# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 21:11:28 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: 4-(2,4-dichlorophenyl)-5-[(E)-phenyldiazenyl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncc(N=Nc2ccccc2)c(n1)c3ccc(Cl)cc3Cl
#
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
 ZZ4  ZZ4  4-(2,4-dichlorophenyl)-5-[(E)-phenyldiazenyl]pyrimidin-2-amine  ligand  34  23  .  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_ZZ4
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
 ZZ4  CL1   CL  CL    0  -0.110   2.5424  -4.3715   0.4721
 ZZ4  C2    C   CR6   0  -0.057   2.0516  -2.7148   0.4339
 ZZ4  C1    C   CR16  0  -0.190   1.2718  -2.2075   1.4612
 ZZ4  C5    C   CR16  0  -0.287   0.8876  -0.8789   1.4120
 ZZ4  C3    C   CR16  0  -0.150   2.4460  -1.9220  -0.6304
 ZZ4  C4    C   CR6   0  -0.110   2.0537  -0.5921  -0.6487
 ZZ4  CL2   CL  CL    0  -0.109   2.5186   0.3760  -2.0029
 ZZ4  C6    C   CR6   0   0.155   1.2760  -0.0472   0.3666
 ZZ4  C7    C   CR6   0   0.201   0.8799   1.3813   0.3697
 ZZ4  N1    N   N     0  -0.436   1.8453   2.2671   0.5095
 ZZ4  C9    C   CR6   0   0.101  -0.4616   1.7556   0.2477
 ZZ4  C10   C   CR16  0  -0.028  -0.7129   3.1332   0.2891
 ZZ4  N3    N   N     0  -0.435   0.2352   4.0265   0.4282
 ZZ4  C8    C   CR6   0   0.570   1.4944   3.5589   0.5333
 ZZ4  N2    N   NH2   0  -0.809   2.4660   4.4590   0.6774
 ZZ4  N4    N   N     0  -0.240  -1.4106   0.7586   0.0738
 ZZ4  N5    N   N     0  -0.284  -2.5929   1.1340   0.0301
 ZZ4  C13   C   CR6   0   0.223  -3.5327   0.1040  -0.1499
 ZZ4  C14   C   CR16  0  -0.286  -4.8589   0.5121  -0.2659
 ZZ4  C15   C   CR16  0  -0.247  -5.8663  -0.4246  -0.4470
 ZZ4  C16   C   CR16  0  -0.255  -5.5517  -1.7748  -0.5083
 ZZ4  C11   C   CR16  0  -0.245  -4.2261  -2.1856  -0.3873
 ZZ4  C12   C   CR16  0  -0.270  -3.2170  -1.2565  -0.2095
 ZZ4  H1    H   HCR6  0   0.289   0.9649  -2.8346   2.2862
 ZZ4  H3    H   HCR6  0   0.305   3.0431  -2.3292  -1.4342
 ZZ4  H5    H   HCR6  0   0.275   0.2821  -0.4759   2.2128
 ZZ4  H10   H   HCR6  0   0.286  -1.7280   3.5028   0.1937
 ZZ4  H21N  H   HNH2  0   0.410   3.4271   4.1701   0.7300
 ZZ4  H22N  H   HNH2  0   0.410   2.2544   5.4412   0.6812
 ZZ4  H14   H   HCR6  0   0.264  -5.0879   1.5691  -0.2147
 ZZ4  H12   H   HCR6  0   0.268  -2.1879  -1.5765  -0.1144
 ZZ4  H15   H   HCR6  0   0.263  -6.8944  -0.1003  -0.5394
 ZZ4  H16   H   HCR6  0   0.265  -6.3345  -2.5087  -0.6478
 ZZ4  H11   H   HCR6  0   0.264  -3.9828  -3.2392  -0.4319

