# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 10:36:38 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: trans-4-{2-[(1R)-1-hydroxyethyl]imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl}cyclohexanecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)c1nc2cnc3[nH]ccc3c2n1[C@H]4CC[C@@H](CC4)C#N
#
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
 1J5  1J5  trans-4-{2-[(1R)-1-hydroxyethyl]imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl}cyclohexanecarbonitrile  ligand  42  23  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1J5
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
 1J5  C1   C  CH3   0  -0.685  -0.8467   3.6287  -1.2604
 1J5  C2   C  CH1   0  -0.048  -1.1818   3.1716   0.1584
 1J5  O4   O  OH1   0  -0.656  -2.2477   3.8987   0.7075
 1J5  C5   C  CR5   0   0.410  -1.5100   1.7016   0.1724
 1J5  N6   N  NR5   0  -0.570  -0.5843   0.6924   0.0927
 1J5  C7   C  CR56  0   0.362  -1.2946  -0.4829   0.0767
 1J5  C8   C  CR56  0   0.022  -2.6396  -0.0950   0.1437
 1J5  N9   N  N     0  -0.495  -2.7341   1.2727   0.2017
 1J5  C10  C  CR16  0  -0.139  -3.6664  -1.0468   0.1465
 1J5  N11  N  N     0  -0.430  -3.4152  -2.3374   0.0879
 1J5  C12  C  CR56  0   0.419  -2.1300  -2.6873   0.0284
 1J5  C13  C  CR56  0   0.018  -0.9859  -1.8520   0.0182
 1J5  C14  C  CR15  0  -0.469   0.1468  -2.7177  -0.0526
 1J5  C15  C  CR15  0  -0.002  -0.3362  -3.9967  -0.0830
 1J5  N16  N  NR15  0  -0.654  -1.6949  -3.9766  -0.0350
 1J5  C18  C  CH1   0  -0.108   0.8609   0.8765   0.0569
 1J5  C20  C  CH2   0  -0.452   1.5404   0.2881   1.2890
 1J5  C21  C  CH2   0  -0.431   3.0417   0.5463   1.2492
 1J5  C22  C  CH1   0  -0.371   3.6453   0.0089  -0.0551
 1J5  C24  C  CH2   0  -0.429   2.9667   0.6317  -1.2823
 1J5  C25  C  CH2   0  -0.462   1.4658   0.3713  -1.2497
 1J5  C26  C  CSP   0   0.139   5.0825   0.2485  -0.0896
 1J5  N27  N  NS    0  -0.269   6.2155   0.4495  -0.1159
 1J5  H1   H  HCH3  0   0.239  -1.6921   3.4630  -1.9294
 1J5  H2   H  HCH3  0   0.252  -0.6002   4.6903  -1.2648
 1J5  H3   H  HCH3  0   0.233   0.0091   3.0885  -1.6657
 1J5  H4   H  HCH1  0   0.256  -0.3196   3.3599   0.8048
 1J5  H5   H  HOH1  0   0.448  -3.0709   3.5175   0.3770
 1J5  H6   H  HCR6  0   0.259  -4.7037  -0.7342   0.1969
 1J5  H8   H  HCR5  0   0.241   1.1914  -2.4586  -0.0777
 1J5  H9   H  HCR5  0   0.289   0.2013  -4.9291  -0.1366
 1J5  H10  H  HCH1  0   0.270   1.0264   1.9556   0.0893
 1J5  H11  H  HCH2  0   0.269   1.1155   0.7401   2.1871
 1J5  H12  H  HCH2  0   0.250   1.3557  -0.7856   1.3624
 1J5  H13  H  HCH2  0   0.251   3.2387   1.6192   1.3235
 1J5  H14  H  HCH2  0   0.272   3.5196   0.0723   2.1070
 1J5  H15  H  HCH1  0   0.313   3.5112  -1.0785  -0.0876
