# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 20:25:38 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 4-{4-(4-fluorophenyl)-1-[1-(1,2-oxazol-3-ylmethyl)piperidin-4-yl]-1H-imidazol-5-yl}pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc(n1)c2n(cnc2c3ccc(F)cc3)C4CCN(CC4)Cc5ccon5
#
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
 PFO  PFO  4-{4-(4-fluorophenyl)-1-[1-(1,2-oxazol-3-ylmethyl)piperidin-4-yl]-1H-imidazol-5-yl}pyrimidin-2-amine  ligand  53  31  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_PFO
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
 PFO  N3   N  NT    0  -0.421  -4.1367   0.0813   0.8926
 PFO  C4   C  CR16  0  -0.400   5.5409  -0.6093  -1.1917
 PFO  N2   N  N     0  -0.453   1.3854  -2.4884   0.4061
 PFO  C7   C  CR5   0   0.081   2.0894  -1.3492   0.1489
 PFO  C6   C  CR6   0   0.033   3.5339  -1.4010  -0.0885
 PFO  C9   C  CR15  0   0.090   0.1392  -2.1178   0.5357
 PFO  C13  C  CH2   0  -0.287  -3.2359   0.4233   1.9794
 PFO  C20  C  CR16  0  -0.384   0.7987   1.8962  -1.0372
 PFO  C21  C  CR16  0  -0.015   1.1639   3.2276  -1.1556
 PFO  C8   C  CR5   0   0.286   1.2314  -0.2703   0.1267
 PFO  N5   N  N     0  -0.451   2.1196   3.7843  -0.4345
 PFO  C18  C  CR15  0   0.097  -7.7010  -1.2861  -0.9506
 PFO  C16  C  CR5   0   0.252  -6.4429   0.1000   0.1492
 PFO  C19  C  CR6   0   0.182   1.4967   1.1554  -0.0875
 PFO  C1   C  CR16  0  -0.281   4.3006  -2.3726   0.5570
 PFO  C2   C  CR16  0  -0.401   5.6678  -2.4659   0.3483
 PFO  C3   C  CR6   0   0.512   6.2661  -1.5760  -0.5220
 PFO  C5   C  CR16  0  -0.294   4.1742  -0.5322  -0.9731
 PFO  N1   N  NR5   0  -0.465  -0.0185  -0.7893   0.3692
 PFO  C10  C  CH1   0  -0.122  -1.2766  -0.0674   0.5262
 PFO  C11  C  CH2   0  -0.434  -2.2478  -0.3750  -0.6057
 PFO  C12  C  CH2   0  -0.288  -3.5454   0.3888  -0.3984
 PFO  C14  C  CH2   0  -0.433  -1.9327  -0.3526   1.8713
 PFO  C15  C  CH2   0  -0.340  -5.4281   0.7129   1.0563
 PFO  C17  C  CR15  0  -0.477  -6.6637  -1.2831  -0.0875
 PFO  O1   O  O     0  -0.323  -8.0752  -0.0346  -1.2181
 PFO  N4   N  N     0  -0.178  -7.2790   0.8305  -0.5292
 PFO  C22  C  CR6   0   0.545   2.7382   2.9829   0.4445
 PFO  N6   N  N     0  -0.453   2.4572   1.6927   0.6519
 PFO  N7   N  NH2   0  -0.825   3.7049   3.5277   1.1999
 PFO  F1   F  F     0  -0.316   7.5910  -1.6581  -0.7290
 PFO  H3   H  HCR5  0   0.291  -0.6873  -2.7762   0.7561
 PFO  H4   H  HCH2  0   0.202  -3.0159   1.5047   2.0034
 PFO  H5   H  HCH2  0   0.251  -3.7186   0.1781   2.9275
 PFO  H6   H  HCR6  0   0.276   0.0367   1.4637  -1.6686
 PFO  H7   H  HCR6  0   0.274   0.6650   3.8679  -1.8750
 PFO  H8   H  HCR5  0   0.305  -8.2542  -2.0735  -1.4387
 PFO  H9   H  HCR6  0   0.259   3.8231  -3.0639   1.2388
 PFO  H10  H  HCR6  0   0.278   6.2562  -3.2184   0.8564
