# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun  5 18:09:09 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 1-[2-[(1~{R},3~{S},5~{R})-3-[[(1~{R})-1-(3-chloranyl-2-fluoranyl-phenyl)ethyl]carbamoyl]-2-azabicyclo[3.1.0]hexan-2-yl]-2-oxidanylidene-ethyl]pyrazolo[3,4-c]pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)[C@@H]1C[C@H]2C[C@H]2N1C(=O)Cn3nc(C(N)=O)c4ccncc34)c5cccc(Cl)c5F
#
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
 5WC  5WC  1-[2-[(1~{R},3~{S},5~{R})-3-[[(1~{R})-1-(3-chloranyl-2-fluoranyl-phenyl)ethyl]carbamoyl]-2-azabicyclo[3.1.0]hexan-2-yl]-2-oxidanylidene-ethyl]pyrazolo[3,4-c]pyridine-3-carboxamide  ligand  56  34  .  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_5WC
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
 5WC  C1   C   CH1   0  -0.270   1.2645   5.2599  -0.1152
 5WC  C2   C   CH2   0  -0.470  -0.0327   5.1002   0.6624
 5WC  C3   C   CH1   0  -0.115   1.8316   3.9050  -0.3369
 5WC  C11  C   CR6   0  -0.098  -3.1863   0.2395  -0.8171
 5WC  C13  C   CH2   0  -0.435   2.6738   1.2975   0.3677
 5WC  C16  C   CR56  0   0.365   2.7730  -1.0731  -0.4326
 5WC  C17  C   CR56  0   0.025   2.9020  -2.3057   0.2170
 5WC  C18  C   CR5   0   0.090   3.0256  -1.9545   1.5893
 5WC  C20  C   CR16  0  -0.079   2.6375  -1.0046  -1.8221
 5WC  C22  C   CR16  0  -0.100   2.7595  -3.2984  -1.9214
 5WC  C23  C   CR16  0  -0.379   2.8912  -3.4669  -0.5621
 5WC  C24  C   C     0   0.480   3.1894  -2.8694   2.7389
 5WC  C27  C   CR6   0   0.651  -2.0245  -0.4690  -1.1003
 5WC  C28  C   CR6   0  -0.228  -1.9193  -1.8290  -0.8681
 5WC  C29  C   CR16  0  -0.227  -3.0019  -2.5260  -0.3523
 5WC  C30  C   CR16  0  -0.260  -4.1728  -1.8427  -0.0725
 5WC  N4   N   NT    0  -0.457   0.9383   2.9782   0.3002
 5WC  C5   C   CH1   0  -0.227  -0.3447   3.5961   0.6271
 5WC  C6   C   C     0   0.595  -1.3319   3.2279  -0.4780
 5WC  N7   N   NH1   0  -0.620  -2.2759   2.3497  -0.1172
 5WC  O8   O   O     0  -0.488  -1.2198   3.6928  -1.6020
 5WC  C9   C   CH1   0  -0.143  -3.2146   1.7377  -1.0418
 5WC  C10  C   CH3   0  -0.671  -4.5955   2.3648  -0.9126
 5WC  N14  N   NR5   0  -0.382   2.8429  -0.1157   0.5311
 5WC  O15  O   O     0  -0.461   0.4366   0.9502   1.1585
 5WC  N19  N   N     0  -0.233   2.9808  -0.6485   1.7296
 5WC  N21  N   N     0  -0.398   2.6384  -2.1046  -2.5358
 5WC  N25  N   NH2   0  -0.810   3.2705  -2.2848   3.9396
 5WC  O26  O   O     0  -0.477   3.2399  -4.0787   2.5567
 5WC  C31  C   CR16  0  -0.293  -4.2601  -0.4753  -0.2994
 5WC  CL   CL  CL    0  -0.083  -0.4403  -2.6358  -1.2249
 5WC  C34  C   CH2   0  -0.474   2.5452   4.8705   0.5642
 5WC  H1   H   HCH1  0   0.278   1.3040   5.9908  -0.9111
 5WC  H2   H   HCH2  0   0.264   0.0769   5.4314   1.6959
 5WC  H3   H   HCH2  0   0.269  -0.8349   5.6882   0.2193
 5WC  H4   H   HCH1  0   0.289   2.2529   3.6119  -1.2910
 5WC  H5   H   HCH2  0   0.295   2.9940   1.5680  -0.6383
 5WC  H6   H   HCH2  0   0.328   3.3422   1.8187   1.0559
