# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 22:03:39 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 5-methyl-7-(naphthalen-2-ylamino)-1H-[1,2,4]triazolo[1,5-a]pyrimidine-3,8-diium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Nc2ccc3ccccc3c2)[n+]4[nH]c[nH+]c4n1
#
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
 JZ8  JZ8  5-methyl-7-(naphthalen-2-ylamino)-1H-[1,2,4]triazolo[1,5-a]pyrimidine-3,8-diium  ligand  36  21  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JZ8
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
 JZ8  C1    C  CR16  0  -0.254   1.5193  -1.7241  -1.0277
 JZ8  N1    N  NH1   0  -0.741  -0.5347  -1.2103   0.1798
 JZ8  C2    C  CR6   0   0.240   0.8655  -1.0120  -0.0024
 JZ8  N2    N  N     1  -0.409  -2.7469  -0.4787   0.2085
 JZ8  C3    C  CR16  0  -0.312   1.5415  -0.1543   0.8188
 JZ8  N3    N  NR15  0  -0.366  -3.3669  -1.5681   0.7198
 JZ8  C4    C  CR66  0   0.120   2.9267   0.0505   0.6334
 JZ8  N4    N  NR15  1  -0.638  -4.8742  -0.1011   0.3354
 JZ8  C5    C  CR16  0  -0.308   3.6596   0.9393   1.4540
 JZ8  N5    N  N     0  -0.436  -3.4764   1.6394  -0.5188
 JZ8  C6    C  CR16  0  -0.252   5.0008   1.1179   1.2545
 JZ8  C7    C  CR16  0  -0.250   5.6696   0.4158   0.2295
 JZ8  C8    C  CR16  0  -0.305   4.9860  -0.4535  -0.5760
 JZ8  C9    C  CR66  0   0.123   3.5988  -0.6592  -0.3956
 JZ8  C10   C  CR16  0  -0.315   2.8617  -1.5498  -1.2115
 JZ8  C11   C  CR6   0   0.807  -1.4238  -0.2656  -0.0603
 JZ8  C12   C  CR16  0  -0.423  -1.1664   1.0061  -0.5844
 JZ8  C13   C  CR6   0   0.303  -2.1823   1.9170  -0.7963
 JZ8  C14   C  CH3   0  -0.721  -1.9028   3.2694  -1.3400
 JZ8  C15   C  CR56  0   0.820  -3.6935   0.4730  -0.0406
 JZ8  C16   C  CR15  0   0.359  -4.6466  -1.3187   0.7892
 JZ8  H1    H  HCR6  0   0.282   0.9539  -2.3953  -1.6607
 JZ8  HN1   H  HNH1  0   0.446  -0.8237  -2.1434   0.4398
 JZ8  H3    H  HCR6  0   0.288   1.0235   0.3714   1.6120
 JZ8  HN4   H  HNR5  0   0.505  -5.7842   0.3462   0.2718
 JZ8  H5    H  HCR6  0   0.263   3.1444   1.4756   2.2414
 JZ8  H6    H  HCR6  0   0.266   5.5569   1.8002   1.8835
 JZ8  H7    H  HCR6  0   0.266   6.7305   0.5691   0.0828
 JZ8  H8    H  HCR6  0   0.263   5.5005  -0.9925  -1.3620
 JZ8  H10   H  HCR6  0   0.270   3.3728  -2.0906  -1.9981
 JZ8  H12   H  HCR6  0   0.340  -0.1500   1.2678  -0.8331
 JZ8  H14   H  HCH3  0   0.286  -2.1523   4.0195  -0.5875
 JZ8  H14A  H  HCH3  0   0.269  -0.8595   3.3875  -1.6180
 JZ8  H14B  H  HCH3  0   0.283  -2.5319   3.4624  -2.2088
 JZ8  H16   H  HCR5  0   0.420  -5.3848  -2.0107   1.1627
 JZ8  HN3   H  HNR5  0   0.507  -2.8912  -2.4104   1.0263

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
