# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 21:35:11 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-(4-{(3S,5S)-5-[(3,3-difluoropyrrolidin-1-yl)carbonyl]pyrrolidin-3-yl}piperazin-1-yl)pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC1(F)CCN(C1)C(=O)[C@@H]2C[C@@H](CN2)N3CCN(CC3)c4ncccn4
#
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
 PF2  PF2  2-(4-{(3S,5S)-5-[(3,3-difluoropyrrolidin-1-yl)carbonyl]pyrrolidin-3-yl}piperazin-1-yl)pyrimidine  ligand  50  26  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PF2
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
 PF2  F26   F  F     0  -0.334  -5.9804  -2.4438  -1.0316
 PF2  C11   C  CR5   0   0.725  -5.1919  -1.7846  -0.1468
 PF2  F25   F  F     0  -0.344  -4.2729  -2.6986   0.2879
 PF2  C10   C  CH2   0  -0.575  -5.9352  -1.1957   1.0262
 PF2  C9    C  CH2   0  -0.243  -4.9540  -0.1529   1.5511
 PF2  C12   C  CH2   0  -0.356  -4.4730  -0.6064  -0.7817
 PF2  N8    N  NR5   0  -0.498  -4.1814   0.2231   0.3682
 PF2  C6    C  C     0   0.579  -3.3043   1.2539   0.4184
 PF2  O7    O  O     0  -0.424  -3.1299   1.8909   1.4352
 PF2  C4    C  CH1   0  -0.257  -2.5088   1.5183  -0.8569
 PF2  N3    N  NH1   0  -0.520  -1.9636   2.8640  -0.8437
 PF2  C2    C  CH2   0  -0.325  -0.6037   2.7464  -0.3565
 PF2  C5    C  CH2   0  -0.496  -1.3034   0.5320  -0.9218
 PF2  C1    C  CH1   0  -0.036  -0.0629   1.4374  -0.9520
 PF2  N13   N  NT    0  -0.416   1.0609   0.8787  -0.2296
 PF2  C18   C  CH2   0  -0.281   2.1728   1.8042  -0.1320
 PF2  C17   C  CH2   0  -0.290   3.2873   1.2334   0.7256
 PF2  N16   N  NT    0  -0.504   3.7042  -0.0582   0.2266
 PF2  C15   C  CH2   0  -0.288   2.6169  -0.9936   0.0464
 PF2  C14   C  CH2   0  -0.278   1.5193  -0.3727  -0.7986
 PF2  C19   C  CR6   0   0.648   4.9987  -0.4576   0.2646
 PF2  N23   N  N     0  -0.449   5.2639  -1.7344  -0.0382
 PF2  C24   C  CR16  0   0.013   6.5301  -2.1002  -0.0182
 PF2  C22   C  CR16  0  -0.381   7.5648  -1.2347   0.2991
 PF2  C21   C  CR16  0   0.011   7.1763   0.0608   0.6015
 PF2  N20   N  N     0  -0.449   5.9197   0.4575   0.5909
 PF2  H10   H  HCH2  0   0.263  -6.8475  -0.7195   0.6650
 PF2  H10A  H  HCH2  0   0.274  -6.2058  -1.9404   1.7727
 PF2  H9    H  HCH2  0   0.259  -5.4636   0.7084   1.9784
 PF2  H9A   H  HCH2  0   0.245  -4.3024  -0.5714   2.3206
 PF2  H12   H  HCH2  0   0.257  -3.5793  -0.9345  -1.3152
 PF2  H12A  H  HCH2  0   0.248  -5.1432  -0.1138  -1.4941
 PF2  H4    H  HCH1  0   0.243  -3.1613   1.4061  -1.7265
 PF2  HN3   H  HNH1  0   0.320  -1.9518   3.2228  -1.7884
 PF2  H2    H  HCH2  0   0.218  -0.0277   3.6280  -0.6403
 PF2  H2A   H  HCH2  0   0.255  -0.6057   2.6800   0.7341
 PF2  H5    H  HCH2  0   0.258  -1.2634  -0.1072  -0.0362
 PF2  H5A   H  HCH2  0   0.228  -1.3619  -0.1222  -1.7923
 PF2  H1    H  HCH1  0   0.178   0.2083   1.6312  -2.0081
 PF2  H18   H  HCH2  0   0.187   2.5763   2.0677  -1.1261
 PF2  H18A  H  HCH2  0   0.237   1.8411   2.7313   0.3374