 5WC  H7   H   HCR6  0   0.277   2.5318  -0.0610  -2.3470
 5WC  H8   H   HCR6  0   0.268   2.7504  -4.1629  -2.5739
 5WC  H9   H   HCR6  0   0.269   2.9867  -4.4522  -0.1314
 5WC  H10  H   HCR6  0   0.288  -2.9223  -3.5896  -0.1741
 5WC  H11  H   HCR6  0   0.272  -5.0225  -2.3778   0.3281
 5WC  H12  H   HCH1  0   0.285  -0.6885   3.2364   1.5975
 5WC  H13  H   HNH1  0   0.403  -2.2741   2.0088   0.8318
 5WC  H14  H   HCH1  0   0.276  -2.8456   1.9447  -2.0478
 5WC  H15  H   HCH3  0   0.242  -5.3023   1.9103  -1.6067
 5WC  H16  H   HCH3  0   0.233  -4.9917   2.2696   0.0986
 5WC  H17  H   HCH3  0   0.255  -4.5306   3.4261  -1.1485
 5WC  H18  H   HNH2  0   0.412   3.2239  -1.2854   4.0450
 5WC  H19  H   HNH2  0   0.408   3.3867  -2.8431   4.7691
 5WC  H20  H   HCR6  0   0.275  -5.1832   0.0367  -0.0650
 5WC  H21  H   HCH2  0   0.266   3.4655   5.3065   0.1970
 5WC  H22  H   HCH2  0   0.259   2.5274   4.6759   1.6306
 5WC  C12  C   C     0   0.546   1.2313   1.7134   0.6432
 5WC  F    F   F     0  -0.286  -0.9768   0.1722  -1.6208

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
 5WC  C22  C23  aromatic  1.376  0.020  1.376
 5WC  C22  N21  aromatic  1.348  0.020  1.348
 5WC  C23  C17  aromatic  1.398  0.020  1.398
 5WC  N21  C20  aromatic  1.311  0.020  1.311
 5WC  O26  C24  double    1.224  0.020  1.224
 5WC  C17  C16  aromatic  1.399  0.020  1.399
 5WC  C17  C18  aromatic  1.422  0.020  1.422
 5WC  C20  C16  aromatic  1.398  0.020  1.398
 5WC  C24  C18  single    1.478  0.020  1.478
 5WC  C24  N25  single    1.338  0.020  1.338
 5WC  C16  N14  aromatic  1.360  0.020  1.360
 5WC  C18  N19  aromatic  1.314  0.020  1.314
 5WC  N14  N19  aromatic  1.319  0.020  1.319
 5WC  N14  C13  single    1.433  0.020  1.433
 5WC  C13  C12  single    1.526  0.020  1.526
 5WC  O15  C12  double    1.216  0.020  1.216
 5WC  C12  N4   single    1.343  0.020  1.343
 5WC  C30  C29  aromatic  1.384  0.020  1.384
 5WC  C30  C31  aromatic  1.389  0.020  1.389
 5WC  O8   C6   double    1.221  0.020  1.221
 5WC  C29  C28  aromatic  1.387  0.020  1.387
 5WC  C31  C11  aromatic  1.390  0.020  1.390
 5WC  N4   C3   single    1.436  0.020  1.436
 5WC  N4   C5   single    1.461  0.020  1.461
 5WC  C3   C34  single    1.501  0.020  1.501
 5WC  C3   C1   single    1.485  0.020  1.485
 5WC  C6   C5   single    1.527  0.020  1.527
 5WC  C6   N7   single    1.339  0.020  1.339
 5WC  C28  C27  aromatic  1.384  0.020  1.384
 5WC  C28  CL   single    1.722  0.020  1.722
 5WC  C11  C27  aromatic  1.390  0.020  1.390
 5WC  C11  C9   single    1.515  0.020  1.515
 5WC  C5   C2   single    1.536  0.020  1.536
 5WC  C34  C1   single    1.501  0.020  1.501
 5WC  C1   C2   single    1.521  0.020  1.521
 5WC  C27  F    single    1.334  0.020  1.334
 5WC  C9   N7   single    1.453  0.020  1.453
 5WC  C9   C10  single    1.522  0.020  1.522
 5WC  C1   H1   single    0.970  0.020  1.090
 5WC  C2   H2   single    0.970  0.020  1.090
 5WC  C2   H3   single    0.970  0.020  1.090
 5WC  C3   H4   single    0.970  0.020  1.090