 PFO  H11  H  HCR6  0   0.256   3.6047   0.2056  -1.5213
 PFO  H12  H  HCH1  0   0.270  -1.0316   0.9961   0.4943
 PFO  H13  H  HCH2  0   0.254  -1.8143  -0.0989  -1.5696
 PFO  H14  H  HCH2  0   0.240  -2.4572  -1.4477  -0.6374
 PFO  H15  H  HCH2  0   0.255  -4.2451   0.1170  -1.1908
 PFO  H16  H  HCH2  0   0.203  -3.3576   1.4721  -0.5044
 PFO  H17  H  HCH2  0   0.258  -1.2650  -0.0636   2.6850
 PFO  H18  H  HCH2  0   0.237  -2.1422  -1.4204   1.9773
 PFO  H19  H  HCH2  0   0.270  -5.7588   0.5580   2.0874
 PFO  H20  H  HCH2  0   0.230  -5.4003   1.8016   0.8936
 PFO  H21  H  HCR5  0   0.279  -6.1282  -2.1217   0.3214
 PFO  H22  H  HNH2  0   0.399   4.0239   4.4607   1.0090
 PFO  H23  H  HNH2  0   0.399   4.2741   2.9401   1.7826
 PFO  H2   H  HCR6  0   0.279   6.0302   0.0641  -1.8831

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
 PFO  O1   C18  aromatic  1.333  0.020  1.333
 PFO  O1   N4   aromatic  1.363  0.020  1.363
 PFO  C18  C17  aromatic  1.349  0.020  1.349
 PFO  N4   C16  aromatic  1.301  0.020  1.301
 PFO  C17  C16  aromatic  1.420  0.020  1.420
 PFO  C16  C15  single    1.493  0.020  1.493
 PFO  C12  C11  single    1.520  0.020  1.520
 PFO  C12  N3   single    1.453  0.020  1.453
 PFO  C11  C10  single    1.523  0.020  1.523
 PFO  C15  N3   single    1.447  0.020  1.447
 PFO  N3   C13  single    1.452  0.020  1.452
 PFO  C10  N1   single    1.459  0.020  1.459
 PFO  C10  C14  single    1.524  0.020  1.524
 PFO  C9   N1   aromatic  1.348  0.020  1.348
 PFO  C9   N2   aromatic  1.307  0.020  1.307
 PFO  N1   C8   aromatic  1.375  0.020  1.375
 PFO  C13  C14  single    1.521  0.020  1.521
 PFO  N2   C7   aromatic  1.364  0.020  1.364
 PFO  C8   C7   aromatic  1.379  0.020  1.379
 PFO  C8   C19  single    1.466  0.020  1.466
 PFO  C7   C6   single    1.465  0.020  1.465
 PFO  C19  C20  aromatic  1.392  0.020  1.392
 PFO  C19  N6   aromatic  1.326  0.020  1.326
 PFO  C5   C6   aromatic  1.396  0.020  1.396
 PFO  C5   C4   aromatic  1.386  0.020  1.386
 PFO  C20  C21  aromatic  1.386  0.020  1.386
 PFO  N6   C22  aromatic  1.337  0.020  1.337
 PFO  C21  N5   aromatic  1.320  0.020  1.320
 PFO  C6   C1   aromatic  1.396  0.020  1.396
 PFO  C22  N7   single    1.342  0.020  1.342
 PFO  C22  N5   aromatic  1.341  0.020  1.341
 PFO  C4   C3   aromatic  1.382  0.020  1.382
 PFO  C1   C2   aromatic  1.386  0.020  1.386
 PFO  C3   C2   aromatic  1.381  0.020  1.381
 PFO  C3   F1   single    1.344  0.020  1.344
 PFO  C4   H2   single    0.930  0.020  1.080
 PFO  C9   H3   single    0.930  0.020  1.080
 PFO  C13  H4   single    0.970  0.020  1.090
 PFO  C13  H5   single    0.970  0.020  1.090
 PFO  C20  H6   single    0.930  0.020  1.080
 PFO  C21  H7   single    0.930  0.020  1.080
 PFO  C18  H8   single    0.930  0.020  1.080
