# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 10:18:19 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 6-[(3S)-3-(acryloylamino)pyrrolidin-1-yl]-2-(4-phenoxyphenoxy)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc(nc1Oc2ccc(Oc3ccccc3)cc2)N4CC[C@@H](C4)NC(=O)C=C
#
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
 GJA  GJA  6-[(3S)-3-(acryloylamino)pyrrolidin-1-yl]-2-(4-phenoxyphenoxy)pyridine-3-carboxamide  ligand  57  33  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GJA
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
 GJA  C2   C  CR6   0   0.504  -3.2520   0.6843  -0.1584
 GJA  C3   C  CR6   0  -0.242  -4.6117   0.3671  -0.2780
 GJA  C9   C  CR6   0   0.365  -1.5760   2.3113   0.0350
 GJA  C10  C  CR16  0  -0.311  -0.9161   2.8358  -1.0631
 GJA  C11  C  CR16  0  -0.304   0.4096   3.2283  -0.9460
 GJA  C12  C  CR6   0   0.298   1.0602   3.0816   0.2689
 GJA  C13  C  CR16  0  -0.309   0.3960   2.5620   1.3703
 GJA  C14  C  CR16  0  -0.285  -0.9307   2.1802   1.2547
 GJA  C15  C  C     0   0.472  -5.6726   1.3936  -0.4334
 GJA  C19  C  CR15  0  -0.114   0.6357  -3.1809  -0.1186
 GJA  C20  C  CH2   0  -0.234  -0.1629  -1.8904   0.0916
 GJA  C22  C  CH2   0  -0.479  -0.2759  -4.2539   0.4716
 GJA  C30  C  CR16  0  -0.245   5.7340   2.3764  -0.2753
 GJA  C31  C  CR16  0  -0.275   5.5345   1.0983  -0.7844
 GJA  C32  C  CR16  0  -0.243   4.2419   0.6096  -0.8971
 GJA  C33  C  CR16  0  -0.349   3.1507   1.3778  -0.5071
 GJA  N1   N  N     0  -0.497  -2.2925  -0.1987  -0.0695
 GJA  C4   C  CR16  0  -0.157  -4.8952  -1.0022  -0.3156
 GJA  C5   C  CR16  0  -0.420  -3.9070  -1.9543  -0.2350
 GJA  C6   C  CR6   0   0.553  -2.5779  -1.5040  -0.1022
 GJA  N7   N  NR5   0  -0.509  -1.5365  -2.3449  -0.0021
 GJA  O8   O  O2    0  -0.504  -2.9060   1.9853  -0.0958
 GJA  O16  O  O     0  -0.482  -5.4923   2.4475  -1.0283
 GJA  N17  N  NH2   0  -0.809  -6.8655   1.0650   0.0998
 GJA  C18  C  CH2   0  -0.281  -1.6655  -3.7929   0.0558
 GJA  O24  O  O     0  -0.499   3.1312  -2.8447  -1.4220
 GJA  C25  C  C1    0  -0.329   4.3044  -2.9586   0.6491
 GJA  C26  C  C2    0  -0.470   5.5162  -2.7963   0.1318
 GJA  O27  O  O2    0  -0.514   2.3640   3.4879   0.4049
 GJA  C28  C  CR6   0   0.365   3.3639   2.6567  -0.0041
 GJA  C29  C  CR16  0  -0.330   4.6578   3.1573   0.1136
 GJA  H1   H  HCR6  0   0.274  -1.4328   2.9419  -2.0082
 GJA  H2   H  HCR6  0   0.279   0.9300   3.6434  -1.7996
 GJA  H3   H  HCR6  0   0.275   0.9115   2.4574   2.3164
 GJA  H4   H  HCR6  0   0.273  -1.4527   1.7747   2.1111
 GJA  H5   H  HCR5  0   0.275   0.7618  -3.3584  -1.1869
 GJA  H6   H  HCH2  0   0.234   0.0521  -1.4564   1.0745
 GJA  H7   H  HCH2  0   0.255   0.0613  -1.1312  -0.6583
 GJA  H8   H  HCH2  0   0.268  -0.0407  -5.2538   0.1110
 GJA  H9   H  HCH2  0   0.249  -0.1912  -4.2568   1.5615
 GJA  H10  H  HCR6  0   0.259   6.7364   2.7727  -0.1784