 5WC  C13  H5   single    0.970  0.020  1.090
 5WC  C13  H6   single    0.970  0.020  1.090
 5WC  C20  H7   single    0.930  0.020  1.080
 5WC  C22  H8   single    0.930  0.020  1.080
 5WC  C23  H9   single    0.930  0.020  1.080
 5WC  C29  H10  single    0.930  0.020  1.080
 5WC  C30  H11  single    0.930  0.020  1.080
 5WC  C5   H12  single    0.970  0.020  1.090
 5WC  N7   H13  single    0.860  0.020  1.020
 5WC  C9   H14  single    0.970  0.020  1.090
 5WC  C10  H15  single    0.970  0.020  1.090
 5WC  C10  H16  single    0.970  0.020  1.090
 5WC  C10  H17  single    0.970  0.020  1.090
 5WC  N25  H18  single    0.860  0.020  1.020
 5WC  N25  H19  single    0.860  0.020  1.020
 5WC  C31  H20  single    0.930  0.020  1.080
 5WC  C34  H21  single    0.970  0.020  1.090
 5WC  C34  H22  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
 5WC  H1   C1   C34  118.51  3.000
 5WC  H1   C1   C3   119.52  3.000
 5WC  C34  C1   C3    60.35  3.000
 5WC  H1   C1   C2   118.59  3.000
 5WC  C34  C1   C2   117.97  3.000
 5WC  C3   C1   C2   107.83  3.000
 5WC  H3   C2   H2   107.19  3.000
 5WC  H3   C2   C5   111.70  3.000
 5WC  H2   C2   C5   109.84  3.000
 5WC  H3   C2   C1   111.32  3.000
 5WC  H2   C2   C1   111.52  3.000
 5WC  C5   C2   C1   105.32  3.000
 5WC  H4   C3   C34  121.18  3.000
 5WC  H4   C3   N4   117.25  3.000
 5WC  C34  C3   N4   116.39  3.000
 5WC  H4   C3   C1   121.78  3.000
 5WC  C34  C3   C1    60.35  3.000
 5WC  N4   C3   C1   106.56  3.000
 5WC  C31  C11  C9   123.32  3.000
 5WC  C9   C11  C27  119.30  3.000
 5WC  C31  C11  C27  117.36  3.000
 5WC  H6   C13  H5   106.47  3.000
 5WC  H6   C13  N14  109.07  3.000
 5WC  H5   C13  N14  108.38  3.000
 5WC  H6   C13  C12  109.55  3.000
 5WC  H5   C13  C12  112.13  3.000
 5WC  N14  C13  C12  111.09  3.000
 5WC  N14  C16  C20  132.44  3.000
 5WC  N14  C16  C17  106.64  3.000
 5WC  C20  C16  C17  120.90  3.000
 5WC  C23  C17  C18  138.03  3.000
 5WC  C18  C17  C16  103.80  3.000
 5WC  C23  C17  C16  118.17  3.000
 5WC  N19  C18  C24  122.40  3.000
 5WC  N19  C18  C17  110.21  3.000
 5WC  C24  C18  C17  127.39  3.000
 5WC  H7   C20  N21  117.79  3.000
 5WC  H7   C20  C16  122.22  3.000
 5WC  N21  C20  C16  119.99  3.000
 5WC  H8   C22  N21  115.56  3.000
 5WC  H8   C22  C23  119.88  3.000
 5WC  N21  C22  C23  124.56  3.000
 5WC  H9   C23  C22  120.96  3.000
 5WC  H9   C23  C17  122.34  3.000
 5WC  C22  C23  C17  116.71  3.000
 5WC  O26  C24  N25  124.25  3.000
 5WC  N25  C24  C18  115.73  3.000
 5WC  O26  C24  C18  120.02  3.000
 5WC  F    C27  C28  118.57  3.000
 5WC  F    C27  C11  119.40  3.000
 5WC  C28  C27  C11  122.03  3.000
 5WC  CL   C28  C29  120.79  3.000
 5WC  CL   C28  C27  119.41  3.000
 5WC  C29  C28  C27  119.80  3.000
 5WC  H10  C29  C30  120.96  3.000
 5WC  H10  C29  C28  119.88  3.000
 5WC  C30  C29  C28  119.16  3.000
 5WC  H11  C30  C31  119.90  3.000
 5WC  H11  C30  C29  119.69  3.000
 5WC  C31  C30  C29  120.41  3.000
 5WC  C5   N4   C12  122.19  3.000
