# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 17:45:09 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N-[(2R)-1-(3-cyanoazetidin-1-yl)-1-oxopropan-2-yl]-2-(6-fluoro-1-methyl-1H-indazol-3-yl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)c1c[nH]c2ncc(nc12)c3nn(C)c4cc(F)ccc34)C(=O)N5C[C@H](C5)C#N
#
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
 VFC  VFC  N-[(2R)-1-(3-cyanoazetidin-1-yl)-1-oxopropan-2-yl]-2-(6-fluoro-1-methyl-1H-indazol-3-yl)-5H-pyrrolo[2,3-b]pyrazine-7-carboxamide  ligand  52  33  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VFC
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
 VFC  F32   F  F     0  -0.315  -4.6159  -5.0127   0.6240
 VFC  C29   C  CR6   0   0.531  -4.4434  -3.6912   0.4636
 VFC  C28   C  CR16  0  -0.422  -3.1264  -3.2199   0.3536
 VFC  C26   C  CR16  0  -0.315  -2.8908  -1.8741   0.1934
 VFC  C24   C  CR56  0  -0.117  -3.9892  -1.0039   0.1446
 VFC  C27   C  CR16  0  -0.483  -5.5519  -2.8883   0.4173
 VFC  C25   C  CR56  0   0.472  -5.2915  -1.5237   0.2500
 VFC  N30   N  NR5   0  -0.383  -6.1377  -0.4709   0.1535
 VFC  C33   C  CH3   0  -0.524  -7.5730  -0.4806   0.2833
 VFC  N31   N  N     0  -0.275  -5.4783   0.6761   0.0121
 VFC  C23   C  CR5   0   0.202  -4.1942   0.4002  -0.0033
 VFC  C5    C  CR6   0   0.121  -3.1893   1.4459  -0.1546
 VFC  N3    N  N     0  -0.408  -1.9211   1.0647  -0.0855
 VFC  C6    C  CR16  0  -0.097  -3.5576   2.7922  -0.3611
 VFC  N4    N  N     0  -0.379  -2.6697   3.7617  -0.4926
 VFC  C2    C  CR56  0   0.476  -1.4157   3.3629  -0.4211
 VFC  N7    N  NR15  0  -0.662  -0.2912   4.1228  -0.5149
 VFC  C8    C  CR15  0  -0.001   0.7945   3.3223  -0.3814
 VFC  C9    C  CR5   0  -0.206   0.4132   2.0134  -0.1942
 VFC  C1    C  CR56  0   0.155  -1.0165   2.0230  -0.2249
 VFC  C10   C  C     0   0.517   1.2774   0.8327  -0.0426
 VFC  O11   O  O     0  -0.483   0.8685  -0.2976  -0.2741
 VFC  N12   N  NH1   0  -0.664   2.5411   1.0844   0.3519
 VFC  C13   C  CH1   0  -0.192   3.5374   0.0542   0.4978
 VFC  C22   C  CH3   0  -0.653   3.4331  -0.6724   1.8429
 VFC  C14   C  C     0   0.535   4.9039   0.7148   0.3770
 VFC  O21   O  O     0  -0.485   5.0829   1.8973   0.6363
 VFC  N15   N  N     0  -0.456   5.9034  -0.0885   0.0163
 VFC  C17   C  C     0  -0.225   7.2959   0.2427  -0.2212
 VFC  C18   C  C     0  -0.445   7.4744  -1.1743  -0.8273
 VFC  C16   C  C     0  -0.237   5.9883  -1.4524  -0.4824
 VFC  C19   C  CSP   0   0.153   8.4406  -2.0244  -0.1662
 VFC  N20   N  NS    0  -0.261   9.2071  -2.6987   0.3640
 VFC  H28   H  HCR6  0   0.280  -2.3073  -3.9249   0.3990
 VFC  H27   H  HCR6  0   0.295  -6.5507  -3.2936   0.5071
 VFC  H26   H  HCR6  0   0.278  -1.8816  -1.4966   0.1065
 VFC  H331  H  HCH3  0   0.259  -7.8764  -0.3990   1.3274
 VFC  H332  H  HCH3  0   0.272  -7.9832   0.3556  -0.2754
 VFC  H333  H  HCH3  0   0.261  -7.9722  -1.4043  -0.1293
 VFC  H6    H  HCR6  0   0.272  -4.6027   3.0682  -0.4185
