# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 16:35:45 2022
#   Inital geometry file: a 117 line input string
#   Ligand name: ~{N}-[(1~{R},3~{R})-3-[7-(4-fluoranyl-2-methoxy-phenyl)-1~{H}-imidazo[4,5-b]pyridin-2-yl]cyclopentyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(F)ccc1c2ccnc3nc([nH]c23)[C@@H]4CC[C@H](C4)NC(C)=O
#
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
 UT5  UT5  "N-((1R,3R)-3-(7-(4-fluoro-2-methoxyphenyl)-3H-imidazo[4,5-b]pyridin-2-yl)cyclopentyl)acetamide"
  ligand  48  27  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UT5
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
 UT5  C1   C  C     0   0.522  -47.3742  -42.1901  -4.2026
 UT5  C2   C  CR15  0  -0.125  -45.6910  -42.2775  -2.4129
 UT5  C3   C  CH2   0  -0.463  -45.4011  -41.5059  -1.1272
 UT5  C7   C  CR5   0   0.482  -42.4273  -40.5637  -3.0633
 UT5  C8   C  CR56  0   0.225  -40.5426  -39.4309  -3.1420
 UT5  C9   C  CR6   0   0.157  -39.4831  -38.5323  -3.1944
 UT5  C10  C  CR16  0  -0.397  -38.2366  -39.1363  -3.3450
 UT5  C11  C  CR16  0  -0.095  -38.1114  -40.5239  -3.4284
 UT5  C12  C  CR56  0   0.262  -40.3217  -40.8189  -3.2373
 UT5  C13  C  CR6   0  -0.060  -39.6220  -37.0656  -3.1460
 UT5  C14  C  CR16  0  -0.264  -39.0152  -36.2813  -4.1196
 UT5  C15  C  CR16  0  -0.433  -39.0957  -34.8963  -4.1056
 UT5  C16  C  CR6   0   0.553  -39.8003  -34.3113  -3.0758
 UT5  C19  C  CH3   0  -0.441  -41.5750  -36.6562  -0.0986
 UT5  F    F  F     0  -0.312  -39.8976  -32.9755  -3.0316
 UT5  C17  C  CR16  0  -0.540  -40.4165  -35.0394  -2.0747
 UT5  C18  C  CR6   0   0.380  -40.3230  -36.4281  -2.1073
 UT5  O1   O  O2    0  -0.462  -40.8557  -37.2283  -1.1751
 UT5  N2   N  N     0  -0.420  -39.1265  -41.3746  -3.3766
 UT5  N1   N  NR15  0  -0.695  -41.8990  -39.3097  -3.0436
 UT5  N3   N  N     0  -0.475  -41.5140  -41.4908  -3.1799
 UT5  C5   C  CR15  0  -0.373  -43.8937  -40.7738  -2.9325
 UT5  C4   C  CH2   0  -0.450  -44.4383  -40.3745  -1.5301
 UT5  C6   C  CH2   0  -0.412  -44.3458  -42.2196  -3.1367
 UT5  N    N  NH1   0  -0.627  -46.7479  -41.6190  -3.1596
 UT5  O    O  O     0  -0.502  -47.0936  -43.3103  -4.6086
 UT5  C    C  CH3   0  -0.774  -48.4685  -41.3658  -4.8361
 UT5  H1   H  HCR5  0   0.260  -45.9943  -43.3057  -2.2086
 UT5  H2   H  HCH2  0   0.253  -46.3069  -41.1438  -0.6384
 UT5  H3   H  HCH2  0   0.254  -44.9116  -42.1829  -0.4261
 UT5  H4   H  HCR6  0   0.264  -37.3438  -38.5259  -3.3853
 UT5  H5   H  HCR6  0   0.254  -37.1233  -40.9564  -3.5390
 UT5  H6   H  HCR6  0   0.271  -38.4747  -36.7683  -4.9211
 UT5  H7   H  HCR6  0   0.278  -38.6275  -34.2977  -4.8747
 UT5  H8   H  HCH3  0   0.265  -41.9144  -37.4860   0.5158
 UT5  H9   H  HCH3  0   0.236  -40.9440  -36.0020   0.5074
