# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:55:35 2021
#   Inital geometry file: a 117 line input string
#   Ligand name: N-(5-{[6-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-2,6-diazaspiro[3.4]octan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1sc(CN2CC3(CCN(C3)c4cc(C)nc5ncnn45)C2)cn1
#
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
 X1A  X1A  N-(5-{[6-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)-2,6-diazaspiro[3.4]octan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide  ligand  50  28  .  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_X1A
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
 X1A  C2   C  C     0   0.521  57.1400   3.5095  37.0856
 X1A  C3   C  CH3   0  -0.785  57.4235   2.0576  36.8375
 X1A  C5   C  CR5   0   0.306  55.5479   5.2685  36.5773
 X1A  C7   C  CR15  0  -0.039  54.2283   6.9727  36.2202
 X1A  C8   C  CR5   0  -0.241  55.1445   7.6283  36.9756
 X1A  N10  N  N     0  -0.406  54.6173   9.3510  38.7152
 X1A  C11  C  C     0  -0.265  55.2490   8.8117  39.9194
 X1A  C12  C  C     0  -0.133  53.8604   8.7217  40.5620
 X1A  C16  C  CH2   0  -0.250  53.4734   9.8791  41.4652
 X1A  C17  C  CR6   0   0.746  51.5023  10.2382  42.8213
 X1A  C18  C  CR16  0  -0.498  51.8570  11.5555  43.1080
 X1A  C19  C  CR6   0   0.255  51.0136  12.3754  43.8637
 X1A  C24  C  CR15  0   0.041  48.5463   8.8810  43.8532
 X1A  C27  C  C     0  -0.250  53.3096   8.8449  39.1274
 X1A  O1   O  O     0  -0.453  57.8462   4.2463  37.7483
 X1A  N4   N  NH1   0  -0.677  55.9994   3.9743  36.4981
 X1A  N6   N  N     0  -0.423  54.4553   5.6447  35.9946
 X1A  C9   C  CH2   0  -0.360  55.1328   9.0694  37.3955
 X1A  C13  C  CH2   0  -0.484  53.4499   7.5211  41.3875
 X1A  C14  C  CH2   0  -0.268  52.1064   7.9428  41.9678
 X1A  N15  N  NT    0  -0.514  52.2478   9.4029  42.1012
 X1A  C20  C  CH3   0  -0.735  51.4462  13.7755  44.1686
 X1A  N21  N  N     0  -0.492  49.8489  11.9789  44.3490
 X1A  C22  C  CR56  0   0.572  49.5044  10.7263  44.0707
 X1A  N23  N  N     0  -0.507  48.3919  10.0930  44.4072
 X1A  N25  N  N     0  -0.284  49.6604   8.6815  43.1912
 X1A  N26  N  N     0  -0.438  50.2908   9.8655  43.3341
 X1A  S28  S  S2    0   0.217  56.3841   6.5081  37.4459
 X1A  H3   H  HCH3  0   0.273  58.3341   1.7600  37.3493
 X1A  H2   H  HCH3  0   0.277  56.5986   1.4379  37.1913
 X1A  H1   H  HCH3  0   0.278  57.5392   1.8692  35.7693
 X1A  H5   H  HCR5  0   0.269  53.3526   7.4400  35.7899
 X1A  H8   H  H     0   0.218  55.6930   7.8144  39.7988
 X1A  H9   H  H     0   0.235  55.9886   9.4650  40.3907
 X1A  H14  H  HCH2  0   0.258  54.2518  10.0674  42.2135
 X1A  H15  H  HCH2  0   0.267  53.2984  10.8042  40.9133
 X1A  H16  H  HCR6  0   0.294  52.8008  11.9487  42.7634
 X1A  H20  H  HCR5  0   0.274  47.8062   8.0987  43.9343
 X1A  H21  H  H     0   0.233  52.4715   9.5271  38.9570
 X1A  H22  H  H     0   0.218  53.0578   7.8628  38.7060
 X1A  H4   H  HNH1  0   0.428  55.4303   3.3482  35.9456
 X1A  H6   H  HCH2  0   0.260  56.1376   9.4932  37.3262
 X1A  H7   H  HCH2  0   0.260  54.5214   9.6149  36.6720
 X1A  H10  H  HCH2  0   0.259  53.3710   6.6047  40.8032
 X1A  H11  H  HCH2  0   0.254  54.1789   7.3526  42.1845
