# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 04:14:46 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: ~{N}8-(2,2-dimethylpropyl)-~{N}2-[2-methoxy-4-(1-methylpyrazol-4-yl)phenyl]pyrido[3,4-d]pyrimidine-2,8-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1Nc2ncc3ccnc(NCC(C)(C)C)c3n2)c4cnn(C)c4
#
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
 5NW  5NW  ~{N}8-(2,2-dimethylpropyl)-~{N}2-[2-methoxy-4-(1-methylpyrazol-4-yl)phenyl]pyrido[3,4-d]pyrimidine-2,8-diamine  ligand  58  31  .  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_5NW
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
 5NW  C1   C  CR66  0   0.092  -2.6544   2.9411   0.1900
 5NW  N5   N  N     0  -0.472  -5.3231   2.1650   0.3169
 5NW  C6   C  CR16  0  -0.347   3.6437   0.9867  -0.6296
 5NW  C7   C  CR6   0   0.133   4.2893  -0.1902  -0.2723
 5NW  C8   C  CR16  0  -0.472   3.5013  -1.2903   0.0823
 5NW  C9   C  CR6   0   0.368   2.1205  -1.2081   0.0894
 5NW  C10  C  CH3   0  -0.406   1.8545  -3.4895   0.7081
 5NW  C11  C  CR5   0  -0.127   5.7452  -0.2913  -0.2607
 5NW  C12  C  CR15  0  -0.084   6.5509  -1.4487  -0.2587
 5NW  C13  C  CR15  0   0.038   6.6693   0.7363  -0.2364
 5NW  C15  C  CR16  0  -0.389  -3.6719   3.9118   0.3525
 5NW  C18  C  CH2   0  -0.189  -6.0854  -0.5318   0.1707
 5NW  C19  C  CT    0  -0.167  -6.2385  -1.9934  -0.2632
 5NW  C20  C  CH3   0  -0.608  -5.8674  -2.1594  -1.7374
 5NW  C21  C  CH3   0  -0.621  -5.3707  -2.9150   0.5973
 5NW  C22  C  CH3   0  -0.612  -7.7066  -2.3708  -0.0629
 5NW  C17  C  CR6   0   0.485  -4.4011   1.2475   0.1520
 5NW  C16  C  CR16  0  -0.067  -4.9566   3.4644   0.4095
 5NW  C    C  CR66  0   0.138  -2.9961   1.5892   0.0892
 5NW  N1   N  N     0  -0.507  -2.0884   0.6197  -0.0540
 5NW  C3   C  CR6   0   0.594  -0.8217   0.9871  -0.1029
 5NW  N    N  N     0  -0.441  -0.3774   2.2582  -0.0305
 5NW  C2   C  CR16  0   0.010  -1.2711   3.1972   0.1140
 5NW  N2   N  NH1   0  -0.756   0.0801  -0.0214  -0.2300
 5NW  C4   C  CR6   0   0.250   1.4726  -0.0021  -0.2514
 5NW  C5   C  CR16  0  -0.271   2.2591   1.0816  -0.6200
 5NW  N4   N  NR5   0  -0.267   7.8882   0.1747  -0.2206
 5NW  C14  C  CH3   0  -0.471   9.1626   0.8481  -0.2169
 5NW  N3   N  N     0  -0.263   7.8349  -1.1519  -0.2368
 5NW  H1   H  HCR6  0   0.221   4.2134   1.8522  -0.9415
 5NW  H2   H  HCR6  0   0.254   3.9843  -2.2107   0.3818
 5NW  H3   H  HCH3  0   0.255   1.0192  -4.1582   0.8956
 5NW  H4   H  HCH3  0   0.220   2.4409  -3.8827  -0.1260
 5NW  H5   H  HCH3  0   0.219   2.4843  -3.4596   1.6005
 5NW  H6   H  HCR5  0   0.229   6.2404  -2.4825  -0.2810
 5NW  H7   H  HCR5  0   0.253   6.5424   1.8061  -0.2123
 5NW  H8   H  HCR6  0   0.231  -3.4371   4.9640   0.4325
 5NW  H9   H  HCH2  0   0.229  -6.7478   0.0955  -0.4309
 5NW  H10  H  HCH2  0   0.219  -6.4208  -0.4230   1.2104
 5NW  H11  H  HCH3  0   0.216  -4.8210  -1.9173  -1.9270
 5NW  H12  H  HCH3  0   0.220  -6.0258  -3.1897  -2.0618
 5NW  H13  H  HCH3  0   0.219  -6.4750  -1.5160  -2.3765
