# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 13:14:13 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: 1-(2-azanylpyrimidin-4-yl)-6-[2-(1-oxidanylcyclohexyl)ethynyl]indole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cn(c2ccnc(N)n2)c3cc(ccc13)C#CC4(O)CCCCC4
#
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
 G5X  G5X  1-(2-azanylpyrimidin-4-yl)-6-[2-(1-oxidanylcyclohexyl)ethynyl]indole-3-carboxamide  ligand  49  28  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G5X
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
 G5X  N12  N  NH2   0  -0.817  -39.6048   9.3415  -14.2457
 G5X  C15  C  CR16  0  -0.339  -33.4697  11.4200  -14.3488
 G5X  C21  C  CH2   0  -0.457  -29.2592   8.3249  -15.7986
 G5X  C22  C  CH2   0  -0.436  -28.2232   7.5315  -16.5874
 G5X  C24  C  CH2   0  -0.441  -28.0861   9.3942  -18.2739
 G5X  C26  C  CR16  0  -0.301  -31.8762  12.8052  -13.1466
 G5X  C28  C  CR56  0   0.077  -34.2188  13.1228  -12.7564
 G5X  C4   C  CR5   0  -0.167  -35.4888  13.5358  -12.2221
 G5X  C5   C  CR15  0   0.011  -36.4376  12.7664  -12.8245
 G5X  C7   C  CR6   0   0.539  -36.5958  11.0570  -14.5504
 G5X  C8   C  CR16  0  -0.427  -36.1912  10.7418  -15.8408
 G5X  C9   C  CR16  0  -0.014  -37.0278   9.8675  -16.5161
 G5X  C11  C  CR6   0   0.568  -38.4522   9.7793  -14.7701
 G5X  C14  C  CR56  0   0.371  -34.4842  12.1081  -13.6985
 G5X  C16  C  CR6   0  -0.150  -32.1550  11.7846  -14.0759
 G5X  C18  C  CSP   0   0.175  -30.1790  10.5436  -15.2918
 G5X  C19  C  CT    0   0.024  -29.0849   9.8420  -15.9833
 G5X  C23  C  CH2   0  -0.430  -28.2604   7.8934  -18.0675
 G5X  C25  C  CH2   0  -0.431  -29.1173  10.1884  -17.4782
 G5X  C27  C  CR16  0  -0.363  -32.8900  13.4602  -12.4829
 G5X  N1   N  NH2   0  -0.817  -34.9444  15.5674  -11.0755
 G5X  N6   N  NR5   0  -0.649  -35.8587  11.9239  -13.7341
 G5X  N10  N  N     0  -0.455  -38.1418   9.3737  -16.0086
 G5X  N13  N  N     0  -0.489  -37.7066  10.5937  -14.0162
 G5X  O3   O  O     0  -0.472  -36.8704  14.4976  -10.5779
 G5X  O20  O  OH1   0  -0.660  -27.8382  10.2850  -15.4864
 G5X  H1   H  HNH2  0   0.402  -40.1352   8.6369  -14.7274
 G5X  H2   H  HNH2  0   0.402  -39.8227   9.5260  -13.2822
 G5X  H3   H  HCR6  0   0.283  -33.6678  10.6098  -15.0355
 G5X  H5   H  HCH2  0   0.242  -29.2090   8.0795  -14.7332
 G5X  H6   H  HCH2  0   0.233  -28.4115   6.4642  -16.4520
 G5X  H7   H  HCH2  0   0.217  -27.2237   7.7201  -16.1861
 G5X  H8   H  HCH2  0   0.220  -27.0766   9.6939  -17.9805
 G5X  H9   H  HCH2  0   0.231  -28.1851   9.6447  -19.3327
 G5X  H10  H  HCR6  0   0.258  -30.8458  13.0634  -12.9431
 G5X  H11  H  HCR5  0   0.310  -37.5079  12.7831  -12.7013
 G5X  H12  H  HCR6  0   0.291  -35.3213  11.1639  -16.3174
 G5X  H13  H  HCR6  0   0.278  -36.7819   9.5638  -17.5281
 G5X  H14  H  HCH2  0   0.211  -29.2206   7.5802  -18.4919
 G5X  H15  H  HCH2  0   0.230  -27.4870   7.3453  -18.6104
 G5X  H16  H  HCH2  0   0.242  -28.9632  11.2629  -17.6032
 G5X  H17  H  HCH2  0   0.232  -30.1194   9.9672  -17.8551
 G5X  H18  H  HCR6  0   0.254  -32.6417  14.2111  -11.7451
 G5X  H19  H  HNH2  0   0.402  -35.1733  16.3332  -10.4616
