# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 14:25:54 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 3-(trans-4-{2-[(1R)-1-hydroxyethyl]imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl}cyclohexyl)propanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)c1nc2cnc3[nH]ccc3c2n1[C@H]4CC[C@H](CCC#N)CC4
#
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
 15T  15T  3-(trans-4-{2-[(1R)-1-hydroxyethyl]imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl}cyclohexyl)propanenitrile  ligand  48  25  .  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_15T
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
 15T  C1   C  CH3   0  -0.700   1.6197  -3.5442  -1.2779
 15T  C2   C  CH1   0  -0.056   2.0653  -3.0767   0.1069
 15T  O4   O  OH1   0  -0.657   3.2573  -3.6966   0.5105
 15T  C5   C  CR5   0   0.434   2.3274  -1.5972   0.1063
 15T  N6   N  NR5   0  -0.572   1.3190  -0.6615   0.1322
 15T  C7   C  CR56  0   0.364   1.9285   0.5658   0.0733
 15T  C8   C  CR56  0   0.003   3.3001   0.2840   0.0141
 15T  N9   N  N     0  -0.461   3.5111  -1.0710   0.0359
 15T  C10  C  CR16  0  -0.144   4.2460   1.3136  -0.0607
 15T  N11  N  N     0  -0.431   3.8936   2.5816  -0.0799
 15T  C12  C  CR56  0   0.416   2.5847   2.8305  -0.0203
 15T  C13  C  CR56  0   0.017   1.5123   1.9084   0.0613
 15T  C14  C  CR15  0  -0.469   0.3141   2.6839   0.1026
 15T  C15  C  CR15  0  -0.006   0.6920   3.9967   0.0446
 15T  N16  N  NR15  0  -0.655   2.0473   4.0826  -0.0282
 15T  C18  C  CH1   0  -0.109  -0.1104  -0.9473   0.2094
 15T  C20  C  CH2   0  -0.443  -0.7263  -0.4230   1.5017
 15T  C21  C  CH2   0  -0.426  -2.2119  -0.7590   1.5582
 15T  C22  C  CH1   0  -0.245  -2.9672  -0.2465   0.3324
 15T  C24  C  CH2   0  -0.437  -2.3365  -0.8071  -0.9418
 15T  C25  C  CH2   0  -0.449  -0.8513  -0.4737  -1.0364
 15T  C26  C  CH2   0  -0.417  -4.4504  -0.5860   0.4572
 15T  C27  C  CH2   0  -0.549  -5.2990   0.0264  -0.6617
 15T  C28  C  CSP   0   0.124  -6.7172  -0.2228  -0.4596
 15T  N29  N  NS    0  -0.279  -7.8359  -0.4287  -0.2835
 15T  H1   H  HCH3  0   0.251   1.3933  -4.6117  -1.2636
 15T  H2   H  HCH3  0   0.238   0.7191  -3.0268  -1.6086
 15T  H3   H  HCH3  0   0.244   2.4040  -3.3605  -2.0126
 15T  H4   H  HCH1  0   0.234   1.2628  -3.2931   0.8258
 15T  H5   H  HOH1  0   0.458   3.1119  -4.6479   0.4923
 15T  H6   H  HCR6  0   0.256   5.3048   1.0822  -0.1071
 15T  H8   H  HCR5  0   0.244  -0.7058   2.3448   0.1670
 15T  H9   H  HCR5  0   0.288   0.0812   4.8844   0.0519
 15T  H10  H  HCH1  0   0.259  -0.2025  -2.0348   0.2379
 15T  H11  H  HCH2  0   0.253  -0.2052  -0.8651   2.3538
 15T  H12  H  HCH2  0   0.240  -0.5938   0.6579   1.5826
 15T  H13  H  HCH2  0   0.222  -2.3394  -1.8452   1.6323
 15T  H14  H  HCH2  0   0.243  -2.6438  -0.3346   2.4675
 15T  H15  H  HCH1  0   0.229  -2.8687   0.8479   0.3083
 15T  H16  H  HCH2  0   0.223  -2.4737  -1.8946  -0.9643
 15T  H17  H  HCH2  0   0.248  -2.8352  -0.4144  -1.8304