 5NW  H14  H  HCH3  0   0.224  -5.5720  -2.7780   1.6613
 5NW  H15  H  HCH3  0   0.228  -5.5681  -3.9605   0.3559
 5NW  H16  H  HCH3  0   0.208  -4.3004  -2.7621   0.4414
 5NW  H17  H  HCH3  0   0.219  -8.3677  -1.7439  -0.6639
 5NW  H18  H  HCH3  0   0.223  -7.8828  -3.4072  -0.3537
 5NW  H19  H  HCH3  0   0.219  -8.0096  -2.2665   0.9811
 5NW  H20  H  HNH1  0   0.381  -3.9682  -0.6962   0.0206
 5NW  H21  H  HCR6  0   0.237  -5.7724   4.1651   0.5409
 5NW  H22  H  HCR6  0   0.252  -0.9044   4.2174   0.1751
 5NW  H23  H  HNH1  0   0.394  -0.3350  -0.9384  -0.1732
 5NW  H24  H  HCR6  0   0.265   1.7932   2.0107  -0.9044
 5NW  H25  H  HCH3  0   0.251   9.7861   0.4651   0.5872
 5NW  H26  H  HCH3  0   0.250   9.6772   0.7103  -1.1659
 5NW  H27  H  HCH3  0   0.237   9.0040   1.9099  -0.0563
 5NW  N6   N  NH1   0  -0.666  -4.7365  -0.0459   0.0264
 5NW  O    O  O2    0  -0.480   1.2990  -2.2265   0.4126

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
 5NW  C22  C19  single    1.529  0.020  1.529
 5NW  C20  C19  single    1.529  0.020  1.529
 5NW  C16  N5   aromatic  1.353  0.020  1.353
 5NW  C16  C15  aromatic  1.362  0.020  1.362
 5NW  N5   C17  aromatic  1.311  0.020  1.311
 5NW  C19  C18  single    1.532  0.020  1.532
 5NW  C19  C21  single    1.531  0.020  1.531
 5NW  C18  N6   single    1.441  0.020  1.441
 5NW  C15  C1   aromatic  1.416  0.020  1.416
 5NW  C17  N6   single    1.342  0.020  1.342
 5NW  C17  C    aromatic  1.447  0.020  1.447
 5NW  C1   C    aromatic  1.398  0.020  1.398
 5NW  C1   C2   aromatic  1.409  0.020  1.409
 5NW  C    N1   aromatic  1.336  0.020  1.336
 5NW  C2   N    aromatic  1.304  0.020  1.304
 5NW  N1   C3   aromatic  1.320  0.020  1.320
 5NW  N    C3   aromatic  1.348  0.020  1.348
 5NW  C3   N2   single    1.359  0.020  1.359
 5NW  C5   C6   aromatic  1.388  0.020  1.388
 5NW  C5   C4   aromatic  1.389  0.020  1.389
 5NW  C6   C7   aromatic  1.389  0.020  1.389
 5NW  N2   C4   single    1.393  0.020  1.393
 5NW  C4   C9   aromatic  1.411  0.020  1.411
 5NW  C13  C11  aromatic  1.382  0.020  1.382
 5NW  C13  N4   aromatic  1.342  0.020  1.342
 5NW  C7   C11  single    1.459  0.020  1.459
 5NW  C7   C8   aromatic  1.399  0.020  1.399
 5NW  C14  N4   single    1.441  0.020  1.441
 5NW  C11  C12  aromatic  1.410  0.020  1.410
 5NW  N4   N3   aromatic  1.328  0.020  1.328
 5NW  C9   C8   aromatic  1.383  0.020  1.383
 5NW  C9   O    single    1.348  0.020  1.348
 5NW  O    C10  single    1.411  0.020  1.411
 5NW  C12  N3   aromatic  1.318  0.020  1.318
 5NW  C6   H1   single    0.930  0.020  1.080
 5NW  C8   H2   single    0.930  0.020  1.080
 5NW  C10  H3   single    0.970  0.020  1.090
 5NW  C10  H4   single    0.970  0.020  1.090
 5NW  C10  H5   single    0.970  0.020  1.090
 5NW  C12  H6   single    0.930  0.020  1.080
 5NW  C13  H7   single    0.930  0.020  1.080
 5NW  C15  H8   single    0.930  0.020  1.080
 5NW  C18  H9   single    0.970  0.020  1.090
 5NW  C18  H10  single    0.970  0.020  1.090
