# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 06:37:03 2022
#   Inital geometry file: a 140 line input string
#   Ligand name: [4-[(4~{Z})-4-[(3,5-dimethoxy-4-oxidanyl-phenyl)methylidene]-2-methyl-5-oxidanylidene-imidazol-1-yl]phenyl]-trimethyl-azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cc(OC)c1O)/C=C/2N=C(C)N(C/2=O)c3ccc(cc3)[N+](C)(C)C
#
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
 V6T  V6T  '[4-[(4~{Z})-4-[(3,5-dimethoxy-4-oxidanyl-phenyl)methylidene]-2-methyl-5-oxidanylidene-imidazol-1-yl]phenyl]-trimethyl-azanium'  ligand  55  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V6T
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
 V6T  C10  C  CH3   0  -0.761   9.3889   -2.7324   -7.0895
 V6T  C01  C  CH3   0  -0.437  11.8666  -12.1468   -6.2620
 V6T  C03  C  CR6   0   0.339  10.5725  -10.3574   -5.4113
 V6T  C04  C  CR16  0  -0.475  11.0524   -9.4541   -6.3480
 V6T  C05  C  CR6   0   0.189  10.6143   -8.1237   -6.3530
 V6T  C07  C  CR5   0   0.089  10.9180   -5.9440   -7.6009
 V6T  C09  C  CR5   0   0.497  10.1472   -3.9395   -7.4847
 V6T  C12  C  CR6   0   0.325  11.3343   -2.8259   -9.3872
 V6T  C13  C  CR16  0  -0.257  10.9293   -2.8231  -10.7113
 V6T  C14  C  CR16  0  -0.304  11.2258   -1.7438  -11.5317
 V6T  C15  C  CR6   0   0.334  11.9222   -0.6636  -11.0166
 V6T  C20  C  CR16  0  -0.262  12.3365   -0.6650   -9.6910
 V6T  C21  C  CR16  0  -0.259  12.0500   -1.7490   -8.8819
 V6T  C22  C  CR5   0   0.526  11.5668   -5.1977   -8.6985
 V6T  C24  C  CR16  0  -0.494   9.6801   -7.7012   -5.3998
 V6T  C25  C  CR6   0   0.360   9.2015   -8.6020   -4.4665
 V6T  C27  C  CH3   0  -0.433   7.8022   -6.9974   -3.4126
 V6T  C28  C  CR6   0   0.195   9.6375   -9.9335   -4.4614
 V6T  N08  N  N     0  -0.481  10.0621   -5.0896   -6.9162
 V6T  N11  N  NR5   0  -0.679  11.0282   -3.9246   -8.5580
 V6T  N16  N  NT    1  -0.482  12.2431    0.5194  -11.8548
 V6T  O23  O  O     0  -0.425  12.3706   -5.5407   -9.5357
 V6T  O26  O  O2    0  -0.490   8.3032   -8.3164   -3.5016
 V6T  O29  O  OH1   0  -0.607   9.1858  -10.8264   -3.5679
 V6T  H1   H  HCH3  0   0.278   8.6935   -2.9867   -6.2942
 V6T  H2   H  HCH3  0   0.275  10.0522   -1.9437   -6.7313
 V6T  H3   H  HCH3  0   0.273   8.8292   -2.3281   -7.9344
 V6T  H4   H  HCH3  0   0.261  12.0193  -13.1956   -6.0196
 V6T  H5   H  HCH3  0   0.228  11.4954  -12.0735   -7.2878
 V6T  H6   H  HCH3  0   0.228  12.8263  -11.6273   -6.1968
 V6T  H7   H  HCR6  0   0.285  11.7737   -9.7651   -7.0922
 V6T  H8   H  H     0   0.269  11.8761   -7.7128   -8.0393
 V6T  H11  H  HCR6  0   0.289  10.3664   -3.6550  -11.1123
 V6T  H12  H  HCR6  0   0.304  10.8885   -1.7789  -12.5560
 V6T  H13  H  HCH3  0   0.302  14.1354    0.8791  -10.9427
 V6T  H14  H  HCH3  0   0.304  14.1667   -0.2069  -12.3545
