# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:18:19 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (2S)-1-{[5-(3-methyl-1H-indazol-5-yl)pyridin-3-yl]oxy}-3-phenylpropan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1n[nH]c2ccc(cc12)c3cncc(OC[C@@H](N)Cc4ccccc4)c3
#
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
 SS3  SS3  (2S)-1-{[5-(3-methyl-1H-indazol-5-yl)pyridin-3-yl]oxy}-3-phenylpropan-2-amine  ligand  49  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SS3
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
 SS3  N1    N  N     0  -0.251  -7.6951   1.1253  -0.4752
 SS3  N3    N  N     0  -0.382  -1.0500  -2.9286   0.7653
 SS3  C4    C  CR56  0   0.415  -5.6544   1.5288   0.3345
 SS3  C5    C  CR16  0  -0.279  -4.5093   2.0803   0.9195
 SS3  C6    C  CR16  0  -0.316  -3.3822   1.2945   0.9423
 SS3  C8    C  CR5   0   0.209  -6.9833   0.0482  -0.6968
 SS3  C13   C  CR16  0  -0.310   7.0959   0.4855   0.8221
 SS3  C15   C  CR16  0  -0.275   8.5616   1.4657  -0.8176
 SS3  C9    C  CH3   0  -0.743  -7.5427  -1.1560  -1.3658
 SS3  C17   C  CR6   0   0.167   6.3374  -0.1139  -0.1798
 SS3  C20   C  CR6   0   0.022  -2.1097  -0.8053   0.4589
 SS3  C21   C  CR16  0  -0.321  -0.8677  -0.2212   0.2598
 SS3  C22   C  CR6   0   0.347   0.2818  -1.0048   0.3167
 SS3  C24   C  CH2   0  -0.174   2.6576  -1.1236   0.2223
 SS3  C1    C  CR6   0   0.068  -3.3544  -0.0174   0.4057
 SS3  C2    C  CR16  0  -0.393  -4.4977  -0.5469  -0.1659
 SS3  C3    C  CR56  0  -0.080  -5.6573   0.2314  -0.2019
 SS3  N5    N  NR15  0  -0.553  -6.9010   2.0100   0.1418
 SS3  C14   C  CR16  0  -0.245   8.2006   1.2666   0.5089
 SS3  C16   C  CR16  0  -0.312   6.7105   0.0915  -1.5064
 SS3  C18   C  CR16  0  -0.196   0.1385  -2.3681   0.5688
 SS3  C19   C  CR16  0  -0.128  -2.1362  -2.1801   0.7170
 SS3  C26   C  CR16  0  -0.241   7.8115   0.8749  -1.8263
 SS3  O1    O  O2    0  -0.475   1.4524  -0.3827   0.1098
 SS3  C23   C  CH1   0  -0.132   3.8245  -0.1519   0.0783
 SS3  C25   C  CH2   0  -0.528   5.1322  -0.9478   0.1465
 SS3  N4    N  NH2   0  -0.774   3.8398   0.9160   1.0575
 SS3  H2    H  HCR6  0   0.257  -4.4922  -1.5390  -0.6010
 SS3  H5    H  HCR6  0   0.272  -4.5064   3.0754   1.3439
 SS3  HA    H  HNR5  0   0.415  -7.2637   2.9128   0.3989
 SS3  H9C1  H  HCH3  0   0.249  -6.9509  -1.4317  -2.2398
 SS3  H9C2  H  HCH3  0   0.250  -7.5433  -2.0160  -0.6941
 SS3  H9C3  H  HCH3  0   0.253  -8.5665  -0.9807  -1.6915
 SS3  H6    H  HCR6  0   0.260  -2.4867   1.6886   1.4062
 SS3  H21   H  HCR6  0   0.273  -0.7763   0.8371   0.0444
 SS3  H19   H  HCR6  0   0.257  -3.0793  -2.6809   0.9087