 GJA  H11  H  HCR6  0   0.252   6.3780   0.4927  -1.0878
 GJA  H12  H  HCR6  0   0.261   4.0680  -0.3839  -1.2892
 GJA  H13  H  HCR6  0   0.272   2.1519   0.9725  -0.6045
 GJA  H14  H  HCR6  0   0.271  -5.9189  -1.3327  -0.4405
 GJA  H15  H  HCR6  0   0.274  -4.1503  -3.0049  -0.2949
 GJA  H16  H  HNH2  0   0.408  -6.9833   0.2823   0.7188
 GJA  H17  H  HNH2  0   0.401  -7.6438   1.6966   0.0048
 GJA  H18  H  HCH2  0   0.246  -1.9492  -4.2010  -0.9196
 GJA  H19  H  HCH2  0   0.255  -2.4277  -4.0962   0.7758
 GJA  H20  H  HNH1  0   0.403   1.9909  -3.2164   1.4854
 GJA  H21  H  H     0   0.269   4.1774  -3.0808   1.7191
 GJA  H22  H  H     0   0.257   5.6677  -2.6699  -0.9324
 GJA  H23  H  H     0   0.262   6.3960  -2.7835   0.7597
 GJA  H24  H  HCR6  0   0.267   4.8153   4.1529   0.5095
 GJA  N21  N  NH1   0  -0.656   1.9423  -3.1500   0.4801
 GJA  C23  C  C     0   0.553   3.0882  -2.9760  -0.2049

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
 GJA  O16  C15  double    1.224  0.020  1.224
 GJA  C4   C5   aromatic  1.375  0.020  1.375
 GJA  C4   C3   aromatic  1.399  0.020  1.399
 GJA  C5   C6   aromatic  1.410  0.020  1.410
 GJA  C26  C25  double    1.328  0.020  1.328
 GJA  O24  C23  double    1.225  0.020  1.225
 GJA  C15  C3   single    1.484  0.020  1.484
 GJA  C15  N17  single    1.347  0.020  1.347
 GJA  C3   C2   aromatic  1.401  0.020  1.401
 GJA  C20  C19  single    1.532  0.020  1.532
 GJA  C20  N7   single    1.450  0.020  1.450
 GJA  C23  C25  single    1.486  0.020  1.486
 GJA  C23  N21  single    1.346  0.020  1.346
 GJA  C6   N7   single    1.342  0.020  1.342
 GJA  C6   N1   aromatic  1.337  0.020  1.337
 GJA  C19  N21  single    1.437  0.020  1.437
 GJA  C19  C22  single    1.527  0.020  1.527
 GJA  N7   C18  single    1.455  0.020  1.455
 GJA  C2   N1   aromatic  1.307  0.020  1.307
 GJA  C2   O8   single    1.348  0.020  1.348
 GJA  O8   C9   single    1.376  0.020  1.376
 GJA  C18  C22  single    1.522  0.020  1.522
 GJA  C9   C10  aromatic  1.384  0.020  1.384
 GJA  C9   C14  aromatic  1.386  0.020  1.386
 GJA  C10  C11  aromatic  1.388  0.020  1.388
 GJA  C14  C13  aromatic  1.385  0.020  1.385
 GJA  C11  C12  aromatic  1.386  0.020  1.386
 GJA  C13  C12  aromatic  1.387  0.020  1.387
 GJA  C12  O27  single    1.372  0.020  1.372
 GJA  C33  C32  aromatic  1.390  0.020  1.390
 GJA  C33  C28  aromatic  1.391  0.020  1.391
 GJA  O27  C28  single    1.363  0.020  1.363
 GJA  C32  C31  aromatic  1.386  0.020  1.386
 GJA  C28  C29  aromatic  1.392  0.020  1.392
 GJA  C31  C30  aromatic  1.390  0.020  1.390
 GJA  C29  C30  aromatic  1.385  0.020  1.385
 GJA  C10  H1   single    0.930  0.020  1.080
 GJA  C11  H2   single    0.930  0.020  1.080
 GJA  C13  H3   single    0.930  0.020  1.080
 GJA  C14  H4   single    0.930  0.020  1.080
 GJA  C19  H5   single    0.970  0.020  1.090
 GJA  C20  H6   single    0.970  0.020  1.090
 GJA  C20  H7   single    0.970  0.020  1.090
