# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 17:37:22 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 2-[4,5-bis(fluoranyl)-2-oxidanylidene-1'-(1~{H}-pyrazolo[3,4-b]pyridin-5-ylcarbonyl)spiro[indole-3,4'-piperidine]-1-yl]-~{N}-[2,2,2-tris(fluoranyl)ethyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc2N(CC(=O)NCC(F)(F)F)C(=O)C3(CCN(CC3)C(=O)c4cnc5[nH]ncc5c4)c2c1F
#
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
 D6Q  D6Q  2-[4,5-bis(fluoranyl)-2-oxidanylidene-1'-(1~{H}-pyrazolo[3,4-b]pyridin-5-ylcarbonyl)spiro[indole-3,4'-piperidine]-1-yl]-~{N}-[2,2,2-tris(fluoranyl)ethyl]ethanamide  ligand  56  37  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D6Q
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
 D6Q  N3   N  N     0  -0.421   6.3305  -0.4067   1.4233
 D6Q  C4   C  CR56  0   0.538   6.4132  -1.7268   1.2906
 D6Q  C7   C  CR15  0  -0.121   6.1682  -3.8387   0.6171
 D6Q  C8   C  CR56  0  -0.116   5.7283  -2.5156   0.3486
 D6Q  N12  N  NR6   0  -0.446   2.6842  -0.0404  -1.6177
 D6Q  C13  C  C     0  -0.331   1.8939   0.7295  -2.5653
 D6Q  C15  C  C     0  -0.334   0.1484   1.1090  -0.7440
 D6Q  C17  C  C     0  -0.335   1.8551  -0.8031  -0.6959
 D6Q  C21  C  CR5   0   0.610  -1.0430   0.3786  -1.3755
 D6Q  C24  C  C     0   0.553  -4.0394  -0.2960  -0.1040
 D6Q  C28  C  CT    0   0.978  -6.3354  -2.6424   0.3959
 D6Q  C1   C  CR6   0  -0.183   4.7567  -0.4958  -0.4107
 D6Q  C14  C  C     0  -0.417   1.0316   1.7504  -1.8361
 D6Q  C16  C  C     0  -0.410   0.9726   0.1356   0.1217
 D6Q  C18  C  CR56  0  -0.108  -0.5514   2.1528   0.0788
 D6Q  C19  C  CR56  0   0.423  -1.9284   2.0436  -0.0987
 D6Q  C2   C  CR16  0  -0.060   5.5209   0.1788   0.5664
 D6Q  C27  C  CH2   0  -0.481  -6.0810  -1.2276   0.8692
 D6Q  C32  C  CR16  0  -0.307  -2.8284   2.8786   0.5313
 D6Q  C33  C  CR16  0  -0.424  -2.3193   3.8659   1.3728
 D6Q  C34  C  CR6   0   0.396  -0.9597   3.9878   1.5546
 D6Q  C35  C  CR6   0   0.376  -0.0712   3.1335   0.9092
 D6Q  C9   C  CR16  0  -0.205   4.8641  -1.8691  -0.5304
 D6Q  F29  F  F     0  -0.307  -6.9922  -3.3473   1.3252
 D6Q  F30  F  F     0  -0.310  -7.0752  -2.6693  -0.7214
 D6Q  F31  F  F     0  -0.302  -5.2019  -3.2983   0.1226
 D6Q  F36  F  F     0  -0.295   1.2401   3.2862   1.1124
 D6Q  F37  F  F     0  -0.310  -0.4650   4.9340   2.3632
 D6Q  N20  N  NR5   0  -0.579  -2.1914   1.0094  -0.9892
 D6Q  N26  N  NH1   0  -0.646  -5.3756  -0.4583  -0.1150
