# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 15:02:31 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: N-[(4-chlorophenyl)methyl]-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ncc2c(NCc3ccc(Cl)cc3)ncnc12
#
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
 6AY  6AY  N-[(4-chlorophenyl)methyl]-1-methyl-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  31  19  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6AY
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
 6AY  C10  C   CR16  0  -0.314  -3.0507  -0.4200  -1.1736
 6AY  C11  C   CR16  0  -0.197  -4.1214   0.0245  -0.4083
 6AY  C12  C   CR6   0  -0.052  -4.0071   0.0205   0.9711
 6AY  C14  C   CR16  0  -0.197  -2.8480  -0.4222   1.5929
 6AY  C15  C   CR16  0  -0.298  -1.7918  -0.8640   0.8132
 6AY  C17  C   CR16  0   0.059   2.6252  -1.7583   1.0394
 6AY  C19  C   CR56  0   0.572   3.5660   0.1105   0.3558
 6AY  N02  N   NR5   0  -0.359   4.4472   1.1184   0.2279
 6AY  N03  N   N     0  -0.252   4.0310   2.0213  -0.6750
 6AY  C04  C   CR15  0  -0.111   2.8813   1.6008  -1.1412
 6AY  C05  C   CR56  0  -0.223   2.5183   0.3815  -0.5258
 6AY  C06  C   CR6   0   0.542   1.4701  -0.5680  -0.5510
 6AY  N07  N   NH1   0  -0.643   0.4156  -0.4297  -1.3600
 6AY  C09  C   CR6   0   0.131  -1.8776  -0.8672  -0.5779
 6AY  CL   CL  CL    0  -0.131  -5.3344   0.5752   1.9398
 6AY  N16  N   N     0  -0.505   1.5560  -1.6294   0.2514
 6AY  N18  N   N     0  -0.463   3.6599  -0.9547   1.1610
 6AY  H1   H   HCR6  0   0.265  -3.1405  -0.4139  -2.2532
 6AY  H2   H   HCR6  0   0.280  -5.0279   0.3709  -0.8856
 6AY  H3   H   HCR6  0   0.279  -2.7696  -0.4271   2.6717
 6AY  H4   H   HCR6  0   0.266  -0.8909  -1.2191   1.2973
 6AY  H5   H   HCR6  0   0.253   2.6332  -2.6465   1.6625
 6AY  H6   H   HCH3  0   0.259   5.6020   2.1621   1.6244
 6AY  H7   H   HCH3  0   0.261   5.8857   0.4172   1.5290
 6AY  H8   H   HCH3  0   0.261   6.4985   1.4790   0.2522
 6AY  H9   H   HCR5  0   0.271   2.3558   2.1729  -1.8909
 6AY  H10  H   HNH1  0   0.407   0.3525   0.4145  -1.9057
 6AY  H11  H   HCH2  0   0.279  -1.0223  -1.4102  -2.4621
 6AY  H12  H   HCH2  0   0.276  -0.3843  -2.3197  -1.1040
 6AY  C08  C   CH2   0  -0.395  -0.7145  -1.3316  -1.4192
 6AY  C01  C   CH3   0  -0.520   5.6796   1.3121   0.9487

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
 6AY  C01  N02  single    1.441  0.020  1.441
 6AY  N02  N03  aromatic  1.343  0.020  1.343
 6AY  N02  C19  aromatic  1.345  0.020  1.345
 6AY  N03  C04  aromatic  1.310  0.020  1.310
 6AY  C19  N18  aromatic  1.339  0.020  1.339
 6AY  C19  C05  aromatic  1.396  0.020  1.396
 6AY  N18  C17  aromatic  1.316  0.020  1.316
 6AY  C04  C05  aromatic  1.413  0.020  1.413
 6AY  C05  C06  aromatic  1.415  0.020  1.415
 6AY  C17  N16  aromatic  1.334  0.020  1.334
 6AY  C06  N16  aromatic  1.333  0.020  1.333
 6AY  C06  N07  single    1.336  0.020  1.336
 6AY  N07  C08  single    1.447  0.020  1.447
 6AY  C10  C11  aromatic  1.389  0.020  1.389
