# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 08:50:08 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 3-{6-[(4R)-6-azaspiro[2.5]oct-4-yloxy]pyrazin-2-yl}-5-(2,6-difluorophenyl)-1H-indazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(F)c1c2ccc3[nH]nc(c4cncc(O[C@H]5CNCCC56CC6)n4)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
 3U1  3U1  3-{6-[(4R)-6-azaspiro[2.5]oct-4-yloxy]pyrazin-2-yl}-5-(2,6-difluorophenyl)-1H-indazole  ligand  53  32  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3U1
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
 3U1  F01  F  F     0  -0.297  -1.3814   1.2358  -2.1865
 3U1  C02  C  CR6   0   0.533  -2.1641   1.7552  -1.2312
 3U1  C03  C  CR16  0  -0.421  -2.3531   3.1231  -1.2050
 3U1  C04  C  CR16  0  -0.227  -3.1627   3.6585  -0.2137
 3U1  C05  C  CR16  0  -0.420  -3.7670   2.8391   0.7284
 3U1  C06  C  CR6   0   0.556  -3.5414   1.4790   0.6571
 3U1  F07  F  F     0  -0.297  -4.1031   0.6835   1.5754
 3U1  C08  C  CR6   0  -0.389  -2.7393   0.8854  -0.3105
 3U1  C09  C  CR6   0   0.119  -2.4758  -0.5696  -0.3287
 3U1  C10  C  CR16  0  -0.292  -3.5333  -1.4959  -0.4905
 3U1  C11  C  CR16  0  -0.282  -3.3151  -2.8536  -0.4998
 3U1  C12  C  CR56  0   0.410  -1.9945  -3.2858  -0.3399
 3U1  N13  N  NR15  0  -0.533  -1.4434  -4.5228  -0.2990
 3U1  N14  N  N     0  -0.244  -0.1294  -4.4891  -0.1336
 3U1  C15  C  CR5   0   0.164   0.2203  -3.2236  -0.0597
 3U1  C16  C  CR6   0   0.183   1.6070  -2.8121   0.1114
 3U1  C17  C  CR16  0  -0.111   2.6542  -3.7114   0.2645
 3U1  N18  N  N     0  -0.347   3.9047  -3.2830   0.4086
 3U1  C19  C  CR16  0  -0.158   4.1321  -1.9870   0.4021
 3U1  C20  C  CR6   0   0.478   3.0696  -1.0812   0.2509
 3U1  O21  O  O2    0  -0.488   3.3560   0.2173   0.2408
 3U1  C22  C  CH1   0   0.030   2.3034   1.1687   0.0807
 3U1  C23  C  CH2   0  -0.346   1.6173   1.4391   1.4260
 3U1  N24  N  NH1   0  -0.577   0.6028   2.4729   1.3548
 3U1  C25  C  CH2   0  -0.318   1.1000   3.7066   0.7659
 3U1  C26  C  CH2   0  -0.455   1.7865   3.5030  -0.5819
 3U1  C27  C  CT    0  -0.028   2.8747   2.4568  -0.4673
 3U1  C28  C  CH2   0  -0.493   3.9838   2.4466  -1.4664
 3U1  C29  C  CH2   0  -0.486   4.2432   2.9059  -0.0566
 3U1  N30  N  N     0  -0.469   1.8353  -1.4972   0.1123
 3U1  C31  C  CR56  0  -0.050  -0.9286  -2.3870  -0.1831
 3U1  C32  C  CR16  0  -0.360  -1.1799  -1.0130  -0.1773
 3U1  H1   H  HCR6  0   0.289  -1.8812   3.7529  -1.9472
 3U1  H2   H  HCR6  0   0.284  -3.3244   4.7268  -0.1749
 3U1  H3   H  HCR6  0   0.288  -4.3929   3.2488   1.5095
 3U1  H4   H  HCR6  0   0.263  -4.5413  -1.1266  -0.6283
 3U1  H5   H  HCR6  0   0.279  -4.1308  -3.5521  -0.6277
 3U1  H6   H  HNR5  0   0.426  -1.9103  -5.4116  -0.3873
 3U1  H7   H  HCR6  0   0.271   2.4853  -4.7802   0.2718
 3U1  H8   H  HCR6  0   0.279   5.1520  -1.6388   0.5156
 3U1  H9   H  HCH1  0   0.235   1.5718   0.7806  -0.6382