 VFC  H7    H  HNR5  0   0.428  -0.2625   5.1186  -0.6701
 VFC  H8    H  HCR5  0   0.310   1.7832   3.7479  -0.4538
 VFC  H12   H  HNH1  0   0.398   2.8085   2.0104   0.6484
 VFC  H13   H  HCH1  0   0.276   3.4070  -0.6718  -0.3087
 VFC  H221  H  HCH3  0   0.239   3.5521   0.0286   2.6690
 VFC  H222  H  HCH3  0   0.255   2.4583  -1.1489   1.9295
 VFC  H223  H  HCH3  0   0.240   4.1917  -1.4491   1.9413
 VFC  H171  H  H     0   0.278   7.4491   1.0528  -0.9330
 VFC  H172  H  H     0   0.273   7.8669   0.4385   0.6864
 VFC  H161  H  H     0   0.276   5.8315  -2.2196   0.2761
 VFC  H162  H  H     0   0.284   5.3611  -1.6608  -1.3488
 VFC  H18   H  H     0   0.355   7.6766  -1.1662  -1.8972

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
 VFC  F32  C29   single    1.342  0.020  1.342
 VFC  C29  C28   aromatic  1.403  0.020  1.403
 VFC  C29  C27   aromatic  1.369  0.020  1.369
 VFC  C28  C26   aromatic  1.376  0.020  1.376
 VFC  C26  C24   aromatic  1.402  0.020  1.402
 VFC  C24  C25   aromatic  1.406  0.020  1.406
 VFC  C24  C23   aromatic  1.427  0.020  1.427
 VFC  C27  C25   aromatic  1.399  0.020  1.399
 VFC  C25  N30   aromatic  1.354  0.020  1.354
 VFC  N30  C33   single    1.441  0.020  1.441
 VFC  N30  N31   aromatic  1.330  0.020  1.330
 VFC  N31  C23   aromatic  1.314  0.020  1.314
 VFC  C23  C5    single    1.458  0.020  1.458
 VFC  C5   N3    aromatic  1.326  0.020  1.326
 VFC  C5   C6    aromatic  1.411  0.020  1.411
 VFC  N3   C1    aromatic  1.325  0.020  1.325
 VFC  C6   N4    aromatic  1.321  0.020  1.321
 VFC  N4   C2    aromatic  1.318  0.020  1.318
 VFC  C2   N7    aromatic  1.360  0.020  1.360
 VFC  C2   C1    aromatic  1.412  0.020  1.412
 VFC  N7   C8    aromatic  1.355  0.020  1.355
 VFC  C8   C9    aromatic  1.376  0.020  1.376
 VFC  C9   C1    aromatic  1.430  0.020  1.430
 VFC  C9   C10   single    1.471  0.020  1.471
 VFC  C10  O11   double    1.224  0.020  1.224
 VFC  C10  N12   single    1.348  0.020  1.348
 VFC  N12  C13   single    1.441  0.020  1.441
 VFC  C13  C22   single    1.532  0.020  1.532
 VFC  C13  C14   single    1.523  0.020  1.523
 VFC  C14  O21   double    1.224  0.020  1.224
 VFC  C14  N15   single    1.332  0.020  1.332
 VFC  N15  C17   single    1.451  0.020  1.451
 VFC  N15  C16   single    1.455  0.020  1.455
 VFC  C17  C18   single    1.551  0.020  1.551
 VFC  C18  C16   single    1.551  0.020  1.551
 VFC  C18  C19   single    1.447  0.020  1.447
 VFC  C19  N20   triple    1.150  0.020  1.150
 VFC  C28  H28   single    0.930  0.020  1.080
 VFC  C27  H27   single    0.930  0.020  1.080
 VFC  C26  H26   single    0.930  0.020  1.080
 VFC  C33  H331  single    0.970  0.020  1.090
 VFC  C33  H332  single    0.970  0.020  1.090
 VFC  C33  H333  single    0.970  0.020  1.090
 VFC  C6   H6    single    0.930  0.020  1.080
 VFC  N7   H7    single    0.860  0.020  1.020
 VFC  C8   H8    single    0.930  0.020  1.080
 VFC  N12  H12   single    0.860  0.020  1.020
