# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 17:40:07 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: (5R)-5-propyl-4,5,6,7-tetrahydro-1H-indazole-3-carbohydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@H]1CCc2[nH]nc(C(=O)NN)c2C1
#
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
 Z46  Z46  (5R)-5-propyl-4,5,6,7-tetrahydro-1H-indazole-3-carbohydrazide  ligand  34  16  .  2021-08-25  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Z46
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
 Z46  N1    N  N     0  -0.293   2.3013  -1.4992  -0.1354
 Z46  N2    N  NR15  0  -0.493   1.2738  -2.3275  -0.1239
 Z46  C3    C  CR5   0   0.400   0.0867  -1.6964  -0.0385
 Z46  C4    C  CR5   0  -0.115   0.3621  -0.3493   0.0048
 Z46  C5    C  CR5   0   0.067   1.7694  -0.2864  -0.0548
 Z46  C6    C  C     0   0.497   2.6148   0.9280  -0.0238
 Z46  N7    N  NH1   0  -0.533   3.9335   0.6851  -0.1378
 Z46  N8    N  NH2   0  -0.635   4.8561   1.7137  -0.1106
 Z46  O9    O  O     0  -0.473   2.1197   2.0381   0.0976
 Z46  C10   C  CH2   0  -0.508  -1.2635  -2.3149   0.0126
 Z46  C11   C  CH2   0  -0.440  -2.2554  -1.2650   0.5178
 Z46  C12   C  CH1   0  -0.242  -2.0871   0.0792  -0.1973
 Z46  C13   C  CH2   0  -0.481  -0.7081   0.6869   0.0983
 Z46  C14   C  CH2   0  -0.404  -3.1839   1.0786   0.1672
 Z46  C15   C  CH2   0  -0.427  -4.5815   0.7080  -0.3170
 Z46  C16   C  CH3   0  -0.665  -5.6129   1.7773   0.0175
 Z46  HN2   H  HNR5  0   0.417   1.4358  -3.3216  -0.1739
 Z46  HN7   H  HNH1  0   0.401   4.2469  -0.2712  -0.2307
 Z46  HN8   H  HNH2  0   0.369   5.4953   1.5656   0.6598
 Z46  HN8A  H  HNH2  0   0.369   5.3996   1.6936  -0.9636
 Z46  H10   H  HCH2  0   0.254  -1.5585  -2.6594  -0.9835
 Z46  H10A  H  HCH2  0   0.261  -1.2686  -3.1939   0.6612
 Z46  H11   H  HCH2  0   0.244  -3.2688  -1.6459   0.3843
 Z46  H11A  H  HCH2  0   0.224  -2.1150  -1.1171   1.5940
 Z46  H12   H  HCH1  0   0.220  -2.1458  -0.1090  -1.2781
 Z46  H13   H  HCH2  0   0.227  -0.7124   1.1321   1.0998
 Z46  H13A  H  HCH2  0   0.242  -0.5112   1.5084  -0.5927
 Z46  H14   H  HCH2  0   0.207  -3.1977   1.2143   1.2553
 Z46  H14A  H  HCH2  0   0.217  -2.9178   2.0551  -0.2527
 Z46  H15   H  HCH2  0   0.210  -4.5582   0.5491  -1.3996
 Z46  H15A  H  HCH2  0   0.216  -4.8954  -0.2419   0.1231
 Z46  H16   H  HCH3  0   0.227  -6.6022   1.5093  -0.3549
 Z46  H16A  H  HCH3  0   0.219  -5.6948   1.9225   1.0963
 Z46  H16B  H  HCH3  0   0.219  -5.3419   2.7387  -0.4232

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
 Z46  N1   N2    aromatic  1.320  0.020  1.320
 Z46  N1   C5    aromatic  1.327  0.020  1.327
 Z46  N2   C3    aromatic  1.347  0.020  1.347
 Z46  C3   C4    aromatic  1.376  0.020  1.376