 UT5  H10  H  HCH3  0   0.235  -42.4450  -36.0932  -0.4451
 UT5  H11  H  HCR6  0   0.303  -40.9448  -34.5164  -1.2888
 UT5  H12  H  HNR5  0   0.423  -42.4268  -38.4549  -2.9564
 UT5  H14  H  HCR5  0   0.280  -44.3812  -40.1432  -3.6829
 UT5  H15  H  HCH2  0   0.249  -43.6346  -40.2707  -0.8003
 UT5  H16  H  HCH2  0   0.250  -44.9418  -39.4091  -1.5792
 UT5  H17  H  HCH2  0   0.241  -43.6544  -42.9092  -2.6476
 UT5  H18  H  HCH2  0   0.254  -44.4077  -42.5039  -4.1863
 UT5  H19  H  HNH1  0   0.401  -47.0406  -40.6999  -2.8684
 UT5  H20  H  HCH3  0   0.261  -48.2866  -41.2821  -5.9071
 UT5  H21  H  HCH3  0   0.263  -49.4238  -41.8755  -4.7091
 UT5  H22  H  HCH3  0   0.246  -48.5571  -40.3636  -4.4207

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
 UT5  O    C1   double    1.224  0.020  1.224
 UT5  C    C1   single    1.509  0.020  1.509
 UT5  C1   N    single    1.344  0.020  1.344
 UT5  C15  C14  aromatic  1.387  0.020  1.387
 UT5  C15  C16  aromatic  1.378  0.020  1.378
 UT5  C14  C13  aromatic  1.390  0.020  1.390
 UT5  F    C16  single    1.340  0.020  1.340
 UT5  C16  C17  aromatic  1.383  0.020  1.383
 UT5  N    C2   single    1.452  0.020  1.452
 UT5  C6   C2   single    1.529  0.020  1.529
 UT5  C6   C5   single    1.529  0.020  1.529
 UT5  C10  C11  aromatic  1.396  0.020  1.396
 UT5  C10  C9   aromatic  1.393  0.020  1.393
 UT5  C11  N2   aromatic  1.325  0.020  1.325
 UT5  C13  C9   single    1.474  0.020  1.474
 UT5  C13  C18  aromatic  1.406  0.020  1.406
 UT5  N2   C12  aromatic  1.325  0.020  1.325
 UT5  C9   C8   aromatic  1.390  0.020  1.390
 UT5  C12  C8   aromatic  1.409  0.020  1.409
 UT5  C12  N3   aromatic  1.370  0.020  1.370
 UT5  C8   N1   aromatic  1.365  0.020  1.365
 UT5  N3   C7   aromatic  1.307  0.020  1.307
 UT5  N1   C7   aromatic  1.361  0.020  1.361
 UT5  C7   C5   single    1.487  0.020  1.487
 UT5  C2   C3   single    1.527  0.020  1.527
 UT5  C5   C4   single    1.557  0.020  1.557
 UT5  C17  C18  aromatic  1.392  0.020  1.392
 UT5  C18  O1   single    1.339  0.020  1.339
 UT5  C3   C4   single    1.539  0.020  1.539
 UT5  O1   C19  single    1.415  0.020  1.415
 UT5  C2   H1   single    0.970  0.020  1.090
 UT5  C3   H2   single    0.970  0.020  1.090
 UT5  C3   H3   single    0.970  0.020  1.090
 UT5  C10  H4   single    0.930  0.020  1.080
 UT5  C11  H5   single    0.930  0.020  1.080
 UT5  C14  H6   single    0.930  0.020  1.080
 UT5  C15  H7   single    0.930  0.020  1.080
 UT5  C19  H8   single    0.970  0.020  1.090
 UT5  C19  H9   single    0.970  0.020  1.090
 UT5  C19  H10  single    0.970  0.020  1.090
 UT5  C17  H11  single    0.930  0.020  1.080
 UT5  N1   H12  single    0.860  0.020  1.020
 UT5  C5   H14  single    0.970  0.020  1.090
 UT5  C4   H15  single    0.970  0.020  1.090