 15T  H18  H  HCH2  0   0.244  -0.7285   0.6031  -1.1699
 15T  H19  H  HCH2  0   0.254  -0.4154  -0.9457  -1.9204
 15T  H20  H  HCH2  0   0.243  -4.5819  -1.6713   0.4608
 15T  H21  H  HCH2  0   0.253  -4.8198  -0.2192   1.4178
 15T  H22  H  HCH2  0   0.303  -5.1506   1.1075  -0.7108
 15T  H23  H  HCH2  0   0.307  -5.0292  -0.3778  -1.6386
 15T  H7   H  HNR5  0   0.411   2.5773   4.9368  -0.0902

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
 15T  C1   C2   single    1.528  0.020  1.528
 15T  N9   C5   aromatic  1.297  0.020  1.297
 15T  N9   C8   aromatic  1.371  0.020  1.371
 15T  C2   C5   single    1.503  0.020  1.503
 15T  C2   O4   single    1.403  0.020  1.403
 15T  C10  C8   aromatic  1.400  0.020  1.400
 15T  C10  N11  aromatic  1.316  0.020  1.316
 15T  C5   N6   aromatic  1.376  0.020  1.376
 15T  C8   C7   aromatic  1.402  0.020  1.402
 15T  C25  C24  single    1.525  0.020  1.525
 15T  C25  C18  single    1.525  0.020  1.525
 15T  N11  C12  aromatic  1.334  0.020  1.334
 15T  N29  C28  triple    1.151  0.020  1.151
 15T  N6   C7   aromatic  1.372  0.020  1.372
 15T  N6   C18  single    1.460  0.020  1.460
 15T  C7   C13  aromatic  1.406  0.020  1.406
 15T  C24  C22  single    1.528  0.020  1.528
 15T  C12  C13  aromatic  1.417  0.020  1.417
 15T  C12  N16  aromatic  1.363  0.020  1.363
 15T  C18  C20  single    1.525  0.020  1.525
 15T  C13  C14  aromatic  1.428  0.020  1.428
 15T  N16  C15  aromatic  1.360  0.020  1.360
 15T  C28  C27  single    1.454  0.020  1.454
 15T  C14  C15  aromatic  1.367  0.020  1.367
 15T  C22  C26  single    1.527  0.020  1.527
 15T  C22  C21  single    1.528  0.020  1.528
 15T  C20  C21  single    1.524  0.020  1.524
 15T  C27  C26  single    1.532  0.020  1.532
 15T  C1   H1   single    0.970  0.020  1.090
 15T  C1   H2   single    0.970  0.020  1.090
 15T  C1   H3   single    0.970  0.020  1.090
 15T  C2   H4   single    0.970  0.020  1.090
 15T  O4   H5   single    0.850  0.020  0.980
 15T  C10  H6   single    0.930  0.020  1.080
 15T  C14  H8   single    0.930  0.020  1.080
 15T  C15  H9   single    0.930  0.020  1.080
 15T  C18  H10  single    0.970  0.020  1.090
 15T  C20  H11  single    0.970  0.020  1.090
 15T  C20  H12  single    0.970  0.020  1.090
 15T  C21  H13  single    0.970  0.020  1.090
 15T  C21  H14  single    0.970  0.020  1.090
 15T  C22  H15  single    0.970  0.020  1.090
 15T  C24  H16  single    0.970  0.020  1.090
 15T  C24  H17  single    0.970  0.020  1.090
 15T  C25  H18  single    0.970  0.020  1.090
 15T  C25  H19  single    0.970  0.020  1.090
 15T  C26  H20  single    0.970  0.020  1.090
 15T  C26  H21  single    0.970  0.020  1.090
 15T  C27  H22  single    0.970  0.020  1.090
 15T  C27  H23  single    0.970  0.020  1.090
 15T  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
 15T  H3   C1   H2   108.06  3.000
 15T  H3   C1   H1   108.83  3.000
 15T  H2   C1   H1   107.27  3.000
 15T  H3   C1   C2   110.45  3.000
 15T  H2   C1   C2   111.76  3.000
 15T  H1   C1   C2   110.36  3.000