 PFO  C1   H9   single    0.930  0.020  1.080
 PFO  C2   H10  single    0.930  0.020  1.080
 PFO  C5   H11  single    0.930  0.020  1.080
 PFO  C10  H12  single    0.970  0.020  1.090
 PFO  C11  H13  single    0.970  0.020  1.090
 PFO  C11  H14  single    0.970  0.020  1.090
 PFO  C12  H15  single    0.970  0.020  1.090
 PFO  C12  H16  single    0.970  0.020  1.090
 PFO  C14  H17  single    0.970  0.020  1.090
 PFO  C14  H18  single    0.970  0.020  1.090
 PFO  C15  H19  single    0.970  0.020  1.090
 PFO  C15  H20  single    0.970  0.020  1.090
 PFO  C17  H21  single    0.930  0.020  1.080
 PFO  N7   H22  single    0.860  0.020  1.020
 PFO  N7   H23  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
 PFO  C15  N3   C12  111.80  3.000
 PFO  C15  N3   C13  111.48  3.000
 PFO  C12  N3   C13  111.26  3.000
 PFO  H2   C4   C5   120.79  3.000
 PFO  H2   C4   C3   120.52  3.000
 PFO  C5   C4   C3   118.69  3.000
 PFO  C9   N2   C7   105.91  3.000
 PFO  C8   C7   C6   129.70  3.000
 PFO  C6   C7   N2   120.67  3.000
 PFO  C8   C7   N2   109.60  3.000
 PFO  C5   C6   C1   118.32  3.000
 PFO  C1   C6   C7   119.43  3.000
 PFO  C5   C6   C7   122.22  3.000
 PFO  H3   C9   N1   122.46  3.000
 PFO  H3   C9   N2   125.28  3.000
 PFO  N1   C9   N2   112.26  3.000
 PFO  H5   C13  H4   106.81  3.000
 PFO  H5   C13  C14  109.03  3.000
 PFO  H4   C13  C14  109.31  3.000
 PFO  H5   C13  N3   108.83  3.000
 PFO  H4   C13  N3   111.75  3.000
 PFO  C14  C13  N3   110.99  3.000
 PFO  H6   C20  C19  122.65  3.000
 PFO  H6   C20  C21  121.39  3.000
 PFO  C19  C20  C21  115.94  3.000
 PFO  H7   C21  N5   116.50  3.000
 PFO  H7   C21  C20  120.18  3.000
 PFO  N5   C21  C20  123.31  3.000
 PFO  N1   C8   C19  123.88  3.000
 PFO  C19  C8   C7   130.60  3.000
 PFO  N1   C8   C7   105.52  3.000
 PFO  C22  N5   C21  116.10  3.000
 PFO  H8   C18  O1   116.77  3.000
 PFO  H8   C18  C17  133.24  3.000
 PFO  O1   C18  C17  109.99  3.000
 PFO  N4   C16  C17  111.09  3.000
 PFO  C17  C16  C15  127.35  3.000
 PFO  N4   C16  C15  121.54  3.000
 PFO  N6   C19  C8   116.35  3.000
 PFO  N6   C19  C20  121.87  3.000
 PFO  C8   C19  C20  121.77  3.000
 PFO  H9   C1   C2   119.15  3.000
 PFO  H9   C1   C6   119.58  3.000
 PFO  C2   C1   C6   121.27  3.000
 PFO  H10  C2   C3   120.56  3.000
 PFO  H10  C2   C1   120.83  3.000
 PFO  C3   C2   C1   118.61  3.000
 PFO  F1   C3   C2   119.01  3.000
 PFO  F1   C3   C4   119.06  3.000
 PFO  C2   C3   C4   121.93  3.000
 PFO  H11  C5   C6   120.30  3.000
 PFO  H11  C5   C4   118.51  3.000
 PFO  C6   C5   C4   121.18  3.000
 PFO  C10  N1   C8   128.03  3.000
 PFO  C8   N1   C9   106.71  3.000
 PFO  C10  N1   C9   125.11  3.000
 PFO  H12  C10  C14  107.74  3.000
 PFO  H12  C10  C11  108.56  3.000
 PFO  C14  C10  C11  110.11  3.000
 PFO  H12  C10  N1   106.58  3.000
