# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 12:47:39 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: 4-azanyl-6-bromanyl-7-methyl-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(Br)c(C#N)c2c(N)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
 QYK  QYK  4-azanyl-6-bromanyl-7-methyl-pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  20  14  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QYK
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
 QYK  C1   C   CH3   0  -0.539  43.1499  1.7697  14.2405
 QYK  N1   N   NR5   0  -0.540  43.1169  3.2160  14.3186
 QYK  C2   C   CR5   0   0.202  42.6392  4.0715  13.3796
 QYK  BR1  BR  BR    0   0.089  41.9156  3.4860  11.7900
 QYK  C3   C   CR5   0  -0.061  42.7779  5.3747  13.8002
 QYK  C4   C   CSP   0  -0.059  42.3911  6.5122  13.0683
 QYK  N2   N   NS    0  -0.240  42.0850  7.4580  12.4819
 QYK  C5   C   CR56  0  -0.025  43.3841  5.3068  15.0938
 QYK  C6   C   CR56  0   0.509  43.5766  3.9577  15.3739
 QYK  N3   N   N     0  -0.456  44.1177  3.4579  16.4804
 QYK  C7   C   CR16  0   0.052  44.4749  4.3951  17.3371
 QYK  N4   N   N     0  -0.464  44.3532  5.7117  17.2082
 QYK  C8   C   CR6   0   0.452  43.8085  6.2079  16.0942
 QYK  N5   N   NH2   0  -0.828  43.6923  7.5320  15.9841
 QYK  H1   H   HCH3  0   0.282  43.5880  1.3942  15.1596
 QYK  H2   H   HCH3  0   0.273  42.1438  1.3688  14.1388
 QYK  H3   H   HCH3  0   0.273  43.7600  1.4451  13.4001
 QYK  H4   H   HCR6  0   0.256  44.9240  4.0536  18.2635
 QYK  H5   H   HNH2  0   0.407  44.0155  8.1223  16.7319
 QYK  H6   H   HNH2  0   0.417  43.2981  7.9790  15.1754

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
 QYK  BR1  C2  single    1.842  0.020  1.842
 QYK  N2   C4  triple    1.154  0.020  1.154
 QYK  C4   C3  single    1.407  0.020  1.407
 QYK  C2   C3  aromatic  1.376  0.020  1.376
 QYK  C2   N1  aromatic  1.357  0.020  1.357
 QYK  C3   C5  aromatic  1.430  0.020  1.430
 QYK  C1   N1  single    1.449  0.020  1.449
 QYK  N1   C6  aromatic  1.369  0.020  1.369
 QYK  C5   C6  aromatic  1.391  0.020  1.391
 QYK  C5   C8  aromatic  1.412  0.020  1.412
 QYK  C6   N3  aromatic  1.329  0.020  1.329
 QYK  N5   C8  single    1.334  0.020  1.334
 QYK  C8   N4  aromatic  1.336  0.020  1.336
 QYK  N3   C7  aromatic  1.319  0.020  1.319
 QYK  N4   C7  aromatic  1.328  0.020  1.328
 QYK  C1   H1  single    0.970  0.020  1.090
 QYK  C1   H2  single    0.970  0.020  1.090
 QYK  C1   H3  single    0.970  0.020  1.090
 QYK  C7   H4  single    0.930  0.020  1.080
 QYK  N5   H5  single    0.860  0.020  1.020
 QYK  N5   H6  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
 QYK  H3   C1  H2   109.66  3.000
 QYK  H3   C1  H1   108.94  3.000
 QYK  H2   C1  H1   108.96  3.000
 QYK  H3   C1  N1   110.63  3.000
 QYK  H2   C1  N1   110.61  3.000
 QYK  H1   C1  N1   108.00  3.000
 QYK  C6   N1  C2   108.06  3.000
 QYK  C6   N1  C1   125.07  3.000
 QYK  C2   N1  C1   126.87  3.000
