# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 07:44:56 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 4-(2,4-dimethylphenyl)-2-(methylsulfanyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1nc2[nH]cc(C#N)c2c(n1)c3ccc(C)cc3C
#
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
 2N6  2N6  4-(2,4-dimethylphenyl)-2-(methylsulfanyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile  ligand  35  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2N6
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
 2N6  C19  C  CH3   0  -0.724  -0.9499   2.0960   1.8154
 2N6  C17  C  CR6   0   0.081  -1.8047   1.4652   0.7586
 2N6  C16  C  CR16  0  -0.329  -3.1506   1.8313   0.6498
 2N6  C15  C  CR6   0   0.246  -4.0017   1.2617  -0.3109
 2N6  C18  C  CH3   0  -0.705  -5.4377   1.6801  -0.3941
 2N6  C14  C  CR16  0  -0.371  -3.4645   0.3238  -1.1915
 2N6  C13  C  CR16  0  -0.309  -2.1381  -0.0646  -1.0867
 2N6  C5   C  CR6   0  -0.017  -1.2940   0.5028  -0.1298
 2N6  C4   C  CR6   0   0.185   0.1184   0.0722  -0.0597
 2N6  C8   C  CR56  0  -0.149   0.5073  -1.2648   0.0711
 2N6  N1   N  N     0  -0.449   1.0621   1.0085  -0.1965
 2N6  C2   C  CR6   0   0.204   2.3445   0.6445  -0.1779
 2N6  S6   S  S2    0   0.098   3.4726   2.0081  -0.3444
 2N6  C7   C  CH3   0  -0.800   5.0639   1.2119  -0.2816
 2N6  N3   N  N     0  -0.432   2.8370  -0.5753  -0.0697
 2N6  C9   C  CR56  0   0.507   1.8935  -1.4921   0.0551
 2N6  N10  N  NR15  0  -0.518   2.1198  -2.8208   0.2207
 2N6  C11  C  CR15  0   0.026   0.9334  -3.4667   0.3279
 2N6  C12  C  CR5   0  -0.055  -0.0880  -2.5594   0.2131
 2N6  C20  C  CSP   0  -0.052  -1.4589  -2.8923   0.2857
 2N6  N21  N  NS    0  -0.222  -2.5786  -3.1653   0.3268
 2N6  H1   H  HCH3  0   0.229  -0.2062   2.7610   1.3879
 2N6  H2   H  HCH3  0   0.267  -1.5647   2.6699   2.5073
 2N6  H3   H  HCH3  0   0.247  -0.4186   1.3419   2.4009
 2N6  H4   H  HCR6  0   0.233  -3.5549   2.5734   1.3306
 2N6  H5   H  HCH3  0   0.178  -6.0621   1.1054   0.3023
 2N6  H6   H  HCH3  0   0.257  -5.5685   2.7291  -0.1473
 2N6  H7   H  HCH3  0   0.276  -5.8324   1.5280  -1.3936
 2N6  H8   H  HCR6  0   0.246  -4.1025  -0.1370  -1.9347
 2N6  H9   H  HCR6  0   0.288  -1.7447  -0.8134  -1.7601
 2N6  H10  H  HCH3  0   0.277   5.2321   0.7250   0.6741
 2N6  H11  H  HCH3  0   0.251   5.1895   0.4766  -1.0732
 2N6  H12  H  HCH3  0   0.306   5.8012   1.9986  -0.4107
 2N6  H13  H  HNR5  0   0.429   3.0392  -3.2514   0.2569
 2N6  H14  H  HCR5  0   0.302   0.8972  -4.5311   0.4593

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
 2N6  N21  C20  triple    1.153  0.020  1.153
 2N6  C20  C12  single    1.413  0.020  1.413
 2N6  C11  C12  aromatic  1.371  0.020  1.371
 2N6  C11  N10  aromatic  1.355  0.020  1.355
 2N6  C12  C8   aromatic  1.432  0.020  1.432
 2N6  C18  C15  single    1.498  0.020  1.498
 2N6  C15  C14  aromatic  1.394  0.020  1.394
 2N6  C15  C16  aromatic  1.404  0.020  1.404
 2N6  C14  C13  aromatic  1.386  0.020  1.386
 2N6  N10  C9   aromatic  1.358  0.020  1.358
 2N6  C16  C17  aromatic  1.399  0.020  1.399
 2N6  C8   C9   aromatic  1.405  0.020  1.405
 2N6  C8   C4   aromatic  1.399  0.020  1.399
 2N6  C13  C5   aromatic  1.396  0.020  1.396
