# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 08:44:30 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 1-cyclopentyl-N-[2-(4-methoxypiperidin-1-yl)pyrimidin-4-yl]-1H-imidazo[4,5-c]pyridin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1CCN(CC1)c2nccc(Nc3cc4n(cnc4cn3)C5CCCC5)n2
#
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
 4YV  4YV  1-cyclopentyl-N-[2-(4-methoxypiperidin-1-yl)pyrimidin-4-yl]-1H-imidazo[4,5-c]pyridin-6-amine  ligand  56  29  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4YV
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
 4YV  C4   C  CH2   0  -0.461   6.2345  -0.0176  -0.1846
 4YV  C5   C  CH2   0  -0.313   5.4158   0.9388   0.6746
 4YV  C11  C  CR16  0  -0.015   2.6477   3.7593  -0.4139
 4YV  C7   C  CH2   0  -0.325   3.6026  -0.6846   0.8359
 4YV  C8   C  CH2   0  -0.471   4.3815  -1.6757  -0.0228
 4YV  C9   C  CR6   0   0.636   3.1059   1.6339   0.1883
 4YV  C12  C  CR16  0  -0.491   1.3041   3.4909  -0.5057
 4YV  C13  C  CR6   0   0.550   0.9288   2.1660  -0.2041
 4YV  C3   C  CH1   0   0.079   5.8840  -1.4616   0.1362
 4YV  O2   O  O2    0  -0.494   6.6574  -2.2937  -0.6991
 4YV  N6   N  NT    0  -0.492   3.9984   0.6774   0.5382
 4YV  N10  N  N     0  -0.505   3.5676   2.8613  -0.0734
 4YV  N14  N  N     0  -0.493   1.8223   1.2622   0.1385
 4YV  N15  N  NH1   0  -0.761  -0.3979   1.8487  -0.2699
 4YV  C16  C  CR6   0   0.508  -1.0880   0.6671  -0.0210
 4YV  C17  C  CR16  0  -0.482  -2.4825   0.7498  -0.0221
 4YV  C18  C  CR56  0   0.458  -3.1490  -0.4410   0.2064
 4YV  C19  C  CR56  0   0.026  -2.4485  -1.6382   0.4278
 4YV  C20  C  CR16  0  -0.119  -1.0640  -1.5896   0.4073
 4YV  N21  N  N     0  -0.421  -0.4092  -0.4627   0.1830
 4YV  N22  N  N     0  -0.457  -3.3306  -2.6756   0.6233
 4YV  C23  C  CR15  0   0.095  -4.5017  -2.1232   0.5238
 4YV  N24  N  NR5   0  -0.527  -4.4684  -0.7786   0.2805
 4YV  C25  C  CH1   0  -0.108  -5.6110   0.0957   0.0550
 4YV  C26  C  CH2   0  -0.458  -6.4086  -0.2769  -1.2143
 4YV  C27  C  CH2   0  -0.452  -7.7043  -0.9020  -0.7035
 4YV  C28  C  CH2   0  -0.448  -8.0007  -0.0825   0.5493
 4YV  C29  C  CH2   0  -0.463  -6.6304   0.0555   1.2164
 4YV  H1   H  HCH2  0   0.228   6.0398   0.1828  -1.2429
 4YV  H2   H  HCH2  0   0.243   7.2968   0.1626  -0.0033
 4YV  H3   H  HCH2  0   0.228   5.7026   0.8214   1.7272
 4YV  H4   H  HCH2  0   0.272   5.6193   1.9678   0.3967
 4YV  H5   H  HCR6  0   0.260   3.0129   4.7585  -0.6279
 4YV  H6   H  HCH2  0   0.293   2.5338  -0.7884   0.6699
 4YV  H7   H  HCH2  0   0.226   3.7914  -0.8899   1.8973
 4YV  H8   H  HCH2  0   0.244   4.0921  -2.6872   0.2720
 4YV  H9   H  HCH2  0   0.227   4.1029  -1.5478  -1.0739
 4YV  H10  H  HCR6  0   0.269   0.5877   4.2514  -0.7831
