# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 13:40:59 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: 5-fluoranyl-4-[[[8-(2-methylpyridin-3-yl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-yl]amino]methyl]-2,3-dihydro-1-benzofuran-7-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncccc1c2cnc(NCc3c(F)cc(C#N)c4OCCc34)n5cnnc25
#
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
 PV5  PV5  5-fluoranyl-4-[[[8-(2-methylpyridin-3-yl)-[1,2,4]triazolo[4,3-c]pyrimidin-5-yl]amino]methyl]-2,3-dihydro-1-benzofuran-7-carbonitrile  ligand  46  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PV5
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
 PV5  C1   C  CR6   0   0.225  -20.2847  27.8253  11.8412
 PV5  C2   C  CR6   0  -0.010  -20.2362  29.1324  11.3322
 PV5  C3   C  CR16  0  -0.168  -19.2577  29.4358  10.3933
 PV5  N6   N  NS    0  -0.244  -19.1781  38.4118   9.4997
 PV5  C7   C  CR16  0  -0.068  -20.7539  31.3169  12.4139
 PV5  C8   C  CR6   0   0.799  -22.8305  32.2744  12.5358
 PV5  C9   C  CR56  0   0.480  -22.5571  30.1175  11.5037
 PV5  C10  C  CR15  0   0.048  -24.6134  30.8238  11.4871
 PV5  C11  C  CH2   0  -0.377  -23.1821  34.4672  13.5091
 PV5  C12  C  CR6   0  -0.124  -22.2956  35.3092  12.6285
 PV5  C13  C  CR6   0   0.533  -22.7280  35.7667  11.3793
 PV5  C14  C  CR16  0  -0.418  -21.9624  36.5556  10.5595
 PV5  C15  C  CR6   0  -0.109  -20.6775  36.9333  10.9781
 PV5  C16  C  CR56  0   0.458  -20.2329  36.4870  12.2138
 PV5  C19  C  CH2   0  -0.185  -18.9243  36.1101  14.0159
 PV5  C20  C  CSP   0   0.059  -19.8501  37.7496  10.1617
 PV5  F    F  F     0  -0.307  -23.9577  35.4193  10.9669
 PV5  O    O  O     0  -0.471  -19.0339  36.7572  12.7261
 PV5  C18  C  CH2   0  -0.541  -20.2542  35.3752  14.2669
 PV5  C17  C  CR56  0  -0.038  -21.0314  35.6904  13.0249
 PV5  N5   N  NH1   0  -0.674  -23.6626  33.2614  12.8739
 PV5  N1   N  N     0  -0.479  -21.5596  32.3371  12.7932
 PV5  N2   N  N     0  -0.594  -23.3538  31.1700  11.8981
 PV5  N4   N  N     0  -0.294  -24.5689  29.6699  10.9022
 PV5  N3   N  N     0  -0.344  -23.2933  29.2178  10.9010
 PV5  C6   C  CR6   0  -0.137  -21.1662  30.1843  11.7766
 PV5  C4   C  CR16  0  -0.326  -18.3770  28.4514   9.9761
 PV5  C5   C  CR16  0  -0.071  -18.5194  27.1877  10.5208
 PV5  N    N  N     0  -0.421  -19.4390  26.8852  11.4292
 PV5  C    C  CH3   0  -0.744  -21.2810  27.4251  12.8860
 PV5  H1   H  HCR6  0   0.266  -19.1965  30.4373   9.9858
 PV5  H2   H  HCR6  0   0.274  -19.7051  31.4434  12.6563
 PV5  H3   H  HCR5  0   0.324  -25.4955  31.4251  11.6347
 PV5  H4   H  HCH2  0   0.286  -22.6479  34.2116  14.4240
