# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 07:02:37 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: N~2~-methyl-N~4~-[(pyrimidin-2-yl)methyl]-5-(quinolin-6-yl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1nc(NCc2ncccn2)c3c([nH]cc3c4ccc5ncccc5c4)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
 8FY  8FY  N~2~-methyl-N~4~-[(pyrimidin-2-yl)methyl]-5-(quinolin-6-yl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diamine  ligand  47  29  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8FY
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
 8FY  C5   C  CR6   0   0.468   2.0102   0.3773   0.0649
 8FY  C7   C  CH2   0  -0.312   0.9482   2.5846   0.0245
 8FY  C8   C  CR6   0   0.360  -0.4556   3.1277   0.0071
 8FY  C10  C  CR16  0  -0.003  -2.6881   2.7484  -0.0104
 8FY  C15  C  CR5   0  -0.009   0.8966  -2.0412   0.0742
 8FY  C21  C  CR6   0   0.003  -0.5486  -1.8472   0.2264
 8FY  C22  C  CR16  0  -0.330  -1.0469  -1.1072   1.3311
 8FY  C24  C  CR66  0   0.197  -3.3140  -1.3881   0.5576
 8FY  C26  C  CR16  0  -0.085  -5.4782  -1.6053  -0.1361
 8FY  C28  C  CR16  0  -0.190  -3.7803  -2.6440  -1.4567
 8FY  C1   C  CH3   0  -0.508   6.7480   0.2386  -0.2502
 8FY  C3   C  CR6   0   0.568   4.3035   0.2004  -0.0515
 8FY  N4   N  N     0  -0.547   3.1971   0.9673   0.0210
 8FY  N6   N  NH1   0  -0.695   0.9166   1.1517   0.0881
 8FY  N9   N  N     0  -0.431  -1.4535   2.2599  -0.0031
 8FY  C11  C  CR16  0  -0.350  -2.9310   4.1085  -0.0161
 8FY  C12  C  CR16  0  -0.024  -1.8136   4.9307  -0.0121
 8FY  N13  N  N     0  -0.412  -0.5789   4.4496   0.0021
 8FY  C14  C  CR56  0  -0.146   1.9241  -1.0366   0.0722
 8FY  C16  C  CR15  0  -0.073   1.5419  -3.2378  -0.0615
 8FY  N17  N  NR15  0  -0.670   2.8967  -3.0209  -0.1390
 8FY  C19  C  CR56  0   0.499   3.1494  -1.6928  -0.0603
 8FY  N20  N  N     0  -0.525   4.3549  -1.1236  -0.1223
 8FY  C23  C  CR16  0  -0.258  -2.3837  -0.8799   1.4915
 8FY  N25  N  N     0  -0.433  -4.6311  -1.1299   0.7379
 8FY  C27  C  CR16  0  -0.327  -5.1043  -2.3735  -1.2589
 8FY  C29  C  CR66  0   0.097  -2.8308  -2.1489  -0.5355
 8FY  C30  C  CR16  0  -0.382  -1.4429  -2.3608  -0.6818
 8FY  H1   H  HCH2  0   0.265   1.4727   2.9387  -0.8693
 8FY  H2   H  HCH2  0   0.265   1.4801   3.0140   0.8789
 8FY  H3   H  HCR6  0   0.278  -3.4978   2.0273  -0.0104
 8FY  H4   H  HCR6  0   0.265  -0.3483  -0.7222   2.0640
 8FY  H5   H  HCR6  0   0.264  -6.5272  -1.3836   0.0310
 8FY  H6   H  HCR6  0   0.272  -3.4501  -3.2263  -2.3086
 8FY  H7   H  HCH3  0   0.229   6.9457  -0.5117   0.5160
 8FY  H8   H  HCH3  0   0.222   6.8268  -0.2522  -1.2238
 8FY  H9   H  HCH3  0   0.245   7.5229   0.9980  -0.1870
 8FY  H10  H  HNH1  0   0.387   5.4155   1.8749  -0.1194