 VFC  C13  H13   single    0.970  0.020  1.090
 VFC  C22  H221  single    0.970  0.020  1.090
 VFC  C22  H222  single    0.970  0.020  1.090
 VFC  C22  H223  single    0.970  0.020  1.090
 VFC  C17  H171  single    0.970  0.020  1.090
 VFC  C17  H172  single    0.970  0.020  1.090
 VFC  C16  H161  single    0.970  0.020  1.090
 VFC  C16  H162  single    0.970  0.020  1.090
 VFC  C18  H18   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
 VFC  C27   C29  C28   124.07  3.000
 VFC  C27   C29  F32   118.50  3.000
 VFC  C28   C29  F32   117.42  3.000
 VFC  H28   C28  C26   120.85  3.000
 VFC  H28   C28  C29   119.25  3.000
 VFC  C26   C28  C29   119.90  3.000
 VFC  H26   C26  C24   120.79  3.000
 VFC  H26   C26  C28   120.72  3.000
 VFC  C24   C26  C28   118.49  3.000
 VFC  C23   C24  C25   103.80  3.000
 VFC  C23   C24  C26   136.63  3.000
 VFC  C25   C24  C26   119.57  3.000
 VFC  H27   C27  C25   123.17  3.000
 VFC  H27   C27  C29   121.67  3.000
 VFC  C25   C27  C29   115.16  3.000
 VFC  N30   C25  C27   130.58  3.000
 VFC  N30   C25  C24   106.62  3.000
 VFC  C27   C25  C24   122.81  3.000
 VFC  N31   N30  C33   120.59  3.000
 VFC  N31   N30  C25   111.60  3.000
 VFC  C33   N30  C25   127.63  3.000
 VFC  H333  C33  H332  108.67  3.000
 VFC  H333  C33  H331  108.95  3.000
 VFC  H332  C33  H331  109.26  3.000
 VFC  H333  C33  N30   109.71  3.000
 VFC  H332  C33  N30   108.94  3.000
 VFC  H331  C33  N30   111.28  3.000
 VFC  C23   N31  N30   107.73  3.000
 VFC  C5    C23  N31   121.62  3.000
 VFC  C5    C23  C24   128.13  3.000
 VFC  N31   C23  C24   110.24  3.000
 VFC  C6    C5   N3    122.11  3.000
 VFC  C6    C5   C23   121.30  3.000
 VFC  N3    C5   C23   116.59  3.000
 VFC  C1    N3   C5    116.07  3.000
 VFC  H6    C6   N4    117.16  3.000
 VFC  H6    C6   C5    120.20  3.000
 VFC  N4    C6   C5    122.64  3.000
 VFC  C2    N4   C6    114.33  3.000
 VFC  C1    C2   N7    107.82  3.000
 VFC  C1    C2   N4    124.32  3.000
 VFC  N7    C2   N4    127.86  3.000
 VFC  H7    N7   C8    125.14  3.000
 VFC  H7    N7   C2    125.86  3.000
 VFC  C8    N7   C2    108.99  3.000
 VFC  H8    C8   C9    129.67  3.000
 VFC  H8    C8   N7    119.63  3.000
 VFC  C9    C8   N7    110.68  3.000
 VFC  C10   C9   C1    126.51  3.000
 VFC  C10   C9   C8    127.93  3.000
 VFC  C1    C9   C8    105.53  3.000
 VFC  C9    C1   C2    106.98  3.000
 VFC  C9    C1   N3    132.48  3.000
 VFC  C2    C1   N3    120.53  3.000
 VFC  N12   C10  O11   122.76  3.000
 VFC  N12   C10  C9    115.54  3.000
 VFC  O11   C10  C9    121.70  3.000
 VFC  H12   N12  C13   116.33  3.000
 VFC  H12   N12  C10   120.41  3.000
 VFC  C13   N12  C10   123.00  3.000
 VFC  H13   C13  C14   109.67  3.000
 VFC  H13   C13  C22   108.94  3.000
 VFC  C14   C13  C22   109.66  3.000
 VFC  H13   C13  N12   108.53  3.000
 VFC  C14   C13  N12   107.60  3.000
 VFC  C22   C13  N12   112.39  3.000
 VFC  H223  C22  H222  107.70  3.000
 VFC  H223  C22  H221  108.28  3.000