 PV5  H5   H  HCH2  0   0.304  -24.0617  35.0383  13.8067
 PV5  H6   H  HCR6  0   0.299  -22.3467  36.8872   9.6042
 PV5  H7   H  HCH2  0   0.255  -18.0733  35.4315  13.9768
 PV5  H8   H  HCH2  0   0.282  -20.7518  35.7391  15.1668
 PV5  H9   H  HNH1  0   0.430  -24.6378  33.2149  12.6315
 PV5  H10  H  HCR6  0   0.268  -17.6074  28.6563   9.2450
 PV5  H11  H  HCR6  0   0.261  -17.8589  26.3822  10.2187
 PV5  H12  H  HCH3  0   0.253  -20.9597  26.5094  13.3777
 PV5  H13  H  HCH3  0   0.245  -21.4105  28.2013  13.6407
 PV5  H14  H  HCH3  0   0.256  -22.2614  27.2430  12.4426
 PV5  H15  H  HCH2  0   0.255  -18.7251  36.8794  14.7604
 PV5  H16  H  HCH2  0   0.284  -20.1141  34.2995  14.3818

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
 PV5  N6   C20  triple    1.152  0.020  1.152
 PV5  C20  C15  single    1.420  0.020  1.420
 PV5  C4   C3   aromatic  1.385  0.020  1.385
 PV5  C4   C5   aromatic  1.383  0.020  1.383
 PV5  C3   C2   aromatic  1.390  0.020  1.390
 PV5  C14  C15  aromatic  1.403  0.020  1.403
 PV5  C14  C13  aromatic  1.371  0.020  1.371
 PV5  N4   N3   aromatic  1.353  0.020  1.353
 PV5  N4   C10  aromatic  1.294  0.020  1.294
 PV5  C5   N    aromatic  1.328  0.020  1.328
 PV5  N3   C9   aromatic  1.310  0.020  1.310
 PV5  C15  C16  aromatic  1.387  0.020  1.387
 PV5  F    C13  single    1.343  0.020  1.343
 PV5  C10  N2   aromatic  1.369  0.020  1.369
 PV5  C9   N2   aromatic  1.378  0.020  1.378
 PV5  C9   C6   aromatic  1.419  0.020  1.419
 PV5  C2   C6   single    1.473  0.020  1.473
 PV5  C2   C1   aromatic  1.404  0.020  1.404
 PV5  C13  C12  aromatic  1.399  0.020  1.399
 PV5  N    C1   aromatic  1.330  0.020  1.330
 PV5  N2   C8   aromatic  1.378  0.020  1.378
 PV5  C6   C7   aromatic  1.363  0.020  1.363
 PV5  C1   C    single    1.498  0.020  1.498
 PV5  C16  O    single    1.332  0.020  1.332
 PV5  C16  C17  aromatic  1.389  0.020  1.389
 PV5  O    C19  single    1.447  0.020  1.447
 PV5  C7   N1   aromatic  1.354  0.020  1.354
 PV5  C8   N5   single    1.334  0.020  1.334
 PV5  C8   N1   aromatic  1.298  0.020  1.298
 PV5  C12  C17  aromatic  1.379  0.020  1.379
 PV5  C12  C11  single    1.507  0.020  1.507
 PV5  C17  C18  single    1.499  0.020  1.499
 PV5  N5   C11  single    1.445  0.020  1.445
 PV5  C19  C18  single    1.540  0.020  1.540
 PV5  C3   H1   single    0.930  0.020  1.080
 PV5  C7   H2   single    0.930  0.020  1.080
 PV5  C10  H3   single    0.930  0.020  1.080
 PV5  C11  H4   single    0.970  0.020  1.090
 PV5  C11  H5   single    0.970  0.020  1.090
 PV5  C14  H6   single    0.930  0.020  1.080
 PV5  C19  H7   single    0.970  0.020  1.090