 SS3  H18   H  HCR6  0   0.277   0.9933  -3.0317   0.6176
 SS3  H241  H  HCH2  0   0.222   2.7086  -1.6239   1.1978
 SS3  H242  H  HCH2  0   0.228   2.7032  -1.8943  -0.5557
 SS3  H23   H  HCH1  0   0.243   3.7589   0.3073  -0.9147
 SS3  H251  H  HCH2  0   0.252   5.0729  -1.7879  -0.5505
 SS3  H252  H  HCH2  0   0.247   5.2345  -1.3797   1.1473
 SS3  H4N1  H  HNH2  0   0.349   2.9817   1.4502   1.0072
 SS3  H4N2  H  HNH2  0   0.337   3.8751   0.5259   1.9929
 SS3  H16   H  HCR6  0   0.244   6.1352  -0.3722  -2.3001
 SS3  H14   H  HCR6  0   0.251   8.7816   1.7201   1.3021
 SS3  H26   H  HCR6  0   0.251   8.0878   1.0180  -2.8632
 SS3  H15   H  HCR6  0   0.252   9.4246   2.0713  -1.0628
 SS3  H13   H  HCR6  0   0.240   6.8233   0.3343   1.8596

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
 SS3  C8   N1    aromatic  1.310  0.020  1.310
 SS3  N5   N1    aromatic  1.339  0.020  1.339
 SS3  C19  N3    aromatic  1.320  0.020  1.320
 SS3  C3   C4    aromatic  1.404  0.020  1.404
 SS3  C4   C5    aromatic  1.399  0.020  1.399
 SS3  C5   C6    aromatic  1.374  0.020  1.374
 SS3  C1   C6    aromatic  1.418  0.020  1.418
 SS3  C3   C8    aromatic  1.427  0.020  1.427
 SS3  C17  C13   aromatic  1.392  0.020  1.392
 SS3  C14  C15   aromatic  1.389  0.020  1.389
 SS3  C26  C15   aromatic  1.389  0.020  1.389
 SS3  C8   C9    single    1.487  0.020  1.487
 SS3  C25  C17   single    1.501  0.020  1.501
 SS3  C1   C20   single    1.474  0.020  1.474
 SS3  C20  C21   aromatic  1.387  0.020  1.387
 SS3  C21  C22   aromatic  1.392  0.020  1.392
 SS3  O1   C24   single    1.419  0.020  1.419
 SS3  C2   C1    aromatic  1.384  0.020  1.384
 SS3  C3   C2    aromatic  1.397  0.020  1.397
 SS3  C4   N5    aromatic  1.350  0.020  1.350
 SS3  C13  C14   aromatic  1.389  0.020  1.389
 SS3  C17  C16   aromatic  1.393  0.020  1.393
 SS3  C22  C18   aromatic  1.394  0.020  1.394
 SS3  N3   C18   aromatic  1.329  0.020  1.329
 SS3  C20  C19   aromatic  1.399  0.020  1.399
 SS3  C16  C26   aromatic  1.389  0.020  1.389
 SS3  C22  O1    single    1.342  0.020  1.342
 SS3  C24  C23   single    1.525  0.020  1.525
 SS3  C23  C25   single    1.532  0.020  1.532
 SS3  C23  N4    single    1.449  0.020  1.449
 SS3  C2   H2    single    0.930  0.020  1.080
 SS3  C5   H5    single    0.930  0.020  1.080
 SS3  N5   HA    single    0.860  0.020  1.020
 SS3  C9   H9C1  single    0.970  0.020  1.090
 SS3  C9   H9C2  single    0.970  0.020  1.090
 SS3  C9   H9C3  single    0.970  0.020  1.090
 SS3  C6   H6    single    0.930  0.020  1.080
 SS3  C21  H21   single    0.930  0.020  1.080
 SS3  C19  H19   single    0.930  0.020  1.080
 SS3  C18  H18   single    0.930  0.020  1.080
