# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 15:29:00 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: 7-[(1R)-3-{[(1R)-2,3-dihydro-1H-inden-1-yl]amino}-1-phenylpropyl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cc([C@H](CCN[C@@H]2CCc3ccccc23)c4ccccc4)c5nn[nH]c5n1
#
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
 XSG  XSG  7-[(1R)-3-{[(1R)-2,3-dihydro-1H-inden-1-yl]amino}-1-phenylpropyl]-3H-[1,2,3]triazolo[4,5-b]pyridin-5-amine  ligand  53  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XSG
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
 XSG  C13  C  CH2   0  -0.255  17.1717  -49.6231  47.6571
 XSG  C18  C  CR56  0   0.103  18.7252  -50.1986  50.1540
 XSG  C17  C  CR56  0   0.095  19.1101  -51.4917  49.8216
 XSG  C16  C  CH2   0  -0.500  19.8149  -51.5182  48.4940
 XSG  C15  C  CH2   0  -0.484  20.1188  -50.0354  48.2257
 XSG  C19  C  CR16  0  -0.313  18.0226  -49.9460  51.3228
 XSG  C20  C  CR16  0  -0.263  17.7227  -51.0042  52.1721
 XSG  C21  C  CR16  0  -0.255  18.1143  -52.2996  51.8446
 XSG  C22  C  CR16  0  -0.321  18.8078  -52.5512  50.6664
 XSG  C11  C  CR16  0  -0.295  16.0979  -50.0809  44.1064
 XSG  C12  C  CH2   0  -0.434  15.9560  -48.9534  47.0348
 XSG  C1   C  CR6   0   0.498  12.2952  -47.5582  45.0782
 XSG  N    N  N     0  -0.487  11.2329  -48.3252  44.8709
 XSG  C2   C  CR56  0   0.473  11.4351  -49.6026  45.1738
 XSG  N4   N  NR15  0  -0.525  10.5779  -50.6398  45.0967
 XSG  N3   N  N     0  -0.080  11.1614  -51.7701  45.5048
 XSG  N2   N  N     0  -0.314  12.3679  -51.5161  45.8459
 XSG  C3   C  CR56  0   0.023  12.5972  -50.1893  45.6621
 XSG  C4   C  CR6   0   0.269  13.7251  -49.3719  45.8842
 XSG  C    C  CR16  0  -0.513  13.5446  -48.0486  45.5857
 XSG  C5   C  CH1   0  -0.408  15.0119  -49.9700  46.3881
 XSG  C6   C  CR6   0   0.166  15.6817  -50.7369  45.2628
 XSG  C10  C  CR16  0  -0.238  16.7335  -50.7763  43.0881
 XSG  C9   C  CR16  0  -0.269  16.9598  -52.1422  43.2094
 XSG  C8   C  CR16  0  -0.240  16.5459  -52.8044  44.3564
 XSG  C7   C  CR16  0  -0.316  15.9096  -52.1045  45.3741
 XSG  N1   N  NH1   0  -0.593  17.9518  -48.6639  48.4181
 XSG  C14  C  CR15  0  -0.166  19.1251  -49.2110  49.0860
 XSG  H1   H  HCH2  0   0.221  16.8308  -50.4116  48.3349
 XSG  H2   H  HCH2  0   0.205  17.7543  -50.1226  46.8704
 XSG  H3   H  HCH2  0   0.245  19.1643  -51.9478  47.7257
 XSG  H4   H  HCH2  0   0.250  20.7183  -52.1308  48.5120
 XSG  H5   H  HCH2  0   0.246  21.1346  -49.8113  48.5567
 XSG  H6   H  HCH2  0   0.239  20.0637  -49.7728  47.1681
 XSG  H7   H  HCR6  0   0.243  17.7163  -48.9377  51.5754
 XSG  H8   H  HCR6  0   0.247  17.1837  -50.8223  53.0933
 XSG  H9   H  HCR6  0   0.248  17.8775  -53.1165  52.5147
 XSG  H10  H  HCR6  0   0.243  19.1054  -53.5623  50.4147
