# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 11:54:01 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: N-[2-(5-chloro-2-fluorophenyl)pyridin-4-yl]-2-[(piperidin-4-yl)methyl]-2H-pyrazolo[4,3-b]pyridin-7-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(Cl)cc1c2cc(Nc3ccnc4cn(CC5CCNCC5)nc34)ccn2
#
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
 8LY  8LY  N-[2-(5-chloro-2-fluorophenyl)pyridin-4-yl]-2-[(piperidin-4-yl)methyl]-2H-pyrazolo[4,3-b]pyridin-7-amine  ligand  53  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_8LY
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
 8LY  C4   C   CR16  0  -0.200   5.9645   2.6070  -0.2534
 8LY  C5   C   CR6   0  -0.043   4.8173   2.6065  -1.0307
 8LY  C7   C   CR16  0  -0.225   3.9691   1.5126  -1.0525
 8LY  C8   C   CR6   0  -0.151   4.2559   0.3822  -0.2903
 8LY  C10  C   CR16  0  -0.429   1.9816  -0.5956  -0.1985
 8LY  N12  N   NH1   0  -0.795  -0.2298  -1.4842  -0.1617
 8LY  C13  C   CR6   0   0.438  -1.2226  -2.3421   0.2308
 8LY  C15  C   CR16  0  -0.110  -2.2238  -4.2925   1.2747
 8LY  C17  C   CR56  0  -0.041  -3.6257  -2.8011   0.3873
 8LY  C20  C   CH2   0  -0.270  -5.1553   0.0376  -1.2115
 8LY  C21  C   CH1   0  -0.267  -4.9901   1.3720  -0.4962
 8LY  C22  C   CH2   0  -0.416  -5.8815   2.4244  -1.1542
 8LY  C26  C   CH2   0  -0.418  -5.2979   1.2872   0.9958
 8LY  C28  C   CR56  0   0.157  -2.5656  -1.9666  -0.0349
 8LY  C2   C   CR6   0   0.539   5.4080   0.4041   0.4861
 8LY  C3   C   CR16  0  -0.414   6.2579   1.4919   0.5153
 8LY  CL6  CL  CL    0  -0.122   4.4402   3.9922  -1.9989
 8LY  C9   C   CR6   0   0.231   3.3486  -0.7865  -0.3195
 8LY  C11  C   CR6   0   0.481   1.1267  -1.7000  -0.2476
 8LY  C14  C   CR16  0  -0.413  -1.0829  -3.5350   0.9087
 8LY  N16  N   N     0  -0.437  -3.4704  -3.9745   1.0404
 8LY  C18  C   CR15  0  -0.001  -4.7666  -2.1209  -0.0325
 8LY  N19  N   NR5   0  -0.252  -4.3290  -1.0078  -0.6359
 8LY  C23  C   CH2   0  -0.291  -5.7593   3.7555  -0.4271
 8LY  N24  N   NH1   0  -0.598  -6.1026   3.5881   0.9734
 8LY  C25  C   CH2   0  -0.297  -5.2028   2.6638   1.6394
 8LY  N27  N   N     0  -0.319  -3.0120  -0.8786  -0.6591
 8LY  C29  C   CR16  0  -0.395   1.7098  -2.9546  -0.4275
 8LY  C30  C   CR16  0  -0.089   3.0883  -3.0289  -0.5262
 8LY  N31  N   N     0  -0.429   3.9063  -1.9873  -0.4713
 8LY  H1   H   HCR6  0   0.293   6.6242   3.4633  -0.2393
 8LY  H2   H   HCR6  0   0.291   3.0850   1.5217  -1.6766
 8LY  H3   H   HCR6  0   0.286   1.5794   0.3982  -0.0456
 8LY  H4   H   HNH1  0   0.415  -0.5369  -0.5457  -0.3735
 8LY  H5   H   HCR6  0   0.258  -2.0519  -5.2221   1.8076
 8LY  H6   H   HCH2  0   0.258  -6.1889  -0.3053  -1.1559
 8LY  H7   H   HCH2  0   0.276  -4.8934   0.1359  -2.2664
 8LY  H8   H   HCH1  0   0.237  -3.9482   1.6927  -0.6142
