# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 02:32:58 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: ~{N},~{N}-dimethyl-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1nccc(n1)c2c[nH]c3ncccc23
#
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
 KQZ  KQZ  ~{N},~{N}-dimethyl-4-(1~{H}-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine  ligand  31  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KQZ
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
 KQZ  C10  C  CR16  0  -0.251  -1.5106  -1.5048  -0.0403
 KQZ  C    C  CH3   0  -0.529   4.6195  -1.3230  -0.0073
 KQZ  C1   C  CH3   0  -0.518   2.4040  -2.4184   0.0710
 KQZ  C11  C  CR16  0  -0.340  -2.6342  -2.3137  -0.0533
 KQZ  C12  C  CR16  0  -0.087  -3.9107  -1.7429  -0.0599
 KQZ  C2   C  CR6   0   0.628   2.5537  -0.0035   0.0001
 KQZ  C3   C  CR16  0  -0.025   2.6306   2.2535  -0.0293
 KQZ  C4   C  CR16  0  -0.424   1.2535   2.3392  -0.0336
 KQZ  C5   C  CR6   0   0.254   0.5622   1.1230  -0.0186
 KQZ  C6   C  CR5   0  -0.079  -0.8884   1.0531  -0.0243
 KQZ  C7   C  CR15  0  -0.033  -1.7573   2.1201  -0.0254
 KQZ  C8   C  CR56  0   0.471  -3.0519   0.3168  -0.0418
 KQZ  C9   C  CR56  0   0.008  -1.7108  -0.1252  -0.0343
 KQZ  N1   N  N     0  -0.483   3.2984   1.1103  -0.0111
 KQZ  N2   N  NR15  0  -0.662  -3.0384   1.6824  -0.0366
 KQZ  N3   N  N     0  -0.422  -4.1369  -0.4370  -0.0544
 KQZ  N4   N  N     0  -0.516   1.2151  -0.0333  -0.0018
 KQZ  H10  H  HCR6  0   0.281  -0.5149  -1.9234  -0.0350
 KQZ  H1   H  HCH3  0   0.261   5.0780  -0.3595  -0.1998
 KQZ  H2   H  HCH3  0   0.233   5.0006  -1.7027   0.9441
 KQZ  H3   H  HCH3  0   0.237   4.9258  -2.0145  -0.7938
 KQZ  H6   H  HCH3  0   0.236   1.7734  -2.5445  -0.8115
 KQZ  H4   H  HCH3  0   0.250   3.0876  -3.2624   0.1221
 KQZ  H5   H  HCH3  0   0.237   1.7587  -2.4518   0.9503
 KQZ  H11  H  HCR6  0   0.264  -2.5373  -3.3907  -0.0588
 KQZ  H12  H  HCR6  0   0.258  -4.7855  -2.3830  -0.0711
 KQZ  H7   H  HCR6  0   0.263   3.2314   3.1573  -0.0403
 KQZ  H8   H  HCR6  0   0.255   0.7567   3.2978  -0.0492
 KQZ  H9   H  HCR5  0   0.301  -1.5513   3.1784  -0.0197
 KQZ  H    H  HNR5  0   0.418  -3.8538   2.2743  -0.0304
 KQZ  N    N  NT    0  -0.484   3.1802  -1.1990   0.0141

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
 KQZ  C    N    single    1.445  0.020  1.445
 KQZ  C1   N    single    1.447  0.020  1.447
 KQZ  N    C2   single    1.350  0.020  1.350
 KQZ  C2   N1   aromatic  1.340  0.020  1.340
 KQZ  C2   N4   aromatic  1.339  0.020  1.339
 KQZ  N1   C3   aromatic  1.324  0.020  1.324
 KQZ  N4   C5   aromatic  1.328  0.020  1.328
 KQZ  C3   C4   aromatic  1.380  0.020  1.380
 KQZ  C5   C4   aromatic  1.399  0.020  1.399
 KQZ  C5   C6   single    1.452  0.020  1.452
 KQZ  C10  C11  aromatic  1.384  0.020  1.384
 KQZ  C10  C9   aromatic  1.394  0.020  1.394
 KQZ  C11  C12  aromatic  1.398  0.020  1.398
 KQZ  C6   C9   aromatic  1.437  0.020  1.437
 KQZ  C6   C7   aromatic  1.376  0.020  1.376