 Z46  C3   C10   single    1.486  0.020  1.486
 Z46  C4   C5    aromatic  1.410  0.020  1.410
 Z46  C4   C13   single    1.493  0.020  1.493
 Z46  C5   C6    single    1.480  0.020  1.480
 Z46  C6   N7    single    1.346  0.020  1.346
 Z46  C6   O9    double    1.222  0.020  1.222
 Z46  N7   N8    single    1.382  0.020  1.382
 Z46  C10  C11   single    1.530  0.020  1.530
 Z46  C11  C12   single    1.532  0.020  1.532
 Z46  C12  C13   single    1.536  0.020  1.536
 Z46  C12  C14   single    1.528  0.020  1.528
 Z46  C14  C15   single    1.525  0.020  1.525
 Z46  C15  C16   single    1.523  0.020  1.523
 Z46  N2   HN2   single    0.860  0.020  1.020
 Z46  N7   HN7   single    0.860  0.020  1.020
 Z46  N8   HN8   single    0.890  0.020  1.040
 Z46  N8   HN8A  single    0.890  0.020  1.040
 Z46  C10  H10   single    0.970  0.020  1.090
 Z46  C10  H10A  single    0.970  0.020  1.090
 Z46  C11  H11   single    0.970  0.020  1.090
 Z46  C11  H11A  single    0.970  0.020  1.090
 Z46  C12  H12   single    0.970  0.020  1.090
 Z46  C13  H13   single    0.970  0.020  1.090
 Z46  C13  H13A  single    0.970  0.020  1.090
 Z46  C14  H14   single    0.970  0.020  1.090
 Z46  C14  H14A  single    0.970  0.020  1.090
 Z46  C15  H15   single    0.970  0.020  1.090
 Z46  C15  H15A  single    0.970  0.020  1.090
 Z46  C16  H16   single    0.970  0.020  1.090
 Z46  C16  H16A  single    0.970  0.020  1.090
 Z46  C16  H16B  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
 Z46  C5    N1   N2    105.13  3.000
 Z46  HN2   N2   C3    127.34  3.000
 Z46  HN2   N2   N1    119.55  3.000
 Z46  C3    N2   N1    113.12  3.000
 Z46  C10   C3   C4    126.05  3.000
 Z46  C10   C3   N2    127.43  3.000
 Z46  C4    C3   N2    106.52  3.000
 Z46  C13   C4   C5    133.42  3.000
 Z46  C13   C4   C3    122.56  3.000
 Z46  C5    C4   C3    104.02  3.000
 Z46  C6    C5   C4    127.29  3.000
 Z46  C6    C5   N1    121.49  3.000
 Z46  C4    C5   N1    111.22  3.000
 Z46  O9    C6   N7    124.73  3.000
 Z46  O9    C6   C5    121.08  3.000
 Z46  N7    C6   C5    114.19  3.000
 Z46  HN7   N7   N8    119.94  3.000
 Z46  HN7   N7   C6    118.85  3.000
 Z46  N8    N7   C6    121.21  3.000
 Z46  HN8A  N8   HN8   107.44  3.000
 Z46  HN8A  N8   N7    109.10  3.000
 Z46  HN8   N8   N7    109.14  3.000
 Z46  H10A  C10  H10   106.61  3.000
 Z46  H10A  C10  C11   110.67  3.000
 Z46  H10   C10  C11   109.98  3.000
 Z46  H10A  C10  C3    111.08  3.000
 Z46  H10   C10  C3    110.16  3.000
 Z46  C11   C10  C3    108.34  3.000
 Z46  H11A  C11  H11   106.64  3.000
 Z46  H11A  C11  C12   109.04  3.000
 Z46  H11   C11  C12   110.57  3.000
 Z46  H11A  C11  C10   109.51  3.000
 Z46  H11   C11  C10   108.80  3.000
