# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 09:42:39 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (1Z,3Z)-3-(2-phenylhydrazinylidene)-2,3-dihydro-1H-isoindol-1-imine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N=C1NC(=N/Nc2ccccc2)\c3ccccc13
#
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
 ZRY  ZRY  "(1Z,3Z)-3-(2-phenylhydrazinylidene)-2,3-dihydro-1H-isoindol-1-imine"
  ligand  30  18  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZRY
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
 ZRY  N1   N  N     0  -0.611  29.3560  3.5318  59.0293
 ZRY  C7   C  CR5   0   0.475  26.1341  4.7450  58.3592
 ZRY  C8   C  CR6   0   0.405  24.6129  7.1847  56.3144
 ZRY  N2   N  N     0  -0.246  25.2581  5.4829  57.8027
 ZRY  C9   C  CR16  0  -0.349  24.9946  8.1280  55.3537
 ZRY  C1   C  CR56  0   0.001  26.9852  3.0907  59.7240
 ZRY  C5   C  CR16  0  -0.312  24.5792  3.2992  59.8388
 ZRY  C6   C  CR56  0   0.028  25.8019  3.7043  59.3285
 ZRY  N3   N  NH1   0  -0.600  25.5897  6.4206  56.9145
 ZRY  C4   C  CR16  0  -0.247  24.5758  2.2622  60.7612
 ZRY  C3   C  CR16  0  -0.253  25.7631  1.6463  61.1606
 ZRY  C2   C  CR16  0  -0.303  26.9848  2.0557  60.6436
 ZRY  N    N  NR15  0  -0.758  27.5139  4.7074  58.2214
 ZRY  C    C  CR5   0   0.390  28.1036  3.7360  59.0086
 ZRY  C10  C  CR16  0  -0.242  24.0418  8.9164  54.7320
 ZRY  C11  C  CR16  0  -0.287  22.6943  8.7878  55.0487
 ZRY  C12  C  CR16  0  -0.242  22.3186  7.8514  56.0032
 ZRY  C13  C  CR16  0  -0.336  23.2588  7.0525  56.6366
 ZRY  H2   H  H     0   0.347  29.5844  2.7793  59.6695
 ZRY  H8   H  HCR6  0   0.260  26.0415  8.2402  55.0954
 ZRY  H6   H  HCR6  0   0.262  23.6568  3.7738  59.5309
 ZRY  H7   H  HNH1  0   0.397  26.5416  6.5476  56.6000
 ZRY  H5   H  HCR6  0   0.267  23.6366  1.9234  61.1783
 ZRY  H4   H  HCR6  0   0.266  25.7286  0.8401  61.8812
 ZRY  H3   H  HCR6  0   0.265  27.9042  1.5753  60.9549
 ZRY  H    H  HNR5  0   0.413  28.0713  5.3083  57.6355
 ZRY  H9   H  HCR6  0   0.252  24.3592  9.6392  53.9911
 ZRY  H10  H  HCR6  0   0.246  21.9527  9.4065  54.5614
 ZRY  H11  H  HCR6  0   0.251  21.2742  7.7358  56.2650
 ZRY  H12  H  HCR6  0   0.262  22.9452  6.3299  57.3765

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
 ZRY  N    C    single    1.383  0.020  1.383
 ZRY  C    N1   double    1.269  0.020  1.269
 ZRY  C1   C    single    1.476  0.020  1.476
 ZRY  C1   C2   aromatic  1.384  0.020  1.384
 ZRY  C2   C3   aromatic  1.388  0.020  1.388
 ZRY  C3   C4   aromatic  1.396  0.020  1.396
 ZRY  C4   C5   aromatic  1.388  0.020  1.388
 ZRY  C5   C6   aromatic  1.385  0.020  1.385
 ZRY  C6   C1   aromatic  1.390  0.020  1.390
 ZRY  C7   C6   single    1.460  0.020  1.460
 ZRY  N    C7   single    1.387  0.020  1.387
 ZRY  N2   C7   double    1.273  0.020  1.273
 ZRY  N3   N2   single    1.333  0.020  1.333
 ZRY  C8   N3   single    1.378  0.020  1.378
 ZRY  C8   C9   aromatic  1.399  0.020  1.399
 ZRY  C9   C10  aromatic  1.384  0.020  1.384
 ZRY  C10  C11  aromatic  1.390  0.020  1.390
