# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 16:51:31 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (5S)-N-methyl-5-(2-methylbutan-2-yl)-4,5,6,7-tetrahydro-2H-indazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(C)(C)[C@H]1CCc2n[nH]c(C(=O)NC)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
 X19  X19  (5S)-N-methyl-5-(2-methylbutan-2-yl)-4,5,6,7-tetrahydro-2H-indazole-3-carboxamide  ligand  41  18  .  2021-08-24  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_X19
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
 X19  N01   N  NR15  0  -0.507   2.6932  -1.6226  -0.0365
 X19  N02   N  N     0  -0.284   1.7670  -2.5680  -0.0345
 X19  N03   N  NH1   0  -0.641   4.2047   0.8175   0.3384
 X19  C04   C  CR5   0   0.232   0.6133  -1.9221  -0.0911
 X19  C05   C  CR5   0  -0.091   0.8028  -0.5326  -0.1527
 X19  C06   C  CR5   0   0.236   2.1743  -0.3748  -0.1172
 X19  C07   C  CH2   0  -0.503  -0.7327  -2.5606  -0.0930
 X19  C08   C  CH2   0  -0.458  -1.7632  -1.5512  -0.5993
 X19  C09   C  CH1   0  -0.200  -1.6521  -0.2051   0.1339
 X19  C10   C  CH2   0  -0.509  -0.3100   0.4610  -0.2126
 X19  C11   C  CT    0  -0.063  -2.8766   0.7283  -0.0845
 X19  C12   C  C     0   0.511   2.9606   0.8725  -0.1622
 X19  C13   C  CH3   0  -0.515   5.0769   1.9694   0.3405
 X19  C14   C  CH3   0  -0.670  -2.5964   2.1022   0.5327
 X19  C15   C  CH3   0  -0.667  -3.1726   0.9106  -1.5757
 X19  C16   C  CH2   0  -0.402  -4.0966   0.0951   0.6186
 X19  C17   C  CH3   0  -0.677  -5.3755   0.9250   0.6372
 X19  O18   O  O     0  -0.482   2.4787   1.8905  -0.6414
 X19  HN01  H  HNR5  0   0.416   3.6639  -1.8899  -0.0845
 X19  HN03  H  HNH1  0   0.404   4.4955   0.0153   0.8713
 X19  H07   H  HCH2  0   0.250  -0.7352  -3.4595  -0.7136
 X19  H07A  H  HCH2  0   0.243  -0.9997  -2.8795   0.9197
 X19  H08   H  HCH2  0   0.227  -1.6183  -1.3960  -1.6735
 X19  H08A  H  HCH2  0   0.242  -2.7580  -1.9810  -0.4811
 X19  H09   H  HCH1  0   0.218  -1.6248  -0.4249   1.2108
 X19  H10   H  HCH2  0   0.248  -0.1026   1.2822   0.4733
 X19  H10A  H  HCH2  0   0.234  -0.3514   0.9066  -1.2114
 X19  H13   H  HCH3  0   0.243   5.2364   2.3447  -0.6697
 X19  H13A  H  HCH3  0   0.240   4.6801   2.7828   0.9499
 X19  H13B  H  HCH3  0   0.254   6.0368   1.6697   0.7500
 X19  H14   H  HCH3  0   0.232  -1.7790   2.6176   0.0269
 X19  H14A  H  HCH3  0   0.234  -3.4686   2.7512   0.4520
 X19  H14B  H  HCH3  0   0.220  -2.3379   2.0221   1.5917
 X19  H15   H  HCH3  0   0.226  -3.5003  -0.0188  -2.0441
 X19  H15A  H  HCH3  0   0.229  -3.9606   1.6490  -1.7321
 X19  H15B  H  HCH3  0   0.226  -2.2956   1.2639  -2.1223
 X19  H16   H  HCH2  0   0.220  -4.3273  -0.8597   0.1403
 X19  H16A  H  HCH2  0   0.214  -3.8165  -0.1434   1.6503
 X19  H17   H  HCH3  0   0.220  -5.2762   1.8307   1.2360
 X19  H17A  H  HCH3  0   0.221  -5.6872   1.2225  -0.3650
 X19  H17B  H  HCH3  0   0.230  -6.1920   0.3446   1.0690

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
 X19  N01  N02   aromatic  1.323  0.020  1.323
 X19  N01  C06   aromatic  1.354  0.020  1.354
 X19  N02  C04   aromatic  1.323  0.020  1.323
 X19  N03  C12   single    1.342  0.020  1.342
 X19  N03  C13   single    1.445  0.020  1.445