 15T  H4   C2   C5   108.76  3.000
 15T  H4   C2   O4   110.20  3.000
 15T  C5   C2   O4   106.68  3.000
 15T  H4   C2   C1   108.64  3.000
 15T  O4   C2   C1   111.92  3.000
 15T  C5   C2   C1   110.59  3.000
 15T  H5   O4   C2   107.63  3.000
 15T  N9   C5   N6   113.19  3.000
 15T  N6   C5   C2   122.81  3.000
 15T  N9   C5   C2   123.96  3.000
 15T  C18  N6   C7   127.77  3.000
 15T  C18  N6   C5   125.84  3.000
 15T  C7   N6   C5   106.39  3.000
 15T  C13  C7   C8   118.78  3.000
 15T  C13  C7   N6   136.35  3.000
 15T  C8   C7   N6   104.88  3.000
 15T  C10  C8   N9   128.57  3.000
 15T  C10  C8   C7   121.03  3.000
 15T  N9   C8   C7   110.40  3.000
 15T  C8   N9   C5   105.14  3.000
 15T  H6   C10  N11  117.78  3.000
 15T  H6   C10  C8   120.32  3.000
 15T  N11  C10  C8   121.90  3.000
 15T  C12  N11  C10  116.22  3.000
 15T  N16  C12  C13  107.45  3.000
 15T  N16  C12  N11  123.94  3.000
 15T  C13  C12  N11  128.61  3.000
 15T  C14  C13  C12  106.46  3.000
 15T  C14  C13  C7   140.08  3.000
 15T  C12  C13  C7   113.46  3.000
 15T  H8   C14  C15  124.52  3.000
 15T  H8   C14  C13  128.72  3.000
 15T  C15  C14  C13  106.76  3.000
 15T  H9   C15  N16  120.88  3.000
 15T  H9   C15  C14  129.34  3.000
 15T  N16  C15  C14  109.78  3.000
 15T  H7   N16  C15  125.54  3.000
 15T  H7   N16  C12  124.90  3.000
 15T  C15  N16  C12  109.55  3.000
 15T  H10  C18  C25  106.84  3.000
 15T  H10  C18  C20  106.64  3.000
 15T  C25  C18  C20  112.92  3.000
 15T  H10  C18  N6   106.20  3.000
 15T  C20  C18  N6   111.90  3.000
 15T  C25  C18  N6   111.83  3.000
 15T  H12  C20  H11  106.56  3.000
 15T  H12  C20  C21  109.49  3.000
 15T  H11  C20  C21  110.29  3.000
 15T  H12  C20  C18  110.74  3.000
 15T  H11  C20  C18  109.23  3.000
 15T  C21  C20  C18  110.45  3.000
 15T  H14  C21  H13  106.42  3.000
 15T  H14  C21  C22  109.99  3.000
 15T  H13  C21  C22  109.21  3.000
 15T  H14  C21  C20  109.31  3.000
 15T  H13  C21  C20  109.53  3.000
 15T  C22  C21  C20  112.21  3.000
 15T  H15  C22  C26  108.08  3.000
 15T  H15  C22  C24  108.06  3.000
 15T  C26  C22  C24  112.80  3.000
 15T  H15  C22  C21  107.89  3.000
 15T  C26  C22  C21  109.88  3.000
 15T  C24  C22  C21  109.98  3.000
 15T  H17  C24  H16  106.43  3.000
 15T  H17  C24  C25  108.40  3.000
 15T  H16  C24  C25  109.72  3.000
 15T  H17  C24  C22  110.98  3.000
 15T  H16  C24  C22  109.23  3.000
 15T  C25  C24  C22  111.92  3.000
 15T  H19  C25  H18  106.38  3.000
 15T  H19  C25  C24  110.13  3.000
 15T  H18  C25  C24  109.43  3.000
 15T  H19  C25  C18  109.44  3.000
 15T  H18  C25  C18  110.58  3.000
 15T  C24  C25  C18  110.77  3.000
 15T  H21  C26  H20  106.84  3.000
 15T  H21  C26  C27  108.71  3.000
 15T  H20  C26  C27  109.43  3.000
 15T  H21  C26  C22  109.00  3.000
 15T  H20  C26  C22  109.75  3.000
 15T  C27  C26  C22  112.93  3.000
 15T  H23  C27  H22  107.02  3.000
 15T  H23  C27  C28  107.59  3.000
 15T  H22  C27  C28  107.96  3.000
 15T  H23  C27  C26  111.65  3.000