 4YV  H11  H  HCH1  0   0.189   6.1474  -1.6548   1.1906
 4YV  H12  H  HCH3  0   0.202   6.9541  -3.7736   0.7328
 4YV  H13  H  HCH3  0   0.206   5.7080  -4.1450  -0.4702
 4YV  H14  H  HCH3  0   0.234   7.4127  -4.1564  -0.9349
 4YV  H15  H  HNH1  0   0.418  -0.9932   2.6300  -0.4965
 4YV  H16  H  HCR6  0   0.287  -2.9950   1.6876  -0.1963
 4YV  H17  H  HCR6  0   0.260  -0.4676  -2.4815   0.5698
 4YV  H18  H  HCR5  0   0.294  -5.4375  -2.6551   0.6201
 4YV  H19  H  HCH1  0   0.282  -5.1955   1.0968  -0.0471
 4YV  H20  H  HCH2  0   0.249  -6.6423   0.6396  -1.7597
 4YV  H21  H  HCH2  0   0.255  -5.8381  -0.9163  -1.8888
 4YV  H22  H  HCH2  0   0.244  -8.5058  -0.8698  -1.4416
 4YV  H23  H  HCH2  0   0.225  -7.5523  -1.9522  -0.4361
 4YV  H24  H  HCH2  0   0.228  -8.3899   0.8992   0.2663
 4YV  H25  H  HCH2  0   0.241  -8.7348  -0.5478   1.2077
 4YV  H26  H  HCH2  0   0.246  -6.4456  -0.8105   1.8559
 4YV  H27  H  HCH2  0   0.258  -6.5495   0.9360   1.8529
 4YV  C1   C  CH3   0  -0.405   6.6716  -3.6471  -0.3194

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
 4YV  C4   C5   single    1.524  0.020  1.524
 4YV  C4   C3   single    1.520  0.020  1.520
 4YV  C5   N6   single    1.448  0.020  1.448
 4YV  O2   C1   single    1.406  0.020  1.406
 4YV  O2   C3   single    1.410  0.020  1.410
 4YV  C3   C8   single    1.526  0.020  1.526
 4YV  N10  C11  aromatic  1.330  0.020  1.330
 4YV  N10  C9   aromatic  1.337  0.020  1.337
 4YV  C11  C12  aromatic  1.373  0.020  1.373
 4YV  N6   C9   single    1.354  0.020  1.354
 4YV  N6   C7   single    1.449  0.020  1.449
 4YV  C9   N14  aromatic  1.337  0.020  1.337
 4YV  C8   C7   single    1.525  0.020  1.525
 4YV  C12  C13  aromatic  1.410  0.020  1.410
 4YV  N14  C13  aromatic  1.316  0.020  1.316
 4YV  C13  N15  single    1.366  0.020  1.366
 4YV  N15  C16  single    1.391  0.020  1.391
 4YV  C16  C17  aromatic  1.397  0.020  1.397
 4YV  C16  N21  aromatic  1.334  0.020  1.334
 4YV  C26  C27  single    1.527  0.020  1.527
 4YV  C26  C25  single    1.545  0.020  1.545
 4YV  C17  C18  aromatic  1.384  0.020  1.384
 4YV  C27  C28  single    1.526  0.020  1.526
 4YV  C25  N24  single    1.456  0.020  1.456
 4YV  C25  C29  single    1.546  0.020  1.546
 4YV  N21  C20  aromatic  1.322  0.020  1.322
 4YV  C18  N24  aromatic  1.364  0.020  1.364
 4YV  C18  C19  aromatic  1.405  0.020  1.405
 4YV  C28  C29  single    1.530  0.020  1.530
 4YV  N24  C23  aromatic  1.367  0.020  1.367
 4YV  C20  C19  aromatic  1.386  0.020  1.386
 4YV  C19  N22  aromatic  1.376  0.020  1.376
 4YV  C23  N22  aromatic  1.299  0.020  1.299
 4YV  C4   H1   single    0.970  0.020  1.090
 4YV  C4   H2   single    0.970  0.020  1.090
 4YV  C5   H3   single    0.970  0.020  1.090
 4YV  C5   H4   single    0.970  0.020  1.090