 QYK  C3   C2  BR1  127.17  3.000
 QYK  C3   C2  N1   110.48  3.000
 QYK  BR1  C2  N1   122.34  3.000
 QYK  C5   C3  C4   128.72  3.000
 QYK  C5   C3  C2   105.91  3.000
 QYK  C4   C3  C2   125.37  3.000
 QYK  N2   C4  C3   180.00  3.000
 QYK  C8   C5  C6   115.77  3.000
 QYK  C8   C5  C3   137.57  3.000
 QYK  C6   C5  C3   106.67  3.000
 QYK  N3   C6  C5   126.05  3.000
 QYK  N3   C6  N1   125.07  3.000
 QYK  C5   C6  N1   108.88  3.000
 QYK  C7   N3  C6   112.57  3.000
 QYK  H4   C7  N4   115.65  3.000
 QYK  H4   C7  N3   116.30  3.000
 QYK  N4   C7  N3   128.05  3.000
 QYK  C8   N4  C7   119.11  3.000
 QYK  N5   C8  N4   118.25  3.000
 QYK  N4   C8  C5   118.46  3.000
 QYK  N5   C8  C5   123.30  3.000
 QYK  H6   N5  H5   117.60  3.000
 QYK  H6   N5  C8   122.85  3.000
 QYK  H5   N5  C8   119.55  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
 QYK  CONST_01  C5  C3  C2  N1      0.00   0.0  0
 QYK  CONST_02  C3  C5  C6  N1      0.00   0.0  0
 QYK  CONST_03  C8  C5  C6  N1    180.00   0.0  0
 QYK  CONST_04  C7  N3  C6  N1    180.00   0.0  0
 QYK  CONST_05  C6  C5  C3  C2      0.00   0.0  0
 QYK  CONST_06  C8  C5  C3  C2    180.00   0.0  0
 QYK  CONST_07  C5  C6  N1  C2      0.00   0.0  0
 QYK  CONST_08  N3  C6  N1  C2    180.00   0.0  0
 QYK  CONST_09  C6  N1  C2  C3      0.00   0.0  0
 QYK  CONST_10  N3  C6  C5  C3    180.00   0.0  0
 QYK  CONST_11  N4  C8  C5  C3    180.00   0.0  0
 QYK  CONST_12  C7  N3  C6  C5      0.00   0.0  0
 QYK  CONST_13  C7  N4  C8  C5      0.00   0.0  0
 QYK  CONST_14  N4  C8  C5  C6      0.00   0.0  0
 QYK  CONST_15  N4  C7  N3  C6      0.00   0.0  0
 QYK  CONST_16  C8  C5  C6  N3      0.00   0.0  0
 QYK  CONST_17  C8  N4  C7  N3      0.00   0.0  0
 QYK  CONST_18  C3  C2  N1  C1    180.00   0.0  0
 QYK  CONST_19  C5  C6  N1  C1    180.00   0.0  0
 QYK  CONST_20  N3  C6  N1  C1      0.00   0.0  0
 QYK  CONST_21  C4  C3  C2  N1    180.00   0.0  0
 QYK  CONST_22  C5  C3  C2  BR1   180.00   0.0  0
 QYK  CONST_23  C6  N1  C2  BR1   180.00   0.0  0
 QYK  CONST_24  N5  C8  C5  C3      0.00   0.0  0
 QYK  CONST_25  C6  C5  C3  C4    180.00   0.0  0
 QYK  CONST_26  C8  C5  C3  C4      0.00   0.0  0
 QYK  CONST_27  N5  C8  C5  C6    180.00   0.0  0
 QYK  CONST_28  N5  C8  N4  C7    180.00   0.0  0
 QYK  CONST_29  H4  C7  N3  C6    180.00   0.0  0
 QYK  CONST_30  H5  N5  C8  C5    180.00   0.0  0
 QYK  CONST_31  H6  N5  C8  C5      0.00   0.0  0
 QYK  Var_01    H1  C1  N1  C2   -179.63  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
 QYK  plan-1  C1   0.020
 QYK  plan-1  N1   0.020
 QYK  plan-1  C2   0.020
 QYK  plan-1  BR1  0.020
 QYK  plan-1  C3   0.020
 QYK  plan-1  C4   0.020
 QYK  plan-1  N2   0.020
 QYK  plan-1  C5   0.020
 QYK  plan-1  C6   0.020
 QYK  plan-1  N3   0.020
 QYK  plan-1  C7   0.020
 QYK  plan-1  N4   0.020
 QYK  plan-1  C8   0.020
 QYK  plan-1  N5   0.020
 QYK  plan-1  H4   0.020
 QYK  plan-2  C8   0.020
 QYK  plan-2  N5   0.020
 QYK  plan-2  H5   0.020
 QYK  plan-2  H6   0.020

