# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 17:17:59 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (2~{S})-4-methyl-1-[5-(3-methyl-2~{H}-indazol-5-yl)pyridin-3-yl]oxy-pentan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)COc1cncc(c1)c2ccc3n[nH]c(C)c3c2
#
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
 EAZ  EAZ  (2~{S})-4-methyl-1-[5-(3-methyl-2~{H}-indazol-5-yl)pyridin-3-yl]oxy-pentan-2-amine  ligand  48  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EAZ
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
 EAZ  C1   C  CR6   0   0.024  -1.1730  -0.6839   0.5960
 EAZ  C2   C  CR16  0  -0.130  -1.0764  -2.0306   0.9637
 EAZ  C11  C  CR16  0  -0.310  -2.6369   1.3352   0.8766
 EAZ  C12  C  CR56  0   0.237  -4.9277   1.3237   0.2252
 EAZ  C13  C  CR56  0  -0.117  -4.7860  -0.0270  -0.1945
 EAZ  C14  C  CR5   0   0.379  -6.0490  -0.3797  -0.6775
 EAZ  C17  C  CH3   0  -0.739  -6.5608  -1.6431  -1.2637
 EAZ  C18  C  CH2   0  -0.151   3.6013  -0.5969   0.3446
 EAZ  C19  C  CH1   0  -0.154   4.6893   0.4169   0.0373
 EAZ  C20  C  CH2   0  -0.411   6.0211  -0.3270  -0.1199
 EAZ  C21  C  CH1   0  -0.242   7.2361   0.5619  -0.3882
 EAZ  C22  C  CH3   0  -0.648   8.5007  -0.2904  -0.4375
 EAZ  C23  C  CH3   0  -0.660   7.0845   1.3711  -1.6733
 EAZ  N3   N  N     0  -0.382   0.0736  -2.6663   1.0870
 EAZ  C4   C  CR16  0  -0.199   1.2088  -2.0128   0.8639
 EAZ  C5   C  CR6   0   0.344   1.2313  -0.6649   0.5063
 EAZ  C6   C  CR16  0  -0.324   0.0139  -0.0020   0.3709
 EAZ  O7   O  O2    0  -0.467   2.3407   0.0491   0.2712
 EAZ  C8   C  CR6   0   0.057  -2.4833  -0.0236   0.4560
 EAZ  C9   C  CR16  0  -0.389  -3.5551  -0.6989  -0.0767
 EAZ  C10  C  CR16  0  -0.283  -3.8188   2.0092   0.7738
 EAZ  N15  N  NR15  0  -0.461  -6.7899   0.7190  -0.5115
 EAZ  N16  N  N     0  -0.319  -6.1693   1.7667   0.0236
 EAZ  N24  N  NH2   0  -0.786   4.6821   1.4579   1.0529
 EAZ  H1   H  HCR6  0   0.255  -1.9726  -2.6013   1.1828
 EAZ  H2   H  HCR6  0   0.255  -1.7843   1.8400   1.3139
 EAZ  H3   H  HCH3  0   0.262  -6.3460  -2.4872  -0.6084
 EAZ  H4   H  HCH3  0   0.262  -7.6379  -1.6044  -1.4194
 EAZ  H5   H  HCH3  0   0.263  -6.0898  -1.8474  -2.2260
 EAZ  H6   H  HCH2  0   0.231   3.6434  -1.4238  -0.3734
 EAZ  H7   H  HCH2  0   0.221   3.7584  -1.0178   1.3461
 EAZ  H8   H  HCH1  0   0.237   4.4360   0.8882  -0.9180
 EAZ  H9   H  HCH2  0   0.219   6.2063  -0.9098   0.7909
 EAZ  H10  H  HCH2  0   0.214   5.9305  -1.0550  -0.9351
 EAZ  H11  H  HCH1  0   0.209   7.3420   1.2635   0.4475
 EAZ  H12  H  HCH3  0   0.225   9.3920   0.3253  -0.5692
 EAZ  H13  H  HCH3  0   0.223   8.6280  -0.8656   0.4817
 EAZ  H14  H  HCH3  0   0.213   8.4604  -0.9982  -1.2687
 EAZ  H15  H  HCH3  0   0.226   6.2288   2.0473  -1.6416
 EAZ  H16  H  HCH3  0   0.228   7.9704   1.9814  -1.8575
 EAZ  H17  H  HCH3  0   0.215   6.9516   0.7112  -2.5346
 EAZ  H18  H  HCR6  0   0.276   2.1214  -2.5847   0.9815
 EAZ  H19  H  HCR6  0   0.271   0.0092   1.0392   0.0705
