# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 02:53:19 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: N-[2-(4-methoxypiperidin-1-yl)pyrimidin-4-yl]-2-(1H-pyrazol-4-yl)-3H-imidazo[4,5-c]pyridin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1CCN(CC1)c2nccc(Nc3cc4nc([nH]c4cn3)c5c[nH]nc5)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
 3R0  3R0  N-[2-(4-methoxypiperidin-1-yl)pyrimidin-4-yl]-2-(1H-pyrazol-4-yl)-3H-imidazo[4,5-c]pyridin-6-amine  ligand  50  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3R0
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
 3R0  C4   C  CH2   0  -0.463   5.5369   1.0264   0.4109
 3R0  C5   C  CH2   0  -0.331   5.4411   0.0153  -0.7288
 3R0  C11  C  CR16  0  -0.020   3.9186  -3.5994   0.4267
 3R0  C7   C  CH2   0  -0.332   3.1938   0.7328  -1.2607
 3R0  C8   C  CH2   0  -0.471   3.2104   1.7725  -0.1434
 3R0  C9   C  CR6   0   0.626   3.5707  -1.5427  -0.4354
 3R0  C12  C  CR16  0  -0.468   2.5708  -3.8622   0.4621
 3R0  C13  C  CR6   0   0.532   1.7409  -2.8197   0.0089
 3R0  C3   C  CH1   0   0.083   4.6411   2.2269   0.1398
 3R0  O2   O  O2    0  -0.494   4.7355   3.0965   1.2465
 3R0  N6   N  NT    0  -0.482   4.0643  -0.3829  -0.9445
 3R0  N10  N  N     0  -0.501   4.4462  -2.4607  -0.0136
 3R0  N14  N  N     0  -0.497   2.2427  -1.6766  -0.4211
 3R0  N15  N  NH1   0  -0.752   0.3892  -2.9781   0.0314
 3R0  C16  C  CR6   0   0.455  -0.5602  -2.0140  -0.3413
 3R0  C17  C  CR16  0  -0.471  -1.5916  -1.7237   0.5415
 3R0  C18  C  CR56  0   0.258  -2.5429  -0.8073   0.1058
 3R0  C19  C  CR56  0   0.239  -2.3830  -0.2245  -1.1609
 3R0  C20  C  CR16  0  -0.119  -1.3134  -0.5741  -1.9664
 3R0  N21  N  N     0  -0.416  -0.4338  -1.4712  -1.5538
 3R0  N22  N  NR15  0  -0.727  -3.4454   0.6299  -1.2891
 3R0  C23  C  CR5   0   0.476  -4.1718   0.5373  -0.1463
 3R0  N24  N  N     0  -0.490  -3.6616  -0.3159   0.7144
 3R0  C26  C  CR5   0  -0.201  -5.3701   1.3051   0.0782
 3R0  C27  C  CR15  0   0.039  -6.1388   1.2992   1.2277
 3R0  N28  N  NR15  0  -0.420  -7.1406   2.1510   1.0062
 3R0  N30  N  N     0  -0.251  -7.0988   2.7199  -0.1956
 3R0  C31  C  CR15  0  -0.098  -6.0292   2.2174  -0.7737
 3R0  H1   H  HCH2  0   0.228   5.2377   0.5463   1.3482
 3R0  H2   H  HCH2  0   0.242   6.5742   1.3508   0.5242
 3R0  H3   H  HCH2  0   0.237   5.8143   0.4660  -1.6538
 3R0  H4   H  HCH2  0   0.270   6.0499  -0.8599  -0.5247
 3R0  H5   H  HCR6  0   0.260   4.6236  -4.3498   0.7702
 3R0  H6   H  HCH2  0   0.280   2.1856   0.3695  -1.4369
 3R0  H7   H  HCH2  0   0.237   3.5490   1.1848  -2.1929
 3R0  H8   H  HCH2  0   0.241   2.5804   2.6159  -0.4382
