# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 16:55:32 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: ~{N}-[2-methoxy-4-(1-methylpyrazol-4-yl)phenyl]-8-(1-methylpyrazol-4-yl)pyrido[3,4-d]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1Nc2ncc3ccnc(c4cnn(C)c4)c3n2)c5cnn(C)c5
#
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
 5OE  5OE  ~{N}-[2-methoxy-4-(1-methylpyrazol-4-yl)phenyl]-8-(1-methylpyrazol-4-yl)pyrido[3,4-d]pyrimidin-2-amine  ligand  51  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5OE
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
 5OE  C21  C  CH3   0  -0.507   7.6329   2.7893   0.8993
 5OE  N6   N  NR5   0  -0.264   6.4376   2.0036   0.7077
 5OE  C19  C  CR15  0   0.067   6.3600   0.7105   0.3836
 5OE  N7   N  N     0  -0.280   5.2385   2.5700   0.8372
 5OE  C20  C  CR15  0  -0.108   4.3667   1.6129   0.5912
 5OE  C18  C  CR5   0  -0.159   5.0131   0.3917   0.2926
 5OE  C17  C  CR6   0   0.142   4.5052  -0.9324  -0.0430
 5OE  N5   N  N     0  -0.429   5.4037  -1.8642  -0.2767
 5OE  C16  C  CR16  0  -0.102   5.0395  -3.1177  -0.5967
 5OE  C15  C  CR16  0  -0.364   3.7349  -3.5139  -0.7048
 5OE  C1   C  CR66  0   0.065   2.7452  -2.5490  -0.4628
 5OE  C    C  CR66  0   0.206   3.1062  -1.2333  -0.1212
 5OE  N1   N  N     0  -0.500   2.1787  -0.2963   0.1251
 5OE  C3   C  CR6   0   0.578   0.9154  -0.6508   0.0308
 5OE  N    N  N     0  -0.427   0.4600  -1.8843  -0.3064
 5OE  C2   C  CR16  0  -0.012   1.3530  -2.7955  -0.5413
 5OE  N2   N  NH1   0  -0.745  -0.0046   0.3112   0.2824
 5OE  C4   C  CR6   0   0.235  -1.3987   0.2001   0.2656
 5OE  C9   C  CR6   0   0.379  -2.1402   1.2524  -0.3004
 5OE  O    O  O2    0  -0.472  -1.4159   2.2663  -0.8086
 5OE  C10  C  CH3   0  -0.439  -2.0902   3.3847  -1.3516
 5OE  C8   C  CR16  0  -0.502  -3.5266   1.2031  -0.3050
 5OE  C7   C  CR6   0   0.140  -4.2126   0.1130   0.2378
 5OE  C6   C  CR16  0  -0.383  -3.4688  -0.9202   0.8025
 5OE  C5   C  CR16  0  -0.250  -2.0845  -0.8691   0.8241
 5OE  C11  C  CR5   0  -0.126  -5.6720   0.0744   0.2137
 5OE  C13  C  CR15  0  -0.109  -6.5749   1.0736  -0.2052
 5OE  N4   N  N     0  -0.277  -7.8281   0.6824  -0.0807
 5OE  N3   N  NR5   0  -0.267  -7.7655  -0.5502   0.4117
 5OE  C14  C  CH3   0  -0.507  -8.9755  -1.3004   0.6494
 5OE  C12  C  CR15  0   0.012  -6.5035  -0.9607   0.6038
 5OE  H1   H  HCH3  0   0.262   7.7062   3.5624   0.1368
 5OE  H2   H  HCH3  0   0.263   7.6200   3.2555   1.8820
 5OE  H3   H  HCH3  0   0.260   8.4988   2.1379   0.8281
 5OE  H4   H  HCR5  0   0.292   7.2388   0.1042   0.2403
 5OE  H5   H  HCR5  0   0.264   3.3104   1.8143   0.6342
 5OE  H6   H  HCR6  0   0.263   5.8487  -3.8162  -0.7711
 5OE  H7   H  HCR6  0   0.273   3.4708  -4.5300  -0.9671
 5OE  H8   H  HCR6  0   0.285   0.9974  -3.7843  -0.8160
 5OE  H9   H  HNH1  0   0.405   0.3815   1.2353   0.4066
 5OE  H10  H  HCH3  0   0.231  -2.6999   3.1118  -2.2167