 8FY  H11  H  HNH1  0   0.428  -0.0034   0.7360   0.0636
 8FY  H12  H  HCR6  0   0.287  -3.9331   4.5106  -0.0235
 8FY  H13  H  HCR6  0   0.282  -1.9182   6.0095  -0.0186
 8FY  H14  H  HCR5  0   0.285   1.1396  -4.2377  -0.0758
 8FY  H15  H  HNR5  0   0.408   3.5965  -3.7393  -0.2296
 8FY  H16  H  HCR6  0   0.259  -2.7530  -0.3111   2.3352
 8FY  H17  H  HCR6  0   0.272  -5.8626  -2.7314  -1.9415
 8FY  H18  H  HCR6  0   0.254  -1.0861  -2.9138  -1.5429
 8FY  N2   N  NH1   0  -0.649   5.4736   0.8741  -0.0513

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
 8FY  C10  C11  aromatic  1.382  0.020  1.382
 8FY  C10  N9   aromatic  1.328  0.020  1.328
 8FY  C11  C12  aromatic  1.387  0.020  1.387
 8FY  N9   C8   aromatic  1.322  0.020  1.322
 8FY  C12  N13  aromatic  1.325  0.020  1.325
 8FY  C8   N13  aromatic  1.328  0.020  1.328
 8FY  C8   C7   single    1.505  0.020  1.505
 8FY  C7   N6   single    1.435  0.020  1.435
 8FY  C27  C26  aromatic  1.411  0.020  1.411
 8FY  C27  C28  aromatic  1.366  0.020  1.366
 8FY  C26  N25  aromatic  1.307  0.020  1.307
 8FY  C28  C29  aromatic  1.413  0.020  1.413
 8FY  N6   C5   single    1.340  0.020  1.340
 8FY  C1   N2   single    1.438  0.020  1.438
 8FY  N4   C5   aromatic  1.326  0.020  1.326
 8FY  N4   C3   aromatic  1.348  0.020  1.348
 8FY  N25  C24  aromatic  1.354  0.020  1.354
 8FY  C29  C24  aromatic  1.417  0.020  1.417
 8FY  C29  C30  aromatic  1.412  0.020  1.412
 8FY  C5   C14  aromatic  1.417  0.020  1.417
 8FY  N2   C3   single    1.350  0.020  1.350
 8FY  C24  C23  aromatic  1.413  0.020  1.413
 8FY  C30  C21  aromatic  1.374  0.020  1.374
 8FY  C3   N20  aromatic  1.327  0.020  1.327
 8FY  C14  C15  aromatic  1.437  0.020  1.437
 8FY  C14  C19  aromatic  1.396  0.020  1.396
 8FY  C23  C22  aromatic  1.365  0.020  1.365
 8FY  C21  C22  aromatic  1.420  0.020  1.420
 8FY  C21  C15  single    1.466  0.020  1.466
 8FY  N20  C19  aromatic  1.335  0.020  1.335
 8FY  C15  C16  aromatic  1.366  0.020  1.366
 8FY  C19  N17  aromatic  1.354  0.020  1.354
 8FY  C16  N17  aromatic  1.374  0.020  1.374
 8FY  C7   H1   single    0.970  0.020  1.090
 8FY  C7   H2   single    0.970  0.020  1.090
 8FY  C10  H3   single    0.930  0.020  1.080
 8FY  C22  H4   single    0.930  0.020  1.080
 8FY  C26  H5   single    0.930  0.020  1.080
 8FY  C28  H6   single    0.930  0.020  1.080
 8FY  C1   H7   single    0.970  0.020  1.090
 8FY  C1   H8   single    0.970  0.020  1.090
 8FY  C1   H9   single    0.970  0.020  1.090
 8FY  N2   H10  single    0.860  0.020  1.020
 8FY  N6   H11  single    0.860  0.020  1.020
 8FY  C11  H12  single    0.930  0.020  1.080
 8FY  C12  H13  single    0.930  0.020  1.080
 8FY  C16  H14  single    0.930  0.020  1.080