 PV5  C18  H8   single    0.970  0.020  1.090
 PV5  N5   H9   single    0.860  0.020  1.020
 PV5  C4   H10  single    0.930  0.020  1.080
 PV5  C5   H11  single    0.930  0.020  1.080
 PV5  C    H12  single    0.970  0.020  1.090
 PV5  C    H13  single    0.970  0.020  1.090
 PV5  C    H14  single    0.970  0.020  1.090
 PV5  C19  H15  single    0.970  0.020  1.090
 PV5  C18  H16  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
 PV5  C    C1   N    116.75  3.000
 PV5  C    C1   C2   121.65  3.000
 PV5  N    C1   C2   121.60  3.000
 PV5  C6   C2   C3   119.51  3.000
 PV5  C6   C2   C1   122.27  3.000
 PV5  C3   C2   C1   118.21  3.000
 PV5  H1   C3   C4   120.53  3.000
 PV5  H1   C3   C2   119.73  3.000
 PV5  C4   C3   C2   119.74  3.000
 PV5  H2   C7   C6   119.61  3.000
 PV5  H2   C7   N1   115.16  3.000
 PV5  C6   C7   N1   125.23  3.000
 PV5  N2   C8   N1   120.14  3.000
 PV5  N1   C8   N5   121.63  3.000
 PV5  N2   C8   N5   118.24  3.000
 PV5  C6   C9   N3   132.22  3.000
 PV5  C6   C9   N2   118.41  3.000
 PV5  N3   C9   N2   109.36  3.000
 PV5  H3   C10  N4   125.97  3.000
 PV5  H3   C10  N2   124.80  3.000
 PV5  N4   C10  N2   109.23  3.000
 PV5  H5   C11  H4   106.81  3.000
 PV5  H5   C11  N5   106.79  3.000
 PV5  H4   C11  N5   109.65  3.000
 PV5  H5   C11  C12  109.97  3.000
 PV5  H4   C11  C12  109.47  3.000
 PV5  N5   C11  C12  113.89  3.000
 PV5  C17  C12  C13  116.73  3.000
 PV5  C17  C12  C11  121.73  3.000
 PV5  C13  C12  C11  121.52  3.000
 PV5  F    C13  C14  118.46  3.000
 PV5  F    C13  C12  118.21  3.000
 PV5  C14  C13  C12  123.33  3.000
 PV5  H6   C14  C15  120.41  3.000
 PV5  H6   C14  C13  120.39  3.000
 PV5  C15  C14  C13  119.20  3.000
 PV5  C20  C15  C16  120.68  3.000
 PV5  C16  C15  C14  118.21  3.000
 PV5  C20  C15  C14  121.11  3.000
 PV5  C17  C16  O    114.16  3.000
 PV5  C17  C16  C15  121.36  3.000
 PV5  O    C16  C15  124.48  3.000
 PV5  H15  C19  H7   108.77  3.000
 PV5  H15  C19  C18  112.56  3.000
 PV5  H7   C19  C18  112.54  3.000
 PV5  H15  C19  O    107.89  3.000
 PV5  H7   C19  O    107.81  3.000
 PV5  C18  C19  O    107.05  3.000
 PV5  C15  C20  N6   180.00  3.000
 PV5  C19  O    C16  108.68  3.000
 PV5  H16  C18  H8   107.50  3.000
 PV5  H16  C18  C17  111.18  3.000
 PV5  H8   C18  C17  112.15  3.000
 PV5  H16  C18  C19  112.13  3.000
 PV5  H8   C18  C19  111.67  3.000
 PV5  C17  C18  C19  102.26  3.000
 PV5  C18  C17  C16  107.84  3.000
 PV5  C18  C17  C12  130.97  3.000
 PV5  C16  C17  C12  121.18  3.000
 PV5  H9   N5   C11  117.82  3.000
 PV5  H9   N5   C8   120.61  3.000
 PV5  C11  N5   C8   121.42  3.000
 PV5  C8   N1   C7   119.37  3.000
