# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 15:16:20 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: [(3,5-difluoro-4-methylpyridine-2,6-diyl)bis(oxybenzene-3,1-diyl)]bis(aminomethaniminium)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(F)c(Oc2cccc(c2)C(N)=[NH2+])nc(Oc3cccc(c3)C(N)=[NH2+])c1F
#
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
 Z23  Z23  '[(3,5-difluoro-4-methylpyridine-2,6-diyl)bis(oxybenzene-3,1-diyl)]bis(aminomethaniminium)'  ligand  48  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_Z23
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
 Z23  C1   C  CR16  0  -0.252   2.5325  -1.6943   1.5091
 Z23  C2   C  CR6   0   0.042   3.1114  -1.3911   0.2812
 Z23  C3   C  CR16  0  -0.385   2.8752  -0.1601  -0.3273
 Z23  C4   C  CR6   0   0.543   2.0712   0.7634   0.3129
 Z23  C5   C  CR16  0  -0.305   1.4993   0.4806   1.5464
 Z23  C6   C  CR16  0  -0.241   1.7320  -0.7510   2.1345
 Z23  O7   O  O2    0  -0.470   1.9126   1.9815  -0.2959
 Z23  C8   C  CR6   0   0.167   0.6689   2.4353  -0.5517
 Z23  N9   N  N     0  -0.365  -0.3640   1.6448  -0.3975
 Z23  C10  C  CR6   0   0.275  -1.5695   2.0900  -0.6432
 Z23  C11  C  CR6   0   0.506   0.5263   3.7379  -0.9966
 Z23  C12  C  CR6   0  -0.221  -0.7311   4.2441  -1.2901
 Z23  C13  C  CR6   0   0.371  -1.7966   3.3799  -1.0982
 Z23  O14  O  O2    0  -0.419  -2.6292   1.2749  -0.4647
 Z23  C15  C  CR6   0   0.396  -2.4222   0.1282   0.2643
 Z23  C16  C  CR16  0  -0.294  -2.2259   0.1977   1.6358
 Z23  C17  C  CR16  0  -0.257  -2.0504  -0.9713   2.3570
 Z23  C18  C  CR16  0  -0.195  -2.0652  -2.2010   1.7174
 Z23  C19  C  CR6   0   0.038  -2.2740  -2.2541   0.3432
 Z23  C20  C  CR16  0  -0.338  -2.4510  -1.0848  -0.3935
 Z23  C21  C  C     0   0.548  -2.3100  -3.5558  -0.3438
 Z23  N22  N  NH2   0  -0.755  -1.4734  -4.4942   0.0247
 Z23  C23  C  C     0   0.597   3.9899  -2.3698  -0.3805
 Z23  N24  N  NH2   0  -0.752   3.7021  -3.6454  -0.3011
 Z23  N25  N  NC2   1  -0.788   5.0441  -1.9441  -1.0308
 Z23  F26  F  F     0  -0.359   1.6045   4.5137  -1.1430
 Z23  C27  C  CH3   0  -0.696  -0.8990   5.6528  -1.7619
 Z23  F28  F  F     0  -0.226  -3.0493   3.7779  -1.3397
 Z23  N38  N  NC2   1  -0.752  -3.1774  -3.7457  -1.3061
 Z23  H29  H  HCR6  0   0.269   2.7286  -2.6387   1.9992
 Z23  H30  H  HCR6  0   0.280   3.2912   0.0771  -1.2984
 Z23  H31  H  HCR6  0   0.315   0.8825   1.2116   2.0507
 Z23  H32  H  HCR6  0   0.284   1.2957  -0.9743   3.0977
 Z23  H33  H  HCR6  0   0.303  -2.2146   1.1558   2.1394
 Z23  H34  H  HCR6  0   0.288  -1.9074  -0.9244   3.4276
 Z23  H35  H  HCR6  0   0.259  -1.9477  -3.1066   2.2978
 Z23  H36  H  HCR6  0   0.273  -2.5835  -1.1105  -1.4678
 Z23  H39  H  HNH2  0   0.451  -0.7381  -4.3020   0.6848
 Z23  H46  H  HNH2  0   0.445  -1.4988  -5.4232  -0.3690
 Z23  H40  H  HNH2  0   0.449   2.8314  -3.9563   0.0971
 Z23  H48  H  HNH2  0   0.394   4.3124  -4.3586  -0.6717
 Z23  H41  H  HNC2  0   0.455   5.6477  -2.5696  -1.5435
 Z23  H47  H  HNC2  0   0.444   5.3269  -0.9784  -0.9818
 Z23  H42  H  HCH3  0   0.305  -0.5526   6.3530  -1.0017
 Z23  H43  H  HCH3  0   0.270  -0.3130   5.8309  -2.6631
 Z23  H44  H  HCH3  0   0.296  -1.9361   5.8847  -1.9837
