# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 18:24:47 2022
#   Inital geometry file: a 124 line input string
#   Ligand name: {amino[3-({6-[3-(ammoniomethyl)phenoxy]-3,5-difluoro-4-methylpyridin-2-yl}oxy)phenyl]methylidene}ammonium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(F)c(Oc2cccc(C[NH3+])c2)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
 ZK9  ZK9  {amino[3-({6-[3-(ammoniomethyl)phenoxy]-3,5-difluoro-4-methylpyridin-2-yl}oxy)phenyl]methylidene}ammonium  ligand  48  28  .  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_ZK9
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
 ZK9  C1   C  CR16  0  -0.273   3.0323  -1.2188   1.7227
 ZK9  C2   C  CR6   0   0.035   2.5274  -1.0918   0.4295
 ZK9  C3   C  CR16  0  -0.301   2.0353   0.1278  -0.0228
 ZK9  C4   C  CR6   0   0.375   2.0506   1.2144   0.8352
 ZK9  C5   C  CR16  0  -0.293   2.5480   1.1019   2.1224
 ZK9  C6   C  CR16  0  -0.239   3.0464  -0.1171   2.5594
 ZK9  O7   O  O2    0  -0.508   1.6212   2.4498   0.4203
 ZK9  C8   C  CR6   0   0.375   0.3171   2.6187   0.1196
 ZK9  N9   N  N     0  -0.451  -0.5121   1.6120   0.2179
 ZK9  C10  C  CR6   0   0.376  -1.7789   1.7757  -0.0724
 ZK9  C11  C  CR6   0   0.395  -0.1033   3.8776  -0.2791
 ZK9  C12  C  CR6   0  -0.173  -1.4364   4.0983  -0.5867
 ZK9  C13  C  CR6   0   0.394  -2.2800   3.0045  -0.4695
 ZK9  O14  O  O2    0  -0.513  -2.6240   0.7317   0.0176
 ZK9  C15  C  CR6   0   0.372  -2.0674  -0.5153   0.2118
 ZK9  C16  C  CR16  0  -0.296  -1.9844  -1.0324   1.4925
 ZK9  C17  C  CR16  0  -0.238  -1.4724  -2.3089   1.6715
 ZK9  C18  C  CR16  0  -0.284  -1.0501  -3.0545   0.5810
 ZK9  C19  C  CR6   0   0.074  -1.1332  -2.5230  -0.7014
 ZK9  C20  C  CR16  0  -0.322  -1.6401  -1.2411  -0.8859
 ZK9  C21  C  CH2   0  -0.406  -0.7217  -3.3396  -1.8881
 ZK9  N22  N  NT3   1  -0.767  -1.9048  -4.0018  -2.5079
 ZK9  C23  C  C     0   0.591   2.5447  -2.2525  -0.4747
 ZK9  N24  N  NH2   0  -0.773   2.3434  -3.4519   0.0150
 ZK9  N25  N  NC2   1  -0.769   2.7592  -2.0693  -1.7550
 ZK9  F26  F  F     0  -0.293   0.7849   4.8736  -0.3607
 ZK9  C27  C  CH3   0  -0.707  -1.9497   5.4377  -1.0099
 ZK9  F28  F  F     0  -0.292  -3.5824   3.1316  -0.7451
 ZK9  H29  H  HCR6  0   0.286   3.4456  -2.1563   2.0700
 ZK9  H30  H  HCR6  0   0.294   1.6259   0.2309  -1.0191
 ZK9  H31  H  HCR6  0   0.291   2.5511   1.9638   2.7765
 ZK9  H32  H  HCR6  0   0.285   3.4492  -0.2054   3.5587
 ZK9  H33  H  HCR6  0   0.280  -2.3166  -0.4475   2.3402