 1J5  H16  H  HCH2  0   0.251   3.1604   1.7077  -1.2953
 1J5  H17  H  HCH2  0   0.272   3.3923   0.2182  -2.1970
 1J5  H18  H  HCH2  0   0.253   1.2771  -0.6962  -1.3793
 1J5  H19  H  HCH2  0   0.269   0.9886   0.8741  -2.0935
 1J5  H7   H  HNR5  0   0.412  -2.2941  -4.7859  -0.0440

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
 1J5  O4   C2   single    1.402  0.020  1.402
 1J5  C10  C8   aromatic  1.400  0.020  1.400
 1J5  C10  N11  aromatic  1.316  0.020  1.316
 1J5  N9   C8   aromatic  1.372  0.020  1.372
 1J5  N9   C5   aromatic  1.297  0.020  1.297
 1J5  C8   C7   aromatic  1.401  0.020  1.401
 1J5  N11  C12  aromatic  1.333  0.020  1.333
 1J5  C2   C5   single    1.506  0.020  1.506
 1J5  C2   C1   single    1.528  0.020  1.528
 1J5  C5   N6   aromatic  1.372  0.020  1.372
 1J5  C20  C21  single    1.524  0.020  1.524
 1J5  C20  C18  single    1.525  0.020  1.525
 1J5  C12  C13  aromatic  1.417  0.020  1.417
 1J5  C12  N16  aromatic  1.362  0.020  1.362
 1J5  C7   N6   aromatic  1.373  0.020  1.373
 1J5  C7   C13  aromatic  1.405  0.020  1.405
 1J5  N6   C18  single    1.457  0.020  1.457
 1J5  C13  C14  aromatic  1.427  0.020  1.427
 1J5  N16  C15  aromatic  1.360  0.020  1.360
 1J5  C21  C22  single    1.534  0.020  1.534
 1J5  C18  C25  single    1.526  0.020  1.526
 1J5  C14  C15  aromatic  1.367  0.020  1.367
 1J5  C22  C26  single    1.457  0.020  1.457
 1J5  C22  C24  single    1.534  0.020  1.534
 1J5  C25  C24  single    1.524  0.020  1.524
 1J5  C26  N27  triple    1.151  0.020  1.151
 1J5  C1   H1   single    0.970  0.020  1.090
 1J5  C1   H2   single    0.970  0.020  1.090
 1J5  C1   H3   single    0.970  0.020  1.090
 1J5  C2   H4   single    0.970  0.020  1.090
 1J5  O4   H5   single    0.850  0.020  0.980
 1J5  C10  H6   single    0.930  0.020  1.080
 1J5  C14  H8   single    0.930  0.020  1.080
 1J5  C15  H9   single    0.930  0.020  1.080
 1J5  C18  H10  single    0.970  0.020  1.090
 1J5  C20  H11  single    0.970  0.020  1.090
 1J5  C20  H12  single    0.970  0.020  1.090
 1J5  C21  H13  single    0.970  0.020  1.090
 1J5  C21  H14  single    0.970  0.020  1.090
 1J5  C22  H15  single    0.970  0.020  1.090
 1J5  C24  H16  single    0.970  0.020  1.090
 1J5  C24  H17  single    0.970  0.020  1.090
 1J5  C25  H18  single    0.970  0.020  1.090
 1J5  C25  H19  single    0.970  0.020  1.090
 1J5  N16  H7   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
 1J5  H3   C1   H2   107.67  3.000
 1J5  H3   C1   H1   107.76  3.000
 1J5  H2   C1   H1   108.71  3.000
 1J5  H3   C1   C2   111.67  3.000
 1J5  H2   C1   C2   110.17  3.000
 1J5  H1   C1   C2   110.74  3.000
 1J5  H4   C2   C5   109.53  3.000
 1J5  H4   C2   O4   106.17  3.000
