# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 16:35:06 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: ~{N}-(2,4-dimethoxyphenyl)-8-(1-methylpyrazol-4-yl)pyrido[3,4-d]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Nc2ncc3ccnc(c4cnn(C)c4)c3n2)c(OC)c1
#
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
 5O7  5O7  ~{N}-(2,4-dimethoxyphenyl)-8-(1-methylpyrazol-4-yl)pyrido[3,4-d]pyrimidin-2-amine  ligand  45  27  .  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_5O7
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
 5O7  C10  C  CH3   0  -0.507   6.4627   2.9004   0.9200
 5O7  C13  C  CR16  0  -0.416  -4.5802  -1.0069   0.9565
 5O7  C14  C  CR6   0   0.398  -5.3371  -0.0375   0.3106
 5O7  C17  C  CH3   0  -0.438  -3.3518   3.2056  -1.4790
 5O7  C18  C  CH3   0  -0.436  -7.3834  -1.1130   0.8385
 5O7  O1   O  O2    0  -0.473  -6.6810  -0.0493   0.2273
 5O7  C12  C  CR16  0  -0.257  -3.1956  -0.8808   0.9807
 5O7  C15  C  CR16  0  -0.488  -4.7047   1.0454  -0.3065
 5O7  C16  C  CR6   0   0.363  -3.3227   1.1467  -0.2955
 5O7  O    O  O2    0  -0.465  -2.6361   2.1487  -0.8692
 5O7  C11  C  CR6   0   0.227  -2.5479   0.1682   0.3549
 5O7  C    C  CR6   0   0.574  -0.2216  -0.6066   0.0590
 5O7  N1   N  N     0  -0.424  -0.6658  -1.8327  -0.3229
 5O7  C3   C  CR16  0  -0.015   0.2357  -2.7204  -0.6071
 5O7  C2   C  CR66  0   0.064   1.6261  -2.4587  -0.5377
 5O7  C4   C  CR16  0  -0.364   2.6244  -3.4009  -0.8283
 5O7  C5   C  CR16  0  -0.103   3.9255  -2.9921  -0.7232
 5O7  N2   N  N     0  -0.429   4.2777  -1.7454  -0.3658
 5O7  C6   C  CR6   0   0.140   3.3705  -0.8344  -0.0875
 5O7  C1   C  CR66  0   0.207   1.9746  -1.1517  -0.1528
 5O7  N    N  N     0  -0.502   1.0389  -0.2378   0.1446
 5O7  C7   C  CR5   0  -0.159   3.8662   0.4857   0.2809
 5O7  C9   C  CR15  0  -0.109   3.2083   1.6909   0.6169
 5O7  N4   N  N     0  -0.281   4.0707   2.6525   0.8781
 5O7  N3   N  NR5   0  -0.264   5.2752   2.1043   0.7231
 5O7  C8   C  CR15  0   0.066   5.2100   0.8189   0.3668
 5O7  H1   H  HCH3  0   0.263   6.4513   3.3493   1.9108
 5O7  H2   H  HCH3  0   0.260   7.3356   2.2606   0.8310
 5O7  H3   H  HCH3  0   0.262   6.5218   3.6877   0.1708
 5O7  H4   H  HCR6  0   0.277  -5.0349  -1.8521   1.4528
 5O7  H5   H  HCH3  0   0.231  -3.9474   2.8583  -2.3270
 5O7  H6   H  HCH3  0   0.232  -4.0094   3.7132  -0.7689
 5O7  H7   H  HCH3  0   0.264  -2.6083   3.9119  -1.8390
 5O7  H8   H  HCH3  0   0.228  -7.1070  -2.0823   0.4156
 5O7  H9   H  HCH3  0   0.228  -7.2225  -1.1409   1.9192
 5O7  H10  H  HCH3  0   0.260  -8.4388  -0.9372   0.6463
 5O7  H11  H  HCR6  0   0.266  -2.6137  -1.6278   1.5021
 5O7  H12  H  HCR6  0   0.287  -5.3174   1.7881  -0.8005
 5O7  H13  H  HNH1  0   0.402  -0.7855   1.2431   0.5588
 5O7  H14  H  HCR6  0   0.284  -0.1105  -3.7025  -0.9164
 5O7  H15  H  HCR6  0   0.272   2.3691  -4.4101  -1.1240
 5O7  H16  H  HCR6  0   0.262   4.7411  -3.6736  -0.9319
 5O7  H17  H  HCR5  0   0.264   2.1501   1.8780   0.6747
 5O7  H18  H  HCR5  0   0.292   6.0946   0.2275   0.1991
 5O7  N5   N  NH1   0  -0.741  -1.1527   0.3209   0.3774

