# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 11:33:49 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (trans-4-{2-[(1R)-1-hydroxyethyl]imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl}cyclohexyl)acetonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)c1nc2cnc3[nH]ccc3c2n1[C@H]4CC[C@@H](CC4)CC#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
 1J6  1J6  (trans-4-{2-[(1R)-1-hydroxyethyl]imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl}cyclohexyl)acetonitrile  ligand  45  24  .  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_1J6
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
 1J6  C1   C  CH3   0  -0.683   1.5680  -3.4926  -1.3267
 1J6  C2   C  CH1   0  -0.041   1.9767  -3.0083   0.0646
 1J6  O4   O  OH1   0  -0.661   3.2106  -3.5454   0.4621
 1J6  C5   C  CR5   0   0.409   2.0545  -1.5049   0.0915
 1J6  N6   N  NR5   0  -0.565   0.9765  -0.6616   0.1301
 1J6  C7   C  CR56  0   0.359   1.4810   0.6143   0.0640
 1J6  C8   C  CR56  0   0.025   2.8711   0.4514  -0.0142
 1J6  N9   N  N     0  -0.502   3.1906  -0.8827   0.0057
 1J6  C10  C  CR16  0  -0.140   3.7245   1.5582  -0.0994
 1J6  N11  N  N     0  -0.430   3.2627   2.7906  -0.1111
 1J6  C12  C  CR56  0   0.419   1.9384   2.9263  -0.0337
 1J6  C13  C  CR56  0   0.015   0.9505   1.9151   0.0603
 1J6  C14  C  CR15  0  -0.472  -0.3095   2.5835   0.1189
 1J6  C15  C  CR15  0  -0.005  -0.0469   3.9240   0.0590
 1J6  N16  N  NR15  0  -0.655   1.2948   4.1269  -0.0323
 1J6  C18  C  CH1   0  -0.111  -0.4184  -1.0738   0.2380
 1J6  C20  C  CH2   0  -0.446  -1.0445  -0.5973   1.5454
 1J6  C21  C  CH2   0  -0.427  -2.5074  -1.0153   1.6312
 1J6  C22  C  CH1   0  -0.264  -3.2992  -0.5411   0.4156
 1J6  C24  C  CH2   0  -0.429  -2.6768  -1.0893  -0.8655
 1J6  C25  C  CH2   0  -0.453  -1.2176  -0.6689  -0.9975
 1J6  C26  C  CH2   0  -0.528  -4.7662  -0.9593   0.5692
 1J6  C27  C  CSP   0   0.117  -5.6076  -0.4624  -0.5085
 1J6  N28  N  NS    0  -0.276  -6.2660  -0.0613  -1.3629
 1J6  H1   H  HCH3  0   0.237   2.2896  -3.1637  -2.0763
 1J6  H2   H  HCH3  0   0.251   1.5194  -4.5813  -1.3454
 1J6  H3   H  HCH3  0   0.233   0.5874  -3.1121  -1.6161
 1J6  H4   H  HCH1  0   0.254   1.2351  -3.3532   0.7923
 1J6  H5   H  HOH1  0   0.448   3.9058  -2.9630   0.1289
 1J6  H6   H  HCR6  0   0.259   4.7986   1.4196  -0.1600
 1J6  H8   H  HCR5  0   0.250  -1.2945   2.1551   0.1967
 1J6  H9   H  HCR5  0   0.290  -0.7323   4.7551   0.0759
 1J6  H10  H  HCH1  0   0.266  -0.4116  -2.1658   0.2691
 1J6  H11  H  HCH2  0   0.259  -0.4859  -1.0180   2.3842
 1J6  H12  H  HCH2  0   0.244  -0.9711   0.4883   1.6364
 1J6  H13  H  HCH2  0   0.230  -2.5782  -2.1065   1.7049
 1J6  H14  H  HCH2  0   0.251  -2.9441  -0.6120   2.5475
 1J6  H15  H  HCH1  0   0.256  -3.2591   0.5541   0.3822
 1J6  H16  H  HCH2  0   0.229  -2.7520  -2.1826  -0.8641