 D6Q  N5   N  NR15  0  -0.514   7.1657  -2.5783   2.0147
 D6Q  N6   N  N     0  -0.219   7.0181  -3.8447   1.6113
 D6Q  O22  O  O     0  -0.440  -1.0034  -0.5894  -2.1030
 D6Q  O25  O  O     0  -0.455  -3.2981  -0.7549   0.7416
 D6Q  H1   H  HCR5  0   0.275   5.8898  -4.7562   0.1224
 D6Q  H2   H  H     0   0.273   2.5507   1.2344  -3.2689
 D6Q  H3   H  H     0   0.266   1.2793   0.0326  -3.1357
 D6Q  H4   H  H     0   0.268   1.2603  -1.5140  -1.2686
 D6Q  H5   H  H     0   0.283   2.4693  -1.3802  -0.0115
 D6Q  H6   H  H     0   0.263   1.6866   2.4846  -1.3632
 D6Q  H7   H  H     0   0.266   0.4103   2.2949  -2.5503
 D6Q  H8   H  H     0   0.258   1.6183   0.7195   0.7821
 D6Q  H9   H  H     0   0.266   0.3102  -0.4479   0.7648
 D6Q  H10  H  HCR6  0   0.273   5.4419   1.2574   0.6448
 D6Q  H11  H  HCH2  0   0.328  -3.4616  -0.1157  -2.1577
 D6Q  H12  H  HCH2  0   0.303  -4.1696   1.3537  -1.5218
 D6Q  H13  H  HCH2  0   0.310  -7.0388  -0.7540   1.0862
 D6Q  H14  H  HCH2  0   0.296  -5.5113  -1.2611   1.7975
 D6Q  H15  H  HCR6  0   0.283  -3.8968   2.7893   0.3902
 D6Q  H16  H  HCR6  0   0.297  -2.9871   4.5429   1.8886
 D6Q  H17  H  HCR6  0   0.289   4.3089  -2.4176  -1.2816
 D6Q  H18  H  HNH1  0   0.420  -5.9167  -0.0106  -0.8379
 D6Q  H19  H  HNR5  0   0.421   7.7826  -2.3596   2.7812
 D6Q  C10  C  C     0   0.522   3.9582   0.3347  -1.3614
 D6Q  C23  C  CH2   0  -0.479  -3.5045   0.5237  -1.2740
 D6Q  O11  O  O     0  -0.479   4.4921   1.2952  -1.8998

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
 D6Q  N6   C7   aromatic  1.308  0.020  1.308
 D6Q  N6   N5   aromatic  1.337  0.020  1.337
 D6Q  C7   C8   aromatic  1.420  0.020  1.420
 D6Q  N5   C4   aromatic  1.347  0.020  1.347
 D6Q  F37  C34  single    1.339  0.020  1.339
 D6Q  C8   C4   aromatic  1.407  0.020  1.407
 D6Q  C8   C9   aromatic  1.392  0.020  1.392
 D6Q  C4   N3   aromatic  1.329  0.020  1.329
 D6Q  F36  C35  single    1.336  0.020  1.336
 D6Q  C9   C1   aromatic  1.383  0.020  1.383
 D6Q  C34  C35  aromatic  1.391  0.020  1.391
 D6Q  C34  C33  aromatic  1.377  0.020  1.377
 D6Q  N3   C2   aromatic  1.316  0.020  1.316
 D6Q  C35  C18  aromatic  1.372  0.020  1.372
 D6Q  C1   C2   aromatic  1.412  0.020  1.412
 D6Q  C1   C10  single    1.494  0.020  1.494
 D6Q  C33  C32  aromatic  1.394  0.020  1.394
 D6Q  O11  C10  double    1.224  0.020  1.224
 D6Q  C10  N12  single    1.353  0.020  1.353
 D6Q  C18  C15  single    1.502  0.020  1.502
 D6Q  C18  C19  aromatic  1.393  0.020  1.393