 GJA  C22  H8   single    0.970  0.020  1.090
 GJA  C22  H9   single    0.970  0.020  1.090
 GJA  C30  H10  single    0.930  0.020  1.080
 GJA  C31  H11  single    0.930  0.020  1.080
 GJA  C32  H12  single    0.930  0.020  1.080
 GJA  C33  H13  single    0.930  0.020  1.080
 GJA  C4   H14  single    0.930  0.020  1.080
 GJA  C5   H15  single    0.930  0.020  1.080
 GJA  N17  H16  single    0.860  0.020  1.020
 GJA  N17  H17  single    0.860  0.020  1.020
 GJA  C18  H18  single    0.970  0.020  1.090
 GJA  C18  H19  single    0.970  0.020  1.090
 GJA  N21  H20  single    0.860  0.020  1.020
 GJA  C25  H21  single    0.930  0.020  1.080
 GJA  C26  H22  single    0.930  0.020  1.080
 GJA  C26  H23  single    0.930  0.020  1.080
 GJA  C29  H24  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
 GJA  O8   C2   N1   117.42  3.000
 GJA  O8   C2   C3   118.14  3.000
 GJA  N1   C2   C3   124.42  3.000
 GJA  C4   C3   C15  121.95  3.000
 GJA  C15  C3   C2   123.09  3.000
 GJA  C4   C3   C2   114.86  3.000
 GJA  O8   C9   C14  120.75  3.000
 GJA  C14  C9   C10  120.79  3.000
 GJA  O8   C9   C10  118.38  3.000
 GJA  H1   C10  C11  120.14  3.000
 GJA  H1   C10  C9   120.14  3.000
 GJA  C11  C10  C9   119.72  3.000
 GJA  H2   C11  C12  120.41  3.000
 GJA  H2   C11  C10  120.08  3.000
 GJA  C12  C11  C10  119.50  3.000
 GJA  O27  C12  C13  119.15  3.000
 GJA  O27  C12  C11  120.10  3.000
 GJA  C13  C12  C11  120.73  3.000
 GJA  H3   C13  C14  120.15  3.000
 GJA  H3   C13  C12  120.14  3.000
 GJA  C14  C13  C12  119.70  3.000
 GJA  H4   C14  C13  119.96  3.000
 GJA  H4   C14  C9   120.49  3.000
 GJA  C13  C14  C9   119.55  3.000
 GJA  N17  C15  O16  122.20  3.000
 GJA  N17  C15  C3   115.01  3.000
 GJA  O16  C15  C3   122.77  3.000
 GJA  H5   C19  N21  107.85  3.000
 GJA  H5   C19  C22  109.47  3.000
 GJA  N21  C19  C22  113.38  3.000
 GJA  H5   C19  C20  109.38  3.000
 GJA  C22  C19  C20  103.16  3.000
 GJA  N21  C19  C20  113.49  3.000
 GJA  H7   C20  H6   107.51  3.000
 GJA  H7   C20  N7   111.63  3.000
 GJA  H6   C20  N7   111.59  3.000
 GJA  H7   C20  C19  112.64  3.000
 GJA  H6   C20  C19  110.75  3.000
 GJA  N7   C20  C19  102.76  3.000
 GJA  H9   C22  H8   108.12  3.000
 GJA  H9   C22  C18  110.11  3.000
 GJA  H8   C22  C18  112.65  3.000
 GJA  H9   C22  C19  109.94  3.000
 GJA  H8   C22  C19  112.86  3.000
 GJA  C18  C22  C19  103.10  3.000
 GJA  H10  C30  C29  119.21  3.000
 GJA  H10  C30  C31  120.16  3.000
 GJA  C29  C30  C31  120.64  3.000
 GJA  H11  C31  C32  120.45  3.000
 GJA  H11  C31  C30  120.36  3.000
 GJA  C32  C31  C30  119.18  3.000
 GJA  H12  C32  C33  118.87  3.000
 GJA  H12  C32  C31  120.19  3.000
 GJA  C33  C32  C31  120.94  3.000
 GJA  H13  C33  C28  121.23  3.000
 GJA  H13  C33  C32  119.48  3.000
 GJA  C28  C33  C32  119.29  3.000
 GJA  C6   N1   C2   120.09  3.000
 GJA  H14  C4   C5   118.36  3.000
 GJA  H14  C4   C3   119.56  3.000
 GJA  C5   C4   C3   122.05  3.000