 3U1  H10  H  HCH2  0   0.249   1.1635   0.5255   1.8147
 3U1  H11  H  HCH2  0   0.240   2.3843   1.7469   2.1446
 3U1  H12  H  HNH1  0   0.333  -0.1945   2.1428   0.8228
 3U1  H14  H  HCH2  0   0.241   0.2666   4.4053   0.6700
 3U1  H15  H  HCH2  0   0.227   1.8091   4.1587   1.4669
 3U1  H16  H  HCH2  0   0.223   1.0458   3.1899  -1.3275
 3U1  H17  H  HCH2  0   0.238   2.2063   4.4470  -0.9387
 3U1  H18  H  HCH2  0   0.249   4.4035   1.4974  -1.7748
 3U1  H19  H  HCH2  0   0.247   3.9586   3.1918  -2.2528
 3U1  H20  H  HCH2  0   0.248   4.3928   3.9648   0.1180
 3U1  H21  H  HCH2  0   0.250   4.8390   2.2659   0.5819
 3U1  H22  H  HCR6  0   0.257  -0.3660  -0.3181  -0.0449

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
 3U1  N13  N14  aromatic  1.325  0.020  1.325
 3U1  N13  C12  aromatic  1.355  0.020  1.355
 3U1  N14  C15  aromatic  1.315  0.020  1.315
 3U1  C12  C11  aromatic  1.399  0.020  1.399
 3U1  C12  C31  aromatic  1.403  0.020  1.403
 3U1  C11  C10  aromatic  1.375  0.020  1.375
 3U1  C17  N18  aromatic  1.330  0.020  1.330
 3U1  C17  C16  aromatic  1.389  0.020  1.389
 3U1  C15  C31  aromatic  1.427  0.020  1.427
 3U1  C15  C16  single    1.457  0.020  1.457
 3U1  N18  C19  aromatic  1.316  0.020  1.316
 3U1  C31  C32  aromatic  1.397  0.020  1.397
 3U1  C16  N30  aromatic  1.335  0.020  1.335
 3U1  C10  C09  aromatic  1.415  0.020  1.415
 3U1  C19  C20  aromatic  1.404  0.020  1.404
 3U1  C32  C09  aromatic  1.378  0.020  1.378
 3U1  N30  C20  aromatic  1.310  0.020  1.310
 3U1  C09  C08  single    1.479  0.020  1.479
 3U1  C20  O21  single    1.330  0.020  1.330
 3U1  F07  C06  single    1.338  0.020  1.338
 3U1  C08  C06  aromatic  1.390  0.020  1.390
 3U1  C08  C02  aromatic  1.391  0.020  1.391
 3U1  C06  C05  aromatic  1.380  0.020  1.380
 3U1  O21  C22  single    1.428  0.020  1.428
 3U1  F01  C02  single    1.340  0.020  1.340
 3U1  C02  C03  aromatic  1.381  0.020  1.381
 3U1  C22  C23  single    1.534  0.020  1.534
 3U1  C22  C27  single    1.512  0.020  1.512
 3U1  C05  C04  aromatic  1.387  0.020  1.387
 3U1  C23  N24  single    1.450  0.020  1.450
 3U1  C03  C04  aromatic  1.387  0.020  1.387
 3U1  C27  C29  single    1.498  0.020  1.498
 3U1  C27  C28  single    1.493  0.020  1.493
 3U1  C27  C26  single    1.514  0.020  1.514
 3U1  C29  C28  single    1.505  0.020  1.505
 3U1  N24  C25  single    1.455  0.020  1.455
 3U1  C26  C25  single    1.526  0.020  1.526
 3U1  C03  H1   single    0.930  0.020  1.080
 3U1  C04  H2   single    0.930  0.020  1.080
 3U1  C05  H3   single    0.930  0.020  1.080
 3U1  C10  H4   single    0.930  0.020  1.080
 3U1  C11  H5   single    0.930  0.020  1.080
 3U1  N13  H6   single    0.860  0.020  1.020
 3U1  C17  H7   single    0.930  0.020  1.080
 3U1  C19  H8   single    0.930  0.020  1.080
 3U1  C22  H9   single    0.970  0.020  1.090