 G5X  H20  H  HNH2  0   0.408  -34.2377  15.7509  -11.7673
 G5X  H21  H  HOH1  0   0.448  -27.7305   9.9604  -14.5852
 G5X  C17  C  CSP   0   0.104  -31.0859  11.1093  -14.7336
 G5X  C2   C  C     0   0.422  -35.8342  14.5667  -11.2246
 G5X  H4   H  HCH2  0   0.232  -30.2638   8.0508  -16.1327

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
 G5X  C24  C23  single    1.525  0.020  1.525
 G5X  C24  C25  single    1.526  0.020  1.526
 G5X  C23  C22  single    1.524  0.020  1.524
 G5X  C25  C19  single    1.535  0.020  1.535
 G5X  C22  C21  single    1.525  0.020  1.525
 G5X  C9   N10  aromatic  1.320  0.020  1.320
 G5X  C9   C8   aromatic  1.386  0.020  1.386
 G5X  C21  C19  single    1.538  0.020  1.538
 G5X  C19  O20  single    1.413  0.020  1.413
 G5X  C19  C18  single    1.472  0.020  1.472
 G5X  N10  C11  aromatic  1.340  0.020  1.340
 G5X  C8   C7   aromatic  1.389  0.020  1.389
 G5X  C18  C17  triple    1.206  0.020  1.206
 G5X  C11  N12  single    1.340  0.020  1.340
 G5X  C11  N13  aromatic  1.337  0.020  1.337
 G5X  C17  C16  single    1.425  0.020  1.425
 G5X  C7   N13  aromatic  1.317  0.020  1.317
 G5X  C7   N6   single    1.400  0.020  1.400
 G5X  C15  C16  aromatic  1.391  0.020  1.391
 G5X  C15  C14  aromatic  1.388  0.020  1.388
 G5X  C16  C26  aromatic  1.408  0.020  1.408
 G5X  N6   C14  aromatic  1.387  0.020  1.387
 G5X  N6   C5   aromatic  1.368  0.020  1.368
 G5X  C14  C28  aromatic  1.410  0.020  1.410
 G5X  C26  C27  aromatic  1.377  0.020  1.377
 G5X  C5   C4   aromatic  1.362  0.020  1.362
 G5X  C28  C27  aromatic  1.398  0.020  1.398
 G5X  C28  C4   aromatic  1.438  0.020  1.438
 G5X  C4   C2   single    1.475  0.020  1.475
 G5X  C2   N1   single    1.347  0.020  1.347
 G5X  C2   O3   double    1.223  0.020  1.223
 G5X  N12  H1   single    0.860  0.020  1.020
 G5X  N12  H2   single    0.860  0.020  1.020
 G5X  C15  H3   single    0.930  0.020  1.080
 G5X  C21  H4   single    0.970  0.020  1.090
 G5X  C21  H5   single    0.970  0.020  1.090
 G5X  C22  H6   single    0.970  0.020  1.090
 G5X  C22  H7   single    0.970  0.020  1.090
 G5X  C24  H8   single    0.970  0.020  1.090
 G5X  C24  H9   single    0.970  0.020  1.090
 G5X  C26  H10  single    0.930  0.020  1.080
 G5X  C5   H11  single    0.930  0.020  1.080
 G5X  C8   H12  single    0.930  0.020  1.080
 G5X  C9   H13  single    0.930  0.020  1.080
 G5X  C23  H14  single    0.970  0.020  1.090
 G5X  C23  H15  single    0.970  0.020  1.090
 G5X  C25  H16  single    0.970  0.020  1.090
 G5X  C25  H17  single    0.970  0.020  1.090
 G5X  C27  H18  single    0.930  0.020  1.080
 G5X  N1   H19  single    0.890  0.020  1.040
 G5X  N1   H20  single    0.890  0.020  1.040
 G5X  O20  H21  single    0.850  0.020  0.980

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
 G5X  H2   N12  H1   118.28  3.000
 G5X  H2   N12  C11  120.12  3.000
 G5X  H1   N12  C11  119.71  3.000
 G5X  H3   C15  C16  119.63  3.000
 G5X  H3   C15  C14  122.39  3.000
 G5X  C16  C15  C14  117.97  3.000
 G5X  H5   C21  H4   106.46  3.000
 G5X  H5   C21  C19  109.44  3.000
 G5X  H4   C21  C19  108.34  3.000
 G5X  H5   C21  C22  110.84  3.000
 G5X  H4   C21  C22  109.62  3.000
 G5X  C19  C21  C22  111.97  3.000