 1J5  C5   C2   O4   109.68  3.000
 1J5  H4   C2   C1   108.93  3.000
 1J5  C5   C2   C1   110.39  3.000
 1J5  O4   C2   C1   112.04  3.000
 1J5  H5   O4   C2   108.02  3.000
 1J5  N9   C5   N6   113.25  3.000
 1J5  N6   C5   C2   124.78  3.000
 1J5  N9   C5   C2   121.90  3.000
 1J5  C18  N6   C7   128.37  3.000
 1J5  C18  N6   C5   125.29  3.000
 1J5  C7   N6   C5   106.33  3.000
 1J5  C13  C7   C8   118.86  3.000
 1J5  C13  C7   N6   136.13  3.000
 1J5  C8   C7   N6   105.01  3.000
 1J5  C10  C8   N9   128.83  3.000
 1J5  N9   C8   C7   110.12  3.000
 1J5  C10  C8   C7   121.05  3.000
 1J5  C8   N9   C5   105.29  3.000
 1J5  H6   C10  N11  117.85  3.000
 1J5  H6   C10  C8   120.37  3.000
 1J5  N11  C10  C8   121.78  3.000
 1J5  C12  N11  C10  116.31  3.000
 1J5  N16  C12  C13  107.44  3.000
 1J5  N16  C12  N11  123.94  3.000
 1J5  C13  C12  N11  128.62  3.000
 1J5  C14  C13  C12  106.48  3.000
 1J5  C14  C13  C7   140.14  3.000
 1J5  C12  C13  C7   113.39  3.000
 1J5  H8   C14  C15  124.56  3.000
 1J5  H8   C14  C13  128.70  3.000
 1J5  C15  C14  C13  106.74  3.000
 1J5  H9   C15  N16  120.86  3.000
 1J5  H9   C15  C14  129.36  3.000
 1J5  N16  C15  C14  109.78  3.000
 1J5  H7   N16  C15  125.62  3.000
 1J5  H7   N16  C12  124.82  3.000
 1J5  C15  N16  C12  109.56  3.000
 1J5  H10  C18  C25  107.00  3.000
 1J5  H10  C18  C20  106.84  3.000
 1J5  C25  C18  C20  112.80  3.000
 1J5  H10  C18  N6   105.92  3.000
 1J5  C25  C18  N6   111.86  3.000
 1J5  C20  C18  N6   111.91  3.000
 1J5  H12  C20  H11  106.62  3.000
 1J5  H12  C20  C21  109.57  3.000
 1J5  H11  C20  C21  109.56  3.000
 1J5  H12  C20  C18  110.99  3.000
 1J5  H11  C20  C18  109.37  3.000
 1J5  C21  C20  C18  110.64  3.000
 1J5  H14  C21  H13  107.11  3.000
 1J5  H14  C21  C22  110.13  3.000
 1J5  H13  C21  C22  109.30  3.000
 1J5  H14  C21  C20  109.73  3.000
 1J5  H13  C21  C20  110.00  3.000
 1J5  C22  C21  C20  110.51  3.000
 1J5  H15  C22  C26  106.44  3.000
 1J5  H15  C22  C24  108.95  3.000
 1J5  C26  C22  C24  110.52  3.000
 1J5  H15  C22  C21  108.94  3.000
 1J5  C24  C22  C21  111.33  3.000
 1J5  C26  C22  C21  110.52  3.000
 1J5  H17  C24  H16  107.10  3.000
 1J5  H17  C24  C25  109.74  3.000
 1J5  H16  C24  C25  110.06  3.000
 1J5  H17  C24  C22  110.14  3.000
 1J5  H16  C24  C22  109.30  3.000
 1J5  C25  C24  C22  110.44  3.000
 1J5  H19  C25  H18  106.44  3.000
 1J5  H19  C25  C24  109.59  3.000
 1J5  H18  C25  C24  109.56  3.000
 1J5  H19  C25  C18  109.63  3.000
 1J5  H18  C25  C18  110.90  3.000
 1J5  C24  C25  C18  110.62  3.000
 1J5  N27  C26  C22  180.00  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
 1J5  CONST_01  C10  C8   N9   C5   180.00   0.0  0
 1J5  CONST_02  C7   C8   N9   C5     0.00   0.0  0
