# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:26:39 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: (5R)-5-(2-methylbutan-2-yl)-4,5,6,7-tetrahydro-1H-indazole-3-carbohydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(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
 X03  X03  (5R)-5-(2-methylbutan-2-yl)-4,5,6,7-tetrahydro-1H-indazole-3-carbohydrazide  ligand  40  18  .  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_X03
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
 X03  N1    N  N     0  -0.292   2.7803  -1.5046  -0.1971
 X03  N2    N  NR15  0  -0.494   1.8070  -2.3954  -0.1561
 X03  C3    C  CR5   0   0.402   0.5857  -1.8381  -0.0446
 X03  C4    C  CR5   0  -0.103   0.7766  -0.4770  -0.0122
 X03  C5    C  CR5   0   0.067   2.1754  -0.3269  -0.1096
 X03  C6    C  C     0   0.496   2.9430   0.9386  -0.1159
 X03  N7    N  NH1   0  -0.532   4.2657   0.7812  -0.3073
 X03  N8    N  NH2   0  -0.637   5.1224   1.8659  -0.3189
 X03  O9    O  O     0  -0.475   2.3865   2.0148   0.0403
 X03  C10   C  CH2   0  -0.503  -0.7247  -2.5302   0.0395
 X03  C11   C  CH2   0  -0.456  -1.7545  -1.5314   0.5703
 X03  C12   C  CH1   0  -0.204  -1.6980  -0.1913  -0.1799
 X03  C13   C  CH2   0  -0.507  -0.3480   0.5012   0.0796
 X03  C14   C  CT    0  -0.061  -2.9216   0.7278   0.0987
 X03  C15   C  CH2   0  -0.402  -4.1663   0.0837  -0.5472
 X03  C16   C  CH3   0  -0.676  -5.4594   0.8889  -0.4820
 X03  C17   C  CH3   0  -0.668  -3.1443   0.9073   1.6028
 X03  C18   C  CH3   0  -0.670  -2.6863   2.1043  -0.5310
 X03  HN2   H  HNR5  0   0.418   2.0288  -3.3779  -0.2042
 X03  HN7   H  HNH1  0   0.402   4.6331  -0.1539  -0.4156
 X03  HN8   H  HNH2  0   0.370   5.7980   1.7634   0.4274
 X03  HN8A  H  HNH2  0   0.371   5.6334   1.8729  -1.1920
 X03  H10   H  HCH2  0   0.254  -1.0267  -2.8926  -0.9482
 X03  H10A  H  HCH2  0   0.261  -0.6685  -3.4052   0.6911
 X03  H11   H  HCH2  0   0.245  -2.7431  -1.9847   0.4949
 X03  H11A  H  HCH2  0   0.231  -1.5696  -1.3642   1.6359
 X03  H12   H  HCH1  0   0.219  -1.7298  -0.4213  -1.2546
 X03  H13   H  HCH2  0   0.230  -0.3450   0.9836   1.0624
 X03  H13A  H  HCH2  0   0.248  -0.1917   1.2988  -0.6457
 X03  H15   H  HCH2  0   0.214  -3.9388  -0.1326  -1.5967
 X03  H15A  H  HCH2  0   0.219  -4.3551  -0.8837  -0.0753
 X03  H16   H  HCH3  0   0.220  -5.4101   1.8066  -1.0688
 X03  H16A  H  HCH3  0   0.230  -6.2869   0.2998  -0.8797
 X03  H16B  H  HCH3  0   0.220  -5.7218   1.1628   0.5407
 X03  H17   H  HCH3  0   0.226  -2.2402   1.2593   2.1043
 X03  H17A  H  HCH3  0   0.229  -3.9239   1.6449   1.7987
 X03  H17B  H  HCH3  0   0.226  -3.4487  -0.0227   2.0860
 X03  H18   H  HCH3  0   0.220  -2.4741   2.0251  -1.6004
 X03  H18A  H  HCH3  0   0.234  -3.5616   2.7433  -0.4127
 X03  H18B  H  HCH3  0   0.233  -1.8530   2.6311  -0.0644

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
 X03  N1   N2    aromatic  1.320  0.020  1.320
 X03  N1   C5    aromatic  1.327  0.020  1.327
 X03  N2   C3    aromatic  1.347  0.020  1.347
 X03  C3   C4    aromatic  1.375  0.020  1.375
