# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 13:18:03 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 2-[4-bromanyl-2-oxidanylidene-1'-(1~{H}-pyrazolo[4,3-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: FC(F)(F)CNC(=O)CN1C(=O)C2(CCN(CC2)C(=O)c3ccc4[nH]ncc4n3)c5c(Br)cccc15
#
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
 D6Z  D6Z  2-[4-bromanyl-2-oxidanylidene-1'-(1~{H}-pyrazolo[4,3-b]pyridin-5-ylcarbonyl)spiro[indole-3,4'-piperidine]-1-yl]-~{N}-[2,2,2-tris(fluoranyl)ethyl]ethanamide  ligand  56  36  .  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_D6Z
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
 D6Z  C4   C   CR16  0  -0.269   2.1088   3.9943  -1.1333
 D6Z  C5   C   CR16  0  -0.309   2.7086   3.0099  -0.3561
 D6Z  C6   C   CR56  0   0.399   1.8804   2.0823   0.2442
 D6Z  C13  C   CT    0   0.978   6.5582  -2.3299  -0.4723
 D6Z  C17  C   CR5   0   0.612   1.1877   0.2851   1.4533
 D6Z  C20  C   CH2   0  -0.411  -0.7751  -0.1031  -0.0504
 D6Z  C21  C   CH2   0  -0.327  -1.5313  -1.1952   0.6999
 D6Z  C24  C   CH2   0  -0.416  -1.0136   1.3617   2.0165
 D6Z  C26  C   CR6   0   0.077  -4.4852  -1.3576   0.5613
 D6Z  C28  C   CR16  0  -0.180  -6.2785  -1.5699  -1.0526
 D6Z  C12  C   CH2   0  -0.481   6.2617  -0.9067  -0.8942
 D6Z  C19  C   CR5   0  -0.357  -0.0793   0.9199   0.8717
 D6Z  C2   C   CR6   0  -0.252  -0.0693   3.0841  -0.6773
 D6Z  C23  C   CH2   0  -0.328  -1.7310   0.1898   2.6728
 D6Z  C27  C   CR16  0  -0.301  -5.5164  -0.7869  -0.2199
 D6Z  C29  C   CR56  0   0.369  -5.9776  -2.9325  -1.0397
 D6Z  C3   C   CR16  0  -0.240   0.7342   4.0420  -1.2964
 D6Z  C30  C   CR56  0   0.023  -4.9421  -3.4165  -0.2198
 D6Z  C32  C   CR15  0  -0.120  -4.9259  -4.8177  -0.4596
 D6Z  C36  C   CR56  0   0.239   0.4905   2.0871   0.0992
 D6Z  C9   C   C     0   0.554   4.1858  -0.0887   0.1058
 D6Z  F14  F   F     0  -0.310   7.3038  -2.3763   0.6406
 D6Z  F15  F   F     0  -0.302   5.4445  -3.0263  -0.2180
 D6Z  F16  F   F     0  -0.307   7.2294  -2.9825  -1.4289
 D6Z  N11  N   NH1   0  -0.646   5.5277  -0.1974   0.1137
 D6Z  N22  N   NT    0  -0.444  -2.4316  -0.6078   1.6793
 D6Z  N31  N   N     0  -0.421  -4.1964  -2.6409   0.5695
 D6Z  N33  N   N     0  -0.212  -5.8505  -5.1362  -1.3290
 D6Z  N34  N   NR15  0  -0.535  -6.4778  -4.0097  -1.6757
 D6Z  N7   N   NR5   0  -0.573   2.2609   1.0359   1.0729
 D6Z  O10  O   O     0  -0.455   3.4652  -0.5404  -0.7612
 D6Z  O18  O   O     0  -0.442   1.2599  -0.7118   2.1382
 D6Z  O35  O   O     0  -0.485  -4.4282   0.3394   2.1716
 D6Z  BR1  BR  BR    0  -0.044  -1.9365   3.2184  -0.9506
 D6Z  H38  H   HCR6  0   0.275   2.7229   4.7395  -1.6205
 D6Z  H39  H   HCR6  0   0.276   3.7830   2.9835  -0.2336
 D6Z  H40  H   HCH2  0   0.327   3.6484  -0.0111   2.1754
 D6Z  H41  H   HCH2  0   0.305   4.2201   1.5265   1.5689
 D6Z  H45  H   HCH2  0   0.261  -0.0423  -0.5665  -0.7155
