# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:05:27 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: N~6~-methyl-N~6~-(3,4,5-trifluorophenyl)pyrido[2,3-d]pyrimidine-2,4,6-triamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(c1cnc2nc(N)nc(N)c2c1)c3cc(F)c(F)c(F)c3
#
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
 IXE  IXE  N~6~-methyl-N~6~-(3,4,5-trifluorophenyl)pyrido[2,3-d]pyrimidine-2,4,6-triamine  ligand  34  23  .  2022-07-25  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_IXE
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
 IXE  C3   C  CR16  0  -0.184   1.5795  -1.1369  -0.1479
 IXE  C4   C  CR66  0  -0.152   2.7789  -0.4612   0.0804
 IXE  C8   C  CR6   0   0.495   3.9458  -1.0270   0.7123
 IXE  N6   N  NH2   0  -0.823   3.9630  -2.2955   1.1217
 IXE  N5   N  N     0  -0.507   5.0221  -0.2995   0.9102
 IXE  C7   C  CR6   0   0.548   5.0003   0.9850   0.4984
 IXE  N4   N  NH2   0  -0.815   6.1345   1.6731   0.7054
 IXE  N3   N  N     0  -0.500   4.0011   1.6133  -0.0979
 IXE  C5   C  CR66  0   0.365   2.8892   0.8943  -0.3075
 IXE  N2   N  N     0  -0.426   1.8639   1.5281  -0.9141
 IXE  C6   C  CR16  0  -0.065   0.7567   0.8647  -1.1339
 IXE  C2   C  CR6   0   0.146   0.5450  -0.4754  -0.7681
 IXE  N1   N  NT    0  -0.598  -0.6801  -1.1139  -1.0532
 IXE  C1   C  CH3   0  -0.553  -0.7497  -1.9929  -2.2035
 IXE  C9   C  CR6   0   0.404  -1.8236  -0.7461  -0.3891
 IXE  C10  C  CR16  0  -0.515  -1.7601   0.0408   0.7734
 IXE  C11  C  CR6   0   0.440  -2.9193   0.3828   1.4299
 IXE  F1   F  F     0  -0.306  -2.8534   1.1277   2.5363
 IXE  C12  C  CR6   0   0.218  -4.1655  -0.0272   0.9916
 IXE  F2   F  F     0  -0.306  -5.2788   0.3147   1.6496
 IXE  C13  C  CR6   0   0.448  -4.2159  -0.8065  -0.1467
 IXE  F3   F  F     0  -0.306  -5.4113  -1.2111  -0.5828
 IXE  C14  C  CR16  0  -0.546  -3.0824  -1.1689  -0.8428
 IXE  H1   H  HCR6  0   0.271   1.4363  -2.1687   0.1500
 IXE  H2   H  HNH2  0   0.419   3.2196  -2.9419   0.9305
 IXE  H3   H  HNH2  0   0.408   4.8087  -2.6729   1.5150
 IXE  H4   H  HNH2  0   0.398   6.8600   1.2772   1.2763
 IXE  H5   H  HNH2  0   0.397   6.1488   2.6646   0.5434
 IXE  H6   H  HCR6  0   0.279  -0.0461   1.4035  -1.6309
 IXE  H7   H  HCH3  0   0.249  -1.2419  -2.9339  -1.9516
 IXE  H8   H  HCH3  0   0.244  -1.2831  -1.5374  -3.0430
 IXE  H9   H  HCH3  0   0.272   0.2594  -2.2224  -2.5330
 IXE  H10  H  HCR6  0   0.299  -0.8172   0.3752   1.1828
 IXE  H11  H  HCR6  0   0.304  -3.1988  -1.7723  -1.7314

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
 IXE  F2   C12  single    1.338  0.020  1.338
 IXE  F3   C13  single    1.335  0.020  1.335
 IXE  C13  C12  aromatic  1.380  0.020  1.380
 IXE  C13  C14  aromatic  1.379  0.020  1.379
 IXE  C12  C11  aromatic  1.383  0.020  1.383
 IXE  F1   C11  single    1.335  0.020  1.335
 IXE  C11  C10  aromatic  1.375  0.020  1.375
 IXE  C14  C9   aromatic  1.403  0.020  1.403
 IXE  N2   C6   aromatic  1.309  0.020  1.309
 IXE  N2   C5   aromatic  1.349  0.020  1.349
 IXE  C6   C2   aromatic  1.405  0.020  1.405
 IXE  C9   C10  aromatic  1.405  0.020  1.405
 IXE  C9   N1   single    1.373  0.020  1.373
 IXE  N3   C5   aromatic  1.341  0.020  1.341
 IXE  N3   C7   aromatic  1.323  0.020  1.323