 4YV  C11  H5   single    0.930  0.020  1.080
 4YV  C7   H6   single    0.970  0.020  1.090
 4YV  C7   H7   single    0.970  0.020  1.090
 4YV  C8   H8   single    0.970  0.020  1.090
 4YV  C8   H9   single    0.970  0.020  1.090
 4YV  C12  H10  single    0.930  0.020  1.080
 4YV  C3   H11  single    0.970  0.020  1.090
 4YV  C1   H12  single    0.970  0.020  1.090
 4YV  C1   H13  single    0.970  0.020  1.090
 4YV  C1   H14  single    0.970  0.020  1.090
 4YV  N15  H15  single    0.860  0.020  1.020
 4YV  C17  H16  single    0.930  0.020  1.080
 4YV  C20  H17  single    0.930  0.020  1.080
 4YV  C23  H18  single    0.930  0.020  1.080
 4YV  C25  H19  single    0.970  0.020  1.090
 4YV  C26  H20  single    0.970  0.020  1.090
 4YV  C26  H21  single    0.970  0.020  1.090
 4YV  C27  H22  single    0.970  0.020  1.090
 4YV  C27  H23  single    0.970  0.020  1.090
 4YV  C28  H24  single    0.970  0.020  1.090
 4YV  C28  H25  single    0.970  0.020  1.090
 4YV  C29  H26  single    0.970  0.020  1.090
 4YV  C29  H27  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
 4YV  H2   C4   H1   107.65  3.000
 4YV  H2   C4   C3   110.24  3.000
 4YV  H1   C4   C3   109.69  3.000
 4YV  H2   C4   C5   108.98  3.000
 4YV  H1   C4   C5   109.55  3.000
 4YV  C3   C4   C5   110.69  3.000
 4YV  H4   C5   H3   107.35  3.000
 4YV  H4   C5   N6   109.31  3.000
 4YV  H3   C5   N6   109.08  3.000
 4YV  H4   C5   C4   110.49  3.000
 4YV  H3   C5   C4   109.46  3.000
 4YV  N6   C5   C4   111.07  3.000
 4YV  H5   C11  N10  116.07  3.000
 4YV  H5   C11  C12  119.73  3.000
 4YV  N10  C11  C12  124.19  3.000
 4YV  H7   C7   H6   107.40  3.000
 4YV  H7   C7   N6   109.12  3.000
 4YV  H6   C7   N6   109.09  3.000
 4YV  H7   C7   C8   109.58  3.000
 4YV  H6   C7   C8   110.74  3.000
 4YV  N6   C7   C8   110.83  3.000
 4YV  H9   C8   H8   107.44  3.000
 4YV  H9   C8   C3   109.53  3.000
 4YV  H8   C8   C3   111.26  3.000
 4YV  H9   C8   C7   109.55  3.000
 4YV  H8   C8   C7   108.32  3.000
 4YV  C3   C8   C7   110.67  3.000
 4YV  N14  C9   N10  125.40  3.000
 4YV  N14  C9   N6   116.48  3.000
 4YV  N10  C9   N6   118.12  3.000
 4YV  H10  C12  C13  122.66  3.000
 4YV  H10  C12  C11  121.88  3.000
 4YV  C13  C12  C11  115.46  3.000
 4YV  N15  C13  N14  120.83  3.000
 4YV  N15  C13  C12  117.82  3.000
 4YV  N14  C13  C12  121.36  3.000
 4YV  H11  C3   O2   109.37  3.000
 4YV  H11  C3   C8   108.05  3.000
 4YV  O2   C3   C8   113.30  3.000
 4YV  H11  C3   C4   108.23  3.000
 4YV  C8   C3   C4   109.77  3.000
 4YV  O2   C3   C4   108.00  3.000
 4YV  C1   O2   C3   114.44  3.000
 4YV  C9   N6   C7   122.47  3.000
 4YV  C7   N6   C5   114.69  3.000
 4YV  C9   N6   C5   122.82  3.000
 4YV  C9   N10  C11  115.54  3.000
 4YV  C13  N14  C9   118.06  3.000