 D6Z  H46  H   HCH2  0   0.258  -1.4868   0.4216  -0.6895
 D6Z  H47  H   HCH2  0   0.282  -2.0789  -1.7943  -0.0190
 D6Z  H48  H   HCH2  0   0.260  -0.8473  -1.8686   1.2167
 D6Z  H51  H   HCH2  0   0.262  -0.4491   1.9194   2.7667
 D6Z  H52  H   HCH2  0   0.260  -1.7651   2.0438   1.6188
 D6Z  H54  H   HCR6  0   0.291  -7.0633  -1.1507  -1.6675
 D6Z  H43  H   HCH2  0   0.310   7.2048  -0.3959  -1.0900
 D6Z  H44  H   HCH2  0   0.296   5.6960  -0.9247  -1.8256
 D6Z  H49  H   HCH2  0   0.265  -1.0276  -0.4613   3.1925
 D6Z  H50  H   HCH2  0   0.271  -2.4359   0.5621   3.4110
 D6Z  H53  H   HCR6  0   0.280  -5.7015   0.2765  -0.1623
 D6Z  H37  H   HCR6  0   0.280   0.2926   4.8214  -1.9020
 D6Z  H55  H   HCR5  0   0.279  -4.2797  -5.5692  -0.0330
 D6Z  H42  H   HNH1  0   0.420   6.0497   0.2367   0.8587
 D6Z  H56  H   HNR5  0   0.425  -7.2359  -4.0431  -2.3379
 D6Z  C8   C   CH2   0  -0.481   3.6170   0.6536   1.3101
 D6Z  C25  C   C     0   0.516  -3.7615  -0.4604   1.5262

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
 D6Z  F16  C13  single    1.338  0.020  1.338
 D6Z  F14  C13  single    1.340  0.020  1.340
 D6Z  C13  F15  single    1.338  0.020  1.338
 D6Z  C13  C12  single    1.514  0.020  1.514
 D6Z  N11  C12  single    1.434  0.020  1.434
 D6Z  N11  C9   single    1.346  0.020  1.346
 D6Z  C8   C9   single    1.525  0.020  1.525
 D6Z  C8   N7   single    1.429  0.020  1.429
 D6Z  O18  C17  double    1.212  0.020  1.212
 D6Z  C9   O10  double    1.215  0.020  1.215
 D6Z  C17  N7   single    1.364  0.020  1.364
 D6Z  C17  C19  single    1.532  0.020  1.532
 D6Z  N7   C6   single    1.388  0.020  1.388
 D6Z  C23  C24  single    1.523  0.020  1.523
 D6Z  C23  N22  single    1.454  0.020  1.454
 D6Z  C24  C19  single    1.542  0.020  1.542
 D6Z  N22  C21  single    1.454  0.020  1.454
 D6Z  N22  C25  single    1.347  0.020  1.347
 D6Z  C21  C20  single    1.526  0.020  1.526
 D6Z  C19  C20  single    1.543  0.020  1.543
 D6Z  C19  C36  single    1.511  0.020  1.511
 D6Z  C6   C5   aromatic  1.381  0.020  1.381
 D6Z  C6   C36  aromatic  1.397  0.020  1.397
 D6Z  O35  C25  double    1.225  0.020  1.225
 D6Z  C25  C26  single    1.503  0.020  1.503
 D6Z  C5   C4   aromatic  1.390  0.020  1.390
 D6Z  C36  C2   aromatic  1.382  0.020  1.382
 D6Z  C26  C27  aromatic  1.414  0.020  1.414
 D6Z  C26  N31  aromatic  1.315  0.020  1.315
 D6Z  C27  C28  aromatic  1.374  0.020  1.374
 D6Z  C4   C3   aromatic  1.385  0.020  1.385
 D6Z  C2   C3   aromatic  1.395  0.020  1.395
 D6Z  C2   BR1  single    1.892  0.020  1.892
 D6Z  N31  C30  aromatic  1.334  0.020  1.334
 D6Z  C28  C29  aromatic  1.395  0.020  1.395
 D6Z  C30  C29  aromatic  1.407  0.020  1.407
 D6Z  C30  C32  aromatic  1.422  0.020  1.422
 D6Z  C29  N34  aromatic  1.347  0.020  1.347
 D6Z  N34  N33  aromatic  1.335  0.020  1.335
 D6Z  C32  N33  aromatic  1.309  0.020  1.309
 D6Z  C4   H38  single    0.930  0.020  1.080
