# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 16:41:41 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: N,4-dimethyl-3-[(1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1ccc(C)c(Nc2ncnc3n(ncc23)c4ccccc4)c1
#
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
 N4D  N4D  N,4-dimethyl-3-[(1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4-yl)amino]benzamide  ligand  45  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N4D
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
 N4D  C13   C  CR6   0   0.062  -3.2286   2.2338   0.3378
 N4D  C18   C  C     0   0.525  -4.9720  -1.5550  -0.7236
 N4D  C17   C  CR6   0   0.522  -0.0748   0.5598  -0.0111
 N4D  C16   C  CR56  0   0.579   2.2238  -0.0300   0.1451
 N4D  C15   C  CR6   0   0.313  -2.4543   1.1818  -0.1669
 N4D  C19   C  CH3   0  -0.747  -2.6045   3.5400   0.7248
 N4D  C20   C  CH3   0  -0.514  -6.7452  -3.1875  -0.3634
 N4D  C11   C  CR56  0  -0.238   1.2705   0.9009  -0.2655
 N4D  C12   C  CR6   0  -0.046  -4.4051  -0.2266  -0.3355
 N4D  C1    C  CR16  0  -0.257   7.2505  -1.1653   0.2768
 N4D  C2    C  CR16  0  -0.250   6.9559  -0.3769  -0.8281
 N4D  C3    C  CR16  0  -0.251   6.2697  -1.4015   1.2299
 N4D  C4    C  CR16  0  -0.290  -5.1858   0.8157   0.1561
 N4D  C5    C  CR16  0  -0.293  -4.5975   2.0288   0.4737
 N4D  C6    C  CR16  0  -0.294   5.6895   0.1633  -0.9894
 N4D  C7    C  CR16  0  -0.294   5.0018  -0.8557   1.0891
 N4D  C8    C  CR16  0  -0.289  -3.0425  -0.0251  -0.5192
 N4D  C9    C  CR15  0  -0.091   2.0184   1.9485  -0.8530
 N4D  C10   C  CR16  0   0.068   0.6744  -1.3996   0.9039
 N4D  C14   C  CR6   0   0.344   4.7139  -0.0782  -0.0274
 N4D  N21   N  N     0  -0.241   3.2948   1.6818  -0.8012
 N4D  N22   N  N     0  -0.455   1.9644  -1.2011   0.7297
 N4D  N23   N  N     0  -0.477  -0.3409  -0.5986   0.5777
 N4D  N24   N  NR5   0  -0.485   3.4320   0.4856  -0.1923
 N4D  N25   N  NH1   0  -0.767  -1.0761   1.3962  -0.3480
 N4D  N26   N  NH1   0  -0.638  -6.0918  -1.9291  -0.0906
 N4D  O27   O  O     0  -0.494  -4.4288  -2.2573  -1.5679
 N4D  H19   H  HCH3  0   0.254  -2.1829   4.0648  -0.1359
 N4D  H19A  H  HCH3  0   0.263  -3.3416   4.2010   1.1759
 N4D  H19B  H  HCH3  0   0.257  -1.7961   3.3980   1.4439
 N4D  H20   H  HCH3  0   0.241  -7.0746  -3.2499  -1.4006
 N4D  H20A  H  HCH3  0   0.238  -6.0907  -4.0363  -0.1606
 N4D  H20B  H  HCH3  0   0.251  -7.6178  -3.2660   0.2781
 N4D  H2    H  HCR6  0   0.265   7.7134  -0.1850  -1.5764
 N4D  H3    H  HCR6  0   0.264   6.4912  -2.0058   2.0997
 N4D  H4    H  HCR6  0   0.259  -6.2567   0.7087   0.2734
 N4D  H5    H  HCR6  0   0.260  -5.2145   2.8369   0.8467
 N4D  H6    H  HCR6  0   0.273   5.4606   0.7690  -1.8553
 N4D  H7    H  HCR6  0   0.276   4.2516  -1.0319   1.8458
 N4D  H8    H  HCR6  0   0.267  -2.4389  -0.8167  -0.9384
 N4D  H9    H  HCR5  0   0.281   1.6748   2.8703  -1.2972
 N4D  H10   H  HCR6  0   0.260   0.3935  -2.3345   1.3760
 N4D  HN25  H  HNH1  0   0.416  -0.8054   2.2981  -0.7091
 N4D  HN26  H  HNH1  0   0.411  -6.4398  -1.3762   0.6738
 N4D  H1    H  HCR6  0   0.262   8.2384  -1.5902   0.3948

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