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
 ZZ4  CL1  C2    single    1.728  0.020  1.728
 ZZ4  C2   C1    aromatic  1.386  0.020  1.386
 ZZ4  C2   C3    aromatic  1.385  0.020  1.385
 ZZ4  C1   C5    aromatic  1.384  0.020  1.384
 ZZ4  C5   C6    aromatic  1.391  0.020  1.391
 ZZ4  C3   C4    aromatic  1.387  0.020  1.387
 ZZ4  C4   CL2   single    1.728  0.020  1.728
 ZZ4  C4   C6    aromatic  1.390  0.020  1.390
 ZZ4  C6   C7    single    1.482  0.020  1.482
 ZZ4  C7   N1    aromatic  1.318  0.020  1.318
 ZZ4  C7   C9    aromatic  1.398  0.020  1.398
 ZZ4  N1   C8    aromatic  1.339  0.020  1.339
 ZZ4  C9   C10   aromatic  1.401  0.020  1.401
 ZZ4  C9   N4    single    1.387  0.020  1.387
 ZZ4  C10  N3    aromatic  1.310  0.020  1.310
 ZZ4  N3   C8    aromatic  1.347  0.020  1.347
 ZZ4  C8   N2    single    1.332  0.020  1.332
 ZZ4  N4   N5    double    1.241  0.020  1.241
 ZZ4  N5   C13   single    1.406  0.020  1.406
 ZZ4  C13  C14   aromatic  1.392  0.020  1.392
 ZZ4  C13  C12   aromatic  1.398  0.020  1.398
 ZZ4  C14  C15   aromatic  1.387  0.020  1.387
 ZZ4  C15  C16   aromatic  1.388  0.020  1.388
 ZZ4  C16  C11   aromatic  1.393  0.020  1.393
 ZZ4  C11  C12   aromatic  1.383  0.020  1.383
 ZZ4  C1   H1    single    0.930  0.020  1.080
 ZZ4  C3   H3    single    0.930  0.020  1.080
 ZZ4  C5   H5    single    0.930  0.020  1.080
 ZZ4  C10  H10   single    0.930  0.020  1.080
 ZZ4  N2   H21N  single    0.860  0.020  1.020
 ZZ4  N2   H22N  single    0.860  0.020  1.020
 ZZ4  C14  H14   single    0.930  0.020  1.080
 ZZ4  C12  H12   single    0.930  0.020  1.080
 ZZ4  C15  H15   single    0.930  0.020  1.080
 ZZ4  C16  H16   single    0.930  0.020  1.080
 ZZ4  C11  H11   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
 ZZ4  C3    C2   C1    121.36  3.000
 ZZ4  C3    C2   CL1   119.01  3.000
 ZZ4  C1    C2   CL1   119.62  3.000
 ZZ4  H1    C1   C5    120.35  3.000
 ZZ4  H1    C1   C2    120.88  3.000
 ZZ4  C5    C1   C2    118.77  3.000
 ZZ4  H5    C5   C6    119.33  3.000
 ZZ4  H5    C5   C1    119.12  3.000
 ZZ4  C6    C5   C1    121.54  3.000
 ZZ4  H3    C3   C4    120.51  3.000
 ZZ4  H3    C3   C2    120.89  3.000
 ZZ4  C4    C3   C2    118.60  3.000
 ZZ4  C6    C4   CL2   120.21  3.000
 ZZ4  C6    C4   C3    121.64  3.000
 ZZ4  CL2   C4   C3    118.13  3.000
 ZZ4  C7    C6   C4    121.92  3.000
 ZZ4  C7    C6   C5    120.00  3.000
 ZZ4  C4    C6   C5    118.08  3.000
 ZZ4  C9    C7   N1    122.16  3.000
 ZZ4  C9    C7   C6    120.95  3.000