 X1A  H13  H  HCH2  0   0.255  51.2899   7.6985  41.2884
 X1A  H12  H  HCH2  0   0.265  51.8983   7.4757  42.9267
 X1A  H18  H  HCH3  0   0.254  50.6316  14.3461  44.6088
 X1A  H17  H  HCH3  0   0.260  52.2812  13.7699  44.8714
 X1A  H19  H  HCH3  0   0.255  51.7884  14.2857  43.2682

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
 X1A  C3   C2   single    1.500  0.020  1.500
 X1A  C2   N4   single    1.365  0.020  1.365
 X1A  C2   O1   double    1.217  0.020  1.217
 X1A  N4   C5   single    1.373  0.020  1.373
 X1A  N6   C5   aromatic  1.294  0.020  1.294
 X1A  N6   C7   aromatic  1.366  0.020  1.366
 X1A  C5   S28  aromatic  1.729  0.020  1.729
 X1A  C7   C8   aromatic  1.356  0.020  1.356
 X1A  S28  C8   aromatic  1.736  0.020  1.736
 X1A  C8   C9   single    1.501  0.020  1.501
 X1A  C9   N10  single    1.445  0.020  1.445
 X1A  N10  C27  single    1.462  0.020  1.462
 X1A  N10  C11  single    1.463  0.020  1.463
 X1A  C27  C12  single    1.542  0.020  1.542
 X1A  C11  C12  single    1.533  0.020  1.533
 X1A  C12  C16  single    1.518  0.020  1.518
 X1A  C12  C13  single    1.514  0.020  1.514
 X1A  C16  N15  single    1.461  0.020  1.461
 X1A  C13  C14  single    1.523  0.020  1.523
 X1A  C20  C19  single    1.497  0.020  1.497
 X1A  C18  C19  aromatic  1.398  0.020  1.398
 X1A  C18  C17  aromatic  1.394  0.020  1.394
 X1A  N15  C14  single    1.473  0.020  1.473
 X1A  N15  C17  single    1.331  0.020  1.331
 X1A  C19  N21  aromatic  1.323  0.020  1.323
 X1A  C17  N26  aromatic  1.367  0.020  1.367
 X1A  N21  C22  aromatic  1.329  0.020  1.329
 X1A  N26  C22  aromatic  1.379  0.020  1.379
 X1A  N26  N25  aromatic  1.349  0.020  1.349
 X1A  C22  N23  aromatic  1.324  0.020  1.324
 X1A  N25  C24  aromatic  1.311  0.020  1.311
 X1A  N23  C24  aromatic  1.341  0.020  1.341
 X1A  C3   H3   single    0.970  0.020  1.090
 X1A  C3   H2   single    0.970  0.020  1.090
 X1A  C3   H1   single    0.970  0.020  1.090
 X1A  C7   H5   single    0.930  0.020  1.080
 X1A  C11  H8   single    0.970  0.020  1.090
 X1A  C11  H9   single    0.970  0.020  1.090
 X1A  C16  H14  single    0.970  0.020  1.090
 X1A  C16  H15  single    0.970  0.020  1.090
 X1A  C18  H16  single    0.930  0.020  1.080
 X1A  C24  H20  single    0.930  0.020  1.080
 X1A  C27  H21  single    0.970  0.020  1.090
 X1A  C27  H22  single    0.970  0.020  1.090
 X1A  N4   H4   single    0.860  0.020  1.020
 X1A  C9   H6   single    0.970  0.020  1.090
 X1A  C9   H7   single    0.970  0.020  1.090
 X1A  C13  H10  single    0.970  0.020  1.090
 X1A  C13  H11  single    0.970  0.020  1.090
 X1A  C14  H13  single    0.970  0.020  1.090
 X1A  C14  H12  single    0.970  0.020  1.090
 X1A  C20  H18  single    0.970  0.020  1.090
 X1A  C20  H17  single    0.970  0.020  1.090
 X1A  C20  H19  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
 X1A  N4   C2   O1   120.88  3.000
 X1A  O1   C2   C3   124.50  3.000
 X1A  N4   C2   C3   114.61  3.000
 X1A  H1   C3   H2   107.44  3.000
 X1A  H1   C3   H3   108.97  3.000
 X1A  H2   C3   H3   108.99  3.000
 X1A  H1   C3   C2   110.44  3.000
 X1A  H2   C3   C2   110.69  3.000
 X1A  H3   C3   C2   110.23  3.000
 X1A  S28  C5   N6   115.22  3.000