 SS3  C24  H241  single    0.970  0.020  1.090
 SS3  C24  H242  single    0.970  0.020  1.090
 SS3  C23  H23   single    0.970  0.020  1.090
 SS3  C25  H251  single    0.970  0.020  1.090
 SS3  C25  H252  single    0.970  0.020  1.090
 SS3  N4   H4N1  single    0.890  0.020  1.040
 SS3  N4   H4N2  single    0.890  0.020  1.040
 SS3  C13  H13   single    0.930  0.020  1.080
 SS3  C16  H16   single    0.930  0.020  1.080
 SS3  C14  H14   single    0.930  0.020  1.080
 SS3  C26  H26   single    0.930  0.020  1.080
 SS3  C15  H15   single    0.930  0.020  1.080

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
 SS3  N5    N1   C8    107.39  3.000
 SS3  C19   N3   C18   119.44  3.000
 SS3  N5    C4   C3    105.83  3.000
 SS3  N5    C4   C5    132.45  3.000
 SS3  C3    C4   C5    121.72  3.000
 SS3  H5    C5   C6    121.15  3.000
 SS3  H5    C5   C4    121.92  3.000
 SS3  C6    C5   C4    116.92  3.000
 SS3  H6    C6   C1    118.86  3.000
 SS3  H6    C6   C5    118.51  3.000
 SS3  C1    C6   C5    122.62  3.000
 SS3  C3    C8   C9    127.56  3.000
 SS3  C9    C8   N1    122.52  3.000
 SS3  C3    C8   N1    109.92  3.000
 SS3  H13   C13  C14   119.65  3.000
 SS3  H13   C13  C17   119.47  3.000
 SS3  C14   C13  C17   120.88  3.000
 SS3  H15   C15  C26   120.27  3.000
 SS3  H15   C15  C14   120.24  3.000
 SS3  C26   C15  C14   119.49  3.000
 SS3  H9C3  C9   H9C2  108.10  3.000
 SS3  H9C3  C9   H9C1  108.13  3.000
 SS3  H9C2  C9   H9C1  107.11  3.000
 SS3  H9C3  C9   C8    110.98  3.000
 SS3  H9C2  C9   C8    111.19  3.000
 SS3  H9C1  C9   C8    111.17  3.000
 SS3  C25   C17  C16   120.25  3.000
 SS3  C16   C17  C13   118.41  3.000
 SS3  C25   C17  C13   121.34  3.000
 SS3  C19   C20  C1    121.06  3.000
 SS3  C19   C20  C21   117.21  3.000
 SS3  C1    C20  C21   121.73  3.000
 SS3  H21   C21  C22   119.21  3.000
 SS3  H21   C21  C20   121.02  3.000
 SS3  C22   C21  C20   119.77  3.000
 SS3  O1    C22  C18   124.83  3.000
 SS3  O1    C22  C21   116.94  3.000
 SS3  C18   C22  C21   118.23  3.000
 SS3  H242  C24  H241  107.97  3.000
 SS3  H242  C24  C23   110.44  3.000
 SS3  H241  C24  C23   109.80  3.000
 SS3  H242  C24  O1    110.25  3.000
 SS3  H241  C24  O1    110.36  3.000
 SS3  C23   C24  O1    108.03  3.000
 SS3  C2    C1   C20   120.54  3.000
 SS3  C2    C1   C6    119.62  3.000
 SS3  C20   C1   C6    119.84  3.000
 SS3  H2    C2   C3    120.26  3.000
 SS3  H2    C2   C1    120.81  3.000
 SS3  C3    C2   C1    118.91  3.000
 SS3  C2    C3   C8    135.13  3.000
 SS3  C2    C3   C4    120.21  3.000
 SS3  C8    C3   C4    104.66  3.000
 SS3  HA    N5   C4    128.03  3.000
 SS3  HA    N5   N1    119.77  3.000