 Z23  H49  H  HNC2  0   0.381  -3.2132  -4.6041  -1.8359
 Z23  H50  H  HNC2  0   0.427  -3.8960  -3.0650  -1.4933

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
 Z23  C1   C2   aromatic  1.391  0.020  1.391
 Z23  C1   C6   aromatic  1.386  0.020  1.386
 Z23  C1   H29  single    0.930  0.020  1.080
 Z23  C2   C3   aromatic  1.393  0.020  1.393
 Z23  C2   C23  single    1.472  0.020  1.472
 Z23  C3   C4   aromatic  1.382  0.020  1.382
 Z23  C3   H30  single    0.930  0.020  1.080
 Z23  C4   C5   aromatic  1.389  0.020  1.389
 Z23  C4   O7   single    1.371  0.020  1.371
 Z23  C5   C6   aromatic  1.384  0.020  1.384
 Z23  C5   H31  single    0.930  0.020  1.080
 Z23  C6   H32  single    0.930  0.020  1.080
 Z23  O7   C8   single    1.348  0.020  1.348
 Z23  C8   N9   aromatic  1.310  0.020  1.310
 Z23  C8   C11  aromatic  1.384  0.020  1.384
 Z23  N9   C10  aromatic  1.308  0.020  1.308
 Z23  C10  C13  aromatic  1.387  0.020  1.387
 Z23  C10  O14  single    1.349  0.020  1.349
 Z23  C11  C12  aromatic  1.387  0.020  1.387
 Z23  C11  F26  single    1.336  0.020  1.336
 Z23  C12  C13  aromatic  1.385  0.020  1.385
 Z23  C12  C27  single    1.495  0.020  1.495
 Z23  C13  F28  single    1.336  0.020  1.336
 Z23  O14  C15  single    1.374  0.020  1.374
 Z23  C15  C16  aromatic  1.387  0.020  1.387
 Z23  C15  C20  aromatic  1.380  0.020  1.380
 Z23  C16  C17  aromatic  1.385  0.020  1.385
 Z23  C16  H33  single    0.930  0.020  1.080
 Z23  C17  C18  aromatic  1.386  0.020  1.386
 Z23  C17  H34  single    0.930  0.020  1.080
 Z23  C18  C19  aromatic  1.391  0.020  1.391
 Z23  C18  H35  single    0.930  0.020  1.080
 Z23  C19  C20  aromatic  1.393  0.020  1.393
 Z23  C19  C21  single    1.472  0.020  1.472
 Z23  C20  H36  single    0.930  0.020  1.080
 Z23  C21  N22  single    1.310  0.020  1.310
 Z23  C21  N38  double    1.309  0.020  1.309
 Z23  N22  H39  single    0.860  0.020  1.020
 Z23  N22  H46  single    0.860  0.020  1.020
 Z23  C23  N24  single    1.310  0.020  1.310
 Z23  C23  N25  double    1.310  0.020  1.310
 Z23  N24  H40  single    0.860  0.020  1.020
 Z23  N24  H48  single    0.860  0.020  1.020
 Z23  N25  H41  single    0.860  0.020  1.020
 Z23  N25  H47  single    0.860  0.020  1.020
 Z23  C27  H42  single    0.970  0.020  1.090
 Z23  C27  H43  single    0.970  0.020  1.090
 Z23  C27  H44  single    0.970  0.020  1.090
 Z23  N38  H49  single    0.860  0.020  1.020
 Z23  N38  H50  single    0.860  0.020  1.020

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
 Z23  H29  C1   C6   119.62  3.000
 Z23  H29  C1   C2   120.98  3.000
 Z23  C6   C1   C2   119.36  3.000
 Z23  C23  C2   C3   119.48  3.000
 Z23  C23  C2   C1   120.02  3.000
 Z23  C3   C2   C1   120.50  3.000
 Z23  H30  C3   C4   119.52  3.000
 Z23  H30  C3   C2   121.34  3.000
 Z23  C4   C3   C2   119.13  3.000
 Z23  O7   C4   C5   121.85  3.000
 Z23  O7   C4   C3   117.09  3.000
 Z23  C5   C4   C3   121.00  3.000
 Z23  H31  C5   C6   119.95  3.000
 Z23  H31  C5   C4   120.76  3.000
 Z23  C6   C5   C4   119.29  3.000
 Z23  H32  C6   C5   119.64  3.000
 Z23  H32  C6   C1   119.64  3.000
 Z23  C5   C6   C1   120.71  3.000
 Z23  C8   O7   C4   119.34  3.000
 Z23  C11  C8   N9   121.65  3.000