 8FY  N17  H15  single    0.860  0.020  1.020
 8FY  C23  H16  single    0.930  0.020  1.080
 8FY  C27  H17  single    0.930  0.020  1.080
 8FY  C30  H18  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
 8FY  C14  C5   N6   121.81  3.000
 8FY  C14  C5   N4   119.91  3.000
 8FY  N6   C5   N4   118.28  3.000
 8FY  H2   C7   H1   106.12  3.000
 8FY  H2   C7   N6   111.59  3.000
 8FY  H1   C7   N6   111.69  3.000
 8FY  H2   C7   C8   108.71  3.000
 8FY  H1   C7   C8   108.70  3.000
 8FY  N6   C7   C8   109.90  3.000
 8FY  N13  C8   N9   125.68  3.000
 8FY  N13  C8   C7   116.48  3.000
 8FY  N9   C8   C7   117.84  3.000
 8FY  H3   C10  C11  121.56  3.000
 8FY  H3   C10  N9   116.73  3.000
 8FY  C11  C10  N9   121.71  3.000
 8FY  C16  C15  C14  105.93  3.000
 8FY  C16  C15  C21  126.28  3.000
 8FY  C14  C15  C21  127.77  3.000
 8FY  C30  C21  C22  118.72  3.000
 8FY  C22  C21  C15  119.72  3.000
 8FY  C30  C21  C15  121.56  3.000
 8FY  H4   C22  C23  119.52  3.000
 8FY  H4   C22  C21  119.03  3.000
 8FY  C23  C22  C21  121.45  3.000
 8FY  C29  C24  N25  122.47  3.000
 8FY  C29  C24  C23  118.60  3.000
 8FY  N25  C24  C23  118.94  3.000
 8FY  H5   C26  C27  119.34  3.000
 8FY  H5   C26  N25  116.71  3.000
 8FY  C27  C26  N25  123.95  3.000
 8FY  H6   C28  C29  119.75  3.000
 8FY  H6   C28  C27  121.05  3.000
 8FY  C29  C28  C27  119.19  3.000
 8FY  H9   C1   H8   108.31  3.000
 8FY  H9   C1   H7   108.10  3.000
 8FY  H8   C1   H7   107.69  3.000
 8FY  H9   C1   N2   108.37  3.000
 8FY  H8   C1   N2   112.68  3.000
 8FY  H7   C1   N2   111.56  3.000
 8FY  N20  C3   N4   127.03  3.000
 8FY  N20  C3   N2   117.67  3.000
 8FY  N4   C3   N2   115.30  3.000
 8FY  C3   N4   C5   118.90  3.000
 8FY  H11  N6   C7   115.48  3.000
 8FY  H11  N6   C5   120.34  3.000
 8FY  C7   N6   C5   123.94  3.000
 8FY  C10  N9   C8   117.41  3.000
 8FY  H12  C11  C12  121.79  3.000
 8FY  H12  C11  C10  121.99  3.000
 8FY  C12  C11  C10  116.22  3.000
 8FY  H13  C12  N13  116.83  3.000
 8FY  H13  C12  C11  120.81  3.000
 8FY  N13  C12  C11  122.37  3.000
 8FY  C12  N13  C8   116.62  3.000
 8FY  C19  C14  C15  107.40  3.000
 8FY  C19  C14  C5   114.54  3.000
 8FY  C15  C14  C5   137.84  3.000
 8FY  H14  C16  N17  120.90  3.000
 8FY  H14  C16  C15  129.61  3.000
 8FY  N17  C16  C15  109.45  3.000
 8FY  H15  N17  C19  125.12  3.000
 8FY  H15  N17  C16  125.28  3.000
 8FY  C19  N17  C16  109.60  3.000
 8FY  N20  C19  N17  125.74  3.000
 8FY  N17  C19  C14  107.62  3.000
 8FY  N20  C19  C14  126.63  3.000
 8FY  C19  N20  C3   112.84  3.000
 8FY  H16  C23  C24  118.66  3.000
 8FY  H16  C23  C22  120.86  3.000
 8FY  C24  C23  C22  120.47  3.000
 8FY  C26  N25  C24  118.17  3.000
 8FY  H17  C27  C28  121.52  3.000
 8FY  H17  C27  C26  119.79  3.000
