# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 04:04:32 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: ~{N}-[4-[chloranyl-bis(fluoranyl)methoxy]phenyl]-6-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-5-(1~{H}-pyrazol-5-yl)pyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCN(C1)c2ncc(cc2c3[nH]ncc3)C(=O)Nc4ccc(OC(F)(F)Cl)cc4
#
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
 AY7  AY7  ~{N}-[4-[chloranyl-bis(fluoranyl)methoxy]phenyl]-6-[(3~{R})-3-oxidanylpyrrolidin-1-yl]-5-(1~{H}-pyrazol-5-yl)pyridine-3-carboxamide  ligand  49  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AY7
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
 AY7  C1   C   CR6   0   0.514   3.8570  -0.5626  -0.2163
 AY7  C3   C   CH2   0  -0.272   5.3594  -2.4473  -0.5553
 AY7  C11  C   CR6   0  -0.062   3.5298   0.7835   0.1227
 AY7  C12  C   CR5   0   0.344   4.5159   1.8236   0.4315
 AY7  C16  C   CR6   0   0.394  -2.5111  -0.2065  -0.4101
 AY7  C17  C   CR16  0  -0.307  -3.1845   0.9103  -0.9079
 AY7  C18  C   CR16  0  -0.290  -4.5706   0.9227  -0.9486
 AY7  C19  C   CR6   0   0.305  -5.2875  -0.1714  -0.5020
 AY7  C20  C   CR16  0  -0.286  -4.6375  -1.2946  -0.0220
 AY7  C21  C   CR16  0  -0.353  -3.2554  -1.3067   0.0213
 AY7  C26  C   CR15  0  -0.095   5.7477   3.4710   1.2148
 AY7  C27  C   CR15  0  -0.493   4.6626   2.6393   1.5335
 AY7  C28  C   CT    0   0.846  -7.3640   0.3020   0.4506
 AY7  N2   N   NR5   0  -0.505   5.0891  -1.0939  -0.0905
 AY7  C4   C   CR15  0   0.019   6.8249  -2.6544  -0.1934
 AY7  C5   C   CH2   0  -0.501   6.9547  -1.8599   1.1006
 AY7  C6   C   CH2   0  -0.297   6.1460  -0.6074   0.8001
 AY7  N7   N   N     0  -0.466   2.9201  -1.3848  -0.7051
 AY7  C8   C   CR16  0  -0.070   1.6613  -0.9995  -0.7526
 AY7  C9   C   CR6   0  -0.177   1.2125   0.2414  -0.3161
 AY7  C10  C   CR16  0  -0.173   2.1998   1.1433   0.0832
 AY7  N14  N   NH1   0  -0.768  -1.1212  -0.3174  -0.3498
 AY7  O15  O   O     0  -0.463  -0.4944   1.8680  -0.3927
 AY7  O22  O   O2    0  -0.498  -6.6786  -0.1723  -0.6002
 AY7  O23  O   OH1   0  -0.666   7.0952  -4.0269  -0.0934
 AY7  N24  N   NR15  0  -0.473   5.4715   2.2083  -0.4384
 AY7  N25  N   N     0  -0.264   6.2296   3.1986   0.0156
 AY7  F29  F   F     0  -0.291  -7.1085  -0.3829   1.5723
 AY7  F30  F   F     0  -0.291  -7.0622   1.5785   0.7186
 AY7  CL   CL  CL    0  -0.104  -9.0752   0.1850   0.0856
 AY7  H1   H   HCH2  0   0.235   4.7386  -3.1837  -0.0335
 AY7  H2   H   HCH2  0   0.253   5.1665  -2.5450  -1.6242
 AY7  H3   H   HCR6  0   0.286  -2.6482   1.7699  -1.2731
 AY7  H4   H   HCR6  0   0.282  -5.0800   1.7875  -1.3523
 AY7  H5   H   HCR6  0   0.284  -5.1935  -2.1619   0.3077
 AY7  H6   H   HCR6  0   0.282  -2.7487  -2.1855   0.4005
 AY7  H7   H   HCR5  0   0.261   6.1924   4.2494   1.8160
 AY7  H8   H   HCR5  0   0.265   4.0786   2.6172   2.4384
 AY7  H9   H   HCR5  0   0.218   7.4532  -2.1844  -0.9628
 AY7  H10  H   HCH2  0   0.242   6.4996  -2.4232   1.9195
 AY7  H11  H   HCH2  0   0.258   7.9845  -1.6276   1.3721
 AY7  H12  H   HCH2  0   0.246   6.7689   0.1425   0.3072
 AY7  H13  H   HCH2  0   0.264   5.7302  -0.1576   1.7009