 3R0  H9   H  HCH2  0   0.228   2.7761   1.3404   0.7640
 3R0  H10  H  HCR6  0   0.268   2.1781  -4.8016   0.8237
 3R0  H11  H  HCH1  0   0.190   5.0188   2.7394  -0.7616
 3R0  H12  H  HCH3  0   0.234   4.4714   4.9996   1.8850
 3R0  H13  H  HCH3  0   0.202   4.7298   4.8554   0.1376
 3R0  H14  H  HCH3  0   0.206   3.1654   4.4200   0.8436
 3R0  H15  H  HNH1  0   0.409   0.0448  -3.7553   0.5727
 3R0  H16  H  HCR6  0   0.272  -1.6443  -2.1832   1.5197
 3R0  H17  H  HCR6  0   0.271  -1.1696  -0.1465  -2.9524
 3R0  H18  H  HNR5  0   0.426  -3.6425   1.2218  -2.0809
 3R0  H20  H  HCR5  0   0.300  -6.0318   0.7597   2.1538
 3R0  H21  H  HNR5  0   0.432  -7.8821   2.3886   1.6471
 3R0  H22  H  HCR5  0   0.266  -5.7624   2.5173  -1.7760
 3R0  C1   C  CH3   0  -0.406   4.2477   4.3930   1.0077

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
 3R0  N28  N30  aromatic  1.330  0.020  1.330
 3R0  N28  C27  aromatic  1.334  0.020  1.334
 3R0  N30  C31  aromatic  1.316  0.020  1.316
 3R0  C27  C26  aromatic  1.383  0.020  1.383
 3R0  C31  C26  aromatic  1.412  0.020  1.412
 3R0  C26  C23  single    1.441  0.020  1.441
 3R0  C23  N22  aromatic  1.357  0.020  1.357
 3R0  C23  N24  aromatic  1.315  0.020  1.315
 3R0  N22  C19  aromatic  1.369  0.020  1.369
 3R0  N24  C18  aromatic  1.365  0.020  1.365
 3R0  C19  C20  aromatic  1.384  0.020  1.384
 3R0  C19  C18  aromatic  1.403  0.020  1.403
 3R0  C20  N21  aromatic  1.322  0.020  1.322
 3R0  C18  C17  aromatic  1.391  0.020  1.391
 3R0  N21  C16  aromatic  1.334  0.020  1.334
 3R0  C17  C16  aromatic  1.388  0.020  1.388
 3R0  C16  N15  single    1.404  0.020  1.404
 3R0  C1   O2   single    1.406  0.020  1.406
 3R0  C4   C5   single    1.527  0.020  1.527
 3R0  C4   C3   single    1.522  0.020  1.522
 3R0  C5   N6   single    1.449  0.020  1.449
 3R0  N15  C13  single    1.361  0.020  1.361
 3R0  O2   C3   single    1.411  0.020  1.411
 3R0  C3   C8   single    1.528  0.020  1.528
 3R0  N14  C13  aromatic  1.320  0.020  1.320
 3R0  N14  C9   aromatic  1.335  0.020  1.335
 3R0  C13  C12  aromatic  1.407  0.020  1.407
 3R0  N6   C9   single    1.359  0.020  1.359
 3R0  N6   C7   single    1.450  0.020  1.450
 3R0  C9   N10  aromatic  1.337  0.020  1.337
 3R0  C8   C7   single    1.526  0.020  1.526
 3R0  C12  C11  aromatic  1.374  0.020  1.374
 3R0  N10  C11  aromatic  1.330  0.020  1.330
 3R0  C4   H1   single    0.970  0.020  1.090
 3R0  C4   H2   single    0.970  0.020  1.090
 3R0  C5   H3   single    0.970  0.020  1.090
 3R0  C5   H4   single    0.970  0.020  1.090
 3R0  C11  H5   single    0.930  0.020  1.080
 3R0  C7   H6   single    0.970  0.020  1.090
 3R0  C7   H7   single    0.970  0.020  1.090