 D6Z  C5   H39  single    0.930  0.020  1.080
 D6Z  C8   H40  single    0.970  0.020  1.090
 D6Z  C8   H41  single    0.970  0.020  1.090
 D6Z  C20  H45  single    0.970  0.020  1.090
 D6Z  C20  H46  single    0.970  0.020  1.090
 D6Z  C21  H47  single    0.970  0.020  1.090
 D6Z  C21  H48  single    0.970  0.020  1.090
 D6Z  C24  H51  single    0.970  0.020  1.090
 D6Z  C24  H52  single    0.970  0.020  1.090
 D6Z  C28  H54  single    0.930  0.020  1.080
 D6Z  C12  H43  single    0.970  0.020  1.090
 D6Z  C12  H44  single    0.970  0.020  1.090
 D6Z  C23  H49  single    0.970  0.020  1.090
 D6Z  C23  H50  single    0.970  0.020  1.090
 D6Z  C27  H53  single    0.930  0.020  1.080
 D6Z  C3   H37  single    0.930  0.020  1.080
 D6Z  C32  H55  single    0.930  0.020  1.080
 D6Z  N11  H42  single    0.860  0.020  1.020
 D6Z  N34  H56  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
 D6Z  H38  C4   C3   119.12  3.000
 D6Z  H38  C4   C5   119.65  3.000
 D6Z  C3   C4   C5   121.22  3.000
 D6Z  H39  C5   C6   122.01  3.000
 D6Z  H39  C5   C4   120.60  3.000
 D6Z  C6   C5   C4   117.39  3.000
 D6Z  N7   C6   C36  109.71  3.000
 D6Z  C36  C6   C5   123.30  3.000
 D6Z  N7   C6   C5   126.99  3.000
 D6Z  F16  C13  F15  107.42  3.000
 D6Z  F15  C13  F14  106.69  3.000
 D6Z  F16  C13  F14  107.32  3.000
 D6Z  F15  C13  C12  112.29  3.000
 D6Z  F14  C13  C12  111.90  3.000
 D6Z  F16  C13  C12  110.94  3.000
 D6Z  O18  C17  N7   124.31  3.000
 D6Z  N7   C17  C19  108.47  3.000
 D6Z  O18  C17  C19  127.22  3.000
 D6Z  H46  C20  H45  106.55  3.000
 D6Z  H46  C20  C19  108.99  3.000
 D6Z  H45  C20  C19  110.02  3.000
 D6Z  H46  C20  C21  108.00  3.000
 D6Z  H45  C20  C21  109.16  3.000
 D6Z  C19  C20  C21  113.84  3.000
 D6Z  H48  C21  H47  106.85  3.000
 D6Z  H48  C21  N22  108.58  3.000
 D6Z  H47  C21  N22  110.92  3.000
 D6Z  H48  C21  C20  111.37  3.000
 D6Z  H47  C21  C20  108.65  3.000
 D6Z  N22  C21  C20  110.42  3.000
 D6Z  H52  C24  H51  106.71  3.000
 D6Z  H52  C24  C23  108.30  3.000
 D6Z  H51  C24  C23  109.90  3.000
 D6Z  H52  C24  C19  109.04  3.000
 D6Z  H51  C24  C19  110.07  3.000
 D6Z  C23  C24  C19  112.63  3.000
 D6Z  N31  C26  C27  123.87  3.000
 D6Z  N31  C26  C25  118.20  3.000
 D6Z  C27  C26  C25  117.70  3.000
 D6Z  H54  C28  C29  122.70  3.000
 D6Z  H54  C28  C27  121.75  3.000
 D6Z  C29  C28  C27  115.55  3.000
 D6Z  H44  C12  H43  107.66  3.000
 D6Z  H44  C12  N11  110.07  3.000
 D6Z  H43  C12  N11  109.70  3.000
 D6Z  H44  C12  C13  108.92  3.000
 D6Z  H43  C12  C13  108.73  3.000
 D6Z  N11  C12  C13  111.67  3.000
 D6Z  C36  C19  C24  112.74  3.000
 D6Z  C36  C19  C20  112.13  3.000
 D6Z  C24  C19  C20  111.12  3.000
 D6Z  C36  C19  C17  101.67  3.000
 D6Z  C20  C19  C17  108.98  3.000
 D6Z  C24  C19  C17  109.75  3.000
 D6Z  BR1  C2   C36  122.15  3.000
 D6Z  BR1  C2   C3   117.10  3.000
 D6Z  C36  C2   C3   120.75  3.000
 D6Z  H50  C23  H49  107.42  3.000