 SS3  C4    N5   N1    112.20  3.000
 SS3  H14   C14  C15   120.00  3.000
 SS3  H14   C14  C13   119.82  3.000
 SS3  C15   C14  C13   120.18  3.000
 SS3  H16   C16  C26   119.55  3.000
 SS3  H16   C16  C17   119.46  3.000
 SS3  C26   C16  C17   120.99  3.000
 SS3  H18   C18  C22   121.75  3.000
 SS3  H18   C18  N3    116.15  3.000
 SS3  C22   C18  N3    122.10  3.000
 SS3  H19   C19  C20   120.17  3.000
 SS3  H19   C19  N3    116.56  3.000
 SS3  C20   C19  N3    123.26  3.000
 SS3  H26   C26  C16   119.84  3.000
 SS3  H26   C26  C15   120.10  3.000
 SS3  C16   C26  C15   120.05  3.000
 SS3  C24   O1   C22   119.12  3.000
 SS3  H23   C23  N4    107.71  3.000
 SS3  H23   C23  C25   107.99  3.000
 SS3  N4    C23  C25   110.10  3.000
 SS3  H23   C23  C24   107.86  3.000
 SS3  N4    C23  C24   114.45  3.000
 SS3  C25   C23  C24   108.53  3.000
 SS3  H252  C25  H251  106.54  3.000
 SS3  H252  C25  C23   108.98  3.000
 SS3  H251  C25  C23   108.93  3.000
 SS3  H252  C25  C17   110.04  3.000
 SS3  H251  C25  C17   109.38  3.000
 SS3  C23   C25  C17   112.76  3.000
 SS3  H4N2  N4   H4N1  106.17  3.000
 SS3  H4N2  N4   C23   109.89  3.000
 SS3  H4N1  N4   C23   110.27  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
 SS3  CONST_01  C4    C3   C8   N1      0.00   0.0  0
 SS3  CONST_02  C2    C3   C8   N1    180.00   0.0  0
 SS3  CONST_03  C3    C4   N5   N1      0.00   0.0  0
 SS3  CONST_04  C5    C4   N5   N1    180.00   0.0  0
 SS3  CONST_05  C1    C20  C19  N3    180.00   0.0  0
 SS3  CONST_06  C21   C20  C19  N3      0.00   0.0  0
 SS3  CONST_07  C21   C22  C18  N3      0.00   0.0  0
 SS3  CONST_08  C1    C2   C3   C4      0.00   0.0  0
 SS3  CONST_09  C1    C6   C5   C4      0.00   0.0  0
 SS3  CONST_10  C8    N1   N5   C4      0.00   0.0  0
 SS3  CONST_11  C8    C3   C4   C5    180.00   0.0  0
 SS3  CONST_12  C2    C3   C4   C5      0.00   0.0  0
 SS3  CONST_13  C20   C1   C6   C5    180.00   0.0  0
 SS3  CONST_14  C2    C1   C6   C5      0.00   0.0  0
 SS3  CONST_15  C3    C4   C5   C6      0.00   0.0  0
 SS3  CONST_16  N5    C4   C5   C6    180.00   0.0  0
 SS3  CONST_19  C3    C2   C1   C6      0.00   0.0  0
 SS3  CONST_20  N5    C4   C3   C8      0.00   0.0  0
 SS3  CONST_21  C1    C2   C3   C8    180.00   0.0  0
 SS3  CONST_22  C26   C16  C17  C13     0.00   0.0  0
 SS3  CONST_23  C26   C15  C14  C13     0.00   0.0  0
 SS3  CONST_24  C17   C13  C14  C15     0.00   0.0  0
 SS3  CONST_25  C17   C16  C26  C15     0.00   0.0  0
 SS3  CONST_26  C3    C2   C1   C20   180.00   0.0  0
 SS3  CONST_27  C18   C22  C21  C20     0.00   0.0  0
 SS3  CONST_28  C18   N3   C19  C20     0.00   0.0  0
 SS3  CONST_30  C1    C20  C21  C22   180.00   0.0  0
