# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 05:50:05 2021
#   Inital geometry file: a 70 line input string
#   Ligand name: 5-fluoro-N-methyl-2-(7H-pyrrolo[2,3-d]pyrimidin-5-yl)pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc(ncc1F)c2c[nH]c3ncncc23
#
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
 PZ4  PZ4  5-fluoro-N-methyl-2-(7H-pyrrolo[2,3-d]pyrimidin-5-yl)pyrimidin-4-amine  ligand  27  18  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_PZ4
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
 PZ4  C1   C  CH3   0  -0.517  -13.7927   -7.4120  25.9601
 PZ4  C3   C  CR6   0   0.425  -11.8466   -6.8967  24.5803
 PZ4  C5   C  CR6   0   0.316   -9.8930   -8.0561  24.8618
 PZ4  C7   C  CR16  0  -0.187   -9.9089   -6.4698  23.2540
 PZ4  C8   C  CR6   0   0.351  -11.2043   -6.1758  23.5533
 PZ4  C11  C  CR15  0   0.002   -7.8836   -9.4774  25.3980
 PZ4  C15  C  CR16  0   0.032   -9.8490  -11.7302  28.6122
 PZ4  C17  C  CR16  0  -0.103  -10.8529  -10.0870  27.3842
 PZ4  C18  C  CR56  0  -0.022   -9.6769   -9.9122  26.6650
 PZ4  N2   N  NH1   0  -0.658  -13.1140   -6.6615  24.9312
 PZ4  N4   N  N     0  -0.494  -11.1572   -7.8383  25.2188
 PZ4  N6   N  N     0  -0.452   -9.2306   -7.4188  23.9075
 PZ4  F9   F  F     0  -0.305  -11.8795   -5.2181  22.8961
 PZ4  C10  C  CR5   0  -0.099   -9.1843   -9.0926  25.5975
 PZ4  N12  N  NR15  0  -0.662   -7.5481  -10.4718  26.2659
 PZ4  C13  C  CR56  0   0.514   -8.6171  -10.7594  27.0501
 PZ4  N14  N  N     0  -0.417   -8.6744  -11.6677  28.0096
 PZ4  N16  N  N     0  -0.414  -10.9294  -10.9930  28.3503
 PZ4  H1   H  HCH3  0   0.258  -14.8053   -7.0286  26.0445
 PZ4  H2   H  HCH3  0   0.239  -13.8445   -8.4748  25.7191
 PZ4  H3   H  HCH3  0   0.240  -13.3010   -7.3049  26.9277
 PZ4  H4   H  HCR6  0   0.285   -9.3918   -5.9309  22.4672
 PZ4  H6   H  HCR6  0   0.258   -9.9457  -12.4603  29.4075
 PZ4  H7   H  HCR6  0   0.275  -11.7352   -9.4933  27.1797
 PZ4  H8   H  HNH1  0   0.410  -13.6372   -5.9661  24.4283
 PZ4  H9   H  HNR5  0   0.424   -6.6474  -10.9222  26.3155
 PZ4  H5   H  HCR5  0   0.304   -7.1655   -9.1035  24.6869

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
 PZ4  F9   C8   single    1.343  0.020  1.343
 PZ4  C7   C8   aromatic  1.362  0.020  1.362
 PZ4  C7   N6   aromatic  1.337  0.020  1.337
 PZ4  C8   C3   aromatic  1.410  0.020  1.410
 PZ4  N6   C5   aromatic  1.325  0.020  1.325
 PZ4  C3   N2   single    1.336  0.020  1.336
 PZ4  C3   N4   aromatic  1.330  0.020  1.330
 PZ4  N2   C1   single    1.443  0.020  1.443
 PZ4  C5   N4   aromatic  1.332  0.020  1.332
 PZ4  C5   C10  single    1.455  0.020  1.455
 PZ4  C11  C10  aromatic  1.371  0.020  1.371
 PZ4  C11  N12  aromatic  1.362  0.020  1.362
 PZ4  C10  C18  aromatic  1.433  0.020  1.433