 D6Z  H50  C23  N22  109.86  3.000
 D6Z  H49  C23  N22  108.00  3.000
 D6Z  H50  C23  C24  109.56  3.000
 D6Z  H49  C23  C24  111.16  3.000
 D6Z  N22  C23  C24  110.77  3.000
 D6Z  H53  C27  C28  119.87  3.000
 D6Z  H53  C27  C26  119.50  3.000
 D6Z  C28  C27  C26  120.62  3.000
 D6Z  N34  C29  C30  105.86  3.000
 D6Z  N34  C29  C28  134.13  3.000
 D6Z  C30  C29  C28  120.01  3.000
 D6Z  H37  C3   C2   120.55  3.000
 D6Z  H37  C3   C4   119.74  3.000
 D6Z  C2   C3   C4   119.71  3.000
 D6Z  N31  C30  C32  131.78  3.000
 D6Z  C32  C30  C29  104.43  3.000
 D6Z  N31  C30  C29  123.79  3.000
 D6Z  H55  C32  N33  121.08  3.000
 D6Z  H55  C32  C30  128.80  3.000
 D6Z  N33  C32  C30  110.12  3.000
 D6Z  C2   C36  C19  133.76  3.000
 D6Z  C2   C36  C6   117.62  3.000
 D6Z  C19  C36  C6   108.62  3.000
 D6Z  O10  C9   N11  124.44  3.000
 D6Z  O10  C9   C8   121.58  3.000
 D6Z  N11  C9   C8   113.98  3.000
 D6Z  H42  N11  C9   119.06  3.000
 D6Z  H42  N11  C12  117.86  3.000
 D6Z  C9   N11  C12  123.08  3.000
 D6Z  C25  N22  C23  119.57  3.000
 D6Z  C25  N22  C21  125.38  3.000
 D6Z  C23  N22  C21  112.55  3.000
 D6Z  C30  N31  C26  116.15  3.000
 D6Z  N34  N33  C32  107.41  3.000
 D6Z  H56  N34  N33  119.76  3.000
 D6Z  H56  N34  C29  128.05  3.000
 D6Z  N33  N34  C29  112.18  3.000
 D6Z  C17  N7   C8   123.59  3.000
 D6Z  C17  N7   C6   111.46  3.000
 D6Z  C8   N7   C6   124.13  3.000
 D6Z  H41  C8   H40  106.44  3.000
 D6Z  H41  C8   N7   110.47  3.000
 D6Z  H40  C8   N7   108.77  3.000
 D6Z  H41  C8   C9   111.74  3.000
 D6Z  H40  C8   C9   108.60  3.000
 D6Z  N7   C8   C9   110.68  3.000
 D6Z  O35  C25  N22  123.30  3.000
 D6Z  O35  C25  C26  117.76  3.000
 D6Z  N22  C25  C26  118.89  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
 D6Z  CONST_01  C36  C6   C5   C4      0.00   0.0  0
 D6Z  CONST_02  C36  C2   C3   C4      0.00   0.0  0
 D6Z  CONST_03  C2   C36  C6   C5      0.00   0.0  0
 D6Z  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 D6Z  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 D6Z  CONST_06  C3   C2   C36  C6      0.00   0.0  0
 D6Z  CONST_07  C29  C28  C27  C26     0.00   0.0  0
 D6Z  CONST_08  C29  C30  N31  C26     0.00   0.0  0
 D6Z  CONST_09  C32  C30  N31  C26   180.00   0.0  0
 D6Z  CONST_10  N31  C26  C27  C28     0.00   0.0  0
 D6Z  CONST_11  N31  C30  C29  C28     0.00   0.0  0
 D6Z  CONST_12  C32  C30  C29  C28   180.00   0.0  0
 D6Z  CONST_13  N33  N34  C29  C28   180.00   0.0  0
 D6Z  CONST_14  C30  N31  C26  C27     0.00   0.0  0
 D6Z  CONST_15  C30  C29  C28  C27     0.00   0.0  0
 D6Z  CONST_16  N34  C29  C28  C27   180.00   0.0  0
 D6Z  CONST_17  N33  C32  C30  C29     0.00   0.0  0
 D6Z  CONST_18  C32  N33  N34  C29     0.00   0.0  0
 D6Z  CONST_19  N33  N34  C29  C30     0.00   0.0  0
 D6Z  CONST_20  N34  N33  C32  C30     0.00   0.0  0
 D6Z  CONST_21  N34  C29  C30  C32     0.00   0.0  0
 D6Z  CONST_22  N34  C29  C30  N31   180.00   0.0  0
