# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 00:51:18 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 7-[(1~{S})-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(pyridin-3-ylamino)pyrrolo[2,3-d]pyrimidin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N1C(=O)C(C)(C)c2cnc(Nc3cccnc3)nc12)c4ccc(F)cc4
#
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
 6Z2  6Z2  7-[(1~{S})-1-(4-fluorophenyl)ethyl]-5,5-dimethyl-2-(pyridin-3-ylamino)pyrrolo[2,3-d]pyrimidin-6-one  ligand  48  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6Z2
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
 6Z2  C4   C  CR16  0  -0.040   1.0512  -2.4323  -0.8787
 6Z2  C14  C  CR5   0   0.617  -2.5277  -2.3413   0.0589
 6Z2  C6   C  CR6   0   0.278   3.7083   0.7404   0.2218
 6Z2  C11  C  CR16  0  -0.212   4.5385  -0.1271  -0.4873
 6Z2  C7   C  CR16  0  -0.153   4.2905   1.9119   0.7285
 6Z2  C13  C  CR5   0  -0.357  -1.4765  -3.1893  -0.6648
 6Z2  N1   N  N     0  -0.487   0.2504  -0.2492   0.5638
 6Z2  N    N  N     0  -0.490   1.9442  -1.4807  -0.5705
 6Z2  C    C  CR6   0   0.615   1.5076  -0.4461   0.1276
 6Z2  C2   C  CR56  0   0.594  -0.5871  -1.1931   0.2307
 6Z2  C3   C  CR56  0  -0.011  -0.2572  -2.3388  -0.4990
 6Z2  N5   N  NH1   0  -0.769   2.3600   0.5593   0.4750
 6Z2  N8   N  N     0  -0.388   5.5598   2.2341   0.5730
 6Z2  C9   C  CR16  0  -0.093   6.3453   1.4027  -0.1055
 6Z2  C10  C  CR16  0  -0.313   5.8718   0.2201  -0.6463
 6Z2  N12  N  NR5   0  -0.581  -1.9255  -1.2024   0.5518
 6Z2  C15  C  CH3   0  -0.628  -1.8802  -3.3721  -2.1294
 6Z2  C16  C  CH3   0  -0.628  -1.3432  -4.5426   0.0383
 6Z2  O    O  O     0  -0.437  -3.6985  -2.6110   0.1846
 6Z2  C17  C  CH1   0  -0.191  -2.6230  -0.1572   1.2968
 6Z2  C18  C  CR6   0   0.128  -2.5220   1.1592   0.5519
 6Z2  C19  C  CR16  0  -0.271  -3.1445   1.2745  -0.6889
 6Z2  C20  C  CR16  0  -0.400  -3.0823   2.4495  -1.4214
 6Z2  C21  C  CR6   0   0.514  -2.3869   3.5185  -0.8889
 6Z2  C22  C  CR16  0  -0.402  -1.7623   3.4454   0.3395
 6Z2  C23  C  CR16  0  -0.268  -1.8329   2.2562   1.0526
 6Z2  C24  C  CH3   0  -0.681  -2.1746  -0.1276   2.7498
 6Z2  F    F  F     0  -0.316  -2.3193   4.6635  -1.5882
 6Z2  H1   H  HCR6  0   0.271   1.4277  -3.2768  -1.4456
 6Z2  H2   H  HCR6  0   0.297   4.1556  -1.0446  -0.9025
 6Z2  H3   H  HCR6  0   0.269   3.6749   2.6120   1.2878
 6Z2  H4   H  HNH1  0   0.409   1.9116   1.2952   1.0005
 6Z2  H5   H  HCR6  0   0.260   7.3837   1.6905  -0.2195
 6Z2  H6   H  HCR6  0   0.271   6.5385  -0.4330  -1.1929
 6Z2  H7   H  HCH3  0   0.242  -1.9893  -2.4152  -2.6406
 6Z2  H8   H  HCH3  0   0.248  -1.1173  -3.9489  -2.6528
 6Z2  H9   H  HCH3  0   0.246  -2.8230  -3.9141  -2.2037
 6Z2  H10  H  HCH3  0   0.246  -2.2747  -5.1054  -0.0243
 6Z2  H11  H  HCH3  0   0.248  -0.5608  -5.1315  -0.4411
 6Z2  H12  H  HCH3  0   0.244  -1.0792  -4.4256   1.0896
 6Z2  H13  H  HCH1  0   0.288  -3.6717  -0.4604   1.2841
 6Z2  H14  H  HCR6  0   0.262  -3.6946   0.4350  -1.0983
 6Z2  H15  H  HCR6  0   0.279  -3.5700   2.5320  -2.3836