 UT5  C4   H16  single    0.970  0.020  1.090
 UT5  C6   H17  single    0.970  0.020  1.090
 UT5  C6   H18  single    0.970  0.020  1.090
 UT5  N    H19  single    0.860  0.020  1.020
 UT5  C    H20  single    0.970  0.020  1.090
 UT5  C    H21  single    0.970  0.020  1.090
 UT5  C    H22  single    0.970  0.020  1.090

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
 UT5  C    C1   O    121.79  3.000
 UT5  C    C1   N    115.56  3.000
 UT5  O    C1   N    122.65  3.000
 UT5  H1   C2   N    108.74  3.000
 UT5  H1   C2   C6   111.65  3.000
 UT5  N    C2   C6   112.32  3.000
 UT5  H1   C2   C3   111.79  3.000
 UT5  C6   C2   C3   102.26  3.000
 UT5  N    C2   C3   110.00  3.000
 UT5  H3   C3   H2   106.89  3.000
 UT5  H3   C3   C4   110.11  3.000
 UT5  H2   C3   C4   113.11  3.000
 UT5  H3   C3   C2   108.23  3.000
 UT5  H2   C3   C2   112.78  3.000
 UT5  C4   C3   C2   105.65  3.000
 UT5  C5   C7   N3   126.64  3.000
 UT5  C5   C7   N1   120.78  3.000
 UT5  N3   C7   N1   112.56  3.000
 UT5  N1   C8   C12  104.36  3.000
 UT5  N1   C8   C9   134.62  3.000
 UT5  C12  C8   C9   120.99  3.000
 UT5  C13  C9   C10  121.27  3.000
 UT5  C13  C9   C8   124.76  3.000
 UT5  C10  C9   C8   113.93  3.000
 UT5  H4   C10  C11  118.98  3.000
 UT5  H4   C10  C9   119.84  3.000
 UT5  C11  C10  C9   121.18  3.000
 UT5  H5   C11  N2   116.48  3.000
 UT5  H5   C11  C10  118.97  3.000
 UT5  N2   C11  C10  124.54  3.000
 UT5  N3   C12  N2   125.71  3.000
 UT5  N3   C12  C8   110.12  3.000
 UT5  N2   C12  C8   124.17  3.000
 UT5  C18  C13  C14  118.65  3.000
 UT5  C18  C13  C9   121.49  3.000
 UT5  C14  C13  C9   119.83  3.000
 UT5  H6   C14  C15  119.05  3.000
 UT5  H6   C14  C13  118.87  3.000
 UT5  C15  C14  C13  122.07  3.000
 UT5  H7   C15  C16  121.19  3.000
 UT5  H7   C15  C14  121.35  3.000
 UT5  C16  C15  C14  117.45  3.000
 UT5  C17  C16  F    117.95  3.000
 UT5  C17  C16  C15  123.05  3.000
 UT5  F    C16  C15  119.01  3.000
 UT5  H10  C19  H9   109.10  3.000
 UT5  H10  C19  H8   108.91  3.000
 UT5  H9   C19  H8   108.91  3.000
 UT5  H10  C19  O1   111.82  3.000
 UT5  H9   C19  O1   111.73  3.000
 UT5  H8   C19  O1   106.27  3.000
 UT5  H11  C17  C18  122.14  3.000
 UT5  H11  C17  C16  119.28  3.000
 UT5  C18  C17  C16  118.58  3.000
 UT5  O1   C18  C17  123.58  3.000
 UT5  O1   C18  C13  116.21  3.000
 UT5  C17  C18  C13  120.20  3.000
 UT5  C18  O1   C19  119.35  3.000
 UT5  C12  N2   C11  115.19  3.000
 UT5  H12  N1   C8   126.97  3.000
 UT5  H12  N1   C7   125.40  3.000
 UT5  C8   N1   C7   107.63  3.000
 UT5  C12  N3   C7   105.32  3.000
 UT5  H14  C5   C6   108.76  3.000
 UT5  H14  C5   C4   108.30  3.000
 UT5  C6   C5   C4   105.04  3.000
 UT5  H14  C5   C7   107.30  3.000
 UT5  C4   C5   C7   112.83  3.000