 JZ8  C1   C2    aromatic  1.409  0.020  1.409
 JZ8  C1   C10   aromatic  1.366  0.020  1.366
 JZ8  N1   C2    single    1.426  0.020  1.426
 JZ8  N1   C11   single    1.319  0.020  1.319
 JZ8  C2   C3    aromatic  1.366  0.020  1.366
 JZ8  N2   N3    aromatic  1.354  0.020  1.354
 JZ8  N2   C11   aromatic  1.367  0.020  1.367
 JZ8  N2   C15   aromatic  1.365  0.020  1.365
 JZ8  C3   C4    aromatic  1.412  0.020  1.412
 JZ8  N3   C16   aromatic  1.306  0.020  1.306
 JZ8  C4   C5    aromatic  1.414  0.020  1.414
 JZ8  C4   C9    aromatic  1.419  0.020  1.419
 JZ8  N4   C15   aromatic  1.366  0.020  1.366
 JZ8  N4   C16   aromatic  1.319  0.020  1.319
 JZ8  C5   C6    aromatic  1.368  0.020  1.368
 JZ8  N5   C13   aromatic  1.352  0.020  1.352
 JZ8  N5   C15   aromatic  1.279  0.020  1.279
 JZ8  C6   C7    aromatic  1.411  0.020  1.411
 JZ8  C7   C8    aromatic  1.368  0.020  1.368
 JZ8  C8   C9    aromatic  1.414  0.020  1.414
 JZ8  C9   C10   aromatic  1.415  0.020  1.415
 JZ8  C11  C12   aromatic  1.399  0.020  1.399
 JZ8  C12  C13   aromatic  1.381  0.020  1.381
 JZ8  C13  C14   single    1.484  0.020  1.484
 JZ8  C1   H1    single    0.930  0.020  1.080
 JZ8  N1   HN1   single    0.860  0.020  1.020
 JZ8  C3   H3    single    0.930  0.020  1.080
 JZ8  N3   HN3   single    0.860  0.020  1.020
 JZ8  N4   HN4   single    0.860  0.020  1.020
 JZ8  C5   H5    single    0.930  0.020  1.080
 JZ8  C6   H6    single    0.930  0.020  1.080
 JZ8  C7   H7    single    0.930  0.020  1.080
 JZ8  C8   H8    single    0.930  0.020  1.080
 JZ8  C10  H10   single    0.930  0.020  1.080
 JZ8  C12  H12   single    0.930  0.020  1.080
 JZ8  C14  H14   single    0.970  0.020  1.090
 JZ8  C14  H14A  single    0.970  0.020  1.090
 JZ8  C14  H14B  single    0.970  0.020  1.090
 JZ8  C16  H16   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
 JZ8  H1    C1   C10   120.93  3.000
 JZ8  H1    C1   C2    119.78  3.000
 JZ8  C10   C1   C2    119.29  3.000
 JZ8  HN1   N1   C11   121.01  3.000
 JZ8  HN1   N1   C2    116.23  3.000
 JZ8  C11   N1   C2    122.61  3.000
 JZ8  C3    C2   N1    119.76  3.000
 JZ8  C3    C2   C1    121.67  3.000
 JZ8  N1    C2   C1    118.57  3.000
 JZ8  C15   N2   C11   121.77  3.000
 JZ8  C15   N2   N3    108.20  3.000
 JZ8  C11   N2   N3    130.02  3.000
 JZ8  H3    C3   C4    119.65  3.000
 JZ8  H3    C3   C2    120.53  3.000
 JZ8  C4    C3   C2    119.82  3.000
 JZ8  HN3   N3   C16   127.02  3.000
 JZ8  HN3   N3   N2    124.56  3.000
 JZ8  C16   N3   N2    108.37  3.000
 JZ8  C9    C4   C5    119.31  3.000
 JZ8  C9    C4   C3    119.15  3.000
 JZ8  C5    C4   C3    121.54  3.000
 JZ8  HN4   N4   C16   125.62  3.000
 JZ8  HN4   N4   C15   124.89  3.000
