# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:05:04 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: (2S)-1-(4-bromophenyl)-3-{[5-(3-methyl-1H-indazol-5-yl)pyridin-3-yl]oxy}propan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1n[nH]c2ccc(cc12)c3cncc(OC[C@@H](N)Cc4ccc(Br)cc4)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
 SS4  SS4  (2S)-1-(4-bromophenyl)-3-{[5-(3-methyl-1H-indazol-5-yl)pyridin-3-yl]oxy}propan-2-amine  ligand  49  28  .  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_SS4
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
 SS4  N1    N   N     0  -0.251   -9.3974   1.6182   0.4673
 SS4  N3    N   N     0  -0.382   -3.1841  -3.0357  -0.8886
 SS4  C4    C   CR56  0   0.415   -7.3313   1.8409  -0.3482
 SS4  C5    C   CR16  0  -0.279   -6.1403   2.2914  -0.9281
 SS4  C6    C   CR16  0  -0.316   -5.0950   1.4004  -0.9760
 SS4  C8    C   CR5   0   0.209   -8.7921   0.4728   0.6606
 SS4  C13   C   CR16  0  -0.316    5.0809  -1.0690   1.3328
 SS4  C15   C   CR6   0  -0.126    6.7638   0.4506   0.5768
 SS4  C9    C   CH3   0  -0.743   -9.4588  -0.6840   1.3150
 SS4  C17   C   CR6   0   0.140    4.4334  -1.0010   0.1025
 SS4  C20   C   CR6   0   0.024   -4.0311  -0.8246  -0.5465
 SS4  C21   C   CR16  0  -0.323   -2.7379  -0.3669  -0.3430
 SS4  C22   C   CR6   0   0.344   -1.6693  -1.2574  -0.4149
 SS4  C24   C   CH2   0  -0.164    0.6675  -1.6314  -0.2228
 SS4  C1    C   CR6   0   0.068   -5.1929   0.0798  -0.4703
 SS4  C2    C   CR16  0  -0.394   -6.3796  -0.3485   0.0974
 SS4  C3    C   CR56  0  -0.080   -7.4576   0.5378   0.1593
 SS4  N5    N   NR15  0  -0.553   -8.5247   2.4355  -0.1361
 SS4  C14   C   CR16  0  -0.213    6.2438  -0.3518   1.5802
 SS4  C16   C   CR16  0  -0.296    4.9818  -0.1856  -0.8851
 SS4  C18   C   CR16  0  -0.199   -1.9463  -2.5963  -0.6880
 SS4  C19   C   CR16  0  -0.129   -4.1924  -2.1861  -0.8252
 SS4  C26   C   CR16  0  -0.213    6.1418   0.5409  -0.6604
 SS4  O1    O   O2    0  -0.465   -0.4450  -0.7540  -0.2031
 SS4  C10   C   CH1   0  -0.134    1.9216  -0.8278   0.0726
 SS4  C25   C   CH2   0  -0.531    3.1489  -1.7371  -0.1376
 SS4  N4    N   NH2   0  -0.782    1.8278  -0.2320   1.3904
 SS4  H5    H   HNR5  0   0.415   -8.7993   3.3752  -0.3688
 SS4  H18   H   HCR6  0   0.277   -1.1601  -3.3386  -0.7513
 SS4  H19   H   HCR6  0   0.257   -5.1802  -2.5898  -1.0208
 SS4  HA    H   HCR6  0   0.272   -6.0415   3.2916  -1.3283
 SS4  H6    H   HCR6  0   0.260   -4.1668   1.7176  -1.4348
 SS4  H9C1  H   HCH3  0   0.250   -9.5071  -1.5432   0.6444
 SS4  H9C2  H   HCH3  0   0.249   -8.9113  -1.0002   2.2042
 SS4  H9C3  H   HCH3  0   0.253  -10.4739  -0.4301   1.6148