 V6T  H15  H  HCH3  0   0.300  13.9427    1.5471  -12.5736
 V6T  H16  H  HCH3  0   0.307  10.6460    0.3034  -13.2400
 V6T  H17  H  HCH3  0   0.315  12.0052    1.2997  -13.7860
 V6T  H18  H  HCH3  0   0.307  12.1831   -0.4620  -13.7392
 V6T  H19  H  HCH3  0   0.303  12.0363    1.9264  -10.2669
 V6T  H20  H  HCH3  0   0.300  11.8508    2.5931  -11.8983
 V6T  H21  H  HCH3  0   0.304  10.5497    1.6006  -11.1907
 V6T  H22  H  HCR6  0   0.301  12.8888    0.1596   -9.2625
 V6T  H23  H  HCR6  0   0.295  12.3880   -1.7509   -7.8542
 V6T  H24  H  HCR6  0   0.300   9.3451   -6.6749   -5.4042
 V6T  H25  H  HCH3  0   0.264   7.1054   -6.9873   -2.5787
 V6T  H26  H  HCH3  0   0.232   8.5984   -6.2746   -3.2180
 V6T  H27  H  HCH3  0   0.232   7.2720   -6.7039   -4.3219
 V6T  H28  H  HOH1  0   0.475   8.5541  -10.4040   -2.9717
 V6T  C06  C  C1    0  -0.379  11.1618   -7.2500   -7.3654
 V6T  C17  C  CH3   0  -0.553  13.7313    0.6949  -11.9329
 V6T  C18  C  CH3   0  -0.586  11.7281    0.3958  -13.2523
 V6T  C19  C  CH3   0  -0.553  11.6242    1.7471  -11.2545
 V6T  O02  O  O2    0  -0.464  10.9323  -11.6512   -5.3254

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
 V6T  C18  N16  single    1.494  0.020  1.494
 V6T  C17  N16  single    1.500  0.020  1.500
 V6T  N16  C19  single    1.500  0.020  1.500
 V6T  N16  C15  single    1.485  0.020  1.485
 V6T  C14  C15  aromatic  1.385  0.020  1.385
 V6T  C14  C13  aromatic  1.388  0.020  1.388
 V6T  C15  C20  aromatic  1.389  0.020  1.389
 V6T  C13  C12  aromatic  1.385  0.020  1.385
 V6T  C20  C21  aromatic  1.383  0.020  1.383
 V6T  C12  C21  aromatic  1.388  0.020  1.388
 V6T  C12  N11  single    1.410  0.020  1.410
 V6T  O23  C22  double    1.210  0.020  1.210
 V6T  N11  C22  single    1.389  0.020  1.389
 V6T  N11  C09  single    1.389  0.020  1.389
 V6T  C22  C07  single    1.477  0.020  1.477
 V6T  C09  C10  single    1.479  0.020  1.479
 V6T  C09  N08  double    1.286  0.020  1.286
 V6T  C07  C06  double    1.349  0.020  1.349
 V6T  C07  N08  single    1.390  0.020  1.390
 V6T  C06  C05  single    1.445  0.020  1.445
 V6T  C01  O02  single    1.413  0.020  1.413
 V6T  C04  C05  aromatic  1.401  0.020  1.401
 V6T  C04  C03  aromatic  1.387  0.020  1.387
 V6T  O02  C03  single    1.346  0.020  1.346
 V6T  C05  C24  aromatic  1.400  0.020  1.400
 V6T  C03  C28  aromatic  1.399  0.020  1.399
 V6T  C24  C25  aromatic  1.383  0.020  1.383
 V6T  C28  C25  aromatic  1.401  0.020  1.401
 V6T  C28  O29  single    1.341  0.020  1.341
 V6T  C25  O26  single    1.349  0.020  1.349
 V6T  O26  C27  single    1.414  0.020  1.414
 V6T  C10  H1   single    0.970  0.020  1.090
 V6T  C10  H2   single    0.970  0.020  1.090
 V6T  C10  H3   single    0.970  0.020  1.090
