# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 06:00:09 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ncc2c(N)nc(nc12)c3cccnc3
#
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
 DXK  DXK  1-methyl-6-pyridin-3-yl-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  27  17  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DXK
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
 DXK  CAC  C  CR16  0  -0.164  -2.8511   1.0516   0.0238
 DXK  CAE  C  CR16  0  -0.314  -4.2081   0.7779   0.0286
 DXK  CAF  C  CR16  0  -0.065  -4.6182  -0.5464   0.0219
 DXK  NAD  N  N     0  -0.402  -3.7693  -1.5689   0.0110
 DXK  CAB  C  CR16  0  -0.073  -2.4716  -1.2998   0.0064
 DXK  CAA  C  CR6   0  -0.109  -1.9470  -0.0069   0.0125
 DXK  C2   C  CR6   0   0.418  -0.4852   0.2215   0.0071
 DXK  N1   N  N     0  -0.513  -0.0939   1.4998   0.0142
 DXK  N3   N  N     0  -0.491   0.2861  -0.8503  -0.0042
 DXK  C4   C  CR56  0   0.606   1.5864  -0.5541  -0.0070
 DXK  NAM  N  NR5   0  -0.380   2.6195  -1.4159  -0.0167
 DXK  CAQ  C  CH3   0  -0.522   2.5711  -2.8555  -0.0327
 DXK  NAN  N  N     0  -0.248   3.7969  -0.7687  -0.0160
 DXK  CAO  C  CR15  0  -0.106   3.5335   0.5145  -0.0051
 DXK  C5   C  CR56  0  -0.253   2.1374   0.7283   0.0009
 DXK  C6   C  CR6   0   0.483   1.2060   1.7908   0.0111
 DXK  NAP  N  NH2   0  -0.818   1.5722   3.0704   0.0201
 DXK  H1   H  HCR6  0   0.269  -2.4918   2.0715   0.0282
 DXK  H2   H  HCR6  0   0.274  -4.9387   1.5747   0.0372
 DXK  H3   H  HCR6  0   0.268  -5.6744  -0.7919   0.0255
 DXK  H4   H  HCR6  0   0.265  -1.8008  -2.1506  -0.0027
 DXK  H5   H  HCH3  0   0.260   3.0435  -3.2426  -0.9336
 DXK  H6   H  HCH3  0   0.260   3.0755  -3.2622   0.8417
 DXK  H7   H  HCH3  0   0.262   1.5305  -3.1668  -0.0174
 DXK  H8   H  HCR5  0   0.274   4.3361   1.2363  -0.0016
 DXK  H9   H  HNH2  0   0.414   2.5381   3.3465   0.0021
 DXK  H10  H  HNH2  0   0.406   0.8741   3.7944   0.0153

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
 DXK  CAO  NAN  aromatic  1.310  0.020  1.310
 DXK  CAO  C5   aromatic  1.412  0.020  1.412
 DXK  NAN  NAM  aromatic  1.344  0.020  1.344
 DXK  NAP  C6   single    1.331  0.020  1.331
 DXK  C5   C6   aromatic  1.413  0.020  1.413
 DXK  C5   C4   aromatic  1.396  0.020  1.396
 DXK  C6   N1   aromatic  1.332  0.020  1.332
 DXK  NAM  C4   aromatic  1.345  0.020  1.345
 DXK  NAM  CAQ  single    1.441  0.020  1.441
 DXK  C4   N3   aromatic  1.334  0.020  1.334
 DXK  N1   C2   aromatic  1.337  0.020  1.337
 DXK  N3   C2   aromatic  1.321  0.020  1.321
 DXK  C2   CAA  single    1.480  0.020  1.480
 DXK  CAA  CAC  aromatic  1.392  0.020  1.392
 DXK  CAA  CAB  aromatic  1.395  0.020  1.395