 6Z2  H16  H  HCR6  0   0.279  -1.2230   4.2967   0.7338
 6Z2  H17  H  HCR6  0   0.261  -1.3335   2.1994   2.0100
 6Z2  H18  H  HCH3  0   0.256  -2.3433  -1.1030   3.2046
 6Z2  H19  H  HCH3  0   0.244  -1.1210   0.1223   2.8574
 6Z2  H20  H  HCH3  0   0.249  -2.7610   0.6029   3.3064

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
 6Z2  F    C21  single    1.343  0.020  1.343
 6Z2  C22  C21  aromatic  1.380  0.020  1.380
 6Z2  C22  C23  aromatic  1.388  0.020  1.388
 6Z2  C21  C20  aromatic  1.382  0.020  1.382
 6Z2  C23  C18  aromatic  1.389  0.020  1.389
 6Z2  C10  C9   aromatic  1.384  0.020  1.384
 6Z2  C10  C11  aromatic  1.387  0.020  1.387
 6Z2  C9   N8   aromatic  1.330  0.020  1.330
 6Z2  C20  C19  aromatic  1.386  0.020  1.386
 6Z2  C18  C19  aromatic  1.393  0.020  1.393
 6Z2  C18  C17  single    1.516  0.020  1.516
 6Z2  C24  C17  single    1.521  0.020  1.521
 6Z2  N8   C7   aromatic  1.319  0.020  1.319
 6Z2  C11  C6   aromatic  1.395  0.020  1.395
 6Z2  C17  N12  single    1.461  0.020  1.461
 6Z2  C7   C6   aromatic  1.403  0.020  1.403
 6Z2  C6   N5   single    1.384  0.020  1.384
 6Z2  N12  C2   single    1.376  0.020  1.376
 6Z2  N12  C14  single    1.379  0.020  1.379
 6Z2  O    C14  double    1.208  0.020  1.208
 6Z2  N1   C2   aromatic  1.305  0.020  1.305
 6Z2  N1   C    aromatic  1.345  0.020  1.345
 6Z2  C2   C3   aromatic  1.398  0.020  1.398
 6Z2  C14  C13  single    1.532  0.020  1.532
 6Z2  N5   C    single    1.363  0.020  1.363
 6Z2  C    N    aromatic  1.322  0.020  1.322
 6Z2  C3   C13  single    1.496  0.020  1.496
 6Z2  C3   C4   aromatic  1.366  0.020  1.366
 6Z2  C13  C15  single    1.530  0.020  1.530
 6Z2  C13  C16  single    1.531  0.020  1.531
 6Z2  N    C4   aromatic  1.341  0.020  1.341
 6Z2  C4   H1   single    0.930  0.020  1.080
 6Z2  C11  H2   single    0.930  0.020  1.080
 6Z2  C7   H3   single    0.930  0.020  1.080
 6Z2  N5   H4   single    0.860  0.020  1.020
 6Z2  C9   H5   single    0.930  0.020  1.080
 6Z2  C10  H6   single    0.930  0.020  1.080
 6Z2  C15  H7   single    0.970  0.020  1.090
 6Z2  C15  H8   single    0.970  0.020  1.090
 6Z2  C15  H9   single    0.970  0.020  1.090
 6Z2  C16  H10  single    0.970  0.020  1.090
 6Z2  C16  H11  single    0.970  0.020  1.090
 6Z2  C16  H12  single    0.970  0.020  1.090
 6Z2  C17  H13  single    0.970  0.020  1.090
 6Z2  C19  H14  single    0.930  0.020  1.080
 6Z2  C20  H15  single    0.930  0.020  1.080
 6Z2  C22  H16  single    0.930  0.020  1.080
 6Z2  C23  H17  single    0.930  0.020  1.080
 6Z2  C24  H18  single    0.970  0.020  1.090
 6Z2  C24  H19  single    0.970  0.020  1.090
 6Z2  C24  H20  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
 6Z2  H1   C4   C3   122.09  3.000
 6Z2  H1   C4   N    116.20  3.000
 6Z2  C3   C4   N    121.71  3.000
 6Z2  O    C14  N12  124.77  3.000
 6Z2  O    C14  C13  126.19  3.000
 6Z2  N12  C14  C13  109.04  3.000
 6Z2  N5   C6   C7   116.59  3.000
 6Z2  N5   C6   C11  126.27  3.000
 6Z2  C7   C6   C11  117.14  3.000
 6Z2  H2   C11  C10  120.71  3.000