 G5X  H7   C22  H6   106.30  3.000
 G5X  H7   C22  C23  109.74  3.000
 G5X  H6   C22  C23  110.37  3.000
 G5X  H7   C22  C21  109.97  3.000
 G5X  H6   C22  C21  109.10  3.000
 G5X  C23  C22  C21  111.24  3.000
 G5X  H9   C24  H8   106.32  3.000
 G5X  H9   C24  C25  108.96  3.000
 G5X  H8   C24  C25  109.96  3.000
 G5X  H9   C24  C23  110.27  3.000
 G5X  H8   C24  C23  109.82  3.000
 G5X  C25  C24  C23  111.38  3.000
 G5X  H10  C26  C27  119.80  3.000
 G5X  H10  C26  C16  119.07  3.000
 G5X  C27  C26  C16  121.13  3.000
 G5X  C27  C28  C14  118.90  3.000
 G5X  C27  C28  C4   134.21  3.000
 G5X  C14  C28  C4   106.78  3.000
 G5X  C5   C4   C2   122.05  3.000
 G5X  C2   C4   C28  131.18  3.000
 G5X  C5   C4   C28  106.77  3.000
 G5X  H11  C5   N6   120.38  3.000
 G5X  H11  C5   C4   129.25  3.000
 G5X  N6   C5   C4   110.31  3.000
 G5X  N13  C7   N6   115.17  3.000
 G5X  N6   C7   C8   121.93  3.000
 G5X  N13  C7   C8   122.88  3.000
 G5X  H12  C8   C9   121.25  3.000
 G5X  H12  C8   C7   123.85  3.000
 G5X  C9   C8   C7   114.85  3.000
 G5X  H13  C9   N10  116.44  3.000
 G5X  H13  C9   C8   119.63  3.000
 G5X  N10  C9   C8   123.92  3.000
 G5X  N13  C11  N10  125.20  3.000
 G5X  N13  C11  N12  117.26  3.000
 G5X  N10  C11  N12  117.54  3.000
 G5X  N6   C14  C28  107.41  3.000
 G5X  C28  C14  C15  122.17  3.000
 G5X  N6   C14  C15  130.28  3.000
 G5X  C26  C16  C17  119.97  3.000
 G5X  C26  C16  C15  120.43  3.000
 G5X  C17  C16  C15  119.61  3.000
 G5X  C19  C18  C17  180.00  3.000
 G5X  O20  C19  C25  106.88  3.000
 G5X  O20  C19  C18  109.94  3.000
 G5X  C25  C19  C18  109.53  3.000
 G5X  C18  C19  C21  109.23  3.000
 G5X  O20  C19  C21  111.52  3.000
 G5X  C25  C19  C21  109.70  3.000
 G5X  H15  C23  H14  106.54  3.000
 G5X  H15  C23  C24  110.22  3.000
 G5X  H14  C23  C24  109.21  3.000
 G5X  H15  C23  C22  110.25  3.000
 G5X  H14  C23  C22  109.25  3.000
 G5X  C24  C23  C22  111.24  3.000
 G5X  H17  C25  H16  106.79  3.000
 G5X  H17  C25  C19  108.02  3.000
 G5X  H16  C25  C19  109.29  3.000
 G5X  H17  C25  C24  109.54  3.000
 G5X  H16  C25  C24  110.92  3.000
 G5X  C19  C25  C24  112.10  3.000
 G5X  H18  C27  C28  121.28  3.000
 G5X  H18  C27  C26  119.33  3.000
 G5X  C28  C27  C26  119.37  3.000
 G5X  H20  N1   H19  116.09  3.000
 G5X  H20  N1   C2   121.56  3.000
 G5X  H19  N1   C2   118.80  3.000
 G5X  C14  N6   C7   128.22  3.000
 G5X  C14  N6   C5   108.68  3.000
 G5X  C7   N6   C5   123.09  3.000
 G5X  C11  N10  C9   115.96  3.000
 G5X  C11  N13  C7   117.13  3.000
 G5X  H21  O20  C19  108.77  3.000
 G5X  C18  C17  C16  180.00  3.000
 G5X  O3   C2   N1   122.88  3.000
 G5X  O3   C2   C4   121.07  3.000
 G5X  N1   C2   C4   116.05  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
 G5X  CONST_01  C27  C26  C16  C15    0.00   0.0  0
 G5X  CONST_02  C7   N6   C14  C15    0.00   0.0  0
 G5X  CONST_03  C5   N6   C14  C15  180.00   0.0  0
 G5X  CONST_04  C27  C28  C14  C15    0.00   0.0  0
 G5X  CONST_05  C4   C28  C14  C15  180.00   0.0  0
 G5X  CONST_06  C14  C15  C16  C26    0.00   0.0  0
 G5X  CONST_07  C14  C28  C27  C26    0.00   0.0  0
 G5X  CONST_08  C4   C28  C27  C26  180.00   0.0  0
