# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 06:03:52 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 4-methoxy-1-(5-methoxy-3H-imidazo[4,5-b]pyridin-2-yl)-3,5-dimethyl-2-(sulfanylmethyl)pyridin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc([nH]c2n1)[n+]3cc(C)c(OC)c(C)c3CS
#
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
 4N1  4N1  4-methoxy-1-(5-methoxy-3H-imidazo[4,5-b]pyridin-2-yl)-3,5-dimethyl-2-(sulfanylmethyl)pyridin-1-ium  ligand  42  23  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4N1
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
 4N1  C1    C  CR6   0   0.512  -4.7550   0.3424  -0.0930
 4N1  O1    O  O2    0  -0.464  -5.9972   0.7315   0.1768
 4N1  N2    N  N     0  -0.484  -3.7408   1.0084   0.4140
 4N1  C3    C  CR56  0   0.482  -2.5520   0.5326   0.0794
 4N1  C4    C  CR56  0   0.100  -2.2851  -0.5715  -0.7330
 4N1  C5    C  CR16  0  -0.207  -3.3794  -1.2623  -1.2603
 4N1  C6    C  CR16  0  -0.388  -4.6274  -0.7940  -0.9316
 4N1  N7    N  NR15  0  -0.668  -1.3278   1.0077   0.4567
 4N1  C8    C  CR5   0   0.609  -0.4246   0.1886  -0.1329
 4N1  N9    N  N     0  -0.411  -0.9308  -0.7572  -0.8512
 4N1  C10   C  CH3   0  -0.419  -6.1813   1.8666   1.0124
 4N1  N11   N  NR6   1  -0.593   0.9681   0.3946   0.0228
 4N1  C12   C  CR6   0   0.430   1.7429  -0.5667   0.5814
 4N1  C13   C  CR6   0  -0.074   3.1183  -0.3787   0.6282
 4N1  C14   C  CR6   0   0.499   3.6456   0.8087   0.1098
 4N1  O14   O  O2    0  -0.466   4.9603   1.0436   0.1414
 4N1  C15   C  CR6   0  -0.100   2.8165   1.8091  -0.4208
 4N1  C16   C  CR16  0   0.016   1.4752   1.5526  -0.4540
 4N1  C17   C  CH2   0  -0.704   1.0887  -1.7974   1.1130
 4N1  C18   C  CH3   0  -0.766   4.0049  -1.4214   1.2368
 4N1  C19   C  CH3   0  -0.711   3.3699   3.0956  -0.9420
 4N1  S20   S  S2    0  -0.169   1.0137  -3.0997  -0.1675
 4N1  C21   C  CH3   0  -0.424   5.7371   0.4168  -0.8899
 4N1  H5    H  HCR6  0   0.284  -3.2552  -2.1267  -1.8985
 4N1  H6    H  HCR6  0   0.284  -5.5196  -1.2806  -1.3006
 4N1  H7    H  HNR5  0   0.445  -1.1431   1.7796   1.0824
 4N1  H101  H  HCH3  0   0.233  -5.7812   1.6975   2.0129
 4N1  H102  H  HCH3  0   0.233  -5.7135   2.7577   0.5929
 4N1  H103  H  HCH3  0   0.251  -7.2554   2.0179   1.0748
 4N1  H16   H  HCR6  0   0.356   0.7669   2.2445  -0.8864
 4N1  H171  H  HCH2  0   0.342   1.6506  -2.1766   1.9615
 4N1  H181  H  HCH3  0   0.272   4.0688  -2.3019   0.5956
 4N1  H182  H  HCH3  0   0.285   5.0112  -1.0472   1.3981
 4N1  H183  H  HCH3  0   0.282   3.6283  -1.7449   2.2061
 4N1  H191  H  HCH3  0   0.265   4.0891   2.9249  -1.7425
 4N1  H192  H  HCH3  0   0.265   2.5751   3.7255  -1.3349
 4N1  H193  H  HCH3  0   0.272   3.8801   3.6452  -0.1516
 4N1  H211  H  HCH3  0   0.265   6.7697   0.7000  -0.7106