 EAZ  H20  H  HCR6  0   0.256  -3.4522  -1.7201  -0.4240
 EAZ  H21  H  HCR6  0   0.258  -3.9095   3.0340   1.1098
 EAZ  H22  H  HNR5  0   0.424  -7.7658   0.8073  -0.7567
 EAZ  H23  H  HNH2  0   0.337   5.0620   1.0911   1.9191
 EAZ  H24  H  HNH2  0   0.350   5.2988   2.2125   0.7800

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
 EAZ  N24  C19  single    1.454  0.020  1.454
 EAZ  C18  C19  single    1.519  0.020  1.519
 EAZ  C18  O7   single    1.418  0.020  1.418
 EAZ  C19  C20  single    1.534  0.020  1.534
 EAZ  C10  C11  aromatic  1.364  0.020  1.364
 EAZ  C10  C12  aromatic  1.414  0.020  1.414
 EAZ  C11  C8   aromatic  1.431  0.020  1.431
 EAZ  O7   C5   single    1.340  0.020  1.340
 EAZ  C6   C5   aromatic  1.393  0.020  1.393
 EAZ  C6   C1   aromatic  1.387  0.020  1.387
 EAZ  C5   C4   aromatic  1.395  0.020  1.395
 EAZ  C12  N16  aromatic  1.334  0.020  1.334
 EAZ  C12  C13  aromatic  1.422  0.020  1.422
 EAZ  N16  N15  aromatic  1.330  0.020  1.330
 EAZ  C8   C1   single    1.474  0.020  1.474
 EAZ  C8   C9   aromatic  1.374  0.020  1.374
 EAZ  C1   C2   aromatic  1.399  0.020  1.399
 EAZ  C4   N3   aromatic  1.329  0.020  1.329
 EAZ  C2   N3   aromatic  1.320  0.020  1.320
 EAZ  C13  C9   aromatic  1.407  0.020  1.407
 EAZ  C13  C14  aromatic  1.397  0.020  1.397
 EAZ  N15  C14  aromatic  1.336  0.020  1.336
 EAZ  C14  C17  single    1.484  0.020  1.484
 EAZ  C20  C21  single    1.529  0.020  1.529
 EAZ  C21  C23  single    1.526  0.020  1.526
 EAZ  C21  C22  single    1.526  0.020  1.526
 EAZ  C2   H1   single    0.930  0.020  1.080
 EAZ  C11  H2   single    0.930  0.020  1.080
 EAZ  C17  H3   single    0.970  0.020  1.090
 EAZ  C17  H4   single    0.970  0.020  1.090
 EAZ  C17  H5   single    0.970  0.020  1.090
 EAZ  C18  H6   single    0.970  0.020  1.090
 EAZ  C18  H7   single    0.970  0.020  1.090
 EAZ  C19  H8   single    0.970  0.020  1.090
 EAZ  C20  H9   single    0.970  0.020  1.090
 EAZ  C20  H10  single    0.970  0.020  1.090
 EAZ  C21  H11  single    0.970  0.020  1.090
 EAZ  C22  H12  single    0.970  0.020  1.090
 EAZ  C22  H13  single    0.970  0.020  1.090
 EAZ  C22  H14  single    0.970  0.020  1.090
 EAZ  C23  H15  single    0.970  0.020  1.090
 EAZ  C23  H16  single    0.970  0.020  1.090
 EAZ  C23  H17  single    0.970  0.020  1.090
 EAZ  C4   H18  single    0.930  0.020  1.080
 EAZ  C6   H19  single    0.930  0.020  1.080
 EAZ  C9   H20  single    0.930  0.020  1.080
 EAZ  C10  H21  single    0.930  0.020  1.080
 EAZ  N15  H22  single    0.860  0.020  1.020
 EAZ  N24  H23  single    0.890  0.020  1.040
 EAZ  N24  H24  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
 EAZ  C8   C1   C6   121.67  3.000
 EAZ  C8   C1   C2   121.16  3.000
 EAZ  C6   C1   C2   117.17  3.000
 EAZ  H1   C2   N3   116.59  3.000
 EAZ  H1   C2   C1   120.15  3.000
 EAZ  N3   C2   C1   123.24  3.000
 EAZ  H2   C11  C10  118.83  3.000
 EAZ  H2   C11  C8   118.47  3.000
 EAZ  C10  C11  C8   122.69  3.000