 ZRY  C11  C12  aromatic  1.389  0.020  1.389
 ZRY  C12  C13  aromatic  1.387  0.020  1.387
 ZRY  C13  C8   aromatic  1.398  0.020  1.398
 ZRY  N1   H2   single    0.890  0.020  1.040
 ZRY  C9   H8   single    0.930  0.020  1.080
 ZRY  C5   H6   single    0.930  0.020  1.080
 ZRY  N3   H7   single    0.860  0.020  1.020
 ZRY  C4   H5   single    0.930  0.020  1.080
 ZRY  C3   H4   single    0.930  0.020  1.080
 ZRY  C2   H3   single    0.930  0.020  1.080
 ZRY  N    H    single    0.860  0.020  1.020
 ZRY  C10  H9   single    0.930  0.020  1.080
 ZRY  C11  H10  single    0.930  0.020  1.080
 ZRY  C12  H11  single    0.930  0.020  1.080
 ZRY  C13  H12  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
 ZRY  H2   N1   C    110.60  3.000
 ZRY  N    C7   C6   105.83  3.000
 ZRY  N    C7   N2   131.04  3.000
 ZRY  C6   C7   N2   123.13  3.000
 ZRY  C13  C8   N3   122.26  3.000
 ZRY  C13  C8   C9   119.08  3.000
 ZRY  N3   C8   C9   118.65  3.000
 ZRY  N3   N2   C7   121.84  3.000
 ZRY  H8   C9   C10  119.92  3.000
 ZRY  H8   C9   C8   119.78  3.000
 ZRY  C10  C9   C8   120.30  3.000
 ZRY  C    C1   C2   130.46  3.000
 ZRY  C2   C1   C6   121.24  3.000
 ZRY  C    C1   C6   108.30  3.000
 ZRY  H6   C5   C4   120.98  3.000
 ZRY  H6   C5   C6   121.28  3.000
 ZRY  C4   C5   C6   117.74  3.000
 ZRY  C5   C6   C1   121.15  3.000
 ZRY  C1   C6   C7   108.05  3.000
 ZRY  C5   C6   C7   130.81  3.000
 ZRY  H7   N3   N2   122.00  3.000
 ZRY  H7   N3   C8   117.55  3.000
 ZRY  N2   N3   C8   120.26  3.000
 ZRY  H5   C4   C3   119.33  3.000
 ZRY  H5   C4   C5   119.49  3.000
 ZRY  C3   C4   C5   121.18  3.000
 ZRY  H4   C3   C2   119.72  3.000
 ZRY  H4   C3   C4   119.49  3.000
 ZRY  C2   C3   C4   120.78  3.000
 ZRY  H3   C2   C3   120.61  3.000
 ZRY  H3   C2   C1   121.48  3.000
 ZRY  C3   C2   C1   117.91  3.000
 ZRY  H    N    C    120.94  3.000
 ZRY  H    N    C7   126.30  3.000
 ZRY  C    N    C7   112.76  3.000
 ZRY  N    C    C1   105.07  3.000
 ZRY  C1   C    N1   132.03  3.000
 ZRY  N    C    N1   122.91  3.000
 ZRY  H9   C10  C11  120.12  3.000
 ZRY  H9   C10  C9   119.07  3.000
 ZRY  C11  C10  C9   120.81  3.000
 ZRY  H10  C11  C12  120.64  3.000
 ZRY  H10  C11  C10  120.60  3.000
 ZRY  C12  C11  C10  118.76  3.000
 ZRY  H11  C12  C13  118.81  3.000
 ZRY  H11  C12  C11  119.93  3.000
 ZRY  C13  C12  C11  121.26  3.000
 ZRY  H12  C13  C12  120.08  3.000
 ZRY  H12  C13  C8   120.13  3.000
 ZRY  C12  C13  C8   119.79  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
 ZRY  CONST_01  C11  C10  C9   C8     0.00   0.0  0
 ZRY  CONST_02  C11  C12  C13  C8     0.00   0.0  0
 ZRY  CONST_03  C12  C13  C8   C9     0.00   0.0  0
 ZRY  CONST_04  C12  C11  C10  C9     0.00   0.0  0
 ZRY  CONST_05  C4   C3   C2   C1     0.00   0.0  0
 ZRY  CONST_06  C4   C5   C6   C1     0.00   0.0  0
 ZRY  CONST_07  C2   C3   C4   C5     0.00   0.0  0
 ZRY  CONST_08  C2   C1   C6   C5     0.00   0.0  0
 ZRY  CONST_09  C3   C4   C5   C6     0.00   0.0  0
 ZRY  CONST_10  C3   C2   C1   C6     0.00   0.0  0
 ZRY  CONST_11  C13  C8   C9   C10    0.00   0.0  0