 4N1  H212  H  HCH3  0   0.246   5.6501  -0.6698  -0.8552
 4N1  H213  H  HCH3  0   0.248   5.4284   0.7699  -1.8746
 4N1  H172  H  HCH2  0   0.340   0.0812  -1.6042   1.4727
 4N1  H1    H  HSH1  0   0.231   1.9819  -3.8714   0.3392

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
 4N1  C1   O1    single    1.329  0.020  1.329
 4N1  C1   N2    aromatic  1.315  0.020  1.315
 4N1  C1   C6    aromatic  1.418  0.020  1.418
 4N1  O1   C10   single    1.421  0.020  1.421
 4N1  N2   C3    aromatic  1.323  0.020  1.323
 4N1  C3   C4    aromatic  1.397  0.020  1.397
 4N1  C3   N7    aromatic  1.366  0.020  1.366
 4N1  C4   C5    aromatic  1.397  0.020  1.397
 4N1  C4   N9    aromatic  1.372  0.020  1.372
 4N1  C5   C6    aromatic  1.373  0.020  1.373
 4N1  N7   C8    aromatic  1.354  0.020  1.354
 4N1  C8   N9    aromatic  1.291  0.020  1.291
 4N1  C8   N11   single    1.416  0.020  1.416
 4N1  N11  C12   aromatic  1.355  0.020  1.355
 4N1  N11  C16   aromatic  1.351  0.020  1.351
 4N1  C12  C13   aromatic  1.389  0.020  1.389
 4N1  C12  C17   single    1.492  0.020  1.492
 4N1  C13  C14   aromatic  1.399  0.020  1.399
 4N1  C13  C18   single    1.498  0.020  1.498
 4N1  C14  O14   single    1.336  0.020  1.336
 4N1  C14  C15   aromatic  1.404  0.020  1.404
 4N1  O14  C21   single    1.435  0.020  1.435
 4N1  C15  C16   aromatic  1.366  0.020  1.366
 4N1  C15  C19   single    1.494  0.020  1.494
 4N1  C17  S20   single    1.828  0.020  1.828
 4N1  C5   H5    single    0.930  0.020  1.080
 4N1  C6   H6    single    0.930  0.020  1.080
 4N1  N7   H7    single    0.860  0.020  1.020
 4N1  C10  H101  single    0.970  0.020  1.090
 4N1  C10  H102  single    0.970  0.020  1.090
 4N1  C10  H103  single    0.970  0.020  1.090
 4N1  C16  H16   single    0.930  0.020  1.080
 4N1  C17  H171  single    0.970  0.020  1.090
 4N1  C18  H181  single    0.970  0.020  1.090
 4N1  C18  H182  single    0.970  0.020  1.090
 4N1  C18  H183  single    0.970  0.020  1.090
 4N1  C19  H191  single    0.970  0.020  1.090
 4N1  C19  H192  single    0.970  0.020  1.090
 4N1  C19  H193  single    0.970  0.020  1.090
 4N1  C21  H211  single    0.970  0.020  1.090
 4N1  C21  H212  single    0.970  0.020  1.090
 4N1  C21  H213  single    0.970  0.020  1.090
 4N1  C17  H172  single    0.970  0.020  1.090
 4N1  S20  H1    single    1.200  0.020  1.300

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
 4N1  C6    C1   N2    124.37  3.000
 4N1  C6    C1   O1    116.02  3.000
 4N1  N2    C1   O1    119.61  3.000
 4N1  C10   O1   C1    118.30  3.000
 4N1  C3    N2   C1    114.41  3.000
 4N1  N7    C3   C4    105.33  3.000
 4N1  N7    C3   N2    127.59  3.000
 4N1  C4    C3   N2    127.08  3.000
 4N1  N9    C4   C5    132.34  3.000
 4N1  N9    C4   C3    110.23  3.000
 4N1  C5    C4   C3    117.43  3.000