 8LY  H9   H   HCH2  0   0.233  -5.6071   2.5534  -2.2045
 8LY  H10  H   HCH2  0   0.217  -6.9249   2.0930  -1.1305
 8LY  H11  H   HCH2  0   0.215  -6.3080   0.8899   1.1435
 8LY  H12  H   HCH2  0   0.234  -4.6062   0.6063   1.4979
 8LY  H13  H   HCR6  0   0.293   7.1411   1.4736   1.1401
 8LY  H14  H   HCR6  0   0.281  -0.1172  -3.9145   1.2058
 8LY  H15  H   HCR5  0   0.302  -5.8155  -2.3510   0.0566
 8LY  H16  H   HCH2  0   0.186  -4.7342   4.1377  -0.5678
 8LY  H17  H   HCH2  0   0.232  -6.4347   4.4883  -0.8729
 8LY  H18  H   HNH1  0   0.353  -6.0699   4.4860   1.4378
 8LY  H20  H   HCH2  0   0.235  -5.4785   2.5990   2.6938
 8LY  H21  H   HCH2  0   0.195  -4.1519   2.9976   1.6044
 8LY  H22  H   HCR6  0   0.303   1.1231  -3.8552  -0.5273
 8LY  H23  H   HCR6  0   0.275   3.5526  -3.9979  -0.6719
 8LY  F1   F   F     0  -0.294   5.6957  -0.6447   1.2636

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
 8LY  N16  C15  aromatic  1.308  0.020  1.308
 8LY  N16  C17  aromatic  1.352  0.020  1.352
 8LY  C15  C14  aromatic  1.418  0.020  1.418
 8LY  C18  C17  aromatic  1.393  0.020  1.393
 8LY  C18  N19  aromatic  1.340  0.020  1.340
 8LY  C17  C28  aromatic  1.414  0.020  1.414
 8LY  N19  C20  single    1.452  0.020  1.452
 8LY  N19  N27  aromatic  1.324  0.020  1.324
 8LY  C14  C13  aromatic  1.379  0.020  1.379
 8LY  C20  C21  single    1.523  0.020  1.523
 8LY  C3   C4   aromatic  1.386  0.020  1.386
 8LY  C3   C2   aromatic  1.381  0.020  1.381
 8LY  C28  C13  aromatic  1.420  0.020  1.420
 8LY  C28  N27  aromatic  1.331  0.020  1.331
 8LY  F1   C2   single    1.337  0.020  1.337
 8LY  C4   C5   aromatic  1.386  0.020  1.386
 8LY  C13  N12  single    1.370  0.020  1.370
 8LY  C2   C8   aromatic  1.389  0.020  1.389
 8LY  C5   CL6  single    1.732  0.020  1.732
 8LY  C5   C7   aromatic  1.384  0.020  1.384
 8LY  C21  C22  single    1.528  0.020  1.528
 8LY  C21  C26  single    1.526  0.020  1.526
 8LY  C22  C23  single    1.522  0.020  1.522
 8LY  C8   C7   aromatic  1.393  0.020  1.393
 8LY  C8   C9   single    1.480  0.020  1.480
 8LY  C10  C9   aromatic  1.386  0.020  1.386
 8LY  C10  C11  aromatic  1.397  0.020  1.397
 8LY  N12  C11  single    1.376  0.020  1.376
 8LY  C26  C25  single    1.523  0.020  1.523
 8LY  C9   N31  aromatic  1.333  0.020  1.333
 8LY  C11  C29  aromatic  1.395  0.020  1.395
 8LY  C23  N24  single    1.452  0.020  1.452
 8LY  C25  N24  single    1.452  0.020  1.452
 8LY  N31  C30  aromatic  1.326  0.020  1.326
 8LY  C29  C30  aromatic  1.384  0.020  1.384
 8LY  C4   H1   single    0.930  0.020  1.080
 8LY  C7   H2   single    0.930  0.020  1.080
 8LY  C10  H3   single    0.930  0.020  1.080
 8LY  N12  H4   single    0.860  0.020  1.020
 8LY  C15  H5   single    0.930  0.020  1.080
 8LY  C20  H6   single    0.970  0.020  1.090
 8LY  C20  H7   single    0.970  0.020  1.090