 AY7  H14  H   HCR6  0   0.266   0.9763  -1.7226  -1.1858
 AY7  H15  H   HCR6  0   0.269   1.9263   2.1572   0.3466
 AY7  H16  H   HNH1  0   0.421  -0.7834  -1.2421  -0.1309
 AY7  H17  H   HOH1  0   0.456   8.0446  -4.1410   0.0102
 AY7  H18  H   HNR5  0   0.419   5.6338   1.8392  -1.3624
 AY7  C13  C   C     0   0.535  -0.1985   0.6855  -0.3606

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
 AY7  F30  C28  single    1.339  0.020  1.339
 AY7  CL   C28  single    1.754  0.020  1.754
 AY7  F29  C28  single    1.339  0.020  1.339
 AY7  C28  O22  single    1.341  0.020  1.341
 AY7  O22  C19  single    1.395  0.020  1.395
 AY7  C19  C18  aromatic  1.382  0.020  1.382
 AY7  C19  C20  aromatic  1.384  0.020  1.384
 AY7  C18  C17  aromatic  1.387  0.020  1.387
 AY7  C20  C21  aromatic  1.383  0.020  1.383
 AY7  C17  C16  aromatic  1.396  0.020  1.396
 AY7  C21  C16  aromatic  1.397  0.020  1.397
 AY7  C16  N14  single    1.396  0.020  1.396
 AY7  C26  C27  aromatic  1.404  0.020  1.404
 AY7  C26  N25  aromatic  1.321  0.020  1.321
 AY7  C27  C12  aromatic  1.379  0.020  1.379
 AY7  N14  C13  single    1.363  0.020  1.363
 AY7  O15  C13  double    1.219  0.020  1.219
 AY7  C13  C9   single    1.480  0.020  1.480
 AY7  N25  N24  aromatic  1.327  0.020  1.327
 AY7  C10  C9   aromatic  1.396  0.020  1.396
 AY7  C10  C11  aromatic  1.378  0.020  1.378
 AY7  C12  N24  aromatic  1.348  0.020  1.348
 AY7  C12  C11  single    1.466  0.020  1.466
 AY7  C9   C8   aromatic  1.390  0.020  1.390
 AY7  C11  C1   aromatic  1.426  0.020  1.426
 AY7  C8   N7   aromatic  1.317  0.020  1.317
 AY7  C1   N7   aromatic  1.339  0.020  1.339
 AY7  C1   N2   single    1.348  0.020  1.348
 AY7  C3   N2   single    1.456  0.020  1.456
 AY7  C3   C4   single    1.524  0.020  1.524
 AY7  N2   C6   single    1.465  0.020  1.465
 AY7  C6   C5   single    1.521  0.020  1.521
 AY7  C4   O23  single    1.402  0.020  1.402
 AY7  C4   C5   single    1.524  0.020  1.524
 AY7  C3   H1   single    0.970  0.020  1.090
 AY7  C3   H2   single    0.970  0.020  1.090
 AY7  C17  H3   single    0.930  0.020  1.080
 AY7  C18  H4   single    0.930  0.020  1.080
 AY7  C20  H5   single    0.930  0.020  1.080
 AY7  C21  H6   single    0.930  0.020  1.080
 AY7  C26  H7   single    0.930  0.020  1.080
 AY7  C27  H8   single    0.930  0.020  1.080
 AY7  C4   H9   single    0.970  0.020  1.090
 AY7  C5   H10  single    0.970  0.020  1.090
 AY7  C5   H11  single    0.970  0.020  1.090
 AY7  C6   H12  single    0.970  0.020  1.090
 AY7  C6   H13  single    0.970  0.020  1.090
 AY7  C8   H14  single    0.930  0.020  1.080
 AY7  C10  H15  single    0.930  0.020  1.080
 AY7  N14  H16  single    0.860  0.020  1.020
 AY7  O23  H17  single    0.850  0.020  0.980
 AY7  N24  H18  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
 AY7  N7   C1   N2   115.58  3.000
 AY7  N2   C1   C11  124.03  3.000
 AY7  N7   C1   C11  120.39  3.000
 AY7  H2   C3   H1   107.84  3.000
 AY7  H2   C3   C4   113.00  3.000
 AY7  H1   C3   C4   109.91  3.000
 AY7  H2   C3   N2   111.31  3.000
 AY7  H1   C3   N2   111.57  3.000
 AY7  C4   C3   N2   103.24  3.000
 AY7  C10  C11  C12  118.03  3.000
 AY7  C12  C11  C1   124.42  3.000