 V6T  C01  H4   single    0.970  0.020  1.090
 V6T  C01  H5   single    0.970  0.020  1.090
 V6T  C01  H6   single    0.970  0.020  1.090
 V6T  C04  H7   single    0.930  0.020  1.080
 V6T  C06  H8   single    0.930  0.020  1.080
 V6T  C13  H11  single    0.930  0.020  1.080
 V6T  C14  H12  single    0.930  0.020  1.080
 V6T  C17  H13  single    0.970  0.020  1.090
 V6T  C17  H14  single    0.970  0.020  1.090
 V6T  C17  H15  single    0.970  0.020  1.090
 V6T  C18  H16  single    0.970  0.020  1.090
 V6T  C18  H17  single    0.970  0.020  1.090
 V6T  C18  H18  single    0.970  0.020  1.090
 V6T  C19  H19  single    0.970  0.020  1.090
 V6T  C19  H20  single    0.970  0.020  1.090
 V6T  C19  H21  single    0.970  0.020  1.090
 V6T  C20  H22  single    0.930  0.020  1.080
 V6T  C21  H23  single    0.930  0.020  1.080
 V6T  C24  H24  single    0.930  0.020  1.080
 V6T  C27  H25  single    0.970  0.020  1.090
 V6T  C27  H26  single    0.970  0.020  1.090
 V6T  C27  H27  single    0.970  0.020  1.090
 V6T  O29  H28  single    0.850  0.020  0.980

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
 V6T  H3   C10  H2   107.36  3.000
 V6T  H3   C10  H1   108.98  3.000
 V6T  H2   C10  H1   108.54  3.000
 V6T  H3   C10  C09  111.00  3.000
 V6T  H2   C10  C09  111.46  3.000
 V6T  H1   C10  C09  109.42  3.000
 V6T  H6   C01  H5   108.79  3.000
 V6T  H6   C01  H4   108.77  3.000
 V6T  H5   C01  H4   108.76  3.000
 V6T  H6   C01  O02  111.98  3.000
 V6T  H5   C01  O02  111.96  3.000
 V6T  H4   C01  O02  106.47  3.000
 V6T  O02  C03  C28  115.27  3.000
 V6T  C28  C03  C04  119.51  3.000
 V6T  O02  C03  C04  125.22  3.000
 V6T  H7   C04  C05  118.62  3.000
 V6T  H7   C04  C03  120.53  3.000
 V6T  C05  C04  C03  120.85  3.000
 V6T  C24  C05  C06  123.19  3.000
 V6T  C24  C05  C04  119.53  3.000
 V6T  C06  C05  C04  117.28  3.000
 V6T  N08  C07  C22  109.02  3.000
 V6T  N08  C07  C06  128.34  3.000
 V6T  C22  C07  C06  122.64  3.000
 V6T  N11  C09  N08  113.17  3.000
 V6T  N08  C09  C10  125.30  3.000
 V6T  N11  C09  C10  121.53  3.000
 V6T  N11  C12  C21  120.15  3.000
 V6T  N11  C12  C13  120.03  3.000
 V6T  C21  C12  C13  119.82  3.000
 V6T  H11  C13  C14  119.36  3.000
 V6T  H11  C13  C12  120.35  3.000
 V6T  C14  C13  C12  120.29  3.000
 V6T  H12  C14  C15  122.40  3.000
 V6T  H12  C14  C13  117.97  3.000
 V6T  C15  C14  C13  119.62  3.000
 V6T  N16  C15  C20  118.37  3.000
 V6T  C20  C15  C14  120.29  3.000
 V6T  N16  C15  C14  121.35  3.000
 V6T  H22  C20  C21  118.16  3.000
 V6T  H22  C20  C15  122.00  3.000
 V6T  C21  C20  C15  119.84  3.000
 V6T  H23  C21  C20  119.51  3.000
 V6T  H23  C21  C12  120.36  3.000
 V6T  C20  C21  C12  120.13  3.000
 V6T  O23  C22  N11  125.94  3.000
 V6T  N11  C22  C07  102.57  3.000
 V6T  O23  C22  C07  131.49  3.000