 GJA  H15  C5   C6   121.90  3.000
 GJA  H15  C5   C4   120.56  3.000
 GJA  C6   C5   C4   117.52  3.000
 GJA  N7   C6   C5   122.58  3.000
 GJA  N7   C6   N1   116.38  3.000
 GJA  C5   C6   N1   121.04  3.000
 GJA  C18  N7   C6   123.90  3.000
 GJA  C18  N7   C20  113.17  3.000
 GJA  C6   N7   C20  122.92  3.000
 GJA  C9   O8   C2   118.78  3.000
 GJA  H17  N17  H16  117.13  3.000
 GJA  H17  N17  C15  119.61  3.000
 GJA  H16  N17  C15  122.52  3.000
 GJA  H19  C18  H18  107.64  3.000
 GJA  H19  C18  N7   111.39  3.000
 GJA  H18  C18  N7   111.01  3.000
 GJA  H19  C18  C22  111.92  3.000
 GJA  H18  C18  C22  111.53  3.000
 GJA  N7   C18  C22  103.38  3.000
 GJA  H21  C25  C26  120.35  3.000
 GJA  H21  C25  C23  118.02  3.000
 GJA  C26  C25  C23  121.64  3.000
 GJA  H23  C26  H22  117.11  3.000
 GJA  H23  C26  C25  121.20  3.000
 GJA  H22  C26  C25  121.69  3.000
 GJA  C28  O27  C12  119.12  3.000
 GJA  C29  C28  O27  115.92  3.000
 GJA  C29  C28  C33  120.25  3.000
 GJA  O27  C28  C33  123.83  3.000
 GJA  H24  C29  C28  119.78  3.000
 GJA  H24  C29  C30  120.52  3.000
 GJA  C28  C29  C30  119.70  3.000
 GJA  H20  N21  C23  118.33  3.000
 GJA  H20  N21  C19  117.23  3.000
 GJA  C23  N21  C19  124.37  3.000
 GJA  C25  C23  O24  122.75  3.000
 GJA  C25  C23  N21  113.94  3.000
 GJA  O24  C23  N21  123.32  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
 GJA  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 GJA  CONST_02  C5   C6   N1   C2      0.00   0.0  0
 GJA  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 GJA  CONST_04  C6   N1   C2   C3      0.00   0.0  0
 GJA  CONST_05  C12  C11  C10  C9      0.00   0.0  0
 GJA  CONST_06  C12  C13  C14  C9      0.00   0.0  0
 GJA  CONST_07  C13  C14  C9   C10     0.00   0.0  0
 GJA  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 GJA  CONST_09  C14  C9   C10  C11     0.00   0.0  0
 GJA  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 GJA  CONST_11  C33  C32  C31  C30     0.00   0.0  0
 GJA  CONST_12  C33  C28  C29  C30     0.00   0.0  0
 GJA  CONST_13  C28  C33  C32  C31     0.00   0.0  0
 GJA  CONST_14  C28  C29  C30  C31     0.00   0.0  0
 GJA  CONST_15  C29  C28  C33  C32     0.00   0.0  0
 GJA  CONST_16  C29  C30  C31  C32     0.00   0.0  0
 GJA  CONST_17  C4   C5   C6   N1      0.00   0.0  0
 GJA  CONST_18  C4   C3   C2   N1      0.00   0.0  0
 GJA  CONST_19  N7   C6   N1   C2    180.00   0.0  0
 GJA  CONST_20  N7   C6   C5   C4    180.00   0.0  0
 GJA  CONST_21  O27  C12  C11  C10   180.00   0.0  0
 GJA  CONST_22  O8   C9   C10  C11   180.00   0.0  0
 GJA  CONST_23  O8   C9   C14  C13   180.00   0.0  0
 GJA  CONST_24  O27  C12  C13  C14   180.00   0.0  0
 GJA  CONST_25  C5   C4   C3   C15   180.00   0.0  0
 GJA  CONST_26  N1   C2   C3   C15   180.00   0.0  0
 GJA  CONST_27  O27  C28  C29  C30   180.00   0.0  0
 GJA  CONST_28  O27  C28  C33  C32   180.00   0.0  0