 XSG  H11  H  HCR6  0   0.252  15.9234  -49.0167  43.9952
 XSG  H12  H  HCH2  0   0.230  16.2854  -48.2141  46.2980
 XSG  H13  H  HCH2  0   0.241  15.4160  -48.4075  47.8129
 XSG  H14  H  HNH2  0   0.393  11.2810  -45.8714  44.5703
 XSG  H15  H  HNH2  0   0.403  12.8886  -45.6000  45.0838
 XSG  H17  H  HCR6  0   0.274  14.3458  -47.3347  45.7251
 XSG  H18  H  HCH1  0   0.270  14.7407  -50.6989  47.1591
 XSG  H19  H  HCR6  0   0.253  17.0520  -50.2516  42.1964
 XSG  H20  H  HCR6  0   0.253  17.4547  -52.6852  42.4146
 XSG  H21  H  HCR6  0   0.253  16.7164  -53.8683  44.4612
 XSG  H22  H  HCR6  0   0.250  15.5896  -52.6282  46.2671
 XSG  H23  H  HNH1  0   0.343  18.2536  -47.9191  47.8002
 XSG  H25  H  HCR5  0   0.248  19.6414  -48.3541  49.5273
 XSG  H16  H  HNR5  0   0.425   9.6159  -50.6508  44.7907
 XSG  N5   N  NH2   0  -0.835  12.1926  -46.2504  44.7633

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
 XSG  N5   C1   single    1.349  0.020  1.349
 XSG  N    C1   aromatic  1.327  0.020  1.327
 XSG  N    C2   aromatic  1.328  0.020  1.328
 XSG  N4   C2   aromatic  1.348  0.020  1.348
 XSG  N4   N3   aromatic  1.336  0.020  1.336
 XSG  C1   C    aromatic  1.435  0.020  1.435
 XSG  C9   C10  aromatic  1.390  0.020  1.390
 XSG  C9   C8   aromatic  1.388  0.020  1.388
 XSG  C10  C11  aromatic  1.387  0.020  1.387
 XSG  C2   C3   aromatic  1.390  0.020  1.390
 XSG  N3   N2   aromatic  1.279  0.020  1.279
 XSG  C8   C7   aromatic  1.389  0.020  1.389
 XSG  C11  C6   aromatic  1.393  0.020  1.393
 XSG  C    C4   aromatic  1.369  0.020  1.369
 XSG  C3   N2   aromatic  1.359  0.020  1.359
 XSG  C3   C4   aromatic  1.410  0.020  1.410
 XSG  C7   C6   aromatic  1.391  0.020  1.391
 XSG  C4   C5   single    1.506  0.020  1.506
 XSG  C6   C5   single    1.518  0.020  1.518
 XSG  C5   C12  single    1.531  0.020  1.531
 XSG  C12  C13  single    1.521  0.020  1.521
 XSG  C16  C15  single    1.537  0.020  1.537
 XSG  C16  C17  single    1.503  0.020  1.503
 XSG  C15  C14  single    1.552  0.020  1.552
 XSG  C13  N1   single    1.452  0.020  1.452
 XSG  N1   C14  single    1.457  0.020  1.457
 XSG  C17  C22  aromatic  1.388  0.020  1.388
 XSG  C17  C18  aromatic  1.390  0.020  1.390
 XSG  C14  C18  single    1.509  0.020  1.509
 XSG  C22  C21  aromatic  1.390  0.020  1.390
 XSG  C18  C19  aromatic  1.387  0.020  1.387
 XSG  C21  C20  aromatic  1.392  0.020  1.392
 XSG  C19  C20  aromatic  1.390  0.020  1.390
 XSG  C13  H1   single    0.970  0.020  1.090
 XSG  C13  H2   single    0.970  0.020  1.090
 XSG  C16  H3   single    0.970  0.020  1.090
 XSG  C16  H4   single    0.970  0.020  1.090
 XSG  C15  H5   single    0.970  0.020  1.090
 XSG  C15  H6   single    0.970  0.020  1.090
 XSG  C19  H7   single    0.930  0.020  1.080
