# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 22:59:20 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: N-[(1S)-1-(5-fluoropyrimidin-2-yl)ethyl]-N'-(1-methyl-1H-imidazol-4-yl)-6-(morpholin-4-yl)-1,3,5-triazine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Nc1nc(Nc2cn(C)cn2)nc(n1)N3CCOCC3)c4ncc(F)cn4
#
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
 XWW  XWW  N-[(1S)-1-(5-fluoropyrimidin-2-yl)ethyl]-N'-(1-methyl-1H-imidazol-4-yl)-6-(morpholin-4-yl)-1,3,5-triazine-2,4-diamine  ligand  50  29  .  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_XWW
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
 XWW  C1    C  CH3   0  -0.665  -2.3533   0.1730  -1.8602
 XWW  C2    C  CH1   0  -0.140  -2.0369  -0.5147  -0.5288
 XWW  C3    C  CR6   0   0.396  -3.0883  -1.5545  -0.2231
 XWW  N1    N  N     0  -0.390  -4.2821  -1.0936   0.1313
 XWW  C4    C  CR16  0  -0.154  -5.2337  -1.9791   0.3739
 XWW  C5    C  CR6   0   0.398  -4.9787  -3.3326   0.2578
 XWW  C6    C  CR16  0  -0.145  -3.7164  -3.7342  -0.1188
 XWW  N2    N  N     0  -0.414  -2.7740  -2.8323  -0.3595
 XWW  F1    F  F     0  -0.288  -5.9339  -4.2276   0.5073
 XWW  N3    N  NH1   0  -0.665  -0.7357  -1.1343  -0.5246
 XWW  C7    C  CR6   0   0.626   0.4217  -0.4735  -0.3895
 XWW  N4    N  N     0  -0.539   0.3687   0.8483  -0.2024
 XWW  C8    C  CR6   0   0.599   1.5583   1.4210  -0.0671
 XWW  N5    N  N     0  -0.551   2.7371   0.8038  -0.1038
 XWW  C9    C  CR6   0   0.652   2.6693  -0.5160  -0.2965
 XWW  N6    N  N     0  -0.548   1.5349  -1.2027  -0.4477
 XWW  N7    N  NT    0  -0.509   3.8276  -1.2035  -0.3416
 XWW  C10   C  CH2   0  -0.320   5.1270  -0.5706  -0.2484
 XWW  C11   C  CH2   0  -0.183   5.9904  -1.3176   0.7534
 XWW  O1    O  O2    0  -0.485   6.0788  -2.6912   0.4451
 XWW  C12   C  CH2   0  -0.183   4.8014  -3.2891   0.4238
 XWW  C13   C  CH2   0  -0.319   3.8874  -2.6295  -0.5936
 XWW  N8    N  NH1   0  -0.736   1.6056   2.7567   0.1251
 XWW  C14   C  CR5   0   0.312   0.5463   3.6488   0.1790
 XWW  C15   C  CR15  0  -0.119  -0.8058   3.4677   0.0370
 XWW  N9    N  NR5   0  -0.402  -1.3426   4.7232   0.1842
 XWW  C16   C  CR15  0   0.096  -0.3277   5.5717   0.3995
 XWW  N10   N  N     0  -0.483   0.8327   4.9588   0.4039
 XWW  C17   C  CH3   0  -0.519  -2.7468   5.0538   0.1139
 XWW  H11C  H  HCH3  0   0.248  -1.6091   0.9424  -2.0603
 XWW  H12C  H  HCH3  0   0.237  -2.3409  -0.5458  -2.6801
 XWW  H13C  H  HCH3  0   0.239  -3.3344   0.6458  -1.8284
 XWW  H2    H  HCH1  0   0.275  -2.0789   0.2335   0.2668
 XWW  H3    H  HNH1  0   0.395  -0.6869  -2.1293  -0.6823
 XWW  H4    H  HCR6  0   0.304  -6.2115  -1.6138   0.6681
 XWW  H6    H  HCR6  0   0.305  -3.4622  -4.7826  -0.2271
 XWW  H8    H  HNH1  0   0.400   2.5234   3.1590   0.2376
 XWW  H101  H  HCH2  0   0.237   5.6112  -0.5742  -1.2322