 8LY  C21  H8   single    0.970  0.020  1.090
 8LY  C22  H9   single    0.970  0.020  1.090
 8LY  C22  H10  single    0.970  0.020  1.090
 8LY  C26  H11  single    0.970  0.020  1.090
 8LY  C26  H12  single    0.970  0.020  1.090
 8LY  C3   H13  single    0.930  0.020  1.080
 8LY  C14  H14  single    0.930  0.020  1.080
 8LY  C18  H15  single    0.930  0.020  1.080
 8LY  C23  H16  single    0.970  0.020  1.090
 8LY  C23  H17  single    0.970  0.020  1.090
 8LY  N24  H18  single    0.890  0.020  1.040
 8LY  C25  H20  single    0.970  0.020  1.090
 8LY  C25  H21  single    0.970  0.020  1.090
 8LY  C29  H22  single    0.930  0.020  1.080
 8LY  C30  H23  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
 8LY  H1   C4   C3   120.06  3.000
 8LY  H1   C4   C5   120.85  3.000
 8LY  C3   C4   C5   119.09  3.000
 8LY  CL6  C5   C7   119.34  3.000
 8LY  C7   C5   C4   121.09  3.000
 8LY  CL6  C5   C4   119.57  3.000
 8LY  H2   C7   C8   119.38  3.000
 8LY  H2   C7   C5   120.19  3.000
 8LY  C8   C7   C5   120.42  3.000
 8LY  C9   C8   C2   122.13  3.000
 8LY  C9   C8   C7   120.25  3.000
 8LY  C2   C8   C7   117.62  3.000
 8LY  H3   C10  C11  120.20  3.000
 8LY  H3   C10  C9   120.35  3.000
 8LY  C11  C10  C9   119.44  3.000
 8LY  H4   N12  C11  115.61  3.000
 8LY  H4   N12  C13  114.95  3.000
 8LY  C11  N12  C13  129.36  3.000
 8LY  C14  C13  C28  114.62  3.000
 8LY  C28  C13  N12  117.81  3.000
 8LY  C14  C13  N12  127.54  3.000
 8LY  H5   C15  N16  116.57  3.000
 8LY  H5   C15  C14  117.20  3.000
 8LY  N16  C15  C14  126.23  3.000
 8LY  C18  C17  N16  131.56  3.000
 8LY  C18  C17  C28  103.65  3.000
 8LY  N16  C17  C28  124.79  3.000
 8LY  H7   C20  H6   107.77  3.000
 8LY  H7   C20  N19  108.15  3.000
 8LY  H6   C20  N19  107.03  3.000
 8LY  H7   C20  C21  110.42  3.000
 8LY  H6   C20  C21  110.76  3.000
 8LY  N19  C20  C21  112.52  3.000
 8LY  H8   C21  C26  108.25  3.000
 8LY  H8   C21  C22  107.85  3.000
 8LY  C26  C21  C22  109.98  3.000
 8LY  H8   C21  C20  107.99  3.000
 8LY  C26  C21  C20  112.87  3.000
 8LY  C22  C21  C20  109.75  3.000
 8LY  H10  C22  H9   107.20  3.000
 8LY  H10  C22  C23  109.32  3.000
 8LY  H9   C22  C23  109.61  3.000
 8LY  H10  C22  C21  109.76  3.000
 8LY  H9   C22  C21  110.40  3.000
 8LY  C23  C22  C21  110.48  3.000
 8LY  H12  C26  H11  107.21  3.000
 8LY  H12  C26  C25  109.24  3.000
 8LY  H11  C26  C25  109.18  3.000
 8LY  H12  C26  C21  110.87  3.000
 8LY  H11  C26  C21  109.76  3.000
 8LY  C25  C26  C21  110.51  3.000
 8LY  N27  C28  C17  111.78  3.000
 8LY  N27  C28  C13  128.39  3.000
 8LY  C17  C28  C13  119.83  3.000
 8LY  C3   C2   F1   118.25  3.000
 8LY  F1   C2   C8   119.41  3.000
 8LY  C3   C2   C8   122.32  3.000
 8LY  H13  C3   C2   120.09  3.000
 8LY  H13  C3   C4   120.45  3.000
 8LY  C2   C3   C4   119.46  3.000
 8LY  N31  C9   C10  123.16  3.000
