# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 09:10:38 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: 8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ncc2C=C(C(=O)N(C[C@H]3OC[C@H](N)CO3)c2n1)c4ccc(cc4Cl)c5cccc(C)n5
#
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
 59T  59T  8-[(trans-5-amino-1,3-dioxan-2-yl)methyl]-6-[2-chloro-4-(6-methylpyridin-2-yl)phenyl]-2-(methylamino)pyrido[2,3-d]pyrimidin-7(8H)-one  ligand  60  35  .  2021-08-04  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_59T
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
 59T  N3   N   N     0  -0.451   5.9987   1.0477  -0.7606
 59T  C4   C   CR6   0   0.226   5.6008  -0.0459  -0.1137
 59T  C5   C   CR16  0  -0.349   6.5099  -0.9208   0.4767
 59T  C6   C   CR16  0  -0.141   7.8622  -0.6432   0.3635
 59T  C7   C   CR16  0  -0.342   8.2668   0.4900  -0.3199
 59T  C8   C   CR6   0   0.055   4.1385  -0.2704  -0.0493
 59T  C10  C   CR6   0  -0.106   2.2378  -1.7162   0.2778
 59T  C13  C   CR16  0  -0.265   3.2522   0.7839  -0.2767
 59T  C15  C   CR6   0   0.564  -0.8758  -0.1243   1.0729
 59T  C20  C   CR6   0   0.607  -4.8185  -2.0569  -0.5788
 59T  C22  C   CR16  0  -0.038  -2.9013  -2.6484  -1.6075
 59T  C24  C   CR16  0  -0.166  -0.7566  -1.6610  -0.8190
 59T  C26  C   CH3   0  -0.512  -6.9393  -3.0716  -1.2848
 59T  C28  C   CH1   0   0.308  -3.3702   1.9806   1.2923
 59T  C2   C   CR6   0   0.238   7.2934   1.3237  -0.8670
 59T  C9   C   CR16  0  -0.263   3.6103  -1.5274   0.2282
 59T  C11  C   CR6   0   0.172   1.3414  -0.6754   0.0509
 59T  C12  C   CR16  0  -0.278   1.8878   0.5802  -0.2175
 59T  C14  C   CR6   0  -0.204  -0.1214  -0.8575   0.0613
 59T  N17  N   NR6   0  -0.599  -2.2674  -0.2199   1.0153
 59T  C18  C   CR66  0   0.572  -2.9165  -1.0789   0.1668
 59T  N19  N   N     0  -0.498  -4.2223  -1.2139   0.2674
 59T  N21  N   N     0  -0.467  -4.2036  -2.7837  -1.5336
 59T  C23  C   CR66  0  -0.109  -2.1639  -1.8092  -0.7734
 59T  N25  N   NH1   0  -0.636  -6.1429  -2.1884  -0.4700
 59T  C27  C   CH2   0  -0.384  -3.0454   0.6298   1.9073
 59T  O30  O   O2    0  -0.479  -2.1871   2.6771   1.0467
 59T  C31  C   CH2   0  -0.180  -2.4177   3.9593   0.4950
 59T  C32  C   CH1   0  -0.148  -3.2294   3.8618  -0.7887
 59T  C34  C   CH2   0  -0.195  -4.4602   3.0099  -0.4916
 59T  O35  O   O2    0  -0.478  -4.0960   1.7848   0.1183
 59T  N36  N   NH2   0  -0.794  -3.5306   5.1927  -1.2755
 59T  CL1  CL  CL    0  -0.124   1.6575  -3.3073   0.6532
 59T  H1   H   HCR6  0   0.269   6.1834  -1.7945   1.0227
 59T  H2   H   HCR6  0   0.273   8.5922  -1.3065   0.8085
 59T  H3   H   HCR6  0   0.266   9.3159   0.7322  -0.4260
 59T  H4   H   HCR6  0   0.259   3.6380   1.7685  -0.4999
 59T  H5   H   HCR6  0   0.278  -2.3862  -3.2315  -2.3657
 59T  H6   H   HCR6  0   0.278  -0.1988  -2.2048  -1.5727
 59T  H7   H   HCH3  0   0.240  -6.8149  -2.8625  -2.3470
 59T  H8   H   HCH3  0   0.237  -6.6942  -4.1209  -1.1138