 AY7  C10  C11  C1   117.44  3.000
 AY7  N24  C12  C27  105.74  3.000
 AY7  N24  C12  C11  122.91  3.000
 AY7  C27  C12  C11  131.27  3.000
 AY7  N14  C16  C21  117.05  3.000
 AY7  N14  C16  C17  124.02  3.000
 AY7  C21  C16  C17  118.90  3.000
 AY7  H3   C17  C18  118.72  3.000
 AY7  H3   C17  C16  121.29  3.000
 AY7  C18  C17  C16  119.99  3.000
 AY7  H4   C18  C19  120.60  3.000
 AY7  H4   C18  C17  119.26  3.000
 AY7  C19  C18  C17  120.12  3.000
 AY7  O22  C19  C20  119.51  3.000
 AY7  C20  C19  C18  120.73  3.000
 AY7  O22  C19  C18  119.68  3.000
 AY7  H5   C20  C21  119.82  3.000
 AY7  H5   C20  C19  121.00  3.000
 AY7  C21  C20  C19  119.17  3.000
 AY7  H6   C21  C20  119.05  3.000
 AY7  H6   C21  C16  119.87  3.000
 AY7  C20  C21  C16  121.07  3.000
 AY7  H7   C26  N25  120.27  3.000
 AY7  H7   C26  C27  128.26  3.000
 AY7  N25  C26  C27  111.46  3.000
 AY7  H8   C27  C26  128.45  3.000
 AY7  H8   C27  C12  126.98  3.000
 AY7  C26  C27  C12  104.56  3.000
 AY7  CL   C28  F30  108.98  3.000
 AY7  CL   C28  F29  109.05  3.000
 AY7  F30  C28  F29  106.08  3.000
 AY7  F29  C28  O22  112.21  3.000
 AY7  CL   C28  O22  108.18  3.000
 AY7  F30  C28  O22  112.26  3.000
 AY7  C6   N2   C3   111.64  3.000
 AY7  C6   N2   C1   125.83  3.000
 AY7  C3   N2   C1   120.41  3.000
 AY7  H9   C4   O23  111.00  3.000
 AY7  H9   C4   C5   108.83  3.000
 AY7  O23  C4   C5   115.67  3.000
 AY7  H9   C4   C3   108.99  3.000
 AY7  C5   C4   C3   102.28  3.000
 AY7  O23  C4   C3   109.59  3.000
 AY7  H11  C5   H10  108.45  3.000
 AY7  H11  C5   C6   112.09  3.000
 AY7  H10  C5   C6   110.55  3.000
 AY7  H11  C5   C4   113.77  3.000
 AY7  H10  C5   C4   109.38  3.000
 AY7  C6   C5   C4   102.49  3.000
 AY7  H13  C6   H12  107.89  3.000
 AY7  H13  C6   C5   112.31  3.000
 AY7  H12  C6   C5   110.56  3.000
 AY7  H13  C6   N2   111.37  3.000
 AY7  H12  C6   N2   111.41  3.000
 AY7  C5   C6   N2   103.31  3.000
 AY7  C8   N7   C1   120.15  3.000
 AY7  H14  C8   C9   121.06  3.000
 AY7  H14  C8   N7   114.98  3.000
 AY7  C9   C8   N7   123.94  3.000
 AY7  C10  C9   C8   116.00  3.000
 AY7  C8   C9   C13  124.50  3.000
 AY7  C10  C9   C13  119.29  3.000
 AY7  H15  C10  C9   119.74  3.000
 AY7  H15  C10  C11  118.76  3.000
 AY7  C9   C10  C11  121.48  3.000
 AY7  H16  N14  C16  114.57  3.000
 AY7  H16  N14  C13  116.73  3.000
 AY7  C16  N14  C13  127.98  3.000
 AY7  C28  O22  C19  117.02  3.000
 AY7  H17  O23  C4   108.30  3.000
 AY7  H18  N24  N25  119.65  3.000
 AY7  H18  N24  C12  126.93  3.000
 AY7  N25  N24  C12  113.40  3.000
 AY7  N24  N25  C26  104.83  3.000
 AY7  O15  C13  N14  123.34  3.000
 AY7  O15  C13  C9   121.55  3.000
 AY7  N14  C13  C9   115.12  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
 AY7  CONST_01  C9   C10  C11  C1      0.00   0.0  0
 AY7  CONST_04  C9   C8   N7   C1      0.00   0.0  0
 AY7  CONST_05  C8   C9   C10  C11     0.00   0.0  0
 AY7  CONST_06  C26  C27  C12  C11   180.00   0.0  0
 AY7  CONST_07  N25  N24  C12  C11   180.00   0.0  0
 AY7  CONST_08  C8   N7   C1   C11     0.00   0.0  0
 AY7  CONST_09  N25  C26  C27  C12     0.00   0.0  0
 AY7  CONST_10  C26  N25  N24  C12     0.00   0.0  0
