C6   N3   121.97  3.000
 HKN  H3   C7   N2   122.91  3.000
 HKN  H3   C7   C6   132.68  3.000
 HKN  N2   C7   C6   104.41  3.000
 HKN  H6   C10  C11  119.13  3.000
 HKN  H6   C10  C9   120.54  3.000
 HKN  C11  C10  C9   120.34  3.000
 HKN  H7   C13  C12  120.18  3.000
 HKN  H7   C13  C14  119.74  3.000
 HKN  C12  C13  C14  120.08  3.000
 HKN  N2   C15  C16  122.97  3.000
 HKN  C16  C15  N3   126.03  3.000
 HKN  N2   C15  N3   110.99  3.000
 HKN  C18  C17  C3   122.65  3.000
 HKN  C18  C17  C21  119.03  3.000
 HKN  C3   C17  C21  118.32  3.000
 HKN  H9   C20  H8   107.65  3.000
 HKN  H9   C20  O3   110.56  3.000
 HKN  H8   C20  O3   107.15  3.000
 HKN  H9   C20  C21  109.52  3.000
 HKN  H8   C20  C21  110.81  3.000
 HKN  O3   C20  C21  111.07  3.000
 HKN  H11  C21  H10  106.16  3.000
 HKN  H11  C21  C20  108.70  3.000
 HKN  H10  C21  C20  110.35  3.000
 HKN  H11  C21  C17  110.43  3.000
 HKN  H10  C21  C17  110.76  3.000
 HKN  C20  C21  C17  110.34  3.000
 HKN  O1   S    O2   121.10  3.000
 HKN  O2   S    C6   109.47  3.000
 HKN  O1   S    C6   107.23  3.000
 HKN  C6   S    N1   106.09  3.000
 HKN  O2   S    N1   105.53  3.000
 HKN  O1   S    N1   106.47  3.000
 HKN  C2   C3   C17  121.19  3.000
 HKN  C17  C3   C4   122.83  3.000
 HKN  C2   C3   C4   115.97  3.000
 HKN  C19  O3   C20  112.02  3.000
 HKN  H13  C19  H12  106.23  3.000
 HKN  H13  C19  C18  108.98  3.000
 HKN  H12  C19  C18  109.53  3.000
 HKN  H13  C19  O3   111.10  3.000
 HKN  H12  C19  O3   107.12  3.000
 HKN  C18  C19  O3   113.59  3.000
 HKN  H14  C18  C19  115.10  3.000
 HKN  H14  C18  C17  121.67  3.000
 HKN  C19  C18  C17  123.22  3.000
 HKN  H15  C2   N    115.15  3.000
 HKN  H15  C2   C3   120.59  3.000
 HKN  N    C2   C3   124.26  3.000
 HKN  C1   N    C2   118.92  3.000
 HKN  O    C1   N    120.60  3.000
 HKN  N    C1   C5   122.37  3.000
 HKN  O    C1   C5   117.03  3.000
 HKN  C    O    C1   118.36  3.000
 HKN  H18  C    H17  108.64  3.000
 HKN  H18  C    H16  109.46  3.000
 HKN  H17  C    H16  109.57  3.000
 HKN  H18  C    O    111.67  3.000
 HKN  H17  C    O    111.64  3.000
 HKN  H16  C    O    105.81  3.000
 HKN  H21  C16  H20  108.07  3.000
 HKN  H21  C16  H19  108.27  3.000
 HKN  H20  C16  H19  107.45  3.000
 HKN  H21  C16  C15  109.44  3.000
 HKN  H20  C16  C15  111.55  3.000
 HKN  H19  C16  C15  111.94  3.000
 HKN  C15  N2   C8   126.08  3.000
 HKN  C8   N2   C7   125.94  3.000
 HKN  C15  N2   C7   107.90  3.000
 HKN  C14  C9   C10  119.12  3.000
 HKN  C14  C9   C8   119.14  3.000
 HKN  C10  C9   C8   121.73  3.000
 HKN  H22  C14  C9   119.69  3.000
 HKN  H22  C14  C13  119.73  3.000
 HKN  C9   C14  C13  120.58  3.000
 HKN  H23  C12  C11  120.16  3.000
 HKN  H23  C12  C13  120.26  3.000
 HKN  C11  C12  C13  119.58  3.000
 HKN  H24  C11  C12  120.10  3.000
 HKN  H24  C11  C10  119.60  3.000
 HKN  C12  C11  C10  120.30  3.000
 HKN  H5   C8   H4   106.57  3.000
 HKN  H5   C8   C9   110.29  3.000
 HKN  H4   C8   C9   110.31  3.000
 HKN  H5   C8   N2   108.93  3.000
 HKN  H4   C8   N2   107.25  3.000
 HKN  C9   C8   N2   113.23  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
 HKN  CONST_01  N2   C7   C6   N3      0.00   0.0  0
 HKN  CONST_02  C7   N2   C15  N3      0.00   0.0  0
 HKN  CONST_03  N    C1   C5   C4      0.00   0.0  0
 HKN  CONST_04  N    C2   C3   C4      0.00   0.0  0
 HKN  CONST_05  C2   C3   C4   C5      0.00   0.0  0