 59T  H9   H   HCH3  0   0.254  -7.9831  -2.9181  -1.0263
 59T  H10  H   HCH1  0   0.199  -3.9865   2.5440   2.0196
 59T  H11  H   HCH3  0   0.255   7.5908   3.4417  -0.9074
 59T  H12  H   HCH3  0   0.245   8.6878   2.5510  -1.9552
 59T  H13  H   HCH3  0   0.250   6.9939   2.7733  -2.4191
 59T  H14  H   HCR6  0   0.275   4.2574  -2.3779   0.3922
 59T  H15  H   HCR6  0   0.259   1.2190   1.4118  -0.3983
 59T  H16  H   HNH1  0   0.403  -6.5949  -1.6545   0.2528
 59T  H17  H   HCH2  0   0.284  -2.4915   0.7793   2.8305
 59T  H18  H   HCH2  0   0.286  -3.9741   0.1220   2.1526
 59T  H19  H   HCH2  0   0.200  -2.9542   4.5944   1.2179
 59T  H20  H   HCH2  0   0.246  -1.4439   4.4142   0.3101
 59T  H21  H   HCH1  0   0.242  -2.6229   3.3519  -1.5435
 59T  H22  H   HCH2  0   0.199  -5.1380   3.5761   0.1669
 59T  H23  H   HCH2  0   0.243  -5.0063   2.7684  -1.4053
 59T  H24  H   HNH2  0   0.355  -3.9768   5.1385  -2.1823
 59T  H25  H   HNH2  0   0.343  -4.1961   5.6468  -0.6601
 59T  C1   C   CH3   0  -0.721   7.6654   2.5864  -1.5825
 59T  O16  O   O     0  -0.454  -0.3345   0.5375   1.9400

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
 59T  N3   C4   aromatic  1.332  0.020  1.332
 59T  N3   C2   aromatic  1.328  0.020  1.328
 59T  C4   C5   aromatic  1.393  0.020  1.393
 59T  C4   C8   single    1.481  0.020  1.481
 59T  C5   C6   aromatic  1.385  0.020  1.385
 59T  C6   C7   aromatic  1.384  0.020  1.384
 59T  C7   C2   aromatic  1.393  0.020  1.393
 59T  C8   C13  aromatic  1.396  0.020  1.396
 59T  C8   C9   aromatic  1.391  0.020  1.391
 59T  C10  C9   aromatic  1.386  0.020  1.386
 59T  C10  C11  aromatic  1.392  0.020  1.392
 59T  C10  CL1  single    1.735  0.020  1.735
 59T  C13  C12  aromatic  1.381  0.020  1.381
 59T  C15  C14  single    1.459  0.020  1.459
 59T  C15  O16  double    1.218  0.020  1.218
 59T  C15  N17  single    1.396  0.020  1.396
 59T  C20  N19  aromatic  1.335  0.020  1.335
 59T  C20  N21  aromatic  1.348  0.020  1.348
 59T  C20  N25  single    1.335  0.020  1.335
 59T  C22  N21  aromatic  1.311  0.020  1.311
 59T  C22  C23  aromatic  1.394  0.020  1.394
 59T  C24  C14  double    1.351  0.020  1.351
 59T  C24  C23  single    1.416  0.020  1.416
 59T  C26  N25  single    1.442  0.020  1.442
 59T  C28  O30  single    1.395  0.020  1.395
 59T  C28  O35  single    1.394  0.020  1.394
 59T  C1   C2   single    1.498  0.020  1.498
 59T  C11  C12  aromatic  1.395  0.020  1.395
 59T  C11  C14  single    1.474  0.020  1.474
 59T  N17  C18  single    1.371  0.020  1.371
 59T  N17  C27  single    1.457  0.020  1.457
 59T  C18  N19  aromatic  1.317  0.020  1.317
 59T  C18  C23  aromatic  1.408  0.020  1.408
 59T  O30  C31  single    1.415  0.020  1.415
 59T  C31  C32  single    1.522  0.020  1.522
 59T  C32  C34  single    1.526  0.020  1.526
 59T  C32  N36  single    1.449  0.020  1.449
 59T  C34  O35  single    1.416  0.020  1.416
 59T  C27  C28  single    1.519  0.020  1.519
 59T  C5   H1   single    0.930  0.020  1.080