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
 5O7  C5   N2   aromatic  1.344  0.020  1.344
 5O7  C5   C4   aromatic  1.368  0.020  1.368
 5O7  C9   N4   aromatic  1.318  0.020  1.318
 5O7  C9   C7   aromatic  1.414  0.020  1.414
 5O7  N2   C6   aromatic  1.315  0.020  1.315
 5O7  N4   N3   aromatic  1.332  0.020  1.332
 5O7  C4   C2   aromatic  1.403  0.020  1.403
 5O7  C6   C7   single    1.457  0.020  1.457
 5O7  C6   C1   aromatic  1.433  0.020  1.433
 5O7  C7   C8   aromatic  1.387  0.020  1.387
 5O7  N3   C8   aromatic  1.335  0.020  1.335
 5O7  N3   C10  single    1.443  0.020  1.443
 5O7  C2   C1   aromatic  1.406  0.020  1.406
 5O7  C2   C3   aromatic  1.417  0.020  1.417
 5O7  C1   N    aromatic  1.341  0.020  1.341
 5O7  C3   N1   aromatic  1.297  0.020  1.297
 5O7  N    C    aromatic  1.316  0.020  1.316
 5O7  N1   C    aromatic  1.359  0.020  1.359
 5O7  C    N5   single    1.352  0.020  1.352
 5O7  C12  C13  aromatic  1.391  0.020  1.391
 5O7  C12  C11  aromatic  1.383  0.020  1.383
 5O7  C13  C14  aromatic  1.389  0.020  1.389
 5O7  N5   C11  single    1.404  0.020  1.404
 5O7  C11  C16  aromatic  1.407  0.020  1.407
 5O7  C18  O1   single    1.414  0.020  1.414
 5O7  C14  O1   single    1.347  0.020  1.347
 5O7  C14  C15  aromatic  1.398  0.020  1.398
 5O7  C16  C15  aromatic  1.386  0.020  1.386
 5O7  C16  O    single    1.343  0.020  1.343
 5O7  O    C17  single    1.415  0.020  1.415
 5O7  C10  H1   single    0.970  0.020  1.090
 5O7  C10  H2   single    0.970  0.020  1.090
 5O7  C10  H3   single    0.970  0.020  1.090
 5O7  C13  H4   single    0.930  0.020  1.080
 5O7  C17  H5   single    0.970  0.020  1.090
 5O7  C17  H6   single    0.970  0.020  1.090
 5O7  C17  H7   single    0.970  0.020  1.090
 5O7  C18  H8   single    0.970  0.020  1.090
 5O7  C18  H9   single    0.970  0.020  1.090
 5O7  C18  H10  single    0.970  0.020  1.090
 5O7  C12  H11  single    0.930  0.020  1.080
 5O7  C15  H12  single    0.930  0.020  1.080
 5O7  N5   H13  single    0.860  0.020  1.020
 5O7  C3   H14  single    0.930  0.020  1.080
 5O7  C4   H15  single    0.930  0.020  1.080
 5O7  C5   H16  single    0.930  0.020  1.080
 5O7  C9   H17  single    0.930  0.020  1.080
 5O7  C8   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
 5O7  H3   C10  H2   109.03  3.000
 5O7  H3   C10  H1   109.21  3.000
 5O7  H2   C10  H1   109.05  3.000
 5O7  H3   C10  N3   110.47  3.000
 5O7  H2   C10  N3   108.98  3.000
 5O7  H1   C10  N3   110.08  3.000
 5O7  H4   C13  C12  118.81  3.000
 5O7  H4   C13  C14  122.01  3.000
 5O7  C12  C13  C14  119.17  3.000
 5O7  C15  C14  O1   115.54  3.000
 5O7  C15  C14  C13  119.96  3.000
 5O7  O1   C14  C13  124.50  3.000
 5O7  H7   C17  H6   108.97  3.000
 5O7  H7   C17  H5   108.80  3.000
 5O7  H6   C17  H5   108.90  3.000
 5O7  H7   C17  O    106.39  3.000
 5O7  H6   C17  O    111.80  3.000
 5O7  H5   C17  O    111.89  3.000
 5O7  H10  C18  H9   108.77  3.000
 5O7  H10  C18  H8   108.69  3.000
 5O7  H9   C18  H8   108.82  3.000
 5O7  H10  C18  O1   106.52  3.000
 5O7  H9   C18  O1   111.93  3.000
 5O7  H8   C18  O1   111.99  3.000