 HKN  CONST_06  C2   N    C1   C5      0.00   0.0  0
 HKN  CONST_07  N2   C15  N3   C6      0.00   0.0  0
 HKN  CONST_08  C15  N2   C7   C6      0.00   0.0  0
 HKN  CONST_09  C15  N3   C6   C7      0.00   0.0  0
 HKN  CONST_10  C13  C12  C11  C10     0.00   0.0  0
 HKN  CONST_11  C13  C14  C9   C10     0.00   0.0  0
 HKN  CONST_12  C1   C5   C4   C3      0.00   0.0  0
 HKN  CONST_13  C1   N    C2   C3      0.00   0.0  0
 HKN  CONST_14  C12  C11  C10  C9      0.00   0.0  0
 HKN  CONST_15  C12  C13  C14  C9      0.00   0.0  0
 HKN  CONST_16  C11  C10  C9   C14     0.00   0.0  0
 HKN  CONST_17  C11  C12  C13  C14     0.00   0.0  0
 HKN  CONST_18  C17  C3   C4   C5    180.00   0.0  0
 HKN  CONST_19  N    C2   C3   C17   180.00   0.0  0
 HKN  CONST_20  C3   C4   C5   N1    180.00   0.0  0
 HKN  CONST_21  N    C1   C5   N1    180.00   0.0  0
 HKN  CONST_22  C8   N2   C15  N3    180.00   0.0  0
 HKN  CONST_23  O    C1   C5   C4    180.00   0.0  0
 HKN  CONST_24  C16  C15  N3   C6    180.00   0.0  0
 HKN  CONST_25  C8   N2   C7   C6    180.00   0.0  0
 HKN  CONST_26  C16  C15  N2   C7    180.00   0.0  0
 HKN  CONST_27  C11  C10  C9   C8    180.00   0.0  0
 HKN  CONST_28  C13  C14  C9   C8    180.00   0.0  0
 HKN  CONST_29  S    C6   N3   C15   180.00   0.0  0
 HKN  CONST_30  N2   C7   C6   S     180.00   0.0  0
 HKN  CONST_31  O    C1   N    C2    180.00   0.0  0
 HKN  CONST_32  H3   C7   C6   N3    180.00   0.0  0
 HKN  CONST_33  H15  C2   C3   C4    180.00   0.0  0
 HKN  CONST_34  H23  C12  C11  C10   180.00   0.0  0
 HKN  CONST_35  H22  C14  C9   C10   180.00   0.0  0
 HKN  CONST_36  H24  C11  C12  C13   180.00   0.0  0
 HKN  CONST_37  H2   C4   C3   C17     0.00   0.0  0
 HKN  CONST_38  H7   C13  C14  C9    180.00   0.0  0
 HKN  CONST_39  H6   C10  C9   C14   180.00   0.0  0
 HKN  Var_01    C18  C17  C3   C4     20.38  30.0  2
 HKN  Var_02    O3   C19  C18  C17   -10.69  30.0  1
 HKN  Var_03    O3   C20  C21  C17    50.32  30.0  1
 HKN  Var_04    C3   C17  C21  C20   162.17  30.0  1
 HKN  Var_05    C18  C19  O3   C20    44.02  30.0  1
 HKN  Var_06    C19  C18  C17  C21    -1.49  30.0  1
 HKN  Var_07    C9   C8   N2   C7   -104.26  30.0  2
 HKN  Var_08    N2   C8   C9   C10    32.70  30.0  2
 HKN  Var_09    N3   C6   S    N1     78.69  30.0  2
 HKN  Var_10    C6   S    N1   C5     59.76  30.0  2
 HKN  Var_11    H19  C16  C15  N3    127.17  30.0  2
 HKN  Var_12    H16  C    O    C1   -174.48  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
 HKN  plan-1  N3   0.020
 HKN  plan-1  C6   0.020
 HKN  plan-1  C7   0.020
 HKN  plan-1  C15  0.020
 HKN  plan-1  S    0.020
 HKN  plan-1  C16  0.020
 HKN  plan-1  N2   0.020
 HKN  plan-1  H3   0.020
 HKN  plan-1  C8   0.020
 HKN  plan-2  N1   0.020
 HKN  plan-2  C4   0.020
 HKN  plan-2  C5   0.020
 HKN  plan-2  C17  0.020
 HKN  plan-2  C3   0.020
 HKN  plan-2  C2   0.020
 HKN  plan-2  N    0.020
 HKN  plan-2  C1   0.020
 HKN  plan-2  O    0.020
 HKN  plan-2  H2   0.020
 HKN  plan-2  H15  0.020
 HKN  plan-3  C10  0.020
 HKN  plan-3  C13  0.020
 HKN  plan-3  C9   0.020
 HKN  plan-3  C14  0.020
 HKN  plan-3  C12  0.020
 HKN  plan-3  C11  0.020
 HKN  plan-3  H7   0.020
 HKN  plan-3  H22  0.020
 HKN  plan-3  H23  0.020
 HKN  plan-3  H24  0.020
 HKN  plan-3  C8   0.020
 HKN  plan-3  H6   0.020
 HKN  plan-4  N1   0.020
 HKN  plan-4  C5   0.020
 HKN  plan-4  S    0.020
 HKN  plan-4  H1   0.020