 IXE  C5   C4   aromatic  1.414  0.020  1.414
 IXE  N4   C7   single    1.343  0.020  1.343
 IXE  C2   N1   single    1.411  0.020  1.411
 IXE  C2   C3   aromatic  1.376  0.020  1.376
 IXE  N1   C1   single    1.449  0.020  1.449
 IXE  C7   N5   aromatic  1.349  0.020  1.349
 IXE  C4   C3   aromatic  1.395  0.020  1.395
 IXE  C4   C8   aromatic  1.443  0.020  1.443
 IXE  N5   C8   aromatic  1.314  0.020  1.314
 IXE  C8   N6   single    1.333  0.020  1.333
 IXE  C3   H1   single    0.930  0.020  1.080
 IXE  N6   H2   single    0.860  0.020  1.020
 IXE  N6   H3   single    0.860  0.020  1.020
 IXE  N4   H4   single    0.860  0.020  1.020
 IXE  N4   H5   single    0.860  0.020  1.020
 IXE  C6   H6   single    0.930  0.020  1.080
 IXE  C1   H7   single    0.970  0.020  1.090
 IXE  C1   H8   single    0.970  0.020  1.090
 IXE  C1   H9   single    0.970  0.020  1.090
 IXE  C10  H10  single    0.930  0.020  1.080
 IXE  C14  H11  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
 IXE  H1   C3   C2   118.85  3.000
 IXE  H1   C3   C4   121.99  3.000
 IXE  C2   C3   C4   119.17  3.000
 IXE  C5   C4   C8   115.66  3.000
 IXE  C8   C4   C3   125.24  3.000
 IXE  C5   C4   C3   119.09  3.000
 IXE  N5   C8   N6   118.03  3.000
 IXE  N6   C8   C4   121.21  3.000
 IXE  N5   C8   C4   120.76  3.000
 IXE  H3   N6   H2   117.09  3.000
 IXE  H3   N6   C8   119.20  3.000
 IXE  H2   N6   C8   123.02  3.000
 IXE  C7   N5   C8   117.90  3.000
 IXE  N3   C7   N4   117.66  3.000
 IXE  N4   C7   N5   115.30  3.000
 IXE  N3   C7   N5   127.03  3.000
 IXE  H5   N4   H4   118.05  3.000
 IXE  H5   N4   C7   119.53  3.000
 IXE  H4   N4   C7   119.72  3.000
 IXE  C5   N3   C7   116.25  3.000
 IXE  N2   C5   N3   116.65  3.000
 IXE  N3   C5   C4   122.40  3.000
 IXE  N2   C5   C4   120.95  3.000
 IXE  C6   N2   C5   118.69  3.000
 IXE  H6   C6   C2   118.71  3.000
 IXE  H6   C6   N2   116.75  3.000
 IXE  C2   C6   N2   124.53  3.000
 IXE  N1   C2   C6   120.66  3.000
 IXE  N1   C2   C3   121.78  3.000
 IXE  C6   C2   C3   117.56  3.000
 IXE  C9   N1   C1   120.43  3.000
 IXE  C1   N1   C2   118.46  3.000
 IXE  C9   N1   C2   120.30  3.000
 IXE  H9   C1   H8   107.95  3.000
 IXE  H9   C1   H7   107.86  3.000
 IXE  H8   C1   H7   108.44  3.000
 IXE  H9   C1   N1   108.93  3.000
 IXE  H8   C1   N1   112.33  3.000
 IXE  H7   C1   N1   111.18  3.000
 IXE  C14  C9   C10  118.47  3.000
 IXE  C10  C9   N1   120.85  3.000
 IXE  C14  C9   N1   120.68  3.000
 IXE  H10  C10  C11  118.51  3.000
 IXE  H10  C10  C9   121.73  3.000
 IXE  C11  C10  C9   119.74  3.000
 IXE  C12  C11  F1   118.18  3.000
 IXE  F1   C11  C10  119.52  3.000
 IXE  C12  C11  C10  122.30  3.000
 IXE  C13  C12  F2   121.30  3.000
 IXE  C13  C12  C11  117.49  3.000
 IXE  F2   C12  C11  121.21  3.000
 IXE  C14  C13  F3   119.44  3.000
 IXE  C14  C13  C12  122.32  3.000
 IXE  F3   C13  C12  118.23  3.000
 IXE  H11  C14  C13  118.26  3.000
 IXE  H11  C14  C9   122.06  3.000
 IXE  C13  C14  C9   119.68  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
 IXE  CONST_01  N2   C6   C2   C3     0.00   0.0  0
 IXE  CONST_02  N2   C5   C4   C3     0.00   0.0  0
 IXE  CONST_03  N3   C5   C4   C3   180.00   0.0  0
 IXE  CONST_04  N5   C8   C4   C3   180.00   0.0  0
 IXE  CONST_05  C6   N2   C5   C4     0.00   0.0  0