 D6Z  CONST_23  N33  C32  C30  N31   180.00   0.0  0
 D6Z  CONST_24  C19  C17  N7   C6      0.00   0.0  0
 D6Z  CONST_25  BR1  C2   C3   C4    180.00   0.0  0
 D6Z  CONST_26  BR1  C2   C36  C6    180.00   0.0  0
 D6Z  CONST_27  C25  C26  C27  C28   180.00   0.0  0
 D6Z  CONST_28  BR1  C2   C36  C19     0.00   0.0  0
 D6Z  CONST_29  C30  N31  C26  C25   180.00   0.0  0
 D6Z  CONST_31  C23  N22  C25  C26   180.00   0.0  0
 D6Z  CONST_32  O18  C17  N7   C6    180.00   0.0  0
 D6Z  CONST_33  C19  C17  N7   C8    180.00   0.0  0
 D6Z  CONST_34  H37  C3   C4   C5    180.00   0.0  0
 D6Z  CONST_35  H38  C4   C5   C6    180.00   0.0  0
 D6Z  CONST_36  H54  C28  C27  C26   180.00   0.0  0
 D6Z  CONST_37  H56  N34  C29  C28     0.00   0.0  0
 D6Z  CONST_38  H53  C27  C28  C29   180.00   0.0  0
 D6Z  CONST_39  H55  C32  C30  C29   180.00   0.0  0
 D6Z  CONST_40  H39  C5   C4   C3    180.00   0.0  0
 D6Z  CONST_42  O35  C25  N22  C23     0.00   0.0  0
 D6Z  CONST_43  O18  C17  N7   C8      0.00   0.0  0
 D6Z  CONST_44  C12  N11  C9   C8    180.00   0.0  0
 D6Z  CONST_45  O10  C9   N11  C12     0.00   0.0  0
 D6Z  CONST_46  H42  N11  C9   C8      0.00   0.0  0
 D6Z  Var_01    C24  C19  C36  C6    117.46  30.0  1
 D6Z  Var_02    C23  C24  C19  C17   -75.13  30.0  3
 D6Z  Var_03    C21  C20  C19  C17    76.30  30.0  3
 D6Z  Var_04    C23  N22  C21  C20   -60.27  30.0  1
 D6Z  Var_05    N7   C17  C19  C20   120.12  30.0  1
 D6Z  Var_06    C24  C23  N22  C21    61.87  30.0  1
 D6Z  Var_07    N22  C23  C24  C19   -53.86  30.0  1
 D6Z  Var_08    N22  C21  C20  C19    51.63  30.0  1
 D6Z  Var_09    N22  C25  C26  C27  -141.01  30.0  1
 D6Z  Var_10    C9   C8   N7   C6    -75.00  30.0  3
 D6Z  Var_11    N7   C8   C9   N11   164.84  30.0  2
 D6Z  Var_12    C9   N11  C12  C13   -95.25  30.0  1
 D6Z  Var_13    N11  C12  C13  F14   -60.89  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
 D6Z  plan-1  C26  0.020
 D6Z  plan-1  C28  0.020
 D6Z  plan-1  C27  0.020
 D6Z  plan-1  C29  0.020
 D6Z  plan-1  C30  0.020
 D6Z  plan-1  C32  0.020
 D6Z  plan-1  N31  0.020
 D6Z  plan-1  N33  0.020
 D6Z  plan-1  N34  0.020
 D6Z  plan-1  H54  0.020
 D6Z  plan-1  H53  0.020
 D6Z  plan-1  H55  0.020
 D6Z  plan-1  H56  0.020
 D6Z  plan-1  C25  0.020
 D6Z  plan-2  C21  0.020
 D6Z  plan-2  C26  0.020
 D6Z  plan-2  C23  0.020
 D6Z  plan-2  N22  0.020
 D6Z  plan-2  O35  0.020
 D6Z  plan-2  C25  0.020
 D6Z  plan-3  C12  0.020
 D6Z  plan-3  C9   0.020
 D6Z  plan-3  N11  0.020
 D6Z  plan-3  O10  0.020
 D6Z  plan-3  H42  0.020
 D6Z  plan-3  C8   0.020
 D6Z  plan-4  C4   0.020
 D6Z  plan-4  C5   0.020
 D6Z  plan-4  C6   0.020
 D6Z  plan-4  C17  0.020
 D6Z  plan-4  C19  0.020
 D6Z  plan-4  C2   0.020
 D6Z  plan-4  C3   0.020
 D6Z  plan-4  C36  0.020
 D6Z  plan-4  N7   0.020
 D6Z  plan-4  O18  0.020
 D6Z  plan-4  BR1  0.020
 D6Z  plan-4  H38  0.020
 D6Z  plan-4  H39  0.020
 D6Z  plan-4  H37  0.020
 D6Z  plan-4  C8   0.020