 JZ8  C16   N4   C15   109.48  3.000
 JZ8  H5    C5   C6    120.52  3.000
 JZ8  H5    C5   C4    119.11  3.000
 JZ8  C6    C5   C4    120.37  3.000
 JZ8  C15   N5   C13   115.23  3.000
 JZ8  H6    C6   C7    119.51  3.000
 JZ8  H6    C6   C5    120.11  3.000
 JZ8  C7    C6   C5    120.38  3.000
 JZ8  H7    C7   C8    120.01  3.000
 JZ8  H7    C7   C6    119.52  3.000
 JZ8  C8    C7   C6    120.47  3.000
 JZ8  H8    C8   C9    119.10  3.000
 JZ8  H8    C8   C7    120.41  3.000
 JZ8  C9    C8   C7    120.50  3.000
 JZ8  C10   C9   C8    121.94  3.000
 JZ8  C10   C9   C4    119.09  3.000
 JZ8  C8    C9   C4    118.97  3.000
 JZ8  H10   C10  C9    119.17  3.000
 JZ8  H10   C10  C1    119.86  3.000
 JZ8  C9    C10  C1    120.97  3.000
 JZ8  C12   C11  N2    113.17  3.000
 JZ8  C12   C11  N1    126.51  3.000
 JZ8  N2    C11  N1    120.32  3.000
 JZ8  H12   C12  C13   119.86  3.000
 JZ8  H12   C12  C11   118.70  3.000
 JZ8  C13   C12  C11   121.44  3.000
 JZ8  C14   C13  C12   121.25  3.000
 JZ8  C14   C13  N5    116.26  3.000
 JZ8  C12   C13  N5    122.49  3.000
 JZ8  H14B  C14  H14A  109.34  3.000
 JZ8  H14B  C14  H14   107.22  3.000
 JZ8  H14A  C14  H14   108.74  3.000
 JZ8  H14B  C14  C13   110.16  3.000
 JZ8  H14A  C14  C13   111.94  3.000
 JZ8  H14   C14  C13   109.31  3.000
 JZ8  N5    C15  N4    129.27  3.000
 JZ8  N5    C15  N2    125.88  3.000
 JZ8  N4    C15  N2    104.84  3.000
 JZ8  H16   C16  N4    126.38  3.000
 JZ8  H16   C16  N3    124.52  3.000
 JZ8  N4    C16  N3    109.10  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
 JZ8  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 JZ8  CONST_02  C4   C9   C10  C1      0.00   0.0  0
 JZ8  CONST_03  C8   C9   C10  C1    180.00   0.0  0
 JZ8  CONST_04  C9   C10  C1   C2      0.00   0.0  0
 JZ8  CONST_05  C5   C4   C3   C2    180.00   0.0  0
 JZ8  CONST_06  C9   C4   C3   C2      0.00   0.0  0
 JZ8  CONST_07  N4   C16  N3   N2      0.00   0.0  0
 JZ8  CONST_08  C13  C12  C11  N2      0.00   0.0  0
 JZ8  CONST_09  C16  N4   C15  N2      0.00   0.0  0
 JZ8  CONST_10  C13  N5   C15  N2      0.00   0.0  0
 JZ8  CONST_11  C10  C1   C2   C3      0.00   0.0  0
 JZ8  CONST_12  C6   C5   C4   C3    180.00   0.0  0
 JZ8  CONST_13  C8   C9   C4   C3    180.00   0.0  0
 JZ8  CONST_14  C10  C9   C4   C3      0.00   0.0  0
 JZ8  CONST_15  C12  C11  N2   N3    180.00   0.0  0
 JZ8  CONST_16  N4   C15  N2   N3      0.00   0.0  0
 JZ8  CONST_17  N5   C15  N2   N3    180.00   0.0  0
 JZ8  CONST_18  C15  N4   C16  N3      0.00   0.0  0
 JZ8  CONST_19  C7   C6   C5   C4      0.00   0.0  0
 JZ8  CONST_20  C7   C8   C9   C4      0.00   0.0  0
 JZ8  CONST_21  C11  N2   C15  N4    180.00   0.0  0