 IXE  CONST_06  C7   N3   C5   C4     0.00   0.0  0
 IXE  CONST_07  C6   C2   C3   C4     0.00   0.0  0
 IXE  CONST_08  C7   N5   C8   C4     0.00   0.0  0
 IXE  CONST_09  N2   C5   C4   C8   180.00   0.0  0
 IXE  CONST_10  N3   C5   C4   C8     0.00   0.0  0
 IXE  CONST_11  C2   C3   C4   C8   180.00   0.0  0
 IXE  CONST_12  N3   C7   N5   C8     0.00   0.0  0
 IXE  CONST_13  C5   N3   C7   N5     0.00   0.0  0
 IXE  CONST_14  C5   C4   C8   N5     0.00   0.0  0
 IXE  CONST_15  N2   C5   N3   C7   180.00   0.0  0
 IXE  CONST_16  C6   N2   C5   N3   180.00   0.0  0
 IXE  CONST_17  C2   C6   N2   C5     0.00   0.0  0
 IXE  CONST_18  C2   C3   C4   C5     0.00   0.0  0
 IXE  CONST_19  C12  C13  C14  C9     0.00   0.0  0
 IXE  CONST_20  C12  C11  C10  C9     0.00   0.0  0
 IXE  CONST_21  C13  C12  C11  C10    0.00   0.0  0
 IXE  CONST_22  C13  C14  C9   C10    0.00   0.0  0
 IXE  CONST_23  C14  C13  C12  C11    0.00   0.0  0
 IXE  CONST_24  C14  C9   C10  C11    0.00   0.0  0
 IXE  CONST_25  N6   C8   C4   C3     0.00   0.0  0
 IXE  CONST_26  N1   C2   C3   C4   180.00   0.0  0
 IXE  CONST_27  N4   C7   N5   C8   180.00   0.0  0
 IXE  CONST_28  C5   C4   C8   N6   180.00   0.0  0
 IXE  CONST_29  C7   N5   C8   N6   180.00   0.0  0
 IXE  CONST_30  C5   N3   C7   N4   180.00   0.0  0
 IXE  CONST_31  N1   C2   C6   N2   180.00   0.0  0
 IXE  CONST_32  C13  C14  C9   N1   180.00   0.0  0
 IXE  CONST_33  C11  C10  C9   N1   180.00   0.0  0
 IXE  CONST_34  F3   C13  C14  C9   180.00   0.0  0
 IXE  CONST_35  F1   C11  C10  C9   180.00   0.0  0
 IXE  CONST_36  F2   C12  C11  C10  180.00   0.0  0
 IXE  CONST_37  F3   C13  C12  C11  180.00   0.0  0
 IXE  CONST_38  C13  C12  C11  F1   180.00   0.0  0
 IXE  CONST_39  C14  C13  C12  F2   180.00   0.0  0
 IXE  CONST_40  H6   C6   C2   C3   180.00   0.0  0
 IXE  CONST_41  H1   C3   C4   C8     0.00   0.0  0
 IXE  CONST_42  H11  C14  C9   C10  180.00   0.0  0
 IXE  CONST_43  H10  C10  C11  C12  180.00   0.0  0
 IXE  CONST_44  H2   N6   C8   C4     0.00   0.0  0
 IXE  CONST_45  H3   N6   C8   C4   180.00   0.0  0
 IXE  CONST_46  H4   N4   C7   N5     0.00   0.0  0
 IXE  CONST_47  H5   N4   C7   N5   180.00   0.0  0
 IXE  Var_01    C9   N1   C2   C3   111.71  30.0  2
 IXE  Var_02    C14  C9   N1   C2   166.95  30.0  2
 IXE  Var_03    H7   C1   N1   C2   133.38  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
 IXE  plan-1  N1   0.020
 IXE  plan-1  C9   0.020
 IXE  plan-1  C10  0.020
 IXE  plan-1  C11  0.020
 IXE  plan-1  F1   0.020
 IXE  plan-1  C12  0.020
 IXE  plan-1  F2   0.020
 IXE  plan-1  C13  0.020
 IXE  plan-1  F3   0.020
 IXE  plan-1  C14  0.020
 IXE  plan-1  H10  0.020
 IXE  plan-1  H11  0.020
 IXE  plan-2  C3   0.020
 IXE  plan-2  C4   0.020
 IXE  plan-2  C8   0.020
 IXE  plan-2  N6   0.020
 IXE  plan-2  N5   0.020
 IXE  plan-2  C7   0.020
 IXE  plan-2  N4   0.020
 IXE  plan-2  N3   0.020
 IXE  plan-2  C5   0.020
 IXE  plan-2  N2   0.020
 IXE  plan-2  C6   0.020
 IXE  plan-2  C2   0.020
 IXE  plan-2  N1   0.020
 IXE  plan-2  H1   0.020
 IXE  plan-2  H6   0.020
 IXE  plan-3  C8   0.020
 IXE  plan-3  N6   0.020
 IXE  plan-3  H2   0.020
 IXE  plan-3  H3   0.020
 IXE  plan-4  C7   0.020
 IXE  plan-4  N4   0.020
 IXE  plan-4  H4   0.020
 IXE  plan-4  H5   0.020