 G5X  CONST_09  C16  C15  C14  C28    0.00   0.0  0
 G5X  CONST_10  C7   N6   C14  C28  180.00   0.0  0
 G5X  CONST_11  C5   N6   C14  C28    0.00   0.0  0
 G5X  CONST_12  C16  C26  C27  C28    0.00   0.0  0
 G5X  CONST_13  N6   C5   C4   C28    0.00   0.0  0
 G5X  CONST_14  C7   N6   C5   C4   180.00   0.0  0
 G5X  CONST_15  C14  N6   C5   C4     0.00   0.0  0
 G5X  CONST_16  N6   C14  C28  C4     0.00   0.0  0
 G5X  CONST_19  C14  C28  C4   C5     0.00   0.0  0
 G5X  CONST_20  C27  C28  C4   C5   180.00   0.0  0
 G5X  CONST_21  N10  C9   C8   C7     0.00   0.0  0
 G5X  CONST_22  N10  C11  N13  C7     0.00   0.0  0
 G5X  CONST_23  C11  N10  C9   C8     0.00   0.0  0
 G5X  CONST_24  C11  N13  C7   C8     0.00   0.0  0
 G5X  CONST_26  N13  C11  N10  C9     0.00   0.0  0
 G5X  CONST_27  N13  C7   C8   C9     0.00   0.0  0
 G5X  CONST_28  N6   C7   C8   C9   180.00   0.0  0
 G5X  CONST_29  N6   C7   N13  C11  180.00   0.0  0
 G5X  CONST_31  N6   C14  C15  C16  180.00   0.0  0
 G5X  CONST_32  N6   C14  C28  C27  180.00   0.0  0
 G5X  CONST_33  C9   N10  C11  N12  180.00   0.0  0
 G5X  CONST_34  C7   N13  C11  N12  180.00   0.0  0
 G5X  CONST_35  C14  C15  C16  C17  180.00   0.0  0
 G5X  CONST_36  C27  C26  C16  C17  180.00   0.0  0
 G5X  CONST_37  N6   C5   C4   C2   180.00   0.0  0
 G5X  CONST_38  C14  C28  C4   C2   180.00   0.0  0
 G5X  CONST_39  C27  C28  C4   C2     0.00   0.0  0
 G5X  CONST_40  H10  C26  C16  C15  180.00   0.0  0
 G5X  CONST_41  H3   C15  C16  C26  180.00   0.0  0
 G5X  CONST_42  H11  C5   C4   C28  180.00   0.0  0
 G5X  CONST_43  H18  C27  C28  C4     0.00   0.0  0
 G5X  CONST_44  H13  C9   C8   C7   180.00   0.0  0
 G5X  CONST_45  H12  C8   C7   N6     0.00   0.0  0
 G5X  CONST_46  H1   N12  C11  N10    0.00   0.0  0
 G5X  CONST_47  H2   N12  C11  N10  180.00   0.0  0
 G5X  CONST_48  H19  N1   C2   C4   180.00   0.0  0
 G5X  Var_01    C24  C23  C22  C21   55.21  30.0  1
 G5X  Var_02    C25  C24  C23  C22  -54.95  30.0  1
 G5X  Var_03    C23  C24  C25  C19   55.50  30.0  1
 G5X  Var_04    C23  C22  C21  C19  -55.99  30.0  1
 G5X  Var_05    N1   C2   C4   C28   23.97  30.0  2

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
 G5X  chir_01  C19  C21  C25  C18  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
 G5X  plan-1  N12  0.020
 G5X  plan-1  C7   0.020
 G5X  plan-1  C8   0.020
 G5X  plan-1  C9   0.020
 G5X  plan-1  C11  0.020
 G5X  plan-1  N6   0.020
 G5X  plan-1  N10  0.020
 G5X  plan-1  N13  0.020
 G5X  plan-1  H12  0.020
 G5X  plan-1  H13  0.020
 G5X  plan-2  C15  0.020
 G5X  plan-2  C26  0.020
 G5X  plan-2  C28  0.020
 G5X  plan-2  C4   0.020
 G5X  plan-2  C5   0.020
 G5X  plan-2  C7   0.020
 G5X  plan-2  C14  0.020
 G5X  plan-2  C16  0.020
 G5X  plan-2  C18  0.020
 G5X  plan-2  C27  0.020
 G5X  plan-2  N6   0.020
 G5X  plan-2  H3   0.020
 G5X  plan-2  H10  0.020
 G5X  plan-2  H11  0.020
 G5X  plan-2  H18  0.020
 G5X  plan-2  C17  0.020
 G5X  plan-2  C2   0.020
 G5X  plan-3  N12  0.020
 G5X  plan-3  C11  0.020
 G5X  plan-3  H1   0.020
 G5X  plan-3  H2   0.020
 G5X  plan-4  C4   0.020
 G5X  plan-4  N1   0.020
 G5X  plan-4  O3   0.020
 G5X  plan-4  H19  0.020
 G5X  plan-4  H20  0.020
 G5X  plan-4  C2   0.020