 UT5  C6   C5   C7   114.43  3.000
 UT5  H16  C4   H15  106.64  3.000
 UT5  H16  C4   C5   110.38  3.000
 UT5  H15  C4   C5   111.68  3.000
 UT5  H16  C4   C3   111.96  3.000
 UT5  H15  C4   C3   110.84  3.000
 UT5  C5   C4   C3   105.43  3.000
 UT5  H18  C6   H17  107.61  3.000
 UT5  H18  C6   C5   113.10  3.000
 UT5  H17  C6   C5   110.50  3.000
 UT5  H18  C6   C2   113.36  3.000
 UT5  H17  C6   C2   108.74  3.000
 UT5  C5   C6   C2   103.47  3.000
 UT5  H19  N    C2   118.45  3.000
 UT5  H19  N    C1   118.47  3.000
 UT5  C2   N    C1   123.06  3.000
 UT5  H22  C    H21  108.34  3.000
 UT5  H22  C    H20  108.54  3.000
 UT5  H21  C    H20  107.26  3.000
 UT5  H22  C    C1   113.69  3.000
 UT5  H21  C    C1   109.33  3.000
 UT5  H20  C    C1   109.48  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
 UT5  CONST_01  N2   C12  N3   C7    180.00   0.0  0
 UT5  CONST_02  C8   C12  N3   C7      0.00   0.0  0
 UT5  CONST_03  C9   C8   N1   C7    180.00   0.0  0
 UT5  CONST_04  C12  C8   N1   C7      0.00   0.0  0
 UT5  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 UT5  CONST_08  C11  N2   C12  C8      0.00   0.0  0
 UT5  CONST_09  N3   C7   N1   C8      0.00   0.0  0
 UT5  CONST_10  N2   C11  C10  C9      0.00   0.0  0
 UT5  CONST_11  C15  C14  C13  C9    180.00   0.0  0
 UT5  CONST_12  C17  C18  C13  C9    180.00   0.0  0
 UT5  CONST_13  N2   C12  C8   C9      0.00   0.0  0
 UT5  CONST_14  N3   C12  C8   C9    180.00   0.0  0
 UT5  CONST_15  C12  N2   C11  C10     0.00   0.0  0
 UT5  CONST_18  C12  C8   C9   C10     0.00   0.0  0
 UT5  CONST_19  N1   C8   C9   C10   180.00   0.0  0
 UT5  CONST_20  C13  C9   C10  C11   180.00   0.0  0
 UT5  CONST_21  N3   C12  N2   C11   180.00   0.0  0
 UT5  CONST_22  C13  C9   C8   C12   180.00   0.0  0
 UT5  CONST_23  N1   C7   N3   C12     0.00   0.0  0
 UT5  CONST_24  C16  C15  C14  C13     0.00   0.0  0
 UT5  CONST_25  N1   C8   C9   C13     0.00   0.0  0
 UT5  CONST_26  C16  C17  C18  C13     0.00   0.0  0
 UT5  CONST_27  C17  C16  C15  C14     0.00   0.0  0
 UT5  CONST_28  C17  C18  C13  C14     0.00   0.0  0
 UT5  CONST_29  C18  C13  C14  C15     0.00   0.0  0
 UT5  CONST_30  C18  C17  C16  C15     0.00   0.0  0
 UT5  CONST_31  N1   C8   C12  N2    180.00   0.0  0
 UT5  CONST_32  N3   C12  C8   N1      0.00   0.0  0
 UT5  CONST_33  C5   C7   N1   C8    180.00   0.0  0
 UT5  CONST_34  C5   C7   N3   C12   180.00   0.0  0
 UT5  CONST_35  O1   C18  C13  C9      0.00   0.0  0
 UT5  CONST_36  F    C16  C15  C14   180.00   0.0  0
 UT5  CONST_37  O1   C18  C13  C14   180.00   0.0  0
 UT5  CONST_38  O1   C18  C17  C16   180.00   0.0  0
 UT5  CONST_39  C18  C17  C16  F     180.00   0.0  0
 UT5  CONST_40  H4   C10  C9   C8    180.00   0.0  0
 UT5  CONST_41  H5   C11  C10  C9    180.00   0.0  0
