# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 20:21:36 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: N-[2-(2,4-diaminopyrido[2,3-d]pyrimidin-7-yl)-2-methylpropyl]-4-phenoxybenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CNC(=O)c1ccc(Oc2ccccc2)cc1)c3ccc4c(N)nc(N)nc4n3
#
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
 3B9  3B9  N-[2-(2,4-diaminopyrido[2,3-d]pyrimidin-7-yl)-2-methylpropyl]-4-phenoxybenzamide  ligand  56  32  .  2022-07-22  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_3B9
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
 3B9  C15   C  CR16  0  -0.319   4.7744  -0.3303   0.5432
 3B9  C1    C  CR6   0   0.539  -6.8023  -2.1207  -0.1282
 3B9  C2    C  CR6   0   0.486  -7.5686   0.0135   0.1109
 3B9  C3    C  CR66  0   0.353  -5.2210  -0.5032  -0.1135
 3B9  C8    C  CT    0  -0.193  -2.0575   1.3937  -0.1678
 3B9  C4    C  CR66  0  -0.154  -6.2115   0.4871   0.0497
 3B9  C5    C  CR16  0  -0.183  -5.8058   1.8221   0.1445
 3B9  C6    C  CR16  0  -0.324  -4.4721   2.1275   0.0740
 3B9  C7    C  CR6   0   0.316  -3.5442   1.0783  -0.0962
 3B9  C9    C  CH2   0  -0.257  -1.2704   0.1005  -0.4487
 3B9  N1    N  N     0  -0.509  -7.8384  -1.2715   0.0234
 3B9  N2    N  N     0  -0.502  -5.5199  -1.8097  -0.2023
 3B9  N3    N  N     0  -0.465  -3.9150  -0.1780  -0.1854
 3B9  N5    N  NH2   0  -0.826  -8.5897   0.8574   0.2664
 3B9  C10   C  CH3   0  -0.654  -1.8097   2.4044  -1.2950
 3B9  C11   C  CH3   0  -0.646  -1.6196   1.9951   1.1736
 3B9  N6    N  NH1   0  -0.654   0.1576   0.3108  -0.5269
 3B9  C12   C  C     0   0.524   1.0202  -0.0383   0.4455
 3B9  O1    O  O     0  -0.489   0.6774  -0.5737   1.4913
 3B9  C13   C  CR6   0  -0.045   2.4572   0.2575   0.1721
 3B9  C14   C  CR16  0  -0.261   3.4254  -0.5559   0.7545
 3B9  C16   C  CR6   0   0.356   5.1719   0.7436  -0.2478
 3B9  C17   C  CR16  0  -0.319   4.2197   1.5842  -0.8136
 3B9  C18   C  CR16  0  -0.282   2.8741   1.3381  -0.6027
 3B9  O2    O  O2    0  -0.507   6.4743   1.0580  -0.4713
 3B9  C19   C  CR6   0   0.317   7.4311   0.0755  -0.4049
 3B9  C20   C  CR16  0  -0.319   8.4854   0.2460   0.4786
 3B9  C21   C  CR16  0  -0.252   9.4985  -0.7039   0.5178
 3B9  C22   C  CR16  0  -0.260   9.4491  -1.8180  -0.3083
 3B9  C23   C  CR16  0  -0.250   8.3839  -1.9768  -1.1867
 3B9  C24   C  CR16  0  -0.303   7.3712  -1.0306  -1.2428
 3B9  H15   H  HCR6  0   0.284   5.5018  -0.9853   1.0041
 3B9  H5    H  HCR6  0   0.262  -6.5237   2.6225   0.2724
 3B9  H6    H  HCR6  0   0.263  -4.1433   3.1543   0.1487
 3B9  H9    H  HCH2  0   0.256  -1.4672  -0.6361   0.3270
 3B9  H9A   H  HCH2  0   0.254  -1.6009  -0.3345  -1.3931
 3B9  HN4   H  HNH2  0   0.394  -8.0700  -3.7082  -0.0073
 3B9  HN4A  H  HNH2  0   0.393  -6.4111  -4.1142  -0.1902
 3B9  HN5   H  HNH2  0   0.417  -8.4758   1.8543   0.2878
 3B9  HN5A  H  HNH2  0   0.406  -9.5303   0.5008   0.2731
 3B9  H10   H  HCH3  0   0.240  -2.3257   3.3477  -1.1144
 3B9  H10A  H  HCH3  0   0.234  -0.7468   2.6368  -1.3762
 3B9  H10B  H  HCH3  0   0.238  -2.1457   2.0181  -2.2590