 6Z2  H2   C11  C6   120.94  3.000
 6Z2  C10  C11  C6   118.35  3.000
 6Z2  H3   C7   N8   116.63  3.000
 6Z2  H3   C7   C6   119.25  3.000
 6Z2  N8   C7   C6   124.12  3.000
 6Z2  C16  C13  C15  110.92  3.000
 6Z2  C16  C13  C3   112.38  3.000
 6Z2  C15  C13  C3   112.89  3.000
 6Z2  C16  C13  C14  109.39  3.000
 6Z2  C15  C13  C14  109.70  3.000
 6Z2  C3   C13  C14  101.08  3.000
 6Z2  C2   N1   C    114.27  3.000
 6Z2  C    N    C4   117.18  3.000
 6Z2  N5   C    N    120.34  3.000
 6Z2  N    C    N1   126.47  3.000
 6Z2  N5   C    N1   113.19  3.000
 6Z2  N12  C2   C3   110.23  3.000
 6Z2  C3   C2   N1   125.07  3.000
 6Z2  N12  C2   N1   124.70  3.000
 6Z2  C2   C3   C13  109.36  3.000
 6Z2  C13  C3   C4   135.33  3.000
 6Z2  C2   C3   C4   115.31  3.000
 6Z2  H4   N5   C    113.12  3.000
 6Z2  H4   N5   C6   115.63  3.000
 6Z2  C    N5   C6   131.24  3.000
 6Z2  C9   N8   C7   118.41  3.000
 6Z2  H5   C9   C10  120.92  3.000
 6Z2  H5   C9   N8   116.98  3.000
 6Z2  C10  C9   N8   122.11  3.000
 6Z2  H6   C10  C9   120.17  3.000
 6Z2  H6   C10  C11  119.96  3.000
 6Z2  C9   C10  C11  119.87  3.000
 6Z2  C17  N12  C2   125.34  3.000
 6Z2  C2   N12  C14  110.29  3.000
 6Z2  C17  N12  C14  124.37  3.000
 6Z2  H9   C15  H8   108.02  3.000
 6Z2  H9   C15  H7   108.53  3.000
 6Z2  H8   C15  H7   108.02  3.000
 6Z2  H9   C15  C13  110.66  3.000
 6Z2  H8   C15  C13  109.75  3.000
 6Z2  H7   C15  C13  111.74  3.000
 6Z2  H12  C16  H11  107.95  3.000
 6Z2  H12  C16  H10  108.53  3.000
 6Z2  H11  C16  H10  108.00  3.000
 6Z2  H12  C16  C13  111.66  3.000
 6Z2  H11  C16  C13  109.75  3.000
 6Z2  H10  C16  C13  110.83  3.000
 6Z2  H13  C17  C24  107.44  3.000
 6Z2  H13  C17  C18  107.43  3.000
 6Z2  C24  C17  C18  115.65  3.000
 6Z2  H13  C17  N12  104.71  3.000
 6Z2  C24  C17  N12  111.12  3.000
 6Z2  C18  C17  N12  109.81  3.000
 6Z2  C23  C18  C19  118.52  3.000
 6Z2  C19  C18  C17  118.67  3.000
 6Z2  C23  C18  C17  122.81  3.000
 6Z2  H14  C19  C20  118.67  3.000
 6Z2  H14  C19  C18  119.94  3.000
 6Z2  C20  C19  C18  121.38  3.000
 6Z2  H15  C20  C21  120.69  3.000
 6Z2  H15  C20  C19  120.96  3.000
 6Z2  C21  C20  C19  118.35  3.000
 6Z2  F    C21  C22  119.06  3.000
 6Z2  C22  C21  C20  121.99  3.000
 6Z2  F    C21  C20  118.95  3.000
 6Z2  H16  C22  C23  120.80  3.000
 6Z2  H16  C22  C21  120.55  3.000
 6Z2  C23  C22  C21  118.66  3.000
 6Z2  H17  C23  C22  118.44  3.000
 6Z2  H17  C23  C18  120.45  3.000
 6Z2  C22  C23  C18  121.10  3.000
 6Z2  H20  C24  H19  108.45  3.000
 6Z2  H20  C24  H18  107.67  3.000
 6Z2  H19  C24  H18  108.32  3.000
 6Z2  H20  C24  C17  110.02  3.000
 6Z2  H19  C24  C17  112.61  3.000
 6Z2  H18  C24  C17  109.62  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
 6Z2  CONST_01  N1   C2   C3   C4      0.00   0.0  0
 6Z2  CONST_02  N1   C    N    C4      0.00   0.0  0
 6Z2  CONST_03  C9   C10  C11  C6      0.00   0.0  0
 6Z2  CONST_04  C9   N8   C7   C6      0.00   0.0  0
 6Z2  CONST_05  N8   C9   C10  C11     0.00   0.0  0
 6Z2  CONST_06  N8   C7   C6   C11     0.00   0.0  0