 PF2  H17   H  HCH2  0   0.268   4.1358   1.9111   0.7289
 PF2  H17A  H  HCH2  0   0.221   2.9306   1.1375   1.7590
 PF2  H15   H  HCH2  0   0.267   2.9875  -1.8947  -0.4337
 PF2  H15A  H  HCH2  0   0.219   2.2029  -1.2799   1.0216
 PF2  H14   H  HCH2  0   0.233   0.6918  -1.0825  -0.8397
 PF2  H14A  H  HCH2  0   0.189   1.8875  -0.2433  -1.8323
 PF2  H24   H  HCR6  0   0.233   6.7302  -3.1381  -0.2646
 PF2  H22   H  HCR6  0   0.233   8.5976  -1.5473   0.3159
 PF2  H21   H  HCR6  0   0.234   7.9117   0.8137   0.8668

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
 PF2  C11  F26   single    1.356  0.020  1.356
 PF2  C10  C11   single    1.508  0.020  1.508
 PF2  C12  C11   single    1.519  0.020  1.519
 PF2  C11  F25   single    1.367  0.020  1.367
 PF2  C9   C10   single    1.525  0.020  1.525
 PF2  C10  H10   single    0.970  0.020  1.090
 PF2  C10  H10A  single    0.970  0.020  1.090
 PF2  C9   N8    single    1.462  0.020  1.462
 PF2  C9   H9    single    0.970  0.020  1.090
 PF2  C9   H9A   single    0.970  0.020  1.090
 PF2  N8   C12   single    1.448  0.020  1.448
 PF2  C12  H12   single    0.970  0.020  1.090
 PF2  C12  H12A  single    0.970  0.020  1.090
 PF2  C6   N8    single    1.354  0.020  1.354
 PF2  C4   C6    single    1.526  0.020  1.526
 PF2  O7   C6    double    1.212  0.020  1.212
 PF2  C5   C4    single    1.559  0.020  1.559
 PF2  N3   C4    single    1.452  0.020  1.452
 PF2  C4   H4    single    0.970  0.020  1.090
 PF2  C2   N3    single    1.449  0.020  1.449
 PF2  N3   HN3   single    0.890  0.020  1.040
 PF2  C1   C2    single    1.536  0.020  1.536
 PF2  C2   H2    single    0.970  0.020  1.090
 PF2  C2   H2A   single    0.970  0.020  1.090
 PF2  C1   C5    single    1.536  0.020  1.536
 PF2  C5   H5    single    0.970  0.020  1.090
 PF2  C5   H5A   single    0.970  0.020  1.090
 PF2  N13  C1    single    1.448  0.020  1.448
 PF2  C1   H1    single    0.970  0.020  1.090
 PF2  C18  N13   single    1.450  0.020  1.450
 PF2  C14  N13   single    1.449  0.020  1.449
 PF2  C17  C18   single    1.518  0.020  1.518
 PF2  C18  H18   single    0.970  0.020  1.090
 PF2  C18  H18A  single    0.970  0.020  1.090
 PF2  N16  C17   single    1.446  0.020  1.446
 PF2  C17  H17   single    0.970  0.020  1.090
 PF2  C17  H17A  single    0.970  0.020  1.090
 PF2  C19  N16   single    1.355  0.020  1.355
 PF2  N16  C15   single    1.446  0.020  1.446
 PF2  C15  C14   single    1.518  0.020  1.518
 PF2  C15  H15   single    0.970  0.020  1.090
 PF2  C15  H15A  single    0.970  0.020  1.090
 PF2  C14  H14   single    0.970  0.020  1.090
 PF2  C14  H14A  single    0.970  0.020  1.090
 PF2  N23  C19   aromatic  1.339  0.020  1.339
 PF2  N20  C19   aromatic  1.339  0.020  1.339
 PF2  C24  N23   aromatic  1.318  0.020  1.318
 PF2  C22  C24   aromatic  1.386  0.020  1.386
 PF2  C24  H24   single    0.930  0.020  1.080
 PF2  C22  C21   aromatic  1.386  0.020  1.386