 X19  C04  C05   aromatic  1.404  0.020  1.404
 X19  C04  C07   single    1.490  0.020  1.490
 X19  C05  C06   aromatic  1.381  0.020  1.381
 X19  C05  C10   single    1.493  0.020  1.493
 X19  C06  C12   single    1.475  0.020  1.475
 X19  C07  C08   single    1.529  0.020  1.529
 X19  C08  C09   single    1.537  0.020  1.537
 X19  C09  C10   single    1.538  0.020  1.538
 X19  C09  C11   single    1.555  0.020  1.555
 X19  C11  C14   single    1.532  0.020  1.532
 X19  C11  C15   single    1.531  0.020  1.531
 X19  C11  C16   single    1.544  0.020  1.544
 X19  C12  O18   double    1.224  0.020  1.224
 X19  C16  C17   single    1.525  0.020  1.525
 X19  N01  HN01  single    0.860  0.020  1.020
 X19  N03  HN03  single    0.860  0.020  1.020
 X19  C07  H07   single    0.970  0.020  1.090
 X19  C07  H07A  single    0.970  0.020  1.090
 X19  C08  H08   single    0.970  0.020  1.090
 X19  C08  H08A  single    0.970  0.020  1.090
 X19  C09  H09   single    0.970  0.020  1.090
 X19  C10  H10   single    0.970  0.020  1.090
 X19  C10  H10A  single    0.970  0.020  1.090
 X19  C13  H13   single    0.970  0.020  1.090
 X19  C13  H13A  single    0.970  0.020  1.090
 X19  C13  H13B  single    0.970  0.020  1.090
 X19  C14  H14   single    0.970  0.020  1.090
 X19  C14  H14A  single    0.970  0.020  1.090
 X19  C14  H14B  single    0.970  0.020  1.090
 X19  C15  H15   single    0.970  0.020  1.090
 X19  C15  H15A  single    0.970  0.020  1.090
 X19  C15  H15B  single    0.970  0.020  1.090
 X19  C16  H16   single    0.970  0.020  1.090
 X19  C16  H16A  single    0.970  0.020  1.090
 X19  C17  H17   single    0.970  0.020  1.090
 X19  C17  H17A  single    0.970  0.020  1.090
 X19  C17  H17B  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
 X19  HN01  N01  C06   127.64  3.000
 X19  HN01  N01  N02   118.99  3.000
 X19  C06   N01  N02   112.97  3.000
 X19  C04   N02  N01   105.15  3.000
 X19  HN03  N03  C13   117.41  3.000
 X19  HN03  N03  C12   119.88  3.000
 X19  C13   N03  C12   121.84  3.000
 X19  C07   C04  C05   123.11  3.000
 X19  C07   C04  N02   125.35  3.000
 X19  C05   C04  N02   111.55  3.000
 X19  C10   C05  C06   131.70  3.000
 X19  C10   C05  C04   124.05  3.000
 X19  C06   C05  C04   104.24  3.000
 X19  C12   C06  C05   128.69  3.000
 X19  C12   C06  N01   125.23  3.000
 X19  C05   C06  N01   106.08  3.000
 X19  H07A  C07  H07   106.57  3.000
 X19  H07A  C07  C08   109.53  3.000
 X19  H07   C07  C08   110.71  3.000
 X19  H07A  C07  C04   110.12  3.000
 X19  H07   C07  C04   110.83  3.000
 X19  C08   C07  C04   109.06  3.000
 X19  H08A  C08  H08   106.45  3.000
 X19  H08A  C08  C09   111.07  3.000
 X19  H08   C08  C09   109.53  3.000
 X19  H08A  C08  C07   108.60  3.000
 X19  H08   C08  C07   109.22  3.000
 X19  C09   C08  C07   111.81  3.000
 X19  H09   C09  C11   106.09  3.000
 X19  H09   C09  C10   106.59  3.000
 X19  C11   C09  C10   113.30  3.000
 X19  H09   C09  C08   107.10  3.000
 X19  C11   C09  C08   113.69  3.000
 X19  C10   C09  C08   109.57  3.000
 X19  H10A  C10  H10   105.95  3.000
 X19  H10A  C10  C09   110.42  3.000
 X19  H10   C10  C09   110.52  3.000
 X19  H10A  C10  C05   109.62  3.000