 SS4  H13   H   HCR6  0   0.261    4.6773  -1.7000   2.1158
 SS4  H14   H   HCR6  0   0.278    6.7262  -0.4252   2.5456
 SS4  H26   H   HCR6  0   0.278    6.5475   1.1647  -1.4456
 SS4  H16   H   HCR6  0   0.260    4.5006  -0.1148  -1.8535
 SS4  H251  H   HCH2  0   0.252    3.1354  -2.1389  -1.1541
 SS4  H252  H   HCH2  0   0.251    3.0821  -2.5899   0.5450
 SS4  H21   H   HCR6  0   0.272   -2.5453   0.6736  -0.1082
 SS4  H241  H   HCH2  0   0.226    0.5456  -2.4237   0.5273
 SS4  H242  H   HCH2  0   0.234    0.7553  -2.1126  -1.2032
 SS4  H10   H   HCH1  0   0.248    1.9790  -0.0119  -0.6561
 SS4  H2    H   HCR6  0   0.256   -6.4673  -1.3465   0.5093
 SS4  H4N1  H   HNH2  0   0.339    1.9254  -0.9456   2.1045
 SS4  H4N2  H   HNH2  0   0.354    2.5881   0.4199   1.5359
 SS4  BR1   BR  BR    0  -0.054    8.3467   1.4331   0.8959

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
 SS4  N1   C8    aromatic  1.310  0.020  1.310
 SS4  N1   N5    aromatic  1.339  0.020  1.339
 SS4  N3   C18   aromatic  1.329  0.020  1.329
 SS4  N3   C19   aromatic  1.320  0.020  1.320
 SS4  C4   C5    aromatic  1.399  0.020  1.399
 SS4  C4   C3    aromatic  1.404  0.020  1.404
 SS4  C4   N5    aromatic  1.350  0.020  1.350
 SS4  C5   C6    aromatic  1.374  0.020  1.374
 SS4  C5   HA    single    0.930  0.020  1.080
 SS4  C6   C1    aromatic  1.418  0.020  1.418
 SS4  C6   H6    single    0.930  0.020  1.080
 SS4  C8   C9    single    1.487  0.020  1.487
 SS4  C8   C3    aromatic  1.427  0.020  1.427
 SS4  C13  C17   aromatic  1.392  0.020  1.392
 SS4  C13  C14   aromatic  1.388  0.020  1.388
 SS4  C13  H13   single    0.930  0.020  1.080
 SS4  C15  C14   aromatic  1.386  0.020  1.386
 SS4  C15  C26   aromatic  1.388  0.020  1.388
 SS4  C15  BR1   single    1.890  0.020  1.890
 SS4  C9   H9C1  single    0.970  0.020  1.090
 SS4  C9   H9C2  single    0.970  0.020  1.090
 SS4  C9   H9C3  single    0.970  0.020  1.090
 SS4  C17  C16   aromatic  1.393  0.020  1.393
 SS4  C17  C25   single    1.500  0.020  1.500
 SS4  C20  C21   aromatic  1.387  0.020  1.387
 SS4  C20  C1    single    1.474  0.020  1.474
 SS4  C20  C19   aromatic  1.399  0.020  1.399
 SS4  C21  C22   aromatic  1.393  0.020  1.393
 SS4  C21  H21   single    0.930  0.020  1.080
 SS4  C22  C18   aromatic  1.394  0.020  1.394
 SS4  C22  O1    single    1.341  0.020  1.341
 SS4  C24  O1    single    1.417  0.020  1.417
 SS4  C24  C10   single    1.519  0.020  1.519
 SS4  C24  H241  single    0.970  0.020  1.090
 SS4  C24  H242  single    0.970  0.020  1.090
 SS4  C1   C2    aromatic  1.383  0.020  1.383
 SS4  C2   C3    aromatic  1.397  0.020  1.397
 SS4  C2   H2    single    0.930  0.020  1.080
 SS4  N5   H5    single    0.860  0.020  1.020