 3B9  H11   H  HCH3  0   0.236  -1.7393   1.2794   1.9882
 3B9  H11A  H  HCH3  0   0.236  -0.5717   2.2945   1.1374
 3B9  H11B  H  HCH3  0   0.238  -2.1981   2.8859   1.4214
 3B9  HN6   H  HNH1  0   0.404   0.5319   0.5996  -1.4153
 3B9  H14   H  HCR6  0   0.266   3.1257  -1.3879   1.3777
 3B9  H17   H  HCR6  0   0.276   4.5329   2.4316  -1.4095
 3B9  H18   H  HCR6  0   0.260   2.1553   2.0200  -1.0402
 3B9  H20   H  HCR6  0   0.272   8.5147   1.1147   1.1239
 3B9  H21   H  HCR6  0   0.264  10.3249  -0.5717   1.2037
 3B9  H22   H  HCR6  0   0.261  10.2377  -2.5575  -0.2715
 3B9  H23   H  HCR6  0   0.265   8.3414  -2.8397  -1.8382
 3B9  H24   H  HCR6  0   0.279   6.5485  -1.1516  -1.9366
 3B9  N4    N  NH2   0  -0.817  -7.1361  -3.4203  -0.2410

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
 3B9  C15  C14   aromatic  1.384  0.020  1.384
 3B9  C15  C16   aromatic  1.392  0.020  1.392
 3B9  C1   N1    aromatic  1.348  0.020  1.348
 3B9  C1   N2    aromatic  1.322  0.020  1.322
 3B9  C1   N4    single    1.346  0.020  1.346
 3B9  C2   C4    aromatic  1.439  0.020  1.439
 3B9  C2   N1    aromatic  1.316  0.020  1.316
 3B9  C2   N5    single    1.334  0.020  1.334
 3B9  C3   C4    aromatic  1.410  0.020  1.410
 3B9  C3   N2    aromatic  1.343  0.020  1.343
 3B9  C3   N3    aromatic  1.348  0.020  1.348
 3B9  C8   C7    single    1.522  0.020  1.522
 3B9  C8   C9    single    1.540  0.020  1.540
 3B9  C8   C10   single    1.534  0.020  1.534
 3B9  C8   C11   single    1.534  0.020  1.534
 3B9  C4   C5    aromatic  1.399  0.020  1.399
 3B9  C5   C6    aromatic  1.370  0.020  1.370
 3B9  C6   C7    aromatic  1.411  0.020  1.411
 3B9  C7   N3    aromatic  1.313  0.020  1.313
 3B9  C9   N6    single    1.446  0.020  1.446
 3B9  N6   C12   single    1.346  0.020  1.346
 3B9  C12  O1    double    1.224  0.020  1.224
 3B9  C12  C13   single    1.492  0.020  1.492
 3B9  C13  C14   aromatic  1.392  0.020  1.392
 3B9  C13  C18   aromatic  1.394  0.020  1.394
 3B9  C16  C17   aromatic  1.390  0.020  1.390
 3B9  C16  O2    single    1.358  0.020  1.358
 3B9  C17  C18   aromatic  1.384  0.020  1.384
 3B9  O2   C19   single    1.373  0.020  1.373
 3B9  C19  C20   aromatic  1.386  0.020  1.386
 3B9  C19  C24   aromatic  1.389  0.020  1.389
 3B9  C20  C21   aromatic  1.389  0.020  1.389
 3B9  C21  C22   aromatic  1.388  0.020  1.388
 3B9  C22  C23   aromatic  1.390  0.020  1.390
 3B9  C23  C24   aromatic  1.387  0.020  1.387
 3B9  C15  H15   single    0.930  0.020  1.080
 3B9  C5   H5    single    0.930  0.020  1.080
 3B9  C6   H6    single    0.930  0.020  1.080
 3B9  C9   H9    single    0.970  0.020  1.090
 3B9  C9   H9A   single    0.970  0.020  1.090
 3B9  N4   HN4   single    0.890  0.020  1.040
 3B9  N4   HN4A  single    0.890  0.020  1.040
 3B9  N5   HN5   single    0.860  0.020  1.020
 3B9  N5   HN5A  single    0.860  0.020  1.020
 3B9  C10  H10   single    0.970  0.020  1.090
 3B9  C10  H10A  single    0.970  0.020  1.090
 3B9  C10  H10B  single    0.970  0.020  1.090
 3B9  C11  H11   single    0.970  0.020  1.090