 5WC  C5   N4   C3   111.87  3.000
 5WC  C12  N4   C3   125.83  3.000
 5WC  H12  C5   C6   111.14  3.000
 5WC  H12  C5   N4   109.66  3.000
 5WC  C6   C5   N4   107.69  3.000
 5WC  H12  C5   C2   111.50  3.000
 5WC  C6   C5   C2   112.58  3.000
 5WC  N4   C5   C2   103.94  3.000
 5WC  O8   C6   N7   124.22  3.000
 5WC  N7   C6   C5   114.77  3.000
 5WC  O8   C6   C5   120.98  3.000
 5WC  H13  N7   C9   117.24  3.000
 5WC  H13  N7   C6   118.30  3.000
 5WC  C9   N7   C6   124.08  3.000
 5WC  H14  C9   C10  107.87  3.000
 5WC  H14  C9   N7   106.76  3.000
 5WC  C10  C9   N7   111.01  3.000
 5WC  H14  C9   C11  108.54  3.000
 5WC  C10  C9   C11  114.31  3.000
 5WC  N7   C9   C11  108.06  3.000
 5WC  H17  C10  H16  107.92  3.000
 5WC  H17  C10  H15  107.88  3.000
 5WC  H16  C10  H15  108.58  3.000
 5WC  H17  C10  C9   109.21  3.000
 5WC  H16  C10  C9   111.87  3.000
 5WC  H15  C10  C9   111.25  3.000
 5WC  N19  N14  C16  111.40  3.000
 5WC  N19  N14  C13  120.96  3.000
 5WC  C16  N14  C13  127.40  3.000
 5WC  N14  N19  C18  107.94  3.000
 5WC  C22  N21  C20  119.66  3.000
 5WC  H19  N25  H18  118.03  3.000
 5WC  H19  N25  C24  120.28  3.000
 5WC  H18  N25  C24  121.69  3.000
 5WC  H20  C31  C30  118.98  3.000
 5WC  H20  C31  C11  119.79  3.000
 5WC  C30  C31  C11  121.24  3.000
 5WC  H22  C34  H21  114.83  3.000
 5WC  H22  C34  C3   117.85  3.000
 5WC  H21  C34  C3   117.36  3.000
 5WC  H22  C34  C1   118.54  3.000
 5WC  H21  C34  C1   117.86  3.000
 5WC  C3   C34  C1    59.31  3.000
 5WC  O15  C12  N4   123.83  3.000
 5WC  N4   C12  C13  114.63  3.000
 5WC  O15  C12  C13  121.53  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
 5WC  CONST_01  C29  C30  C31  C11     0.00   0.0  0
 5WC  CONST_02  C29  C28  C27  C11     0.00   0.0  0
 5WC  CONST_03  C22  C23  C17  C16     0.00   0.0  0
 5WC  CONST_04  N19  C18  C17  C16     0.00   0.0  0
 5WC  CONST_05  C22  N21  C20  C16     0.00   0.0  0
 5WC  CONST_06  C18  N19  N14  C16     0.00   0.0  0
 5WC  CONST_07  N21  C22  C23  C17     0.00   0.0  0
 5WC  CONST_08  N21  C20  C16  C17     0.00   0.0  0
 5WC  CONST_09  N19  N14  C16  C17     0.00   0.0  0
 5WC  CONST_10  N14  N19  C18  C17     0.00   0.0  0
 5WC  CONST_11  C22  C23  C17  C18   180.00   0.0  0
 5WC  CONST_12  C20  C16  C17  C18   180.00   0.0  0
 5WC  CONST_13  N14  C16  C17  C18     0.00   0.0  0
 5WC  CONST_14  C23  C22  N21  C20     0.00   0.0  0
 5WC  CONST_15  C23  C17  C16  C20     0.00   0.0  0
 5WC  CONST_16  N19  N14  C16  C20   180.00   0.0  0
 5WC  CONST_17  N14  C16  C17  C23   180.00   0.0  0
 5WC  CONST_18  N19  C18  C17  C23   180.00   0.0  0
 5WC  CONST_19  C30  C29  C28  C27     0.00   0.0  0
 5WC  CONST_20  C30  C31  C11  C27     0.00   0.0  0
 5WC  CONST_21  C31  C30  C29  C28     0.00   0.0  0
 5WC  CONST_22  C31  C11  C27  C28     0.00   0.0  0
 5WC  CONST_23  N21  C20  C16  N14   180.00   0.0  0
 5WC  CONST_24  CL   C28  C27  C11   180.00   0.0  0
 5WC  CONST_25  C17  C16  N14  C13   180.00   0.0  0