 Z46  C12   C11  C10   112.13  3.000
 Z46  H12   C12  C14   107.96  3.000
 Z46  H12   C12  C13   107.77  3.000
 Z46  C14   C12  C13   109.87  3.000
 Z46  H12   C12  C11   107.64  3.000
 Z46  C14   C12  C11   112.57  3.000
 Z46  C13   C12  C11   110.86  3.000
 Z46  H13A  C13  H13   105.87  3.000
 Z46  H13A  C13  C12   109.76  3.000
 Z46  H13   C13  C12   109.45  3.000
 Z46  H13A  C13  C4    110.71  3.000
 Z46  H13   C13  C4    110.00  3.000
 Z46  C12   C13  C4    110.92  3.000
 Z46  H14A  C14  H14   105.84  3.000
 Z46  H14A  C14  C15   108.51  3.000
 Z46  H14   C14  C15   109.49  3.000
 Z46  H14A  C14  C12   108.49  3.000
 Z46  H14   C14  C12   109.06  3.000
 Z46  C15   C14  C12   115.04  3.000
 Z46  H15A  C15  H15   106.16  3.000
 Z46  H15A  C15  C16   109.11  3.000
 Z46  H15   C15  C16   109.49  3.000
 Z46  H15A  C15  C14   110.28  3.000
 Z46  H15   C15  C14   109.26  3.000
 Z46  C16   C15  C14   112.36  3.000
 Z46  H16B  C16  H16A  107.49  3.000
 Z46  H16B  C16  H16   107.68  3.000
 Z46  H16A  C16  H16   107.59  3.000
 Z46  H16B  C16  C15   111.19  3.000
 Z46  H16A  C16  C15   111.18  3.000
 Z46  H16   C16  C15   111.52  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
 Z46  CONST_01  C4   C3   N2   N1      0.00   0.0  0
 Z46  CONST_02  C3   C4   C5   N1      0.00   0.0  0
 Z46  CONST_03  C4   C5   N1   N2      0.00   0.0  0
 Z46  CONST_04  C5   C4   C3   N2      0.00   0.0  0
 Z46  CONST_05  C5   N1   N2   C3      0.00   0.0  0
 Z46  CONST_06  C6   C5   N1   N2    180.00   0.0  0
 Z46  CONST_07  C6   C5   C4   C3    180.00   0.0  0
 Z46  CONST_08  C13  C4   C5   C6      0.00   0.0  0
 Z46  CONST_09  HN2  N2   C3   C4    180.00   0.0  0
 Z46  CONST_10  N8   N7   C6   C5    180.00   0.0  0
 Z46  CONST_11  HN7  N7   C6   C5      0.00   0.0  0
 Z46  CONST_12  O9   C6   N7   N8      0.00   0.0  0
 Z46  Var_01    C11  C10  C3   N2    163.40  30.0  1
 Z46  Var_02    C12  C13  C4   C3    -13.47  30.0  1
 Z46  Var_03    C12  C11  C10  C3     46.99  30.0  1
 Z46  Var_04    N7   C6   C5   N1      2.52  30.0  2
 Z46  Var_05    C16  C15  C14  C12  -177.12  30.0  3
 Z46  Var_06    HN8  N8   N7   C6    120.58  30.0  2
 Z46  Var_07    H16  C16  C15  C14   178.68  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 Z46  chir_01  C12  C11  C13  C14  positiv

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
 Z46  plan-1  C5   0.020
 Z46  plan-1  C6   0.020
 Z46  plan-1  N7   0.020
 Z46  plan-1  N8   0.020
 Z46  plan-1  O9   0.020
 Z46  plan-1  HN7  0.020
 Z46  plan-2  N1   0.020
 Z46  plan-2  N2   0.020
 Z46  plan-2  C3   0.020
 Z46  plan-2  C4   0.020
 Z46  plan-2  C5   0.020
 Z46  plan-2  C6   0.020
 Z46  plan-2  C10  0.020
 Z46  plan-2  C13  0.020
 Z46  plan-2  HN2  0.020