 8FY  C28  C27  C26  118.69  3.000
 8FY  C30  C29  C28  122.73  3.000
 8FY  C30  C29  C24  119.73  3.000
 8FY  C28  C29  C24  117.53  3.000
 8FY  H18  C30  C29  118.85  3.000
 8FY  H18  C30  C21  120.11  3.000
 8FY  C29  C30  C21  121.02  3.000
 8FY  H10  N2   C3   116.55  3.000
 8FY  H10  N2   C1   118.82  3.000
 8FY  C3   N2   C1   123.20  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
 8FY  CONST_01  N20  C3   N4   C5     0.00   0.0  0
 8FY  CONST_02  C21  C15  C14  C5     0.00   0.0  0
 8FY  CONST_03  C16  C15  C14  C5   180.00   0.0  0
 8FY  CONST_04  N20  C19  C14  C5     0.00   0.0  0
 8FY  CONST_05  N17  C19  C14  C5   180.00   0.0  0
 8FY  CONST_06  C11  C10  N9   C8     0.00   0.0  0
 8FY  CONST_07  C11  C12  N13  C8     0.00   0.0  0
 8FY  CONST_08  N13  C12  C11  C10    0.00   0.0  0
 8FY  CONST_09  N13  C8   N9   C10    0.00   0.0  0
 8FY  CONST_10  N4   C5   C14  C15  180.00   0.0  0
 8FY  CONST_11  N20  C19  C14  C15  180.00   0.0  0
 8FY  CONST_12  N17  C19  C14  C15    0.00   0.0  0
 8FY  CONST_13  C29  C30  C21  C15  180.00   0.0  0
 8FY  CONST_14  C23  C22  C21  C15  180.00   0.0  0
 8FY  CONST_15  C19  N17  C16  C15    0.00   0.0  0
 8FY  CONST_16  C28  C29  C30  C21  180.00   0.0  0
 8FY  CONST_17  C24  C29  C30  C21    0.00   0.0  0
 8FY  CONST_18  C24  C23  C22  C21    0.00   0.0  0
 8FY  CONST_19  C19  C14  C15  C21  180.00   0.0  0
 8FY  CONST_20  N17  C16  C15  C21  180.00   0.0  0
 8FY  CONST_21  N25  C24  C23  C22  180.00   0.0  0
 8FY  CONST_22  C29  C24  C23  C22    0.00   0.0  0
 8FY  CONST_23  C29  C30  C21  C22    0.00   0.0  0
 8FY  CONST_26  C27  C26  N25  C24    0.00   0.0  0
 8FY  CONST_27  C27  C28  C29  C24    0.00   0.0  0
 8FY  CONST_28  C29  C28  C27  C26    0.00   0.0  0
 8FY  CONST_29  C29  C24  N25  C26    0.00   0.0  0
 8FY  CONST_30  C23  C24  N25  C26  180.00   0.0  0
 8FY  CONST_31  N25  C26  C27  C28    0.00   0.0  0
 8FY  CONST_32  N25  C24  C29  C28    0.00   0.0  0
 8FY  CONST_33  C23  C24  C29  C28  180.00   0.0  0
 8FY  CONST_34  C14  C5   N4   C3     0.00   0.0  0
 8FY  CONST_35  C14  C19  N20  C3     0.00   0.0  0
 8FY  CONST_36  N17  C19  N20  C3   180.00   0.0  0
 8FY  CONST_37  C19  C14  C5   N4     0.00   0.0  0
 8FY  CONST_38  C19  N20  C3   N4     0.00   0.0  0
 8FY  CONST_39  C12  C11  C10  N9     0.00   0.0  0
 8FY  CONST_40  C12  N13  C8   N9     0.00   0.0  0
 8FY  CONST_42  N17  C16  C15  C14    0.00   0.0  0
 8FY  CONST_43  C16  N17  C19  C14    0.00   0.0  0
 8FY  CONST_44  C19  C14  C15  C16    0.00   0.0  0
 8FY  CONST_46  N20  C19  N17  C16  180.00   0.0  0
 8FY  CONST_47  C30  C29  C24  C23    0.00   0.0  0
 8FY  CONST_48  C30  C21  C22  C23    0.00   0.0  0
 8FY  CONST_49  C30  C29  C24  N25  180.00   0.0  0