 4YV  H15  N15  C16  113.93  3.000
 4YV  H15  N15  C13  113.86  3.000
 4YV  C16  N15  C13  132.13  3.000
 4YV  N21  C16  C17  123.94  3.000
 4YV  N21  C16  N15  119.64  3.000
 4YV  C17  C16  N15  116.42  3.000
 4YV  H16  C17  C18  122.95  3.000
 4YV  H16  C17  C16  121.59  3.000
 4YV  C18  C17  C16  115.46  3.000
 4YV  N24  C18  C19  105.24  3.000
 4YV  C19  C18  C17  121.29  3.000
 4YV  N24  C18  C17  133.47  3.000
 4YV  N22  C19  C20  132.01  3.000
 4YV  N22  C19  C18  110.21  3.000
 4YV  C20  C19  C18  117.78  3.000
 4YV  H17  C20  N21  116.98  3.000
 4YV  H17  C20  C19  121.21  3.000
 4YV  N21  C20  C19  121.81  3.000
 4YV  C20  N21  C16  119.72  3.000
 4YV  C23  N22  C19  104.27  3.000
 4YV  H18  C23  N24  121.40  3.000
 4YV  H18  C23  N22  124.38  3.000
 4YV  N24  C23  N22  114.21  3.000
 4YV  C25  N24  C23  126.80  3.000
 4YV  C23  N24  C18  106.07  3.000
 4YV  C25  N24  C18  127.01  3.000
 4YV  H19  C25  C29  110.25  3.000
 4YV  H19  C25  C26  109.98  3.000
 4YV  C29  C25  C26  105.70  3.000
 4YV  H19  C25  N24  105.49  3.000
 4YV  C29  C25  N24  112.67  3.000
 4YV  C26  C25  N24  112.80  3.000
 4YV  H21  C26  H20  107.17  3.000
 4YV  H21  C26  C27  114.26  3.000
 4YV  H20  C26  C27  109.22  3.000
 4YV  H21  C26  C25  112.31  3.000
 4YV  H20  C26  C25  108.58  3.000
 4YV  C27  C26  C25  105.19  3.000
 4YV  H23  C27  H22  107.22  3.000
 4YV  H23  C27  C28  109.98  3.000
 4YV  H22  C27  C28  113.40  3.000
 4YV  H23  C27  C26  110.91  3.000
 4YV  H22  C27  C26  112.67  3.000
 4YV  C28  C27  C26  102.68  3.000
 4YV  H25  C28  H24  107.45  3.000
 4YV  H25  C28  C29  112.22  3.000
 4YV  H24  C28  C29  110.53  3.000
 4YV  H25  C28  C27  113.41  3.000
 4YV  H24  C28  C27  109.80  3.000
 4YV  C29  C28  C27  103.44  3.000
 4YV  H27  C29  H26  106.63  3.000
 4YV  H27  C29  C28  113.21  3.000
 4YV  H26  C29  C28  109.59  3.000
 4YV  H27  C29  C25  111.65  3.000
 4YV  H26  C29  C25  110.42  3.000
 4YV  C28  C29  C25  105.39  3.000
 4YV  H14  C1   H13  107.95  3.000
 4YV  H14  C1   H12  108.23  3.000
 4YV  H13  C1   H12  107.84  3.000
 4YV  H14  C1   O2   107.71  3.000
 4YV  H13  C1   O2   113.06  3.000
 4YV  H12  C1   O2   111.88  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
 4YV  CONST_01  N14  C9   N10  C11     0.00   0.0  0
 4YV  CONST_02  N14  C13  C12  C11     0.00   0.0  0
 4YV  CONST_03  C12  C11  N10  C9      0.00   0.0  0
 4YV  CONST_04  C12  C13  N14  C9      0.00   0.0  0
 4YV  CONST_05  N10  C11  C12  C13     0.00   0.0  0
 4YV  CONST_06  N10  C9   N14  C13     0.00   0.0  0
 4YV  CONST_07  N24  C18  C17  C16   180.00   0.0  0
 4YV  CONST_08  C19  C18  C17  C16     0.00   0.0  0
 4YV  CONST_09  C19  C20  N21  C16     0.00   0.0  0
 4YV  CONST_10  C20  N21  C16  C17     0.00   0.0  0