 59T  C6   H2   single    0.930  0.020  1.080
 59T  C7   H3   single    0.930  0.020  1.080
 59T  C13  H4   single    0.930  0.020  1.080
 59T  C22  H5   single    0.930  0.020  1.080
 59T  C24  H6   single    0.930  0.020  1.080
 59T  C26  H7   single    0.970  0.020  1.090
 59T  C26  H8   single    0.970  0.020  1.090
 59T  C26  H9   single    0.970  0.020  1.090
 59T  C28  H10  single    0.970  0.020  1.090
 59T  C1   H11  single    0.970  0.020  1.090
 59T  C1   H12  single    0.970  0.020  1.090
 59T  C1   H13  single    0.970  0.020  1.090
 59T  C9   H14  single    0.930  0.020  1.080
 59T  C12  H15  single    0.930  0.020  1.080
 59T  N25  H16  single    0.860  0.020  1.020
 59T  C27  H17  single    0.970  0.020  1.090
 59T  C27  H18  single    0.970  0.020  1.090
 59T  C31  H19  single    0.970  0.020  1.090
 59T  C31  H20  single    0.970  0.020  1.090
 59T  C32  H21  single    0.970  0.020  1.090
 59T  C34  H22  single    0.970  0.020  1.090
 59T  C34  H23  single    0.970  0.020  1.090
 59T  N36  H24  single    0.890  0.020  1.040
 59T  N36  H25  single    0.890  0.020  1.040

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
 59T  C2   N3   C4   120.07  3.000
 59T  C8   C4   C5   122.06  3.000
 59T  C8   C4   N3   116.15  3.000
 59T  C5   C4   N3   121.78  3.000
 59T  H1   C5   C6   119.88  3.000
 59T  H1   C5   C4   121.64  3.000
 59T  C6   C5   C4   118.47  3.000
 59T  H2   C6   C7   120.52  3.000
 59T  H2   C6   C5   120.15  3.000
 59T  C7   C6   C5   119.34  3.000
 59T  H3   C7   C2   120.33  3.000
 59T  H3   C7   C6   121.01  3.000
 59T  C2   C7   C6   118.66  3.000
 59T  C9   C8   C13  118.28  3.000
 59T  C9   C8   C4   121.36  3.000
 59T  C13  C8   C4   120.36  3.000
 59T  CL1  C10  C11  120.37  3.000
 59T  CL1  C10  C9   117.64  3.000
 59T  C11  C10  C9   121.99  3.000
 59T  H4   C13  C12  119.74  3.000
 59T  H4   C13  C8   119.67  3.000
 59T  C12  C13  C8   120.60  3.000
 59T  N17  C15  O16  120.64  3.000
 59T  N17  C15  C14  116.89  3.000
 59T  O16  C15  C14  122.46  3.000
 59T  N25  C20  N21  117.18  3.000
 59T  N25  C20  N19  116.97  3.000
 59T  N21  C20  N19  125.85  3.000
 59T  H5   C22  C23  119.33  3.000
 59T  H5   C22  N21  117.05  3.000
 59T  C23  C22  N21  123.62  3.000
 59T  H6   C24  C23  118.78  3.000
 59T  H6   C24  C14  120.64  3.000
 59T  C23  C24  C14  120.58  3.000
 59T  H9   C26  H8   108.32  3.000
 59T  H9   C26  H7   108.33  3.000
 59T  H8   C26  H7   108.16  3.000
 59T  H9   C26  N25  108.05  3.000
 59T  H8   C26  N25  112.12  3.000
 59T  H7   C26  N25  111.73  3.000
 59T  H10  C28  O35  109.56  3.000
 59T  H10  C28  O30  109.49  3.000
 59T  O35  C28  O30  111.32  3.000
 59T  H10  C28  C27  107.78  3.000
 59T  O35  C28  C27  109.11  3.000
 59T  O30  C28  C27  109.50  3.000
 59T  C1   C2   C7   121.21  3.000
 59T  C1   C2   N3   117.10  3.000
 59T  C7   C2   N3   121.68  3.000
 59T  H14  C9   C10  118.68  3.000
 59T  H14  C9   C8   120.91  3.000
 59T  C10  C9   C8   120.40  3.000
 59T  C14  C11  C12  120.07  3.000