 PF2  C22  H22   single    0.930  0.020  1.080
 PF2  C21  N20   aromatic  1.318  0.020  1.318
 PF2  C21  H21   single    0.930  0.020  1.080

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
 PF2  C12   C11  C10  104.80  3.000
 PF2  C12   C11  F25  109.47  3.000
 PF2  C10   C11  F25  110.19  3.000
 PF2  F25   C11  F26  105.87  3.000
 PF2  C12   C11  F26  112.29  3.000
 PF2  C10   C11  F26  114.24  3.000
 PF2  H10A  C10  H10  108.54  3.000
 PF2  H10A  C10  C9   113.06  3.000
 PF2  H10   C10  C9   110.70  3.000
 PF2  H10A  C10  C11  112.87  3.000
 PF2  H10   C10  C11  108.97  3.000
 PF2  C9    C10  C11  102.57  3.000
 PF2  H9A   C9   H9   107.83  3.000
 PF2  H9A   C9   N8   110.70  3.000
 PF2  H9    C9   N8   111.20  3.000
 PF2  H9A   C9   C10  111.37  3.000
 PF2  H9    C9   C10  112.03  3.000
 PF2  N8    C9   C10  103.73  3.000
 PF2  H12A  C12  H12  108.56  3.000
 PF2  H12A  C12  N8   112.47  3.000
 PF2  H12   C12  N8   113.30  3.000
 PF2  H12A  C12  C11  109.34  3.000
 PF2  H12   C12  C11  111.02  3.000
 PF2  N8    C12  C11  101.99  3.000
 PF2  C6    N8   C12  126.59  3.000
 PF2  C6    N8   C9   120.53  3.000
 PF2  C12   N8   C9   112.89  3.000
 PF2  C4    C6   O7   122.33  3.000
 PF2  O7    C6   N8   121.60  3.000
 PF2  C4    C6   N8   116.00  3.000
 PF2  H4    C4   C5   111.32  3.000
 PF2  H4    C4   N3   109.06  3.000
 PF2  C5    C4   N3   107.25  3.000
 PF2  H4    C4   C6   109.63  3.000
 PF2  N3    C4   C6   110.40  3.000
 PF2  C5    C4   C6   109.16  3.000
 PF2  HN3   N3   C2   109.39  3.000
 PF2  HN3   N3   C4   108.96  3.000
 PF2  C2    N3   C4   106.27  3.000
 PF2  H2A   C2   H2   108.04  3.000
 PF2  H2A   C2   C1   109.62  3.000
 PF2  H2    C2   C1   113.70  3.000
 PF2  H2A   C2   N3   109.80  3.000
 PF2  H2    C2   N3   110.03  3.000
 PF2  C1    C2   N3   105.61  3.000
 PF2  H5A   C5   H5   107.34  3.000
 PF2  H5A   C5   C1   112.41  3.000
 PF2  H5    C5   C1   109.34  3.000
 PF2  H5A   C5   C4   111.80  3.000
 PF2  H5    C5   C4   111.38  3.000
 PF2  C1    C5   C4   104.61  3.000
 PF2  H1    C1   N13  110.68  3.000
 PF2  H1    C1   C5   108.64  3.000
 PF2  N13   C1   C5   112.92  3.000
 PF2  H1    C1   C2   107.87  3.000
 PF2  N13   C1   C2   114.11  3.000
 PF2  C5    C1   C2   102.14  3.000
 PF2  C14   N13  C18  109.58  3.000
 PF2  C14   N13  C1   112.51  3.000
 PF2  C18   N13  C1   112.49  3.000
 PF2  H18A  C18  H18  107.19  3.000
 PF2  H18A  C18  C17  107.44  3.000
 PF2  H18   C18  C17  109.27  3.000
 PF2  H18A  C18  N13  109.77  3.000
 PF2  H18   C18  N13  111.83  3.000
 PF2  C17   C18  N13  111.17  3.000
 PF2  H17A  C17  H17  107.79  3.000
 PF2  H17A  C17  N16  109.91  3.000
 PF2  H17   C17  N16  109.47  3.000
 PF2  H17A  C17  C18  109.04  3.000
 PF2  H17   C17  C18  109.92  3.000
 PF2  N16   C17  C18  110.65  3.000
 PF2  C19   N16  C15  122.09  3.000
 PF2  C15   N16  C17  113.84  3.000
 PF2  C19   N16  C17  121.94  3.000
 PF2  H15A  C15  H15  107.76  3.000
 PF2  H15A  C15  C14  109.18  3.000