 5OE  H11  H  HCH3  0   0.232  -2.7263   3.8759  -0.6109
 5OE  H12  H  HCH3  0   0.264  -1.3199   4.0812  -1.6723
 5OE  H13  H  HCR6  0   0.273  -4.0889   2.0110  -0.7528
 5OE  H14  H  HCR6  0   0.243  -3.9632  -1.7723   1.2498
 5OE  H15  H  HCR6  0   0.266  -1.5332  -1.6743   1.2866
 5OE  H16  H  HCR5  0   0.257  -6.3554   2.0612  -0.5837
 5OE  H17  H  HCH3  0   0.261  -9.4739  -1.5304  -0.2907
 5OE  H18  H  HCH3  0   0.259  -8.7209  -2.2291   1.1516
 5OE  H19  H  HCH3  0   0.263  -9.6508  -0.7299   1.2831
 5OE  H20  H  HCR5  0   0.290  -6.2843  -1.9419   0.9932

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
 5OE  C20  N7   aromatic  1.318  0.020  1.318
 5OE  C20  C18  aromatic  1.414  0.020  1.414
 5OE  C16  N5   aromatic  1.344  0.020  1.344
 5OE  C16  C15  aromatic  1.368  0.020  1.368
 5OE  N7   N6   aromatic  1.332  0.020  1.332
 5OE  N5   C17  aromatic  1.315  0.020  1.315
 5OE  C18  C17  single    1.457  0.020  1.457
 5OE  C18  C19  aromatic  1.387  0.020  1.387
 5OE  C15  C1   aromatic  1.403  0.020  1.403
 5OE  C17  C    aromatic  1.433  0.020  1.433
 5OE  N6   C19  aromatic  1.335  0.020  1.335
 5OE  N6   C21  single    1.443  0.020  1.443
 5OE  C1   C    aromatic  1.406  0.020  1.406
 5OE  C1   C2   aromatic  1.416  0.020  1.416
 5OE  C    N1   aromatic  1.341  0.020  1.341
 5OE  N1   C3   aromatic  1.315  0.020  1.315
 5OE  C2   N    aromatic  1.297  0.020  1.297
 5OE  C3   N    aromatic  1.357  0.020  1.357
 5OE  C3   N2   single    1.355  0.020  1.355
 5OE  C5   C6   aromatic  1.385  0.020  1.385
 5OE  C5   C4   aromatic  1.388  0.020  1.388
 5OE  C6   C7   aromatic  1.393  0.020  1.393
 5OE  N2   C4   single    1.399  0.020  1.399
 5OE  C4   C9   aromatic  1.406  0.020  1.406
 5OE  C12  C11  aromatic  1.384  0.020  1.384
 5OE  C12  N3   aromatic  1.341  0.020  1.341
 5OE  C7   C11  single    1.460  0.020  1.460
 5OE  C7   C8   aromatic  1.398  0.020  1.398
 5OE  C14  N3   single    1.443  0.020  1.443
 5OE  C11  C13  aromatic  1.410  0.020  1.410
 5OE  N3   N4   aromatic  1.329  0.020  1.329
 5OE  C9   C8   aromatic  1.387  0.020  1.387
 5OE  C9   O    single    1.346  0.020  1.346
 5OE  O    C10  single    1.414  0.020  1.414
 5OE  C13  N4   aromatic  1.319  0.020  1.319
 5OE  C21  H1   single    0.970  0.020  1.090
 5OE  C21  H2   single    0.970  0.020  1.090
 5OE  C21  H3   single    0.970  0.020  1.090
 5OE  C19  H4   single    0.930  0.020  1.080
 5OE  C20  H5   single    0.930  0.020  1.080
 5OE  C16  H6   single    0.930  0.020  1.080
 5OE  C15  H7   single    0.930  0.020  1.080
 5OE  C2   H8   single    0.930  0.020  1.080
 5OE  N2   H9   single    0.860  0.020  1.020
 5OE  C10  H10  single    0.970  0.020  1.090
 5OE  C10  H11  single    0.970  0.020  1.090
 5OE  C10  H12  single    0.970  0.020  1.090
 5OE  C8   H13  single    0.930  0.020  1.080
 5OE  C6   H14  single    0.930  0.020  1.080