 X1A  S28  C5   N4   123.07  3.000
 X1A  N6   C5   N4   121.71  3.000
 X1A  H5   C7   N6   119.26  3.000
 X1A  H5   C7   C8   124.02  3.000
 X1A  N6   C7   C8   116.72  3.000
 X1A  S28  C8   C9   123.33  3.000
 X1A  C9   C8   C7   127.92  3.000
 X1A  S28  C8   C7   108.74  3.000
 X1A  C9   N10  C27  120.63  3.000
 X1A  C27  N10  C11   91.52  3.000
 X1A  C9   N10  C11  121.74  3.000
 X1A  H9   C11  H8   108.45  3.000
 X1A  H9   C11  C12  117.85  3.000
 X1A  H8   C11  C12  111.04  3.000
 X1A  H9   C11  N10  115.25  3.000
 X1A  H8   C11  N10  114.76  3.000
 X1A  C12  C11  N10   88.60  3.000
 X1A  C13  C12  C27  118.30  3.000
 X1A  C13  C12  C16  102.19  3.000
 X1A  C27  C12  C16  113.68  3.000
 X1A  C13  C12  C11  121.39  3.000
 X1A  C16  C12  C11  115.82  3.000
 X1A  C27  C12  C11   85.92  3.000
 X1A  H15  C16  H14  108.27  3.000
 X1A  H15  C16  N15  111.22  3.000
 X1A  H14  C16  N15  110.77  3.000
 X1A  H15  C16  C12  112.72  3.000
 X1A  H14  C16  C12  110.86  3.000
 X1A  N15  C16  C12  102.97  3.000
 X1A  N26  C17  N15  121.88  3.000
 X1A  N26  C17  C18  113.94  3.000
 X1A  N15  C17  C18  124.18  3.000
 X1A  H16  C18  C19  119.12  3.000
 X1A  H16  C18  C17  120.08  3.000
 X1A  C19  C18  C17  120.79  3.000
 X1A  N21  C19  C20  117.40  3.000
 X1A  N21  C19  C18  123.63  3.000
 X1A  C20  C19  C18  118.97  3.000
 X1A  H20  C24  N25  120.66  3.000
 X1A  H20  C24  N23  123.00  3.000
 X1A  N25  C24  N23  116.34  3.000
 X1A  H22  C27  H21  108.80  3.000
 X1A  H22  C27  C12  111.56  3.000
 X1A  H21  C27  C12  117.93  3.000
 X1A  H22  C27  N10  114.00  3.000
 X1A  H21  C27  N10  115.19  3.000
 X1A  C12  C27  N10   88.31  3.000
 X1A  H4   N4   C5   115.49  3.000
 X1A  H4   N4   C2   119.68  3.000
 X1A  C5   N4   C2   124.83  3.000
 X1A  C7   N6   C5   110.40  3.000
 X1A  H7   C9   H6   106.19  3.000
 X1A  H7   C9   N10  107.92  3.000
 X1A  H6   C9   N10  108.09  3.000
 X1A  H7   C9   C8   107.36  3.000
 X1A  H6   C9   C8   110.33  3.000
 X1A  N10  C9   C8   116.45  3.000
 X1A  H11  C13  H10  108.04  3.000
 X1A  H11  C13  C14  110.68  3.000
 X1A  H10  C13  C14  111.92  3.000
 X1A  H11  C13  C12  109.82  3.000
 X1A  H10  C13  C12  113.22  3.000
 X1A  C14  C13  C12  103.14  3.000
 X1A  H12  C14  H13  108.08  3.000
 X1A  H12  C14  N15  111.38  3.000
 X1A  H13  C14  N15  110.52  3.000
 X1A  H12  C14  C13  112.71  3.000
 X1A  H13  C14  C13  111.18  3.000
 X1A  N15  C14  C13  102.96  3.000
 X1A  C14  N15  C17  128.11  3.000
 X1A  C17  N15  C16  120.06  3.000
 X1A  C14  N15  C16  111.36  3.000
 X1A  H19  C20  H17  107.11  3.000
 X1A  H19  C20  H18  108.90  3.000
 X1A  H17  C20  H18  108.37  3.000
 X1A  H19  C20  C19  111.12  3.000
 X1A  H17  C20  C19  110.33  3.000
 X1A  H18  C20  C19  110.89  3.000
 X1A  C22  N21  C19  115.72  3.000
 X1A  N26  C22  N23  108.44  3.000
 X1A  N23  C22  N21  128.01  3.000
 X1A  N26  C22  N21  123.54  3.000
 X1A  C22  N23  C24  103.33  3.000
 X1A  N26  N25  C24  102.13  3.000
 X1A  N25  N26  C22  109.75  3.000
 X1A  N25  N26  C17  127.85  3.000
 X1A  C22  N26  C17  122.37  3.000
 X1A  C8   S28  C5    88.92  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
 X1A  CONST_01  C8   C7   N6   C5      0.00   0.0  0
 X1A  CONST_02  C7   C8   S28  C5      0.00   0.0  0
