# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 12:14:00 2021
#   Inital geometry file: a 106 line input string
#   Ligand name: N-{5-[(E)-2-(4,4-difluorocyclohexyl)ethenyl]-6-methoxypyridin-3-yl}methanesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(N[S](C)(=O)=O)cc1/C=C/C2CCC(F)(F)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
 QLV  QLV  N-{5-[(E)-2-(4,4-difluorocyclohexyl)ethenyl]-6-methoxypyridin-3-yl}methanesulfonamide  ligand  43  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QLV
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
 QLV  C4   C  CR6   0   0.174  -33.7985   8.2439  21.2736
 QLV  C5   C  CR16  0  -0.082  -35.0803   8.7458  21.3869
 QLV  C6   C  CH3   0  -0.797  -34.9205   5.1582  21.0224
 QLV  N1   N  NC1   0  -0.826  -33.3498   7.1641  22.0722
 QLV  C7   C  C1    0  -0.318  -32.4084  10.5158  18.6515
 QLV  C8   C  C1    0  -0.170  -32.5009  11.6172  17.9009
 QLV  C9   C  CH1   0  -0.321  -31.4038  12.0876  17.0005
 QLV  C10  C  CH2   0  -0.437  -31.9074  12.2164  15.5577
 QLV  C11  C  CH2   0  -0.561  -30.8233  12.7509  14.6248
 QLV  C12  C  CT    0   0.760  -30.2595  14.0542  15.1375
 QLV  C13  C  CH2   0  -0.561  -29.7634  13.9688  16.5602
 QLV  C14  C  CH2   0  -0.436  -30.8522  13.4340  17.4873
 QLV  N    N  N     0  -0.454  -35.5080   9.7785  20.6696
 QLV  C    C  CH3   0  -0.414  -36.4992  11.7816  19.2609
 QLV  O    O  O2    0  -0.465  -35.1535  11.3618  19.0758
 QLV  C1   C  CR6   0   0.484  -34.7003  10.3447  19.8022
 QLV  C2   C  CR6   0   0.001  -33.3631   9.9282  19.5904
 QLV  C3   C  CR16  0  -0.195  -32.9422   8.8560  20.3626
 QLV  F    F  F     0  -0.359  -31.2242  15.0326  15.0511
 QLV  F1   F  F     0  -0.356  -29.2498  14.4840  14.3129
 QLV  O1   O  OS    0  -0.656  -32.5299   5.7911  20.1433
 QLV  O2   O  OS    0  -0.664  -32.7330   4.7779  22.4361
 QLV  S    S  S     0   1.317  -33.2531   5.6476  21.3952
 QLV  H1   H  HCR6  0   0.277  -35.7870   8.3100  22.0862
 QLV  H2   H  HCH3  0   0.296  -35.4974   5.1227  21.9436
 QLV  H3   H  HCH3  0   0.293  -35.3613   5.8657  20.3232
 QLV  H4   H  HCH3  0   0.311  -34.8833   4.1693  20.5680
 QLV  H5   H  HNC1  0   0.421  -33.7139   7.1419  23.0189
 QLV  H6   H  H     0   0.243  -31.4802   9.9526  18.5863
 QLV  H7   H  H     0   0.261  -33.3859  12.2412  17.9220
 QLV  H8   H  HCH1  0   0.240  -30.5858  11.3566  17.0162
 QLV  H9   H  HCH2  0   0.231  -32.7792  12.8779  15.5353
 QLV  H10  H  HCH2  0   0.252  -32.2449  11.2451  15.1925
 QLV  H11  H  HCH2  0   0.267  -31.2134  12.8850  13.6129
 QLV  H12  H  HCH2  0   0.251  -30.0046  12.0288  14.5632
 QLV  H13  H  HCH2  0   0.251  -28.9027  13.2947  16.5784
 QLV  H14  H  HCH2  0   0.267  -29.4165  14.9492  16.8948
 QLV  H15  H  HCH2  0   0.252  -30.4434  13.3259  18.4933
 QLV  H16  H  HCH2  0   0.232  -31.6690  14.1588  17.5607
 QLV  H17  H  HCH3  0   0.249  -36.6474  12.6070  18.5699
 QLV  H18  H  HCH3  0   0.232  -37.2060  10.9844  19.0291
 QLV  H19  H  HCH3  0   0.232  -36.6779  12.1252  20.2799
 QLV  H20  H  HCR6  0   0.277  -31.9248   8.5006  20.2642

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
 QLV  F1   C12  single    1.373  0.020  1.373
 QLV  F    C12  single    1.377  0.020  1.377
 QLV  C11  C12  single    1.510  0.020  1.510
 QLV  C11  C10  single    1.527  0.020  1.527