 3U1  C23  H10  single    0.970  0.020  1.090
 3U1  C23  H11  single    0.970  0.020  1.090
 3U1  N24  H12  single    0.890  0.020  1.040
 3U1  C25  H14  single    0.970  0.020  1.090
 3U1  C25  H15  single    0.970  0.020  1.090
 3U1  C26  H16  single    0.970  0.020  1.090
 3U1  C26  H17  single    0.970  0.020  1.090
 3U1  C28  H18  single    0.970  0.020  1.090
 3U1  C28  H19  single    0.970  0.020  1.090
 3U1  C29  H20  single    0.970  0.020  1.090
 3U1  C29  H21  single    0.970  0.020  1.090
 3U1  C32  H22  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
 3U1  C08  C02  C03  123.37  3.000
 3U1  C03  C02  F01  118.52  3.000
 3U1  C08  C02  F01  118.11  3.000
 3U1  H1   C03  C04  121.34  3.000
 3U1  H1   C03  C02  120.26  3.000
 3U1  C04  C03  C02  118.41  3.000
 3U1  H2   C04  C05  119.62  3.000
 3U1  H2   C04  C03  119.62  3.000
 3U1  C05  C04  C03  120.76  3.000
 3U1  H3   C05  C06  120.34  3.000
 3U1  H3   C05  C04  121.25  3.000
 3U1  C06  C05  C04  118.41  3.000
 3U1  C08  C06  F07  117.77  3.000
 3U1  C08  C06  C05  123.44  3.000
 3U1  F07  C06  C05  118.79  3.000
 3U1  C09  C08  C06  122.11  3.000
 3U1  C06  C08  C02  115.62  3.000
 3U1  C09  C08  C02  122.23  3.000
 3U1  C32  C09  C10  120.31  3.000
 3U1  C32  C09  C08  118.87  3.000
 3U1  C10  C09  C08  120.82  3.000
 3U1  H4   C10  C11  118.93  3.000
 3U1  H4   C10  C09  119.15  3.000
 3U1  C11  C10  C09  121.91  3.000
 3U1  H5   C11  C12  121.74  3.000
 3U1  H5   C11  C10  121.26  3.000
 3U1  C12  C11  C10  117.01  3.000
 3U1  C31  C12  N13  105.81  3.000
 3U1  C31  C12  C11  122.15  3.000
 3U1  N13  C12  C11  132.04  3.000
 3U1  H6   N13  N14  119.53  3.000
 3U1  H6   N13  C12  127.89  3.000
 3U1  N14  N13  C12  112.58  3.000
 3U1  C15  N14  N13  107.17  3.000
 3U1  C31  C15  C16  127.68  3.000
 3U1  C16  C15  N14  122.11  3.000
 3U1  C31  C15  N14  110.20  3.000
 3U1  N30  C16  C17  120.59  3.000
 3U1  N30  C16  C15  116.18  3.000
 3U1  C17  C16  C15  123.23  3.000
 3U1  H7   C17  N18  117.66  3.000
 3U1  H7   C17  C16  121.51  3.000
 3U1  N18  C17  C16  120.83  3.000
 3U1  C19  N18  C17  118.64  3.000
 3U1  H8   C19  C20  121.07  3.000
 3U1  H8   C19  N18  118.59  3.000
 3U1  C20  C19  N18  120.34  3.000
 3U1  N30  C20  O21  120.82  3.000
 3U1  O21  C20  C19  117.88  3.000
 3U1  N30  C20  C19  121.29  3.000
 3U1  C22  O21  C20  119.52  3.000
 3U1  H9   C22  C27  108.42  3.000
 3U1  H9   C22  C23  109.81  3.000
 3U1  C27  C22  C23  109.67  3.000
 3U1  H9   C22  O21  109.24  3.000
 3U1  C27  C22  O21  109.25  3.000
 3U1  C23  C22  O21  110.41  3.000
 3U1  H11  C23  H10  107.02  3.000
 3U1  H11  C23  N24  108.77  3.000
 3U1  H10  C23  N24  108.86  3.000
 3U1  H11  C23  C22  108.16  3.000
 3U1  H10  C23  C22  110.53  3.000
 3U1  N24  C23  C22  113.30  3.000
 3U1  H12  N24  C25  109.42  3.000
 3U1  H12  N24  C23  110.11  3.000
 3U1  C25  N24  C23  112.67  3.000
 3U1  H15  C25  H14  106.64  3.000