 2N6  C17  C5   aromatic  1.406  0.020  1.406
 2N6  C17  C19  single    1.499  0.020  1.499
 2N6  C5   C4   single    1.478  0.020  1.478
 2N6  C9   N3   aromatic  1.322  0.020  1.322
 2N6  C4   N1   aromatic  1.336  0.020  1.336
 2N6  N3   C2   aromatic  1.320  0.020  1.320
 2N6  N1   C2   aromatic  1.333  0.020  1.333
 2N6  C2   S6   single    1.778  0.020  1.778
 2N6  C7   S6   single    1.781  0.020  1.781
 2N6  C19  H1   single    0.970  0.020  1.090
 2N6  C19  H2   single    0.970  0.020  1.090
 2N6  C19  H3   single    0.970  0.020  1.090
 2N6  C16  H4   single    0.930  0.020  1.080
 2N6  C18  H5   single    0.970  0.020  1.090
 2N6  C18  H6   single    0.970  0.020  1.090
 2N6  C18  H7   single    0.970  0.020  1.090
 2N6  C14  H8   single    0.930  0.020  1.080
 2N6  C13  H9   single    0.930  0.020  1.080
 2N6  C7   H10  single    0.970  0.020  1.090
 2N6  C7   H11  single    0.970  0.020  1.090
 2N6  C7   H12  single    0.970  0.020  1.090
 2N6  N10  H13  single    0.860  0.020  1.020
 2N6  C11  H14  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
 2N6  H3   C19  H2   107.32  3.000
 2N6  H3   C19  H1   107.50  3.000
 2N6  H2   C19  H1   108.32  3.000
 2N6  H3   C19  C17  111.39  3.000
 2N6  H2   C19  C17  110.36  3.000
 2N6  H1   C19  C17  111.78  3.000
 2N6  C5   C17  C16  118.66  3.000
 2N6  C5   C17  C19  121.78  3.000
 2N6  C16  C17  C19  119.56  3.000
 2N6  H4   C16  C15  118.74  3.000
 2N6  H4   C16  C17  119.25  3.000
 2N6  C15  C16  C17  122.01  3.000
 2N6  C14  C15  C18  121.48  3.000
 2N6  C14  C15  C16  118.13  3.000
 2N6  C18  C15  C16  120.38  3.000
 2N6  H7   C18  H6   107.52  3.000
 2N6  H7   C18  H5   107.70  3.000
 2N6  H6   C18  H5   107.05  3.000
 2N6  H7   C18  C15  111.14  3.000
 2N6  H6   C18  C15  111.88  3.000
 2N6  H5   C18  C15  111.33  3.000
 2N6  H8   C14  C13  119.78  3.000
 2N6  H8   C14  C15  119.54  3.000
 2N6  C13  C14  C15  120.63  3.000
 2N6  H9   C13  C5   119.23  3.000
 2N6  H9   C13  C14  119.68  3.000
 2N6  C5   C13  C14  121.09  3.000
 2N6  C4   C5   C13  119.45  3.000
 2N6  C4   C5   C17  121.10  3.000
 2N6  C13  C5   C17  119.44  3.000
 2N6  N1   C4   C8   118.88  3.000
 2N6  N1   C4   C5   117.76  3.000
 2N6  C8   C4   C5   123.27  3.000
 2N6  C12  C8   C9   105.37  3.000
 2N6  C9   C8   C4   115.34  3.000
 2N6  C12  C8   C4   139.28  3.000
 2N6  C2   N1   C4   119.12  3.000
 2N6  N3   C2   S6   118.67  3.000
 2N6  S6   C2   N1   113.56  3.000
 2N6  N3   C2   N1   127.76  3.000
 2N6  C7   S6   C2   102.76  3.000
 2N6  H12  C7   H11  108.95  3.000
 2N6  H12  C7   H10  108.93  3.000
 2N6  H11  C7   H10  108.64  3.000
 2N6  H12  C7   S6   106.18  3.000
 2N6  H11  C7   S6   112.32  3.000
 2N6  H10  C7   S6   111.72  3.000
 2N6  C9   N3   C2   112.49  3.000
 2N6  N10  C9   N3   124.84  3.000
 2N6  N3   C9   C8   126.40  3.000
 2N6  N10  C9   C8   108.75  3.000
 2N6  H13  N10  C11  125.98  3.000
 2N6  H13  N10  C9   124.74  3.000
 2N6  C11  N10  C9   109.28  3.000
 2N6  H14  C11  C12  129.91  3.000
 2N6  H14  C11  N10  120.80  3.000
 2N6  C12  C11  N10  109.28  3.000
 2N6  C20  C12  C11  124.25  3.000
 2N6  C11  C12  C8   107.27  3.000
 2N6  C20  C12  C8   128.43  3.000
 2N6  N21  C20  C12  180.00  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
