# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 05:40:36 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (3R,4S)-1-[6-(6-methoxypyridin-3-yl)pyrimidin-4-yl]-4-(2,4,5-trifluorophenyl)pyrrolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cn1)c2cc(ncn2)N3C[C@H](N)[C@H](C3)c4cc(F)c(F)cc4F
#
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
 PZF  PZF  (3R,4S)-1-[6-(6-methoxypyridin-3-yl)pyrimidin-4-yl]-4-(2,4,5-trifluorophenyl)pyrrolidin-3-amine  ligand  47  29  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PZF
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
 PZF  N3    N  N     0  -0.461  -6.0755  -0.8218  -0.9026
 PZF  C4    C  CR6   0   0.538  -7.0688  -0.2856  -0.2244
 PZF  C6    C  CR16  0  -0.159  -5.5906   1.0692   1.0511
 PZF  C13   C  CR15  0  -0.400   2.5307  -0.8576   0.3266
 PZF  C21   C  CR6   0  -0.021   3.9928  -0.5735   0.1438
 PZF  C8    C  CR16  0   0.053  -1.7264   2.3945   1.5932
 PZF  C16   C  CH2   0  -0.274   0.3667  -1.2570  -0.5573
 PZF  C19   C  CH3   0  -0.418  -8.5392  -1.6488  -1.4754
 PZF  C26   C  CR16  0  -0.459   4.4328   0.3395  -0.8154
 PZF  C24   C  CR6   0   0.404   6.7179  -0.0699  -0.2262
 PZF  C23   C  CR16  0  -0.555   6.3237  -0.9788   0.7296
 PZF  C22   C  CR6   0   0.517   4.9690  -1.2113   0.8927
 PZF  F27   F  F     0  -0.302   4.6054  -2.1003   1.8276
 PZF  C25   C  CR6   0   0.412   5.7738   0.5874  -0.9972
 PZF  F28   F  F     0  -0.305   6.1820   1.4655  -1.9186
 PZF  C17   C  CR15  0  -0.085   1.8375  -1.4210  -0.9187
 PZF  N20   N  NH2   0  -0.794   2.1887  -2.8008  -1.1698
 PZF  N15   N  NR5   0  -0.511   0.3511  -0.0442   0.2383
 PZF  C14   C  CH2   0  -0.224   1.6803   0.3701   0.6580
 PZF  C12   C  CR6   0   0.576  -0.7626   0.6126   0.5844
 PZF  N7    N  N     0  -0.473  -0.6176   1.7578   1.2662
 PZF  C11   C  CR16  0  -0.453  -2.0472   0.1298   0.2628
 PZF  C10   C  CR6   0   0.281  -3.1281   0.8979   0.6431
 PZF  N9    N  N     0  -0.469  -2.9688   2.0487   1.3188
 PZF  C1    C  CR6   0  -0.058  -4.5158   0.4996   0.3529
 PZF  C5    C  CR16  0  -0.379  -6.8773   0.6796   0.7737
 PZF  O18   O  O2    0  -0.467  -8.3200  -0.6560  -0.4817
 PZF  C2    C  CR16  0  -0.097  -4.8352  -0.4360  -0.6193
 PZF  H6    H  HCR6  0   0.270  -5.4047   1.8120   1.8147
 PZF  H13   H  HCR5  0   0.281   2.3928  -1.5904   1.1251
 PZF  H8    H  HCR6  0   0.251  -1.5960   3.3170   2.1512
 PZF  H161  H  HCH2  0   0.259  -0.2677  -1.1646  -1.4415
 PZF  H162  H  HCH2  0   0.242   0.0234  -2.1246   0.0183
 PZF  H191  H  HCH3  0   0.232  -8.1738  -1.3322  -2.4525
 PZF  H192  H  HCH3  0   0.232  -8.0630  -2.5940  -1.2125
 PZF  H193  H  HCH3  0   0.248  -9.6158  -1.7892  -1.5209
 PZF  H26   H  HCR6  0   0.296   3.7202   0.8688  -1.4359
 PZF  H23   H  HCR6  0   0.315   7.0544  -1.4966   1.3371
 PZF  H17   H  HCR5  0   0.231   2.0565  -0.7542  -1.7671
 PZF  H201  H  HNH2  0   0.355   1.6886  -3.1315  -1.9863
 PZF  H202  H  HNH2  0   0.352   3.1693  -2.8560  -1.4184
 PZF  H141  H  HCH2  0   0.264   1.7102   0.6130   1.7199
 PZF  H142  H  HCH2  0   0.243   2.0080   1.2579   0.1081