 N4D  C13  C15   aromatic  1.400  0.020  1.400
 N4D  C13  C19   single    1.498  0.020  1.498
 N4D  C13  C5    aromatic  1.391  0.020  1.391
 N4D  C18  C12   single    1.496  0.020  1.496
 N4D  C18  N26   single    1.340  0.020  1.340
 N4D  C18  O27   double    1.225  0.020  1.225
 N4D  C17  C11   aromatic  1.411  0.020  1.411
 N4D  C17  N23   aromatic  1.326  0.020  1.326
 N4D  C17  N25   single    1.347  0.020  1.347
 N4D  C16  C11   aromatic  1.394  0.020  1.394
 N4D  C16  N22   aromatic  1.334  0.020  1.334
 N4D  C16  N24   aromatic  1.356  0.020  1.356
 N4D  C15  C8    aromatic  1.388  0.020  1.388
 N4D  C15  N25   single    1.407  0.020  1.407
 N4D  C20  N26   single    1.444  0.020  1.444
 N4D  C11  C9    aromatic  1.415  0.020  1.415
 N4D  C12  C4    aromatic  1.392  0.020  1.392
 N4D  C12  C8    aromatic  1.390  0.020  1.390
 N4D  C1   C2    aromatic  1.389  0.020  1.389
 N4D  C1   C3    aromatic  1.388  0.020  1.388
 N4D  C2   C6    aromatic  1.386  0.020  1.386
 N4D  C3   C7    aromatic  1.388  0.020  1.388
 N4D  C4   C5    aromatic  1.385  0.020  1.385
 N4D  C6   C14   aromatic  1.391  0.020  1.391
 N4D  C7   C14   aromatic  1.391  0.020  1.391
 N4D  C9   N21   aromatic  1.305  0.020  1.305
 N4D  C10  N22   aromatic  1.317  0.020  1.317
 N4D  C10  N23   aromatic  1.334  0.020  1.334
 N4D  C14  N24   single    1.410  0.020  1.410
 N4D  N21  N24   aromatic  1.349  0.020  1.349
 N4D  C19  H19   single    0.970  0.020  1.090
 N4D  C19  H19A  single    0.970  0.020  1.090
 N4D  C19  H19B  single    0.970  0.020  1.090
 N4D  C20  H20   single    0.970  0.020  1.090
 N4D  C20  H20A  single    0.970  0.020  1.090
 N4D  C20  H20B  single    0.970  0.020  1.090
 N4D  C1   H1    single    0.930  0.020  1.080
 N4D  C2   H2    single    0.930  0.020  1.080
 N4D  C3   H3    single    0.930  0.020  1.080
 N4D  C4   H4    single    0.930  0.020  1.080
 N4D  C5   H5    single    0.930  0.020  1.080
 N4D  C6   H6    single    0.930  0.020  1.080
 N4D  C7   H7    single    0.930  0.020  1.080
 N4D  C8   H8    single    0.930  0.020  1.080
 N4D  C9   H9    single    0.930  0.020  1.080
 N4D  C10  H10   single    0.930  0.020  1.080
 N4D  N25  HN25  single    0.860  0.020  1.020
 N4D  N26  HN26  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
 N4D  C5    C13  C19   120.88  3.000
 N4D  C5    C13  C15   117.95  3.000
 N4D  C19   C13  C15   121.17  3.000
 N4D  O27   C18  N26   122.43  3.000
 N4D  O27   C18  C12   121.33  3.000
 N4D  N26   C18  C12   116.24  3.000
 N4D  N25   C17  N23   120.27  3.000
 N4D  N25   C17  C11   120.89  3.000
 N4D  N23   C17  C11   118.84  3.000
 N4D  N24   C16  N22   128.01  3.000
 N4D  N24   C16  C11   106.38  3.000
 N4D  N22   C16  C11   125.60  3.000
 N4D  N25   C15  C8    121.00  3.000
 N4D  N25   C15  C13   118.28  3.000
 N4D  C8    C15  C13   120.69  3.000
 N4D  H19B  C19  H19A  107.92  3.000
 N4D  H19B  C19  H19   107.20  3.000
 N4D  H19A  C19  H19   107.23  3.000
 N4D  H19B  C19  C13   111.43  3.000
 N4D  H19A  C19  C13   110.76  3.000
 N4D  H19   C19  C13   112.09  3.000
 N4D  H20B  C20  H20A  108.42  3.000
 N4D  H20B  C20  H20   108.37  3.000
 N4D  H20A  C20  H20   108.28  3.000
 N4D  H20B  C20  N26   108.36  3.000