 1J6  H17  H  HCH2  0   0.253  -3.2249  -0.7399  -1.7437
 1J6  H18  H  HCH2  0   0.247  -1.1646   0.4105  -1.1538
 1J6  H19  H  HCH2  0   0.259  -0.7724  -1.1305  -1.8821
 1J6  H20  H  HCH2  0   0.303  -4.8557  -2.0483   0.5942
 1J6  H21  H  HCH2  0   0.314  -5.1761  -0.5830   1.5093
 1J6  H7   H  HNR5  0   0.411   1.7480   5.0243  -0.0957

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
 1J6  C1   C2   single    1.529  0.020  1.529
 1J6  N9   C5   aromatic  1.298  0.020  1.298
 1J6  N9   C8   aromatic  1.372  0.020  1.372
 1J6  C2   C5   single    1.506  0.020  1.506
 1J6  C2   O4   single    1.403  0.020  1.403
 1J6  C10  C8   aromatic  1.400  0.020  1.400
 1J6  C10  N11  aromatic  1.316  0.020  1.316
 1J6  C5   N6   aromatic  1.369  0.020  1.369
 1J6  C8   C7   aromatic  1.402  0.020  1.402
 1J6  C25  C24  single    1.524  0.020  1.524
 1J6  C25  C18  single    1.526  0.020  1.526
 1J6  N11  C12  aromatic  1.333  0.020  1.333
 1J6  N6   C7   aromatic  1.374  0.020  1.374
 1J6  N6   C18  single    1.459  0.020  1.459
 1J6  C7   C13  aromatic  1.405  0.020  1.405
 1J6  C24  C22  single    1.526  0.020  1.526
 1J6  C12  C13  aromatic  1.417  0.020  1.417
 1J6  C12  N16  aromatic  1.362  0.020  1.362
 1J6  C18  C20  single    1.526  0.020  1.526
 1J6  C13  C14  aromatic  1.428  0.020  1.428
 1J6  N16  C15  aromatic  1.360  0.020  1.360
 1J6  N28  C27  triple    1.151  0.020  1.151
 1J6  C14  C15  aromatic  1.367  0.020  1.367
 1J6  C27  C26  single    1.455  0.020  1.455
 1J6  C22  C26  single    1.533  0.020  1.533
 1J6  C22  C21  single    1.526  0.020  1.526
 1J6  C20  C21  single    1.524  0.020  1.524
 1J6  C1   H1   single    0.970  0.020  1.090
 1J6  C1   H2   single    0.970  0.020  1.090
 1J6  C1   H3   single    0.970  0.020  1.090
 1J6  C2   H4   single    0.970  0.020  1.090
 1J6  O4   H5   single    0.850  0.020  0.980
 1J6  C10  H6   single    0.930  0.020  1.080
 1J6  C14  H8   single    0.930  0.020  1.080
 1J6  C15  H9   single    0.930  0.020  1.080
 1J6  C18  H10  single    0.970  0.020  1.090
 1J6  C20  H11  single    0.970  0.020  1.090
 1J6  C20  H12  single    0.970  0.020  1.090
 1J6  C21  H13  single    0.970  0.020  1.090
 1J6  C21  H14  single    0.970  0.020  1.090
 1J6  C22  H15  single    0.970  0.020  1.090
 1J6  C24  H16  single    0.970  0.020  1.090
 1J6  C24  H17  single    0.970  0.020  1.090
 1J6  C25  H18  single    0.970  0.020  1.090
 1J6  C25  H19  single    0.970  0.020  1.090
 1J6  C26  H20  single    0.970  0.020  1.090
 1J6  C26  H21  single    0.970  0.020  1.090
 1J6  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
 1J6  H3   C1   H2   107.67  3.000
 1J6  H3   C1   H1   107.88  3.000
 1J6  H2   C1   H1   108.59  3.000
 1J6  H3   C1   C2   111.80  3.000
 1J6  H2   C1   C2   110.12  3.000
 1J6  H1   C1   C2   110.67  3.000
 1J6  H4   C2   C5   109.74  3.000
 1J6  H4   C2   O4   106.67  3.000