 ZZ4  N1    C7   C6    116.89  3.000
 ZZ4  C8    N1   C7    117.29  3.000
 ZZ4  N4    C9   C10   125.99  3.000
 ZZ4  N4    C9   C7    118.35  3.000
 ZZ4  C10   C9   C7    115.65  3.000
 ZZ4  H10   C10  N3    117.02  3.000
 ZZ4  H10   C10  C9    120.04  3.000
 ZZ4  N3    C10  C9    122.94  3.000
 ZZ4  C8    N3   C10   116.61  3.000
 ZZ4  N2    C8   N3    117.10  3.000
 ZZ4  N2    C8   N1    117.56  3.000
 ZZ4  N3    C8   N1    125.34  3.000
 ZZ4  H22N  N2   H21N  118.83  3.000
 ZZ4  H22N  N2   C8    120.48  3.000
 ZZ4  H21N  N2   C8    120.59  3.000
 ZZ4  N5    N4   C9    116.02  3.000
 ZZ4  C13   N5   N4    114.81  3.000
 ZZ4  C12   C13  C14   119.79  3.000
 ZZ4  C12   C13  N5    124.58  3.000
 ZZ4  C14   C13  N5    115.63  3.000
 ZZ4  H14   C14  C15   120.77  3.000
 ZZ4  H14   C14  C13   118.92  3.000
 ZZ4  C15   C14  C13   120.30  3.000
 ZZ4  H15   C15  C16   120.21  3.000
 ZZ4  H15   C15  C14   119.92  3.000
 ZZ4  C16   C15  C14   119.87  3.000
 ZZ4  H16   C16  C11   119.98  3.000
 ZZ4  H16   C16  C15   120.11  3.000
 ZZ4  C11   C16  C15   119.92  3.000
 ZZ4  H11   C11  C12   119.69  3.000
 ZZ4  H11   C11  C16   119.82  3.000
 ZZ4  C12   C11  C16   120.49  3.000
 ZZ4  H12   C12  C11   120.44  3.000
 ZZ4  H12   C12  C13   119.93  3.000
 ZZ4  C11   C12  C13   119.63  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
 ZZ4  CONST_01  C6    C5   C1   C2     0.00  0.0  0
 ZZ4  CONST_02  C6    C4   C3   C2     0.00  0.0  0
 ZZ4  CONST_03  C4    C3   C2   C1     0.00  0.0  0
 ZZ4  CONST_04  C4    C6   C5   C1     0.00  0.0  0
 ZZ4  CONST_05  C7    C6   C5   C1   180.00  0.0  0
 ZZ4  CONST_06  C3    C2   C1   C5     0.00  0.0  0
 ZZ4  CONST_07  C3    C4   C6   C5     0.00  0.0  0
 ZZ4  CONST_10  C7    C6   C4   C3   180.00  0.0  0
 ZZ4  CONST_13  C8    N1   C7   C6   180.00  0.0  0
 ZZ4  CONST_14  C10   C9   C7   C6   180.00  0.0  0
 ZZ4  CONST_15  N3    C8   N1   C7     0.00  0.0  0
 ZZ4  CONST_16  N3    C10  C9   C7     0.00  0.0  0
 ZZ4  CONST_17  C10   C9   C7   N1     0.00  0.0  0
 ZZ4  CONST_18  C10   N3   C8   N1     0.00  0.0  0
 ZZ4  CONST_19  C8    N1   C7   C9     0.00  0.0  0
 ZZ4  CONST_20  C8    N3   C10  C9     0.00  0.0  0
 ZZ4  CONST_21  C16   C15  C14  C13    0.00  0.0  0
 ZZ4  CONST_22  C16   C11  C12  C13    0.00  0.0  0
 ZZ4  CONST_23  C11   C12  C13  C14    0.00  0.0  0
 ZZ4  CONST_24  C11   C16  C15  C14    0.00  0.0  0
 ZZ4  CONST_25  C12   C13  C14  C15    0.00  0.0  0
 ZZ4  CONST_26  C12   C11  C16  C15    0.00  0.0  0