 Z23  C11  C8   O7   118.22  3.000
 Z23  N9   C8   O7   120.13  3.000
 Z23  C10  N9   C8   119.95  3.000
 Z23  O14  C10  C13  118.48  3.000
 Z23  O14  C10  N9   119.57  3.000
 Z23  C13  C10  N9   121.94  3.000
 Z23  F26  C11  C12  119.76  3.000
 Z23  F26  C11  C8   119.90  3.000
 Z23  C12  C11  C8   120.33  3.000
 Z23  C27  C12  C13  123.03  3.000
 Z23  C27  C12  C11  120.83  3.000
 Z23  C13  C12  C11  116.13  3.000
 Z23  F28  C13  C12  120.68  3.000
 Z23  F28  C13  C10  119.33  3.000
 Z23  C12  C13  C10  119.99  3.000
 Z23  C15  O14  C10  117.13  3.000
 Z23  C20  C15  C16  121.21  3.000
 Z23  C20  C15  O14  118.51  3.000
 Z23  C16  C15  O14  120.26  3.000
 Z23  H33  C16  C17  120.23  3.000
 Z23  H33  C16  C15  120.39  3.000
 Z23  C17  C16  C15  119.38  3.000
 Z23  H34  C17  C18  119.79  3.000
 Z23  H34  C17  C16  119.74  3.000
 Z23  C18  C17  C16  120.48  3.000
 Z23  H35  C18  C19  120.95  3.000
 Z23  H35  C18  C17  119.59  3.000
 Z23  C19  C18  C17  119.43  3.000
 Z23  C21  C19  C20  119.48  3.000
 Z23  C21  C19  C18  119.89  3.000
 Z23  C20  C19  C18  120.63  3.000
 Z23  H36  C20  C19  121.35  3.000
 Z23  H36  C20  C15  119.76  3.000
 Z23  C19  C20  C15  118.87  3.000
 Z23  N38  C21  N22  121.73  3.000
 Z23  N38  C21  C19  119.17  3.000
 Z23  N22  C21  C19  119.11  3.000
 Z23  H46  N22  H39  116.74  3.000
 Z23  H46  N22  C21  122.24  3.000
 Z23  H39  N22  C21  120.94  3.000
 Z23  N25  C23  N24  121.56  3.000
 Z23  N25  C23  C2   119.17  3.000
 Z23  N24  C23  C2   119.27  3.000
 Z23  H48  N24  H40  116.75  3.000
 Z23  H48  N24  C23  122.21  3.000
 Z23  H40  N24  C23  120.98  3.000
 Z23  H47  N25  H41  116.80  3.000
 Z23  H47  N25  C23  120.89  3.000
 Z23  H41  N25  C23  122.16  3.000
 Z23  H44  C27  H43  108.05  3.000
 Z23  H44  C27  H42  107.99  3.000
 Z23  H43  C27  H42  107.51  3.000
 Z23  H44  C27  C12  111.90  3.000
 Z23  H43  C27  C12  110.77  3.000
 Z23  H42  C27  C12  110.46  3.000
 Z23  H50  N38  H49  116.86  3.000
 Z23  H50  N38  C21  120.74  3.000
 Z23  H49  N38  C21  122.18  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
 Z23  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 Z23  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 Z23  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 Z23  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 Z23  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 Z23  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 Z23  CONST_07  C13  C10  N9   C8     0.00   0.0  0
 Z23  CONST_08  C13  C12  C11  C8     0.00   0.0  0
 Z23  CONST_09  C12  C11  C8   N9     0.00   0.0  0
 Z23  CONST_10  C12  C13  C10  N9     0.00   0.0  0
 Z23  CONST_11  C11  C8   N9   C10    0.00   0.0  0
 Z23  CONST_12  C11  C12  C13  C10    0.00   0.0  0
 Z23  CONST_13  C18  C17  C16  C15    0.00   0.0  0
 Z23  CONST_14  C18  C19  C20  C15    0.00   0.0  0
 Z23  CONST_15  C19  C20  C15  C16    0.00   0.0  0
 Z23  CONST_16  C19  C18  C17  C16    0.00   0.0  0
 Z23  CONST_17  C20  C15  C16  C17    0.00   0.0  0
 Z23  CONST_18  C20  C19  C18  C17    0.00   0.0  0
 Z23  CONST_19  O7   C4   C3   C2   180.00   0.0  0
 Z23  CONST_20  C23  C2   C3   C4   180.00   0.0  0
 Z23  CONST_21  C23  C2   C1   C6   180.00   0.0  0
