# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:30:22 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (3R)-3-methyl-5-[(pyrimidin-4-yl)amino]-2,3-dihydro-1H-isoindol-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1NC(=O)c2ccc(Nc3ccncn3)cc12
#
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
 F67  F67  (3R)-3-methyl-5-[(pyrimidin-4-yl)amino]-2,3-dihydro-1H-isoindol-1-one  ligand  30  18  .  2021-08-09  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F67
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
 F67  O1   O  O     0  -0.484  -4.8413   0.9310  -0.1035
 F67  C16  C  CR5   0   0.522  -3.8316   0.2508  -0.1992
 F67  N15  N  NR15  0  -0.669  -3.7681  -1.0844  -0.4013
 F67  C14  C  CR15  0  -0.083  -2.4265  -1.6332  -0.4621
 F67  C18  C  CH3   0  -0.655  -2.1802  -2.6939   0.6024
 F67  C10  C  CR56  0   0.158  -1.5954  -0.3938  -0.2786
 F67  C9   C  CR16  0  -0.397  -0.2186  -0.2789  -0.2474
 F67  C11  C  CR56  0  -0.122  -2.4279   0.6990  -0.1214
 F67  C12  C  CR16  0  -0.288  -1.9016   1.9666   0.0746
 F67  C13  C  CR16  0  -0.369  -0.5294   2.1053   0.1065
 F67  C8   C  CR6   0   0.384   0.3248   0.9959  -0.0518
 F67  N7   N  NH1   0  -0.776   1.6838   1.2751  -0.0045
 F67  C3   C  CR6   0   0.570   2.7752   0.4675  -0.0757
 F67  N2   N  N     0  -0.470   2.6386  -0.8467  -0.2123
 F67  C4   C  CR16  0  -0.414   4.0542   1.0489  -0.0006
 F67  C5   C  CR16  0  -0.031   5.1240   0.1955  -0.0733
 F67  N6   N  N     0  -0.427   4.9916  -1.1304  -0.2087
 F67  C1   C  CR16  0   0.075   3.7499  -1.5673  -0.2702
 F67  H1   H  HNR5  0   0.400  -4.5891  -1.6584  -0.5107
 F67  H2   H  HCR5  0   0.276  -2.2434  -2.0655  -1.4517
 F67  H3   H  HCH3  0   0.246  -2.8556  -3.5387   0.4647
 F67  H4   H  HCH3  0   0.239  -1.1596  -3.0705   0.5361
 F67  H5   H  HCH3  0   0.235  -2.3339  -2.2834   1.6005
 F67  H6   H  HCR6  0   0.291   0.4201  -1.1391  -0.3668
 F67  H7   H  HCR6  0   0.265  -2.5414   2.8307   0.2003
 F67  H8   H  HCR6  0   0.275  -0.0962   3.0866   0.2608
 F67  H9   H  HNH1  0   0.422   1.9004   2.2530   0.1172
 F67  H10  H  HCR6  0   0.289   4.1904   2.1163   0.1062
 F67  H11  H  HCR6  0   0.279   6.1348   0.5831  -0.0225
 F67  H12  H  HCR6  0   0.260   3.6119  -2.6379  -0.3801

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
 F67  O1   C16  double    1.221  0.020  1.221
 F67  C16  C11  single    1.476  0.020  1.476
 F67  C16  N15  single    1.352  0.020  1.352
 F67  C12  C11  aromatic  1.386  0.020  1.386
 F67  C12  C13  aromatic  1.380  0.020  1.380
 F67  C11  C10  aromatic  1.383  0.020  1.383
 F67  N15  C14  single    1.451  0.020  1.451
 F67  C13  C8   aromatic  1.409  0.020  1.409
 F67  C1   N2   aromatic  1.326  0.020  1.326
 F67  C1   N6   aromatic  1.318  0.020  1.318
 F67  N2   C3   aromatic  1.328  0.020  1.328
 F67  C10  C14  single    1.504  0.020  1.504
 F67  C10  C9   aromatic  1.382  0.020  1.382
 F67  C14  C18  single    1.523  0.020  1.523
 F67  N6   C5   aromatic  1.339  0.020  1.339
 F67  C8   C9   aromatic  1.400  0.020  1.400
 F67  C8   N7   single    1.388  0.020  1.388
 F67  C3   N7   single    1.360  0.020  1.360
 F67  C3   C4   aromatic  1.407  0.020  1.407
 F67  C5   C4   aromatic  1.370  0.020  1.370
 F67  N15  H1   single    0.860  0.020  1.020
 F67  C14  H2   single    0.970  0.020  1.090
 F67  C18  H3   single    0.970  0.020  1.090
 F67  C18  H4   single    0.970  0.020  1.090
 F67  C18  H5   single    0.970  0.020  1.090
 F67  C9   H6   single    0.930  0.020  1.080
 F67  C12  H7   single    0.930  0.020  1.080
 F67  C13  H8   single    0.930  0.020  1.080
 F67  N7   H9   single    0.860  0.020  1.020
 F67  C4   H10  single    0.930  0.020  1.080
 F67  C5   H11  single    0.930  0.020  1.080
 F67  C1   H12  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
 F67  C11  C16  N15  105.26  3.000
 F67  N15  C16  O1   126.91  3.000
 F67  C11  C16  O1   127.83  3.000
 F67  H1   N15  C14  122.24  3.000