 X19  H10   C10  C05   109.53  3.000
 X19  C09   C10  C05   110.68  3.000
 X19  C16   C11  C15   109.86  3.000
 X19  C16   C11  C14   109.20  3.000
 X19  C15   C11  C14   108.72  3.000
 X19  C16   C11  C09   108.18  3.000
 X19  C15   C11  C09   111.13  3.000
 X19  C14   C11  C09   109.73  3.000
 X19  O18   C12  C06   120.35  3.000
 X19  O18   C12  N03   123.02  3.000
 X19  C06   C12  N03   116.62  3.000
 X19  H13B  C13  H13A  108.46  3.000
 X19  H13B  C13  H13   108.38  3.000
 X19  H13A  C13  H13   108.32  3.000
 X19  H13B  C13  N03   108.31  3.000
 X19  H13A  C13  N03   112.06  3.000
 X19  H13   C13  N03   111.21  3.000
 X19  H14B  C14  H14A  107.73  3.000
 X19  H14B  C14  H14   107.86  3.000
 X19  H14A  C14  H14   106.50  3.000
 X19  H14B  C14  C11   111.58  3.000
 X19  H14A  C14  C11   110.96  3.000
 X19  H14   C14  C11   111.97  3.000
 X19  H15B  C15  H15A  106.82  3.000
 X19  H15B  C15  H15   107.57  3.000
 X19  H15A  C15  H15   107.33  3.000
 X19  H15B  C15  C11   111.77  3.000
 X19  H15A  C15  C11   111.08  3.000
 X19  H15   C15  C11   112.01  3.000
 X19  H16A  C16  H16   106.03  3.000
 X19  H16A  C16  C17   108.76  3.000
 X19  H16   C16  C17   107.69  3.000
 X19  H16A  C16  C11   108.43  3.000
 X19  H16   C16  C11   109.02  3.000
 X19  C17   C16  C11   116.43  3.000
 X19  H17B  C17  H17A  107.15  3.000
 X19  H17B  C17  H17   107.02  3.000
 X19  H17A  C17  H17   107.70  3.000
 X19  H17B  C17  C16   110.07  3.000
 X19  H17A  C17  C16   112.14  3.000
 X19  H17   C17  C16   112.48  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
 X19  CONST_01  C05   C04  N02  N01     0.00   0.0  0
 X19  CONST_02  C04   C05  C06  N01     0.00   0.0  0
 X19  CONST_03  C05   C06  N01  N02     0.00   0.0  0
 X19  CONST_04  C06   C05  C04  N02     0.00   0.0  0
 X19  CONST_05  C06   N01  N02  C04     0.00   0.0  0
 X19  CONST_06  C12   C06  N01  N02   180.00   0.0  0
 X19  CONST_07  C12   C06  C05  C04   180.00   0.0  0
 X19  CONST_08  C12   C06  C05  C10     0.00   0.0  0
 X19  CONST_09  HN01  N01  N02  C04   180.00   0.0  0
 X19  CONST_10  C13   N03  C12  C06   180.00   0.0  0
 X19  CONST_11  HN03  N03  C12  C06     0.00   0.0  0
 X19  CONST_12  O18   C12  N03  C13     0.00   0.0  0
 X19  Var_01    C08   C07  C04  N02  -162.47  30.0  1
 X19  Var_02    C09   C10  C05  C04    13.36  30.0  1
 X19  Var_03    C09   C08  C07  C04   -50.12  30.0  1
 X19  Var_04    N03   C12  C06  N01   -22.68  30.0  2
 X19  Var_05    C17   C16  C11  C09   174.31  30.0  3
 X19  Var_06    H14   C14  C11  C09    65.09  30.0  3
 X19  Var_07    H15   C15  C11  C09    66.16  30.0  3
 X19  Var_08    H17   C17  C16  C11   -66.29  30.0  3
 X19  Var_09    H13   C13  N03  C12   -58.40  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
 X19  chir_01  C09  C08  C10  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
 X19  plan-1  N03   0.020
 X19  plan-1  C06   0.020
 X19  plan-1  C12   0.020
 X19  plan-1  C13   0.020
 X19  plan-1  O18   0.020
 X19  plan-1  HN03  0.020
 X19  plan-2  N01   0.020
 X19  plan-2  N02   0.020
 X19  plan-2  C04   0.020
 X19  plan-2  C05   0.020
 X19  plan-2  C06   0.020
 X19  plan-2  C07   0.020
 X19  plan-2  C10   0.020
 X19  plan-2  C12   0.020
 X19  plan-2  HN01  0.020