 D6Q  C16  C15  single    1.542  0.020  1.542
 D6Q  C16  C17  single    1.526  0.020  1.526
 D6Q  C32  C19  aromatic  1.380  0.020  1.380
 D6Q  C14  C15  single    1.544  0.020  1.544
 D6Q  C14  C13  single    1.522  0.020  1.522
 D6Q  C15  C21  single    1.534  0.020  1.534
 D6Q  N12  C17  single    1.456  0.020  1.456
 D6Q  N12  C13  single    1.454  0.020  1.454
 D6Q  C19  N20  single    1.390  0.020  1.390
 D6Q  C21  N20  single    1.366  0.020  1.366
 D6Q  C21  O22  double    1.211  0.020  1.211
 D6Q  N20  C23  single    1.429  0.020  1.429
 D6Q  O25  C24  double    1.215  0.020  1.215
 D6Q  C23  C24  single    1.525  0.020  1.525
 D6Q  C24  N26  single    1.346  0.020  1.346
 D6Q  N26  C27  single    1.435  0.020  1.435
 D6Q  C27  C28  single    1.513  0.020  1.513
 D6Q  F30  C28  single    1.340  0.020  1.340
 D6Q  C28  F31  single    1.338  0.020  1.338
 D6Q  C28  F29  single    1.339  0.020  1.339
 D6Q  C7   H1   single    0.930  0.020  1.080
 D6Q  C13  H2   single    0.970  0.020  1.090
 D6Q  C13  H3   single    0.970  0.020  1.090
 D6Q  C17  H4   single    0.970  0.020  1.090
 D6Q  C17  H5   single    0.970  0.020  1.090
 D6Q  C14  H6   single    0.970  0.020  1.090
 D6Q  C14  H7   single    0.970  0.020  1.090
 D6Q  C16  H8   single    0.970  0.020  1.090
 D6Q  C16  H9   single    0.970  0.020  1.090
 D6Q  C2   H10  single    0.930  0.020  1.080
 D6Q  C23  H11  single    0.970  0.020  1.090
 D6Q  C23  H12  single    0.970  0.020  1.090
 D6Q  C27  H13  single    0.970  0.020  1.090
 D6Q  C27  H14  single    0.970  0.020  1.090
 D6Q  C32  H15  single    0.930  0.020  1.080
 D6Q  C33  H16  single    0.930  0.020  1.080
 D6Q  C9   H17  single    0.930  0.020  1.080
 D6Q  N26  H18  single    0.860  0.020  1.020
 D6Q  N5   H19  single    0.860  0.020  1.020

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
 D6Q  C2   N3   C4   114.52  3.000
 D6Q  N5   C4   C8   106.11  3.000
 D6Q  C8   C4   N3   126.40  3.000
 D6Q  N5   C4   N3   127.49  3.000
 D6Q  H1   C7   N6   120.82  3.000
 D6Q  H1   C7   C8   128.73  3.000
 D6Q  N6   C7   C8   110.45  3.000
 D6Q  C9   C8   C7   138.12  3.000
 D6Q  C9   C8   C4   117.70  3.000
 D6Q  C7   C8   C4   104.18  3.000
 D6Q  C17  N12  C13  112.36  3.000
 D6Q  C13  N12  C10  119.24  3.000
 D6Q  C17  N12  C10  124.18  3.000
 D6Q  H3   C13  H2   107.39  3.000
 D6Q  H3   C13  C14  111.10  3.000
 D6Q  H2   C13  C14  109.93  3.000
 D6Q  H3   C13  N12  107.99  3.000
 D6Q  H2   C13  N12  109.83  3.000