 V6T  H24  C24  C25  120.98  3.000
 V6T  H24  C24  C05  119.41  3.000
 V6T  C25  C24  C05  119.60  3.000
 V6T  O26  C25  C28  113.94  3.000
 V6T  O26  C25  C24  125.13  3.000
 V6T  C28  C25  C24  120.93  3.000
 V6T  H27  C27  H26  108.91  3.000
 V6T  H27  C27  H25  108.96  3.000
 V6T  H26  C27  H25  108.92  3.000
 V6T  H27  C27  O26  111.73  3.000
 V6T  H26  C27  O26  111.73  3.000
 V6T  H25  C27  O26  106.51  3.000
 V6T  O29  C28  C25  122.02  3.000
 V6T  O29  C28  C03  118.40  3.000
 V6T  C25  C28  C03  119.58  3.000
 V6T  C09  N08  C07  106.94  3.000
 V6T  C22  N11  C12  124.78  3.000
 V6T  C22  N11  C09  108.31  3.000
 V6T  C12  N11  C09  126.91  3.000
 V6T  C19  N16  C18  107.44  3.000
 V6T  C19  N16  C17  109.53  3.000
 V6T  C18  N16  C17  107.63  3.000
 V6T  C19  N16  C15  109.69  3.000
 V6T  C17  N16  C15  109.69  3.000
 V6T  C18  N16  C15  112.80  3.000
 V6T  C27  O26  C25  118.59  3.000
 V6T  H28  O29  C28  109.90  3.000
 V6T  H8   C06  C07  115.03  3.000
 V6T  H8   C06  C05  115.24  3.000
 V6T  C07  C06  C05  129.72  3.000
 V6T  H15  C17  H14  110.12  3.000
 V6T  H15  C17  H13  109.41  3.000
 V6T  H14  C17  H13  110.23  3.000
 V6T  H15  C17  N16  108.38  3.000
 V6T  H14  C17  N16  108.70  3.000
 V6T  H13  C17  N16  109.98  3.000
 V6T  H18  C18  H17  109.29  3.000
 V6T  H18  C18  H16  110.80  3.000
 V6T  H17  C18  H16  109.31  3.000
 V6T  H18  C18  N16  109.88  3.000
 V6T  H17  C18  N16  107.63  3.000
 V6T  H16  C18  N16  109.87  3.000
 V6T  H21  C19  H20  110.24  3.000
 V6T  H21  C19  H19  110.15  3.000
 V6T  H20  C19  H19  109.35  3.000
 V6T  H21  C19  N16  108.73  3.000
 V6T  H20  C19  N16  108.29  3.000
 V6T  H19  C19  N16  110.04  3.000
 V6T  C03  O02  C01  118.15  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
 V6T  CONST_01  C24  C05  C04  C03     0.00   0.0  0
 V6T  CONST_02  C24  C25  C28  C03     0.00   0.0  0
 V6T  CONST_03  C25  C24  C05  C04     0.00   0.0  0
 V6T  CONST_04  C25  C28  C03  C04     0.00   0.0  0
 V6T  CONST_05  C28  C03  C04  C05     0.00   0.0  0
 V6T  CONST_06  C28  C25  C24  C05     0.00   0.0  0
 V6T  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 V6T  CONST_08  C15  C20  C21  C12     0.00   0.0  0
 V6T  CONST_09  C20  C15  C14  C13     0.00   0.0  0
 V6T  CONST_10  C20  C21  C12  C13     0.00   0.0  0
 V6T  CONST_11  C21  C20  C15  C14     0.00   0.0  0
 V6T  CONST_12  C21  C12  C13  C14     0.00   0.0  0
 V6T  CONST_13  N11  C12  C13  C14   180.00   0.0  0
 V6T  CONST_14  N11  C12  C21  C20   180.00   0.0  0
 V6T  CONST_15  C12  N11  C22  C07   180.00   0.0  0
 V6T  CONST_16  C09  N11  C22  C07     0.00   0.0  0
 V6T  CONST_17  N11  C09  N08  C07     0.00   0.0  0
 V6T  CONST_18  C22  C07  N08  C09     0.00   0.0  0
 V6T  CONST_19  N08  C09  N11  C12   180.00   0.0  0