 6AY  C10  C09  aromatic  1.390  0.020  1.390
 6AY  C11  C12  aromatic  1.384  0.020  1.384
 6AY  C08  C09  single    1.509  0.020  1.509
 6AY  C09  C15  aromatic  1.394  0.020  1.394
 6AY  C12  CL   single    1.734  0.020  1.734
 6AY  C12  C14  aromatic  1.388  0.020  1.388
 6AY  C15  C14  aromatic  1.385  0.020  1.385
 6AY  C10  H1   single    0.930  0.020  1.080
 6AY  C11  H2   single    0.930  0.020  1.080
 6AY  C14  H3   single    0.930  0.020  1.080
 6AY  C15  H4   single    0.930  0.020  1.080
 6AY  C17  H5   single    0.930  0.020  1.080
 6AY  C01  H6   single    0.970  0.020  1.090
 6AY  C01  H7   single    0.970  0.020  1.090
 6AY  C01  H8   single    0.970  0.020  1.090
 6AY  C04  H9   single    0.930  0.020  1.080
 6AY  N07  H10  single    0.860  0.020  1.020
 6AY  C08  H11  single    0.970  0.020  1.090
 6AY  C08  H12  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
 6AY  H1   C10  C09  119.93  3.000
 6AY  H1   C10  C11  118.90  3.000
 6AY  C09  C10  C11  121.17  3.000
 6AY  H2   C11  C12  120.67  3.000
 6AY  H2   C11  C10  120.36  3.000
 6AY  C12  C11  C10  118.97  3.000
 6AY  CL   C12  C14  119.40  3.000
 6AY  C14  C12  C11  121.10  3.000
 6AY  CL   C12  C11  119.50  3.000
 6AY  H3   C14  C15  120.31  3.000
 6AY  H3   C14  C12  120.59  3.000
 6AY  C15  C14  C12  119.10  3.000
 6AY  H4   C15  C09  119.79  3.000
 6AY  H4   C15  C14  119.17  3.000
 6AY  C09  C15  C14  121.04  3.000
 6AY  H5   C17  N18  116.18  3.000
 6AY  H5   C17  N16  115.09  3.000
 6AY  N18  C17  N16  128.73  3.000
 6AY  N18  C19  C05  125.95  3.000
 6AY  C05  C19  N02  106.63  3.000
 6AY  N18  C19  N02  127.42  3.000
 6AY  N03  N02  C01  120.74  3.000
 6AY  N03  N02  C19  111.39  3.000
 6AY  C01  N02  C19  127.85  3.000
 6AY  C04  N03  N02  107.19  3.000
 6AY  H9   C04  C05  129.39  3.000
 6AY  H9   C04  N03  120.29  3.000
 6AY  C05  C04  N03  110.32  3.000
 6AY  C06  C05  C04  139.61  3.000
 6AY  C06  C05  C19  115.92  3.000
 6AY  C04  C05  C19  104.47  3.000
 6AY  N16  C06  N07  119.84  3.000
 6AY  N07  C06  C05  121.74  3.000
 6AY  N16  C06  C05  118.42  3.000
 6AY  H10  N07  C08  116.82  3.000
 6AY  H10  N07  C06  117.66  3.000
 6AY  C08  N07  C06  125.21  3.000
 6AY  C08  C09  C15  120.65  3.000
 6AY  C15  C09  C10  118.63  3.000
 6AY  C08  C09  C10  120.72  3.000
 6AY  C06  N16  C17  118.94  3.000
 6AY  C19  N18  C17  112.04  3.000
 6AY  H12  C08  H11  107.29  3.000
 6AY  H12  C08  C09  110.60  3.000
 6AY  H11  C08  C09  109.75  3.000
 6AY  H12  C08  N07  108.48  3.000
 6AY  H11  C08  N07  107.73  3.000
 6AY  C09  C08  N07  112.79  3.000
 6AY  H8   C01  H7   109.01  3.000
 6AY  H8   C01  H6   109.34  3.000
 6AY  H7   C01  H6   108.97  3.000
 6AY  H8   C01  N02  110.13  3.000
 6AY  H7   C01  N02  108.59  3.000
 6AY  H6   C01  N02  110.76  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
 6AY  CONST_01  C14  C12  C11  C10     0.00   0.0  0
 6AY  CONST_02  C14  C15  C09  C10     0.00   0.0  0
 6AY  CONST_03  C15  C09  C10  C11     0.00   0.0  0