 3R0  C8   H8   single    0.970  0.020  1.090
 3R0  C8   H9   single    0.970  0.020  1.090
 3R0  C12  H10  single    0.930  0.020  1.080
 3R0  C3   H11  single    0.970  0.020  1.090
 3R0  C1   H12  single    0.970  0.020  1.090
 3R0  C1   H13  single    0.970  0.020  1.090
 3R0  C1   H14  single    0.970  0.020  1.090
 3R0  N15  H15  single    0.860  0.020  1.020
 3R0  C17  H16  single    0.930  0.020  1.080
 3R0  C20  H17  single    0.930  0.020  1.080
 3R0  N22  H18  single    0.860  0.020  1.020
 3R0  C27  H20  single    0.930  0.020  1.080
 3R0  N28  H21  single    0.860  0.020  1.020
 3R0  C31  H22  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
 3R0  H2   C4   H1   107.51  3.000
 3R0  H2   C4   C3   110.06  3.000
 3R0  H1   C4   C3   109.72  3.000
 3R0  H2   C4   C5   109.49  3.000
 3R0  H1   C4   C5   109.36  3.000
 3R0  C3   C4   C5   110.64  3.000
 3R0  H4   C5   H3   107.44  3.000
 3R0  H4   C5   N6   109.83  3.000
 3R0  H3   C5   N6   108.13  3.000
 3R0  H4   C5   C4   111.00  3.000
 3R0  H3   C5   C4   109.68  3.000
 3R0  N6   C5   C4   110.65  3.000
 3R0  H5   C11  N10  116.04  3.000
 3R0  H5   C11  C12  119.79  3.000
 3R0  N10  C11  C12  124.16  3.000
 3R0  H7   C7   H6   107.52  3.000
 3R0  H7   C7   N6   107.96  3.000
 3R0  H6   C7   N6   109.59  3.000
 3R0  H7   C7   C8   109.78  3.000
 3R0  H6   C7   C8   110.90  3.000
 3R0  N6   C7   C8   110.97  3.000
 3R0  H9   C8   H8   107.42  3.000
 3R0  H9   C8   C3   109.59  3.000
 3R0  H8   C8   C3   111.12  3.000
 3R0  H9   C8   C7   109.48  3.000
 3R0  H8   C8   C7   108.77  3.000
 3R0  C3   C8   C7   110.40  3.000
 3R0  N14  C9   N10  125.40  3.000
 3R0  N10  C9   N6   117.79  3.000
 3R0  N14  C9   N6   116.80  3.000
 3R0  H10  C12  C13  122.51  3.000
 3R0  H10  C12  C11  122.11  3.000
 3R0  C13  C12  C11  115.37  3.000
 3R0  N15  C13  N14  118.92  3.000
 3R0  N14  C13  C12  121.47  3.000
 3R0  N15  C13  C12  119.60  3.000
 3R0  H11  C3   O2   109.37  3.000
 3R0  H11  C3   C8   107.89  3.000
 3R0  O2   C3   C8   113.05  3.000
 3R0  H11  C3   C4   108.08  3.000
 3R0  C8   C3   C4   110.46  3.000
 3R0  O2   C3   C4   107.89  3.000
 3R0  C1   O2   C3   114.34  3.000
 3R0  C9   N6   C7   121.34  3.000
 3R0  C7   N6   C5   113.04  3.000
 3R0  C9   N6   C5   121.57  3.000
 3R0  C9   N10  C11  115.64  3.000
 3R0  C13  N14  C9   117.93  3.000
 3R0  H15  N15  C16  116.18  3.000
 3R0  H15  N15  C13  115.98  3.000
 3R0  C16  N15  C13  125.98  3.000
 3R0  N21  C16  C17  124.27  3.000
 3R0  C17  C16  N15  118.51  3.000
 3R0  N21  C16  N15  117.17  3.000
 3R0  H16  C17  C18  121.98  3.000
 3R0  H16  C17  C16  121.48  3.000
 3R0  C18  C17  C16  116.53  3.000