 59T  C14  C11  C10  123.06  3.000
 59T  C12  C11  C10  116.87  3.000
 59T  H15  C12  C11  118.79  3.000
 59T  H15  C12  C13  119.34  3.000
 59T  C11  C12  C13  121.87  3.000
 59T  C11  C14  C24  122.39  3.000
 59T  C11  C14  C15  117.11  3.000
 59T  C24  C14  C15  120.50  3.000
 59T  C27  N17  C18  119.44  3.000
 59T  C27  N17  C15  117.85  3.000
 59T  C18  N17  C15  122.71  3.000
 59T  C23  C18  N19  121.86  3.000
 59T  C23  C18  N17  119.02  3.000
 59T  N19  C18  N17  119.11  3.000
 59T  C18  N19  C20  117.34  3.000
 59T  C22  N21  C20  115.92  3.000
 59T  C18  C23  C24  119.89  3.000
 59T  C18  C23  C22  115.39  3.000
 59T  C24  C23  C22  124.72  3.000
 59T  H16  N25  C26  118.89  3.000
 59T  H16  N25  C20  116.86  3.000
 59T  C26  N25  C20  124.21  3.000
 59T  H18  C27  H17  107.95  3.000
 59T  H18  C27  N17  108.79  3.000
 59T  H17  C27  N17  109.15  3.000
 59T  H18  C27  C28  108.91  3.000
 59T  H17  C27  C28  109.30  3.000
 59T  N17  C27  C28  112.63  3.000
 59T  C31  O30  C28  112.52  3.000
 59T  H20  C31  H19  107.79  3.000
 59T  H20  C31  C32  111.10  3.000
 59T  H19  C31  C32  109.31  3.000
 59T  H20  C31  O30  107.37  3.000
 59T  H19  C31  O30  110.24  3.000
 59T  C32  C31  O30  110.97  3.000
 59T  H21  C32  N36  108.15  3.000
 59T  H21  C32  C34  108.73  3.000
 59T  N36  C32  C34  114.24  3.000
 59T  H21  C32  C31  108.42  3.000
 59T  N36  C32  C31  109.60  3.000
 59T  C34  C32  C31  107.56  3.000
 59T  H23  C34  H22  107.83  3.000
 59T  H23  C34  O35  107.32  3.000
 59T  H22  C34  O35  110.21  3.000
 59T  H23  C34  C32  111.35  3.000
 59T  H22  C34  C32  109.01  3.000
 59T  O35  C34  C32  111.06  3.000
 59T  C34  O35  C28  112.03  3.000
 59T  H25  N36  H24  106.16  3.000
 59T  H25  N36  C32  110.12  3.000
 59T  H24  N36  C32  110.09  3.000
 59T  H13  C1   H12  108.76  3.000
 59T  H13  C1   H11  107.36  3.000
 59T  H12  C1   H11  107.53  3.000
 59T  H13  C1   C2   111.01  3.000
 59T  H12  C1   C2   111.67  3.000
 59T  H11  C1   C2   110.35  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
 59T  CONST_01  C6   C5   C4   N3     0.00   0.0  0
 59T  CONST_04  C6   C7   C2   N3     0.00   0.0  0
 59T  CONST_05  C7   C2   N3   C4     0.00   0.0  0
 59T  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 59T  CONST_07  C12  C13  C8   C4   180.00   0.0  0
 59T  CONST_08  C10  C9   C8   C4   180.00   0.0  0
 59T  CONST_09  C2   N3   C4   C5     0.00   0.0  0
 59T  CONST_12  C2   C7   C6   C5     0.00   0.0  0
 59T  CONST_13  C8   C4   C5   C6   180.00   0.0  0
 59T  CONST_14  C2   N3   C4   C8   180.00   0.0  0
 59T  CONST_15  C11  C12  C13  C8     0.00   0.0  0
 59T  CONST_16  C11  C10  C9   C8     0.00   0.0  0
 59T  CONST_17  C13  C8   C9   C10    0.00   0.0  0
 59T  CONST_18  C13  C12  C11  C10    0.00   0.0  0
 59T  CONST_19  C23  C18  N19  C20    0.00   0.0  0
 59T  CONST_20  C23  C22  N21  C20    0.00   0.0  0
 59T  CONST_21  N19  C20  N21  C22    0.00   0.0  0
 59T  CONST_22  N19  C18  C23  C22    0.00   0.0  0