 ZK9  H34  H  HCR6  0   0.273  -1.4027  -2.7230   2.6681
 ZK9  H35  H  HCR6  0   0.272  -0.6620  -4.0546   0.7300
 ZK9  H36  H  HCR6  0   0.281  -1.7073  -0.8115  -1.8790
 ZK9  H37  H  HCH2  0   0.316  -0.2637  -2.7346  -2.6672
 ZK9  H38  H  HCH2  0   0.308  -0.0368  -4.1385  -1.6146
 ZK9  H39  H  HNT3  0   0.476  -2.3809  -4.6207  -1.8512
 ZK9  H45  H  HNT3  0   0.474  -2.5929  -3.3259  -2.8393
 ZK9  H46  H  HNT3  0   0.482  -1.6335  -4.5680  -3.3120
 ZK9  H40  H  HNH2  0   0.445   2.4664  -4.2877  -0.5378
 ZK9  H48  H  HNH2  0   0.448   2.0808  -3.5834   0.9784
 ZK9  H41  H  HNC2  0   0.450   3.0581  -1.1740  -2.1071
 ZK9  H47  H  HNC2  0   0.442   2.7800  -2.8368  -2.4102
 ZK9  H42  H  HCH3  0   0.277  -2.4090   5.9510  -0.1643
 ZK9  H43  H  HCH3  0   0.267  -1.1525   6.0703  -1.3905
 ZK9  H44  H  HCH3  0   0.268  -2.7044   5.3414  -1.7873

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
 ZK9  C1   C2   aromatic  1.394  0.020  1.394
 ZK9  C1   C6   aromatic  1.384  0.020  1.384
 ZK9  C1   H29  single    0.930  0.020  1.080
 ZK9  C2   C3   aromatic  1.391  0.020  1.391
 ZK9  C2   C23  single    1.471  0.020  1.471
 ZK9  C3   C4   aromatic  1.385  0.020  1.385
 ZK9  C3   H30  single    0.930  0.020  1.080
 ZK9  C4   C5   aromatic  1.385  0.020  1.385
 ZK9  C4   O7   single    1.372  0.020  1.372
 ZK9  C5   C6   aromatic  1.387  0.020  1.387
 ZK9  C5   H31  single    0.930  0.020  1.080
 ZK9  C6   H32  single    0.930  0.020  1.080
 ZK9  O7   C8   single    1.349  0.020  1.349
 ZK9  C8   N9   aromatic  1.308  0.020  1.308
 ZK9  C8   C11  aromatic  1.386  0.020  1.386
 ZK9  N9   C10  aromatic  1.310  0.020  1.310
 ZK9  C10  C13  aromatic  1.385  0.020  1.385
 ZK9  C10  O14  single    1.346  0.020  1.346
 ZK9  C11  C12  aromatic  1.386  0.020  1.386
 ZK9  C11  F26  single    1.337  0.020  1.337
 ZK9  C12  C13  aromatic  1.386  0.020  1.386
 ZK9  C12  C27  single    1.496  0.020  1.496
 ZK9  C13  F28  single    1.337  0.020  1.337
 ZK9  O14  C15  single    1.379  0.020  1.379
 ZK9  C15  C16  aromatic  1.384  0.020  1.384
 ZK9  C15  C20  aromatic  1.384  0.020  1.384
 ZK9  C16  C17  aromatic  1.387  0.020  1.387
 ZK9  C16  H33  single    0.930  0.020  1.080
 ZK9  C17  C18  aromatic  1.387  0.020  1.387
 ZK9  C17  H34  single    0.930  0.020  1.080
 ZK9  C18  C19  aromatic  1.391  0.020  1.391
 ZK9  C18  H35  single    0.930  0.020  1.080
 ZK9  C19  C20  aromatic  1.391  0.020  1.391
 ZK9  C19  C21  single    1.498  0.020  1.498
 ZK9  C20  H36  single    0.930  0.020  1.080
 ZK9  C21  N22  single    1.491  0.020  1.491
