# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 18:01:37 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: (5R)-5-tert-butyl-4,5,6,7-tetrahydro-1H-indazole-3-carbohydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)[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
 Z30  Z30  (5R)-5-tert-butyl-4,5,6,7-tetrahydro-1H-indazole-3-carbohydrazide  ligand  37  17  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Z30
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
 Z30  N1    N  N     0  -0.293   2.3949  -1.5946  -0.0071
 Z30  N2    N  NR15  0  -0.494   1.3713  -2.4279  -0.0025
 Z30  C3    C  CR5   0   0.401   0.1799  -1.8005   0.0346
 Z30  C4    C  CH2   0  -0.503  -1.1695  -2.4190   0.0671
 Z30  C5    C  CH2   0  -0.455  -2.1655  -1.3558   0.5327
 Z30  C6    C  CH1   0  -0.200  -1.9955  -0.0368  -0.2344
 Z30  C7    C  CT    0  -0.080  -3.1758   0.9483  -0.0285
 Z30  C8    C  CH3   0  -0.654  -3.4450   1.2144   1.4547
 Z30  C9    C  CH3   0  -0.655  -2.8789   2.2811  -0.7231
 Z30  C10   C  CH3   0  -0.645  -4.4464   0.3653  -0.6569
 Z30  C11   C  CH2   0  -0.504  -0.6241   0.5891   0.0740
 Z30  C12   C  CR5   0  -0.105   0.4467  -0.4517   0.0518
 Z30  C13   C  CR5   0   0.068   1.8552  -0.3830   0.0272
 Z30  C14   C  C     0   0.496   2.6948   0.8355   0.0428
 Z30  N15   N  NH1   0  -0.532   4.0167   0.5956  -0.0374
 Z30  N16   N  NH2   0  -0.637   4.9342   1.6289  -0.0215
 Z30  O17   O  O     0  -0.475   2.1934   1.9465   0.1229
 Z30  HN2   H  HNR5  0   0.418   1.5388  -3.4222  -0.0201
 Z30  H4    H  HCH2  0   0.254  -1.4449  -2.7830  -0.9277
 Z30  H4A   H  HCH2  0   0.261  -1.1899  -3.2839   0.7343
 Z30  H5    H  HCH2  0   0.244  -3.1756  -1.7479   0.4106
 Z30  H5A   H  HCH2  0   0.230  -2.0244  -1.1814   1.6038
 Z30  H6    H  HCH1  0   0.219  -1.9920  -0.2871  -1.3049
 Z30  H8    H  HCH3  0   0.224  -2.5618   1.5919   1.9740
 Z30  H8A   H  HCH3  0   0.226  -4.2327   1.9626   1.5690
 Z30  H8B   H  HCH3  0   0.226  -3.7766   0.3151   1.9762
 Z30  H9    H  HCH3  0   0.221  -2.6207   2.1383  -1.7752
 Z30  H9A   H  HCH3  0   0.226  -3.7564   2.9293  -0.6824
 Z30  H9B   H  HCH3  0   0.228  -2.0580   2.8219  -0.2494
 Z30  H10   H  HCH3  0   0.224  -4.7718  -0.5466  -0.1553
 Z30  H10A  H  HCH3  0   0.225  -5.2686   1.0808  -0.5897
 Z30  H10B  H  HCH3  0   0.221  -4.2972   0.1310  -1.7134
 Z30  H11   H  HCH2  0   0.248  -0.3943   1.3649  -0.6559
 Z30  H11A  H  HCH2  0   0.230  -0.6369   1.0901   1.0472
 Z30  HN15  H  HNH1  0   0.402   4.3359  -0.3612  -0.0988
 Z30  HN16  H  HNH2  0   0.370   5.5587   1.5066   0.7651
 Z30  HN1A  H  HNH2  0   0.370   5.4936   1.5884  -0.8635

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
 Z30  N1   N2    aromatic  1.320  0.020  1.320
 Z30  N1   C13   aromatic  1.327  0.020  1.327
 Z30  N2   C3    aromatic  1.347  0.020  1.347
 Z30  C3   C4    single    1.485  0.020  1.485
 Z30  C3   C12   aromatic  1.375  0.020  1.375