 PFO  C14  C10  N1   111.94  3.000
 PFO  C11  C10  N1   111.72  3.000
 PFO  H14  C11  H13  107.36  3.000
 PFO  H14  C11  C12  109.48  3.000
 PFO  H13  C11  C12  109.40  3.000
 PFO  H14  C11  C10  109.99  3.000
 PFO  H13  C11  C10  110.59  3.000
 PFO  C12  C11  C10  109.97  3.000
 PFO  H16  C12  H15  106.47  3.000
 PFO  H16  C12  C11  109.55  3.000
 PFO  H15  C12  C11  108.85  3.000
 PFO  H16  C12  N3   111.23  3.000
 PFO  H15  C12  N3   109.36  3.000
 PFO  C11  C12  N3   111.24  3.000
 PFO  H18  C14  H17  107.67  3.000
 PFO  H18  C14  C10  110.55  3.000
 PFO  H17  C14  C10  110.19  3.000
 PFO  H18  C14  C13  109.10  3.000
 PFO  H17  C14  C13  109.64  3.000
 PFO  C10  C14  C13  109.65  3.000
 PFO  H20  C15  H19  106.67  3.000
 PFO  H20  C15  C16  109.47  3.000
 PFO  H19  C15  C16  108.00  3.000
 PFO  H20  C15  N3   113.11  3.000
 PFO  H19  C15  N3   108.34  3.000
 PFO  C16  C15  N3   111.03  3.000
 PFO  H21  C17  C16  128.19  3.000
 PFO  H21  C17  C18  128.61  3.000
 PFO  C16  C17  C18  103.20  3.000
 PFO  N4   O1   C18  109.30  3.000
 PFO  O1   N4   C16  106.42  3.000
 PFO  N7   C22  N6   117.12  3.000
 PFO  N7   C22  N5   117.30  3.000
 PFO  N6   C22  N5   125.57  3.000
 PFO  C22  N6   C19  117.19  3.000
 PFO  H23  N7   H22  118.29  3.000
 PFO  H23  N7   C22  119.81  3.000
 PFO  H22  N7   C22  119.92  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
 PFO  CONST_01  C7   C6   C5   C4    180.00   0.0  0
 PFO  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 PFO  CONST_03  C1   C2   C3   C4      0.00   0.0  0
 PFO  CONST_04  C8   N1   C9   N2      0.00   0.0  0
 PFO  CONST_05  N1   C8   C7   N2      0.00   0.0  0
 PFO  CONST_06  C19  C8   C7   N2    180.00   0.0  0
 PFO  CONST_09  N1   C9   N2   C7      0.00   0.0  0
 PFO  CONST_10  C9   N1   C8   C7      0.00   0.0  0
 PFO  CONST_13  C2   C1   C6   C7    180.00   0.0  0
 PFO  CONST_14  C9   N2   C7   C6    180.00   0.0  0
 PFO  CONST_15  N1   C8   C7   C6    180.00   0.0  0
 PFO  CONST_16  C19  C8   C7   C6      0.00   0.0  0
 PFO  CONST_17  C3   C4   C5   C6      0.00   0.0  0
 PFO  CONST_18  C3   C2   C1   C6      0.00   0.0  0
 PFO  CONST_19  C19  C8   N1   C9    180.00   0.0  0
 PFO  CONST_20  C8   C7   N2   C9      0.00   0.0  0
 PFO  CONST_22  C22  N6   C19  C20     0.00   0.0  0
 PFO  CONST_23  C22  N5   C21  C20     0.00   0.0  0
 PFO  CONST_24  C8   C19  C20  C21   180.00   0.0  0
 PFO  CONST_25  N6   C19  C20  C21     0.00   0.0  0
 PFO  CONST_26  N6   C22  N5   C21     0.00   0.0  0
 PFO  CONST_29  C22  N6   C19  C8    180.00   0.0  0
 PFO  CONST_30  C19  C20  C21  N5      0.00   0.0  0
 PFO  CONST_31  C19  N6   C22  N5      0.00   0.0  0
 PFO  CONST_32  C16  N4   O1   C18     0.00   0.0  0
 PFO  CONST_33  N4   C16  C17  C18     0.00   0.0  0
 PFO  CONST_34  O1   C18  C17  C16     0.00   0.0  0