 5O7  C18  O1   C14  118.41  3.000
 5O7  H11  C12  C11  119.37  3.000
 5O7  H11  C12  C13  118.80  3.000
 5O7  C11  C12  C13  121.83  3.000
 5O7  H12  C15  C16  121.20  3.000
 5O7  H12  C15  C14  118.50  3.000
 5O7  C16  C15  C14  120.29  3.000
 5O7  C11  C16  O    115.76  3.000
 5O7  O    C16  C15  124.12  3.000
 5O7  C11  C16  C15  120.12  3.000
 5O7  C16  O    C17  118.86  3.000
 5O7  N5   C11  C16  118.62  3.000
 5O7  C16  C11  C12  118.61  3.000
 5O7  N5   C11  C12  122.75  3.000
 5O7  N    C    N1   125.75  3.000
 5O7  N1   C    N5   117.39  3.000
 5O7  N    C    N5   116.86  3.000
 5O7  C3   N1   C    116.87  3.000
 5O7  H14  C3   C2   119.59  3.000
 5O7  H14  C3   N1   117.37  3.000
 5O7  C2   C3   N1   123.04  3.000
 5O7  C1   C2   C4   120.30  3.000
 5O7  C1   C2   C3   115.36  3.000
 5O7  C4   C2   C3   124.35  3.000
 5O7  H15  C4   C5   121.61  3.000
 5O7  H15  C4   C2   120.99  3.000
 5O7  C5   C4   C2   117.39  3.000
 5O7  H16  C5   N2   115.95  3.000
 5O7  H16  C5   C4   120.89  3.000
 5O7  N2   C5   C4   123.16  3.000
 5O7  C6   N2   C5   121.19  3.000
 5O7  C7   C6   C1   122.91  3.000
 5O7  C1   C6   N2   120.59  3.000
 5O7  C7   C6   N2   116.50  3.000
 5O7  N    C1   C6   121.24  3.000
 5O7  N    C1   C2   121.40  3.000
 5O7  C6   C1   C2   117.36  3.000
 5O7  C1   N    C    117.56  3.000
 5O7  C8   C7   C9   103.38  3.000
 5O7  C8   C7   C6   124.24  3.000
 5O7  C9   C7   C6   132.38  3.000
 5O7  H17  C9   N4   120.40  3.000
 5O7  H17  C9   C7   128.22  3.000
 5O7  N4   C9   C7   111.38  3.000
 5O7  N3   N4   C9   105.56  3.000
 5O7  C8   N3   N4   112.51  3.000
 5O7  C8   N3   C10  127.41  3.000
 5O7  N4   N3   C10  120.07  3.000
 5O7  H18  C8   N3   121.99  3.000
 5O7  H18  C8   C7   130.84  3.000
 5O7  N3   C8   C7   107.16  3.000
 5O7  H13  N5   C    114.75  3.000
 5O7  H13  N5   C11  117.65  3.000
 5O7  C    N5   C11  127.30  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
 5O7  CONST_01  C16  C11  C12  C13     0.00   0.0  0
 5O7  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 5O7  CONST_03  C11  C12  C13  C14     0.00   0.0  0
 5O7  CONST_04  C11  C16  C15  C14     0.00   0.0  0
 5O7  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 5O7  CONST_06  C15  C16  C11  C12     0.00   0.0  0
 5O7  CONST_07  C6   C1   N    C     180.00   0.0  0
 5O7  CONST_08  C2   C1   N    C       0.00   0.0  0
 5O7  CONST_09  C2   C3   N1   C       0.00   0.0  0
 5O7  CONST_10  C4   C2   C3   N1    180.00   0.0  0
 5O7  CONST_11  C1   C2   C3   N1      0.00   0.0  0
 5O7  CONST_12  C1   N    C    N1      0.00   0.0  0
 5O7  CONST_13  C5   C4   C2   C3    180.00   0.0  0
 5O7  CONST_14  C6   C1   C2   C3    180.00   0.0  0
 5O7  CONST_15  N    C1   C2   C3      0.00   0.0  0
 5O7  CONST_16  N    C    N1   C3      0.00   0.0  0
 5O7  CONST_17  N2   C5   C4   C2      0.00   0.0  0
 5O7  CONST_18  N2   C6   C1   C2      0.00   0.0  0
 5O7  CONST_19  C7   C6   C1   C2    180.00   0.0  0
 5O7  CONST_20  C6   N2   C5   C4      0.00   0.0  0
 5O7  CONST_21  C6   C1   C2   C4      0.00   0.0  0
 5O7  CONST_22  N    C1   C2   C4    180.00   0.0  0