 QLV  C12  C13  single    1.509  0.020  1.509
 QLV  C10  C9   single    1.534  0.020  1.534
 QLV  C13  C14  single    1.527  0.020  1.527
 QLV  C9   C14  single    1.534  0.020  1.534
 QLV  C9   C8   single    1.495  0.020  1.495
 QLV  C8   C7   double    1.336  0.020  1.336
 QLV  C7   C2   single    1.462  0.020  1.462
 QLV  O    C    single    1.422  0.020  1.422
 QLV  O    C1   single    1.329  0.020  1.329
 QLV  C2   C1   aromatic  1.416  0.020  1.416
 QLV  C2   C3   aromatic  1.387  0.020  1.387
 QLV  C1   N    aromatic  1.314  0.020  1.314
 QLV  C6   S    single    1.777  0.020  1.777
 QLV  O1   S    double    1.453  0.020  1.453
 QLV  C3   C4   aromatic  1.392  0.020  1.392
 QLV  N    C5   aromatic  1.328  0.020  1.328
 QLV  S    N1   single    1.664  0.020  1.664
 QLV  S    O2   double    1.453  0.020  1.453
 QLV  C4   C5   aromatic  1.381  0.020  1.381
 QLV  C4   N1   single    1.416  0.020  1.416
 QLV  C5   H1   single    0.930  0.020  1.080
 QLV  C6   H2   single    0.970  0.020  1.090
 QLV  C6   H3   single    0.970  0.020  1.090
 QLV  C6   H4   single    0.970  0.020  1.090
 QLV  N1   H5   single    0.890  0.020  1.040
 QLV  C7   H6   single    0.930  0.020  1.080
 QLV  C8   H7   single    0.930  0.020  1.080
 QLV  C9   H8   single    0.970  0.020  1.090
 QLV  C10  H9   single    0.970  0.020  1.090
 QLV  C10  H10  single    0.970  0.020  1.090
 QLV  C11  H11  single    0.970  0.020  1.090
 QLV  C11  H12  single    0.970  0.020  1.090
 QLV  C13  H13  single    0.970  0.020  1.090
 QLV  C13  H14  single    0.970  0.020  1.090
 QLV  C14  H15  single    0.970  0.020  1.090
 QLV  C14  H16  single    0.970  0.020  1.090
 QLV  C    H17  single    0.970  0.020  1.090
 QLV  C    H18  single    0.970  0.020  1.090
 QLV  C    H19  single    0.970  0.020  1.090
 QLV  C3   H20  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
 QLV  C3   C4   N1   120.63  3.000
 QLV  N1   C4   C5   121.66  3.000
 QLV  C3   C4   C5   117.70  3.000
 QLV  H1   C5   N    116.78  3.000
 QLV  H1   C5   C4   120.74  3.000
 QLV  N    C5   C4   122.48  3.000
 QLV  H4   C6   H3   109.65  3.000
 QLV  H4   C6   H2   109.99  3.000
 QLV  H3   C6   H2   110.53  3.000
 QLV  H4   C6   S    107.79  3.000
 QLV  H3   C6   S    109.63  3.000
 QLV  H2   C6   S    109.20  3.000
 QLV  H5   N1   S    112.37  3.000
 QLV  H5   N1   C4   115.42  3.000
 QLV  S    N1   C4   118.95  3.000
 QLV  H6   C7   C2   112.81  3.000
 QLV  H6   C7   C8   116.89  3.000
 QLV  C2   C7   C8   130.30  3.000
 QLV  H7   C8   C9   115.47  3.000
 QLV  H7   C8   C7   121.37  3.000
 QLV  C9   C8   C7   123.15  3.000
 QLV  H8   C9   C14  108.19  3.000
 QLV  H8   C9   C10  108.31  3.000
 QLV  C14  C9   C10  110.05  3.000
 QLV  H8   C9   C8   109.20  3.000
 QLV  C14  C9   C8   110.42  3.000
 QLV  C10  C9   C8   110.61  3.000
 QLV  H10  C10  H9   106.54  3.000
 QLV  H10  C10  C11  109.07  3.000
 QLV  H9   C10  C11  109.97  3.000
 QLV  H10  C10  C9   109.98  3.000
 QLV  H9   C10  C9   109.36  3.000
 QLV  C11  C10  C9   111.78  3.000
 QLV  H12  C11  H11  107.22  3.000
 QLV  H12  C11  C12  108.04  3.000
 QLV  H11  C11  C12  109.99  3.000
 QLV  H12  C11  C10  109.57  3.000
 QLV  H11  C11  C10  110.81  3.000
 QLV  C12  C11  C10  111.09  3.000
 QLV  F1   C12  F    104.79  3.000
 QLV  F    C12  C13  109.25  3.000
 QLV  F1   C12  C13  110.01  3.000