 XSG  C20  H8   single    0.930  0.020  1.080
 XSG  C21  H9   single    0.930  0.020  1.080
 XSG  C22  H10  single    0.930  0.020  1.080
 XSG  C11  H11  single    0.930  0.020  1.080
 XSG  C12  H12  single    0.970  0.020  1.090
 XSG  C12  H13  single    0.970  0.020  1.090
 XSG  N5   H14  single    0.890  0.020  1.040
 XSG  N5   H15  single    0.890  0.020  1.040
 XSG  N4   H16  single    0.860  0.020  1.020
 XSG  C    H17  single    0.930  0.020  1.080
 XSG  C5   H18  single    0.970  0.020  1.090
 XSG  C10  H19  single    0.930  0.020  1.080
 XSG  C9   H20  single    0.930  0.020  1.080
 XSG  C8   H21  single    0.930  0.020  1.080
 XSG  C7   H22  single    0.930  0.020  1.080
 XSG  N1   H23  single    0.890  0.020  1.040
 XSG  C14  H25  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
 XSG  H2   C13  H1   106.32  3.000
 XSG  H2   C13  N1   112.99  3.000
 XSG  H1   C13  N1   108.59  3.000
 XSG  H2   C13  C12  109.32  3.000
 XSG  H1   C13  C12  108.77  3.000
 XSG  N1   C13  C12  110.67  3.000
 XSG  C14  C18  C19  127.71  3.000
 XSG  C19  C18  C17  120.76  3.000
 XSG  C14  C18  C17  111.50  3.000
 XSG  C22  C17  C16  128.76  3.000
 XSG  C22  C17  C18  120.28  3.000
 XSG  C16  C17  C18  110.95  3.000
 XSG  H4   C16  H3   106.45  3.000
 XSG  H4   C16  C15  112.37  3.000
 XSG  H3   C16  C15  111.94  3.000
 XSG  H4   C16  C17  112.54  3.000
 XSG  H3   C16  C17  110.37  3.000
 XSG  C15  C16  C17  103.29  3.000
 XSG  H6   C15  H5   106.94  3.000
 XSG  H6   C15  C14  112.16  3.000
 XSG  H5   C15  C14  108.59  3.000
 XSG  H6   C15  C16  113.04  3.000
 XSG  H5   C15  C16  109.22  3.000
 XSG  C14  C15  C16  106.81  3.000
 XSG  H7   C19  C20  120.33  3.000
 XSG  H7   C19  C18  120.60  3.000
 XSG  C20  C19  C18  119.06  3.000
 XSG  H8   C20  C21  119.77  3.000
 XSG  H8   C20  C19  119.97  3.000
 XSG  C21  C20  C19  120.26  3.000
 XSG  H9   C21  C22  119.81  3.000
 XSG  H9   C21  C20  119.66  3.000
 XSG  C22  C21  C20  120.53  3.000
 XSG  H10  C22  C21  120.18  3.000
 XSG  H10  C22  C17  120.72  3.000
 XSG  C21  C22  C17  119.10  3.000
 XSG  H11  C11  C10  119.38  3.000
 XSG  H11  C11  C6   119.95  3.000
 XSG  C10  C11  C6   120.68  3.000
 XSG  H13  C12  H12  106.89  3.000
 XSG  H13  C12  C5   109.12  3.000
 XSG  H12  C12  C5   110.48  3.000
 XSG  H13  C12  C13  108.87  3.000
 XSG  H12  C12  C13  109.41  3.000
 XSG  C5   C12  C13  111.93  3.000
 XSG  C    C1   N    123.71  3.000
 XSG  C    C1   N5   118.69  3.000
 XSG  N    C1   N5   117.59  3.000
 XSG  C2   N    C1   113.48  3.000
 XSG  C3   C2   N4   103.12  3.000
 XSG  C3   C2   N    127.82  3.000
 XSG  N4   C2   N    129.06  3.000
 XSG  H16  N4   N3   119.97  3.000
 XSG  H16  N4   C2   129.18  3.000
 XSG  N3   N4   C2   110.85  3.000
 XSG  N2   N3   N4   108.99  3.000