 Z30  C4   C5    single    1.529  0.020  1.529
 Z30  C5   C6    single    1.535  0.020  1.535
 Z30  C6   C7    single    1.551  0.020  1.551
 Z30  C6   C11   single    1.539  0.020  1.539
 Z30  C7   C8    single    1.531  0.020  1.531
 Z30  C7   C9    single    1.532  0.020  1.532
 Z30  C7   C10   single    1.533  0.020  1.533
 Z30  C11  C12   single    1.493  0.020  1.493
 Z30  C12  C13   aromatic  1.410  0.020  1.410
 Z30  C13  C14   single    1.480  0.020  1.480
 Z30  C14  N15   single    1.346  0.020  1.346
 Z30  C14  O17   double    1.222  0.020  1.222
 Z30  N15  N16   single    1.382  0.020  1.382
 Z30  N2   HN2   single    0.860  0.020  1.020
 Z30  C4   H4    single    0.970  0.020  1.090
 Z30  C4   H4A   single    0.970  0.020  1.090
 Z30  C5   H5    single    0.970  0.020  1.090
 Z30  C5   H5A   single    0.970  0.020  1.090
 Z30  C6   H6    single    0.970  0.020  1.090
 Z30  C8   H8    single    0.970  0.020  1.090
 Z30  C8   H8A   single    0.970  0.020  1.090
 Z30  C8   H8B   single    0.970  0.020  1.090
 Z30  C9   H9    single    0.970  0.020  1.090
 Z30  C9   H9A   single    0.970  0.020  1.090
 Z30  C9   H9B   single    0.970  0.020  1.090
 Z30  C10  H10   single    0.970  0.020  1.090
 Z30  C10  H10A  single    0.970  0.020  1.090
 Z30  C10  H10B  single    0.970  0.020  1.090
 Z30  C11  H11   single    0.970  0.020  1.090
 Z30  C11  H11A  single    0.970  0.020  1.090
 Z30  N15  HN15  single    0.860  0.020  1.020
 Z30  N16  HN16  single    0.890  0.020  1.040
 Z30  N16  HN1A  single    0.890  0.020  1.040

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
 Z30  C13   N1   N2    105.13  3.000
 Z30  HN2   N2   C3    127.34  3.000
 Z30  HN2   N2   N1    119.58  3.000
 Z30  C3    N2   N1    113.07  3.000
 Z30  C12   C3   C4    125.78  3.000
 Z30  C12   C3   N2    106.60  3.000
 Z30  C4    C3   N2    127.62  3.000
 Z30  H4A   C4   H4    106.69  3.000
 Z30  H4A   C4   C5    110.63  3.000
 Z30  H4    C4   C5    110.12  3.000
 Z30  H4A   C4   C3    111.11  3.000
 Z30  H4    C4   C3    110.32  3.000
 Z30  C5    C4   C3    107.99  3.000
 Z30  H5A   C5   H5    106.64  3.000
 Z30  H5A   C5   C6    109.74  3.000
 Z30  H5    C5   C6    110.82  3.000
 Z30  H5A   C5   C4    108.96  3.000
 Z30  H5    C5   C4    108.62  3.000
 Z30  C6    C5   C4    111.90  3.000
 Z30  H6    C6   C11   106.55  3.000
 Z30  H6    C6   C7    106.04  3.000
 Z30  C11   C6   C7    113.16  3.000
 Z30  H6    C6   C5    106.94  3.000
 Z30  C11   C6   C5    110.37  3.000
 Z30  C7    C6   C5    113.27  3.000
 Z30  C10   C7   C9    107.80  3.000
 Z30  C10   C7   C8    108.52  3.000
 Z30  C9    C7   C8    108.79  3.000
 Z30  C10   C7   C6    109.56  3.000
 Z30  C9    C7   C6    110.17  3.000
 Z30  C8    C7   C6    111.89  3.000
 Z30  H8B   C8   H8A   107.18  3.000
 Z30  H8B   C8   H8    107.67  3.000
 Z30  H8A   C8   H8    107.26  3.000
 Z30  H8B   C8   C7    111.91  3.000
 Z30  H8A   C8   C7    110.32  3.000