 VFC  H222  C22  H221  108.61  3.000
 VFC  H223  C22  C13   111.70  3.000
 VFC  H222  C22  C13   109.78  3.000
 VFC  H221  C22  C13   110.67  3.000
 VFC  N15   C14  O21   122.04  3.000
 VFC  N15   C14  C13   115.67  3.000
 VFC  O21   C14  C13   122.25  3.000
 VFC  C16   N15  C17    95.85  3.000
 VFC  C16   N15  C14   134.59  3.000
 VFC  C17   N15  C14   128.81  3.000
 VFC  H172  C17  H171  109.69  3.000
 VFC  H172  C17  C18   115.41  3.000
 VFC  H171  C17  C18   114.06  3.000
 VFC  H172  C17  N15   114.05  3.000
 VFC  H171  C17  N15   114.31  3.000
 VFC  C18   C17  N15    88.04  3.000
 VFC  H18   C18  C19   109.22  3.000
 VFC  H18   C18  C16   113.44  3.000
 VFC  C19   C18  C16   115.66  3.000
 VFC  H18   C18  C17   113.48  3.000
 VFC  C19   C18  C17   115.79  3.000
 VFC  C16   C18  C17    88.09  3.000
 VFC  H162  C16  H161  109.62  3.000
 VFC  H162  C16  C18   114.15  3.000
 VFC  H161  C16  C18   114.76  3.000
 VFC  H162  C16  N15   114.73  3.000
 VFC  H161  C16  N15   114.39  3.000
 VFC  C18   C16  N15    87.93  3.000
 VFC  N20   C19  C18   180.00  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
 VFC  CONST_01  C24   C26  C28  C29     0.00   0.0  0
 VFC  CONST_02  C24   C25  C27  C29     0.00   0.0  0
 VFC  CONST_03  N30   C25  C27  C29   180.00   0.0  0
 VFC  CONST_04  C25   C27  C29  C28     0.00   0.0  0
 VFC  CONST_05  C25   C24  C26  C28     0.00   0.0  0
 VFC  CONST_06  C23   C24  C26  C28   180.00   0.0  0
 VFC  CONST_07  C27   C29  C28  C26     0.00   0.0  0
 VFC  CONST_08  C27   C25  C24  C26     0.00   0.0  0
 VFC  CONST_09  N30   C25  C24  C26   180.00   0.0  0
 VFC  CONST_10  N31   C23  C24  C26   180.00   0.0  0
 VFC  CONST_11  C5    C23  C24  C26     0.00   0.0  0
 VFC  CONST_12  N31   N30  C25  C24     0.00   0.0  0
 VFC  CONST_13  N30   N31  C23  C24     0.00   0.0  0
 VFC  CONST_14  N3    C5   C23  C24     0.00   0.0  0
 VFC  CONST_15  C6    C5   C23  C24   180.00   0.0  0
 VFC  CONST_16  C23   C24  C25  C27   180.00   0.0  0
 VFC  CONST_17  N31   N30  C25  C27   180.00   0.0  0
 VFC  CONST_18  N31   C23  C24  C25     0.00   0.0  0
 VFC  CONST_19  C5    C23  C24  C25   180.00   0.0  0
 VFC  CONST_20  C23   N31  N30  C25     0.00   0.0  0
 VFC  CONST_21  C23   C24  C25  N30     0.00   0.0  0
 VFC  CONST_22  C5    C23  N31  N30   180.00   0.0  0
 VFC  CONST_23  N3    C5   C23  N31   180.00   0.0  0
 VFC  CONST_24  C6    C5   C23  N31     0.00   0.0  0
 VFC  CONST_25  C1    N3   C5   C23   180.00   0.0  0
 VFC  CONST_26  N4    C6   C5   C23   180.00   0.0  0
 VFC  CONST_27  C2    C1   N3   C5      0.00   0.0  0
 VFC  CONST_28  C9    C1   N3   C5    180.00   0.0  0
 VFC  CONST_29  C2    N4   C6   C5      0.00   0.0  0
 VFC  CONST_30  N4    C6   C5   N3      0.00   0.0  0
 VFC  CONST_31  N4    C2   C1   N3      0.00   0.0  0
 VFC  CONST_32  N7    C2   C1   N3    180.00   0.0  0
 VFC  CONST_33  C8    C9   C1   N3    180.00   0.0  0
 VFC  CONST_34  C1    N3   C5   C6      0.00   0.0  0
 VFC  CONST_35  N7    C2   N4   C6    180.00   0.0  0