 XSG  C3   N2   N3   108.48  3.000
 XSG  C4   C3   N2   132.80  3.000
 XSG  C4   C3   C2   118.63  3.000
 XSG  N2   C3   C2   108.57  3.000
 XSG  C5   C4   C    124.74  3.000
 XSG  C5   C4   C3   120.38  3.000
 XSG  C    C4   C3   114.87  3.000
 XSG  H17  C    C4   120.81  3.000
 XSG  H17  C    C1   117.70  3.000
 XSG  C4   C    C1   121.50  3.000
 XSG  H18  C5   C6   107.16  3.000
 XSG  H18  C5   C4   106.76  3.000
 XSG  C6   C5   C4   109.25  3.000
 XSG  H18  C5   C12  107.30  3.000
 XSG  C6   C5   C12  112.12  3.000
 XSG  C4   C5   C12  113.87  3.000
 XSG  C7   C6   C5   120.65  3.000
 XSG  C5   C6   C11  120.63  3.000
 XSG  C7   C6   C11  118.71  3.000
 XSG  H19  C10  C9   120.03  3.000
 XSG  H19  C10  C11  119.76  3.000
 XSG  C9   C10  C11  120.21  3.000
 XSG  H20  C9   C8   120.26  3.000
 XSG  H20  C9   C10  120.22  3.000
 XSG  C8   C9   C10  119.51  3.000
 XSG  H21  C8   C7   119.76  3.000
 XSG  H21  C8   C9   120.13  3.000
 XSG  C7   C8   C9   120.11  3.000
 XSG  H22  C7   C8   119.70  3.000
 XSG  H22  C7   C6   119.52  3.000
 XSG  C8   C7   C6   120.78  3.000
 XSG  H23  N1   C14  108.40  3.000
 XSG  H23  N1   C13  109.02  3.000
 XSG  C14  N1   C13  115.15  3.000
 XSG  H25  C14  N1   105.73  3.000
 XSG  H25  C14  C15  109.74  3.000
 XSG  N1   C14  C15  117.47  3.000
 XSG  H25  C14  C18  110.64  3.000
 XSG  N1   C14  C18  110.91  3.000
 XSG  C15  C14  C18  102.38  3.000
 XSG  H15  N5   H14  116.42  3.000
 XSG  H15  N5   C1   120.02  3.000
 XSG  H14  N5   C1   118.61  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
 XSG  CONST_01  C21  C22  C17  C18     0.00   0.0  0
 XSG  CONST_02  C21  C20  C19  C18     0.00   0.0  0
 XSG  CONST_03  C20  C21  C22  C17     0.00   0.0  0
 XSG  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 XSG  CONST_05  C22  C17  C18  C19     0.00   0.0  0
 XSG  CONST_06  C22  C21  C20  C19     0.00   0.0  0
 XSG  CONST_07  C8   C9   C10  C11     0.00   0.0  0
 XSG  CONST_08  C8   C7   C6   C11     0.00   0.0  0
 XSG  CONST_09  N4   C2   N    C1    180.00   0.0  0
 XSG  CONST_10  C3   C2   N    C1      0.00   0.0  0
 XSG  CONST_11  C3   C4   C    C1      0.00   0.0  0
 XSG  CONST_12  C4   C    C1   N       0.00   0.0  0
 XSG  CONST_13  N3   N4   C2   N     180.00   0.0  0
 XSG  CONST_14  N2   C3   C2   N     180.00   0.0  0
 XSG  CONST_15  C4   C3   C2   N       0.00   0.0  0
 XSG  CONST_16  C    C1   N    C2      0.00   0.0  0
 XSG  CONST_17  N2   N3   N4   C2      0.00   0.0  0
 XSG  CONST_18  N3   N2   C3   C2      0.00   0.0  0
 XSG  CONST_19  C    C4   C3   C2      0.00   0.0  0
 XSG  CONST_20  N2   C3   C2   N4      0.00   0.0  0
 XSG  CONST_21  C4   C3   C2   N4    180.00   0.0  0
 XSG  CONST_22  C3   N2   N3   N4      0.00   0.0  0
 XSG  CONST_23  C3   C2   N4   N3      0.00   0.0  0