 GJA  CONST_29  O8   C2   C3   C4    180.00   0.0  0
 GJA  CONST_30  O8   C2   N1   C6    180.00   0.0  0
 GJA  CONST_31  H14  C4   C3   C2    180.00   0.0  0
 GJA  CONST_32  H15  C5   C4   C3    180.00   0.0  0
 GJA  CONST_33  H2   C11  C10  C9    180.00   0.0  0
 GJA  CONST_34  H3   C13  C14  C9    180.00   0.0  0
 GJA  CONST_35  H4   C14  C9   C10   180.00   0.0  0
 GJA  CONST_36  H1   C10  C11  C12   180.00   0.0  0
 GJA  CONST_37  H12  C32  C31  C30   180.00   0.0  0
 GJA  CONST_38  H13  C33  C32  C31   180.00   0.0  0
 GJA  CONST_39  H24  C29  C30  C31   180.00   0.0  0
 GJA  CONST_40  H10  C30  C31  C32   180.00   0.0  0
 GJA  CONST_41  H11  C31  C32  C33   180.00   0.0  0
 GJA  CONST_42  O24  C23  N21  C19     0.00   0.0  0
 GJA  CONST_43  C25  C23  N21  C19   180.00   0.0  0
 GJA  CONST_44  H16  N17  C15  C3      0.00   0.0  0
 GJA  CONST_45  H17  N17  C15  C3    180.00   0.0  0
 GJA  CONST_46  H20  N21  C23  O24   180.00   0.0  0
 GJA  Var_01    C6   N7   C20  C19  -168.34  30.0  1
 GJA  Var_02    N7   C18  C22  C19   -30.03  30.0  1
 GJA  Var_03    C5   C6   N7   C20   177.96  30.0  1
 GJA  Var_04    C22  C18  N7   C20    10.74  30.0  1
 GJA  Var_05    C10  C9   O8   C2    106.77  30.0  2
 GJA  Var_06    N1   C2   O8   C9      1.03  30.0  2
 GJA  Var_07    C33  C28  O27  C12    -2.89  30.0  2
 GJA  Var_08    O16  C15  C3   C2     32.84  30.0  2
 GJA  Var_09    C26  C25  C23  N21  -179.99  30.0  2
 GJA  Var_10    H22  C26  C25  C23     0.00   0.0  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
 GJA  chir_01  C19  C20  N21  C22  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
 GJA  plan-1  C9   0.020
 GJA  plan-1  C10  0.020
 GJA  plan-1  C11  0.020
 GJA  plan-1  C12  0.020
 GJA  plan-1  C13  0.020
 GJA  plan-1  C14  0.020
 GJA  plan-1  O8   0.020
 GJA  plan-1  O27  0.020
 GJA  plan-1  H1   0.020
 GJA  plan-1  H2   0.020
 GJA  plan-1  H3   0.020
 GJA  plan-1  H4   0.020
 GJA  plan-2  C30  0.020
 GJA  plan-2  C31  0.020
 GJA  plan-2  C32  0.020
 GJA  plan-2  C33  0.020
 GJA  plan-2  O27  0.020
 GJA  plan-2  C28  0.020
 GJA  plan-2  C29  0.020
 GJA  plan-2  H10  0.020
 GJA  plan-2  H11  0.020
 GJA  plan-2  H12  0.020
 GJA  plan-2  H13  0.020
 GJA  plan-2  H24  0.020
 GJA  plan-3  C2   0.020
 GJA  plan-3  C3   0.020
 GJA  plan-3  C15  0.020
 GJA  plan-3  N1   0.020
 GJA  plan-3  C4   0.020
 GJA  plan-3  C5   0.020
 GJA  plan-3  C6   0.020
 GJA  plan-3  N7   0.020
 GJA  plan-3  O8   0.020
 GJA  plan-3  H14  0.020
 GJA  plan-3  H15  0.020
 GJA  plan-4  C19  0.020
 GJA  plan-4  O24  0.020
 GJA  plan-4  C25  0.020
 GJA  plan-4  H20  0.020
 GJA  plan-4  N21  0.020
 GJA  plan-4  C23  0.020
 GJA  plan-5  C3   0.020
 GJA  plan-5  C15  0.020
 GJA  plan-5  O16  0.020
 GJA  plan-5  N17  0.020
 GJA  plan-5  H16  0.020
 GJA  plan-5  H17  0.020
 GJA  plan-6  C25  0.020
 GJA  plan-6  C26  0.020
 GJA  plan-6  H21  0.020
 GJA  plan-6  H22  0.020
 GJA  plan-6  H23  0.020
 GJA  plan-6  C23  0.020