 5O7  CONST_23  C7   C6   N2   C5    180.00   0.0  0
 5O7  CONST_24  C1   C6   N2   C5      0.00   0.0  0
 5O7  CONST_25  C1   C2   C4   C5      0.00   0.0  0
 5O7  CONST_26  C9   C7   C6   N2    180.00   0.0  0
 5O7  CONST_27  C8   C7   C6   N2      0.00   0.0  0
 5O7  CONST_28  N    C1   C6   N2    180.00   0.0  0
 5O7  CONST_29  N4   C9   C7   C6    180.00   0.0  0
 5O7  CONST_30  N3   C8   C7   C6    180.00   0.0  0
 5O7  CONST_31  C9   C7   C6   C1      0.00   0.0  0
 5O7  CONST_32  C8   C7   C6   C1    180.00   0.0  0
 5O7  CONST_33  C7   C6   C1   N       0.00   0.0  0
 5O7  CONST_34  N3   N4   C9   C7      0.00   0.0  0
 5O7  CONST_35  N4   N3   C8   C7      0.00   0.0  0
 5O7  CONST_36  C8   N3   N4   C9      0.00   0.0  0
 5O7  CONST_37  N3   C8   C7   C9      0.00   0.0  0
 5O7  CONST_38  C8   C7   C9   N4      0.00   0.0  0
 5O7  CONST_39  C9   N4   N3   C10   180.00   0.0  0
 5O7  CONST_40  C7   C8   N3   C10   180.00   0.0  0
 5O7  CONST_41  N5   C11  C12  C13   180.00   0.0  0
 5O7  CONST_42  O    C16  C15  C14   180.00   0.0  0
 5O7  CONST_43  C12  C13  C14  O1    180.00   0.0  0
 5O7  CONST_44  C16  C15  C14  O1    180.00   0.0  0
 5O7  CONST_45  O    C16  C11  C12   180.00   0.0  0
 5O7  CONST_46  N5   C11  C16  C15   180.00   0.0  0
 5O7  CONST_47  C1   N    C    N5    180.00   0.0  0
 5O7  CONST_48  C3   N1   C    N5    180.00   0.0  0
 5O7  CONST_49  H12  C15  C14  C13   180.00   0.0  0
 5O7  CONST_50  H11  C12  C13  C14   180.00   0.0  0
 5O7  CONST_51  H4   C13  C14  C15   180.00   0.0  0
 5O7  CONST_52  H14  C3   N1   C     180.00   0.0  0
 5O7  CONST_53  H15  C4   C2   C3      0.00   0.0  0
 5O7  CONST_54  H16  C5   C4   C2    180.00   0.0  0
 5O7  CONST_55  H17  C9   C7   C6      0.00   0.0  0
 5O7  CONST_56  H18  C8   C7   C6      0.00   0.0  0
 5O7  Var_01    C    N5   C11  C12    51.21  30.0  1
 5O7  Var_02    N    C    N5   C11   179.56  30.0  1
 5O7  Var_03    C11  C16  O    C17  -176.64  30.0  2
 5O7  Var_04    C15  C14  O1   C18  -179.59  30.0  2
 5O7  Var_05    H1   C10  N3   N4     55.77  30.0  2
 5O7  Var_06    H8   C18  O1   C14   -60.73  30.0  3
 5O7  Var_07    H5   C17  O    C16   -63.38  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
 5O7  plan-1  C10  0.020
 5O7  plan-1  C6   0.020
 5O7  plan-1  C7   0.020
 5O7  plan-1  C9   0.020
 5O7  plan-1  N4   0.020
 5O7  plan-1  N3   0.020
 5O7  plan-1  C8   0.020
 5O7  plan-1  H17  0.020
 5O7  plan-1  H18  0.020
 5O7  plan-2  C13  0.020
 5O7  plan-2  C14  0.020
 5O7  plan-2  O1   0.020
 5O7  plan-2  C12  0.020
 5O7  plan-2  C15  0.020
 5O7  plan-2  C16  0.020
 5O7  plan-2  O    0.020
 5O7  plan-2  C11  0.020
 5O7  plan-2  H4   0.020
 5O7  plan-2  H11  0.020
 5O7  plan-2  H12  0.020
 5O7  plan-2  N5   0.020
 5O7  plan-3  C    0.020
 5O7  plan-3  N1   0.020
 5O7  plan-3  C3   0.020
 5O7  plan-3  C2   0.020
 5O7  plan-3  C4   0.020
 5O7  plan-3  C5   0.020
 5O7  plan-3  N2   0.020
 5O7  plan-3  C6   0.020
 5O7  plan-3  C1   0.020
 5O7  plan-3  N    0.020
 5O7  plan-3  C7   0.020
 5O7  plan-3  H14  0.020
 5O7  plan-3  H15  0.020
 5O7  plan-3  H16  0.020
 5O7  plan-3  N5   0.020