 V6T  CONST_20  N08  C09  N11  C22     0.00   0.0  0
 V6T  CONST_21  N11  C22  C07  N08     0.00   0.0  0
 V6T  CONST_22  C06  C05  C04  C03   180.00   0.0  0
 V6T  CONST_23  O26  C25  C28  C03   180.00   0.0  0
 V6T  CONST_24  O29  C28  C03  C04   180.00   0.0  0
 V6T  CONST_25  O02  C03  C04  C05   180.00   0.0  0
 V6T  CONST_26  O26  C25  C24  C05   180.00   0.0  0
 V6T  CONST_27  C25  C24  C05  C06   180.00   0.0  0
 V6T  CONST_28  N16  C15  C14  C13   180.00   0.0  0
 V6T  CONST_29  N16  C15  C20  C21   180.00   0.0  0
 V6T  CONST_30  O29  C28  C25  C24   180.00   0.0  0
 V6T  CONST_31  O02  C03  C28  C25   180.00   0.0  0
 V6T  CONST_32  C12  N11  C09  C10     0.00   0.0  0
 V6T  CONST_33  C22  N11  C09  C10   180.00   0.0  0
 V6T  CONST_34  C07  N08  C09  C10   180.00   0.0  0
 V6T  CONST_35  O23  C22  N11  C09   180.00   0.0  0
 V6T  CONST_36  O23  C22  N11  C12     0.00   0.0  0
 V6T  CONST_37  H24  C24  C05  C04   180.00   0.0  0
 V6T  CONST_38  H12  C14  C13  C12   180.00   0.0  0
 V6T  CONST_39  H22  C20  C21  C12   180.00   0.0  0
 V6T  CONST_40  H23  C21  C12  C13   180.00   0.0  0
 V6T  CONST_41  H11  C13  C14  C15   180.00   0.0  0
 V6T  CONST_42  H7   C04  C05  C24   180.00   0.0  0
 V6T  Var_01    C13  C12  N11  C09  -111.44  30.0  3
 V6T  Var_02    C22  C07  C06  C05  -179.58   0.0  2
 V6T  Var_03    C07  C06  C05  C04   179.81  30.0  3
 V6T  Var_04    C04  C03  O02  C01    -0.42  30.0  2
 V6T  Var_05    C18  N16  C15  C14     0.49  30.0  2
 V6T  Var_06    C28  C25  O26  C27   179.68  30.0  3
 V6T  Var_07    H1   C10  C09  N08    -4.29  30.0  3
 V6T  Var_08    H4   C01  O02  C03   179.88  30.0  3
 V6T  Var_09    H16  C18  N16  C15    60.94  30.0  3
 V6T  Var_10    H13  C17  N16  C15   -62.07  30.0  3
 V6T  Var_11    H19  C19  N16  C15    61.98  30.0  3
 V6T  Var_12    H25  C27  O26  C25  -179.87  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
 V6T  plan-1  C10  0.020
 V6T  plan-1  C05  0.020
 V6T  plan-1  C07  0.020
 V6T  plan-1  C09  0.020
 V6T  plan-1  C12  0.020
 V6T  plan-1  C22  0.020
 V6T  plan-1  N08  0.020
 V6T  plan-1  N11  0.020
 V6T  plan-1  O23  0.020
 V6T  plan-1  H8   0.020
 V6T  plan-1  C06  0.020
 V6T  plan-2  C03  0.020
 V6T  plan-2  C04  0.020
 V6T  plan-2  C05  0.020
 V6T  plan-2  C24  0.020
 V6T  plan-2  C25  0.020
 V6T  plan-2  C28  0.020
 V6T  plan-2  O26  0.020
 V6T  plan-2  O29  0.020
 V6T  plan-2  H7   0.020
 V6T  plan-2  H24  0.020
 V6T  plan-2  C06  0.020
 V6T  plan-2  O02  0.020
 V6T  plan-3  C12  0.020
 V6T  plan-3  C13  0.020
 V6T  plan-3  C14  0.020
 V6T  plan-3  C15  0.020
 V6T  plan-3  C20  0.020
 V6T  plan-3  C21  0.020
 V6T  plan-3  N11  0.020
 V6T  plan-3  N16  0.020
 V6T  plan-3  H11  0.020
 V6T  plan-3  H12  0.020
 V6T  plan-3  H22  0.020
 V6T  plan-3  H23  0.020