 X1A  CONST_03  S28  C5   N6   C7      0.00   0.0  0
 X1A  CONST_04  N6   C5   S28  C8      0.00   0.0  0
 X1A  CONST_05  N21  C19  C18  C17     0.00   0.0  0
 X1A  CONST_06  N21  C22  N26  C17     0.00   0.0  0
 X1A  CONST_07  N23  C22  N26  C17   180.00   0.0  0
 X1A  CONST_08  C24  N25  N26  C17   180.00   0.0  0
 X1A  CONST_09  C22  N21  C19  C18     0.00   0.0  0
 X1A  CONST_10  C22  N26  C17  C18     0.00   0.0  0
 X1A  CONST_11  N25  N26  C17  C18   180.00   0.0  0
 X1A  CONST_12  N26  C17  C18  C19     0.00   0.0  0
 X1A  CONST_13  N26  C22  N21  C19     0.00   0.0  0
 X1A  CONST_14  N23  C22  N21  C19   180.00   0.0  0
 X1A  CONST_15  C22  N26  N25  C24     0.00   0.0  0
 X1A  CONST_16  N21  C22  N23  C24   180.00   0.0  0
 X1A  CONST_17  N26  C22  N23  C24     0.00   0.0  0
 X1A  CONST_18  S28  C8   C7   N6      0.00   0.0  0
 X1A  CONST_19  N25  N26  C22  N21   180.00   0.0  0
 X1A  CONST_20  N25  C24  N23  C22     0.00   0.0  0
 X1A  CONST_21  N25  N26  C22  N23     0.00   0.0  0
 X1A  CONST_22  N26  N25  C24  N23     0.00   0.0  0
 X1A  CONST_23  N15  C17  C18  C19   180.00   0.0  0
 X1A  CONST_24  C22  N26  C17  N15   180.00   0.0  0
 X1A  CONST_25  N25  N26  C17  N15     0.00   0.0  0
 X1A  CONST_26  C9   C8   S28  C5    180.00   0.0  0
 X1A  CONST_27  N4   C5   N6   C7    180.00   0.0  0
 X1A  CONST_28  N4   C5   S28  C8    180.00   0.0  0
 X1A  CONST_29  C20  C19  C18  C17   180.00   0.0  0
 X1A  CONST_30  C9   C8   C7   N6    180.00   0.0  0
 X1A  CONST_31  C22  N21  C19  C20   180.00   0.0  0
 X1A  CONST_32  H5   C7   N6   C5    180.00   0.0  0
 X1A  CONST_33  H16  C18  C17  N15     0.00   0.0  0
 X1A  CONST_34  H20  C24  N23  C22   180.00   0.0  0
 X1A  CONST_35  N6   C5   N4   C2    180.00   0.0  0
 X1A  CONST_36  S28  C5   N4   C2      0.00   0.0  0
 X1A  CONST_37  H4   N4   C5   N6      0.00   0.0  0
 X1A  CONST_38  C5   N4   C2   C3    180.00   0.0  0
 X1A  CONST_39  O1   C2   N4   C5      0.00   0.0  0
 X1A  Var_01    C11  C12  C27  N10   -17.42  30.0  3
 X1A  Var_02    N15  C16  C12  C11  -170.11  30.0  1
 X1A  Var_03    C14  C13  C12  C11   172.54  30.0  1
 X1A  Var_04    C14  N15  C16  C12    17.23  30.0  1
 X1A  Var_05    N15  C14  C13  C12   -30.95  30.0  1
 X1A  Var_06    C13  C14  N15  C16     8.52  30.0  1
 X1A  Var_07    C18  C17  N15  C16    -4.94  30.0  2
 X1A  Var_08    N10  C9   C8   C7     97.17  30.0  2
 X1A  Var_09    H18  C20  C19  C18   170.23  30.0  2
 X1A  Var_10    H3   C3   C2   O1      1.12  30.0  3

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
 X1A  plan-1  C5   0.020
 X1A  plan-1  C7   0.020
 X1A  plan-1  C8   0.020
 X1A  plan-1  N4   0.020
 X1A  plan-1  N6   0.020
 X1A  plan-1  C9   0.020
 X1A  plan-1  S28  0.020
 X1A  plan-1  H5   0.020
 X1A  plan-2  C17  0.020
 X1A  plan-2  C18  0.020
 X1A  plan-2  C19  0.020
 X1A  plan-2  C24  0.020
 X1A  plan-2  N15  0.020
 X1A  plan-2  C20  0.020
 X1A  plan-2  N21  0.020
 X1A  plan-2  C22  0.020
 X1A  plan-2  N23  0.020
 X1A  plan-2  N25  0.020
 X1A  plan-2  N26  0.020
 X1A  plan-2  H16  0.020
 X1A  plan-2  H20  0.020
 X1A  plan-3  C2   0.020
 X1A  plan-3  C3   0.020
 X1A  plan-3  C5   0.020
 X1A  plan-3  O1   0.020
 X1A  plan-3  N4   0.020
 X1A  plan-3  H4   0.020