 5WC  CONST_26  C20  C16  N14  C13     0.00   0.0  0
 5WC  CONST_27  C18  N19  N14  C13   180.00   0.0  0
 5WC  CONST_28  C24  C18  C17  C16   180.00   0.0  0
 5WC  CONST_29  C24  C18  C17  C23     0.00   0.0  0
 5WC  CONST_30  N14  N19  C18  C24   180.00   0.0  0
 5WC  CONST_31  C9   C11  C27  C28   180.00   0.0  0
 5WC  CONST_32  F    C27  C28  C29   180.00   0.0  0
 5WC  CONST_33  CL   C28  C29  C30   180.00   0.0  0
 5WC  CONST_34  C9   C11  C31  C30   180.00   0.0  0
 5WC  CONST_35  F    C27  C11  C31   180.00   0.0  0
 5WC  CONST_36  H11  C30  C31  C11   180.00   0.0  0
 5WC  CONST_37  H9   C23  C17  C16   180.00   0.0  0
 5WC  CONST_38  H8   C22  C23  C17   180.00   0.0  0
 5WC  CONST_39  H7   C20  C16  C17   180.00   0.0  0
 5WC  CONST_40  H10  C29  C28  C27   180.00   0.0  0
 5WC  CONST_41  H20  C31  C11  C27   180.00   0.0  0
 5WC  CONST_42  C13  C12  N4   C3      0.00   0.0  0
 5WC  CONST_43  O15  C12  N4   C3    180.00   0.0  0
 5WC  CONST_44  C5   N4   C12  C13   180.00   0.0  0
 5WC  CONST_45  O15  C12  N4   C5      0.00   0.0  0
 5WC  CONST_46  C9   N7   C6   C5    180.00   0.0  0
 5WC  CONST_47  H18  N25  C24  C18     0.00   0.0  0
 5WC  CONST_48  H19  N25  C24  C18   180.00   0.0  0
 5WC  CONST_49  H13  N7   C6   C5      0.00   0.0  0
 5WC  CONST_50  C9   N7   C6   O8      0.00   0.0  0
 5WC  Var_01    C5   N4   C3   C1     14.68  30.0  1
 5WC  Var_02    N4   C3   C34  C1    -94.79  30.0  1
 5WC  Var_03    C5   C2   C1   C3    -11.51  30.0  1
 5WC  Var_04    C16  N14  C13  C12    94.06  30.0  2
 5WC  Var_05    O26  C24  C18  C17     0.48  30.0  2
 5WC  Var_06    N14  C13  C12  N4   -169.54  30.0  1

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
 5WC  chir_03  C5  N4  C6   C2   positiv
 5WC  chir_04  C9  N7  C11  C10  negativ
 5WC  chir_05  C1  C3  C34  C2   both
 5WC  chir_06  C3  N4  C1   C34  both

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
 5WC  plan-1  C11  0.020
 5WC  plan-1  C27  0.020
 5WC  plan-1  C28  0.020
 5WC  plan-1  C29  0.020
 5WC  plan-1  C30  0.020
 5WC  plan-1  C9   0.020
 5WC  plan-1  C31  0.020
 5WC  plan-1  CL   0.020
 5WC  plan-1  H10  0.020
 5WC  plan-1  H11  0.020
 5WC  plan-1  H20  0.020
 5WC  plan-1  F    0.020
 5WC  plan-2  C13  0.020
 5WC  plan-2  C16  0.020
 5WC  plan-2  C17  0.020
 5WC  plan-2  C18  0.020
 5WC  plan-2  C20  0.020
 5WC  plan-2  C22  0.020
 5WC  plan-2  C23  0.020
 5WC  plan-2  C24  0.020
 5WC  plan-2  N14  0.020
 5WC  plan-2  N19  0.020
 5WC  plan-2  N21  0.020
 5WC  plan-2  H7   0.020
 5WC  plan-2  H8   0.020
 5WC  plan-2  H9   0.020
 5WC  plan-3  C5   0.020
 5WC  plan-3  C6   0.020
 5WC  plan-3  N7   0.020
 5WC  plan-3  O8   0.020
 5WC  plan-3  C9   0.020
 5WC  plan-3  H13  0.020
 5WC  plan-4  C3   0.020
 5WC  plan-4  C13  0.020
 5WC  plan-4  N4   0.020
 5WC  plan-4  C5   0.020
 5WC  plan-4  O15  0.020
 5WC  plan-4  C12  0.020
 5WC  plan-5  C18  0.020
 5WC  plan-5  C24  0.020
 5WC  plan-5  N25  0.020
 5WC  plan-5  O26  0.020
 5WC  plan-5  H18  0.020
 5WC  plan-5  H19  0.020