 1J6  C5   C2   O4   109.37  3.000
 1J6  H4   C2   C1   108.90  3.000
 1J6  O4   C2   C1   111.81  3.000
 1J6  C5   C2   C1   110.26  3.000
 1J6  H5   O4   C2   107.71  3.000
 1J6  N9   C5   N6   113.31  3.000
 1J6  N6   C5   C2   125.09  3.000
 1J6  N9   C5   C2   121.51  3.000
 1J6  C18  N6   C7   128.12  3.000
 1J6  C18  N6   C5   125.52  3.000
 1J6  C7   N6   C5   106.35  3.000
 1J6  C13  C7   C8   118.81  3.000
 1J6  C13  C7   N6   136.18  3.000
 1J6  C8   C7   N6   105.01  3.000
 1J6  C10  C8   N9   128.88  3.000
 1J6  C10  C8   C7   121.06  3.000
 1J6  N9   C8   C7   110.06  3.000
 1J6  C8   N9   C5   105.26  3.000
 1J6  H6   C10  N11  117.81  3.000
 1J6  H6   C10  C8   120.40  3.000
 1J6  N11  C10  C8   121.79  3.000
 1J6  C12  N11  C10  116.31  3.000
 1J6  N16  C12  C13  107.43  3.000
 1J6  N16  C12  N11  123.98  3.000
 1J6  C13  C12  N11  128.59  3.000
 1J6  C14  C13  C12  106.50  3.000
 1J6  C14  C13  C7   140.06  3.000
 1J6  C12  C13  C7   113.44  3.000
 1J6  H8   C14  C15  124.67  3.000
 1J6  H8   C14  C13  128.62  3.000
 1J6  C15  C14  C13  106.72  3.000
 1J6  H9   C15  N16  120.90  3.000
 1J6  H9   C15  C14  129.30  3.000
 1J6  N16  C15  C14  109.80  3.000
 1J6  H7   N16  C15  125.52  3.000
 1J6  H7   N16  C12  124.93  3.000
 1J6  C15  N16  C12  109.55  3.000
 1J6  H10  C18  C25  106.94  3.000
 1J6  H10  C18  C20  106.88  3.000
 1J6  C25  C18  C20  113.32  3.000
 1J6  H10  C18  N6   106.18  3.000
 1J6  C20  C18  N6   111.57  3.000
 1J6  C25  C18  N6   111.47  3.000
 1J6  H12  C20  H11  106.54  3.000
 1J6  H12  C20  C21  109.43  3.000
 1J6  H11  C20  C21  110.01  3.000
 1J6  H12  C20  C18  110.75  3.000
 1J6  H11  C20  C18  109.14  3.000
 1J6  C21  C20  C18  110.88  3.000
 1J6  H14  C21  H13  106.58  3.000
 1J6  H14  C21  C22  110.24  3.000
 1J6  H13  C21  C22  109.23  3.000
 1J6  H14  C21  C20  109.26  3.000
 1J6  H13  C21  C20  109.81  3.000
 1J6  C22  C21  C20  111.59  3.000
 1J6  H15  C22  C26  108.08  3.000
 1J6  H15  C22  C24  108.56  3.000
 1J6  C26  C22  C24  112.11  3.000
 1J6  H15  C22  C21  108.40  3.000
 1J6  C26  C22  C21  109.38  3.000
 1J6  C24  C22  C21  110.21  3.000
 1J6  H17  C24  H16  106.60  3.000
 1J6  H17  C24  C25  108.82  3.000
 1J6  H16  C24  C25  109.94  3.000
 1J6  H17  C24  C22  110.81  3.000
 1J6  H16  C24  C22  109.22  3.000
 1J6  C25  C24  C22  111.35  3.000
 1J6  H19  C25  H18  106.38  3.000
 1J6  H19  C25  C24  110.10  3.000
 1J6  H18  C25  C24  109.35  3.000
 1J6  H19  C25  C18  109.26  3.000
 1J6  H18  C25  C18  110.66  3.000
 1J6  C24  C25  C18  110.98  3.000
 1J6  H21  C26  H20  107.03  3.000
 1J6  H21  C26  C27  107.63  3.000
 1J6  H20  C26  C27  108.05  3.000
 1J6  H21  C26  C22  110.57  3.000
 1J6  H20  C26  C22  110.63  3.000
 1J6  C27  C26  C22  112.71  3.000
 1J6  N28  C27  C26  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