 KQZ  C9   C8   aromatic  1.412  0.020  1.412
 KQZ  C12  N3   aromatic  1.325  0.020  1.325
 KQZ  C7   N2   aromatic  1.354  0.020  1.354
 KQZ  C8   N3   aromatic  1.321  0.020  1.321
 KQZ  C8   N2   aromatic  1.366  0.020  1.366
 KQZ  C10  H10  single    0.930  0.020  1.080
 KQZ  C    H1   single    0.970  0.020  1.090
 KQZ  C    H2   single    0.970  0.020  1.090
 KQZ  C    H3   single    0.970  0.020  1.090
 KQZ  C1   H6   single    0.970  0.020  1.090
 KQZ  C1   H4   single    0.970  0.020  1.090
 KQZ  C1   H5   single    0.970  0.020  1.090
 KQZ  C11  H11  single    0.930  0.020  1.080
 KQZ  C12  H12  single    0.930  0.020  1.080
 KQZ  C3   H7   single    0.930  0.020  1.080
 KQZ  C4   H8   single    0.930  0.020  1.080
 KQZ  C7   H9   single    0.930  0.020  1.080
 KQZ  N2   H    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
 KQZ  H10  C10  C9   121.06  3.000
 KQZ  H10  C10  C11  121.44  3.000
 KQZ  C9   C10  C11  117.50  3.000
 KQZ  H3   C    H2   108.03  3.000
 KQZ  H3   C    H1   108.45  3.000
 KQZ  H2   C    H1   108.41  3.000
 KQZ  H3   C    N    110.16  3.000
 KQZ  H2   C    N    111.37  3.000
 KQZ  H1   C    N    110.34  3.000
 KQZ  H5   C1   H4   108.07  3.000
 KQZ  H5   C1   H6   107.84  3.000
 KQZ  H4   C1   H6   108.15  3.000
 KQZ  H5   C1   N    112.01  3.000
 KQZ  H4   C1   N    108.59  3.000
 KQZ  H6   C1   N    112.05  3.000
 KQZ  H11  C11  C12  119.23  3.000
 KQZ  H11  C11  C10  120.62  3.000
 KQZ  C12  C11  C10  120.15  3.000
 KQZ  H12  C12  N3   116.37  3.000
 KQZ  H12  C12  C11  119.71  3.000
 KQZ  N3   C12  C11  123.92  3.000
 KQZ  N4   C2   N1   125.04  3.000
 KQZ  N4   C2   N    116.38  3.000
 KQZ  N1   C2   N    118.58  3.000
 KQZ  H7   C3   N1   116.10  3.000
 KQZ  H7   C3   C4   120.05  3.000
 KQZ  N1   C3   C4   123.85  3.000
 KQZ  H8   C4   C5   122.99  3.000
 KQZ  H8   C4   C3   120.96  3.000
 KQZ  C5   C4   C3   116.05  3.000
 KQZ  N4   C5   C6   116.69  3.000
 KQZ  C6   C5   C4   122.37  3.000
 KQZ  N4   C5   C4   120.94  3.000
 KQZ  C9   C6   C7   105.93  3.000
 KQZ  C7   C6   C5   126.40  3.000
 KQZ  C9   C6   C5   127.67  3.000
 KQZ  H9   C7   N2   119.88  3.000
 KQZ  H9   C7   C6   129.83  3.000
 KQZ  N2   C7   C6   110.29  3.000
 KQZ  N3   C8   N2   125.36  3.000
 KQZ  N2   C8   C9   107.67  3.000
 KQZ  N3   C8   C9   126.97  3.000
 KQZ  C8   C9   C6   106.68  3.000
 KQZ  C8   C9   C10  116.49  3.000
 KQZ  C6   C9   C10  136.83  3.000
 KQZ  C3   N1   C2   115.94  3.000
 KQZ  H    N2   C8   125.41  3.000
 KQZ  H    N2   C7   125.15  3.000
 KQZ  C8   N2   C7   109.43  3.000
 KQZ  C8   N3   C12  114.96  3.000
 KQZ  C5   N4   C2   118.17  3.000
 KQZ  C2   N    C1   119.86  3.000
 KQZ  C2   N    C    122.56  3.000
 KQZ  C1   N    C    117.57  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
 KQZ  CONST_01  N3   C12  C11  C10    0.00   0.0  0
 KQZ  CONST_02  C5   C6   C9   C10    0.00   0.0  0
 KQZ  CONST_03  C7   C6   C9   C10  180.00   0.0  0
 KQZ  CONST_04  N3   C8   C9   C10    0.00   0.0  0