 8FY  CONST_50  C30  C29  C28  C27  180.00   0.0  0
 8FY  CONST_51  N2   C3   N4   C5   180.00   0.0  0
 8FY  CONST_52  C10  N9   C8   C7   180.00   0.0  0
 8FY  CONST_53  C12  N13  C8   C7   180.00   0.0  0
 8FY  CONST_54  N6   C5   C14  C15    0.00   0.0  0
 8FY  CONST_55  C19  N20  C3   N2   180.00   0.0  0
 8FY  CONST_56  N6   C5   N4   C3   180.00   0.0  0
 8FY  CONST_57  C19  C14  C5   N6   180.00   0.0  0
 8FY  CONST_58  H3   C10  N9   C8   180.00   0.0  0
 8FY  CONST_59  H13  C12  N13  C8   180.00   0.0  0
 8FY  CONST_60  H18  C30  C21  C15    0.00   0.0  0
 8FY  CONST_61  H4   C22  C21  C15    0.00   0.0  0
 8FY  CONST_62  H15  N17  C16  C15  180.00   0.0  0
 8FY  CONST_63  H16  C23  C22  C21  180.00   0.0  0
 8FY  CONST_64  H14  C16  C15  C21    0.00   0.0  0
 8FY  CONST_65  H5   C26  N25  C24  180.00   0.0  0
 8FY  CONST_66  H6   C28  C29  C24  180.00   0.0  0
 8FY  CONST_67  H12  C11  C10  N9   180.00   0.0  0
 8FY  CONST_68  H17  C27  C26  N25  180.00   0.0  0
 8FY  CONST_69  N4   C5   N6   C7     0.00   0.0  0
 8FY  CONST_70  C14  C5   N6   C7   180.00   0.0  0
 8FY  CONST_71  N4   C3   N2   C1   180.00   0.0  0
 8FY  CONST_72  N20  C3   N2   C1     0.00   0.0  0
 8FY  CONST_73  H11  N6   C5   N4   180.00   0.0  0
 8FY  CONST_74  H10  N2   C3   N4     0.00   0.0  0
 8FY  Var_01    C8   C7   N6   C5   177.31  30.0  2
 8FY  Var_02    N9   C8   C7   N6    -2.62  30.0  2
 8FY  Var_03    H7   C1   N2   C3   -60.15  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
 8FY  plan-1  C7   0.020
 8FY  plan-1  C8   0.020
 8FY  plan-1  C10  0.020
 8FY  plan-1  N9   0.020
 8FY  plan-1  C11  0.020
 8FY  plan-1  C12  0.020
 8FY  plan-1  N13  0.020
 8FY  plan-1  H3   0.020
 8FY  plan-1  H12  0.020
 8FY  plan-1  H13  0.020
 8FY  plan-2  C5   0.020
 8FY  plan-2  C15  0.020
 8FY  plan-2  C21  0.020
 8FY  plan-2  C3   0.020
 8FY  plan-2  N4   0.020
 8FY  plan-2  N6   0.020
 8FY  plan-2  C14  0.020
 8FY  plan-2  C16  0.020
 8FY  plan-2  N17  0.020
 8FY  plan-2  C19  0.020
 8FY  plan-2  N20  0.020
 8FY  plan-2  H14  0.020
 8FY  plan-2  H15  0.020
 8FY  plan-2  N2   0.020
 8FY  plan-3  C15  0.020
 8FY  plan-3  C21  0.020
 8FY  plan-3  C22  0.020
 8FY  plan-3  C24  0.020
 8FY  plan-3  C26  0.020
 8FY  plan-3  C28  0.020
 8FY  plan-3  C23  0.020
 8FY  plan-3  N25  0.020
 8FY  plan-3  C27  0.020
 8FY  plan-3  C29  0.020
 8FY  plan-3  C30  0.020
 8FY  plan-3  H4   0.020
 8FY  plan-3  H5   0.020
 8FY  plan-3  H6   0.020
 8FY  plan-3  H16  0.020
 8FY  plan-3  H17  0.020
 8FY  plan-3  H18  0.020
 8FY  plan-4  C5   0.020
 8FY  plan-4  C7   0.020
 8FY  plan-4  N6   0.020
 8FY  plan-4  H11  0.020
 8FY  plan-5  C1   0.020
 8FY  plan-5  C3   0.020
 8FY  plan-5  H10  0.020
 8FY  plan-5  N2   0.020