 XSG  CONST_24  C4   C3   N2   N3    180.00   0.0  0
 XSG  CONST_25  C    C4   C3   N2    180.00   0.0  0
 XSG  CONST_26  C9   C10  C11  C6      0.00   0.0  0
 XSG  CONST_27  C9   C8   C7   C6      0.00   0.0  0
 XSG  CONST_28  C7   C8   C9   C10     0.00   0.0  0
 XSG  CONST_29  C7   C6   C11  C10     0.00   0.0  0
 XSG  CONST_30  C2   N    C1   N5    180.00   0.0  0
 XSG  CONST_31  C4   C    C1   N5    180.00   0.0  0
 XSG  CONST_32  C5   C4   C    C1    180.00   0.0  0
 XSG  CONST_33  C5   C4   C3   C2    180.00   0.0  0
 XSG  CONST_34  C5   C4   C3   N2      0.00   0.0  0
 XSG  CONST_35  C10  C11  C6   C5    180.00   0.0  0
 XSG  CONST_36  C8   C7   C6   C5    180.00   0.0  0
 XSG  CONST_37  H10  C22  C17  C18   180.00   0.0  0
 XSG  CONST_38  H8   C20  C19  C18   180.00   0.0  0
 XSG  CONST_39  H9   C21  C22  C17   180.00   0.0  0
 XSG  CONST_40  H7   C19  C18  C17   180.00   0.0  0
 XSG  CONST_41  H20  C9   C10  C11   180.00   0.0  0
 XSG  CONST_42  H22  C7   C6   C11   180.00   0.0  0
 XSG  CONST_43  H17  C    C1   N     180.00   0.0  0
 XSG  CONST_44  H16  N4   C2   N       0.00   0.0  0
 XSG  CONST_45  H19  C10  C11  C6    180.00   0.0  0
 XSG  CONST_46  H21  C8   C7   C6    180.00   0.0  0
 XSG  CONST_47  H11  C11  C10  C9    180.00   0.0  0
 XSG  CONST_48  H14  N5   C1   N       0.00   0.0  0
 XSG  CONST_49  H15  N5   C1   N     180.00   0.0  0
 XSG  Var_01    C15  C16  C17  C18    13.63  30.0  1
 XSG  Var_02    C14  C15  C16  C17   -21.68  30.0  1
 XSG  Var_03    C14  N1   C13  C12   178.53  30.0  3
 XSG  Var_04    N1   C13  C12  C5   -172.17  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
 XSG  chir_01  C5   C4  C6   C12  negativ
 XSG  chir_02  C14  N1  C15  C18  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
 XSG  plan-1  C11  0.020
 XSG  plan-1  C5   0.020
 XSG  plan-1  C6   0.020
 XSG  plan-1  C10  0.020
 XSG  plan-1  C9   0.020
 XSG  plan-1  C8   0.020
 XSG  plan-1  C7   0.020
 XSG  plan-1  H11  0.020
 XSG  plan-1  H19  0.020
 XSG  plan-1  H20  0.020
 XSG  plan-1  H21  0.020
 XSG  plan-1  H22  0.020
 XSG  plan-2  C18  0.020
 XSG  plan-2  C17  0.020
 XSG  plan-2  C16  0.020
 XSG  plan-2  C19  0.020
 XSG  plan-2  C20  0.020
 XSG  plan-2  C21  0.020
 XSG  plan-2  C22  0.020
 XSG  plan-2  C14  0.020
 XSG  plan-2  H7   0.020
 XSG  plan-2  H8   0.020
 XSG  plan-2  H9   0.020
 XSG  plan-2  H10  0.020
 XSG  plan-3  C1   0.020
 XSG  plan-3  N    0.020
 XSG  plan-3  C2   0.020
 XSG  plan-3  N4   0.020
 XSG  plan-3  N3   0.020
 XSG  plan-3  N2   0.020
 XSG  plan-3  C3   0.020
 XSG  plan-3  C4   0.020
 XSG  plan-3  C    0.020
 XSG  plan-3  C5   0.020
 XSG  plan-3  H17  0.020
 XSG  plan-3  H16  0.020
 XSG  plan-3  N5   0.020
 XSG  plan-4  C1   0.020
 XSG  plan-4  H14  0.020
 XSG  plan-4  H15  0.020
 XSG  plan-4  N5   0.020