 5NW  C20  H11  single    0.970  0.020  1.090
 5NW  C20  H12  single    0.970  0.020  1.090
 5NW  C20  H13  single    0.970  0.020  1.090
 5NW  C21  H14  single    0.970  0.020  1.090
 5NW  C21  H15  single    0.970  0.020  1.090
 5NW  C21  H16  single    0.970  0.020  1.090
 5NW  C22  H17  single    0.970  0.020  1.090
 5NW  C22  H18  single    0.970  0.020  1.090
 5NW  C22  H19  single    0.970  0.020  1.090
 5NW  N6   H20  single    0.860  0.020  1.020
 5NW  C16  H21  single    0.930  0.020  1.080
 5NW  C2   H22  single    0.930  0.020  1.080
 5NW  N2   H23  single    0.860  0.020  1.020
 5NW  C5   H24  single    0.930  0.020  1.080
 5NW  C14  H25  single    0.970  0.020  1.090
 5NW  C14  H26  single    0.970  0.020  1.090
 5NW  C14  H27  single    0.970  0.020  1.090

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
 5NW  C2   C1   C    114.32  3.000
 5NW  C2   C1   C15  125.97  3.000
 5NW  C    C1   C15  119.72  3.000
 5NW  C16  N5   C17  119.34  3.000
 5NW  H1   C6   C5   118.20  3.000
 5NW  H1   C6   C7   120.47  3.000
 5NW  C5   C6   C7   121.32  3.000
 5NW  C11  C7   C8   120.36  3.000
 5NW  C8   C7   C6   118.01  3.000
 5NW  C11  C7   C6   121.63  3.000
 5NW  H2   C8   C9   119.66  3.000
 5NW  H2   C8   C7   119.19  3.000
 5NW  C9   C8   C7   121.13  3.000
 5NW  O    C9   C4   115.08  3.000
 5NW  O    C9   C8   124.39  3.000
 5NW  C4   C9   C8   120.53  3.000
 5NW  H5   C10  H4   108.90  3.000
 5NW  H5   C10  H3   108.60  3.000
 5NW  H4   C10  H3   108.84  3.000
 5NW  H5   C10  O    111.92  3.000
 5NW  H4   C10  O    111.93  3.000
 5NW  H3   C10  O    106.53  3.000
 5NW  C13  C11  C12  103.19  3.000
 5NW  C12  C11  C7   128.81  3.000
 5NW  C13  C11  C7   127.99  3.000
 5NW  H6   C12  N3   119.74  3.000
 5NW  H6   C12  C11  128.43  3.000
 5NW  N3   C12  C11  111.83  3.000
 5NW  H7   C13  N4   121.48  3.000
 5NW  H7   C13  C11  131.28  3.000
 5NW  N4   C13  C11  107.23  3.000
 5NW  H8   C15  C16  121.45  3.000
 5NW  H8   C15  C1   121.31  3.000
 5NW  C16  C15  C1   117.24  3.000
 5NW  H10  C18  H9   106.22  3.000
 5NW  H10  C18  N6   110.33  3.000
 5NW  H9   C18  N6   108.59  3.000
 5NW  H10  C18  C19  109.40  3.000
 5NW  H9   C18  C19  109.33  3.000
 5NW  N6   C18  C19  112.76  3.000
 5NW  C22  C19  C21  108.79  3.000
 5NW  C21  C19  C20  109.82  3.000
 5NW  C22  C19  C20  109.42  3.000
 5NW  C21  C19  C18  111.01  3.000
 5NW  C20  C19  C18  110.63  3.000
 5NW  C22  C19  C18  107.11  3.000
 5NW  H13  C20  H12  107.55  3.000
 5NW  H13  C20  H11  107.54  3.000
 5NW  H12  C20  H11  107.28  3.000
 5NW  H13  C20  C19  111.43  3.000
 5NW  H12  C20  C19  110.71  3.000
 5NW  H11  C20  C19  112.10  3.000
 5NW  H16  C21  H15  106.25  3.000
 5NW  H16  C21  H14  107.60  3.000
 5NW  H15  C21  H14  107.61  3.000
 5NW  H16  C21  C19  113.01  3.000
 5NW  H15  C21  C19  110.49  3.000
 5NW  H14  C21  C19  111.59  3.000
 5NW  H19  C22  H18  107.50  3.000
 5NW  H19  C22  H17  107.66  3.000
 5NW  H18  C22  H17  107.52  3.000
 5NW  H19  C22  C19  111.60  3.000