 DXK  CAC  CAE  aromatic  1.384  0.020  1.384
 DXK  CAB  NAD  aromatic  1.325  0.020  1.325
 DXK  CAE  CAF  aromatic  1.386  0.020  1.386
 DXK  NAD  CAF  aromatic  1.329  0.020  1.329
 DXK  CAC  H1   single    0.930  0.020  1.080
 DXK  CAE  H2   single    0.930  0.020  1.080
 DXK  CAF  H3   single    0.930  0.020  1.080
 DXK  CAB  H4   single    0.930  0.020  1.080
 DXK  CAQ  H5   single    0.970  0.020  1.090
 DXK  CAQ  H6   single    0.970  0.020  1.090
 DXK  CAQ  H7   single    0.970  0.020  1.090
 DXK  CAO  H8   single    0.930  0.020  1.080
 DXK  NAP  H9   single    0.860  0.020  1.020
 DXK  NAP  H10  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
 DXK  H1   CAC  CAA  120.09  3.000
 DXK  H1   CAC  CAE  120.81  3.000
 DXK  CAA  CAC  CAE  119.10  3.000
 DXK  H2   CAE  CAF  120.28  3.000
 DXK  H2   CAE  CAC  121.11  3.000
 DXK  CAF  CAE  CAC  118.61  3.000
 DXK  H3   CAF  NAD  116.62  3.000
 DXK  H3   CAF  CAE  120.29  3.000
 DXK  NAD  CAF  CAE  123.09  3.000
 DXK  CAB  NAD  CAF  117.99  3.000
 DXK  H4   CAB  CAA  119.66  3.000
 DXK  H4   CAB  NAD  116.54  3.000
 DXK  CAA  CAB  NAD  123.80  3.000
 DXK  C2   CAA  CAB  120.96  3.000
 DXK  CAB  CAA  CAC  117.42  3.000
 DXK  C2   CAA  CAC  121.62  3.000
 DXK  N3   C2   N1   127.24  3.000
 DXK  N3   C2   CAA  116.86  3.000
 DXK  N1   C2   CAA  115.90  3.000
 DXK  C6   N1   C2   119.64  3.000
 DXK  C4   N3   C2   112.91  3.000
 DXK  C5   C4   NAM  106.58  3.000
 DXK  NAM  C4   N3   127.34  3.000
 DXK  C5   C4   N3   126.08  3.000
 DXK  NAN  NAM  CAQ  120.72  3.000
 DXK  CAQ  NAM  C4   127.91  3.000
 DXK  NAN  NAM  C4   111.37  3.000
 DXK  H7   CAQ  H6   109.00  3.000
 DXK  H7   CAQ  H5   109.00  3.000
 DXK  H6   CAQ  H5   109.33  3.000
 DXK  H7   CAQ  NAM  108.57  3.000
 DXK  H6   CAQ  NAM  110.43  3.000
 DXK  H5   CAQ  NAM  110.49  3.000
 DXK  CAO  NAN  NAM  107.20  3.000
 DXK  H8   CAO  C5   129.33  3.000
 DXK  H8   CAO  NAN  120.37  3.000
 DXK  C5   CAO  NAN  110.30  3.000
 DXK  C6   C5   CAO  139.94  3.000
 DXK  C6   C5   C4   115.51  3.000
 DXK  CAO  C5   C4   104.55  3.000
 DXK  NAP  C6   C5   122.79  3.000
 DXK  C5   C6   N1   118.62  3.000
 DXK  NAP  C6   N1   118.59  3.000
 DXK  H10  NAP  H9   117.99  3.000
 DXK  H10  NAP  C6   120.07  3.000
 DXK  H9   NAP  C6   121.91  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
 DXK  CONST_01  N1   C2   CAA  CAC    0.00   0.0  0
 DXK  CONST_02  N3   C2   CAA  CAC  180.00   0.0  0
 DXK  CONST_03  NAD  CAB  CAA  CAC    0.00   0.0  0
 DXK  CONST_04  NAD  CAF  CAE  CAC    0.00   0.0  0
 DXK  CONST_05  C2   CAA  CAC  CAE  180.00   0.0  0
 DXK  CONST_06  CAB  CAA  CAC  CAE    0.00   0.0  0
 DXK  CONST_07  CAB  NAD  CAF  CAE    0.00   0.0  0
