# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 13:45:38 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: 4-azanyl-2-methyl-6-pyridin-3-yl-7~{H}-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)c2c([nH]c(c3cccnc3)c2C#N)n1
#
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
 QYW  QYW  4-azanyl-2-methyl-6-pyridin-3-yl-7~{H}-pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  29  19  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_QYW
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
 QYW  C1   C  CH3   0  -0.729  45.0213  3.9571  18.0719
 QYW  C2   C  CR6   0   0.348  44.3845  4.5119  16.8374
 QYW  N1   N  N     0  -0.476  44.2119  5.8371  16.8132
 QYW  C3   C  CR6   0   0.442  43.6509  6.4160  15.7528
 QYW  N2   N  NH2   0  -0.831  43.4893  7.7419  15.7681
 QYW  C4   C  CR56  0  -0.037  43.2505  5.6031  14.6703
 QYW  C5   C  CR56  0   0.475  43.4884  4.2424  14.8299
 QYW  N3   N  NR15  0  -0.727  43.0503  3.6065  13.7088
 QYW  C6   C  CR5   0   0.436  42.5445  4.5054  12.8211
 QYW  C7   C  CR5   0  -0.134  42.6427  5.7647  13.3843
 QYW  C8   C  CSP   0  -0.083  42.1511  6.9571  12.8199
 QYW  N4   N  NS    0  -0.245  41.7477  7.9486  12.3868
 QYW  C9   C  CR6   0  -0.053  41.9955  4.1008  11.5341
 QYW  C10  C  CR16  0  -0.176  41.2404  2.9375  11.3939
 QYW  C11  C  CR16  0  -0.313  40.7418  2.6108  10.1461
 QYW  C12  C  CR16  0  -0.056  41.0094  3.4578   9.0806
 QYW  N5   N  N     0  -0.391  41.7351  4.5638   9.1977
 QYW  C13  C  CR16  0  -0.089  42.2177  4.8704  10.3910
 QYW  N6   N  N     0  -0.466  44.0498  3.6575  15.8838
 QYW  H1   H  HCH3  0   0.245  45.1053  2.8746  18.0178
 QYW  H2   H  HCH3  0   0.253  46.0179  4.3784  18.2110
 QYW  H3   H  HCH3  0   0.252  44.4377  4.2204  18.9547
 QYW  H4   H  HNH2  0   0.404  43.8312  8.2732  16.5509
 QYW  H5   H  HNH2  0   0.414  43.1290  8.2522  14.9814
 QYW  H6   H  HNR5  0   0.429  43.1508  2.6158  13.5385
 QYW  H7   H  HCR6  0   0.281  41.0302  2.3041  12.2470
 QYW  H8   H  HCR6  0   0.281  40.1469  1.7201  10.0006
 QYW  H9   H  HCR6  0   0.274  40.6253  3.2321   8.0924
 QYW  H10  H  HCR6  0   0.271  42.8336  5.7618  10.4450

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
 QYW  C12  N5   aromatic  1.328  0.020  1.328
 QYW  C12  C11  aromatic  1.387  0.020  1.387
 QYW  N5   C13  aromatic  1.323  0.020  1.323
 QYW  C11  C10  aromatic  1.383  0.020  1.383
 QYW  C13  C9   aromatic  1.396  0.020  1.396
 QYW  C10  C9   aromatic  1.394  0.020  1.394
 QYW  C9   C6   single    1.456  0.020  1.456
 QYW  N4   C8   triple    1.155  0.020  1.155
 QYW  C6   C7   aromatic  1.383  0.020  1.383
 QYW  C6   N3   aromatic  1.361  0.020  1.361
 QYW  C8   C7   single    1.408  0.020  1.408
 QYW  C7   C4   aromatic  1.432  0.020  1.432
 QYW  N3   C5   aromatic  1.361  0.020  1.361
 QYW  C4   C5   aromatic  1.390  0.020  1.390