 5NW  H18  C22  C19  110.78  3.000
 5NW  H17  C22  C19  111.57  3.000
 5NW  C    C17  N6   117.78  3.000
 5NW  C    C17  N5   121.53  3.000
 5NW  N6   C17  N5   120.69  3.000
 5NW  H21  C16  C15  120.20  3.000
 5NW  H21  C16  N5   115.17  3.000
 5NW  C15  C16  N5   124.62  3.000
 5NW  N1   C    C17  119.54  3.000
 5NW  N1   C    C1   122.92  3.000
 5NW  C17  C    C1   117.54  3.000
 5NW  C3   N1   C    117.01  3.000
 5NW  N2   C3   N    119.07  3.000
 5NW  N2   C3   N1   115.71  3.000
 5NW  N    C3   N1   125.21  3.000
 5NW  C2   N    C3   117.31  3.000
 5NW  H22  C2   N    116.82  3.000
 5NW  H22  C2   C1   119.96  3.000
 5NW  N    C2   C1   123.22  3.000
 5NW  H23  N2   C4   115.16  3.000
 5NW  H23  N2   C3   113.36  3.000
 5NW  C4   N2   C3   130.90  3.000
 5NW  C5   C4   N2   125.52  3.000
 5NW  N2   C4   C9   116.33  3.000
 5NW  C5   C4   C9   118.10  3.000
 5NW  H24  C5   C4   119.86  3.000
 5NW  H24  C5   C6   119.24  3.000
 5NW  C4   C5   C6   120.89  3.000
 5NW  N3   N4   C14  120.15  3.000
 5NW  N3   N4   C13  112.43  3.000
 5NW  C14  N4   C13  127.41  3.000
 5NW  H27  C14  H26  108.78  3.000
 5NW  H27  C14  H25  108.60  3.000
 5NW  H26  C14  H25  109.22  3.000
 5NW  H27  C14  N4   109.15  3.000
 5NW  H26  C14  N4   110.90  3.000
 5NW  H25  C14  N4   110.14  3.000
 5NW  N4   N3   C12  105.32  3.000
 5NW  H20  N6   C17  115.62  3.000
 5NW  H20  N6   C18  119.82  3.000
 5NW  C17  N6   C18  123.34  3.000
 5NW  C10  O    C9   119.12  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
 5NW  CONST_01  N5   C16  C15  C1      0.00   0.0  0
 5NW  CONST_02  N5   C17  C    C1      0.00   0.0  0
 5NW  CONST_03  C3   N1   C    C1      0.00   0.0  0
 5NW  CONST_04  C3   N    C2   C1      0.00   0.0  0
 5NW  CONST_05  N1   C    C17  N5    180.00   0.0  0
 5NW  CONST_06  C9   C4   C5   C6      0.00   0.0  0
 5NW  CONST_09  C9   C8   C7   C6      0.00   0.0  0
 5NW  CONST_10  C4   C5   C6   C7      0.00   0.0  0
 5NW  CONST_11  N4   C13  C11  C7    180.00   0.0  0
 5NW  CONST_12  N3   C12  C11  C7    180.00   0.0  0
 5NW  CONST_13  C4   C9   C8   C7      0.00   0.0  0
 5NW  CONST_14  C5   C6   C7   C8      0.00   0.0  0
 5NW  CONST_17  C5   C4   C9   C8      0.00   0.0  0
 5NW  CONST_18  C11  C7   C8   C9    180.00   0.0  0
 5NW  CONST_19  N3   N4   C13  C11     0.00   0.0  0
 5NW  CONST_20  C5   C6   C7   C11   180.00   0.0  0
 5NW  CONST_21  N4   N3   C12  C11     0.00   0.0  0
 5NW  CONST_22  N4   C13  C11  C12     0.00   0.0  0
 5NW  CONST_23  C13  N4   N3   C12     0.00   0.0  0
 5NW  CONST_24  N3   C12  C11  C13     0.00   0.0  0
 5NW  CONST_25  C17  N5   C16  C15     0.00   0.0  0
 5NW  CONST_26  C17  C    C1   C15     0.00   0.0  0
 5NW  CONST_27  N1   C    C1   C15   180.00   0.0  0
 5NW  CONST_28  N    C2   C1   C15   180.00   0.0  0
 5NW  CONST_29  C2   C1   C    C17   180.00   0.0  0
 5NW  CONST_30  C3   N1   C    C17   180.00   0.0  0
 5NW  CONST_31  C    C17  N5   C16     0.00   0.0  0
 5NW  CONST_32  C    C1   C15  C16     0.00   0.0  0