 KQZ  CONST_05  N2   C8   C9   C10  180.00   0.0  0
 KQZ  CONST_06  C6   C9   C10  C11  180.00   0.0  0
 KQZ  CONST_07  C8   C9   C10  C11    0.00   0.0  0
 KQZ  CONST_08  C8   N3   C12  C11    0.00   0.0  0
 KQZ  CONST_09  C9   C10  C11  C12    0.00   0.0  0
 KQZ  CONST_10  C9   C8   N3   C12    0.00   0.0  0
 KQZ  CONST_11  N2   C8   N3   C12  180.00   0.0  0
 KQZ  CONST_12  C4   C3   N1   C2     0.00   0.0  0
 KQZ  CONST_13  C4   C5   N4   C2     0.00   0.0  0
 KQZ  CONST_14  C6   C5   N4   C2   180.00   0.0  0
 KQZ  CONST_15  N4   C2   N1   C3     0.00   0.0  0
 KQZ  CONST_16  N4   C5   C4   C3     0.00   0.0  0
 KQZ  CONST_17  C6   C5   C4   C3   180.00   0.0  0
 KQZ  CONST_18  C9   C6   C5   C4   180.00   0.0  0
 KQZ  CONST_19  C7   C6   C5   C4     0.00   0.0  0
 KQZ  CONST_20  N1   C2   N4   C5     0.00   0.0  0
 KQZ  CONST_21  N1   C3   C4   C5     0.00   0.0  0
 KQZ  CONST_22  C8   C9   C6   C5   180.00   0.0  0
 KQZ  CONST_23  N2   C7   C6   C5   180.00   0.0  0
 KQZ  CONST_24  N3   C8   C9   C6   180.00   0.0  0
 KQZ  CONST_25  N2   C8   C9   C6     0.00   0.0  0
 KQZ  CONST_26  C8   N2   C7   C6     0.00   0.0  0
 KQZ  CONST_27  N4   C5   C6   C7   180.00   0.0  0
 KQZ  CONST_28  C8   C9   C6   C7     0.00   0.0  0
 KQZ  CONST_29  C9   C8   N2   C7     0.00   0.0  0
 KQZ  CONST_30  N3   C8   N2   C7   180.00   0.0  0
 KQZ  CONST_31  N4   C5   C6   C9     0.00   0.0  0
 KQZ  CONST_32  N2   C7   C6   C9     0.00   0.0  0
 KQZ  CONST_33  C3   N1   C2   N    180.00   0.0  0
 KQZ  CONST_34  C5   N4   C2   N    180.00   0.0  0
 KQZ  CONST_35  H12  C12  C11  C10  180.00   0.0  0
 KQZ  CONST_36  H10  C10  C11  C12  180.00   0.0  0
 KQZ  CONST_37  H7   C3   N1   C2   180.00   0.0  0
 KQZ  CONST_38  H9   C7   C6   C5     0.00   0.0  0
 KQZ  CONST_39  H8   C4   C5   C6     0.00   0.0  0
 KQZ  CONST_40  H    N2   C7   C6   180.00   0.0  0
 KQZ  CONST_41  H11  C11  C10  C9   180.00   0.0  0
 KQZ  CONST_42  N1   C2   N    C      0.00   0.0  0
 KQZ  CONST_43  N4   C2   N    C    180.00   0.0  0
 KQZ  CONST_44  N1   C2   N    C1   180.00   0.0  0
 KQZ  CONST_45  N4   C2   N    C1     0.00   0.0  0
 KQZ  Var_01    H1   C    N    C2    -9.35  30.0  3
 KQZ  Var_02    H6   C1   N    C2    63.30  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
 KQZ  plan-1  C2   0.020
 KQZ  plan-1  C3   0.020
 KQZ  plan-1  C4   0.020
 KQZ  plan-1  C5   0.020
 KQZ  plan-1  C6   0.020
 KQZ  plan-1  N1   0.020
 KQZ  plan-1  N4   0.020
 KQZ  plan-1  H7   0.020
 KQZ  plan-1  H8   0.020
 KQZ  plan-1  N    0.020
 KQZ  plan-2  C10  0.020
 KQZ  plan-2  C11  0.020
 KQZ  plan-2  C12  0.020
 KQZ  plan-2  C5   0.020
 KQZ  plan-2  C6   0.020
 KQZ  plan-2  C7   0.020
 KQZ  plan-2  C8   0.020
 KQZ  plan-2  C9   0.020
 KQZ  plan-2  N2   0.020
 KQZ  plan-2  N3   0.020
 KQZ  plan-2  H10  0.020
 KQZ  plan-2  H11  0.020
 KQZ  plan-2  H12  0.020
 KQZ  plan-2  H9   0.020
 KQZ  plan-2  H    0.020
 KQZ  plan-3  C    0.020
 KQZ  plan-3  C1   0.020
 KQZ  plan-3  C2   0.020
 KQZ  plan-3  N    0.020