 PZF  H11   H  HCR6  0   0.275  -2.1765  -0.8178  -0.2380
 PZF  H5    H  HCR6  0   0.277  -7.7207   1.0963   1.3072
 PZF  H2    H  HCR6  0   0.261  -4.0607  -0.8972  -1.2220
 PZF  F29   F  F     0  -0.299   8.0130   0.1828  -0.4179

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
 PZF  N3   C4    aromatic  1.317  0.020  1.317
 PZF  N3   C2    aromatic  1.329  0.020  1.329
 PZF  C4   O18   single    1.330  0.020  1.330
 PZF  C4   C5    aromatic  1.402  0.020  1.402
 PZF  C6   C5    aromatic  1.373  0.020  1.373
 PZF  C6   C1    aromatic  1.402  0.020  1.402
 PZF  C6   H6    single    0.930  0.020  1.080
 PZF  C13  C14   single    1.530  0.020  1.530
 PZF  C13  C17   single    1.532  0.020  1.532
 PZF  C13  C21   single    1.501  0.020  1.501
 PZF  C13  H13   single    0.970  0.020  1.090
 PZF  C21  C22   aromatic  1.386  0.020  1.386
 PZF  C21  C26   aromatic  1.395  0.020  1.395
 PZF  C8   N9    aromatic  1.319  0.020  1.319
 PZF  C8   N7    aromatic  1.320  0.020  1.320
 PZF  C8   H8    single    0.930  0.020  1.080
 PZF  C16  N15   single    1.451  0.020  1.451
 PZF  C16  C17   single    1.523  0.020  1.523
 PZF  C16  H161  single    0.970  0.020  1.090
 PZF  C16  H162  single    0.970  0.020  1.090
 PZF  C19  O18   single    1.422  0.020  1.422
 PZF  C19  H191  single    0.970  0.020  1.090
 PZF  C19  H192  single    0.970  0.020  1.090
 PZF  C19  H193  single    0.970  0.020  1.090
 PZF  C26  C25   aromatic  1.376  0.020  1.376
 PZF  C26  H26   single    0.930  0.020  1.080
 PZF  F29  C24   single    1.333  0.020  1.333
 PZF  C24  C23   aromatic  1.377  0.020  1.377
 PZF  C24  C25   aromatic  1.385  0.020  1.385
 PZF  C23  C22   aromatic  1.384  0.020  1.384
 PZF  C23  H23   single    0.930  0.020  1.080
 PZF  C22  F27   single    1.340  0.020  1.340
 PZF  C25  F28   single    1.337  0.020  1.337
 PZF  C17  N20   single    1.446  0.020  1.446
 PZF  C17  H17   single    0.970  0.020  1.090
 PZF  N20  H201  single    0.890  0.020  1.040
 PZF  N20  H202  single    0.890  0.020  1.040
 PZF  N15  C12   single    1.338  0.020  1.338
 PZF  N15  C14   single    1.454  0.020  1.454
 PZF  C14  H141  single    0.970  0.020  1.090
 PZF  C14  H142  single    0.970  0.020  1.090
 PZF  C12  C11   aromatic  1.409  0.020  1.409
 PZF  C12  N7    aromatic  1.341  0.020  1.341
 PZF  C11  C10   aromatic  1.379  0.020  1.379
 PZF  C11  H11   single    0.930  0.020  1.080
 PZF  C10  C1    single    1.473  0.020  1.473
 PZF  C10  N9    aromatic  1.344  0.020  1.344
 PZF  C1   C2    aromatic  1.387  0.020  1.387
 PZF  C5   H5    single    0.930  0.020  1.080
 PZF  C2   H2    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
 PZF  C2    N3   C4    118.41  3.000
 PZF  O18   C4   C5    117.26  3.000
 PZF  C5    C4   N3    122.96  3.000
 PZF  O18   C4   N3    119.78  3.000
 PZF  H6    C6   C5    119.91  3.000
 PZF  H6    C6   C1    119.92  3.000
 PZF  C5    C6   C1    120.17  3.000
 PZF  H13   C13  C14   108.05  3.000
 PZF  H13   C13  C17   106.88  3.000
 PZF  C14   C13  C17   102.69  3.000
 PZF  H13   C13  C21   109.81  3.000
 PZF  C17   C13  C21   114.29  3.000
 PZF  C14   C13  C21   114.58  3.000
