# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 00:49:20 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: [(1S)-2,2-difluorocyclopropyl][(1R,5S)-3-{2-[(1-methyl-1H-pyrazol-4-yl)amino]pyrimidin-4-yl}-3,8-diazabicyclo[3.2.1]octan-8-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(Nc2nccc(n2)N3C[C@H]4CC[C@@H](C3)N4C(=O)[C@@H]5CC5(F)F)cn1
#
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
 G4J  G4J  '[(1S)-2,2-difluorocyclopropyl][(1R,5S)-3-{2-[(1-methyl-1H-pyrazol-4-yl)amino]pyrimidin-4-yl}-3,8-diazabicyclo[3.2.1]octan-8-yl]methanone'  ligand  49  28  .  2022-07-25  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_G4J
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
 G4J  N3   N  NH1   0  -0.754  -3.8744  -0.3082  -0.4085
 G4J  C4   C  CR15  0  -0.085  -6.1095   0.1200   0.7419
 G4J  N2   N  N     0  -0.284  -7.3661  -0.2178   0.4907
 G4J  C7   C  CR16  0  -0.459  -1.1055   1.4213   1.9386
 G4J  C6   C  CR16  0  -0.017  -2.4417   1.4471   2.2493
 G4J  C9   C  CH2   0  -0.279   0.8205  -0.1869  -0.8547
 G4J  C13  C  CR15  0  -0.161   2.8494   1.4371   0.2776
 G4J  C8   C  CR6   0   0.586  -0.7565   0.7579   0.7384
 G4J  N5   N  N     0  -0.544  -1.7052   0.1923  -0.0014
 G4J  C18  C  CT    0   0.739   6.4811  -0.6844   0.4341
 G4J  C16  C  CH1   0  -0.527   5.0470  -0.4699   0.6756
 G4J  N1   N  NR5   0  -0.251  -7.3382  -0.9307  -0.6198
 G4J  C2   C  CR15  0  -0.033  -6.0913  -1.0685  -1.1123
 G4J  C3   C  CR5   0   0.079  -5.2496  -0.3954  -0.2481
 G4J  C5   C  CR6   0   0.581  -2.9696   0.2885   0.4079
 G4J  N4   N  N     0  -0.490  -3.4017   0.8938   1.5087
 G4J  N6   N  NT    0  -0.514   0.5199   0.6705   0.2847
 G4J  C10  C  CR15  0  -0.154   2.0748   0.3055  -1.5655
 G4J  C11  C  CH2   0  -0.444   1.9589   1.7874  -1.9511
 G4J  C12  C  CH2   0  -0.438   2.5008   2.5463  -0.7226
 G4J  C14  C  CH2   0  -0.271   1.6422   1.0499   1.1269
 G4J  N7   N  NR5   0  -0.433   3.1661   0.3244  -0.6031
 G4J  C15  C  C     0   0.537   4.0568  -0.6627  -0.4390
 G4J  O1   O  O     0  -0.486   4.0807  -1.6647  -1.1386
 G4J  C17  C  CH2   0  -0.594   6.0451   0.6968   0.6696
 G4J  F1   F  F     0  -0.312   6.9117  -1.0390  -0.7886
 G4J  F2   F  F     0  -0.319   7.2194  -1.3297   1.3555
 G4J  H9   H  HNH1  0   0.403  -3.4836  -0.7536  -1.2233
 G4J  H8   H  HCR5  0   0.267  -5.8573   0.7054   1.6080
 G4J  H11  H  HCR6  0   0.270  -0.3922   1.8892   2.5972
 G4J  H10  H  HCR6  0   0.262  -2.7676   1.9429   3.1576
 G4J  H13  H  HCH2  0   0.246   0.9587  -1.2269  -0.5348
 G4J  H12  H  HCH2  0   0.275  -0.0193  -0.1666  -1.5438
 G4J  H2   H  HCR5  0   0.300   3.6759   1.6926   0.9372
 G4J  H3   H  HCH1  0   0.339   4.6764  -0.7577   1.6561
 G4J  H4   H  HCH3  0   0.257  -9.1400  -0.6024  -1.6361
 G4J  H5   H  HCH3  0   0.258  -8.3216  -2.1302  -1.9912
 G4J  H6   H  HCH3  0   0.261  -9.1608  -1.9208  -0.4496
 G4J  H7   H  HCR5  0   0.293  -5.8840  -1.6216  -2.0145
 G4J  H1   H  HCR5  0   0.281   2.2999  -0.3485  -2.4051
 G4J  H15  H  HCH2  0   0.255   2.5623   1.9943  -2.8344
 G4J  H14  H  HCH2  0   0.249   0.9295   2.0546  -2.1879