 N4D  H20A  C20  N26   111.81  3.000
 N4D  H20   C20  N26   111.50  3.000
 N4D  C9    C11  C16   104.79  3.000
 N4D  C9    C11  C17   139.27  3.000
 N4D  C16   C11  C17   115.94  3.000
 N4D  C8    C12  C4    119.21  3.000
 N4D  C8    C12  C18   117.79  3.000
 N4D  C4    C12  C18   122.97  3.000
 N4D  H1    C1   C3    120.23  3.000
 N4D  H1    C1   C2    120.22  3.000
 N4D  C3    C1   C2    119.54  3.000
 N4D  H2    C2   C6    119.34  3.000
 N4D  H2    C2   C1    120.16  3.000
 N4D  C6    C2   C1    120.50  3.000
 N4D  H3    C3   C7    119.23  3.000
 N4D  H3    C3   C1    120.17  3.000
 N4D  C7    C3   C1    120.60  3.000
 N4D  H4    C4   C5    118.80  3.000
 N4D  H4    C4   C12   121.27  3.000
 N4D  C5    C4   C12   119.91  3.000
 N4D  H5    C5   C4    119.38  3.000
 N4D  H5    C5   C13   118.97  3.000
 N4D  C4    C5   C13   121.65  3.000
 N4D  H6    C6   C14   120.17  3.000
 N4D  H6    C6   C2    120.32  3.000
 N4D  C14   C6   C2    119.51  3.000
 N4D  H7    C7   C14   120.66  3.000
 N4D  H7    C7   C3    119.96  3.000
 N4D  C14   C7   C3    119.38  3.000
 N4D  H8    C8   C12   119.54  3.000
 N4D  H8    C8   C15   119.93  3.000
 N4D  C12   C8   C15   120.54  3.000
 N4D  H9    C9   N21   120.15  3.000
 N4D  H9    C9   C11   129.41  3.000
 N4D  N21   C9   C11   110.44  3.000
 N4D  H10   C10  N23   115.28  3.000
 N4D  H10   C10  N22   116.19  3.000
 N4D  N23   C10  N22   128.53  3.000
 N4D  N24   C14  C7    120.38  3.000
 N4D  N24   C14  C6    119.16  3.000
 N4D  C7    C14  C6    120.46  3.000
 N4D  N24   N21  C9    107.37  3.000
 N4D  C10   N22  C16   112.38  3.000
 N4D  C10   N23  C17   118.71  3.000
 N4D  N21   N24  C14   119.98  3.000
 N4D  N21   N24  C16   111.02  3.000
 N4D  C14   N24  C16   128.96  3.000
 N4D  HN25  N25  C15   116.45  3.000
 N4D  HN25  N25  C17   116.44  3.000
 N4D  C15   N25  C17   126.97  3.000
 N4D  HN26  N26  C20   117.79  3.000
 N4D  HN26  N26  C18   119.67  3.000
 N4D  C20   N26  C18   122.16  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
 N4D  CONST_01  C12   C8   C15  C13    0.00   0.0  0
 N4D  CONST_02  C12   C4   C5   C13    0.00   0.0  0
 N4D  CONST_03  N22   C16  C11  C17    0.00   0.0  0
 N4D  CONST_04  N24   C16  C11  C17  180.00   0.0  0
 N4D  CONST_05  N21   C9   C11  C17  180.00   0.0  0
 N4D  CONST_06  N22   C10  N23  C17    0.00   0.0  0
 N4D  CONST_07  N23   C17  C11  C16    0.00   0.0  0
 N4D  CONST_08  N21   C9   C11  C16    0.00   0.0  0
 N4D  CONST_09  N23   C10  N22  C16    0.00   0.0  0
 N4D  CONST_12  C9    N21  N24  C16    0.00   0.0  0
 N4D  CONST_13  C4    C5   C13  C15    0.00   0.0  0
 N4D  CONST_14  C4    C12  C8   C15    0.00   0.0  0
 N4D  CONST_15  C10   N23  C17  C11    0.00   0.0  0
 N4D  CONST_16  C10   N22  C16  C11    0.00   0.0  0
 N4D  CONST_17  C14   N24  C16  C11  180.00   0.0  0
 N4D  CONST_18  N21   N24  C16  C11    0.00   0.0  0
 N4D  CONST_19  N24   N21  C9   C11    0.00   0.0  0
 N4D  CONST_20  C14   C6   C2   C1     0.00   0.0  0
 N4D  CONST_21  C14   C7   C3   C1     0.00   0.0  0
 N4D  CONST_22  C7    C3   C1   C2     0.00   0.0  0
 N4D  CONST_23  C7    C14  C6   C2     0.00   0.0  0
 N4D  CONST_24  N24   C14  C6   C2   180.00   0.0  0
 N4D  CONST_25  C6    C2   C1   C3     0.00   0.0  0