 15T  H22  C27  C26  110.68  3.000
 15T  C28  C27  C26  111.73  3.000
 15T  N29  C28  C27  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
 15T  CONST_01  C10  C8   N9   C5    180.00   0.0  0
 15T  CONST_02  C7   C8   N9   C5      0.00   0.0  0
 15T  CONST_03  C8   C7   N6   C5      0.00   0.0  0
 15T  CONST_04  C13  C7   N6   C5    180.00   0.0  0
 15T  CONST_05  C8   N9   C5   N6      0.00   0.0  0
 15T  CONST_06  N9   C8   C7   N6      0.00   0.0  0
 15T  CONST_07  C10  C8   C7   N6    180.00   0.0  0
 15T  CONST_08  C12  C13  C7   N6    180.00   0.0  0
 15T  CONST_09  C14  C13  C7   N6      0.00   0.0  0
 15T  CONST_10  N11  C10  C8   C7      0.00   0.0  0
 15T  CONST_11  N9   C5   N6   C7      0.00   0.0  0
 15T  CONST_12  N11  C12  C13  C7      0.00   0.0  0
 15T  CONST_13  N16  C12  C13  C7    180.00   0.0  0
 15T  CONST_14  C15  C14  C13  C7    180.00   0.0  0
 15T  CONST_15  C12  N11  C10  C8      0.00   0.0  0
 15T  CONST_16  C12  C13  C7   C8      0.00   0.0  0
 15T  CONST_17  C14  C13  C7   C8    180.00   0.0  0
 15T  CONST_18  N11  C10  C8   N9    180.00   0.0  0
 15T  CONST_19  C13  C7   C8   N9    180.00   0.0  0
 15T  CONST_20  C13  C7   C8   C10     0.00   0.0  0
 15T  CONST_21  C13  C12  N11  C10     0.00   0.0  0
 15T  CONST_22  N16  C12  N11  C10   180.00   0.0  0
 15T  CONST_23  C14  C13  C12  N11   180.00   0.0  0
 15T  CONST_24  C15  N16  C12  N11   180.00   0.0  0
 15T  CONST_25  C15  C14  C13  C12     0.00   0.0  0
 15T  CONST_26  C14  C15  N16  C12     0.00   0.0  0
 15T  CONST_27  C15  N16  C12  C13     0.00   0.0  0
 15T  CONST_28  N16  C15  C14  C13     0.00   0.0  0
 15T  CONST_29  N16  C12  C13  C14     0.00   0.0  0
 15T  CONST_30  C18  N6   C7   C8    180.00   0.0  0
 15T  CONST_31  C18  N6   C5   N9    180.00   0.0  0
 15T  CONST_32  C18  N6   C7   C13     0.00   0.0  0
 15T  CONST_33  C8   N9   C5   C2    180.00   0.0  0
 15T  CONST_34  C7   N6   C5   C2    180.00   0.0  0
 15T  CONST_35  C18  N6   C5   C2      0.00   0.0  0
 15T  CONST_36  H6   C10  C8   C7    180.00   0.0  0
 15T  CONST_37  H8   C14  C13  C7      0.00   0.0  0
 15T  CONST_38  H7   N16  C12  N11     0.00   0.0  0
 15T  CONST_39  H9   C15  N16  C12   180.00   0.0  0
 15T  Var_01    C22  C24  C25  C18    54.87  30.0  1
 15T  Var_02    C22  C21  C20  C18   -55.05  30.0  1
 15T  Var_03    C28  C27  C26  C22  -175.42  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
 15T  chir_01  C2   C1   C5   O4   positiv
 15T  chir_02  C18  N6   C20  C25  negativ
 15T  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
 15T  plan-1  C2   0.020
 15T  plan-1  C5   0.020
 15T  plan-1  N6   0.020
 15T  plan-1  C7   0.020
 15T  plan-1  C8   0.020
 15T  plan-1  N9   0.020
 15T  plan-1  C10  0.020
 15T  plan-1  N11  0.020
 15T  plan-1  C12  0.020
 15T  plan-1  C13  0.020
 15T  plan-1  C14  0.020
 15T  plan-1  C15  0.020
 15T  plan-1  N16  0.020
 15T  plan-1  C18  0.020
 15T  plan-1  H6   0.020
 15T  plan-1  H8   0.020
 15T  plan-1  H9   0.020
 15T  plan-1  H7   0.020