 PZF  C22   C21  C26   116.77  3.000
 PZF  C26   C21  C13   120.99  3.000
 PZF  C22   C21  C13   122.23  3.000
 PZF  H8    C8   N9    116.29  3.000
 PZF  H8    C8   N7    115.86  3.000
 PZF  N9    C8   N7    127.85  3.000
 PZF  H162  C16  H161  108.06  3.000
 PZF  H162  C16  N15   111.74  3.000
 PZF  H161  C16  N15   111.53  3.000
 PZF  H162  C16  C17   109.99  3.000
 PZF  H161  C16  C17   112.20  3.000
 PZF  N15   C16  C17   103.32  3.000
 PZF  H193  C19  H192  109.31  3.000
 PZF  H193  C19  H191  109.39  3.000
 PZF  H192  C19  H191  108.75  3.000
 PZF  H193  C19  O18   105.80  3.000
 PZF  H192  C19  O18   111.69  3.000
 PZF  H191  C19  O18   111.84  3.000
 PZF  H26   C26  C25   118.52  3.000
 PZF  H26   C26  C21   120.41  3.000
 PZF  C25   C26  C21   121.07  3.000
 PZF  C25   C24  C23   120.31  3.000
 PZF  C25   C24  F29   119.48  3.000
 PZF  C23   C24  F29   120.21  3.000
 PZF  H23   C23  C22   120.95  3.000
 PZF  H23   C23  C24   120.82  3.000
 PZF  C22   C23  C24   118.23  3.000
 PZF  F27   C22  C23   117.33  3.000
 PZF  F27   C22  C21   119.41  3.000
 PZF  C23   C22  C21   123.26  3.000
 PZF  F28   C25  C24   119.17  3.000
 PZF  F28   C25  C26   120.48  3.000
 PZF  C24   C25  C26   120.36  3.000
 PZF  H17   C17  N20   113.32  3.000
 PZF  H17   C17  C16   108.04  3.000
 PZF  N20   C17  C16   112.24  3.000
 PZF  H17   C17  C13   108.27  3.000
 PZF  N20   C17  C13   112.46  3.000
 PZF  C16   C17  C13   101.79  3.000
 PZF  H202  N20  H201  105.21  3.000
 PZF  H202  N20  C17   109.25  3.000
 PZF  H201  N20  C17   109.36  3.000
 PZF  C12   N15  C14   123.11  3.000
 PZF  C14   N15  C16   112.75  3.000
 PZF  C12   N15  C16   124.12  3.000
 PZF  H142  C14  H141  107.49  3.000
 PZF  H142  C14  N15   111.08  3.000
 PZF  H141  C14  N15   111.70  3.000
 PZF  H142  C14  C13   112.06  3.000
 PZF  H141  C14  C13   112.01  3.000
 PZF  N15   C14  C13   102.53  3.000
 PZF  C11   C12  N7    120.47  3.000
 PZF  N7    C12  N15   117.43  3.000
 PZF  C11   C12  N15   122.10  3.000
 PZF  C12   N7   C8    116.56  3.000
 PZF  H11   C11  C10   121.52  3.000
 PZF  H11   C11  C12   121.04  3.000
 PZF  C10   C11  C12   117.42  3.000
 PZF  C1    C10  N9    116.26  3.000
 PZF  N9    C10  C11   121.50  3.000
 PZF  C1    C10  C11   122.24  3.000
 PZF  C10   N9   C8    116.16  3.000
 PZF  C2    C1   C10   122.53  3.000
 PZF  C2    C1   C6    116.53  3.000
 PZF  C10   C1   C6    120.94  3.000
 PZF  H5    C5   C6    121.47  3.000
 PZF  H5    C5   C4    120.67  3.000
 PZF  C6    C5   C4    117.86  3.000
 PZF  C19   O18  C4    118.34  3.000
 PZF  H2    C2   C1    120.82  3.000
 PZF  H2    C2   N3    115.12  3.000
 PZF  C1    C2   N3    124.06  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
 PZF  CONST_01  C6    C5   C4   N3      0.00   0.0  0
 PZF  CONST_02  C6    C1   C2   N3      0.00   0.0  0
 PZF  CONST_03  C10   C1   C2   N3    180.00   0.0  0
 PZF  CONST_04  C1    C2   N3   C4      0.00   0.0  0
 PZF  CONST_05  C1    C6   C5   C4      0.00   0.0  0
 PZF  CONST_08  C24   C23  C22  C21     0.00   0.0  0
 PZF  CONST_09  C24   C25  C26  C21     0.00   0.0  0