 ZRY  CONST_12  C13  C12  C11  C10    0.00   0.0  0
 ZRY  CONST_13  C1   C    N    C7     0.00   0.0  0
 ZRY  CONST_14  C    N    C7   C6     0.00   0.0  0
 ZRY  CONST_15  C10  C9   C8   N3   180.00   0.0  0
 ZRY  CONST_16  C12  C13  C8   N3   180.00   0.0  0
 ZRY  CONST_17  C7   N    C    N1   180.00   0.0  0
 ZRY  CONST_18  C    N    C7   N2   180.00   0.0  0
 ZRY  CONST_19  H6   C5   C6   C7     0.00   0.0  0
 ZRY  CONST_20  H9   C10  C9   C8   180.00   0.0  0
 ZRY  CONST_21  H11  C12  C13  C8   180.00   0.0  0
 ZRY  CONST_22  H12  C13  C8   C9   180.00   0.0  0
 ZRY  CONST_23  H10  C11  C10  C9   180.00   0.0  0
 ZRY  CONST_24  H4   C3   C2   C1   180.00   0.0  0
 ZRY  CONST_25  H6   C5   C6   C1   180.00   0.0  0
 ZRY  CONST_26  H4   C3   C4   C5   180.00   0.0  0
 ZRY  CONST_27  H5   C4   C5   C6   180.00   0.0  0
 ZRY  CONST_28  H3   C2   C1   C6   180.00   0.0  0
 ZRY  CONST_29  H3   C2   C3   C4   180.00   0.0  0
 ZRY  CONST_30  H6   C5   C4   C3   180.00   0.0  0
 ZRY  CONST_31  H5   C4   C3   C2   180.00   0.0  0
 ZRY  CONST_32  H3   C2   C1   C      0.00   0.0  0
 ZRY  CONST_33  H11  C12  C11  C10  180.00   0.0  0
 ZRY  CONST_34  H8   C9   C10  C11  180.00   0.0  0
 ZRY  CONST_35  H12  C13  C12  C11  180.00   0.0  0
 ZRY  CONST_36  H9   C10  C11  C12  180.00   0.0  0
 ZRY  CONST_37  H10  C11  C12  C13  180.00   0.0  0
 ZRY  CONST_38  H8   C9   C8   C13  180.00   0.0  0
 ZRY  CONST_39  H    N    C    C1   180.00   0.0  0
 ZRY  CONST_40  H    N    C7   C6   180.00   0.0  0
 ZRY  CONST_41  C8   N3   N2   C7   180.00   0.0  0
 ZRY  CONST_42  C9   C8   N3   N2   180.00   0.0  0
 ZRY  CONST_43  C13  C8   N3   N2     0.00   0.0  0
 ZRY  CONST_44  N3   N2   C7   C6   180.00   0.0  0
 ZRY  CONST_45  N    C7   N2   N3     0.00   0.0  0
 ZRY  CONST_46  H7   N3   C8   C9     0.00   0.0  0
 ZRY  CONST_47  H7   N3   C8   C13  180.00   0.0  0
 ZRY  CONST_48  H    N    C    N1     0.00   0.0  0
 ZRY  CONST_49  H    N    C7   N2     0.00   0.0  0
 ZRY  CONST_50  H2   N1   C    C1     0.00   0.0  0
 ZRY  CONST_51  H2   N1   C    N    180.00   0.0  0
 ZRY  Var_01    H7   N3   N2   C7     3.99  30.0  1

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
 ZRY  plan-1  C8   0.020
 ZRY  plan-1  C9   0.020
 ZRY  plan-1  N3   0.020
 ZRY  plan-1  C10  0.020
 ZRY  plan-1  C11  0.020
 ZRY  plan-1  C12  0.020
 ZRY  plan-1  C13  0.020
 ZRY  plan-1  H8   0.020
 ZRY  plan-1  H9   0.020
 ZRY  plan-1  H10  0.020
 ZRY  plan-1  H11  0.020
 ZRY  plan-1  H12  0.020
 ZRY  plan-2  N1   0.020
 ZRY  plan-2  C7   0.020
 ZRY  plan-2  N2   0.020
 ZRY  plan-2  C1   0.020
 ZRY  plan-2  C5   0.020
 ZRY  plan-2  C6   0.020
 ZRY  plan-2  N3   0.020
 ZRY  plan-2  C4   0.020
 ZRY  plan-2  C3   0.020
 ZRY  plan-2  C2   0.020
 ZRY  plan-2  N    0.020
 ZRY  plan-2  C    0.020
 ZRY  plan-2  H2   0.020
 ZRY  plan-2  H6   0.020
 ZRY  plan-2  H5   0.020
 ZRY  plan-2  H4   0.020
 ZRY  plan-2  H3   0.020
 ZRY  plan-2  H    0.020
 ZRY  plan-3  C8   0.020
 ZRY  plan-3  N2   0.020
 ZRY  plan-3  N3   0.020
 ZRY  plan-3  H7   0.020