 6AY  CONST_04  C15  C14  C12  C11     0.00   0.0  0
 6AY  CONST_05  C09  C10  C11  C12     0.00   0.0  0
 6AY  CONST_06  C09  C15  C14  C12     0.00   0.0  0
 6AY  CONST_07  N02  C19  N18  C17   180.00   0.0  0
 6AY  CONST_08  C05  C19  N18  C17     0.00   0.0  0
 6AY  CONST_09  C05  C06  N16  C17     0.00   0.0  0
 6AY  CONST_10  C04  N03  N02  C19     0.00   0.0  0
 6AY  CONST_11  N16  C17  N18  C19     0.00   0.0  0
 6AY  CONST_12  N03  C04  C05  C19     0.00   0.0  0
 6AY  CONST_13  N16  C06  C05  C19     0.00   0.0  0
 6AY  CONST_14  C05  C04  N03  N02     0.00   0.0  0
 6AY  CONST_15  C04  C05  C19  N02     0.00   0.0  0
 6AY  CONST_16  C06  C05  C19  N02   180.00   0.0  0
 6AY  CONST_17  N18  C19  N02  N03   180.00   0.0  0
 6AY  CONST_18  C05  C19  N02  N03     0.00   0.0  0
 6AY  CONST_19  C06  C05  C04  N03   180.00   0.0  0
 6AY  CONST_20  N18  C19  C05  C04   180.00   0.0  0
 6AY  CONST_21  N16  C06  C05  C04   180.00   0.0  0
 6AY  CONST_22  N18  C19  C05  C06     0.00   0.0  0
 6AY  CONST_23  N18  C17  N16  C06     0.00   0.0  0
 6AY  CONST_24  CL   C12  C11  C10   180.00   0.0  0
 6AY  CONST_25  C08  C09  C10  C11   180.00   0.0  0
 6AY  CONST_26  C08  C09  C15  C14   180.00   0.0  0
 6AY  CONST_27  CL   C12  C14  C15   180.00   0.0  0
 6AY  CONST_28  N07  C06  N16  C17   180.00   0.0  0
 6AY  CONST_29  N07  C06  C05  C19   180.00   0.0  0
 6AY  CONST_30  C04  N03  N02  C01   180.00   0.0  0
 6AY  CONST_31  N18  C19  N02  C01     0.00   0.0  0
 6AY  CONST_32  C05  C19  N02  C01   180.00   0.0  0
 6AY  CONST_33  N07  C06  C05  C04     0.00   0.0  0
 6AY  CONST_34  H4   C15  C09  C10   180.00   0.0  0
 6AY  CONST_35  H3   C14  C12  C11   180.00   0.0  0
 6AY  CONST_36  H1   C10  C11  C12   180.00   0.0  0
 6AY  CONST_37  H2   C11  C12  C14   180.00   0.0  0
 6AY  CONST_38  H5   C17  N18  C19   180.00   0.0  0
 6AY  CONST_39  H9   C04  C05  C19   180.00   0.0  0
 6AY  CONST_40  C08  N07  C06  C05   180.00   0.0  0
 6AY  CONST_41  N16  C06  N07  C08     0.00   0.0  0
 6AY  CONST_42  H10  N07  C06  C05     0.00   0.0  0
 6AY  Var_01    N07  C08  C09  C10   110.56  30.0  3
 6AY  Var_02    C09  C08  N07  C06    96.05  30.0  3
 6AY  Var_03    H6   C01  N02  C19  -110.78  30.0  2

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
 6AY  plan-1  C10  0.020
 6AY  plan-1  C11  0.020
 6AY  plan-1  C12  0.020
 6AY  plan-1  C14  0.020
 6AY  plan-1  C15  0.020
 6AY  plan-1  C09  0.020
 6AY  plan-1  CL   0.020
 6AY  plan-1  H1   0.020
 6AY  plan-1  H2   0.020
 6AY  plan-1  H3   0.020
 6AY  plan-1  H4   0.020
 6AY  plan-1  C08  0.020
 6AY  plan-2  C17  0.020
 6AY  plan-2  C19  0.020
 6AY  plan-2  N02  0.020
 6AY  plan-2  N03  0.020
 6AY  plan-2  C04  0.020
 6AY  plan-2  C05  0.020
 6AY  plan-2  C06  0.020
 6AY  plan-2  N07  0.020
 6AY  plan-2  N16  0.020
 6AY  plan-2  N18  0.020
 6AY  plan-2  H5   0.020
 6AY  plan-2  H9   0.020
 6AY  plan-2  C01  0.020
 6AY  plan-3  C06  0.020
 6AY  plan-3  N07  0.020
 6AY  plan-3  H10  0.020
 6AY  plan-3  C08  0.020