 PV5  C10  N2   C9   104.65  3.000
 PV5  C9   N2   C8   121.67  3.000
 PV5  C10  N2   C8   133.67  3.000
 PV5  N3   N4   C10  109.30  3.000
 PV5  N4   N3   C9   107.46  3.000
 PV5  C9   C6   C7   115.17  3.000
 PV5  C7   C6   C2   122.92  3.000
 PV5  C9   C6   C2   121.83  3.000
 PV5  H10  C4   C5   120.84  3.000
 PV5  H10  C4   C3   121.44  3.000
 PV5  C5   C4   C3   117.72  3.000
 PV5  H11  C5   N    116.31  3.000
 PV5  H11  C5   C4   120.40  3.000
 PV5  N    C5   C4   123.29  3.000
 PV5  C5   N    C1   119.43  3.000
 PV5  H14  C    H13  107.05  3.000
 PV5  H14  C    H12  107.96  3.000
 PV5  H13  C    H12  108.76  3.000
 PV5  H14  C    C1   111.02  3.000
 PV5  H13  C    C1   111.81  3.000
 PV5  H12  C    C1   110.10  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
 PV5  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 PV5  CONST_04  C4   C5   N    C1      0.00   0.0  0
 PV5  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 PV5  CONST_06  N3   C9   C6   C2      0.00   0.0  0
 PV5  CONST_07  N2   C9   C6   C2    180.00   0.0  0
 PV5  CONST_08  N1   C7   C6   C2    180.00   0.0  0
 PV5  CONST_09  C5   N    C1   C2      0.00   0.0  0
 PV5  CONST_10  N    C5   C4   C3      0.00   0.0  0
 PV5  CONST_13  N    C1   C2   C3      0.00   0.0  0
 PV5  CONST_14  N3   C9   C6   C7    180.00   0.0  0
 PV5  CONST_15  N2   C9   C6   C7      0.00   0.0  0
 PV5  CONST_16  N2   C8   N1   C7      0.00   0.0  0
 PV5  CONST_17  N4   C10  N2   C8    180.00   0.0  0
 PV5  CONST_18  N3   C9   N2   C8    180.00   0.0  0
 PV5  CONST_19  C6   C9   N2   C8      0.00   0.0  0
 PV5  CONST_20  C6   C7   N1   C8      0.00   0.0  0
 PV5  CONST_21  C10  N4   N3   C9      0.00   0.0  0
 PV5  CONST_22  N4   C10  N2   C9      0.00   0.0  0
 PV5  CONST_23  N1   C8   N2   C9      0.00   0.0  0
 PV5  CONST_24  N1   C7   C6   C9      0.00   0.0  0
 PV5  CONST_25  N3   C9   N2   C10     0.00   0.0  0
 PV5  CONST_26  C6   C9   N2   C10   180.00   0.0  0
 PV5  CONST_27  N1   C8   N2   C10   180.00   0.0  0
 PV5  CONST_28  C15  C14  C13  C12     0.00   0.0  0
 PV5  CONST_29  C15  C16  C17  C12     0.00   0.0  0
 PV5  CONST_30  C16  C15  C14  C13     0.00   0.0  0
 PV5  CONST_31  C16  C17  C12  C13     0.00   0.0  0
 PV5  CONST_32  C17  C16  C15  C14     0.00   0.0  0
 PV5  CONST_33  C17  C12  C13  C14     0.00   0.0  0
 PV5  CONST_34  N3   N4   C10  N2      0.00   0.0  0
 PV5  CONST_35  N4   N3   C9   N2      0.00   0.0  0
 PV5  CONST_36  C6   C9   N3   N4    180.00   0.0  0
 PV5  CONST_37  C4   C3   C2   C6    180.00   0.0  0
 PV5  CONST_38  N    C1   C2   C6    180.00   0.0  0
 PV5  CONST_39  C    C1   C2   C3    180.00   0.0  0