 4YV  CONST_11  C23  N24  C18  C17   180.00   0.0  0
 4YV  CONST_12  C20  C19  C18  C17     0.00   0.0  0
 4YV  CONST_13  N22  C19  C18  C17   180.00   0.0  0
 4YV  CONST_14  N21  C16  C17  C18     0.00   0.0  0
 4YV  CONST_15  N22  C23  N24  C18     0.00   0.0  0
 4YV  CONST_16  N21  C20  C19  C18     0.00   0.0  0
 4YV  CONST_17  C23  N22  C19  C18     0.00   0.0  0
 4YV  CONST_18  C23  N24  C18  C19     0.00   0.0  0
 4YV  CONST_19  N24  C23  N22  C19     0.00   0.0  0
 4YV  CONST_20  N24  C18  C19  C20   180.00   0.0  0
 4YV  CONST_21  C23  N22  C19  C20   180.00   0.0  0
 4YV  CONST_22  N22  C19  C20  N21   180.00   0.0  0
 4YV  CONST_23  N24  C18  C19  N22     0.00   0.0  0
 4YV  CONST_24  N6   C9   N10  C11   180.00   0.0  0
 4YV  CONST_25  N6   C9   N14  C13   180.00   0.0  0
 4YV  CONST_26  C25  N24  C18  C17     0.00   0.0  0
 4YV  CONST_27  C25  N24  C18  C19   180.00   0.0  0
 4YV  CONST_28  C25  N24  C23  N22   180.00   0.0  0
 4YV  CONST_29  N15  C13  C12  C11   180.00   0.0  0
 4YV  CONST_30  N15  C13  N14  C9    180.00   0.0  0
 4YV  CONST_31  C18  C17  C16  N15   180.00   0.0  0
 4YV  CONST_32  C20  N21  C16  N15   180.00   0.0  0
 4YV  CONST_33  H5   C11  N10  C9    180.00   0.0  0
 4YV  CONST_34  H10  C12  C11  N10   180.00   0.0  0
 4YV  CONST_35  H17  C20  N21  C16   180.00   0.0  0
 4YV  CONST_36  H18  C23  N24  C18   180.00   0.0  0
 4YV  CONST_37  H16  C17  C18  C19   180.00   0.0  0
 4YV  Var_01    C9   N6   C5   C4   -125.62  30.0  1
 4YV  Var_02    N10  C9   N6   C5      1.74  30.0  2
 4YV  Var_03    C8   C7   N6   C5    -55.74  30.0  1
 4YV  Var_04    N6   C5   C4   C3    -54.71  30.0  1
 4YV  Var_05    N6   C7   C8   C3     54.74  30.0  1
 4YV  Var_06    C28  C27  C26  C25    36.04  30.0  1
 4YV  Var_07    C27  C28  C29  C25    32.32  30.0  1
 4YV  Var_08    C29  C28  C27  C26   -42.28  30.0  1
 4YV  Var_09    C16  N15  C13  C12  -178.95  30.0  2
 4YV  Var_10    C17  C16  N15  C13   171.91  30.0  2
 4YV  Var_11    H12  C1   O2   C3    -52.60  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
 4YV  chir_01  C3   C4   O2   C8   positiv
 4YV  chir_02  C25  C26  N24  C29  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
 4YV  plan-1  C11  0.020
 4YV  plan-1  C9   0.020
 4YV  plan-1  C12  0.020
 4YV  plan-1  C13  0.020
 4YV  plan-1  N6   0.020
 4YV  plan-1  N10  0.020
 4YV  plan-1  N14  0.020
 4YV  plan-1  N15  0.020
 4YV  plan-1  H5   0.020
 4YV  plan-1  H10  0.020
 4YV  plan-2  N15  0.020
 4YV  plan-2  C16  0.020
 4YV  plan-2  C17  0.020
 4YV  plan-2  C18  0.020
 4YV  plan-2  C19  0.020
 4YV  plan-2  C20  0.020
 4YV  plan-2  N21  0.020
 4YV  plan-2  N22  0.020
 4YV  plan-2  C23  0.020
 4YV  plan-2  N24  0.020
 4YV  plan-2  C25  0.020
 4YV  plan-2  H16  0.020
 4YV  plan-2  H17  0.020
 4YV  plan-2  H18  0.020