 3R0  N24  C18  C19  110.26  3.000
 3R0  C19  C18  C17  118.58  3.000
 3R0  N24  C18  C17  131.15  3.000
 3R0  N22  C19  C20  134.65  3.000
 3R0  C20  C19  C18  120.56  3.000
 3R0  N22  C19  C18  104.79  3.000
 3R0  H17  C20  N21  117.58  3.000
 3R0  H17  C20  C19  122.15  3.000
 3R0  N21  C20  C19  120.26  3.000
 3R0  C20  N21  C16  119.76  3.000
 3R0  H18  N22  C23  126.64  3.000
 3R0  H18  N22  C19  126.27  3.000
 3R0  C23  N22  C19  107.08  3.000
 3R0  C26  C23  N24  124.51  3.000
 3R0  N24  C23  N22  112.82  3.000
 3R0  C26  C23  N22  122.68  3.000
 3R0  C23  N24  C18  105.05  3.000
 3R0  C31  C26  C27  104.17  3.000
 3R0  C31  C26  C23  129.70  3.000
 3R0  C27  C26  C23  126.13  3.000
 3R0  H20  C27  N28  122.50  3.000
 3R0  H20  C27  C26  131.42  3.000
 3R0  N28  C27  C26  106.07  3.000
 3R0  H21  N28  N30  119.77  3.000
 3R0  H21  N28  C27  126.68  3.000
 3R0  N30  N28  C27  113.55  3.000
 3R0  C31  N30  N28  105.03  3.000
 3R0  H22  C31  N30  120.18  3.000
 3R0  H22  C31  C26  128.64  3.000
 3R0  N30  C31  C26  111.18  3.000
 3R0  H14  C1   H13  107.76  3.000
 3R0  H14  C1   H12  108.04  3.000
 3R0  H13  C1   H12  108.28  3.000
 3R0  H14  C1   O2   113.03  3.000
 3R0  H13  C1   O2   111.78  3.000
 3R0  H12  C1   O2   107.78  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
 3R0  CONST_01  N14  C13  C12  C11     0.00   0.0  0
 3R0  CONST_02  N14  C9   N10  C11     0.00   0.0  0
 3R0  CONST_03  C12  C13  N14  C9      0.00   0.0  0
 3R0  CONST_04  C12  C11  N10  C9      0.00   0.0  0
 3R0  CONST_05  N10  C9   N14  C13     0.00   0.0  0
 3R0  CONST_06  N10  C11  C12  C13     0.00   0.0  0
 3R0  CONST_07  C19  C20  N21  C16     0.00   0.0  0
 3R0  CONST_08  N24  C18  C17  C16   180.00   0.0  0
 3R0  CONST_09  C19  C18  C17  C16     0.00   0.0  0
 3R0  CONST_10  C23  N24  C18  C17   180.00   0.0  0
 3R0  CONST_11  N22  C19  C18  C17   180.00   0.0  0
 3R0  CONST_12  C20  C19  C18  C17     0.00   0.0  0
 3R0  CONST_13  C20  N21  C16  C17     0.00   0.0  0
 3R0  CONST_14  C26  C23  N24  C18   180.00   0.0  0
 3R0  CONST_15  N22  C23  N24  C18     0.00   0.0  0
 3R0  CONST_16  C23  N22  C19  C18     0.00   0.0  0
 3R0  CONST_17  N21  C20  C19  C18     0.00   0.0  0
 3R0  CONST_18  N21  C16  C17  C18     0.00   0.0  0
 3R0  CONST_19  C26  C23  N22  C19   180.00   0.0  0
 3R0  CONST_20  N24  C23  N22  C19     0.00   0.0  0
 3R0  CONST_21  C23  N24  C18  C19     0.00   0.0  0
 3R0  CONST_22  C23  N22  C19  C20   180.00   0.0  0
 3R0  CONST_23  N24  C18  C19  C20   180.00   0.0  0
 3R0  CONST_24  N22  C19  C20  N21   180.00   0.0  0
 3R0  CONST_25  C27  C26  C23  N22   180.00   0.0  0
 3R0  CONST_26  C31  C26  C23  N22     0.00   0.0  0