 3B9  C11  H11A  single    0.970  0.020  1.090
 3B9  C11  H11B  single    0.970  0.020  1.090
 3B9  N6   HN6   single    0.860  0.020  1.020
 3B9  C14  H14   single    0.930  0.020  1.080
 3B9  C17  H17   single    0.930  0.020  1.080
 3B9  C18  H18   single    0.930  0.020  1.080
 3B9  C20  H20   single    0.930  0.020  1.080
 3B9  C21  H21   single    0.930  0.020  1.080
 3B9  C22  H22   single    0.930  0.020  1.080
 3B9  C23  H23   single    0.930  0.020  1.080
 3B9  C24  H24   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
 3B9  H15   C15  C16   121.15  3.000
 3B9  H15   C15  C14   119.45  3.000
 3B9  C16   C15  C14   119.40  3.000
 3B9  N4    C1   N2    117.57  3.000
 3B9  N4    C1   N1    115.27  3.000
 3B9  N2    C1   N1    127.14  3.000
 3B9  N5    C2   N1    117.94  3.000
 3B9  N5    C2   C4    121.26  3.000
 3B9  N1    C2   C4    120.80  3.000
 3B9  N3    C3   N2    116.54  3.000
 3B9  N3    C3   C4    121.16  3.000
 3B9  N2    C3   C4    122.30  3.000
 3B9  C11   C8   C10   109.77  3.000
 3B9  C11   C8   C9    110.05  3.000
 3B9  C10   C8   C9    109.68  3.000
 3B9  C11   C8   C7    108.61  3.000
 3B9  C10   C8   C7    109.21  3.000
 3B9  C9    C8   C7    109.51  3.000
 3B9  C5    C4   C3    118.32  3.000
 3B9  C5    C4   C2    125.81  3.000
 3B9  C3    C4   C2    115.87  3.000
 3B9  H5    C5   C6    119.13  3.000
 3B9  H5    C5   C4    121.42  3.000
 3B9  C6    C5   C4    119.45  3.000
 3B9  H6    C6   C7    120.98  3.000
 3B9  H6    C6   C5    120.29  3.000
 3B9  C7    C6   C5    118.73  3.000
 3B9  N3    C7   C6    122.28  3.000
 3B9  N3    C7   C8    118.11  3.000
 3B9  C6    C7   C8    119.61  3.000
 3B9  H9A   C9   H9    107.01  3.000
 3B9  H9A   C9   N6    108.08  3.000
 3B9  H9    C9   N6    108.41  3.000
 3B9  H9A   C9   C8    109.75  3.000
 3B9  H9    C9   C8    110.26  3.000
 3B9  N6    C9   C8    113.12  3.000
 3B9  C2    N1   C1    117.71  3.000
 3B9  C3    N2   C1    116.17  3.000
 3B9  C7    N3   C3    120.06  3.000
 3B9  HN5A  N5   HN5   117.27  3.000
 3B9  HN5A  N5   C2    119.49  3.000
 3B9  HN5   N5   C2    122.96  3.000
 3B9  H10B  C10  H10A  108.03  3.000
 3B9  H10B  C10  H10   107.87  3.000
 3B9  H10A  C10  H10   106.81  3.000
 3B9  H10B  C10  C8    111.47  3.000
 3B9  H10A  C10  C8    110.63  3.000
 3B9  H10   C10  C8    111.83  3.000
 3B9  H11B  C11  H11A  107.03  3.000
 3B9  H11B  C11  H11   107.94  3.000
 3B9  H11A  C11  H11   108.08  3.000
 3B9  H11B  C11  C8    111.56  3.000
 3B9  H11A  C11  C8    110.67  3.000
 3B9  H11   C11  C8    111.37  3.000
 3B9  HN6   N6   C12   118.28  3.000
 3B9  HN6   N6   C9    117.19  3.000
 3B9  C12   N6   C9    123.80  3.000
 3B9  C13   C12  O1    120.86  3.000
 3B9  C13   C12  N6    115.68  3.000
 3B9  O1    C12  N6    123.46  3.000
 3B9  C18   C13  C14   118.53  3.000
 3B9  C18   C13  C12   122.93  3.000
 3B9  C14   C13  C12   118.50  3.000
 3B9  H14   C14  C13   119.85  3.000
 3B9  H14   C14  C15   118.90  3.000
 3B9  C13   C14  C15   121.25  3.000
 3B9  O2    C16  C17   116.73  3.000
 3B9  O2    C16  C15   123.09  3.000
 3B9  C17   C16  C15   120.14  3.000