 59T  CONST_23  C12  C13  C8   C9     0.00   0.0  0
 59T  CONST_24  C12  C11  C10  C9     0.00   0.0  0
 59T  CONST_25  N21  C20  N19  C18    0.00   0.0  0
 59T  CONST_26  N21  C22  C23  C18    0.00   0.0  0
 59T  CONST_27  C14  C11  C12  C13  180.00   0.0  0
 59T  CONST_28  C14  C11  C10  C9   180.00   0.0  0
 59T  CONST_29  C18  N17  C15  C14    0.00   0.0  0
 59T  CONST_30  C1   C2   N3   C4   180.00   0.0  0
 59T  CONST_31  C1   C2   C7   C6   180.00   0.0  0
 59T  CONST_32  CL1  C10  C9   C8   180.00   0.0  0
 59T  CONST_33  N25  C20  N21  C22  180.00   0.0  0
 59T  CONST_34  CL1  C10  C11  C12  180.00   0.0  0
 59T  CONST_35  CL1  C10  C11  C14    0.00   0.0  0
 59T  CONST_36  N25  C20  N19  C18  180.00   0.0  0
 59T  CONST_37  C27  N17  C15  C14  180.00   0.0  0
 59T  CONST_38  C18  N17  C15  O16  180.00   0.0  0
 59T  CONST_39  H1   C5   C4   N3   180.00   0.0  0
 59T  CONST_40  H3   C7   C2   N3   180.00   0.0  0
 59T  CONST_41  H2   C6   C5   C4   180.00   0.0  0
 59T  CONST_42  H4   C13  C8   C4     0.00   0.0  0
 59T  CONST_43  H14  C9   C8   C4     0.00   0.0  0
 59T  CONST_44  H15  C12  C13  C8   180.00   0.0  0
 59T  CONST_45  H5   C22  N21  C20  180.00   0.0  0
 59T  CONST_46  N19  C20  N25  C26  180.00   0.0  0
 59T  CONST_47  N21  C20  N25  C26    0.00   0.0  0
 59T  CONST_48  C27  N17  C15  O16    0.00   0.0  0
 59T  CONST_49  H16  N25  C20  N19    0.00   0.0  0
 59T  Var_01    C15  C14  C11  C10  117.70  30.0  2
 59T  Var_02    C32  C31  O30  C28  -56.75  30.0  1
 59T  Var_03    C32  C34  O35  C28   57.16  30.0  1
 59T  Var_04    C28  C27  N17  C15   89.24  30.0  3
 59T  Var_05    H11  C1   C2   N3    82.30  30.0  2
 59T  Var_06    H7   C26  N25  C20  -56.88  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 59T  chir_01  C28  O30  O35  C27  negativ
 59T  chir_02  C32  N36  C31  C34  negativ

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
 59T  plan-1  N3   0.020
 59T  plan-1  C4   0.020
 59T  plan-1  C5   0.020
 59T  plan-1  C6   0.020
 59T  plan-1  C7   0.020
 59T  plan-1  C8   0.020
 59T  plan-1  C2   0.020
 59T  plan-1  H1   0.020
 59T  plan-1  H2   0.020
 59T  plan-1  H3   0.020
 59T  plan-1  C1   0.020
 59T  plan-2  C4   0.020
 59T  plan-2  C8   0.020
 59T  plan-2  C10  0.020
 59T  plan-2  C13  0.020
 59T  plan-2  C9   0.020
 59T  plan-2  C11  0.020
 59T  plan-2  C12  0.020
 59T  plan-2  C14  0.020
 59T  plan-2  CL1  0.020
 59T  plan-2  H4   0.020
 59T  plan-2  H14  0.020
 59T  plan-2  H15  0.020
 59T  plan-3  C15  0.020
 59T  plan-3  C20  0.020
 59T  plan-3  C22  0.020
 59T  plan-3  C24  0.020
 59T  plan-3  C11  0.020
 59T  plan-3  C14  0.020
 59T  plan-3  N17  0.020
 59T  plan-3  C18  0.020
 59T  plan-3  N19  0.020
 59T  plan-3  N21  0.020
 59T  plan-3  C23  0.020
 59T  plan-3  N25  0.020
 59T  plan-3  C27  0.020
 59T  plan-3  H5   0.020
 59T  plan-3  H6   0.020
 59T  plan-3  O16  0.020
 59T  plan-4  C20  0.020
 59T  plan-4  C26  0.020
 59T  plan-4  N25  0.020
 59T  plan-4  H16  0.020