 Z30  H8    C8   C7    112.25  3.000
 Z30  H9B   C9   H9A   107.11  3.000
 Z30  H9B   C9   H9    107.76  3.000
 Z30  H9A   C9   H9    107.66  3.000
 Z30  H9B   C9   C7    112.34  3.000
 Z30  H9A   C9   C7    110.12  3.000
 Z30  H9    C9   C7    111.63  3.000
 Z30  H10B  C10  H10A  107.63  3.000
 Z30  H10B  C10  H10   107.83  3.000
 Z30  H10A  C10  H10   107.16  3.000
 Z30  H10B  C10  C7    111.40  3.000
 Z30  H10A  C10  C7    110.47  3.000
 Z30  H10   C10  C7    112.14  3.000
 Z30  H11A  C11  H11   105.79  3.000
 Z30  H11A  C11  C12   109.91  3.000
 Z30  H11   C11  C12   109.57  3.000
 Z30  H11A  C11  C6    110.73  3.000
 Z30  H11   C11  C6    110.08  3.000
 Z30  C12   C11  C6    110.64  3.000
 Z30  C13   C12  C11   133.03  3.000
 Z30  C13   C12  C3    103.96  3.000
 Z30  C11   C12  C3    123.00  3.000
 Z30  C14   C13  C12   127.34  3.000
 Z30  C14   C13  N1    121.43  3.000
 Z30  C12   C13  N1    111.23  3.000
 Z30  O17   C14  N15   124.69  3.000
 Z30  O17   C14  C13   121.11  3.000
 Z30  N15   C14  C13   114.20  3.000
 Z30  HN15  N15  N16   119.93  3.000
 Z30  HN15  N15  C14   118.86  3.000
 Z30  N16   N15  C14   121.21  3.000
 Z30  HN1A  N16  HN16  107.51  3.000
 Z30  HN1A  N16  N15   109.12  3.000
 Z30  HN16  N16  N15   109.17  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
 Z30  CONST_01  C12   C3   N2   N1     0.00   0.0  0
 Z30  CONST_02  C3    C12  C13  N1     0.00   0.0  0
 Z30  CONST_03  C12   C13  N1   N2     0.00   0.0  0
 Z30  CONST_04  C13   C12  C3   N2     0.00   0.0  0
 Z30  CONST_05  C13   N1   N2   C3     0.00   0.0  0
 Z30  CONST_06  C14   C13  N1   N2   180.00   0.0  0
 Z30  CONST_07  C14   C13  C12  C3   180.00   0.0  0
 Z30  CONST_08  C14   C13  C12  C11    0.00   0.0  0
 Z30  CONST_09  HN2   N2   C3   C4     0.00   0.0  0
 Z30  CONST_10  N16   N15  C14  C13  180.00   0.0  0
 Z30  CONST_11  HN15  N15  C14  C13    0.00   0.0  0
 Z30  CONST_12  O17   C14  N15  N16    0.00   0.0  0
 Z30  Var_01    C5    C4   C3   N2   162.78  30.0  1
 Z30  Var_02    C6    C5   C4   C3    48.51  30.0  1
 Z30  Var_03    C6    C11  C12  C3   -12.40  30.0  1
 Z30  Var_04    N15   C14  C13  N1     2.65  30.0  2
 Z30  Var_05    H8    C8   C7   C6    56.50  30.0  3
 Z30  Var_06    H9    C9   C7   C6    53.60  30.0  3
 Z30  Var_07    H10   C10  C7   C6    64.97  30.0  3
 Z30  Var_08    HN16  N16  N15  C14  120.61  30.0  2

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
 Z30  chir_01  C6  C5  C7  C11  negativ

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
 Z30  plan-1  C13   0.020
 Z30  plan-1  C14   0.020
 Z30  plan-1  N15   0.020
 Z30  plan-1  N16   0.020
 Z30  plan-1  O17   0.020
 Z30  plan-1  HN15  0.020
 Z30  plan-2  N1    0.020
 Z30  plan-2  N2    0.020
 Z30  plan-2  C3    0.020
 Z30  plan-2  C4    0.020
 Z30  plan-2  C11   0.020
 Z30  plan-2  C12   0.020
 Z30  plan-2  C13   0.020
 Z30  plan-2  C14   0.020
 Z30  plan-2  HN2   0.020