 6Z2  CONST_07  C10  C9   N8   C7      0.00   0.0  0
 6Z2  CONST_08  C10  C11  C6   C7      0.00   0.0  0
 6Z2  CONST_09  C2   N1   C    N       0.00   0.0  0
 6Z2  CONST_10  C2   C3   C4   N       0.00   0.0  0
 6Z2  CONST_11  C3   C2   N1   C       0.00   0.0  0
 6Z2  CONST_12  C3   C4   N    C       0.00   0.0  0
 6Z2  CONST_13  C21  C22  C23  C18     0.00   0.0  0
 6Z2  CONST_14  C21  C20  C19  C18     0.00   0.0  0
 6Z2  CONST_15  C22  C21  C20  C19     0.00   0.0  0
 6Z2  CONST_16  C22  C23  C18  C19     0.00   0.0  0
 6Z2  CONST_17  C23  C22  C21  C20     0.00   0.0  0
 6Z2  CONST_18  C23  C18  C19  C20     0.00   0.0  0
 6Z2  CONST_19  C2   N12  C14  C13     0.00   0.0  0
 6Z2  CONST_20  N5   C    N    C4    180.00   0.0  0
 6Z2  CONST_21  N5   C    N1   C2    180.00   0.0  0
 6Z2  CONST_22  C10  C11  C6   N5    180.00   0.0  0
 6Z2  CONST_23  N8   C7   C6   N5    180.00   0.0  0
 6Z2  CONST_24  C22  C23  C18  C17   180.00   0.0  0
 6Z2  CONST_25  C20  C19  C18  C17   180.00   0.0  0
 6Z2  CONST_26  F    C21  C20  C19   180.00   0.0  0
 6Z2  CONST_27  F    C21  C22  C23   180.00   0.0  0
 6Z2  CONST_28  C17  N12  C14  C13   180.00   0.0  0
 6Z2  CONST_29  O    C14  N12  C2    180.00   0.0  0
 6Z2  CONST_30  H6   C10  C11  C6    180.00   0.0  0
 6Z2  CONST_31  H5   C9   C10  C11   180.00   0.0  0
 6Z2  CONST_32  H3   C7   C6   C11   180.00   0.0  0
 6Z2  CONST_33  H2   C11  C6   C7    180.00   0.0  0
 6Z2  CONST_34  H1   C4   C3   C13     0.00   0.0  0
 6Z2  CONST_35  H16  C22  C23  C18   180.00   0.0  0
 6Z2  CONST_36  H15  C20  C19  C18   180.00   0.0  0
 6Z2  CONST_37  H17  C23  C18  C19   180.00   0.0  0
 6Z2  CONST_38  H14  C19  C20  C21   180.00   0.0  0
 6Z2  CONST_39  C17  N12  C14  O       0.00   0.0  0
 6Z2  Var_01    C15  C13  C3   C4    -62.57  30.0  1
 6Z2  Var_02    N1   C    N5   C6   -179.68  30.0  2
 6Z2  Var_03    C    N5   C6   C11    -0.19  30.0  2
 6Z2  Var_04    H7   C15  C13  C14    58.43  30.0  3
 6Z2  Var_05    H10  C16  C13  C14    63.64  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
 6Z2  chir_01  C17  C18  C24  N12  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
 6Z2  plan-1  C6   0.020
 6Z2  plan-1  C11  0.020
 6Z2  plan-1  C7   0.020
 6Z2  plan-1  N5   0.020
 6Z2  plan-1  N8   0.020
 6Z2  plan-1  C9   0.020
 6Z2  plan-1  C10  0.020
 6Z2  plan-1  H2   0.020
 6Z2  plan-1  H3   0.020
 6Z2  plan-1  H5   0.020
 6Z2  plan-1  H6   0.020
 6Z2  plan-2  C17  0.020
 6Z2  plan-2  C18  0.020
 6Z2  plan-2  C19  0.020
 6Z2  plan-2  C20  0.020
 6Z2  plan-2  C21  0.020
 6Z2  plan-2  C22  0.020
 6Z2  plan-2  C23  0.020
 6Z2  plan-2  F    0.020
 6Z2  plan-2  H14  0.020
 6Z2  plan-2  H15  0.020
 6Z2  plan-2  H16  0.020
 6Z2  plan-2  H17  0.020
 6Z2  plan-3  C4   0.020
 6Z2  plan-3  C14  0.020
 6Z2  plan-3  C13  0.020
 6Z2  plan-3  N1   0.020
 6Z2  plan-3  N    0.020
 6Z2  plan-3  C    0.020
 6Z2  plan-3  C2   0.020
 6Z2  plan-3  C3   0.020
 6Z2  plan-3  N5   0.020
 6Z2  plan-3  N12  0.020
 6Z2  plan-3  O    0.020
 6Z2  plan-3  C17  0.020
 6Z2  plan-3  H1   0.020