 3B9  H17   C17  C18   120.30  3.000
 3B9  H17   C17  C16   119.94  3.000
 3B9  C18   C17  C16   119.75  3.000
 3B9  H18   C18  C17   118.15  3.000
 3B9  H18   C18  C13   120.94  3.000
 3B9  C17   C18  C13   120.89  3.000
 3B9  C19   O2   C16   119.64  3.000
 3B9  C24   C19  C20   121.02  3.000
 3B9  C24   C19  O2    120.70  3.000
 3B9  C20   C19  O2    118.22  3.000
 3B9  H20   C20  C21   120.80  3.000
 3B9  H20   C20  C19   119.95  3.000
 3B9  C21   C20  C19   119.25  3.000
 3B9  H21   C21  C22   120.17  3.000
 3B9  H21   C21  C20   119.43  3.000
 3B9  C22   C21  C20   120.40  3.000
 3B9  H22   C22  C23   120.14  3.000
 3B9  H22   C22  C21   120.17  3.000
 3B9  C23   C22  C21   119.69  3.000
 3B9  H23   C23  C24   119.40  3.000
 3B9  H23   C23  C22   120.12  3.000
 3B9  C24   C23  C22   120.48  3.000
 3B9  H24   C24  C23   120.29  3.000
 3B9  H24   C24  C19   120.55  3.000
 3B9  C23   C24  C19   119.16  3.000
 3B9  HN4A  N4   HN4   117.45  3.000
 3B9  HN4A  N4   C1    118.91  3.000
 3B9  HN4   N4   C1    119.17  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
 3B9  CONST_01  C18   C13  C14  C15     0.00   0.0  0
 3B9  CONST_02  C18   C17  C16  C15     0.00   0.0  0
 3B9  CONST_03  C4    C2   N1   C1      0.00   0.0  0
 3B9  CONST_04  C4    C3   N2   C1      0.00   0.0  0
 3B9  CONST_05  N3    C3   N2   C1    180.00   0.0  0
 3B9  CONST_06  N2    C3   C4   C2      0.00   0.0  0
 3B9  CONST_07  N3    C3   C4   C2    180.00   0.0  0
 3B9  CONST_08  C6    C5   C4   C2    180.00   0.0  0
 3B9  CONST_09  N2    C1   N1   C2      0.00   0.0  0
 3B9  CONST_10  N1    C2   C4   C3      0.00   0.0  0
 3B9  CONST_11  C6    C5   C4   C3      0.00   0.0  0
 3B9  CONST_12  N1    C1   N2   C3      0.00   0.0  0
 3B9  CONST_13  C6    C7   N3   C3      0.00   0.0  0
 3B9  CONST_14  C7    N3   C3   C4      0.00   0.0  0
 3B9  CONST_15  C7    C6   C5   C4      0.00   0.0  0
 3B9  CONST_16  N1    C2   C4   C5    180.00   0.0  0
 3B9  CONST_17  N2    C3   C4   C5    180.00   0.0  0
 3B9  CONST_18  N3    C3   C4   C5      0.00   0.0  0
 3B9  CONST_19  N3    C7   C6   C5      0.00   0.0  0
 3B9  CONST_20  N2    C3   N3   C7    180.00   0.0  0
 3B9  CONST_21  C16   C15  C14  C13     0.00   0.0  0
 3B9  CONST_22  C16   C17  C18  C13     0.00   0.0  0
 3B9  CONST_23  C17   C16  C15  C14     0.00   0.0  0
 3B9  CONST_24  C17   C18  C13  C14     0.00   0.0  0
 3B9  CONST_25  C22   C21  C20  C19     0.00   0.0  0
 3B9  CONST_26  C22   C23  C24  C19     0.00   0.0  0
 3B9  CONST_27  C23   C24  C19  C20     0.00   0.0  0
 3B9  CONST_28  C23   C22  C21  C20     0.00   0.0  0
 3B9  CONST_29  C24   C19  C20  C21     0.00   0.0  0
 3B9  CONST_30  C24   C23  C22  C21     0.00   0.0  0
 3B9  CONST_31  C12   C13  C14  C15   180.00   0.0  0
 3B9  CONST_32  N5    C2   N1   C1    180.00   0.0  0
 3B9  CONST_33  N4    C1   N1   C2    180.00   0.0  0
 3B9  CONST_34  N5    C2   C4   C3    180.00   0.0  0
 3B9  CONST_35  N4    C1   N2   C3    180.00   0.0  0
 3B9  CONST_36  C8    C7   N3   C3    180.00   0.0  0
 3B9  CONST_37  C5    C6   C7   C8    180.00   0.0  0