 5OE  C5   H15  single    0.930  0.020  1.080
 5OE  C13  H16  single    0.930  0.020  1.080
 5OE  C14  H17  single    0.970  0.020  1.090
 5OE  C14  H18  single    0.970  0.020  1.090
 5OE  C14  H19  single    0.970  0.020  1.090
 5OE  C12  H20  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
 5OE  H3   C21  H2   109.02  3.000
 5OE  H3   C21  H1   109.05  3.000
 5OE  H2   C21  H1   109.23  3.000
 5OE  H3   C21  N6   108.98  3.000
 5OE  H2   C21  N6   110.09  3.000
 5OE  H1   C21  N6   110.45  3.000
 5OE  N7   N6   C19  112.52  3.000
 5OE  C19  N6   C21  127.41  3.000
 5OE  N7   N6   C21  120.07  3.000
 5OE  H4   C19  C18  130.85  3.000
 5OE  H4   C19  N6   122.00  3.000
 5OE  C18  C19  N6   107.15  3.000
 5OE  C20  N7   N6   105.57  3.000
 5OE  H5   C20  C18  128.23  3.000
 5OE  H5   C20  N7   120.39  3.000
 5OE  C18  C20  N7   111.37  3.000
 5OE  C17  C18  C20  132.40  3.000
 5OE  C17  C18  C19  124.22  3.000
 5OE  C20  C18  C19  103.39  3.000
 5OE  C    C17  N5   120.55  3.000
 5OE  C    C17  C18  122.92  3.000
 5OE  N5   C17  C18  116.52  3.000
 5OE  C16  N5   C17  121.20  3.000
 5OE  H6   C16  C15  120.87  3.000
 5OE  H6   C16  N5   115.94  3.000
 5OE  C15  C16  N5   123.19  3.000
 5OE  H7   C15  C1   121.02  3.000
 5OE  H7   C15  C16  121.60  3.000
 5OE  C1   C15  C16  117.38  3.000
 5OE  C2   C1   C    115.38  3.000
 5OE  C2   C1   C15  124.35  3.000
 5OE  C    C1   C15  120.27  3.000
 5OE  N1   C    C1   121.37  3.000
 5OE  N1   C    C17  121.22  3.000
 5OE  C1   C    C17  117.40  3.000
 5OE  C3   N1   C    117.56  3.000
 5OE  N2   C3   N    117.62  3.000
 5OE  N2   C3   N1   116.58  3.000
 5OE  N    C3   N1   125.80  3.000
 5OE  C2   N    C3   116.89  3.000
 5OE  H8   C2   N    117.38  3.000
 5OE  H8   C2   C1   119.62  3.000
 5OE  N    C2   C1   122.99  3.000
 5OE  H9   N2   C4   117.09  3.000
 5OE  H9   N2   C3   114.41  3.000
 5OE  C4   N2   C3   128.20  3.000
 5OE  C5   C4   C9   118.56  3.000
 5OE  C9   C4   N2   118.10  3.000
 5OE  C5   C4   N2   123.29  3.000
 5OE  C8   C9   O    124.29  3.000
 5OE  O    C9   C4   115.60  3.000
 5OE  C8   C9   C4   120.11  3.000
 5OE  C10  O    C9   118.96  3.000
 5OE  H12  C10  H11  108.93  3.000
 5OE  H12  C10  H10  108.77  3.000
 5OE  H11  C10  H10  108.90  3.000
 5OE  H12  C10  O    106.39  3.000
 5OE  H11  C10  O    111.89  3.000
 5OE  H10  C10  O    111.86  3.000
 5OE  H13  C8   C7   119.23  3.000
 5OE  H13  C8   C9   119.64  3.000
 5OE  C7   C8   C9   121.12  3.000
 5OE  C11  C7   C6   121.39  3.000
 5OE  C11  C7   C8   120.31  3.000
 5OE  C6   C7   C8   118.29  3.000
 5OE  H14  C6   C5   118.63  3.000
 5OE  H14  C6   C7   120.52  3.000
 5OE  C5   C6   C7   120.84  3.000
 5OE  H15  C5   C6   119.30  3.000
 5OE  H15  C5   C4   119.64  3.000
 5OE  C6   C5   C4   121.06  3.000
 5OE  C12  C11  C13  103.24  3.000
 5OE  C13  C11  C7   128.76  3.000
 5OE  C12  C11  C7   128.00  3.000
 5OE  H16  C13  N4   119.83  3.000