 SS4  C14  H14   single    0.930  0.020  1.080
 SS4  C16  C26   aromatic  1.387  0.020  1.387
 SS4  C16  H16   single    0.930  0.020  1.080
 SS4  C18  H18   single    0.930  0.020  1.080
 SS4  C19  H19   single    0.930  0.020  1.080
 SS4  C26  H26   single    0.930  0.020  1.080
 SS4  C10  C25   single    1.542  0.020  1.542
 SS4  C10  N4    single    1.449  0.020  1.449
 SS4  C10  H10   single    0.970  0.020  1.090
 SS4  C25  H251  single    0.970  0.020  1.090
 SS4  C25  H252  single    0.970  0.020  1.090
 SS4  N4   H4N1  single    0.890  0.020  1.040
 SS4  N4   H4N2  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
 SS4  N5    N1   C8    107.40  3.000
 SS4  C19   N3   C18   119.44  3.000
 SS4  N5    C4   C3    105.81  3.000
 SS4  N5    C4   C5    132.51  3.000
 SS4  C3    C4   C5    121.68  3.000
 SS4  HA    C5   C6    121.13  3.000
 SS4  HA    C5   C4    121.92  3.000
 SS4  C6    C5   C4    116.94  3.000
 SS4  H6    C6   C1    118.89  3.000
 SS4  H6    C6   C5    118.48  3.000
 SS4  C1    C6   C5    122.61  3.000
 SS4  C3    C8   C9    127.54  3.000
 SS4  C3    C8   N1    109.91  3.000
 SS4  C9    C8   N1    122.55  3.000
 SS4  H13   C13  C14   118.95  3.000
 SS4  H13   C13  C17   119.60  3.000
 SS4  C14   C13  C17   121.45  3.000
 SS4  BR1   C15  C26   119.48  3.000
 SS4  BR1   C15  C14   119.53  3.000
 SS4  C26   C15  C14   120.99  3.000
 SS4  H9C3  C9   H9C2  108.13  3.000
 SS4  H9C3  C9   H9C1  108.16  3.000
 SS4  H9C2  C9   H9C1  107.15  3.000
 SS4  H9C3  C9   C8    110.97  3.000
 SS4  H9C2  C9   C8    111.05  3.000
 SS4  H9C1  C9   C8    111.22  3.000
 SS4  C25   C17  C16   120.73  3.000
 SS4  C25   C17  C13   121.05  3.000
 SS4  C16   C17  C13   118.17  3.000
 SS4  C19   C20  C1    121.10  3.000
 SS4  C19   C20  C21   117.25  3.000
 SS4  C1    C20  C21   121.65  3.000
 SS4  H21   C21  C22   119.25  3.000
 SS4  H21   C21  C20   120.95  3.000
 SS4  C22   C21  C20   119.79  3.000
 SS4  O1    C22  C18   124.96  3.000
 SS4  O1    C22  C21   116.90  3.000
 SS4  C18   C22  C21   118.14  3.000
 SS4  H242  C24  H241  107.66  3.000
 SS4  H242  C24  C10   109.89  3.000
 SS4  H241  C24  C10   109.92  3.000
 SS4  H242  C24  O1    110.32  3.000
 SS4  H241  C24  O1    110.50  3.000
 SS4  C10   C24  O1    108.54  3.000
 SS4  C2    C1   C20   120.48  3.000
 SS4  C2    C1   C6    119.60  3.000
 SS4  C20   C1   C6    119.91  3.000
 SS4  H2    C2   C3    120.34  3.000
 SS4  H2    C2   C1    120.71  3.000
 SS4  C3    C2   C1    118.93  3.000
 SS4  C2    C3   C8    135.10  3.000
 SS4  C2    C3   C4    120.22  3.000
 SS4  C8    C3   C4    104.68  3.000
 SS4  H5    N5   C4    128.04  3.000
 SS4  H5    N5   N1    119.75  3.000