 ZK9  C21  H37  single    0.970  0.020  1.090
 ZK9  C21  H38  single    0.970  0.020  1.090
 ZK9  N22  H39  single    0.890  0.020  1.040
 ZK9  N22  H45  single    0.890  0.020  1.040
 ZK9  N22  H46  single    0.890  0.020  1.040
 ZK9  C23  N24  single    1.311  0.020  1.311
 ZK9  C23  N25  double    1.311  0.020  1.311
 ZK9  N24  H40  single    0.860  0.020  1.020
 ZK9  N24  H48  single    0.860  0.020  1.020
 ZK9  N25  H41  single    0.860  0.020  1.020
 ZK9  N25  H47  single    0.860  0.020  1.020
 ZK9  C27  H42  single    0.970  0.020  1.090
 ZK9  C27  H43  single    0.970  0.020  1.090
 ZK9  C27  H44  single    0.970  0.020  1.090

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
 ZK9  H29  C1   C6   119.47  3.000
 ZK9  H29  C1   C2   121.01  3.000
 ZK9  C6   C1   C2   119.48  3.000
 ZK9  C23  C2   C3   119.74  3.000
 ZK9  C23  C2   C1   119.60  3.000
 ZK9  C3   C2   C1   120.65  3.000
 ZK9  H30  C3   C4   120.00  3.000
 ZK9  H30  C3   C2   121.12  3.000
 ZK9  C4   C3   C2   118.87  3.000
 ZK9  O7   C4   C5   117.82  3.000
 ZK9  O7   C4   C3   121.05  3.000
 ZK9  C5   C4   C3   121.09  3.000
 ZK9  H31  C5   C6   120.56  3.000
 ZK9  H31  C5   C4   119.89  3.000
 ZK9  C6   C5   C4   119.55  3.000
 ZK9  H32  C6   C5   119.78  3.000
 ZK9  H32  C6   C1   119.85  3.000
 ZK9  C5   C6   C1   120.36  3.000
 ZK9  C8   O7   C4   118.86  3.000
 ZK9  C11  C8   N9   121.90  3.000
 ZK9  C11  C8   O7   118.11  3.000
 ZK9  N9   C8   O7   119.99  3.000
 ZK9  C10  N9   C8   120.02  3.000
 ZK9  O14  C10  C13  118.69  3.000
 ZK9  O14  C10  N9   119.69  3.000
 ZK9  C13  C10  N9   121.62  3.000
 ZK9  F26  C11  C12  120.46  3.000
 ZK9  F26  C11  C8   119.52  3.000
 ZK9  C12  C11  C8   120.02  3.000
 ZK9  C27  C12  C13  121.44  3.000
 ZK9  C27  C12  C11  122.39  3.000
 ZK9  C13  C12  C11  116.17  3.000
 ZK9  F28  C13  C12  120.02  3.000
 ZK9  F28  C13  C10  119.72  3.000
 ZK9  C12  C13  C10  120.26  3.000
 ZK9  C15  O14  C10  117.21  3.000
 ZK9  C20  C15  C16  121.31  3.000
 ZK9  C20  C15  O14  119.16  3.000
 ZK9  C16  C15  O14  119.50  3.000
 ZK9  H33  C16  C17  120.64  3.000
 ZK9  H33  C16  C15  120.31  3.000
 ZK9  C17  C16  C15  119.05  3.000
 ZK9  H34  C17  C18  119.94  3.000
 ZK9  H34  C17  C16  119.68  3.000
 ZK9  C18  C17  C16  120.38  3.000
 ZK9  H35  C18  C19  120.08  3.000
 ZK9  H35  C18  C17  119.82  3.000
 ZK9  C19  C18  C17  120.09  3.000
 ZK9  C21  C19  C20  119.83  3.000
 ZK9  C21  C19  C18  120.38  3.000
 ZK9  C20  C19  C18  119.76  3.000