 1J6  CONST_01  C10  C8   N9   C5    180.00   0.0  0
 1J6  CONST_02  C7   C8   N9   C5      0.00   0.0  0
 1J6  CONST_03  C8   C7   N6   C5      0.00   0.0  0
 1J6  CONST_04  C13  C7   N6   C5    180.00   0.0  0
 1J6  CONST_05  C8   N9   C5   N6      0.00   0.0  0
 1J6  CONST_06  N9   C8   C7   N6      0.00   0.0  0
 1J6  CONST_07  C10  C8   C7   N6    180.00   0.0  0
 1J6  CONST_08  C12  C13  C7   N6    180.00   0.0  0
 1J6  CONST_09  C14  C13  C7   N6      0.00   0.0  0
 1J6  CONST_10  N11  C10  C8   C7      0.00   0.0  0
 1J6  CONST_11  N9   C5   N6   C7      0.00   0.0  0
 1J6  CONST_12  N11  C12  C13  C7      0.00   0.0  0
 1J6  CONST_13  N16  C12  C13  C7    180.00   0.0  0
 1J6  CONST_14  C15  C14  C13  C7    180.00   0.0  0
 1J6  CONST_15  C12  N11  C10  C8      0.00   0.0  0
 1J6  CONST_16  C12  C13  C7   C8      0.00   0.0  0
 1J6  CONST_17  C14  C13  C7   C8    180.00   0.0  0
 1J6  CONST_18  N11  C10  C8   N9    180.00   0.0  0
 1J6  CONST_19  C13  C7   C8   N9    180.00   0.0  0
 1J6  CONST_20  C13  C7   C8   C10     0.00   0.0  0
 1J6  CONST_21  C13  C12  N11  C10     0.00   0.0  0
 1J6  CONST_22  N16  C12  N11  C10   180.00   0.0  0
 1J6  CONST_23  C14  C13  C12  N11   180.00   0.0  0
 1J6  CONST_24  C15  N16  C12  N11   180.00   0.0  0
 1J6  CONST_25  C15  C14  C13  C12     0.00   0.0  0
 1J6  CONST_26  C14  C15  N16  C12     0.00   0.0  0
 1J6  CONST_27  C15  N16  C12  C13     0.00   0.0  0
 1J6  CONST_28  N16  C15  C14  C13     0.00   0.0  0
 1J6  CONST_29  N16  C12  C13  C14     0.00   0.0  0
 1J6  CONST_30  C18  N6   C7   C8    180.00   0.0  0
 1J6  CONST_31  C18  N6   C5   N9    180.00   0.0  0
 1J6  CONST_32  C18  N6   C7   C13     0.00   0.0  0
 1J6  CONST_33  C8   N9   C5   C2    180.00   0.0  0
 1J6  CONST_34  C7   N6   C5   C2    180.00   0.0  0
 1J6  CONST_35  C18  N6   C5   C2      0.00   0.0  0
 1J6  CONST_36  H6   C10  C8   C7    180.00   0.0  0
 1J6  CONST_37  H8   C14  C13  C7      0.00   0.0  0
 1J6  CONST_38  H7   N16  C12  N11     0.00   0.0  0
 1J6  CONST_39  H9   C15  N16  C12   180.00   0.0  0
 1J6  Var_01    C22  C24  C25  C18    54.82  30.0  1
 1J6  Var_02    C22  C21  C20  C18   -54.57  30.0  1
 1J6  Var_03    H20  C26  C27  N28  -145.97  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
 1J6  chir_01  C2   C1   C5   O4   positiv
 1J6  chir_02  C18  N6   C20  C25  negativ
 1J6  chir_03  C22  C21  C26  C24  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
 1J6  plan-1  C2   0.020
 1J6  plan-1  C5   0.020
 1J6  plan-1  N6   0.020
 1J6  plan-1  C7   0.020
 1J6  plan-1  C8   0.020
 1J6  plan-1  N9   0.020
 1J6  plan-1  C10  0.020
 1J6  plan-1  N11  0.020
 1J6  plan-1  C12  0.020
 1J6  plan-1  C13  0.020
 1J6  plan-1  C14  0.020
 1J6  plan-1  C15  0.020
 1J6  plan-1  N16  0.020
 1J6  plan-1  C18  0.020
 1J6  plan-1  H6   0.020
 1J6  plan-1  H8   0.020
 1J6  plan-1  H9   0.020
 1J6  plan-1  H7   0.020