 G4J  H17  H  HCH2  0   0.249   1.7826   3.2502  -0.3028
 G4J  H16  H  HCH2  0   0.256   3.3998   3.1075  -0.9771
 G4J  H19  H  HCH2  0   0.251   1.9137   0.2363   1.8115
 G4J  H18  H  HCH2  0   0.270   1.3794   1.9144   1.7329
 G4J  H20  H  HCH2  0   0.299   6.2686   1.1626   1.6209
 G4J  H21  H  HCH2  0   0.293   6.0251   1.3679  -0.1808
 G4J  C1   C  CH3   0  -0.507  -8.5621  -1.4193  -1.2061

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
 G4J  F1   C18  single    1.344  0.020  1.344
 G4J  O1   C15  double    1.222  0.020  1.222
 G4J  C17  C18  single    1.467  0.020  1.467
 G4J  C17  C16  single    1.535  0.020  1.535
 G4J  C18  F2   single    1.346  0.020  1.346
 G4J  C18  C16  single    1.470  0.020  1.470
 G4J  C15  C16  single    1.503  0.020  1.503
 G4J  C15  N7   single    1.340  0.020  1.340
 G4J  C1   N1   single    1.442  0.020  1.442
 G4J  C10  N7   single    1.455  0.020  1.455
 G4J  C10  C11  single    1.536  0.020  1.536
 G4J  C10  C9   single    1.523  0.020  1.523
 G4J  N7   C13  single    1.454  0.020  1.454
 G4J  C11  C12  single    1.542  0.020  1.542
 G4J  N1   N2   aromatic  1.320  0.020  1.320
 G4J  N1   C2   aromatic  1.348  0.020  1.348
 G4J  C9   N6   single    1.457  0.020  1.457
 G4J  C12  C13  single    1.534  0.020  1.534
 G4J  C13  C14  single    1.526  0.020  1.526
 G4J  N2   C4   aromatic  1.325  0.020  1.325
 G4J  C2   C3   aromatic  1.381  0.020  1.381
 G4J  N6   C14  single    1.454  0.020  1.454
 G4J  N6   C8   single    1.357  0.020  1.357
 G4J  C4   C3   aromatic  1.409  0.020  1.409
 G4J  C3   N3   single    1.387  0.020  1.387
 G4J  N5   C8   aromatic  1.329  0.020  1.329
 G4J  N5   C5   aromatic  1.332  0.020  1.332
 G4J  C8   C7   aromatic  1.415  0.020  1.415
 G4J  N3   C5   single    1.357  0.020  1.357
 G4J  C5   N4   aromatic  1.329  0.020  1.329
 G4J  C7   C6   aromatic  1.372  0.020  1.372
 G4J  N4   C6   aromatic  1.333  0.020  1.333
 G4J  N3   H9   single    0.860  0.020  1.020
 G4J  C4   H8   single    0.930  0.020  1.080
 G4J  C7   H11  single    0.930  0.020  1.080
 G4J  C6   H10  single    0.930  0.020  1.080
 G4J  C9   H13  single    0.970  0.020  1.090
 G4J  C9   H12  single    0.970  0.020  1.090
 G4J  C13  H2   single    0.970  0.020  1.090
 G4J  C16  H3   single    0.970  0.020  1.090
 G4J  C1   H4   single    0.970  0.020  1.090
 G4J  C1   H5   single    0.970  0.020  1.090
 G4J  C1   H6   single    0.970  0.020  1.090
 G4J  C2   H7   single    0.930  0.020  1.080
 G4J  C10  H1   single    0.970  0.020  1.090
 G4J  C11  H15  single    0.970  0.020  1.090
 G4J  C11  H14  single    0.970  0.020  1.090
 G4J  C12  H17  single    0.970  0.020  1.090
 G4J  C12  H16  single    0.970  0.020  1.090
 G4J  C14  H19  single    0.970  0.020  1.090
 G4J  C14  H18  single    0.970  0.020  1.090
 G4J  C17  H20  single    0.970  0.020  1.090
 G4J  C17  H21  single    0.970  0.020  1.090

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
 G4J  H9   N3   C5   114.98  3.000
 G4J  H9   N3   C3   116.76  3.000
 G4J  C5   N3   C3   128.25  3.000
 G4J  H8   C4   C3   128.46  3.000