 JZ8  CONST_22  C13  N5   C15  N4    180.00   0.0  0
 JZ8  CONST_23  C8   C9   C4   C5      0.00   0.0  0
 JZ8  CONST_24  C10  C9   C4   C5    180.00   0.0  0
 JZ8  CONST_25  C8   C7   C6   C5      0.00   0.0  0
 JZ8  CONST_26  C11  C12  C13  N5      0.00   0.0  0
 JZ8  CONST_27  C11  N2   C15  N5      0.00   0.0  0
 JZ8  CONST_28  C16  N4   C15  N5    180.00   0.0  0
 JZ8  CONST_29  C9   C4   C5   C6      0.00   0.0  0
 JZ8  CONST_30  C9   C8   C7   C6      0.00   0.0  0
 JZ8  CONST_31  C10  C9   C8   C7    180.00   0.0  0
 JZ8  CONST_32  C16  N3   N2   C11   180.00   0.0  0
 JZ8  CONST_33  C15  N2   C11  C12     0.00   0.0  0
 JZ8  CONST_34  C15  N5   C13  C12     0.00   0.0  0
 JZ8  CONST_35  C16  N3   N2   C15     0.00   0.0  0
 JZ8  CONST_36  C10  C1   C2   N1    180.00   0.0  0
 JZ8  CONST_37  C4   C3   C2   N1    180.00   0.0  0
 JZ8  CONST_38  N3   N2   C11  N1      0.00   0.0  0
 JZ8  CONST_39  C15  N2   C11  N1    180.00   0.0  0
 JZ8  CONST_40  C13  C12  C11  N1    180.00   0.0  0
 JZ8  CONST_41  C14  C13  C12  C11   180.00   0.0  0
 JZ8  CONST_42  C15  N5   C13  C14   180.00   0.0  0
 JZ8  CONST_43  H3   C3   C2   C1    180.00   0.0  0
 JZ8  CONST_44  H10  C10  C1   C2    180.00   0.0  0
 JZ8  CONST_45  H16  C16  N3   N2    180.00   0.0  0
 JZ8  CONST_46  H12  C12  C11  N2    180.00   0.0  0
 JZ8  CONST_47  HN4  N4   C15  N2    180.00   0.0  0
 JZ8  CONST_48  H1   C1   C2   C3    180.00   0.0  0
 JZ8  CONST_49  H5   C5   C4   C3      0.00   0.0  0
 JZ8  CONST_50  H6   C6   C5   C4    180.00   0.0  0
 JZ8  CONST_51  H8   C8   C9   C4    180.00   0.0  0
 JZ8  CONST_52  HN3  N3   C16  N4    180.00   0.0  0
 JZ8  CONST_53  H7   C7   C6   C5    180.00   0.0  0
 JZ8  Var_01    C11  N1   C2   C1   -112.61  30.0  2
 JZ8  Var_02    N2   C11  N1   C2   -175.95  30.0  2
 JZ8  Var_03    H14  C14  C13  N5     64.42  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
 JZ8  plan-1  N1   0.020
 JZ8  plan-1  N2   0.020
 JZ8  plan-1  N3   0.020
 JZ8  plan-1  N4   0.020
 JZ8  plan-1  N5   0.020
 JZ8  plan-1  C11  0.020
 JZ8  plan-1  C12  0.020
 JZ8  plan-1  C13  0.020
 JZ8  plan-1  C14  0.020
 JZ8  plan-1  C15  0.020
 JZ8  plan-1  C16  0.020
 JZ8  plan-1  HN4  0.020
 JZ8  plan-1  H12  0.020
 JZ8  plan-1  H16  0.020
 JZ8  plan-1  HN3  0.020
 JZ8  plan-2  C1   0.020
 JZ8  plan-2  N1   0.020
 JZ8  plan-2  C2   0.020
 JZ8  plan-2  C3   0.020
 JZ8  plan-2  C4   0.020
 JZ8  plan-2  C5   0.020
 JZ8  plan-2  C6   0.020
 JZ8  plan-2  C7   0.020
 JZ8  plan-2  C8   0.020
 JZ8  plan-2  C9   0.020
 JZ8  plan-2  C10  0.020
 JZ8  plan-2  H1   0.020
 JZ8  plan-2  H3   0.020
 JZ8  plan-2  H5   0.020
 JZ8  plan-2  H6   0.020
 JZ8  plan-2  H7   0.020
 JZ8  plan-2  H8   0.020
 JZ8  plan-2  H10  0.020