 8LY  N31  C9   C8   117.21  3.000
 8LY  C10  C9   C8   119.63  3.000
 8LY  C29  C11  N12  124.12  3.000
 8LY  C29  C11  C10  117.36  3.000
 8LY  N12  C11  C10  118.48  3.000
 8LY  H14  C14  C15  117.46  3.000
 8LY  H14  C14  C13  122.01  3.000
 8LY  C15  C14  C13  120.51  3.000
 8LY  C17  N16  C15  114.02  3.000
 8LY  H15  C18  N19  122.18  3.000
 8LY  H15  C18  C17  131.92  3.000
 8LY  N19  C18  C17  105.90  3.000
 8LY  N27  N19  C18  114.46  3.000
 8LY  N27  N19  C20  119.29  3.000
 8LY  C18  N19  C20  126.23  3.000
 8LY  H17  C23  H16  106.88  3.000
 8LY  H17  C23  N24  108.96  3.000
 8LY  H16  C23  N24  112.51  3.000
 8LY  H17  C23  C22  110.02  3.000
 8LY  H16  C23  C22  108.47  3.000
 8LY  N24  C23  C22  109.95  3.000
 8LY  H18  N24  C25  109.54  3.000
 8LY  H18  N24  C23  109.45  3.000
 8LY  C25  N24  C23  111.68  3.000
 8LY  H21  C25  H20  106.80  3.000
 8LY  H21  C25  N24  112.53  3.000
 8LY  H20  C25  N24  108.92  3.000
 8LY  H21  C25  C26  108.64  3.000
 8LY  H20  C25  C26  109.81  3.000
 8LY  N24  C25  C26  110.06  3.000
 8LY  N19  N27  C28  104.22  3.000
 8LY  H22  C29  C30  119.34  3.000
 8LY  H22  C29  C11  122.34  3.000
 8LY  C30  C29  C11  118.28  3.000
 8LY  H23  C30  N31  116.33  3.000
 8LY  H23  C30  C29  118.95  3.000
 8LY  N31  C30  C29  124.71  3.000
 8LY  C30  N31  C9   117.04  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
 8LY  CONST_01  C8   C2   C3   C4      0.00   0.0  0
 8LY  CONST_02  C8   C7   C5   C4      0.00   0.0  0
 8LY  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 8LY  CONST_04  C2   C8   C7   C5      0.00   0.0  0
 8LY  CONST_05  C9   C8   C7   C5    180.00   0.0  0
 8LY  CONST_06  C3   C4   C5   C7      0.00   0.0  0
 8LY  CONST_07  C3   C2   C8   C7      0.00   0.0  0
 8LY  CONST_10  C11  C10  C9   C8    180.00   0.0  0
 8LY  CONST_11  C30  N31  C9   C8    180.00   0.0  0
 8LY  CONST_13  C30  N31  C9   C10     0.00   0.0  0
 8LY  CONST_14  C30  C29  C11  C10     0.00   0.0  0
 8LY  CONST_15  N16  C15  C14  C13     0.00   0.0  0
 8LY  CONST_16  N16  C17  C28  C13     0.00   0.0  0
 8LY  CONST_17  C18  C17  C28  C13   180.00   0.0  0
 8LY  CONST_18  N19  N27  C28  C13   180.00   0.0  0
 8LY  CONST_19  C18  C17  N16  C15   180.00   0.0  0
 8LY  CONST_20  C28  C17  N16  C15     0.00   0.0  0
 8LY  CONST_21  C28  C13  C14  C15     0.00   0.0  0
 8LY  CONST_22  C14  C15  N16  C17     0.00   0.0  0
 8LY  CONST_23  N27  N19  C18  C17     0.00   0.0  0
 8LY  CONST_24  C14  C13  C28  C17     0.00   0.0  0
 8LY  CONST_25  N19  N27  C28  C17     0.00   0.0  0
 8LY  CONST_26  N19  C18  C17  C28     0.00   0.0  0
 8LY  CONST_27  C18  N19  N27  C28     0.00   0.0  0
 8LY  CONST_29  C9   C8   C2   C3    180.00   0.0  0
 8LY  CONST_30  C29  C11  C10  C9      0.00   0.0  0
 8LY  CONST_31  C29  C30  N31  C9      0.00   0.0  0