 3R0  CONST_27  N24  C18  C19  N22     0.00   0.0  0
 3R0  CONST_28  N28  C27  C26  C23   180.00   0.0  0
 3R0  CONST_29  N30  C31  C26  C23   180.00   0.0  0
 3R0  CONST_30  C27  C26  C23  N24     0.00   0.0  0
 3R0  CONST_31  C31  C26  C23  N24   180.00   0.0  0
 3R0  CONST_32  N30  N28  C27  C26     0.00   0.0  0
 3R0  CONST_33  N28  N30  C31  C26     0.00   0.0  0
 3R0  CONST_34  C31  N30  N28  C27     0.00   0.0  0
 3R0  CONST_35  N30  C31  C26  C27     0.00   0.0  0
 3R0  CONST_36  C31  C26  C27  N28     0.00   0.0  0
 3R0  CONST_37  N6   C9   N10  C11   180.00   0.0  0
 3R0  CONST_38  N6   C9   N14  C13   180.00   0.0  0
 3R0  CONST_39  N15  C13  C12  C11   180.00   0.0  0
 3R0  CONST_40  N15  C13  N14  C9    180.00   0.0  0
 3R0  CONST_41  C20  N21  C16  N15   180.00   0.0  0
 3R0  CONST_42  C18  C17  C16  N15   180.00   0.0  0
 3R0  CONST_43  H5   C11  N10  C9    180.00   0.0  0
 3R0  CONST_44  H10  C12  C11  N10   180.00   0.0  0
 3R0  CONST_45  H17  C20  N21  C16   180.00   0.0  0
 3R0  CONST_46  H18  N22  C19  C18   180.00   0.0  0
 3R0  CONST_47  H16  C17  C18  C19   180.00   0.0  0
 3R0  CONST_48  H20  C27  C26  C23     0.00   0.0  0
 3R0  CONST_49  H22  C31  C26  C23     0.00   0.0  0
 3R0  CONST_50  H21  N28  C27  C26   180.00   0.0  0
 3R0  Var_01    C9   N6   C5   C4    -98.92  30.0  1
 3R0  Var_02    N14  C9   N6   C5    165.13  30.0  2
 3R0  Var_03    C8   C7   N6   C5    -58.69  30.0  1
 3R0  Var_04    N6   C5   C4   C3    -55.72  30.0  1
 3R0  Var_05    N6   C7   C8   C3     55.27  30.0  1
 3R0  Var_06    C16  N15  C13  C12   177.57  30.0  2
 3R0  Var_07    N21  C16  N15  C13    53.85  30.0  2
 3R0  Var_08    H12  C1   O2   C3   -173.82  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
 3R0  chir_01  C3  C4  O2  C8  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
 3R0  plan-1  C23  0.020
 3R0  plan-1  C26  0.020
 3R0  plan-1  C27  0.020
 3R0  plan-1  N28  0.020
 3R0  plan-1  N30  0.020
 3R0  plan-1  C31  0.020
 3R0  plan-1  H20  0.020
 3R0  plan-1  H21  0.020
 3R0  plan-1  H22  0.020
 3R0  plan-2  C11  0.020
 3R0  plan-2  C9   0.020
 3R0  plan-2  C12  0.020
 3R0  plan-2  C13  0.020
 3R0  plan-2  N6   0.020
 3R0  plan-2  N10  0.020
 3R0  plan-2  N14  0.020
 3R0  plan-2  N15  0.020
 3R0  plan-2  H5   0.020
 3R0  plan-2  H10  0.020
 3R0  plan-3  N15  0.020
 3R0  plan-3  C16  0.020
 3R0  plan-3  C17  0.020
 3R0  plan-3  C18  0.020
 3R0  plan-3  C19  0.020
 3R0  plan-3  C20  0.020
 3R0  plan-3  N21  0.020
 3R0  plan-3  N22  0.020
 3R0  plan-3  C23  0.020
 3R0  plan-3  N24  0.020
 3R0  plan-3  C26  0.020
 3R0  plan-3  H16  0.020
 3R0  plan-3  H17  0.020
 3R0  plan-3  H18  0.020