 3U1  H15  C25  C26  109.22  3.000
 3U1  H14  C25  C26  110.56  3.000
 3U1  H15  C25  N24  108.20  3.000
 3U1  H14  C25  N24  108.51  3.000
 3U1  C26  C25  N24  113.46  3.000
 3U1  H17  C26  H16  106.51  3.000
 3U1  H17  C26  C27  110.21  3.000
 3U1  H16  C26  C27  109.86  3.000
 3U1  H17  C26  C25  110.23  3.000
 3U1  H16  C26  C25  109.55  3.000
 3U1  C27  C26  C25  110.41  3.000
 3U1  C29  C27  C28   60.45  3.000
 3U1  C28  C27  C26  119.21  3.000
 3U1  C29  C27  C26  118.06  3.000
 3U1  C26  C27  C22  110.16  3.000
 3U1  C28  C27  C22  121.17  3.000
 3U1  C29  C27  C22  120.09  3.000
 3U1  H19  C28  H18  113.90  3.000
 3U1  H19  C28  C29  118.29  3.000
 3U1  H18  C28  C29  117.86  3.000
 3U1  H19  C28  C27  117.63  3.000
 3U1  H18  C28  C27  118.99  3.000
 3U1  C29  C28  C27   59.94  3.000
 3U1  H21  C29  H20  114.00  3.000
 3U1  H21  C29  C28  117.83  3.000
 3U1  H20  C29  C28  118.22  3.000
 3U1  H21  C29  C27  119.16  3.000
 3U1  H20  C29  C27  117.60  3.000
 3U1  C28  C29  C27   59.61  3.000
 3U1  C20  N30  C16  118.31  3.000
 3U1  C32  C31  C15  136.17  3.000
 3U1  C32  C31  C12  119.60  3.000
 3U1  C15  C31  C12  104.23  3.000
 3U1  H22  C32  C31  119.91  3.000
 3U1  H22  C32  C09  121.06  3.000
 3U1  C31  C32  C09  119.03  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
 3U1  CONST_03  C05  C06  C08  C02    0.00   0.0  0
 3U1  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 3U1  CONST_05  C09  C08  C02  C03  180.00   0.0  0
 3U1  CONST_06  C06  C08  C02  C03    0.00   0.0  0
 3U1  CONST_07  C06  C05  C04  C03    0.00   0.0  0
 3U1  CONST_08  C08  C06  C05  C04    0.00   0.0  0
 3U1  CONST_09  C08  C02  C03  C04    0.00   0.0  0
 3U1  CONST_10  C09  C08  C06  C05  180.00   0.0  0
 3U1  CONST_13  C11  C10  C09  C08  180.00   0.0  0
 3U1  CONST_14  C31  C32  C09  C08  180.00   0.0  0
 3U1  CONST_15  C12  C11  C10  C09    0.00   0.0  0
 3U1  CONST_16  C12  C31  C32  C09    0.00   0.0  0
 3U1  CONST_17  C15  C31  C32  C09  180.00   0.0  0
 3U1  CONST_18  N13  C12  C11  C10  180.00   0.0  0
 3U1  CONST_19  C31  C12  C11  C10    0.00   0.0  0
 3U1  CONST_20  C31  C32  C09  C10    0.00   0.0  0
 3U1  CONST_21  N14  N13  C12  C11  180.00   0.0  0
 3U1  CONST_22  C15  C31  C12  C11  180.00   0.0  0
 3U1  CONST_23  C32  C31  C12  C11    0.00   0.0  0
 3U1  CONST_24  C32  C09  C10  C11    0.00   0.0  0
 3U1  CONST_25  C15  N14  N13  C12    0.00   0.0  0
 3U1  CONST_26  N14  C15  C31  C12    0.00   0.0  0
 3U1  CONST_27  C16  C15  C31  C12  180.00   0.0  0
 3U1  CONST_28  C31  C15  N14  N13    0.00   0.0  0
 3U1  CONST_29  C16  C15  N14  N13  180.00   0.0  0
 3U1  CONST_30  C15  C31  C12  N13    0.00   0.0  0
 3U1  CONST_31  C32  C31  C12  N13  180.00   0.0  0
 3U1  CONST_32  C31  C12  N13  N14    0.00   0.0  0
 3U1  CONST_33  C32  C31  C15  N14  180.00   0.0  0
 3U1  CONST_34  C17  C16  C15  N14    0.00   0.0  0