 QYW  C4   C3   aromatic  1.412  0.020  1.412
 QYW  C5   N6   aromatic  1.330  0.020  1.330
 QYW  N2   C3   single    1.336  0.020  1.336
 QYW  C3   N1   aromatic  1.332  0.020  1.332
 QYW  N6   C2   aromatic  1.323  0.020  1.323
 QYW  N1   C2   aromatic  1.337  0.020  1.337
 QYW  C2   C1   single    1.496  0.020  1.496
 QYW  C1   H1   single    0.970  0.020  1.090
 QYW  C1   H2   single    0.970  0.020  1.090
 QYW  C1   H3   single    0.970  0.020  1.090
 QYW  N2   H4   single    0.860  0.020  1.020
 QYW  N2   H5   single    0.860  0.020  1.020
 QYW  N3   H6   single    0.860  0.020  1.020
 QYW  C10  H7   single    0.930  0.020  1.080
 QYW  C11  H8   single    0.930  0.020  1.080
 QYW  C12  H9   single    0.930  0.020  1.080
 QYW  C13  H10  single    0.930  0.020  1.080

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
 QYW  H3   C1   H2   107.00  3.000
 QYW  H3   C1   H1   108.79  3.000
 QYW  H2   C1   H1   108.68  3.000
 QYW  H3   C1   C2   110.53  3.000
 QYW  H2   C1   C2   110.54  3.000
 QYW  H1   C1   C2   111.17  3.000
 QYW  N6   C2   N1   126.47  3.000
 QYW  N1   C2   C1   115.96  3.000
 QYW  N6   C2   C1   117.57  3.000
 QYW  C3   N1   C2   119.98  3.000
 QYW  C4   C3   N2   123.10  3.000
 QYW  N2   C3   N1   118.24  3.000
 QYW  C4   C3   N1   118.66  3.000
 QYW  H5   N2   H4   117.58  3.000
 QYW  H5   N2   C3   122.59  3.000
 QYW  H4   N2   C3   119.48  3.000
 QYW  C7   C4   C5   106.64  3.000
 QYW  C5   C4   C3   115.27  3.000
 QYW  C7   C4   C3   138.09  3.000
 QYW  N6   C5   N3   125.67  3.000
 QYW  N6   C5   C4   126.42  3.000
 QYW  N3   C5   C4   107.91  3.000
 QYW  H6   N3   C6   125.09  3.000
 QYW  H6   N3   C5   124.39  3.000
 QYW  C6   N3   C5   110.38  3.000
 QYW  C9   C6   C7   129.76  3.000
 QYW  C7   C6   N3   108.02  3.000
 QYW  C9   C6   N3   122.21  3.000
 QYW  C8   C7   C6   125.67  3.000
 QYW  C8   C7   C4   127.16  3.000
 QYW  C6   C7   C4   107.05  3.000
 QYW  N4   C8   C7   180.00  3.000
 QYW  C13  C9   C10  117.64  3.000
 QYW  C10  C9   C6   121.66  3.000
 QYW  C13  C9   C6   120.70  3.000
 QYW  H7   C10  C11  120.17  3.000
 QYW  H7   C10  C9   120.93  3.000
 QYW  C11  C10  C9   118.90  3.000
 QYW  H8   C11  C12  120.39  3.000
 QYW  H8   C11  C10  120.97  3.000
 QYW  C12  C11  C10  118.64  3.000
 QYW  H9   C12  N5   116.58  3.000
 QYW  H9   C12  C11  120.31  3.000
 QYW  N5   C12  C11  123.11  3.000
 QYW  C13  N5   C12  118.15  3.000
 QYW  H10  C13  N5   116.25  3.000
 QYW  H10  C13  C9   120.18  3.000
 QYW  N5   C13  C9   123.56  3.000
 QYW  C5   N6   C2   113.20  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
 QYW  CONST_01  N3   C5   N6   C2   180.00   0.0  0
 QYW  CONST_02  C4   C5   N6   C2     0.00   0.0  0
 QYW  CONST_03  C4   C3   N1   C2     0.00   0.0  0
 QYW  CONST_04  C7   C4   C3   N1   180.00   0.0  0
 QYW  CONST_05  C5   C4   C3   N1     0.00   0.0  0