 X03  C3   C10   single    1.484  0.020  1.484
 X03  C4   C5    aromatic  1.410  0.020  1.410
 X03  C4   C13   single    1.493  0.020  1.493
 X03  C5   C6    single    1.480  0.020  1.480
 X03  C6   N7    single    1.346  0.020  1.346
 X03  C6   O9    double    1.222  0.020  1.222
 X03  N7   N8    single    1.382  0.020  1.382
 X03  C10  C11   single    1.530  0.020  1.530
 X03  C11  C12   single    1.537  0.020  1.537
 X03  C12  C13   single    1.539  0.020  1.539
 X03  C12  C14   single    1.556  0.020  1.556
 X03  C14  C15   single    1.543  0.020  1.543
 X03  C14  C17   single    1.531  0.020  1.531
 X03  C14  C18   single    1.532  0.020  1.532
 X03  C15  C16   single    1.525  0.020  1.525
 X03  N2   HN2   single    0.860  0.020  1.020
 X03  N7   HN7   single    0.860  0.020  1.020
 X03  N8   HN8   single    0.890  0.020  1.040
 X03  N8   HN8A  single    0.890  0.020  1.040
 X03  C10  H10   single    0.970  0.020  1.090
 X03  C10  H10A  single    0.970  0.020  1.090
 X03  C11  H11   single    0.970  0.020  1.090
 X03  C11  H11A  single    0.970  0.020  1.090
 X03  C12  H12   single    0.970  0.020  1.090
 X03  C13  H13   single    0.970  0.020  1.090
 X03  C13  H13A  single    0.970  0.020  1.090
 X03  C15  H15   single    0.970  0.020  1.090
 X03  C15  H15A  single    0.970  0.020  1.090
 X03  C16  H16   single    0.970  0.020  1.090
 X03  C16  H16A  single    0.970  0.020  1.090
 X03  C16  H16B  single    0.970  0.020  1.090
 X03  C17  H17   single    0.970  0.020  1.090
 X03  C17  H17A  single    0.970  0.020  1.090
 X03  C17  H17B  single    0.970  0.020  1.090
 X03  C18  H18   single    0.970  0.020  1.090
 X03  C18  H18A  single    0.970  0.020  1.090
 X03  C18  H18B  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
 X03  C5    N1   N2    105.12  3.000
 X03  HN2   N2   C3    127.34  3.000
 X03  HN2   N2   N1    119.60  3.000
 X03  C3    N2   N1    113.07  3.000
 X03  C10   C3   C4    125.65  3.000
 X03  C10   C3   N2    127.74  3.000
 X03  C4    C3   N2    106.60  3.000
 X03  C13   C4   C5    132.96  3.000
 X03  C13   C4   C3    123.05  3.000
 X03  C5    C4   C3    103.97  3.000
 X03  C6    C5   C4    127.28  3.000
 X03  C6    C5   N1    121.48  3.000
 X03  C4    C5   N1    111.24  3.000
 X03  O9    C6   N7    124.68  3.000
 X03  O9    C6   C5    121.10  3.000
 X03  N7    C6   C5    114.23  3.000
 X03  HN7   N7   N8    120.00  3.000
 X03  HN7   N7   C6    118.74  3.000
 X03  N8    N7   C6    121.24  3.000
 X03  HN8A  N8   HN8   107.45  3.000
 X03  HN8A  N8   N7    109.01  3.000
 X03  HN8   N8   N7    109.16  3.000
 X03  H10A  C10  H10   106.70  3.000
 X03  H10A  C10  C11   110.52  3.000
 X03  H10   C10  C11   110.10  3.000
 X03  H10A  C10  C3    111.21  3.000
 X03  H10   C10  C3    110.29  3.000
 X03  C11   C10  C3    108.03  3.000
 X03  H11A  C11  H11   106.51  3.000
 X03  H11A  C11  C12   109.62  3.000
 X03  H11   C11  C12   111.23  3.000
 X03  H11A  C11  C10   108.90  3.000
 X03  H11   C11  C10   108.36  3.000
 X03  C12   C11  C10   112.04  3.000
 X03  H12   C12  C14   106.02  3.000
 X03  H12   C12  C13   106.52  3.000
 X03  C14   C12  C13   113.20  3.000