 5OE  H16  C13  C11  128.44  3.000
 5OE  N4   C13  C11  111.72  3.000
 5OE  N3   N4   C13  105.39  3.000
 5OE  C12  N3   C14  127.32  3.000
 5OE  C14  N3   N4   120.24  3.000
 5OE  C12  N3   N4   112.42  3.000
 5OE  H19  C14  H18  108.95  3.000
 5OE  H19  C14  H17  109.24  3.000
 5OE  H18  C14  H17  109.02  3.000
 5OE  H19  C14  N3   110.11  3.000
 5OE  H18  C14  N3   108.92  3.000
 5OE  H17  C14  N3   110.57  3.000
 5OE  H20  C12  N3   121.45  3.000
 5OE  H20  C12  C11  131.33  3.000
 5OE  N3   C12  C11  107.22  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
 5OE  CONST_01  C18  C20  N7   N6      0.00   0.0  0
 5OE  CONST_02  C20  C18  C19  N6      0.00   0.0  0
 5OE  CONST_03  C17  C18  C19  N6    180.00   0.0  0
 5OE  CONST_04  N7   C20  C18  C19     0.00   0.0  0
 5OE  CONST_05  N5   C17  C18  C19     0.00   0.0  0
 5OE  CONST_06  C    C17  C18  C19   180.00   0.0  0
 5OE  CONST_07  C20  N7   N6   C19     0.00   0.0  0
 5OE  CONST_08  C17  C18  C20  N7    180.00   0.0  0
 5OE  CONST_09  C18  C19  N6   N7      0.00   0.0  0
 5OE  CONST_10  N5   C17  C18  C20   180.00   0.0  0
 5OE  CONST_11  C    C17  C18  C20     0.00   0.0  0
 5OE  CONST_12  C16  N5   C17  C18   180.00   0.0  0
 5OE  CONST_13  C1   C    C17  C18   180.00   0.0  0
 5OE  CONST_14  N1   C    C17  C18     0.00   0.0  0
 5OE  CONST_15  C15  C16  N5   C17     0.00   0.0  0
 5OE  CONST_16  C15  C1   C    C17     0.00   0.0  0
 5OE  CONST_17  C2   C1   C    C17   180.00   0.0  0
 5OE  CONST_18  C3   N1   C    C17   180.00   0.0  0
 5OE  CONST_19  C1   C15  C16  N5      0.00   0.0  0
 5OE  CONST_20  C1   C    C17  N5      0.00   0.0  0
 5OE  CONST_21  N1   C    C17  N5    180.00   0.0  0
 5OE  CONST_22  C    C17  N5   C16     0.00   0.0  0
 5OE  CONST_23  C    C1   C15  C16     0.00   0.0  0
 5OE  CONST_24  C2   C1   C15  C16   180.00   0.0  0
 5OE  CONST_25  N1   C    C1   C15   180.00   0.0  0
 5OE  CONST_26  N    C2   C1   C15   180.00   0.0  0
 5OE  CONST_27  C3   N1   C    C1      0.00   0.0  0
 5OE  CONST_28  C3   N    C2   C1      0.00   0.0  0
 5OE  CONST_29  N    C2   C1   C       0.00   0.0  0
 5OE  CONST_30  N    C3   N1   C       0.00   0.0  0
 5OE  CONST_31  C2   C1   C    N1      0.00   0.0  0
 5OE  CONST_32  C2   N    C3   N1      0.00   0.0  0
 5OE  CONST_33  C7   C6   C5   C4      0.00   0.0  0
 5OE  CONST_34  C7   C8   C9   C4      0.00   0.0  0
 5OE  CONST_35  C6   C5   C4   C9      0.00   0.0  0
 5OE  CONST_36  C6   C7   C8   C9      0.00   0.0  0
 5OE  CONST_37  C11  C7   C8   C9    180.00   0.0  0
 5OE  CONST_38  C5   C6   C7   C8      0.00   0.0  0
 5OE  CONST_39  C12  C11  C7   C8    180.00   0.0  0
 5OE  CONST_40  C13  C11  C7   C8      0.00   0.0  0
 5OE  CONST_41  C5   C4   C9   C8      0.00   0.0  0
 5OE  CONST_42  N3   C12  C11  C7    180.00   0.0  0
 5OE  CONST_43  N4   C13  C11  C7    180.00   0.0  0
 5OE  CONST_44  C12  C11  C7   C6      0.00   0.0  0