 EAZ  N16  C12  C10  128.87  3.000
 EAZ  N16  C12  C13  111.33  3.000
 EAZ  C10  C12  C13  119.80  3.000
 EAZ  C9   C13  C14  134.34  3.000
 EAZ  C14  C13  C12  104.58  3.000
 EAZ  C9   C13  C12  121.07  3.000
 EAZ  N15  C14  C17  123.94  3.000
 EAZ  C17  C14  C13  131.54  3.000
 EAZ  N15  C14  C13  104.52  3.000
 EAZ  H5   C17  H4   107.91  3.000
 EAZ  H5   C17  H3   107.48  3.000
 EAZ  H4   C17  H3   107.96  3.000
 EAZ  H5   C17  C14  111.05  3.000
 EAZ  H4   C17  C14  111.55  3.000
 EAZ  H3   C17  C14  110.73  3.000
 EAZ  H7   C18  H6   107.64  3.000
 EAZ  H7   C18  O7   110.43  3.000
 EAZ  H6   C18  O7   110.12  3.000
 EAZ  H7   C18  C19  109.76  3.000
 EAZ  H6   C18  C19  110.10  3.000
 EAZ  O7   C18  C19  108.80  3.000
 EAZ  H8   C19  N24  107.46  3.000
 EAZ  H8   C19  C20  108.68  3.000
 EAZ  N24  C19  C20  115.03  3.000
 EAZ  H8   C19  C18  107.35  3.000
 EAZ  C20  C19  C18  108.61  3.000
 EAZ  N24  C19  C18  109.45  3.000
 EAZ  H10  C20  H9   106.16  3.000
 EAZ  H10  C20  C21  108.73  3.000
 EAZ  H9   C20  C21  108.68  3.000
 EAZ  H10  C20  C19  109.05  3.000
 EAZ  H9   C20  C19  108.62  3.000
 EAZ  C21  C20  C19  115.22  3.000
 EAZ  H11  C21  C23  108.19  3.000
 EAZ  H11  C21  C22  107.58  3.000
 EAZ  C23  C21  C22  110.56  3.000
 EAZ  H11  C21  C20  108.36  3.000
 EAZ  C22  C21  C20  109.84  3.000
 EAZ  C23  C21  C20  112.15  3.000
 EAZ  H14  C22  H13  107.67  3.000
 EAZ  H14  C22  H12  107.69  3.000
 EAZ  H13  C22  H12  107.68  3.000
 EAZ  H14  C22  C21  110.85  3.000
 EAZ  H13  C22  C21  111.33  3.000
 EAZ  H12  C22  C21  111.45  3.000
 EAZ  H17  C23  H16  107.66  3.000
 EAZ  H17  C23  H15  107.56  3.000
 EAZ  H16  C23  H15  107.15  3.000
 EAZ  H17  C23  C21  110.83  3.000
 EAZ  H16  C23  C21  110.98  3.000
 EAZ  H15  C23  C21  112.45  3.000
 EAZ  C4   N3   C2   119.46  3.000
 EAZ  H18  C4   C5   121.63  3.000
 EAZ  H18  C4   N3   116.21  3.000
 EAZ  C5   C4   N3   122.15  3.000
 EAZ  O7   C5   C6   116.93  3.000
 EAZ  C6   C5   C4   118.09  3.000
 EAZ  O7   C5   C4   124.98  3.000
 EAZ  H19  C6   C5   119.21  3.000
 EAZ  H19  C6   C1   120.90  3.000
 EAZ  C5   C6   C1   119.87  3.000
 EAZ  C5   O7   C18  118.94  3.000
 EAZ  C9   C8   C11  119.79  3.000
 EAZ  C9   C8   C1   120.67  3.000
 EAZ  C11  C8   C1   119.54  3.000
 EAZ  H20  C9   C8   120.88  3.000
 EAZ  H20  C9   C13  120.41  3.000
 EAZ  C8   C9   C13  118.69  3.000
 EAZ  H21  C10  C12  120.91  3.000
 EAZ  H21  C10  C11  121.12  3.000
 EAZ  C12  C10  C11  117.96  3.000
 EAZ  H22  N15  N16  118.66  3.000
 EAZ  H22  N15  C14  125.29  3.000
 EAZ  N16  N15  C14  116.05  3.000
 EAZ  N15  N16  C12  103.51  3.000
 EAZ  H24  N24  H23  105.76  3.000
 EAZ  H24  N24  C19  110.02  3.000
 EAZ  H23  N24  C19  109.61  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
 EAZ  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 EAZ  CONST_02  C10  C11  C8   C1    180.00   0.0  0
 EAZ  CONST_03  C13  C9   C8   C1    180.00   0.0  0
 EAZ  CONST_04  C4   N3   C2   C1      0.00   0.0  0