 ZZ4  CONST_27  C5    C1   C2   CL1  180.00  0.0  0
 ZZ4  CONST_28  C4    C3   C2   CL1  180.00  0.0  0
 ZZ4  CONST_29  CL2   C4   C3   C2   180.00  0.0  0
 ZZ4  CONST_30  CL2   C4   C6   C5   180.00  0.0  0
 ZZ4  CONST_31  C7    C6   C4   CL2    0.00  0.0  0
 ZZ4  CONST_32  N4    C9   C7   C6     0.00  0.0  0
 ZZ4  CONST_33  N2    C8   N1   C7   180.00  0.0  0
 ZZ4  CONST_34  N4    C9   C7   N1   180.00  0.0  0
 ZZ4  CONST_35  N2    C8   N3   C10  180.00  0.0  0
 ZZ4  CONST_36  N4    C9   C10  N3   180.00  0.0  0
 ZZ4  CONST_37  C15   C14  C13  N5   180.00  0.0  0
 ZZ4  CONST_38  C11   C12  C13  N5   180.00  0.0  0
 ZZ4  CONST_39  H5    C5   C1   C2   180.00  0.0  0
 ZZ4  CONST_40  H3    C3   C2   C1   180.00  0.0  0
 ZZ4  CONST_41  H1    C1   C2   C3   180.00  0.0  0
 ZZ4  CONST_42  H10   C10  C9   C7   180.00  0.0  0
 ZZ4  CONST_43  H15   C15  C14  C13  180.00  0.0  0
 ZZ4  CONST_44  H11   C11  C12  C13  180.00  0.0  0
 ZZ4  CONST_45  H12   C12  C13  C14  180.00  0.0  0
 ZZ4  CONST_46  H16   C16  C15  C14  180.00  0.0  0
 ZZ4  CONST_47  H14   C14  C15  C16  180.00  0.0  0
 ZZ4  CONST_48  N5    N4   C9   C7   180.00  0.0  0
 ZZ4  CONST_49  N5    N4   C9   C10    0.00  0.0  0
 ZZ4  CONST_50  C14   C13  N5   N4   180.00  0.0  0
 ZZ4  CONST_51  C12   C13  N5   N4     0.00  0.0  0
 ZZ4  CONST_52  H21N  N2   C8   N1     0.00  0.0  0
 ZZ4  CONST_53  H22N  N2   C8   N1   180.00  0.0  0

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
 ZZ4  plan-1  CL1   0.020
 ZZ4  plan-1  C2    0.020
 ZZ4  plan-1  C1    0.020
 ZZ4  plan-1  C5    0.020
 ZZ4  plan-1  C3    0.020
 ZZ4  plan-1  C4    0.020
 ZZ4  plan-1  CL2   0.020
 ZZ4  plan-1  C6    0.020
 ZZ4  plan-1  C7    0.020
 ZZ4  plan-1  H1    0.020
 ZZ4  plan-1  H3    0.020
 ZZ4  plan-1  H5    0.020
 ZZ4  plan-2  C6    0.020
 ZZ4  plan-2  C7    0.020
 ZZ4  plan-2  N1    0.020
 ZZ4  plan-2  C9    0.020
 ZZ4  plan-2  C10   0.020
 ZZ4  plan-2  N3    0.020
 ZZ4  plan-2  C8    0.020
 ZZ4  plan-2  N2    0.020
 ZZ4  plan-2  N4    0.020
 ZZ4  plan-2  N5    0.020
 ZZ4  plan-2  C13   0.020
 ZZ4  plan-2  H10   0.020
 ZZ4  plan-3  N4    0.020
 ZZ4  plan-3  N5    0.020
 ZZ4  plan-3  C13   0.020
 ZZ4  plan-3  C14   0.020
 ZZ4  plan-3  C15   0.020
 ZZ4  plan-3  C16   0.020
 ZZ4  plan-3  C11   0.020
 ZZ4  plan-3  C12   0.020
 ZZ4  plan-3  H14   0.020
 ZZ4  plan-3  H12   0.020
 ZZ4  plan-3  H15   0.020
 ZZ4  plan-3  H16   0.020
 ZZ4  plan-3  H11   0.020
 ZZ4  plan-4  C8    0.020
 ZZ4  plan-4  N2    0.020
 ZZ4  plan-4  H21N  0.020
 ZZ4  plan-4  H22N  0.020