 SS4  C4    N5   N1    112.21  3.000
 SS4  H14   C14  C15   121.20  3.000
 SS4  H14   C14  C13   119.83  3.000
 SS4  C15   C14  C13   118.97  3.000
 SS4  H16   C16  C26   118.81  3.000
 SS4  H16   C16  C17   119.80  3.000
 SS4  C26   C16  C17   121.39  3.000
 SS4  H18   C18  C22   121.69  3.000
 SS4  H18   C18  N3    116.15  3.000
 SS4  C22   C18  N3    122.16  3.000
 SS4  H19   C19  C20   120.20  3.000
 SS4  H19   C19  N3    116.57  3.000
 SS4  C20   C19  N3    123.22  3.000
 SS4  H26   C26  C16   119.87  3.000
 SS4  H26   C26  C15   121.10  3.000
 SS4  C16   C26  C15   119.03  3.000
 SS4  C24   O1   C22   118.83  3.000
 SS4  H10   C10  N4    107.59  3.000
 SS4  H10   C10  C25   107.87  3.000
 SS4  N4    C10  C25   114.71  3.000
 SS4  H10   C10  C24   107.94  3.000
 SS4  N4    C10  C24   109.93  3.000
 SS4  C25   C10  C24   108.59  3.000
 SS4  H252  C25  H251  107.03  3.000
 SS4  H252  C25  C10   109.02  3.000
 SS4  H251  C25  C10   109.49  3.000
 SS4  H252  C25  C17   109.57  3.000
 SS4  H251  C25  C17   109.87  3.000
 SS4  C10   C25  C17   111.74  3.000
 SS4  H4N2  N4   H4N1  106.24  3.000
 SS4  H4N2  N4   C10   110.29  3.000
 SS4  H4N1  N4   C10   110.17  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
 SS4  CONST_01  C4    C3   C8   N1      0.00   0.0  0
 SS4  CONST_02  C2    C3   C8   N1    180.00   0.0  0
 SS4  CONST_03  C5    C4   N5   N1    180.00   0.0  0
 SS4  CONST_04  C3    C4   N5   N1      0.00   0.0  0
 SS4  CONST_05  C21   C22  C18  N3      0.00   0.0  0
 SS4  CONST_06  C21   C20  C19  N3      0.00   0.0  0
 SS4  CONST_07  C1    C20  C19  N3    180.00   0.0  0
 SS4  CONST_08  C1    C6   C5   C4      0.00   0.0  0
 SS4  CONST_09  C1    C2   C3   C4      0.00   0.0  0
 SS4  CONST_10  C8    N1   N5   C4      0.00   0.0  0
 SS4  CONST_11  C8    C3   C4   C5    180.00   0.0  0
 SS4  CONST_12  C2    C3   C4   C5      0.00   0.0  0
 SS4  CONST_13  C20   C1   C6   C5    180.00   0.0  0
 SS4  CONST_14  C2    C1   C6   C5      0.00   0.0  0
 SS4  CONST_15  C3    C4   C5   C6      0.00   0.0  0
 SS4  CONST_16  N5    C4   C5   C6    180.00   0.0  0
 SS4  CONST_19  C3    C2   C1   C6      0.00   0.0  0
 SS4  CONST_20  N5    C4   C3   C8      0.00   0.0  0
 SS4  CONST_21  C1    C2   C3   C8    180.00   0.0  0
 SS4  CONST_22  C26   C16  C17  C13     0.00   0.0  0
 SS4  CONST_23  C26   C15  C14  C13     0.00   0.0  0
 SS4  CONST_24  C17   C13  C14  C15     0.00   0.0  0
 SS4  CONST_25  C17   C16  C26  C15     0.00   0.0  0
 SS4  CONST_26  C18   C22  C21  C20     0.00   0.0  0
 SS4  CONST_27  C3    C2   C1   C20   180.00   0.0  0
 SS4  CONST_28  C18   N3   C19  C20     0.00   0.0  0
 SS4  CONST_30  C1    C20  C21  C22   180.00   0.0  0