 G4J  H8   C4   N2   120.91  3.000
 G4J  C3   C4   N2   110.63  3.000
 G4J  N1   N2   C4   106.09  3.000
 G4J  H11  C7   C8   123.95  3.000
 G4J  H11  C7   C6   119.87  3.000
 G4J  C8   C7   C6   116.17  3.000
 G4J  H10  C6   N4   116.01  3.000
 G4J  H10  C6   C7   119.39  3.000
 G4J  N4   C6   C7   124.60  3.000
 G4J  H12  C9   H13  107.46  3.000
 G4J  H12  C9   C10  109.53  3.000
 G4J  H13  C9   C10  109.80  3.000
 G4J  H12  C9   N6   109.00  3.000
 G4J  H13  C9   N6   110.85  3.000
 G4J  C10  C9   N6   110.15  3.000
 G4J  H2   C13  N7   112.43  3.000
 G4J  H2   C13  C14  108.85  3.000
 G4J  N7   C13  C14  108.38  3.000
 G4J  H2   C13  C12  113.47  3.000
 G4J  C14  C13  C12  111.51  3.000
 G4J  N7   C13  C12  102.00  3.000
 G4J  N6   C8   N5   117.23  3.000
 G4J  N5   C8   C7   119.70  3.000
 G4J  N6   C8   C7   123.07  3.000
 G4J  C5   N5   C8   118.39  3.000
 G4J  F2   C18  F1   108.70  3.000
 G4J  F2   C18  C17  120.30  3.000
 G4J  F1   C18  C17  119.31  3.000
 G4J  F2   C18  C16  119.52  3.000
 G4J  C17  C18  C16   63.03  3.000
 G4J  F1   C18  C16  120.04  3.000
 G4J  H3   C16  C17  115.24  3.000
 G4J  H3   C16  C15  114.22  3.000
 G4J  C17  C16  C15  121.52  3.000
 G4J  H3   C16  C18  116.25  3.000
 G4J  C15  C16  C18  120.13  3.000
 G4J  C17  C16  C18   58.40  3.000
 G4J  C2   N1   C1   127.00  3.000
 G4J  C2   N1   N2   112.47  3.000
 G4J  C1   N1   N2   120.47  3.000
 G4J  H7   C2   C3   131.01  3.000
 G4J  H7   C2   N1   122.41  3.000
 G4J  C3   C2   N1   106.57  3.000
 G4J  C2   C3   C4   104.24  3.000
 G4J  C4   C3   N3   131.55  3.000
 G4J  C2   C3   N3   124.21  3.000
 G4J  N4   C5   N5   126.59  3.000
 G4J  N4   C5   N3   118.82  3.000
 G4J  N5   C5   N3   114.60  3.000
 G4J  C5   N4   C6   114.54  3.000
 G4J  C14  N6   C8   121.03  3.000
 G4J  C8   N6   C9   119.55  3.000
 G4J  C14  N6   C9   116.57  3.000
 G4J  H1   C10  N7   111.29  3.000
 G4J  H1   C10  C11  113.70  3.000
 G4J  N7   C10  C11  102.13  3.000
 G4J  H1   C10  C9   109.65  3.000
 G4J  C11  C10  C9   111.53  3.000
 G4J  N7   C10  C9   108.24  3.000
 G4J  H14  C11  H15  107.49  3.000
 G4J  H14  C11  C12  112.61  3.000
 G4J  H15  C11  C12  110.96  3.000
 G4J  H14  C11  C10  111.26  3.000
 G4J  H15  C11  C10  110.18  3.000
 G4J  C12  C11  C10  104.38  3.000
 G4J  H16  C12  H17  107.51  3.000
 G4J  H16  C12  C11  110.93  3.000
 G4J  H17  C12  C11  113.15  3.000
 G4J  H16  C12  C13  109.71  3.000
 G4J  H17  C12  C13  111.45  3.000
 G4J  C11  C12  C13  104.09  3.000
 G4J  H18  C14  H19  107.54  3.000
 G4J  H18  C14  N6   110.10  3.000
 G4J  H19  C14  N6   111.04  3.000
 G4J  H18  C14  C13  107.43  3.000
 G4J  H19  C14  C13  109.85  3.000
 G4J  N6   C14  C13  110.77  3.000
 G4J  C15  N7   C10  124.75  3.000
 G4J  C10  N7   C13  104.31  3.000
 G4J  C15  N7   C13  129.38  3.000
 G4J  O1   C15  N7   123.15  3.000
 G4J  N7   C15  C16  115.74  3.000
 G4J  O1   C15  C16  121.11  3.000
 G4J  H21  C17  H20  115.28  3.000
 G4J  H21  C17  C16  117.50  3.000
 G4J  H20  C17  C16  117.24  3.000
 G4J  H21  C17  C18  117.55  3.000
 G4J  H20  C17  C18  118.99  3.000