 PZF  CONST_10  C11   C10  N9   C8      0.00   0.0  0
 PZF  CONST_11  C1    C10  N9   C8    180.00   0.0  0
 PZF  CONST_12  C11   C12  N7   C8      0.00   0.0  0
 PZF  CONST_13  C23   C22  C21  C26     0.00   0.0  0
 PZF  CONST_14  C23   C24  C25  C26     0.00   0.0  0
 PZF  CONST_15  C25   C26  C21  C22     0.00   0.0  0
 PZF  CONST_16  C25   C24  C23  C22     0.00   0.0  0
 PZF  CONST_17  C1    C10  C11  C12   180.00   0.0  0
 PZF  CONST_18  N9    C10  C11  C12     0.00   0.0  0
 PZF  CONST_19  N9    C8   N7   C12     0.00   0.0  0
 PZF  CONST_20  C10   N9   C8   N7      0.00   0.0  0
 PZF  CONST_21  C10   C11  C12  N7      0.00   0.0  0
 PZF  CONST_23  C5    C6   C1   C10   180.00   0.0  0
 PZF  CONST_25  C2    N3   C4   C5      0.00   0.0  0
 PZF  CONST_26  C2    C1   C6   C5      0.00   0.0  0
 PZF  CONST_27  C23   C22  C21  C13   180.00   0.0  0
 PZF  CONST_28  C25   C26  C21  C13   180.00   0.0  0
 PZF  CONST_29  N15   C12  N7   C8    180.00   0.0  0
 PZF  CONST_30  C10   C11  C12  N15   180.00   0.0  0
 PZF  CONST_31  O18   C4   C5   C6    180.00   0.0  0
 PZF  CONST_32  F27   C22  C21  C13     0.00   0.0  0
 PZF  CONST_33  F28   C25  C26  C21   180.00   0.0  0
 PZF  CONST_34  F27   C22  C21  C26   180.00   0.0  0
 PZF  CONST_35  F29   C24  C25  C26   180.00   0.0  0
 PZF  CONST_36  C22   C23  C24  F29   180.00   0.0  0
 PZF  CONST_37  F27   C22  C23  C24   180.00   0.0  0
 PZF  CONST_38  F28   C25  C24  C23   180.00   0.0  0
 PZF  CONST_39  C2    N3   C4   O18   180.00   0.0  0
 PZF  CONST_40  H5    C5   C4   N3    180.00   0.0  0
 PZF  CONST_41  H2    C2   N3   C4    180.00   0.0  0
 PZF  CONST_42  H6    C6   C5   C4    180.00   0.0  0
 PZF  CONST_43  H26   C26  C21  C13     0.00   0.0  0
 PZF  CONST_44  H23   C23  C22  C21   180.00   0.0  0
 PZF  CONST_45  H11   C11  C12  N15     0.00   0.0  0
 PZF  CONST_46  H8    C8   N7   C12   180.00   0.0  0
 PZF  Var_01    C16   N15  C14  C13   -12.27  30.0  1
 PZF  Var_02    C11   C12  N15  C16     3.77  30.0  2
 PZF  Var_03    C5    C4   O18  C19  -179.03  30.0  2
 PZF  Var_04    H191  C19  O18  C4    -60.74  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
 PZF  chir_01  C13  C14  C17  C21  negativ
 PZF  chir_02  C17  N20  C13  C16  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
 PZF  plan-1  N3   0.020
 PZF  plan-1  C4   0.020
 PZF  plan-1  C6   0.020
 PZF  plan-1  C10  0.020
 PZF  plan-1  C1   0.020
 PZF  plan-1  C5   0.020
 PZF  plan-1  O18  0.020
 PZF  plan-1  C2   0.020
 PZF  plan-1  H6   0.020
 PZF  plan-1  H5   0.020
 PZF  plan-1  H2   0.020
 PZF  plan-2  C13  0.020
 PZF  plan-2  C21  0.020
 PZF  plan-2  C26  0.020
 PZF  plan-2  C24  0.020
 PZF  plan-2  C23  0.020
 PZF  plan-2  C22  0.020
 PZF  plan-2  F27  0.020
 PZF  plan-2  C25  0.020
 PZF  plan-2  F28  0.020
 PZF  plan-2  H26  0.020
 PZF  plan-2  H23  0.020
 PZF  plan-2  F29  0.020
 PZF  plan-3  C8   0.020
 PZF  plan-3  N15  0.020
 PZF  plan-3  C12  0.020
 PZF  plan-3  N7   0.020
 PZF  plan-3  C11  0.020
 PZF  plan-3  C10  0.020
 PZF  plan-3  N9   0.020
 PZF  plan-3  C1   0.020
 PZF  plan-3  H8   0.020
 PZF  plan-3  H11  0.020