 3U1  CONST_35  N30  C16  C15  N14  180.00   0.0  0
 3U1  CONST_36  N18  C17  C16  C15  180.00   0.0  0
 3U1  CONST_37  C20  N30  C16  C15  180.00   0.0  0
 3U1  CONST_38  C19  N18  C17  C16    0.00   0.0  0
 3U1  CONST_39  C32  C31  C15  C16    0.00   0.0  0
 3U1  CONST_40  C19  C20  N30  C16    0.00   0.0  0
 3U1  CONST_41  C20  C19  N18  C17    0.00   0.0  0
 3U1  CONST_42  C31  C15  C16  C17  180.00   0.0  0
 3U1  CONST_43  C20  N30  C16  C17    0.00   0.0  0
 3U1  CONST_44  N30  C16  C17  N18    0.00   0.0  0
 3U1  CONST_45  N30  C20  C19  N18    0.00   0.0  0
 3U1  CONST_46  C31  C15  C16  N30    0.00   0.0  0
 3U1  CONST_47  C09  C08  C02  F01    0.00   0.0  0
 3U1  CONST_48  C06  C08  C02  F01  180.00   0.0  0
 3U1  CONST_49  C04  C03  C02  F01  180.00   0.0  0
 3U1  CONST_50  F07  C06  C08  C02  180.00   0.0  0
 3U1  CONST_51  F07  C06  C05  C04  180.00   0.0  0
 3U1  CONST_52  C09  C08  C06  F07    0.00   0.0  0
 3U1  CONST_53  O21  C20  N30  C16  180.00   0.0  0
 3U1  CONST_54  O21  C20  C19  N18  180.00   0.0  0
 3U1  CONST_55  H2   C04  C03  C02  180.00   0.0  0
 3U1  CONST_56  H3   C05  C04  C03  180.00   0.0  0
 3U1  CONST_57  H1   C03  C04  C05  180.00   0.0  0
 3U1  CONST_58  H4   C10  C09  C08    0.00   0.0  0
 3U1  CONST_59  H22  C32  C09  C08    0.00   0.0  0
 3U1  CONST_60  H5   C11  C10  C09  180.00   0.0  0
 3U1  CONST_61  H6   N13  C12  C11    0.00   0.0  0
 3U1  CONST_62  H7   C17  C16  C15    0.00   0.0  0
 3U1  CONST_63  H8   C19  N18  C17  180.00   0.0  0
 3U1  Var_01    C25  N24  C23  C22  -52.94  30.0  1
 3U1  Var_02    C28  C29  C27  C22  111.04  30.0  3
 3U1  Var_03    C25  C26  C27  C22   55.64  30.0  1
 3U1  Var_04    C26  C25  N24  C23   52.11  30.0  1
 3U1  Var_05    C27  C26  C25  N24  -53.62  30.0  1
 3U1  Var_06    N30  C20  O21  C22    0.19  30.0  2

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
 3U1  chir_01  C22  O21  C23  C27  negativ

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
 3U1  plan-1  F01  0.020
 3U1  plan-1  C02  0.020
 3U1  plan-1  C03  0.020
 3U1  plan-1  C04  0.020
 3U1  plan-1  C05  0.020
 3U1  plan-1  C06  0.020
 3U1  plan-1  F07  0.020
 3U1  plan-1  C08  0.020
 3U1  plan-1  C09  0.020
 3U1  plan-1  H1   0.020
 3U1  plan-1  H2   0.020
 3U1  plan-1  H3   0.020
 3U1  plan-2  C15  0.020
 3U1  plan-2  C16  0.020
 3U1  plan-2  C17  0.020
 3U1  plan-2  N18  0.020
 3U1  plan-2  C19  0.020
 3U1  plan-2  C20  0.020
 3U1  plan-2  O21  0.020
 3U1  plan-2  N30  0.020
 3U1  plan-2  H7   0.020
 3U1  plan-2  H8   0.020
 3U1  plan-3  C08  0.020
 3U1  plan-3  C09  0.020
 3U1  plan-3  C10  0.020
 3U1  plan-3  C11  0.020
 3U1  plan-3  C12  0.020
 3U1  plan-3  N13  0.020
 3U1  plan-3  N14  0.020
 3U1  plan-3  C15  0.020
 3U1  plan-3  C16  0.020
 3U1  plan-3  C31  0.020
 3U1  plan-3  C32  0.020
 3U1  plan-3  H4   0.020
 3U1  plan-3  H5   0.020
 3U1  plan-3  H6   0.020
 3U1  plan-3  H22  0.020