 G4J  C16  C17  C18   58.57  3.000
 G4J  H6   C1   H5   108.84  3.000
 G4J  H6   C1   H4   109.18  3.000
 G4J  H5   C1   H4   108.85  3.000
 G4J  H6   C1   N1   109.91  3.000
 G4J  H5   C1   N1   109.13  3.000
 G4J  H4   C1   N1   110.89  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
 G4J  CONST_01  C2   N1   N2   C4      0.00   0.0  0
 G4J  CONST_02  N1   C2   C3   C4      0.00   0.0  0
 G4J  CONST_03  C3   C2   N1   N2      0.00   0.0  0
 G4J  CONST_04  C2   C3   C4   N2      0.00   0.0  0
 G4J  CONST_05  C5   N5   C8   C7      0.00   0.0  0
 G4J  CONST_06  C5   N4   C6   C7      0.00   0.0  0
 G4J  CONST_07  N5   C8   C7   C6      0.00   0.0  0
 G4J  CONST_08  N5   C5   N4   C6      0.00   0.0  0
 G4J  CONST_09  N4   C5   N5   C8      0.00   0.0  0
 G4J  CONST_10  N4   C6   C7   C8      0.00   0.0  0
 G4J  CONST_11  C3   C4   N2   N1      0.00   0.0  0
 G4J  CONST_12  N6   C8   C7   C6    180.00   0.0  0
 G4J  CONST_13  N6   C8   N5   C5    180.00   0.0  0
 G4J  CONST_14  N1   C2   C3   N3    180.00   0.0  0
 G4J  CONST_15  N2   C4   C3   N3    180.00   0.0  0
 G4J  CONST_16  C8   N5   C5   N3    180.00   0.0  0
 G4J  CONST_17  C6   N4   C5   N3    180.00   0.0  0
 G4J  CONST_18  C1   N1   N2   C4    180.00   0.0  0
 G4J  CONST_19  C3   C2   N1   C1    180.00   0.0  0
 G4J  CONST_20  C16  C15  N7   C13     0.00   0.0  0
 G4J  CONST_21  C10  N7   C15  C16   180.00   0.0  0
 G4J  CONST_22  H7   C2   C3   C4    180.00   0.0  0
 G4J  CONST_23  H10  C6   C7   C8    180.00   0.0  0
 G4J  CONST_24  H11  C7   C8   N5    180.00   0.0  0
 G4J  CONST_25  H8   C4   N2   N1    180.00   0.0  0
 G4J  CONST_26  O1   C15  N7   C13   180.00   0.0  0
 G4J  CONST_27  O1   C15  N7   C10     0.00   0.0  0
 G4J  Var_01    C9   N6   C8   C7    171.36  30.0  2
 G4J  Var_02    C13  C14  N6   C9     43.39  30.0  1
 G4J  Var_03    C10  C11  C12  C13    -1.36  30.0  3
 G4J  Var_04    C10  C9   N6   C8    154.87  30.0  1
 G4J  Var_05    C5   N3   C3   C4      2.30  30.0  2
 G4J  Var_06    C3   N3   C5   N5    179.06  30.0  1
 G4J  Var_07    C15  C16  C17  C18  -108.31  30.0  1
 G4J  Var_08    N7   C15  C16  C18  -131.67  30.0  3
 G4J  Var_09    F1   C18  C17  C16   111.00  30.0  1
 G4J  Var_10    H4   C1   N1   N2     70.78  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
 G4J  chir_01  C13  N7   C12  C14  negativ
 G4J  chir_03  C10  N7   C11  C9   positiv
 G4J  chir_04  C16  C17  C18  C15  both

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
 G4J  plan-1  N3   0.020
 G4J  plan-1  C4   0.020
 G4J  plan-1  N2   0.020
 G4J  plan-1  N1   0.020
 G4J  plan-1  C2   0.020
 G4J  plan-1  C3   0.020
 G4J  plan-1  H8   0.020
 G4J  plan-1  H7   0.020
 G4J  plan-1  C1   0.020
 G4J  plan-2  N3   0.020
 G4J  plan-2  C7   0.020
 G4J  plan-2  C6   0.020
 G4J  plan-2  C8   0.020
 G4J  plan-2  N5   0.020
 G4J  plan-2  C5   0.020
 G4J  plan-2  N4   0.020
 G4J  plan-2  N6   0.020
 G4J  plan-2  H11  0.020
 G4J  plan-2  H10  0.020
 G4J  plan-3  C13  0.020
 G4J  plan-3  C16  0.020
 G4J  plan-3  C10  0.020
 G4J  plan-3  N7   0.020
 G4J  plan-3  C15  0.020
 G4J  plan-3  O1   0.020