 4N1  H5    C5   C6    121.21  3.000
 4N1  H5    C5   C4    121.86  3.000
 4N1  C6    C5   C4    116.93  3.000
 4N1  H6    C6   C5    120.99  3.000
 4N1  H6    C6   C1    119.23  3.000
 4N1  C5    C6   C1    119.78  3.000
 4N1  H7    N7   C8    127.55  3.000
 4N1  H7    N7   C3    126.89  3.000
 4N1  C8    N7   C3    105.49  3.000
 4N1  N11   C8   N9    123.59  3.000
 4N1  N11   C8   N7    121.32  3.000
 4N1  N9    C8   N7    115.08  3.000
 4N1  C8    N9   C4    103.88  3.000
 4N1  H103  C10  H102  109.42  3.000
 4N1  H103  C10  H101  109.36  3.000
 4N1  H102  C10  H101  108.79  3.000
 4N1  H103  C10  O1    105.84  3.000
 4N1  H102  C10  O1    111.77  3.000
 4N1  H101  C10  O1    111.59  3.000
 4N1  C16   N11  C12   122.61  3.000
 4N1  C16   N11  C8    117.06  3.000
 4N1  C12   N11  C8    120.28  3.000
 4N1  C17   C12  C13   122.27  3.000
 4N1  C17   C12  N11   118.78  3.000
 4N1  C13   C12  N11   118.95  3.000
 4N1  C18   C13  C14   121.22  3.000
 4N1  C18   C13  C12   120.37  3.000
 4N1  C14   C13  C12   118.40  3.000
 4N1  C15   C14  O14   117.71  3.000
 4N1  C15   C14  C13   121.50  3.000
 4N1  O14   C14  C13   120.76  3.000
 4N1  C21   O14  C14   116.03  3.000
 4N1  C19   C15  C16   121.12  3.000
 4N1  C19   C15  C14   121.78  3.000
 4N1  C16   C15  C14   117.09  3.000
 4N1  H16   C16  C15   122.23  3.000
 4N1  H16   C16  N11   116.36  3.000
 4N1  C15   C16  N11   121.39  3.000
 4N1  H172  C17  H171  106.44  3.000
 4N1  H172  C17  S20   108.68  3.000
 4N1  H171  C17  S20   108.64  3.000
 4N1  H172  C17  C12   112.19  3.000
 4N1  H171  C17  C12   109.86  3.000
 4N1  S20   C17  C12   110.86  3.000
 4N1  H183  C18  H182  106.90  3.000
 4N1  H183  C18  H181  107.68  3.000
 4N1  H182  C18  H181  108.13  3.000
 4N1  H183  C18  C13   111.33  3.000
 4N1  H182  C18  C13   111.65  3.000
 4N1  H181  C18  C13   110.96  3.000
 4N1  H193  C19  H192  108.19  3.000
 4N1  H193  C19  H191  107.63  3.000
 4N1  H192  C19  H191  107.92  3.000
 4N1  H193  C19  C15   110.77  3.000
 4N1  H192  C19  C15   110.73  3.000
 4N1  H191  C19  C15   111.46  3.000
 4N1  H1    S20  C17    96.66  3.000
 4N1  H213  C21  H212  109.19  3.000
 4N1  H213  C21  H211  109.51  3.000
 4N1  H212  C21  H211  109.30  3.000
 4N1  H213  C21  O14   110.75  3.000
 4N1  H212  C21  O14   111.65  3.000
 4N1  H211  C21  O14   106.39  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
 4N1  CONST_01  C4    C3   N2   C1      0.00   0.0  0
 4N1  CONST_02  N7    C3   N2   C1    180.00   0.0  0
 4N1  CONST_03  C4    C5   C6   C1      0.00   0.0  0
 4N1  CONST_04  C5    C6   C1   N2      0.00   0.0  0
 4N1  CONST_05  C5    C4   C3   N2      0.00   0.0  0
 4N1  CONST_06  N9    C4   C3   N2    180.00   0.0  0
 4N1  CONST_07  C8    N7   C3   N2    180.00   0.0  0
 4N1  CONST_08  C6    C1   N2   C3      0.00   0.0  0