 PF2  H15   C15  C14  109.87  3.000
 PF2  H15A  C15  N16  109.99  3.000
 PF2  H15   C15  N16  109.59  3.000
 PF2  C14   C15  N16  110.40  3.000
 PF2  H14A  C14  H14  107.08  3.000
 PF2  H14A  C14  C15  109.13  3.000
 PF2  H14   C14  C15  107.66  3.000
 PF2  H14A  C14  N13  111.81  3.000
 PF2  H14   C14  N13  109.67  3.000
 PF2  C15   C14  N13  111.30  3.000
 PF2  N20   C19  N23  124.81  3.000
 PF2  N20   C19  N16  117.54  3.000
 PF2  N23   C19  N16  117.64  3.000
 PF2  C24   N23  C19  116.84  3.000
 PF2  H24   C24  C22  120.77  3.000
 PF2  H24   C24  N23  116.04  3.000
 PF2  C22   C24  N23  123.19  3.000
 PF2  H22   C22  C21  122.39  3.000
 PF2  H22   C22  C24  122.50  3.000
 PF2  C21   C22  C24  115.12  3.000
 PF2  H21   C21  N20  116.05  3.000
 PF2  H21   C21  C22  120.78  3.000
 PF2  N20   C21  C22  123.16  3.000
 PF2  C21   N20  C19  116.88  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
 PF2  CONST_01  C22  C24  N23  C19     0.00   0.0  0
 PF2  CONST_02  C22  C21  N20  C19     0.00   0.0  0
 PF2  CONST_03  C21  N20  C19  N23     0.00   0.0  0
 PF2  CONST_04  C21  C22  C24  N23     0.00   0.0  0
 PF2  CONST_05  N20  C19  N23  C24     0.00   0.0  0
 PF2  CONST_06  N20  C21  C22  C24     0.00   0.0  0
 PF2  CONST_07  C24  N23  C19  N16   180.00   0.0  0
 PF2  CONST_08  C21  N20  C19  N16   180.00   0.0  0
 PF2  CONST_09  C4   C6   N8   C9    180.00   0.0  0
 PF2  CONST_10  C4   C6   N8   C12     0.00   0.0  0
 PF2  CONST_11  H24  C24  N23  C19   180.00   0.0  0
 PF2  CONST_12  H21  C21  N20  C19   180.00   0.0  0
 PF2  CONST_13  H22  C22  C24  N23   180.00   0.0  0
 PF2  CONST_14  O7   C6   N8   C9      0.00   0.0  0
 PF2  CONST_15  O7   C6   N8   C12   180.00   0.0  0
 PF2  Var_01    N8   C9   C10  C11    27.52  30.0  1
 PF2  Var_02    C9   N8   C12  C11   -15.50  30.0  1
 PF2  Var_03    N8   C12  C11  C10    32.77  30.0  1
 PF2  Var_04    C12  N8   C9   C10    -7.55  30.0  1
 PF2  Var_05    C12  C11  C10  C9    -37.72  30.0  1
 PF2  Var_06    C1   C2   N3   C4     37.21  30.0  1
 PF2  Var_07    C17  C18  N13  C1    175.34  30.0  1
 PF2  Var_08    C15  C14  N13  C1   -175.11  30.0  1
 PF2  Var_09    N16  C17  C18  N13    55.07  30.0  1
 PF2  Var_10    N16  C15  C14  N13   -55.35  30.0  1
 PF2  Var_11    C19  N16  C17  C18   143.89  30.0  1
 PF2  Var_12    N23  C19  N16  C17   170.57  30.0  3
 PF2  Var_13    C14  C15  N16  C17    52.45  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
 PF2  chir_01  C4  C6   C5  N3  positiv
 PF2  chir_02  C1  N13  C2  C5  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
 PF2  plan-1  C9   0.020
 PF2  plan-1  C12  0.020
 PF2  plan-1  N8   0.020
 PF2  plan-1  C6   0.020
 PF2  plan-1  O7   0.020
 PF2  plan-1  C4   0.020
 PF2  plan-2  N16  0.020
 PF2  plan-2  C19  0.020
 PF2  plan-2  N23  0.020
 PF2  plan-2  C24  0.020
 PF2  plan-2  C22  0.020
 PF2  plan-2  C21  0.020
 PF2  plan-2  N20  0.020
 PF2  plan-2  H24  0.020
 PF2  plan-2  H22  0.020
 PF2  plan-2  H21  0.020