 2N6  CONST_01  C14  C15  C16  C17     0.00   0.0  0
 2N6  CONST_02  C14  C13  C5   C17     0.00   0.0  0
 2N6  CONST_05  C13  C14  C15  C16     0.00   0.0  0
 2N6  CONST_06  C13  C5   C17  C16     0.00   0.0  0
 2N6  CONST_07  C4   C5   C17  C16   180.00   0.0  0
 2N6  CONST_08  C5   C13  C14  C15     0.00   0.0  0
 2N6  CONST_09  C5   C17  C16  C15     0.00   0.0  0
 2N6  CONST_10  C4   C5   C13  C14   180.00   0.0  0
 2N6  CONST_13  C12  C8   C4   C5      0.00   0.0  0
 2N6  CONST_14  C9   C8   C4   C5    180.00   0.0  0
 2N6  CONST_15  C2   N1   C4   C5    180.00   0.0  0
 2N6  CONST_16  C11  C12  C8   C4    180.00   0.0  0
 2N6  CONST_17  N10  C9   C8   C4    180.00   0.0  0
 2N6  CONST_18  N3   C9   C8   C4      0.00   0.0  0
 2N6  CONST_19  N3   C2   N1   C4      0.00   0.0  0
 2N6  CONST_20  N10  C11  C12  C8      0.00   0.0  0
 2N6  CONST_21  C11  N10  C9   C8      0.00   0.0  0
 2N6  CONST_22  C2   N3   C9   C8      0.00   0.0  0
 2N6  CONST_23  C2   N1   C4   C8      0.00   0.0  0
 2N6  CONST_24  C12  C8   C4   N1    180.00   0.0  0
 2N6  CONST_25  C9   C8   C4   N1      0.00   0.0  0
 2N6  CONST_26  C9   N3   C2   N1      0.00   0.0  0
 2N6  CONST_27  N10  C9   N3   C2    180.00   0.0  0
 2N6  CONST_28  C11  N10  C9   N3    180.00   0.0  0
 2N6  CONST_29  C12  C8   C9   N3    180.00   0.0  0
 2N6  CONST_30  C12  C11  N10  C9      0.00   0.0  0
 2N6  CONST_31  C11  C12  C8   C9      0.00   0.0  0
 2N6  CONST_32  C12  C8   C9   N10     0.00   0.0  0
 2N6  CONST_33  C15  C16  C17  C19   180.00   0.0  0
 2N6  CONST_34  C13  C5   C17  C19   180.00   0.0  0
 2N6  CONST_35  C4   C5   C17  C19     0.00   0.0  0
 2N6  CONST_36  C18  C15  C16  C17   180.00   0.0  0
 2N6  CONST_37  C13  C14  C15  C18   180.00   0.0  0
 2N6  CONST_38  C20  C12  C8   C4      0.00   0.0  0
 2N6  CONST_39  S6   C2   N1   C4    180.00   0.0  0
 2N6  CONST_40  C9   N3   C2   S6    180.00   0.0  0
 2N6  CONST_41  C20  C12  C8   C9    180.00   0.0  0
 2N6  CONST_42  C20  C12  C11  N10   180.00   0.0  0
 2N6  CONST_43  H9   C13  C5   C17   180.00   0.0  0
 2N6  CONST_44  H8   C14  C15  C16   180.00   0.0  0
 2N6  CONST_45  H4   C16  C15  C14   180.00   0.0  0
 2N6  CONST_46  H14  C11  C12  C8    180.00   0.0  0
 2N6  CONST_47  H13  N10  C9   C8    180.00   0.0  0
 2N6  Var_01    N3   C2   S6   C7     -0.87  30.0  1
 2N6  Var_02    H5   C18  C15  C16   -85.66  30.0  2
 2N6  Var_03    H1   C19  C17  C16  -110.67  30.0  2
 2N6  Var_04    H10  C7   S6   C2    -63.10  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
 2N6  plan-1  C19  0.020
 2N6  plan-1  C17  0.020
 2N6  plan-1  C16  0.020
 2N6  plan-1  C15  0.020
 2N6  plan-1  C18  0.020
 2N6  plan-1  C14  0.020
 2N6  plan-1  C13  0.020
 2N6  plan-1  C5   0.020
 2N6  plan-1  C4   0.020
 2N6  plan-1  H4   0.020
 2N6  plan-1  H8   0.020
 2N6  plan-1  H9   0.020
 2N6  plan-2  C5   0.020
 2N6  plan-2  C4   0.020
 2N6  plan-2  C8   0.020
 2N6  plan-2  N1   0.020
 2N6  plan-2  C2   0.020
 2N6  plan-2  S6   0.020
 2N6  plan-2  N3   0.020
 2N6  plan-2  C9   0.020
 2N6  plan-2  N10  0.020
 2N6  plan-2  C11  0.020
 2N6  plan-2  C12  0.020
 2N6  plan-2  C20  0.020
 2N6  plan-2  N21  0.020
 2N6  plan-2  H13  0.020
 2N6  plan-2  H14  0.020