 1J5  CONST_03  C8   C7   N6   C5     0.00   0.0  0
 1J5  CONST_04  C13  C7   N6   C5   180.00   0.0  0
 1J5  CONST_05  C8   N9   C5   N6     0.00   0.0  0
 1J5  CONST_06  C10  C8   C7   N6   180.00   0.0  0
 1J5  CONST_07  N9   C8   C7   N6     0.00   0.0  0
 1J5  CONST_08  C12  C13  C7   N6   180.00   0.0  0
 1J5  CONST_09  C14  C13  C7   N6     0.00   0.0  0
 1J5  CONST_10  N11  C10  C8   C7     0.00   0.0  0
 1J5  CONST_11  N9   C5   N6   C7     0.00   0.0  0
 1J5  CONST_12  N11  C12  C13  C7     0.00   0.0  0
 1J5  CONST_13  N16  C12  C13  C7   180.00   0.0  0
 1J5  CONST_14  C15  C14  C13  C7   180.00   0.0  0
 1J5  CONST_15  C12  N11  C10  C8     0.00   0.0  0
 1J5  CONST_16  C12  C13  C7   C8     0.00   0.0  0
 1J5  CONST_17  C14  C13  C7   C8   180.00   0.0  0
 1J5  CONST_18  N11  C10  C8   N9   180.00   0.0  0
 1J5  CONST_19  C13  C7   C8   N9   180.00   0.0  0
 1J5  CONST_20  C13  C7   C8   C10    0.00   0.0  0
 1J5  CONST_21  C13  C12  N11  C10    0.00   0.0  0
 1J5  CONST_22  N16  C12  N11  C10  180.00   0.0  0
 1J5  CONST_23  C14  C13  C12  N11  180.00   0.0  0
 1J5  CONST_24  C15  N16  C12  N11  180.00   0.0  0
 1J5  CONST_25  C15  C14  C13  C12    0.00   0.0  0
 1J5  CONST_26  C14  C15  N16  C12    0.00   0.0  0
 1J5  CONST_27  C15  N16  C12  C13    0.00   0.0  0
 1J5  CONST_28  N16  C15  C14  C13    0.00   0.0  0
 1J5  CONST_29  N16  C12  C13  C14    0.00   0.0  0
 1J5  CONST_30  C18  N6   C7   C8   180.00   0.0  0
 1J5  CONST_31  C18  N6   C5   N9   180.00   0.0  0
 1J5  CONST_32  C18  N6   C7   C13    0.00   0.0  0
 1J5  CONST_33  C8   N9   C5   C2   180.00   0.0  0
 1J5  CONST_34  C7   N6   C5   C2   180.00   0.0  0
 1J5  CONST_35  C18  N6   C5   C2     0.00   0.0  0
 1J5  CONST_36  H6   C10  C8   C7   180.00   0.0  0
 1J5  CONST_37  H8   C14  C13  C7     0.00   0.0  0
 1J5  CONST_38  H7   N16  C12  N11    0.00   0.0  0
 1J5  CONST_39  H9   C15  N16  C12  180.00   0.0  0
 1J5  Var_01    C22  C21  C20  C18  -55.23  30.0  1
 1J5  Var_02    C22  C24  C25  C18   55.39  30.0  1

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
 1J5  chir_01  C2   O4   C5   C1   negativ
 1J5  chir_02  C18  N6   C25  C20  positiv
 1J5  chir_03  C22  C24  C26  C21  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
 1J5  plan-1  C2   0.020
 1J5  plan-1  C5   0.020
 1J5  plan-1  N6   0.020
 1J5  plan-1  C7   0.020
 1J5  plan-1  C8   0.020
 1J5  plan-1  N9   0.020
 1J5  plan-1  C10  0.020
 1J5  plan-1  N11  0.020
 1J5  plan-1  C12  0.020
 1J5  plan-1  C13  0.020
 1J5  plan-1  C14  0.020
 1J5  plan-1  C15  0.020
 1J5  plan-1  N16  0.020
 1J5  plan-1  C18  0.020
 1J5  plan-1  H6   0.020
 1J5  plan-1  H8   0.020
 1J5  plan-1  H9   0.020
 1J5  plan-1  H7   0.020