 X03  H12   C12  C11   107.08  3.000
 X03  C14   C12  C11   113.50  3.000
 X03  C13   C12  C11   110.01  3.000
 X03  H13A  C13  H13   105.94  3.000
 X03  H13A  C13  C12   110.05  3.000
 X03  H13   C13  C12   110.61  3.000
 X03  H13A  C13  C4    109.31  3.000
 X03  H13   C13  C4    109.99  3.000
 X03  C12   C13  C4    110.82  3.000
 X03  C18   C14  C17   108.71  3.000
 X03  C18   C14  C15   109.08  3.000
 X03  C17   C14  C15   110.05  3.000
 X03  C18   C14  C12   109.66  3.000
 X03  C17   C14  C12   111.08  3.000
 X03  C15   C14  C12   108.24  3.000
 X03  H15A  C15  H15   105.95  3.000
 X03  H15A  C15  C16   107.61  3.000
 X03  H15   C15  C16   108.75  3.000
 X03  H15A  C15  C14   109.15  3.000
 X03  H15   C15  C14   108.42  3.000
 X03  C16   C15  C14   116.47  3.000
 X03  H16B  C16  H16A  107.15  3.000
 X03  H16B  C16  H16   107.71  3.000
 X03  H16A  C16  H16   107.02  3.000
 X03  H16B  C16  C15   112.13  3.000
 X03  H16A  C16  C15   110.03  3.000
 X03  H16   C16  C15   112.52  3.000
 X03  H17B  C17  H17A  107.30  3.000
 X03  H17B  C17  H17   107.60  3.000
 X03  H17A  C17  H17   106.93  3.000
 X03  H17B  C17  C14   112.06  3.000
 X03  H17A  C17  C14   111.08  3.000
 X03  H17   C17  C14   111.62  3.000
 X03  H18B  C18  H18A  106.49  3.000
 X03  H18B  C18  H18   107.76  3.000
 X03  H18A  C18  H18   107.73  3.000
 X03  H18B  C18  C14   112.06  3.000
 X03  H18A  C18  C14   111.03  3.000
 X03  H18   C18  C14   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
 X03  CONST_01  C4   C3   N2   N1      0.00   0.0  0
 X03  CONST_02  C3   C4   C5   N1      0.00   0.0  0
 X03  CONST_03  C4   C5   N1   N2      0.00   0.0  0
 X03  CONST_04  C5   C4   C3   N2      0.00   0.0  0
 X03  CONST_05  C5   N1   N2   C3      0.00   0.0  0
 X03  CONST_06  C6   C5   N1   N2    180.00   0.0  0
 X03  CONST_07  C6   C5   C4   C3    180.00   0.0  0
 X03  CONST_08  C13  C4   C5   C6      0.00   0.0  0
 X03  CONST_09  HN2  N2   C3   C4    180.00   0.0  0
 X03  CONST_10  N8   N7   C6   C5    180.00   0.0  0
 X03  CONST_11  HN7  N7   C6   C5      0.00   0.0  0
 X03  CONST_12  O9   C6   N7   N8      0.00   0.0  0
 X03  Var_01    C11  C10  C3   N2    163.18  30.0  1
 X03  Var_02    C12  C13  C4   C3    -12.47  30.0  1
 X03  Var_03    C12  C11  C10  C3     48.61  30.0  1
 X03  Var_04    N7   C6   C5   N1      4.27  30.0  2
 X03  Var_05    C16  C15  C14  C12  -175.31  30.0  3
 X03  Var_06    H17  C17  C14  C12    53.90  30.0  3
 X03  Var_07    H18  C18  C14  C12    55.65  30.0  3
 X03  Var_08    HN8  N8   N7   C6    119.12  30.0  2
 X03  Var_09    H16  C16  C15  C14    66.23  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
 X03  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
 X03  plan-1  C5   0.020
 X03  plan-1  C6   0.020
 X03  plan-1  N7   0.020
 X03  plan-1  N8   0.020
 X03  plan-1  O9   0.020
 X03  plan-1  HN7  0.020
 X03  plan-2  N1   0.020
 X03  plan-2  N2   0.020
 X03  plan-2  C3   0.020
 X03  plan-2  C4   0.020
 X03  plan-2  C5   0.020
 X03  plan-2  C6   0.020
 X03  plan-2  C10  0.020
 X03  plan-2  C13  0.020
 X03  plan-2  HN2  0.020