 D6Q  C14  C13  N12  110.53  3.000
 D6Q  C18  C15  C16  112.35  3.000
 D6Q  C16  C15  C14  110.71  3.000
 D6Q  C18  C15  C14  111.42  3.000
 D6Q  C14  C15  C21  110.55  3.000
 D6Q  C16  C15  C21  110.24  3.000
 D6Q  C18  C15  C21  101.22  3.000
 D6Q  H5   C17  H4   107.06  3.000
 D6Q  H5   C17  C16  108.45  3.000
 D6Q  H4   C17  C16  111.55  3.000
 D6Q  H5   C17  N12  110.82  3.000
 D6Q  H4   C17  N12  108.65  3.000
 D6Q  C16  C17  N12  110.27  3.000
 D6Q  O22  C21  N20  124.49  3.000
 D6Q  O22  C21  C15  127.04  3.000
 D6Q  N20  C21  C15  108.47  3.000
 D6Q  O25  C24  N26  124.47  3.000
 D6Q  N26  C24  C23  113.99  3.000
 D6Q  O25  C24  C23  121.54  3.000
 D6Q  F31  C28  F30  106.71  3.000
 D6Q  F31  C28  F29  107.42  3.000
 D6Q  F30  C28  F29  107.30  3.000
 D6Q  F29  C28  C27  110.96  3.000
 D6Q  F31  C28  C27  112.32  3.000
 D6Q  F30  C28  C27  111.85  3.000
 D6Q  C9   C1   C2   119.50  3.000
 D6Q  C2   C1   C10  117.65  3.000
 D6Q  C9   C1   C10  122.59  3.000
 D6Q  H7   C14  H6   106.82  3.000
 D6Q  H7   C14  C15  110.14  3.000
 D6Q  H6   C14  C15  108.43  3.000
 D6Q  H7   C14  C13  110.08  3.000
 D6Q  H6   C14  C13  108.58  3.000
 D6Q  C15  C14  C13  112.59  3.000
 D6Q  H9   C16  H8   106.74  3.000
 D6Q  H9   C16  C17  109.73  3.000
 D6Q  H8   C16  C17  108.11  3.000
 D6Q  H9   C16  C15  110.10  3.000
 D6Q  H8   C16  C15  108.54  3.000
 D6Q  C17  C16  C15  113.37  3.000
 D6Q  C35  C18  C19  118.64  3.000
 D6Q  C19  C18  C15  109.65  3.000
 D6Q  C35  C18  C15  131.71  3.000
 D6Q  N20  C19  C32  128.27  3.000
 D6Q  N20  C19  C18  109.10  3.000
 D6Q  C32  C19  C18  122.63  3.000
 D6Q  H10  C2   C1   119.07  3.000
 D6Q  H10  C2   N3   116.12  3.000
 D6Q  C1   C2   N3   124.81  3.000
 D6Q  H14  C27  H13  107.64  3.000
 D6Q  H14  C27  N26  110.11  3.000
 D6Q  H13  C27  N26  109.61  3.000
 D6Q  H14  C27  C28  108.99  3.000
 D6Q  H13  C27  C28  108.70  3.000
 D6Q  N26  C27  C28  111.68  3.000
 D6Q  H15  C32  C33  119.89  3.000
 D6Q  H15  C32  C19  122.33  3.000
 D6Q  C33  C32  C19  117.78  3.000
 D6Q  H16  C33  C34  119.42  3.000
 D6Q  H16  C33  C32  120.38  3.000
 D6Q  C34  C33  C32  120.21  3.000
 D6Q  F37  C34  C35  118.55  3.000
 D6Q  C35  C34  C33  120.99  3.000
 D6Q  F37  C34  C33  120.46  3.000
 D6Q  F36  C35  C34  119.09  3.000
 D6Q  C34  C35  C18  119.75  3.000
 D6Q  F36  C35  C18  121.16  3.000
 D6Q  H17  C9   C1   121.54  3.000
 D6Q  H17  C9   C8   121.40  3.000
 D6Q  C1   C9   C8   117.06  3.000