 PFO  CONST_35  C5   C6   C1   C2      0.00   0.0  0
 PFO  CONST_36  C5   C4   C3   C2      0.00   0.0  0
 PFO  CONST_38  N4   O1   C18  C17     0.00   0.0  0
 PFO  CONST_39  O1   N4   C16  C17     0.00   0.0  0
 PFO  CONST_40  C10  N1   C9   N2    180.00   0.0  0
 PFO  CONST_41  C10  N1   C8   C7    180.00   0.0  0
 PFO  CONST_42  C10  N1   C8   C19     0.00   0.0  0
 PFO  CONST_43  N7   C22  N5   C21   180.00   0.0  0
 PFO  CONST_44  C15  C16  C17  C18   180.00   0.0  0
 PFO  CONST_45  N7   C22  N6   C19   180.00   0.0  0
 PFO  CONST_46  F1   C3   C2   C1    180.00   0.0  0
 PFO  CONST_47  F1   C3   C4   C5    180.00   0.0  0
 PFO  CONST_48  O1   N4   C16  C15   180.00   0.0  0
 PFO  CONST_49  H10  C2   C3   C4    180.00   0.0  0
 PFO  CONST_50  H3   C9   N2   C7    180.00   0.0  0
 PFO  CONST_51  H11  C5   C6   C7      0.00   0.0  0
 PFO  CONST_52  H9   C1   C6   C7      0.00   0.0  0
 PFO  CONST_53  H2   C4   C5   C6    180.00   0.0  0
 PFO  CONST_54  H6   C20  C19  C8      0.00   0.0  0
 PFO  CONST_55  H8   C18  C17  C16   180.00   0.0  0
 PFO  CONST_56  H7   C21  C20  C19   180.00   0.0  0
 PFO  CONST_57  H21  C17  C18  O1    180.00   0.0  0
 PFO  CONST_58  H22  N7   C22  N5      0.00   0.0  0
 PFO  CONST_59  H23  N7   C22  N5    180.00   0.0  0
 PFO  Var_01    C10  C11  C12  N3    -56.62  30.0  1
 PFO  Var_02    C10  C14  C13  N3     57.69  30.0  1
 PFO  Var_03    C11  C12  N3   C13    59.53  30.0  1
 PFO  Var_04    C14  C13  N3   C12   -60.09  30.0  1
 PFO  Var_05    N4   C16  C15  N3   -135.97  30.0  2
 PFO  Var_06    C16  C15  N3   C13  -165.69  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
 PFO  chir_01  C10  C11  N1  C14  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
 PFO  plan-1  N2   0.020
 PFO  plan-1  C7   0.020
 PFO  plan-1  C6   0.020
 PFO  plan-1  C9   0.020
 PFO  plan-1  C8   0.020
 PFO  plan-1  C19  0.020
 PFO  plan-1  N1   0.020
 PFO  plan-1  C10  0.020
 PFO  plan-1  H3   0.020
 PFO  plan-2  C18  0.020
 PFO  plan-2  C16  0.020
 PFO  plan-2  C15  0.020
 PFO  plan-2  C17  0.020
 PFO  plan-2  O1   0.020
 PFO  plan-2  N4   0.020
 PFO  plan-2  H8   0.020
 PFO  plan-2  H21  0.020
 PFO  plan-3  C20  0.020
 PFO  plan-3  C21  0.020
 PFO  plan-3  C8   0.020
 PFO  plan-3  N5   0.020
 PFO  plan-3  C19  0.020
 PFO  plan-3  C22  0.020
 PFO  plan-3  N6   0.020
 PFO  plan-3  N7   0.020
 PFO  plan-3  H6   0.020
 PFO  plan-3  H7   0.020
 PFO  plan-4  C4   0.020
 PFO  plan-4  C7   0.020
 PFO  plan-4  C6   0.020
 PFO  plan-4  C1   0.020
 PFO  plan-4  C2   0.020
 PFO  plan-4  C3   0.020
 PFO  plan-4  C5   0.020
 PFO  plan-4  F1   0.020
 PFO  plan-4  H9   0.020
 PFO  plan-4  H10  0.020
 PFO  plan-4  H11  0.020
 PFO  plan-4  H2   0.020
 PFO  plan-5  C22  0.020
 PFO  plan-5  N7   0.020
 PFO  plan-5  H22  0.020
 PFO  plan-5  H23  0.020