 VFC  CONST_36  C1    C2   N4   C6      0.00   0.0  0
 VFC  CONST_37  C8    N7   C2   N4    180.00   0.0  0
 VFC  CONST_38  C9    C1   C2   N4    180.00   0.0  0
 VFC  CONST_39  C9    C8   N7   C2      0.00   0.0  0
 VFC  CONST_40  C8    C9   C1   C2      0.00   0.0  0
 VFC  CONST_41  C9    C1   C2   N7      0.00   0.0  0
 VFC  CONST_42  C1    C9   C8   N7      0.00   0.0  0
 VFC  CONST_43  C1    C2   N7   C8      0.00   0.0  0
 VFC  CONST_44  C26   C28  C29  F32   180.00   0.0  0
 VFC  CONST_45  C25   C27  C29  F32   180.00   0.0  0
 VFC  CONST_46  C33   N30  C25  C24   180.00   0.0  0
 VFC  CONST_47  C33   N30  C25  C27     0.00   0.0  0
 VFC  CONST_48  C23   N31  N30  C33   180.00   0.0  0
 VFC  CONST_49  C10   C9   C1   N3      0.00   0.0  0
 VFC  CONST_50  C10   C9   C1   C2    180.00   0.0  0
 VFC  CONST_51  C10   C9   C8   N7    180.00   0.0  0
 VFC  CONST_52  H26   C26  C28  C29   180.00   0.0  0
 VFC  CONST_53  H27   C27  C29  C28   180.00   0.0  0
 VFC  CONST_54  H28   C28  C26  C24   180.00   0.0  0
 VFC  CONST_55  H6    C6   C5   C23     0.00   0.0  0
 VFC  CONST_56  H7    N7   C2   N4      0.00   0.0  0
 VFC  CONST_57  H8    C8   N7   C2    180.00   0.0  0
 VFC  CONST_58  C17   N15  C14  C13   180.00   0.0  0
 VFC  CONST_59  C16   N15  C14  C13     0.00   0.0  0
 VFC  CONST_60  C17   N15  C14  O21     0.00   0.0  0
 VFC  CONST_61  C16   N15  C14  O21   180.00   0.0  0
 VFC  CONST_62  C13   N12  C10  C9    180.00   0.0  0
 VFC  CONST_63  H12   N12  C10  C9      0.00   0.0  0
 VFC  CONST_64  C13   N12  C10  O11     0.00   0.0  0
 VFC  Var_01    C18   C16  N15  C17    -2.21  30.0  1
 VFC  Var_02    O11   C10  C9   C8   -157.98  30.0  2
 VFC  Var_03    H331  C33  N30  C25    85.51  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
 VFC  chir_01  C13  N12  C22  C14  positiv
 VFC  chir_02  C18  C17  C16  C19  positiv

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
 VFC  plan-1  F32  0.020
 VFC  plan-1  C29  0.020
 VFC  plan-1  C28  0.020
 VFC  plan-1  C26  0.020
 VFC  plan-1  C24  0.020
 VFC  plan-1  C27  0.020
 VFC  plan-1  C25  0.020
 VFC  plan-1  N30  0.020
 VFC  plan-1  C33  0.020
 VFC  plan-1  N31  0.020
 VFC  plan-1  C23  0.020
 VFC  plan-1  C5   0.020
 VFC  plan-1  H28  0.020
 VFC  plan-1  H27  0.020
 VFC  plan-1  H26  0.020
 VFC  plan-2  C23  0.020
 VFC  plan-2  C5   0.020
 VFC  plan-2  N3   0.020
 VFC  plan-2  C6   0.020
 VFC  plan-2  N4   0.020
 VFC  plan-2  C2   0.020
 VFC  plan-2  N7   0.020
 VFC  plan-2  C8   0.020
 VFC  plan-2  C9   0.020
 VFC  plan-2  C1   0.020
 VFC  plan-2  C10  0.020
 VFC  plan-2  H6   0.020
 VFC  plan-2  H7   0.020
 VFC  plan-2  H8   0.020
 VFC  plan-3  C13  0.020
 VFC  plan-3  C14  0.020
 VFC  plan-3  O21  0.020
 VFC  plan-3  N15  0.020
 VFC  plan-3  C17  0.020
 VFC  plan-3  C16  0.020
 VFC  plan-4  C9   0.020
 VFC  plan-4  C10  0.020
 VFC  plan-4  O11  0.020
 VFC  plan-4  N12  0.020
 VFC  plan-4  C13  0.020
 VFC  plan-4  H12  0.020