 ZK9  H36  C20  C19  120.62  3.000
 ZK9  H36  C20  C15  119.98  3.000
 ZK9  C19  C20  C15  119.40  3.000
 ZK9  H38  C21  H37  108.88  3.000
 ZK9  H38  C21  N22  106.14  3.000
 ZK9  H37  C21  N22  106.46  3.000
 ZK9  H38  C21  C19  111.98  3.000
 ZK9  H37  C21  C19  112.33  3.000
 ZK9  N22  C21  C19  110.70  3.000
 ZK9  H46  N22  H45  106.92  3.000
 ZK9  H46  N22  H39  107.15  3.000
 ZK9  H45  N22  H39  107.25  3.000
 ZK9  H46  N22  C21  111.30  3.000
 ZK9  H45  N22  C21  112.09  3.000
 ZK9  H39  N22  C21  111.85  3.000
 ZK9  N25  C23  N24  121.18  3.000
 ZK9  N25  C23  C2   119.46  3.000
 ZK9  N24  C23  C2   119.36  3.000
 ZK9  H48  N24  H40  116.57  3.000
 ZK9  H48  N24  C23  121.12  3.000
 ZK9  H40  N24  C23  122.29  3.000
 ZK9  H47  N25  H41  116.28  3.000
 ZK9  H47  N25  C23  122.08  3.000
 ZK9  H41  N25  C23  120.94  3.000
 ZK9  H44  C27  H43  108.07  3.000
 ZK9  H44  C27  H42  107.67  3.000
 ZK9  H43  C27  H42  107.85  3.000
 ZK9  H44  C27  C12  111.17  3.000
 ZK9  H43  C27  C12  111.64  3.000
 ZK9  H42  C27  C12  110.28  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
 ZK9  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 ZK9  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 ZK9  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 ZK9  CONST_04  C5   C4   C3   C2     0.00   0.0  0
 ZK9  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 ZK9  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 ZK9  CONST_07  C13  C10  N9   C8     0.00   0.0  0
 ZK9  CONST_08  C13  C12  C11  C8     0.00   0.0  0
 ZK9  CONST_09  C12  C11  C8   N9     0.00   0.0  0
 ZK9  CONST_10  C12  C13  C10  N9     0.00   0.0  0
 ZK9  CONST_11  C11  C8   N9   C10    0.00   0.0  0
 ZK9  CONST_12  C11  C12  C13  C10    0.00   0.0  0
 ZK9  CONST_13  C18  C17  C16  C15    0.00   0.0  0
 ZK9  CONST_14  C18  C19  C20  C15    0.00   0.0  0
 ZK9  CONST_15  C19  C20  C15  C16    0.00   0.0  0
 ZK9  CONST_16  C19  C18  C17  C16    0.00   0.0  0
 ZK9  CONST_17  C20  C15  C16  C17    0.00   0.0  0
 ZK9  CONST_18  C20  C19  C18  C17    0.00   0.0  0
 ZK9  CONST_19  O7   C4   C3   C2   180.00   0.0  0
 ZK9  CONST_20  C23  C2   C3   C4   180.00   0.0  0
 ZK9  CONST_21  C23  C2   C1   C6   180.00   0.0  0
 ZK9  CONST_22  O7   C4   C5   C6   180.00   0.0  0
 ZK9  CONST_23  C10  N9   C8   O7   180.00   0.0  0
 ZK9  CONST_24  C12  C11  C8   O7   180.00   0.0  0
 ZK9  CONST_25  O14  C10  N9   C8   180.00   0.0  0
 ZK9  CONST_26  C27  C12  C11  C8   180.00   0.0  0
 ZK9  CONST_27  F26  C11  C8   N9   180.00   0.0  0