 N4D  CONST_26  C6    C14  C7   C3     0.00   0.0  0
 N4D  CONST_27  N24   C14  C7   C3   180.00   0.0  0
 N4D  CONST_28  C8    C15  C13  C5     0.00   0.0  0
 N4D  CONST_29  C8    C12  C4   C5     0.00   0.0  0
 N4D  CONST_32  N23   C17  C11  C9   180.00   0.0  0
 N4D  CONST_33  N22   C16  C11  C9   180.00   0.0  0
 N4D  CONST_34  N24   C16  C11  C9     0.00   0.0  0
 N4D  CONST_35  C14   N24  N21  C9   180.00   0.0  0
 N4D  CONST_36  N24   C16  N22  C10  180.00   0.0  0
 N4D  CONST_37  N22   C16  N24  C14    0.00   0.0  0
 N4D  CONST_38  N22   C16  N24  N21  180.00   0.0  0
 N4D  CONST_39  C5    C4   C12  C18  180.00   0.0  0
 N4D  CONST_40  C15   C8   C12  C18  180.00   0.0  0
 N4D  CONST_41  N25   C17  C11  C16  180.00   0.0  0
 N4D  CONST_42  C8    C15  C13  C19  180.00   0.0  0
 N4D  CONST_43  C4    C5   C13  C19  180.00   0.0  0
 N4D  CONST_44  N25   C15  C8   C12  180.00   0.0  0
 N4D  CONST_45  N25   C15  C13  C5   180.00   0.0  0
 N4D  CONST_46  N25   C17  C11  C9     0.00   0.0  0
 N4D  CONST_47  N25   C17  N23  C10  180.00   0.0  0
 N4D  CONST_48  H8    C8   C15  C13  180.00   0.0  0
 N4D  CONST_49  H4    C4   C5   C13  180.00   0.0  0
 N4D  CONST_50  H9    C9   C11  C17    0.00   0.0  0
 N4D  CONST_51  H10   C10  N23  C17  180.00   0.0  0
 N4D  CONST_52  H5    C5   C13  C15  180.00   0.0  0
 N4D  CONST_53  H6    C6   C2   C1   180.00   0.0  0
 N4D  CONST_54  H7    C7   C3   C1   180.00   0.0  0
 N4D  CONST_55  H3    C3   C1   C2   180.00   0.0  0
 N4D  CONST_56  H2    C2   C1   C3   180.00   0.0  0
 N4D  CONST_57  H1    C1   C2   C6   180.00   0.0  0
 N4D  CONST_58  C12   C18  N26  C20  180.00   0.0  0
 N4D  CONST_59  HN26  N26  C18  C12    0.00   0.0  0
 N4D  CONST_60  O27   C18  N26  C20    0.00   0.0  0
 N4D  Var_01    C17   N25  C15  C13  135.54  30.0  2
 N4D  Var_02    C11   C17  N25  C15  179.35  30.0  2
 N4D  Var_03    N26   C18  C12  C4   -27.52  30.0  2
 N4D  Var_04    H19   C19  C13  C15   65.33  30.0  2
 N4D  Var_05    H20   C20  N26  C18  -61.48  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
 N4D  plan-1  C13   0.020
 N4D  plan-1  C18   0.020
 N4D  plan-1  C15   0.020
 N4D  plan-1  C19   0.020
 N4D  plan-1  C12   0.020
 N4D  plan-1  C4    0.020
 N4D  plan-1  C5    0.020
 N4D  plan-1  C8    0.020
 N4D  plan-1  N25   0.020
 N4D  plan-1  H4    0.020
 N4D  plan-1  H5    0.020
 N4D  plan-1  H8    0.020
 N4D  plan-2  C1    0.020
 N4D  plan-2  C2    0.020
 N4D  plan-2  C3    0.020
 N4D  plan-2  C6    0.020
 N4D  plan-2  C7    0.020
 N4D  plan-2  C14   0.020
 N4D  plan-2  N24   0.020
 N4D  plan-2  H2    0.020
 N4D  plan-2  H3    0.020
 N4D  plan-2  H6    0.020
 N4D  plan-2  H7    0.020
 N4D  plan-2  H1    0.020
 N4D  plan-3  C17   0.020
 N4D  plan-3  C16   0.020
 N4D  plan-3  C11   0.020
 N4D  plan-3  C9    0.020
 N4D  plan-3  C10   0.020
 N4D  plan-3  C14   0.020
 N4D  plan-3  N21   0.020
 N4D  plan-3  N22   0.020
 N4D  plan-3  N23   0.020
 N4D  plan-3  N24   0.020
 N4D  plan-3  N25   0.020
 N4D  plan-3  H9    0.020
 N4D  plan-3  H10   0.020
 N4D  plan-4  C18   0.020
 N4D  plan-4  C20   0.020
 N4D  plan-4  C12   0.020
 N4D  plan-4  N26   0.020
 N4D  plan-4  O27   0.020
 N4D  plan-4  HN26  0.020