 AY7  CONST_11  C9   C10  C11  C12   180.00   0.0  0
 AY7  CONST_12  N7   C1   C11  C12   180.00   0.0  0
 AY7  CONST_13  C19  C18  C17  C16     0.00   0.0  0
 AY7  CONST_14  C19  C20  C21  C16     0.00   0.0  0
 AY7  CONST_15  C20  C19  C18  C17     0.00   0.0  0
 AY7  CONST_16  C20  C21  C16  C17     0.00   0.0  0
 AY7  CONST_17  C21  C20  C19  C18     0.00   0.0  0
 AY7  CONST_18  C21  C16  C17  C18     0.00   0.0  0
 AY7  CONST_19  N24  C12  C27  C26     0.00   0.0  0
 AY7  CONST_20  N24  N25  C26  C27     0.00   0.0  0
 AY7  CONST_21  N25  N24  C12  C27     0.00   0.0  0
 AY7  CONST_23  C10  C9   C8   N7      0.00   0.0  0
 AY7  CONST_24  C10  C11  C1   N7      0.00   0.0  0
 AY7  CONST_26  N2   C1   C11  C12     0.00   0.0  0
 AY7  CONST_27  C10  C11  C1   N2    180.00   0.0  0
 AY7  CONST_28  C8   N7   C1   N2    180.00   0.0  0
 AY7  CONST_29  C13  C9   C10  C11   180.00   0.0  0
 AY7  CONST_30  N7   C8   C9   C13   180.00   0.0  0
 AY7  CONST_31  O22  C19  C18  C17   180.00   0.0  0
 AY7  CONST_32  N14  C16  C17  C18   180.00   0.0  0
 AY7  CONST_33  N14  C16  C21  C20   180.00   0.0  0
 AY7  CONST_34  O22  C19  C20  C21   180.00   0.0  0
 AY7  CONST_35  H15  C10  C11  C1    180.00   0.0  0
 AY7  CONST_36  H14  C8   N7   C1    180.00   0.0  0
 AY7  CONST_37  H8   C27  C12  C11     0.00   0.0  0
 AY7  CONST_38  H18  N24  C12  C11     0.00   0.0  0
 AY7  CONST_39  H7   C26  C27  C12   180.00   0.0  0
 AY7  CONST_40  H4   C18  C17  C16   180.00   0.0  0
 AY7  CONST_41  H5   C20  C21  C16   180.00   0.0  0
 AY7  CONST_42  H6   C21  C16  C17   180.00   0.0  0
 AY7  CONST_43  H3   C17  C18  C19   180.00   0.0  0
 AY7  CONST_44  C9   C13  N14  C16   180.00   0.0  0
 AY7  CONST_47  H16  N14  C16  C17   180.00   0.0  0
 AY7  CONST_48  O15  C13  N14  C16     0.00   0.0  0
 AY7  Var_01    C4   C3   N2   C1   -178.50  30.0  1
 AY7  Var_02    C5   C6   N2   C1    151.67  30.0  1
 AY7  Var_03    C11  C1   N2   C3   -175.31  30.0  1
 AY7  Var_04    C4   C5   C6   N2     32.60  30.0  1
 AY7  Var_05    N14  C13  C9   C8     25.01  30.0  2
 AY7  Var_06    F30  C28  O22  C19    60.05  30.0  3

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
 AY7  chir_01  C4  C3  O23  C5  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
 AY7  plan-1  C11  0.020
 AY7  plan-1  C12  0.020
 AY7  plan-1  C26  0.020
 AY7  plan-1  C27  0.020
 AY7  plan-1  N24  0.020
 AY7  plan-1  N25  0.020
 AY7  plan-1  H7   0.020
 AY7  plan-1  H8   0.020
 AY7  plan-1  H18  0.020
 AY7  plan-2  C16  0.020
 AY7  plan-2  C17  0.020
 AY7  plan-2  C18  0.020
 AY7  plan-2  C19  0.020
 AY7  plan-2  C20  0.020
 AY7  plan-2  C21  0.020
 AY7  plan-2  N14  0.020
 AY7  plan-2  O22  0.020
 AY7  plan-2  H3   0.020
 AY7  plan-2  H4   0.020
 AY7  plan-2  H5   0.020
 AY7  plan-2  H6   0.020
 AY7  plan-3  C1   0.020
 AY7  plan-3  C11  0.020
 AY7  plan-3  C12  0.020
 AY7  plan-3  N2   0.020
 AY7  plan-3  N7   0.020
 AY7  plan-3  C8   0.020
 AY7  plan-3  C9   0.020
 AY7  plan-3  C10  0.020
 AY7  plan-3  H14  0.020
 AY7  plan-3  H15  0.020
 AY7  plan-3  C13  0.020
 AY7  plan-4  C16  0.020
 AY7  plan-4  C9   0.020
 AY7  plan-4  N14  0.020
 AY7  plan-4  O15  0.020
 AY7  plan-4  H16  0.020
 AY7  plan-4  C13  0.020