 5OE  CONST_45  C13  C11  C7   C6    180.00   0.0  0
 5OE  CONST_46  C11  C7   C6   C5    180.00   0.0  0
 5OE  CONST_47  N4   N3   C12  C11     0.00   0.0  0
 5OE  CONST_48  N3   N4   C13  C11     0.00   0.0  0
 5OE  CONST_49  N3   C12  C11  C13     0.00   0.0  0
 5OE  CONST_50  C12  N3   N4   C13     0.00   0.0  0
 5OE  CONST_51  C12  C11  C13  N4      0.00   0.0  0
 5OE  CONST_52  C20  N7   N6   C21   180.00   0.0  0
 5OE  CONST_53  C18  C19  N6   C21   180.00   0.0  0
 5OE  CONST_54  N2   C3   N1   C     180.00   0.0  0
 5OE  CONST_55  N2   C3   N    C2    180.00   0.0  0
 5OE  CONST_56  C6   C5   C4   N2    180.00   0.0  0
 5OE  CONST_57  C8   C9   C4   N2    180.00   0.0  0
 5OE  CONST_58  C5   C4   C9   O     180.00   0.0  0
 5OE  CONST_59  C7   C8   C9   O     180.00   0.0  0
 5OE  CONST_60  C14  N3   C12  C11   180.00   0.0  0
 5OE  CONST_61  C14  N3   N4   C13   180.00   0.0  0
 5OE  CONST_62  H5   C20  N7   N6    180.00   0.0  0
 5OE  CONST_63  H4   C19  N6   N7    180.00   0.0  0
 5OE  CONST_64  H6   C16  N5   C17   180.00   0.0  0
 5OE  CONST_65  H7   C15  C16  N5    180.00   0.0  0
 5OE  CONST_66  H8   C2   C1   C15     0.00   0.0  0
 5OE  CONST_67  H14  C6   C5   C4    180.00   0.0  0
 5OE  CONST_68  H13  C8   C9   C4    180.00   0.0  0
 5OE  CONST_69  H15  C5   C4   C9    180.00   0.0  0
 5OE  CONST_70  H20  C12  C11  C7      0.00   0.0  0
 5OE  CONST_71  H16  C13  C11  C7      0.00   0.0  0
 5OE  Var_01    C4   N2   C3   N1   -179.31  30.0  2
 5OE  Var_02    C5   C4   N2   C3     43.54  30.0  2
 5OE  Var_03    C8   C9   O    C10     2.04  30.0  3
 5OE  Var_04    H1   C21  N6   C19   114.57  30.0  2
 5OE  Var_05    H17  C14  N3   N4     66.49  30.0  2
 5OE  Var_06    H10  C10  O    C9    -62.92  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
 5OE  plan-1  C21  0.020
 5OE  plan-1  N6   0.020
 5OE  plan-1  C19  0.020
 5OE  plan-1  N7   0.020
 5OE  plan-1  C20  0.020
 5OE  plan-1  C18  0.020
 5OE  plan-1  C17  0.020
 5OE  plan-1  H4   0.020
 5OE  plan-1  H5   0.020
 5OE  plan-2  C7   0.020
 5OE  plan-2  C11  0.020
 5OE  plan-2  C13  0.020
 5OE  plan-2  N4   0.020
 5OE  plan-2  N3   0.020
 5OE  plan-2  C14  0.020
 5OE  plan-2  C12  0.020
 5OE  plan-2  H16  0.020
 5OE  plan-2  H20  0.020
 5OE  plan-3  N2   0.020
 5OE  plan-3  C4   0.020
 5OE  plan-3  C9   0.020
 5OE  plan-3  O    0.020
 5OE  plan-3  C8   0.020
 5OE  plan-3  C7   0.020
 5OE  plan-3  C6   0.020
 5OE  plan-3  C5   0.020
 5OE  plan-3  C11  0.020
 5OE  plan-3  H13  0.020
 5OE  plan-3  H14  0.020
 5OE  plan-3  H15  0.020
 5OE  plan-4  C18  0.020
 5OE  plan-4  C17  0.020
 5OE  plan-4  N5   0.020
 5OE  plan-4  C16  0.020
 5OE  plan-4  C15  0.020
 5OE  plan-4  C1   0.020
 5OE  plan-4  C    0.020
 5OE  plan-4  N1   0.020
 5OE  plan-4  C3   0.020
 5OE  plan-4  N    0.020
 5OE  plan-4  C2   0.020
 5OE  plan-4  N2   0.020
 5OE  plan-4  H6   0.020
 5OE  plan-4  H7   0.020
 5OE  plan-4  H8   0.020