 PZ4  N12  C13  aromatic  1.357  0.020  1.357
 PZ4  C18  C13  aromatic  1.410  0.020  1.410
 PZ4  C18  C17  aromatic  1.389  0.020  1.389
 PZ4  C13  N14  aromatic  1.322  0.020  1.322
 PZ4  C17  N16  aromatic  1.327  0.020  1.327
 PZ4  N14  C15  aromatic  1.322  0.020  1.322
 PZ4  N16  C15  aromatic  1.334  0.020  1.334
 PZ4  C1   H1   single    0.970  0.020  1.090
 PZ4  C1   H2   single    0.970  0.020  1.090
 PZ4  C1   H3   single    0.970  0.020  1.090
 PZ4  C7   H4   single    0.930  0.020  1.080
 PZ4  C11  H5   single    0.930  0.020  1.080
 PZ4  C15  H6   single    0.930  0.020  1.080
 PZ4  C17  H7   single    0.930  0.020  1.080
 PZ4  N2   H8   single    0.860  0.020  1.020
 PZ4  N12  H9   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
 PZ4  H3   C1   H2   108.24  3.000
 PZ4  H3   C1   H1   108.46  3.000
 PZ4  H2   C1   H1   108.47  3.000
 PZ4  H3   C1   N2   111.69  3.000
 PZ4  H2   C1   N2   111.80  3.000
 PZ4  H1   C1   N2   108.08  3.000
 PZ4  N4   C3   N2   119.35  3.000
 PZ4  N4   C3   C8   118.40  3.000
 PZ4  N2   C3   C8   122.25  3.000
 PZ4  C10  C5   N6   117.60  3.000
 PZ4  C10  C5   N4   116.32  3.000
 PZ4  N6   C5   N4   126.09  3.000
 PZ4  H4   C7   N6   117.72  3.000
 PZ4  H4   C7   C8   120.38  3.000
 PZ4  N6   C7   C8   121.90  3.000
 PZ4  F9   C8   C7   121.63  3.000
 PZ4  C7   C8   C3   118.90  3.000
 PZ4  F9   C8   C3   119.47  3.000
 PZ4  H5   C11  N12  120.64  3.000
 PZ4  H5   C11  C10  129.12  3.000
 PZ4  N12  C11  C10  110.24  3.000
 PZ4  H6   C15  N16  116.36  3.000
 PZ4  H6   C15  N14  116.47  3.000
 PZ4  N16  C15  N14  127.17  3.000
 PZ4  H7   C17  N16  117.70  3.000
 PZ4  H7   C17  C18  121.53  3.000
 PZ4  N16  C17  C18  120.77  3.000
 PZ4  C13  C18  C10  106.78  3.000
 PZ4  C13  C18  C17  114.78  3.000
 PZ4  C10  C18  C17  138.44  3.000
 PZ4  H8   N2   C3   118.96  3.000
 PZ4  H8   N2   C1   118.15  3.000
 PZ4  C3   N2   C1   122.81  3.000
 PZ4  C5   N4   C3   118.63  3.000
 PZ4  C7   N6   C5   116.09  3.000
 PZ4  C18  C10  C11  105.90  3.000
 PZ4  C18  C10  C5   128.06  3.000
 PZ4  C11  C10  C5   126.04  3.000
 PZ4  H9   N12  C13  125.51  3.000
 PZ4  H9   N12  C11  125.28  3.000
 PZ4  C13  N12  C11  109.21  3.000
 PZ4  N14  C13  N12  126.81  3.000
 PZ4  N14  C13  C18  125.32  3.000
 PZ4  N12  C13  C18  107.87  3.000
 PZ4  C13  N14  C15  113.69  3.000
 PZ4  C17  N16  C15  118.28  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
 PZ4  CONST_01  N6   C7   C8   C3      0.00   0.0  0
 PZ4  CONST_02  N6   C5   N4   C3      0.00   0.0  0
 PZ4  CONST_03  C10  C5   N4   C3    180.00   0.0  0
 PZ4  CONST_04  C8   C7   N6   C5      0.00   0.0  0
 PZ4  CONST_05  C8   C3   N4   C5      0.00   0.0  0
 PZ4  CONST_06  N12  C11  C10  C5    180.00   0.0  0
 PZ4  CONST_07  C13  C18  C10  C5    180.00   0.0  0