 SS3  CONST_31  C19   C20  C21  C22     0.00   0.0  0
 SS3  CONST_32  C19   N3   C18  C22     0.00   0.0  0
 SS3  CONST_34  N5    C4   C3   C2    180.00   0.0  0
 SS3  CONST_35  N5    N1   C8   C3      0.00   0.0  0
 SS3  CONST_36  C16   C26  C15  C14     0.00   0.0  0
 SS3  CONST_37  C16   C17  C13  C14     0.00   0.0  0
 SS3  CONST_38  O1    C22  C18  N3    180.00   0.0  0
 SS3  CONST_39  C9    C8   C3   C4    180.00   0.0  0
 SS3  CONST_40  N5    N1   C8   C9    180.00   0.0  0
 SS3  CONST_41  C2    C3   C8   C9      0.00   0.0  0
 SS3  CONST_42  O1    C22  C21  C20   180.00   0.0  0
 SS3  CONST_43  C25   C17  C13  C14   180.00   0.0  0
 SS3  CONST_44  C25   C17  C16  C26   180.00   0.0  0
 SS3  CONST_45  H2    C2   C3   C4    180.00   0.0  0
 SS3  CONST_46  H6    C6   C5   C4    180.00   0.0  0
 SS3  CONST_47  HA    N5   C4   C5      0.00   0.0  0
 SS3  CONST_48  H16   C16  C17  C13   180.00   0.0  0
 SS3  CONST_49  H15   C15  C14  C13   180.00   0.0  0
 SS3  CONST_50  H13   C13  C14  C15   180.00   0.0  0
 SS3  CONST_51  H14   C14  C13  C17   180.00   0.0  0
 SS3  CONST_52  H26   C26  C16  C17   180.00   0.0  0
 SS3  CONST_53  H19   C19  C20  C21   180.00   0.0  0
 SS3  CONST_54  H18   C18  C22  C21   180.00   0.0  0
 SS3  CONST_55  H5    C5   C6   C1    180.00   0.0  0
 SS3  CONST_56  H21   C21  C20  C1      0.00   0.0  0
 SS3  Var_01    C23   C25  C17  C13    95.25  30.0  2
 SS3  Var_02    C18   C22  O1   C24    -3.72  30.0  1
 SS3  Var_03    H9C1  C9   C8   N1    124.38  30.0  2
 SS3  Var_04    C23   C24  O1   C22  -174.42  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
 SS3  chir_01  C23  C24  C25  N4  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
 SS3  plan-1  C13  0.020
 SS3  plan-1  C15  0.020
 SS3  plan-1  C17  0.020
 SS3  plan-1  C14  0.020
 SS3  plan-1  C16  0.020
 SS3  plan-1  C26  0.020
 SS3  plan-1  C25  0.020
 SS3  plan-1  H16  0.020
 SS3  plan-1  H14  0.020
 SS3  plan-1  H26  0.020
 SS3  plan-1  H15  0.020
 SS3  plan-1  H13  0.020
 SS3  plan-2  N3   0.020
 SS3  plan-2  C20  0.020
 SS3  plan-2  C21  0.020
 SS3  plan-2  C22  0.020
 SS3  plan-2  C1   0.020
 SS3  plan-2  C18  0.020
 SS3  plan-2  C19  0.020
 SS3  plan-2  O1   0.020
 SS3  plan-2  H21  0.020
 SS3  plan-2  H19  0.020
 SS3  plan-2  H18  0.020
 SS3  plan-3  N1   0.020
 SS3  plan-3  C4   0.020
 SS3  plan-3  C5   0.020
 SS3  plan-3  C6   0.020
 SS3  plan-3  C8   0.020
 SS3  plan-3  C9   0.020
 SS3  plan-3  C20  0.020
 SS3  plan-3  C1   0.020
 SS3  plan-3  C2   0.020
 SS3  plan-3  C3   0.020
 SS3  plan-3  N5   0.020
 SS3  plan-3  H2   0.020
 SS3  plan-3  H5   0.020
 SS3  plan-3  HA   0.020
 SS3  plan-3  H6   0.020