 QYW  CONST_06  C5   N6   C2   N1     0.00   0.0  0
 QYW  CONST_07  C6   C7   C4   C3   180.00   0.0  0
 QYW  CONST_08  N3   C5   C4   C3   180.00   0.0  0
 QYW  CONST_09  N6   C5   C4   C3     0.00   0.0  0
 QYW  CONST_10  N6   C2   N1   C3     0.00   0.0  0
 QYW  CONST_11  C9   C6   C7   C4   180.00   0.0  0
 QYW  CONST_12  N3   C6   C7   C4     0.00   0.0  0
 QYW  CONST_13  C6   N3   C5   C4     0.00   0.0  0
 QYW  CONST_14  C9   C6   N3   C5   180.00   0.0  0
 QYW  CONST_15  C7   C6   N3   C5     0.00   0.0  0
 QYW  CONST_16  C6   C7   C4   C5     0.00   0.0  0
 QYW  CONST_19  C7   C4   C5   N3     0.00   0.0  0
 QYW  CONST_20  N5   C13  C9   C6   180.00   0.0  0
 QYW  CONST_21  C11  C10  C9   C6   180.00   0.0  0
 QYW  CONST_22  N6   C5   N3   C6   180.00   0.0  0
 QYW  CONST_25  N6   C5   C4   C7   180.00   0.0  0
 QYW  CONST_26  C12  N5   C13  C9     0.00   0.0  0
 QYW  CONST_27  C12  C11  C10  C9     0.00   0.0  0
 QYW  CONST_28  N5   C12  C11  C10    0.00   0.0  0
 QYW  CONST_29  N5   C13  C9   C10    0.00   0.0  0
 QYW  CONST_30  C13  N5   C12  C11    0.00   0.0  0
 QYW  CONST_31  C13  C9   C10  C11    0.00   0.0  0
 QYW  CONST_32  C5   N6   C2   C1   180.00   0.0  0
 QYW  CONST_33  C3   N1   C2   C1   180.00   0.0  0
 QYW  CONST_34  N2   C3   N1   C2   180.00   0.0  0
 QYW  CONST_35  C8   C7   C4   C3     0.00   0.0  0
 QYW  CONST_36  C7   C4   C3   N2     0.00   0.0  0
 QYW  CONST_37  C5   C4   C3   N2   180.00   0.0  0
 QYW  CONST_38  C8   C7   C4   C5   180.00   0.0  0
 QYW  CONST_39  C8   C7   C6   N3   180.00   0.0  0
 QYW  CONST_40  C9   C6   C7   C8     0.00   0.0  0
 QYW  CONST_41  H6   N3   C5   C4   180.00   0.0  0
 QYW  CONST_42  H10  C13  C9   C6     0.00   0.0  0
 QYW  CONST_43  H7   C10  C9   C6     0.00   0.0  0
 QYW  CONST_44  H8   C11  C10  C9   180.00   0.0  0
 QYW  CONST_45  H9   C12  C11  C10  180.00   0.0  0
 QYW  CONST_46  H4   N2   C3   N1     0.00   0.0  0
 QYW  CONST_47  H5   N2   C3   N1   180.00   0.0  0
 QYW  Var_01    H1   C1   C2   N1   178.83  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
 QYW  plan-1  C6   0.020
 QYW  plan-1  C9   0.020
 QYW  plan-1  C10  0.020
 QYW  plan-1  C11  0.020
 QYW  plan-1  C12  0.020
 QYW  plan-1  N5   0.020
 QYW  plan-1  C13  0.020
 QYW  plan-1  H7   0.020
 QYW  plan-1  H8   0.020
 QYW  plan-1  H9   0.020
 QYW  plan-1  H10  0.020
 QYW  plan-2  C1   0.020
 QYW  plan-2  C2   0.020
 QYW  plan-2  N1   0.020
 QYW  plan-2  C3   0.020
 QYW  plan-2  N2   0.020
 QYW  plan-2  C4   0.020
 QYW  plan-2  C5   0.020
 QYW  plan-2  N3   0.020
 QYW  plan-2  C6   0.020
 QYW  plan-2  C7   0.020
 QYW  plan-2  C8   0.020
 QYW  plan-2  N4   0.020
 QYW  plan-2  C9   0.020
 QYW  plan-2  N6   0.020
 QYW  plan-2  H6   0.020
 QYW  plan-3  C3   0.020
 QYW  plan-3  N2   0.020
 QYW  plan-3  H4   0.020
 QYW  plan-3  H5   0.020