 SS4  CONST_31  C19   C20  C21  C22     0.00   0.0  0
 SS4  CONST_32  C19   N3   C18  C22     0.00   0.0  0
 SS4  CONST_34  N5    C4   C3   C2    180.00   0.0  0
 SS4  CONST_35  N5    N1   C8   C3      0.00   0.0  0
 SS4  CONST_36  C16   C17  C13  C14     0.00   0.0  0
 SS4  CONST_37  C16   C26  C15  C14     0.00   0.0  0
 SS4  CONST_38  O1    C22  C18  N3    180.00   0.0  0
 SS4  CONST_39  C9    C8   C3   C4    180.00   0.0  0
 SS4  CONST_40  BR1   C15  C14  C13   180.00   0.0  0
 SS4  CONST_41  N5    N1   C8   C9    180.00   0.0  0
 SS4  CONST_42  C2    C3   C8   C9      0.00   0.0  0
 SS4  CONST_43  O1    C22  C21  C20   180.00   0.0  0
 SS4  CONST_44  C25   C17  C13  C14   180.00   0.0  0
 SS4  CONST_45  BR1   C15  C26  C16   180.00   0.0  0
 SS4  CONST_46  C25   C17  C16  C26   180.00   0.0  0
 SS4  CONST_47  H6    C6   C5   C4    180.00   0.0  0
 SS4  CONST_48  H2    C2   C3   C4    180.00   0.0  0
 SS4  CONST_49  H5    N5   C4   C5      0.00   0.0  0
 SS4  CONST_50  H16   C16  C17  C13   180.00   0.0  0
 SS4  CONST_51  H13   C13  C14  C15   180.00   0.0  0
 SS4  CONST_52  H14   C14  C13  C17   180.00   0.0  0
 SS4  CONST_53  H26   C26  C16  C17   180.00   0.0  0
 SS4  CONST_54  H19   C19  C20  C21   180.00   0.0  0
 SS4  CONST_55  H18   C18  C22  C21   180.00   0.0  0
 SS4  CONST_56  HA    C5   C6   C1    180.00   0.0  0
 SS4  CONST_57  H21   C21  C20  C1      0.00   0.0  0
 SS4  Var_01    C10   C25  C17  C13    96.31  30.0  2
 SS4  Var_02    C18   C22  O1   C24    -1.51  30.0  1
 SS4  Var_03    H9C1  C9   C8   N1    119.15  30.0  2
 SS4  Var_04    C10   C24  O1   C22  -178.72  30.0  1

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
 SS4  chir_01  C10  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
 SS4  plan-1  N3   0.020
 SS4  plan-1  C20  0.020
 SS4  plan-1  C21  0.020
 SS4  plan-1  C22  0.020
 SS4  plan-1  C1   0.020
 SS4  plan-1  C18  0.020
 SS4  plan-1  C19  0.020
 SS4  plan-1  O1   0.020
 SS4  plan-1  H18  0.020
 SS4  plan-1  H19  0.020
 SS4  plan-1  H21  0.020
 SS4  plan-2  C13  0.020
 SS4  plan-2  C15  0.020
 SS4  plan-2  C17  0.020
 SS4  plan-2  C14  0.020
 SS4  plan-2  C16  0.020
 SS4  plan-2  C26  0.020
 SS4  plan-2  C25  0.020
 SS4  plan-2  H13  0.020
 SS4  plan-2  H14  0.020
 SS4  plan-2  H26  0.020
 SS4  plan-2  H16  0.020
 SS4  plan-2  BR1  0.020
 SS4  plan-3  N1   0.020
 SS4  plan-3  C4   0.020
 SS4  plan-3  C5   0.020
 SS4  plan-3  C6   0.020
 SS4  plan-3  C8   0.020
 SS4  plan-3  C9   0.020
 SS4  plan-3  C20  0.020
 SS4  plan-3  C1   0.020
 SS4  plan-3  C2   0.020
 SS4  plan-3  C3   0.020
 SS4  plan-3  N5   0.020
 SS4  plan-3  H5   0.020
 SS4  plan-3  HA   0.020
 SS4  plan-3  H6   0.020
 SS4  plan-3  H2   0.020