 8LY  CONST_32  N31  C9   C10  C11     0.00   0.0  0
 8LY  CONST_33  N31  C30  C29  C11     0.00   0.0  0
 8LY  CONST_34  N27  C28  C13  C14   180.00   0.0  0
 8LY  CONST_35  N19  C18  C17  N16   180.00   0.0  0
 8LY  CONST_36  N27  C28  C17  N16   180.00   0.0  0
 8LY  CONST_37  N27  C28  C17  C18     0.00   0.0  0
 8LY  CONST_38  F1   C2   C3   C4    180.00   0.0  0
 8LY  CONST_39  F1   C2   C8   C7    180.00   0.0  0
 8LY  CONST_40  CL6  C5   C7   C8    180.00   0.0  0
 8LY  CONST_41  C15  C14  C13  N12   180.00   0.0  0
 8LY  CONST_42  C17  C28  C13  N12   180.00   0.0  0
 8LY  CONST_43  N27  C28  C13  N12     0.00   0.0  0
 8LY  CONST_44  C9   C10  C11  N12   180.00   0.0  0
 8LY  CONST_45  C30  C29  C11  N12   180.00   0.0  0
 8LY  CONST_46  C20  N19  C18  C17   180.00   0.0  0
 8LY  CONST_47  C28  N27  N19  C20   180.00   0.0  0
 8LY  CONST_48  C9   C8   C2   F1      0.00   0.0  0
 8LY  CONST_49  CL6  C5   C4   C3    180.00   0.0  0
 8LY  CONST_50  H2   C7   C5   C4    180.00   0.0  0
 8LY  CONST_51  H13  C3   C4   C5    180.00   0.0  0
 8LY  CONST_52  H1   C4   C5   C7    180.00   0.0  0
 8LY  CONST_53  H3   C10  C9   C8      0.00   0.0  0
 8LY  CONST_54  H22  C29  C11  C10   180.00   0.0  0
 8LY  CONST_55  H5   C15  C14  C13   180.00   0.0  0
 8LY  CONST_56  H15  C18  C17  C28   180.00   0.0  0
 8LY  CONST_57  H14  C14  C13  C28   180.00   0.0  0
 8LY  CONST_58  H23  C30  N31  C9    180.00   0.0  0
 8LY  Var_01    N24  C23  C22  C21   -57.27  30.0  1
 8LY  Var_02    N24  C25  C26  C21    57.00  30.0  1
 8LY  Var_03    C25  N24  C23  C22    61.71  30.0  1
 8LY  Var_04    C23  N24  C25  C26   -61.58  30.0  1
 8LY  Var_05    C13  N12  C11  C10  -157.09  30.0  2
 8LY  Var_06    C18  N19  C20  C21   115.91  30.0  2
 8LY  Var_07    C11  N12  C13  C28  -167.02  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
 8LY  chir_01  C21  C20  C22  C26  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
 8LY  plan-1  C8   0.020
 8LY  plan-1  C10  0.020
 8LY  plan-1  N12  0.020
 8LY  plan-1  C9   0.020
 8LY  plan-1  C11  0.020
 8LY  plan-1  C29  0.020
 8LY  plan-1  C30  0.020
 8LY  plan-1  N31  0.020
 8LY  plan-1  H3   0.020
 8LY  plan-1  H22  0.020
 8LY  plan-1  H23  0.020
 8LY  plan-2  C4   0.020
 8LY  plan-2  C5   0.020
 8LY  plan-2  C7   0.020
 8LY  plan-2  C8   0.020
 8LY  plan-2  C2   0.020
 8LY  plan-2  C3   0.020
 8LY  plan-2  CL6  0.020
 8LY  plan-2  C9   0.020
 8LY  plan-2  H1   0.020
 8LY  plan-2  H2   0.020
 8LY  plan-2  H13  0.020
 8LY  plan-2  F1   0.020
 8LY  plan-3  N12  0.020
 8LY  plan-3  C13  0.020
 8LY  plan-3  C15  0.020
 8LY  plan-3  C17  0.020
 8LY  plan-3  C20  0.020
 8LY  plan-3  C28  0.020
 8LY  plan-3  C14  0.020
 8LY  plan-3  N16  0.020
 8LY  plan-3  C18  0.020
 8LY  plan-3  N19  0.020
 8LY  plan-3  N27  0.020
 8LY  plan-3  H5   0.020
 8LY  plan-3  H14  0.020
 8LY  plan-3  H15  0.020