 EAZ  CONST_05  C5   C6   C1   C2      0.00   0.0  0
 EAZ  CONST_08  C5   C4   N3   C2      0.00   0.0  0
 EAZ  CONST_09  N16  C12  C10  C11   180.00   0.0  0
 EAZ  CONST_10  C13  C12  C10  C11     0.00   0.0  0
 EAZ  CONST_12  C13  C9   C8   C11     0.00   0.0  0
 EAZ  CONST_13  C8   C11  C10  C12     0.00   0.0  0
 EAZ  CONST_14  C14  N15  N16  C12     0.00   0.0  0
 EAZ  CONST_15  C8   C9   C13  C12     0.00   0.0  0
 EAZ  CONST_16  N15  C14  C13  C12     0.00   0.0  0
 EAZ  CONST_17  N15  N16  C12  C13     0.00   0.0  0
 EAZ  CONST_18  N16  N15  C14  C13     0.00   0.0  0
 EAZ  CONST_19  C10  C12  C13  C14   180.00   0.0  0
 EAZ  CONST_20  N16  C12  C13  C14     0.00   0.0  0
 EAZ  CONST_21  C8   C9   C13  C14   180.00   0.0  0
 EAZ  CONST_22  C6   C5   C4   N3      0.00   0.0  0
 EAZ  CONST_23  C6   C1   C2   N3      0.00   0.0  0
 EAZ  CONST_24  C8   C1   C2   N3    180.00   0.0  0
 EAZ  CONST_25  C8   C1   C6   C5    180.00   0.0  0
 EAZ  CONST_27  C10  C11  C8   C9      0.00   0.0  0
 EAZ  CONST_28  C10  C12  C13  C9      0.00   0.0  0
 EAZ  CONST_29  N16  C12  C13  C9    180.00   0.0  0
 EAZ  CONST_30  N15  C14  C13  C9    180.00   0.0  0
 EAZ  CONST_31  N15  N16  C12  C10   180.00   0.0  0
 EAZ  CONST_32  O7   C5   C6   C1    180.00   0.0  0
 EAZ  CONST_33  C17  C14  C13  C12   180.00   0.0  0
 EAZ  CONST_34  C9   C13  C14  C17     0.00   0.0  0
 EAZ  CONST_35  N16  N15  C14  C17   180.00   0.0  0
 EAZ  CONST_36  O7   C5   C4   N3    180.00   0.0  0
 EAZ  CONST_37  H2   C11  C8   C1      0.00   0.0  0
 EAZ  CONST_38  H20  C9   C8   C1      0.00   0.0  0
 EAZ  CONST_39  H19  C6   C1   C2    180.00   0.0  0
 EAZ  CONST_40  H18  C4   N3   C2    180.00   0.0  0
 EAZ  CONST_41  H22  N15  N16  C12   180.00   0.0  0
 EAZ  CONST_42  H21  C10  C12  C13   180.00   0.0  0
 EAZ  CONST_43  H1   C2   N3   C4    180.00   0.0  0
 EAZ  Var_01    C6   C5   O7   C18  -177.51  30.0  2
 EAZ  Var_02    H3   C17  C14  C13    52.61  30.0  2
 EAZ  Var_03    H6   C18  O7   C5     59.11  30.0  1
 EAZ  Var_04    C23  C21  C20  C19   -60.10  30.0  3
 EAZ  Var_05    H15  C23  C21  C20    61.23  30.0  3
 EAZ  Var_06    H12  C22  C21  C20  -176.64  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
 EAZ  chir_01  C19  N24  C18  C20  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
 EAZ  plan-1  C1   0.020
 EAZ  plan-1  C2   0.020
 EAZ  plan-1  N3   0.020
 EAZ  plan-1  C4   0.020
 EAZ  plan-1  C5   0.020
 EAZ  plan-1  C6   0.020
 EAZ  plan-1  O7   0.020
 EAZ  plan-1  C8   0.020
 EAZ  plan-1  H1   0.020
 EAZ  plan-1  H18  0.020
 EAZ  plan-1  H19  0.020
 EAZ  plan-2  C1   0.020
 EAZ  plan-2  C11  0.020
 EAZ  plan-2  C12  0.020
 EAZ  plan-2  C13  0.020
 EAZ  plan-2  C14  0.020
 EAZ  plan-2  C17  0.020
 EAZ  plan-2  C8   0.020
 EAZ  plan-2  C9   0.020
 EAZ  plan-2  C10  0.020
 EAZ  plan-2  N15  0.020
 EAZ  plan-2  N16  0.020
 EAZ  plan-2  H2   0.020
 EAZ  plan-2  H20  0.020
 EAZ  plan-2  H21  0.020
 EAZ  plan-2  H22  0.020