 DXK  CONST_08  CAA  CAC  CAE  CAF    0.00   0.0  0
 DXK  CONST_09  CAA  CAB  NAD  CAF    0.00   0.0  0
 DXK  CONST_10  C2   CAA  CAB  NAD  180.00   0.0  0
 DXK  CONST_11  N1   C2   CAA  CAB  180.00   0.0  0
 DXK  CONST_12  N3   C2   CAA  CAB    0.00   0.0  0
 DXK  CONST_13  C6   N1   C2   CAA  180.00   0.0  0
 DXK  CONST_14  C4   N3   C2   CAA  180.00   0.0  0
 DXK  CONST_15  C5   C6   N1   C2     0.00   0.0  0
 DXK  CONST_16  C5   C4   N3   C2     0.00   0.0  0
 DXK  CONST_17  NAM  C4   N3   C2   180.00   0.0  0
 DXK  CONST_18  CAO  C5   C6   N1   180.00   0.0  0
 DXK  CONST_19  C4   C5   C6   N1     0.00   0.0  0
 DXK  CONST_20  C4   N3   C2   N1     0.00   0.0  0
 DXK  CONST_21  CAO  C5   C4   N3   180.00   0.0  0
 DXK  CONST_22  C6   C5   C4   N3     0.00   0.0  0
 DXK  CONST_23  NAN  NAM  C4   N3   180.00   0.0  0
 DXK  CONST_24  C6   N1   C2   N3     0.00   0.0  0
 DXK  CONST_25  NAN  CAO  C5   C4     0.00   0.0  0
 DXK  CONST_26  CAO  NAN  NAM  C4     0.00   0.0  0
 DXK  CONST_27  C5   CAO  NAN  NAM    0.00   0.0  0
 DXK  CONST_28  CAO  C5   C4   NAM    0.00   0.0  0
 DXK  CONST_29  C6   C5   C4   NAM  180.00   0.0  0
 DXK  CONST_30  C6   C5   CAO  NAN  180.00   0.0  0
 DXK  CONST_31  C5   C4   NAM  NAN    0.00   0.0  0
 DXK  CONST_32  NAP  C6   N1   C2   180.00   0.0  0
 DXK  CONST_33  CAQ  NAM  C4   N3     0.00   0.0  0
 DXK  CONST_34  NAP  C6   C5   C4   180.00   0.0  0
 DXK  CONST_35  CAO  NAN  NAM  CAQ  180.00   0.0  0
 DXK  CONST_36  C5   C4   NAM  CAQ  180.00   0.0  0
 DXK  CONST_37  NAP  C6   C5   CAO    0.00   0.0  0
 DXK  CONST_38  H4   CAB  CAA  CAC  180.00   0.0  0
 DXK  CONST_39  H3   CAF  CAE  CAC  180.00   0.0  0
 DXK  CONST_40  H1   CAC  CAE  CAF  180.00   0.0  0
 DXK  CONST_41  H2   CAE  CAF  NAD  180.00   0.0  0
 DXK  CONST_42  H8   CAO  C5   C4   180.00   0.0  0
 DXK  CONST_43  H9   NAP  C6   N1   180.00   0.0  0
 DXK  CONST_44  H10  NAP  C6   N1     0.00   0.0  0
 DXK  Var_01    H5   CAQ  NAM  C4   118.44  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
 DXK  plan-1  CAC  0.020
 DXK  plan-1  CAE  0.020
 DXK  plan-1  CAF  0.020
 DXK  plan-1  NAD  0.020
 DXK  plan-1  CAB  0.020
 DXK  plan-1  CAA  0.020
 DXK  plan-1  C2   0.020
 DXK  plan-1  H1   0.020
 DXK  plan-1  H2   0.020
 DXK  plan-1  H3   0.020
 DXK  plan-1  H4   0.020
 DXK  plan-2  CAA  0.020
 DXK  plan-2  C2   0.020
 DXK  plan-2  N1   0.020
 DXK  plan-2  N3   0.020
 DXK  plan-2  C4   0.020
 DXK  plan-2  NAM  0.020
 DXK  plan-2  CAQ  0.020
 DXK  plan-2  NAN  0.020
 DXK  plan-2  CAO  0.020
 DXK  plan-2  C5   0.020
 DXK  plan-2  C6   0.020
 DXK  plan-2  NAP  0.020
 DXK  plan-2  H8   0.020
 DXK  plan-3  C6   0.020
 DXK  plan-3  NAP  0.020
 DXK  plan-3  H9   0.020
 DXK  plan-3  H10  0.020