 3B9  CONST_38  N5    C2   C4   C5      0.00   0.0  0
 3B9  CONST_39  C17   C18  C13  C12   180.00   0.0  0
 3B9  CONST_40  O2    C16  C15  C14   180.00   0.0  0
 3B9  CONST_41  O2    C16  C17  C18   180.00   0.0  0
 3B9  CONST_42  C21   C20  C19  O2    180.00   0.0  0
 3B9  CONST_43  C23   C24  C19  O2    180.00   0.0  0
 3B9  CONST_44  H17   C17  C16  C15   180.00   0.0  0
 3B9  CONST_45  H5    C5   C4   C2      0.00   0.0  0
 3B9  CONST_46  H6    C6   C5   C4    180.00   0.0  0
 3B9  CONST_47  H15   C15  C14  C13   180.00   0.0  0
 3B9  CONST_48  H18   C18  C13  C14   180.00   0.0  0
 3B9  CONST_49  H14   C14  C15  C16   180.00   0.0  0
 3B9  CONST_50  H21   C21  C20  C19   180.00   0.0  0
 3B9  CONST_51  H23   C23  C24  C19   180.00   0.0  0
 3B9  CONST_52  H24   C24  C19  C20   180.00   0.0  0
 3B9  CONST_53  H22   C22  C21  C20   180.00   0.0  0
 3B9  CONST_54  H20   C20  C21  C22   180.00   0.0  0
 3B9  CONST_55  HN5   N5   C2   C4      0.00   0.0  0
 3B9  CONST_56  HN5A  N5   C2   C4    180.00   0.0  0
 3B9  CONST_57  HN4   N4   C1   N1      0.00   0.0  0
 3B9  CONST_58  HN4A  N4   C1   N1    180.00   0.0  0
 3B9  CONST_59  C13   C12  N6   C9    180.00   0.0  0
 3B9  CONST_60  HN6   N6   C12  C13     0.00   0.0  0
 3B9  CONST_61  O1    C12  N6   C9      0.00   0.0  0
 3B9  Var_01    C20   C19  O2   C16  -123.18  30.0  2
 3B9  Var_02    C9    C8   C7   C6   -176.24  30.0  3
 3B9  Var_03    C14   C13  C12  N6   -150.99  30.0  2
 3B9  Var_04    N6    C9   C8   C7   -179.75  30.0  3
 3B9  Var_05    H10   C10  C8   C7     61.88  30.0  3
 3B9  Var_06    H11   C11  C8   C7     63.44  30.0  3
 3B9  Var_07    C12   N6   C9   C8    104.80  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
 3B9  plan-1  C15   0.020
 3B9  plan-1  C12   0.020
 3B9  plan-1  C13   0.020
 3B9  plan-1  C14   0.020
 3B9  plan-1  C16   0.020
 3B9  plan-1  C17   0.020
 3B9  plan-1  C18   0.020
 3B9  plan-1  O2    0.020
 3B9  plan-1  H15   0.020
 3B9  plan-1  H14   0.020
 3B9  plan-1  H17   0.020
 3B9  plan-1  H18   0.020
 3B9  plan-2  O2    0.020
 3B9  plan-2  C19   0.020
 3B9  plan-2  C20   0.020
 3B9  plan-2  C21   0.020
 3B9  plan-2  C22   0.020
 3B9  plan-2  C23   0.020
 3B9  plan-2  C24   0.020
 3B9  plan-2  H20   0.020
 3B9  plan-2  H21   0.020
 3B9  plan-2  H22   0.020
 3B9  plan-2  H23   0.020
 3B9  plan-2  H24   0.020
 3B9  plan-3  C1    0.020
 3B9  plan-3  C2    0.020
 3B9  plan-3  C3    0.020
 3B9  plan-3  C8    0.020
 3B9  plan-3  C4    0.020
 3B9  plan-3  C5    0.020
 3B9  plan-3  C6    0.020
 3B9  plan-3  C7    0.020
 3B9  plan-3  N1    0.020
 3B9  plan-3  N2    0.020
 3B9  plan-3  N3    0.020
 3B9  plan-3  N5    0.020
 3B9  plan-3  H5    0.020
 3B9  plan-3  H6    0.020
 3B9  plan-3  N4    0.020
 3B9  plan-4  C9    0.020
 3B9  plan-4  N6    0.020
 3B9  plan-4  C12   0.020
 3B9  plan-4  O1    0.020
 3B9  plan-4  C13   0.020
 3B9  plan-4  HN6   0.020
 3B9  plan-5  C2    0.020
 3B9  plan-5  N5    0.020
 3B9  plan-5  HN5   0.020
 3B9  plan-5  HN5A  0.020
 3B9  plan-6  C1    0.020
 3B9  plan-6  HN4   0.020
 3B9  plan-6  HN4A  0.020
 3B9  plan-6  N4    0.020