 UT5  CONST_42  H6   C14  C13  C9      0.00   0.0  0
 UT5  CONST_43  H12  N1   C8   C9      0.00   0.0  0
 UT5  CONST_44  H5   C11  N2   C12   180.00   0.0  0
 UT5  CONST_45  H12  N1   C8   C12   180.00   0.0  0
 UT5  CONST_46  H7   C15  C14  C13   180.00   0.0  0
 UT5  CONST_47  H4   C10  C9   C13     0.00   0.0  0
 UT5  CONST_48  H11  C17  C18  C13   180.00   0.0  0
 UT5  CONST_49  H11  C17  C16  C15   180.00   0.0  0
 UT5  CONST_50  H6   C14  C15  C16   180.00   0.0  0
 UT5  CONST_51  H7   C15  C16  C17   180.00   0.0  0
 UT5  CONST_52  H6   C14  C13  C18   180.00   0.0  0
 UT5  CONST_53  H4   C10  C11  N2    180.00   0.0  0
 UT5  CONST_54  H12  N1   C7   N3    180.00   0.0  0
 UT5  CONST_55  H12  N1   C7   C5      0.00   0.0  0
 UT5  CONST_56  O    C1   N    C2      0.00   0.0  0
 UT5  CONST_57  C    C1   N    C2    180.00   0.0  0
 UT5  CONST_58  H19  N    C1   O     180.00   0.0  0
 UT5  CONST_59  H19  N    C1   C       0.00   0.0  0
 UT5  Var_01    C5   C4   C3   C2    -15.73  30.0  1
 UT5  Var_02    H15  C4   C3   C2   -136.74  30.0  1
 UT5  Var_03    H16  C4   C3   C2    104.33  30.0  1
 UT5  Var_04    H2   C3   C4   C5   -139.56  30.0  1
 UT5  Var_05    H3   C3   C4   C5    100.92  30.0  1
 UT5  Var_06    C19  O1   C18  C13   179.96  30.0  2
 UT5  Var_07    C17  C18  O1   C19     0.99  30.0  2
 UT5  Var_08    H8   C19  O1   C18   179.57  30.0  3
 UT5  Var_09    H9   C19  O1   C18   -61.77  30.0  3
 UT5  Var_10    H10  C19  O1   C18    60.85  30.0  3
 UT5  Var_11    H20  C    C1   N     126.72  30.0  3
 UT5  Var_12    H21  C    C1   N    -116.04  30.0  3
 UT5  Var_13    H22  C    C1   N       5.15  30.0  3
 UT5  Var_14    H20  C    C1   O     -54.13  30.0  3
 UT5  Var_15    H21  C    C1   O      63.11  30.0  3
 UT5  Var_16    H22  C    C1   O    -175.70  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
 UT5  chir_01  C2  N   C6  C3  negativ
 UT5  chir_02  C5  C4  C7  C6  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
 UT5  plan-1  C9   0.020
 UT5  plan-1  C13  0.020
 UT5  plan-1  C14  0.020
 UT5  plan-1  C15  0.020
 UT5  plan-1  C16  0.020
 UT5  plan-1  F    0.020
 UT5  plan-1  C17  0.020
 UT5  plan-1  C18  0.020
 UT5  plan-1  O1   0.020
 UT5  plan-1  H6   0.020
 UT5  plan-1  H7   0.020
 UT5  plan-1  H11  0.020
 UT5  plan-2  C7   0.020
 UT5  plan-2  C8   0.020
 UT5  plan-2  C9   0.020
 UT5  plan-2  C10  0.020
 UT5  plan-2  C11  0.020
 UT5  plan-2  C12  0.020
 UT5  plan-2  C13  0.020
 UT5  plan-2  N2   0.020
 UT5  plan-2  N1   0.020
 UT5  plan-2  N3   0.020
 UT5  plan-2  C5   0.020
 UT5  plan-2  H4   0.020
 UT5  plan-2  H5   0.020
 UT5  plan-2  H12  0.020
 UT5  plan-3  C1   0.020
 UT5  plan-3  C2   0.020
 UT5  plan-3  N    0.020
 UT5  plan-3  O    0.020
 UT5  plan-3  C    0.020
 UT5  plan-3  H19  0.020