 D6Q  C23  N20  C19  123.68  3.000
 D6Q  C23  N20  C21  124.01  3.000
 D6Q  C19  N20  C21  111.45  3.000
 D6Q  H18  N26  C27  117.79  3.000
 D6Q  H18  N26  C24  119.03  3.000
 D6Q  C27  N26  C24  123.17  3.000
 D6Q  H19  N5   N6   120.17  3.000
 D6Q  H19  N5   C4   127.83  3.000
 D6Q  N6   N5   C4   112.01  3.000
 D6Q  N5   N6   C7   107.26  3.000
 D6Q  O11  C10  C1   118.89  3.000
 D6Q  O11  C10  N12  123.04  3.000
 D6Q  C1   C10  N12  118.03  3.000
 D6Q  H12  C23  H11  106.58  3.000
 D6Q  H12  C23  N20  110.28  3.000
 D6Q  H11  C23  N20  108.93  3.000
 D6Q  H12  C23  C24  111.65  3.000
 D6Q  H11  C23  C24  108.66  3.000
 D6Q  N20  C23  C24  110.61  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
 D6Q  CONST_01  N6   N5   C4   N3    180.00   0.0  0
 D6Q  CONST_02  C7   C8   C4   N3    180.00   0.0  0
 D6Q  CONST_03  C9   C8   C4   N3      0.00   0.0  0
 D6Q  CONST_04  C9   C1   C2   N3      0.00   0.0  0
 D6Q  CONST_05  C7   N6   N5   C4      0.00   0.0  0
 D6Q  CONST_06  N6   C7   C8   C4      0.00   0.0  0
 D6Q  CONST_07  C1   C9   C8   C4      0.00   0.0  0
 D6Q  CONST_08  C1   C2   N3   C4      0.00   0.0  0
 D6Q  CONST_09  N5   C4   C8   C7      0.00   0.0  0
 D6Q  CONST_10  C1   C9   C8   C7    180.00   0.0  0
 D6Q  CONST_11  N5   N6   C7   C8      0.00   0.0  0
 D6Q  CONST_12  N6   N5   C4   C8      0.00   0.0  0
 D6Q  CONST_13  C2   N3   C4   C8      0.00   0.0  0
 D6Q  CONST_14  C2   C1   C9   C8      0.00   0.0  0
 D6Q  CONST_15  C33  C34  C35  C18     0.00   0.0  0
 D6Q  CONST_16  C33  C32  C19  C18     0.00   0.0  0
 D6Q  CONST_17  C34  C35  C18  C19     0.00   0.0  0
 D6Q  CONST_18  C34  C33  C32  C19     0.00   0.0  0
 D6Q  CONST_19  N5   C4   N3   C2    180.00   0.0  0
 D6Q  CONST_20  C35  C34  C33  C32     0.00   0.0  0
 D6Q  CONST_21  C35  C18  C19  C32     0.00   0.0  0
 D6Q  CONST_22  N6   C7   C8   C9    180.00   0.0  0
 D6Q  CONST_23  N5   C4   C8   C9    180.00   0.0  0
 D6Q  CONST_24  C34  C35  C18  C15   180.00   0.0  0
 D6Q  CONST_25  C32  C19  C18  C15   180.00   0.0  0
 D6Q  CONST_26  N20  C19  C18  C15     0.00   0.0  0
 D6Q  CONST_27  C19  N20  C21  C15     0.00   0.0  0
 D6Q  CONST_28  C10  C1   C2   N3    180.00   0.0  0
 D6Q  CONST_29  C10  C1   C9   C8    180.00   0.0  0
 D6Q  CONST_30  F36  C35  C18  C15     0.00   0.0  0
 D6Q  CONST_31  F37  C34  C35  C18   180.00   0.0  0
 D6Q  CONST_32  F36  C35  C18  C19   180.00   0.0  0
 D6Q  CONST_33  F37  C34  C33  C32   180.00   0.0  0
 D6Q  CONST_34  F36  C35  C34  C33   180.00   0.0  0