 4N1  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 4N1  CONST_10  C8    N9   C4   C3      0.00   0.0  0
 4N1  CONST_11  N9    C8   N7   C3      0.00   0.0  0
 4N1  CONST_12  N11   C8   N7   C3    180.00   0.0  0
 4N1  CONST_13  C8    N7   C3   C4      0.00   0.0  0
 4N1  CONST_14  N7    C8   N9   C4      0.00   0.0  0
 4N1  CONST_15  N11   C8   N9   C4    180.00   0.0  0
 4N1  CONST_16  N7    C3   C4   C5    180.00   0.0  0
 4N1  CONST_17  C8    N9   C4   C5    180.00   0.0  0
 4N1  CONST_18  N9    C4   C5   C6    180.00   0.0  0
 4N1  CONST_19  N9    C4   C3   N7      0.00   0.0  0
 4N1  CONST_22  C13   C12  N11  C8    180.00   0.0  0
 4N1  CONST_23  C15   C16  N11  C8    180.00   0.0  0
 4N1  CONST_26  C14   C13  C12  N11     0.00   0.0  0
 4N1  CONST_27  C14   C15  C16  N11     0.00   0.0  0
 4N1  CONST_28  C15   C16  N11  C12     0.00   0.0  0
 4N1  CONST_29  C15   C14  C13  C12     0.00   0.0  0
 4N1  CONST_30  C16   N11  C12  C13     0.00   0.0  0
 4N1  CONST_31  C16   C15  C14  C13     0.00   0.0  0
 4N1  CONST_32  C3    N2   C1   O1    180.00   0.0  0
 4N1  CONST_33  C5    C6   C1   O1    180.00   0.0  0
 4N1  CONST_34  C17   C12  N11  C8      0.00   0.0  0
 4N1  CONST_35  C18   C13  C12  N11   180.00   0.0  0
 4N1  CONST_36  C19   C15  C16  N11   180.00   0.0  0
 4N1  CONST_37  O14   C14  C13  C12   180.00   0.0  0
 4N1  CONST_38  C19   C15  C14  C13   180.00   0.0  0
 4N1  CONST_39  C17   C12  C13  C14   180.00   0.0  0
 4N1  CONST_40  C16   C15  C14  O14   180.00   0.0  0
 4N1  CONST_41  C18   C13  C14  C15   180.00   0.0  0
 4N1  CONST_42  C17   C12  N11  C16   180.00   0.0  0
 4N1  CONST_43  H5    C5   C6   C1    180.00   0.0  0
 4N1  CONST_44  H6    C6   C1   N2    180.00   0.0  0
 4N1  CONST_45  H7    N7   C3   N2      0.00   0.0  0
 4N1  CONST_46  H16   C16  N11  C8      0.00   0.0  0
 4N1  Var_01    S20   C17  C12  N11    91.52  30.0  2
 4N1  Var_02    H181  C18  C13  C12    71.79  30.0  2
 4N1  Var_03    H191  C19  C15  C14    58.23  30.0  2
 4N1  Var_04    H101  C10  O1   C1    -62.63  30.0  3
 4N1  Var_05    H211  C21  O14  C14  -179.38  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
 4N1  plan-1  C8   0.020
 4N1  plan-1  N11  0.020
 4N1  plan-1  C12  0.020
 4N1  plan-1  C13  0.020
 4N1  plan-1  C14  0.020
 4N1  plan-1  O14  0.020
 4N1  plan-1  C15  0.020
 4N1  plan-1  C16  0.020
 4N1  plan-1  C17  0.020
 4N1  plan-1  C18  0.020
 4N1  plan-1  C19  0.020
 4N1  plan-1  H16  0.020
 4N1  plan-2  C1   0.020
 4N1  plan-2  O1   0.020
 4N1  plan-2  N2   0.020
 4N1  plan-2  C3   0.020
 4N1  plan-2  C4   0.020
 4N1  plan-2  C5   0.020
 4N1  plan-2  C6   0.020
 4N1  plan-2  N7   0.020
 4N1  plan-2  C8   0.020
 4N1  plan-2  N9   0.020
 4N1  plan-2  N11  0.020
 4N1  plan-2  H5   0.020
 4N1  plan-2  H6   0.020
 4N1  plan-2  H7   0.020