 PZ4  CONST_08  C17  C18  C10  C5      0.00   0.0  0
 PZ4  CONST_09  N4   C3   C8   C7      0.00   0.0  0
 PZ4  CONST_10  N4   C5   N6   C7      0.00   0.0  0
 PZ4  CONST_11  C10  C5   N6   C7    180.00   0.0  0
 PZ4  CONST_12  N6   C5   C10  C11     0.00   0.0  0
 PZ4  CONST_13  N4   C5   C10  C11   180.00   0.0  0
 PZ4  CONST_14  C13  C18  C10  C11     0.00   0.0  0
 PZ4  CONST_15  C17  C18  C10  C11   180.00   0.0  0
 PZ4  CONST_16  C18  C13  N12  C11     0.00   0.0  0
 PZ4  CONST_17  N14  C13  N12  C11   180.00   0.0  0
 PZ4  CONST_18  N12  C13  N14  C15   180.00   0.0  0
 PZ4  CONST_19  C18  C13  N14  C15     0.00   0.0  0
 PZ4  CONST_20  C18  C17  N16  C15     0.00   0.0  0
 PZ4  CONST_21  N12  C13  C18  C17   180.00   0.0  0
 PZ4  CONST_22  N14  C13  C18  C17     0.00   0.0  0
 PZ4  CONST_23  N14  C15  N16  C17     0.00   0.0  0
 PZ4  CONST_24  N6   C5   C10  C18   180.00   0.0  0
 PZ4  CONST_25  N4   C5   C10  C18     0.00   0.0  0
 PZ4  CONST_26  N12  C11  C10  C18     0.00   0.0  0
 PZ4  CONST_27  C13  N12  C11  C10     0.00   0.0  0
 PZ4  CONST_28  N12  C13  C18  C10     0.00   0.0  0
 PZ4  CONST_29  N14  C13  C18  C10   180.00   0.0  0
 PZ4  CONST_30  N16  C17  C18  C10   180.00   0.0  0
 PZ4  CONST_31  N16  C17  C18  C13     0.00   0.0  0
 PZ4  CONST_32  N16  C15  N14  C13     0.00   0.0  0
 PZ4  CONST_33  N2   C3   N4   C5    180.00   0.0  0
 PZ4  CONST_34  N2   C3   C8   C7    180.00   0.0  0
 PZ4  CONST_35  F9   C8   C3   N4    180.00   0.0  0
 PZ4  CONST_36  F9   C8   C7   N6    180.00   0.0  0
 PZ4  CONST_37  H4   C7   C8   C3    180.00   0.0  0
 PZ4  CONST_38  H5   C11  C10  C5      0.00   0.0  0
 PZ4  CONST_39  H7   C17  N16  C15   180.00   0.0  0
 PZ4  CONST_40  H6   C15  N16  C17   180.00   0.0  0
 PZ4  CONST_41  H9   N12  C13  C18   180.00   0.0  0
 PZ4  CONST_42  C8   C3   N2   C1    180.00   0.0  0
 PZ4  CONST_43  N4   C3   N2   C1      0.00   0.0  0
 PZ4  CONST_44  H8   N2   C3   C8      0.00   0.0  0
 PZ4  Var_01    H1   C1   N2   C3   -179.68  30.0  3

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
 PZ4  plan-1  C3   0.020
 PZ4  plan-1  C5   0.020
 PZ4  plan-1  C7   0.020
 PZ4  plan-1  C8   0.020
 PZ4  plan-1  N2   0.020
 PZ4  plan-1  N4   0.020
 PZ4  plan-1  N6   0.020
 PZ4  plan-1  F9   0.020
 PZ4  plan-1  C10  0.020
 PZ4  plan-1  H4   0.020
 PZ4  plan-2  C5   0.020
 PZ4  plan-2  C11  0.020
 PZ4  plan-2  C15  0.020
 PZ4  plan-2  C17  0.020
 PZ4  plan-2  C18  0.020
 PZ4  plan-2  C10  0.020
 PZ4  plan-2  N12  0.020
 PZ4  plan-2  C13  0.020
 PZ4  plan-2  N14  0.020
 PZ4  plan-2  N16  0.020
 PZ4  plan-2  H6   0.020
 PZ4  plan-2  H7   0.020
 PZ4  plan-2  H9   0.020
 PZ4  plan-2  H5   0.020
 PZ4  plan-3  C1   0.020
 PZ4  plan-3  C3   0.020
 PZ4  plan-3  N2   0.020
 PZ4  plan-3  H8   0.020