 PV5  CONST_40  N5   C8   N1   C7    180.00   0.0  0
 PV5  CONST_41  N5   C8   N2   C9    180.00   0.0  0
 PV5  CONST_42  N5   C8   N2   C10     0.00   0.0  0
 PV5  CONST_43  C14  C13  C12  C11   180.00   0.0  0
 PV5  CONST_44  C16  C17  C12  C11   180.00   0.0  0
 PV5  CONST_45  C18  C17  C12  C11     0.00   0.0  0
 PV5  CONST_46  C20  C15  C14  C13   180.00   0.0  0
 PV5  CONST_47  F    C13  C14  C15   180.00   0.0  0
 PV5  CONST_48  O    C16  C15  C20     0.00   0.0  0
 PV5  CONST_49  C17  C16  C15  C20   180.00   0.0  0
 PV5  CONST_50  C17  C12  C13  F     180.00   0.0  0
 PV5  CONST_51  C    C1   C2   C6      0.00   0.0  0
 PV5  CONST_52  C    C1   N    C5    180.00   0.0  0
 PV5  CONST_53  H1   C3   C2   C1    180.00   0.0  0
 PV5  CONST_54  H11  C5   N    C1    180.00   0.0  0
 PV5  CONST_55  H10  C4   C3   C2    180.00   0.0  0
 PV5  CONST_56  H2   C7   C6   C2      0.00   0.0  0
 PV5  CONST_57  H3   C10  N2   C8      0.00   0.0  0
 PV5  CONST_58  H6   C14  C13  C12   180.00   0.0  0
 PV5  CONST_59  N2   C8   N5   C11   180.00   0.0  0
 PV5  CONST_60  N1   C8   N5   C11     0.00   0.0  0
 PV5  CONST_61  H9   N5   C8   N1    180.00   0.0  0
 PV5  Var_01    C19  C18  C17  C12   178.96  30.0  1
 PV5  Var_02    C18  C19  O    C16    -0.25  30.0  1
 PV5  Var_03    C17  C16  O    C19     0.23  30.0  1
 PV5  Var_04    C17  C18  C19  O       0.18  30.0  1
 PV5  Var_05    C12  C11  N5   C8     66.37  30.0  3
 PV5  Var_06    N5   C11  C12  C13    56.15  30.0  2
 PV5  Var_07    H12  C    C1   C2   -161.31  30.0  2

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
 PV5  plan-1  C1   0.020
 PV5  plan-1  C2   0.020
 PV5  plan-1  C3   0.020
 PV5  plan-1  C6   0.020
 PV5  plan-1  C4   0.020
 PV5  plan-1  C5   0.020
 PV5  plan-1  N    0.020
 PV5  plan-1  C    0.020
 PV5  plan-1  H1   0.020
 PV5  plan-1  H10  0.020
 PV5  plan-1  H11  0.020
 PV5  plan-2  N6   0.020
 PV5  plan-2  C11  0.020
 PV5  plan-2  C12  0.020
 PV5  plan-2  C13  0.020
 PV5  plan-2  C14  0.020
 PV5  plan-2  C15  0.020
 PV5  plan-2  C16  0.020
 PV5  plan-2  C20  0.020
 PV5  plan-2  F    0.020
 PV5  plan-2  O    0.020
 PV5  plan-2  C18  0.020
 PV5  plan-2  C17  0.020
 PV5  plan-2  H6   0.020
 PV5  plan-3  C2   0.020
 PV5  plan-3  C7   0.020
 PV5  plan-3  C8   0.020
 PV5  plan-3  C9   0.020
 PV5  plan-3  C10  0.020
 PV5  plan-3  N5   0.020
 PV5  plan-3  N1   0.020
 PV5  plan-3  N2   0.020
 PV5  plan-3  N4   0.020
 PV5  plan-3  N3   0.020
 PV5  plan-3  C6   0.020
 PV5  plan-3  H2   0.020
 PV5  plan-3  H3   0.020
 PV5  plan-4  C8   0.020
 PV5  plan-4  C11  0.020
 PV5  plan-4  N5   0.020
 PV5  plan-4  H9   0.020