 QLV  C13  C12  C11  113.20  3.000
 QLV  F    C12  C11  109.30  3.000
 QLV  F1   C12  C11  109.94  3.000
 QLV  H14  C13  H13  107.34  3.000
 QLV  H14  C13  C14  110.78  3.000
 QLV  H13  C13  C14  109.60  3.000
 QLV  H14  C13  C12  110.02  3.000
 QLV  H13  C13  C12  108.02  3.000
 QLV  C14  C13  C12  110.97  3.000
 QLV  H16  C14  H15  106.46  3.000
 QLV  H16  C14  C13  109.94  3.000
 QLV  H15  C14  C13  109.10  3.000
 QLV  H16  C14  C9   109.52  3.000
 QLV  H15  C14  C9   109.89  3.000
 QLV  C13  C14  C9   111.78  3.000
 QLV  C1   N    C5   119.59  3.000
 QLV  H19  C    H18  108.83  3.000
 QLV  H19  C    H17  109.43  3.000
 QLV  H18  C    H17  109.38  3.000
 QLV  H19  C    O    111.71  3.000
 QLV  H18  C    O    111.72  3.000
 QLV  H17  C    O    105.70  3.000
 QLV  C1   O    C    118.52  3.000
 QLV  C2   C1   O    117.72  3.000
 QLV  C2   C1   N    123.54  3.000
 QLV  O    C1   N    118.74  3.000
 QLV  C3   C2   C1   115.51  3.000
 QLV  C3   C2   C7   118.04  3.000
 QLV  C1   C2   C7   126.45  3.000
 QLV  H20  C3   C2   119.25  3.000
 QLV  H20  C3   C4   119.57  3.000
 QLV  C2   C3   C4   121.18  3.000
 QLV  O2   S    O1   119.89  3.000
 QLV  O2   S    N1   105.96  3.000
 QLV  O1   S    N1   106.83  3.000
 QLV  O2   S    C6   108.74  3.000
 QLV  N1   S    C6   106.37  3.000
 QLV  O1   S    C6   108.26  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
 QLV  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 QLV  CONST_02  C1   N    C5   C4      0.00   0.0  0
 QLV  CONST_03  C2   C1   N    C5      0.00   0.0  0
 QLV  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 QLV  CONST_05  C3   C2   C1   N       0.00   0.0  0
 QLV  CONST_06  C3   C4   C5   N       0.00   0.0  0
 QLV  CONST_07  C7   C2   C3   C4    180.00   0.0  0
 QLV  CONST_08  O    C1   N    C5    180.00   0.0  0
 QLV  CONST_09  C2   C3   C4   N1    180.00   0.0  0
 QLV  CONST_10  N    C5   C4   N1    180.00   0.0  0
 QLV  CONST_11  N    C1   C2   C7    180.00   0.0  0
 QLV  CONST_12  C3   C2   C1   O     180.00   0.0  0
 QLV  CONST_13  H20  C3   C4   C5    180.00   0.0  0
 QLV  CONST_14  H1   C5   N    C1    180.00   0.0  0
 QLV  Var_01    C12  C11  C10  C9    -54.50  30.0  1
 QLV  Var_02    C12  C13  C14  C9     54.75  30.0  1
 QLV  Var_03    C13  C12  C11  C10    53.99  30.0  1
 QLV  Var_04    C14  C13  C12  C11   -54.08  30.0  1
 QLV  Var_05    C2   C7   C8   C9    178.98   0.0  2
 QLV  Var_06    C1   C2   C7   C8      7.59  30.0  2
 QLV  Var_07    C2   C1   O    C     179.11  30.0  2
 QLV  Var_08    C6   S    N1   C4    -65.96  30.0  1
 QLV  Var_09    H17  C    O    C1   -179.63  30.0  3
 QLV  Var_10    H2   C6   S    N1    -61.06  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 QLV  chir_01  C9  C10  C14  C8  negativ

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
 QLV  plan-1  C4   0.020
 QLV  plan-1  C5   0.020
 QLV  plan-1  N1   0.020
 QLV  plan-1  C7   0.020
 QLV  plan-1  N    0.020
 QLV  plan-1  O    0.020
 QLV  plan-1  C1   0.020
 QLV  plan-1  C2   0.020
 QLV  plan-1  C3   0.020
 QLV  plan-1  H1   0.020
 QLV  plan-1  H20  0.020
 QLV  plan-2  C4   0.020
 QLV  plan-2  N1   0.020
 QLV  plan-2  S    0.020
 QLV  plan-2  H5   0.020
 QLV  plan-3  C7   0.020
 QLV  plan-3  C8   0.020
 QLV  plan-3  C9   0.020
 QLV  plan-3  C2   0.020
 QLV  plan-3  H6   0.020
 QLV  plan-3  H7   0.020