 ZK9  CONST_28  F28  C13  C10  N9   180.00   0.0  0
 ZK9  CONST_29  C27  C12  C13  C10  180.00   0.0  0
 ZK9  CONST_30  F28  C13  C12  C11  180.00   0.0  0
 ZK9  CONST_31  O14  C10  C13  C12  180.00   0.0  0
 ZK9  CONST_32  F26  C11  C12  C13  180.00   0.0  0
 ZK9  CONST_33  C17  C16  C15  O14  180.00   0.0  0
 ZK9  CONST_34  C19  C20  C15  O14  180.00   0.0  0
 ZK9  CONST_35  C21  C19  C20  C15  180.00   0.0  0
 ZK9  CONST_36  C21  C19  C18  C17  180.00   0.0  0
 ZK9  CONST_37  H30  C3   C2   C1   180.00   0.0  0
 ZK9  CONST_38  H31  C5   C6   C1   180.00   0.0  0
 ZK9  CONST_39  H32  C6   C1   C2   180.00   0.0  0
 ZK9  CONST_40  H29  C1   C2   C3   180.00   0.0  0
 ZK9  CONST_41  H34  C17  C16  C15  180.00   0.0  0
 ZK9  CONST_42  H36  C20  C15  C16  180.00   0.0  0
 ZK9  CONST_43  H35  C18  C17  C16  180.00   0.0  0
 ZK9  CONST_44  H33  C16  C17  C18  180.00   0.0  0
 ZK9  CONST_45  H40  N24  C23  C2   180.00   0.0  0
 ZK9  CONST_46  H48  N24  C23  C2     0.00   0.0  0
 ZK9  CONST_47  H41  N25  C23  C2     0.00   0.0  0
 ZK9  CONST_48  H47  N25  C23  C2   180.00   0.0  0
 ZK9  Var_01    N9   C8   O7   C4    -0.41  30.0  2
 ZK9  Var_02    C16  C15  O14  C10   96.59  30.0  2
 ZK9  Var_03    N24  C23  C2   C1    35.57  30.0  2
 ZK9  Var_04    N22  C21  C19  C18   95.85  30.0  2
 ZK9  Var_05    H42  C27  C12  C11  -98.88  30.0  2
 ZK9  Var_06    H39  N22  C21  C19  -59.63  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
 ZK9  plan-1  C1   0.020
 ZK9  plan-1  C2   0.020
 ZK9  plan-1  C3   0.020
 ZK9  plan-1  C4   0.020
 ZK9  plan-1  C5   0.020
 ZK9  plan-1  C6   0.020
 ZK9  plan-1  O7   0.020
 ZK9  plan-1  C23  0.020
 ZK9  plan-1  H29  0.020
 ZK9  plan-1  H30  0.020
 ZK9  plan-1  H31  0.020
 ZK9  plan-1  H32  0.020
 ZK9  plan-2  O7   0.020
 ZK9  plan-2  C8   0.020
 ZK9  plan-2  N9   0.020
 ZK9  plan-2  C10  0.020
 ZK9  plan-2  C11  0.020
 ZK9  plan-2  C12  0.020
 ZK9  plan-2  C13  0.020
 ZK9  plan-2  O14  0.020
 ZK9  plan-2  F26  0.020
 ZK9  plan-2  C27  0.020
 ZK9  plan-2  F28  0.020
 ZK9  plan-3  O14  0.020
 ZK9  plan-3  C15  0.020
 ZK9  plan-3  C16  0.020
 ZK9  plan-3  C17  0.020
 ZK9  plan-3  C18  0.020
 ZK9  plan-3  C19  0.020
 ZK9  plan-3  C20  0.020
 ZK9  plan-3  C21  0.020
 ZK9  plan-3  H33  0.020
 ZK9  plan-3  H34  0.020
 ZK9  plan-3  H35  0.020
 ZK9  plan-3  H36  0.020
 ZK9  plan-4  C2   0.020
 ZK9  plan-4  C23  0.020
 ZK9  plan-4  N24  0.020
 ZK9  plan-4  N25  0.020
 ZK9  plan-4  H40  0.020
 ZK9  plan-4  H48  0.020
 ZK9  plan-4  H41  0.020
 ZK9  plan-4  H47  0.020