 F67  H1   N15  C16  122.72  3.000
 F67  C14  N15  C16  115.04  3.000
 F67  H2   C14  C10  110.08  3.000
 F67  H2   C14  C18  109.24  3.000
 F67  C10  C14  C18  113.54  3.000
 F67  H2   C14  N15  109.99  3.000
 F67  C18  C14  N15  112.56  3.000
 F67  C10  C14  N15  101.20  3.000
 F67  H5   C18  H4   108.53  3.000
 F67  H5   C18  H3   108.66  3.000
 F67  H4   C18  H3   107.74  3.000
 F67  H5   C18  C14  110.79  3.000
 F67  H4   C18  C14  110.46  3.000
 F67  H3   C18  C14  110.56  3.000
 F67  C11  C10  C9   122.11  3.000
 F67  C9   C10  C14  128.46  3.000
 F67  C11  C10  C14  109.43  3.000
 F67  H6   C9   C8   120.81  3.000
 F67  H6   C9   C10  121.43  3.000
 F67  C8   C9   C10  117.75  3.000
 F67  C12  C11  C10  120.67  3.000
 F67  C10  C11  C16  109.07  3.000
 F67  C12  C11  C16  130.26  3.000
 F67  H7   C12  C13  120.33  3.000
 F67  H7   C12  C11  121.46  3.000
 F67  C13  C12  C11  118.21  3.000
 F67  H8   C13  C8   119.12  3.000
 F67  H8   C13  C12  119.47  3.000
 F67  C8   C13  C12  121.42  3.000
 F67  N7   C8   C13  115.55  3.000
 F67  N7   C8   C9   124.62  3.000
 F67  C13  C8   C9   119.83  3.000
 F67  H9   N7   C3   114.19  3.000
 F67  H9   N7   C8   114.16  3.000
 F67  C3   N7   C8   131.65  3.000
 F67  C4   C3   N2   120.52  3.000
 F67  C4   C3   N7   118.79  3.000
 F67  N2   C3   N7   120.70  3.000
 F67  C1   N2   C3   117.13  3.000
 F67  H10  C4   C5   121.44  3.000
 F67  H10  C4   C3   121.84  3.000
 F67  C5   C4   C3   116.71  3.000
 F67  H11  C5   N6   116.81  3.000
 F67  H11  C5   C4   120.19  3.000
 F67  N6   C5   C4   123.01  3.000
 F67  C1   N6   C5   115.22  3.000
 F67  H12  C1   N6   116.85  3.000
 F67  H12  C1   N2   115.73  3.000
 F67  N6   C1   N2   127.42  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
 F67  CONST_01  C13  C12  C11  C10    0.00   0.0  0
 F67  CONST_02  C13  C8   C9   C10    0.00   0.0  0
 F67  CONST_03  C12  C11  C10  C9     0.00   0.0  0
 F67  CONST_04  C12  C13  C8   C9     0.00   0.0  0
 F67  CONST_05  C8   C13  C12  C11    0.00   0.0  0
 F67  CONST_06  C8   C9   C10  C11    0.00   0.0  0
 F67  CONST_07  N6   C1   N2   C3     0.00   0.0  0
 F67  CONST_08  N6   C5   C4   C3     0.00   0.0  0
 F67  CONST_09  C5   N6   C1   N2     0.00   0.0  0
 F67  CONST_10  C5   C4   C3   N2     0.00   0.0  0
 F67  CONST_11  C1   N2   C3   C4     0.00   0.0  0
 F67  CONST_12  C1   N6   C5   C4     0.00   0.0  0
 F67  CONST_13  C11  C16  N15  C14    0.00   0.0  0
 F67  CONST_14  N7   C8   C9   C10  180.00   0.0  0
 F67  CONST_15  N7   C8   C13  C12  180.00   0.0  0
 F67  CONST_16  C1   N2   C3   N7   180.00   0.0  0
 F67  CONST_17  C5   C4   C3   N7   180.00   0.0  0
 F67  CONST_18  C14  N15  C16  O1   180.00   0.0  0
 F67  CONST_19  H7   C12  C11  C16    0.00   0.0  0
 F67  CONST_20  H6   C9   C10  C14    0.00   0.0  0
 F67  CONST_21  H8   C13  C8   C9   180.00   0.0  0
 F67  CONST_22  H12  C1   N2   C3   180.00   0.0  0
 F67  CONST_23  H11  C5   C4   C3   180.00   0.0  0
 F67  CONST_24  H10  C4   C3   N2   180.00   0.0  0
 F67  CONST_25  H1   N15  C16  C11  180.00   0.0  0
 F67  Var_01    C3   N7   C8   C9    -2.64  30.0  2
 F67  Var_02    N2   C3   N7   C8    -0.22  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
 F67  chir_01  C14  N15  C10  C18  negativ

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
 F67  plan-1  N7   0.020
 F67  plan-1  C3   0.020
 F67  plan-1  N2   0.020
 F67  plan-1  C4   0.020
 F67  plan-1  C5   0.020
 F67  plan-1  N6   0.020
 F67  plan-1  C1   0.020
 F67  plan-1  H10  0.020
 F67  plan-1  H11  0.020
 F67  plan-1  H12  0.020
 F67  plan-2  O1   0.020
 F67  plan-2  C16  0.020
 F67  plan-2  N15  0.020
 F67  plan-2  C14  0.020
 F67  plan-2  C10  0.020
 F67  plan-2  C9   0.020
 F67  plan-2  C11  0.020
 F67  plan-2  C12  0.020
 F67  plan-2  C13  0.020
 F67  plan-2  C8   0.020
 F67  plan-2  N7   0.020
 F67  plan-2  H1   0.020
 F67  plan-2  H6   0.020
 F67  plan-2  H7   0.020
 F67  plan-2  H8   0.020