 D6Q  CONST_35  C1   C10  N12  C13   180.00   0.0  0
 D6Q  CONST_37  C23  N20  C21  C15   180.00   0.0  0
 D6Q  CONST_38  O22  C21  N20  C19   180.00   0.0  0
 D6Q  CONST_39  H19  N5   C4   N3      0.00   0.0  0
 D6Q  CONST_40  H1   C7   C8   C4    180.00   0.0  0
 D6Q  CONST_41  H17  C9   C8   C4    180.00   0.0  0
 D6Q  CONST_42  H10  C2   N3   C4    180.00   0.0  0
 D6Q  CONST_43  H15  C32  C19  C18   180.00   0.0  0
 D6Q  CONST_44  H16  C33  C32  C19   180.00   0.0  0
 D6Q  CONST_45  O11  C10  N12  C13     0.00   0.0  0
 D6Q  CONST_47  O22  C21  N20  C23     0.00   0.0  0
 D6Q  CONST_48  C27  N26  C24  C23   180.00   0.0  0
 D6Q  CONST_49  O25  C24  N26  C27     0.00   0.0  0
 D6Q  CONST_50  H18  N26  C24  C23     0.00   0.0  0
 D6Q  Var_01    C15  C16  C17  N12    52.90  30.0  1
 D6Q  Var_02    C15  C14  C13  N12   -54.29  30.0  1
 D6Q  Var_03    C18  C15  C14  C13   172.42  30.0  3
 D6Q  Var_04    C16  C17  N12  C13   -60.84  30.0  1
 D6Q  Var_05    C14  C13  N12  C17    61.89  30.0  1
 D6Q  Var_06    C35  C18  C15  C14   -63.32  30.0  1
 D6Q  Var_07    N20  C21  C15  C14  -115.18  30.0  1
 D6Q  Var_08    C9   C1   C10  N12    50.62  30.0  2
 D6Q  Var_09    C24  C23  N20  C21    94.93  30.0  3
 D6Q  Var_10    O25  C24  C23  N20   -18.75  30.0  3
 D6Q  Var_11    C28  C27  N26  C24   -95.90  30.0  3
 D6Q  Var_12    N26  C27  C28  F29   179.91  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
 D6Q  plan-1  N3   0.020
 D6Q  plan-1  C4   0.020
 D6Q  plan-1  C7   0.020
 D6Q  plan-1  C8   0.020
 D6Q  plan-1  C1   0.020
 D6Q  plan-1  C2   0.020
 D6Q  plan-1  C9   0.020
 D6Q  plan-1  N5   0.020
 D6Q  plan-1  N6   0.020
 D6Q  plan-1  H1   0.020
 D6Q  plan-1  H10  0.020
 D6Q  plan-1  H17  0.020
 D6Q  plan-1  H19  0.020
 D6Q  plan-1  C10  0.020
 D6Q  plan-2  N12  0.020
 D6Q  plan-2  C13  0.020
 D6Q  plan-2  C17  0.020
 D6Q  plan-2  C1   0.020
 D6Q  plan-2  C10  0.020
 D6Q  plan-2  O11  0.020
 D6Q  plan-3  C24  0.020
 D6Q  plan-3  C27  0.020
 D6Q  plan-3  N26  0.020
 D6Q  plan-3  O25  0.020
 D6Q  plan-3  H18  0.020
 D6Q  plan-3  C23  0.020
 D6Q  plan-4  C15  0.020
 D6Q  plan-4  C21  0.020
 D6Q  plan-4  C18  0.020
 D6Q  plan-4  C19  0.020
 D6Q  plan-4  C32  0.020
 D6Q  plan-4  C33  0.020
 D6Q  plan-4  C34  0.020
 D6Q  plan-4  C35  0.020
 D6Q  plan-4  F36  0.020
 D6Q  plan-4  F37  0.020
 D6Q  plan-4  N20  0.020
 D6Q  plan-4  O22  0.020
 D6Q  plan-4  H15  0.020
 D6Q  plan-4  H16  0.020
 D6Q  plan-4  C23  0.020