 5NW  CONST_33  C2   C1   C15  C16   180.00   0.0  0
 5NW  CONST_34  N    C2   C1   C       0.00   0.0  0
 5NW  CONST_35  N    C3   N1   C       0.00   0.0  0
 5NW  CONST_36  C2   C1   C    N1      0.00   0.0  0
 5NW  CONST_37  C2   N    C3   N1      0.00   0.0  0
 5NW  CONST_38  N6   C17  C    C1    180.00   0.0  0
 5NW  CONST_39  N2   C4   C5   C6    180.00   0.0  0
 5NW  CONST_40  O    C9   C8   C7    180.00   0.0  0
 5NW  CONST_41  N2   C4   C9   C8    180.00   0.0  0
 5NW  CONST_42  C14  N4   C13  C11   180.00   0.0  0
 5NW  CONST_43  C14  N4   N3   C12   180.00   0.0  0
 5NW  CONST_44  C16  N5   C17  N6    180.00   0.0  0
 5NW  CONST_45  N1   C    C17  N6      0.00   0.0  0
 5NW  CONST_46  N2   C3   N1   C     180.00   0.0  0
 5NW  CONST_47  N2   C3   N    C2    180.00   0.0  0
 5NW  CONST_48  C5   C4   C9   O     180.00   0.0  0
 5NW  CONST_49  H21  C16  C15  C1    180.00   0.0  0
 5NW  CONST_50  H8   C15  C16  N5    180.00   0.0  0
 5NW  CONST_51  H2   C8   C7   C6    180.00   0.0  0
 5NW  CONST_52  H24  C5   C6   C7    180.00   0.0  0
 5NW  CONST_53  H7   C13  C11  C7      0.00   0.0  0
 5NW  CONST_54  H6   C12  C11  C7      0.00   0.0  0
 5NW  CONST_55  H1   C6   C7   C8    180.00   0.0  0
 5NW  CONST_56  H22  C2   C1   C15     0.00   0.0  0
 5NW  CONST_57  C18  N6   C17  N5      0.00   0.0  0
 5NW  CONST_58  C    C17  N6   C18   180.00   0.0  0
 5NW  CONST_59  H20  N6   C17  N5    180.00   0.0  0
 5NW  Var_01    C3   N2   C4   C9    157.57  30.0  2
 5NW  Var_02    C4   N2   C3   N1   -176.73  30.0  2
 5NW  Var_03    C4   C9   O    C10   177.12  30.0  3
 5NW  Var_04    H25  C14  N4   C13   128.84  30.0  2
 5NW  Var_05    C17  N6   C18  C19   169.76  30.0  3
 5NW  Var_06    H3   C10  O    C9   -177.64  30.0  3
 5NW  Var_07    N6   C18  C19  C20   -60.63  30.0  3
 5NW  Var_08    H17  C22  C19  C18    60.35  30.0  3
 5NW  Var_09    H11  C20  C19  C18    63.20  30.0  3
 5NW  Var_10    H14  C21  C19  C18    54.09  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
 5NW  plan-1  C7   0.020
 5NW  plan-1  C11  0.020
 5NW  plan-1  C12  0.020
 5NW  plan-1  C13  0.020
 5NW  plan-1  N4   0.020
 5NW  plan-1  C14  0.020
 5NW  plan-1  N3   0.020
 5NW  plan-1  H6   0.020
 5NW  plan-1  H7   0.020
 5NW  plan-2  C6   0.020
 5NW  plan-2  C7   0.020
 5NW  plan-2  C8   0.020
 5NW  plan-2  C9   0.020
 5NW  plan-2  C11  0.020
 5NW  plan-2  N2   0.020
 5NW  plan-2  C4   0.020
 5NW  plan-2  C5   0.020
 5NW  plan-2  H1   0.020
 5NW  plan-2  H2   0.020
 5NW  plan-2  H24  0.020
 5NW  plan-2  O    0.020
 5NW  plan-3  C1   0.020
 5NW  plan-3  N5   0.020
 5NW  plan-3  C15  0.020
 5NW  plan-3  C17  0.020
 5NW  plan-3  C16  0.020
 5NW  plan-3  C    0.020
 5NW  plan-3  N1   0.020
 5NW  plan-3  C3   0.020
 5NW  plan-3  N    0.020
 5NW  plan-3  C2   0.020
 5NW  plan-3  N2   0.020
 5NW  plan-3  H8   0.020
 5NW  plan-3  H21  0.020
 5NW  plan-3  H22  0.020
 5NW  plan-3  N6   0.020
 5NW  plan-4  C18  0.020
 5NW  plan-4  C17  0.020
 5NW  plan-4  H20  0.020
 5NW  plan-4  N6   0.020