 Z23  CONST_22  O7   C4   C5   C6   180.00   0.0  0
 Z23  CONST_23  C10  N9   C8   O7   180.00   0.0  0
 Z23  CONST_24  C12  C11  C8   O7   180.00   0.0  0
 Z23  CONST_25  O14  C10  N9   C8   180.00   0.0  0
 Z23  CONST_26  C27  C12  C11  C8   180.00   0.0  0
 Z23  CONST_27  F26  C11  C8   N9   180.00   0.0  0
 Z23  CONST_28  F28  C13  C10  N9   180.00   0.0  0
 Z23  CONST_29  C27  C12  C13  C10  180.00   0.0  0
 Z23  CONST_30  F28  C13  C12  C11  180.00   0.0  0
 Z23  CONST_31  O14  C10  C13  C12  180.00   0.0  0
 Z23  CONST_32  F26  C11  C12  C13  180.00   0.0  0
 Z23  CONST_33  C17  C16  C15  O14  180.00   0.0  0
 Z23  CONST_34  C19  C20  C15  O14  180.00   0.0  0
 Z23  CONST_35  C21  C19  C20  C15  180.00   0.0  0
 Z23  CONST_36  C21  C19  C18  C17  180.00   0.0  0
 Z23  CONST_37  H30  C3   C2   C1   180.00   0.0  0
 Z23  CONST_38  H31  C5   C6   C1   180.00   0.0  0
 Z23  CONST_39  H32  C6   C1   C2   180.00   0.0  0
 Z23  CONST_40  H29  C1   C2   C3   180.00   0.0  0
 Z23  CONST_41  H34  C17  C16  C15  180.00   0.0  0
 Z23  CONST_42  H36  C20  C15  C16  180.00   0.0  0
 Z23  CONST_43  H35  C18  C17  C16  180.00   0.0  0
 Z23  CONST_44  H33  C16  C17  C18  180.00   0.0  0
 Z23  CONST_45  H40  N24  C23  C2     0.00   0.0  0
 Z23  CONST_46  H48  N24  C23  C2   180.00   0.0  0
 Z23  CONST_47  H41  N25  C23  C2   180.00   0.0  0
 Z23  CONST_48  H47  N25  C23  C2     0.00   0.0  0
 Z23  CONST_49  H39  N22  C21  C19    0.00   0.0  0
 Z23  CONST_50  H46  N22  C21  C19  180.00   0.0  0
 Z23  CONST_51  H49  N38  C21  C19  180.00   0.0  0
 Z23  CONST_52  H50  N38  C21  C19    0.00   0.0  0
 Z23  Var_01    N9   C8   O7   C4    -9.69  30.0  2
 Z23  Var_02    C16  C15  O14  C10   71.78  30.0  2
 Z23  Var_03    N24  C23  C2   C1    37.18  30.0  2
 Z23  Var_04    N22  C21  C19  C18  -38.97  30.0  2
 Z23  Var_05    H42  C27  C12  C11  -61.79  30.0  2

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
 Z23  plan-1  C1   0.020
 Z23  plan-1  C2   0.020
 Z23  plan-1  C3   0.020
 Z23  plan-1  C4   0.020
 Z23  plan-1  C5   0.020
 Z23  plan-1  C6   0.020
 Z23  plan-1  O7   0.020
 Z23  plan-1  C23  0.020
 Z23  plan-1  H29  0.020
 Z23  plan-1  H30  0.020
 Z23  plan-1  H31  0.020
 Z23  plan-1  H32  0.020
 Z23  plan-2  O7   0.020
 Z23  plan-2  C8   0.020
 Z23  plan-2  N9   0.020
 Z23  plan-2  C10  0.020
 Z23  plan-2  C11  0.020
 Z23  plan-2  C12  0.020
 Z23  plan-2  C13  0.020
 Z23  plan-2  O14  0.020
 Z23  plan-2  F26  0.020
 Z23  plan-2  C27  0.020
 Z23  plan-2  F28  0.020
 Z23  plan-3  O14  0.020
 Z23  plan-3  C15  0.020
 Z23  plan-3  C16  0.020
 Z23  plan-3  C17  0.020
 Z23  plan-3  C18  0.020
 Z23  plan-3  C19  0.020
 Z23  plan-3  C20  0.020
 Z23  plan-3  C21  0.020
 Z23  plan-3  H33  0.020
 Z23  plan-3  H34  0.020
 Z23  plan-3  H35  0.020
 Z23  plan-3  H36  0.020
 Z23  plan-4  C19  0.020
 Z23  plan-4  C21  0.020
 Z23  plan-4  N22  0.020
 Z23  plan-4  N38  0.020
 Z23  plan-4  H39  0.020
 Z23  plan-4  H46  0.020
 Z23  plan-4  H49  0.020
 Z23  plan-4  H50  0.020
 Z23  plan-5  C2   0.020
 Z23  plan-5  C23  0.020
 Z23  plan-5  N24  0.020
 Z23  plan-5  N25  0.020
 Z23  plan-5  H40  0.020
 Z23  plan-5  H48  0.020
 Z23  plan-5  H41  0.020
 Z23  plan-5  H47  0.020