 XWW  H102  H  HCH2  0   0.272   5.0141   0.4644   0.0613
 XWW  H131  H  HCH2  0   0.272   2.8915  -3.0578  -0.5283
 XWW  H132  H  HCH2  0   0.237   4.2646  -2.8088  -1.6072
 XWW  H111  H  HCH2  0   0.242   7.0034  -0.9132   0.7414
 XWW  H112  H  HCH2  0   0.206   5.5809  -1.1762   1.7638
 XWW  H121  H  HCH2  0   0.241   4.9370  -4.3413   0.1693
 XWW  H122  H  HCH2  0   0.206   4.3357  -3.2365   1.4181
 XWW  H15   H  HCR5  0   0.298  -1.4061   2.5965  -0.1438
 XWW  H16   H  HCR5  0   0.281  -0.4797   6.6302   0.5478
 XWW  H171  H  HCH3  0   0.260  -3.3061   4.5102   0.8729
 XWW  H172  H  HCH3  0   0.263  -2.8704   6.1194   0.2865
 XWW  H173  H  HCH3  0   0.258  -3.1504   4.8100  -0.8673

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
 XWW  C1   C2    single    1.531  0.020  1.531
 XWW  C2   C3    single    1.510  0.020  1.510
 XWW  C2   N3    single    1.441  0.020  1.441
 XWW  C3   N1    aromatic  1.328  0.020  1.328
 XWW  C3   N2    aromatic  1.323  0.020  1.323
 XWW  N1   C4    aromatic  1.322  0.020  1.322
 XWW  C4   C5    aromatic  1.382  0.020  1.382
 XWW  C5   C6    aromatic  1.377  0.020  1.377
 XWW  C5   F1    single    1.333  0.020  1.333
 XWW  C6   N2    aromatic  1.326  0.020  1.326
 XWW  N3   C7    single    1.340  0.020  1.340
 XWW  C7   N4    aromatic  1.336  0.020  1.336
 XWW  C7   N6    aromatic  1.332  0.020  1.332
 XWW  N4   C8    aromatic  1.327  0.020  1.327
 XWW  C8   N5    aromatic  1.331  0.020  1.331
 XWW  C8   N8    single    1.350  0.020  1.350
 XWW  N5   C9    aromatic  1.336  0.020  1.336
 XWW  C9   N6    aromatic  1.335  0.020  1.335
 XWW  C9   N7    single    1.348  0.020  1.348
 XWW  N7   C10   single    1.448  0.020  1.448
 XWW  N7   C13   single    1.449  0.020  1.449
 XWW  C10  C11   single    1.519  0.020  1.519
 XWW  C11  O1    single    1.411  0.020  1.411
 XWW  O1   C12   single    1.411  0.020  1.411
 XWW  C12  C13   single    1.518  0.020  1.518
 XWW  N8   C14   single    1.386  0.020  1.386
 XWW  C14  C15   aromatic  1.371  0.020  1.371
 XWW  C14  N10   aromatic  1.360  0.020  1.360
 XWW  C15  N9    aromatic  1.373  0.020  1.373
 XWW  N9   C16   aromatic  1.340  0.020  1.340
 XWW  N9   C17   single    1.444  0.020  1.444
 XWW  C16  N10   aromatic  1.312  0.020  1.312
 XWW  C1   H11C  single    0.970  0.020  1.090
 XWW  C1   H12C  single    0.970  0.020  1.090
 XWW  C1   H13C  single    0.970  0.020  1.090
 XWW  C2   H2    single    0.970  0.020  1.090
 XWW  N3   H3    single    0.860  0.020  1.020
 XWW  C4   H4    single    0.930  0.020  1.080
 XWW  C6   H6    single    0.930  0.020  1.080
 XWW  N8   H8    single    0.860  0.020  1.020
 XWW  C10  H101  single    0.970  0.020  1.090
 XWW  C10  H102  single    0.970  0.020  1.090
 XWW  C13  H131  single    0.970  0.020  1.090
 XWW  C13  H132  single    0.970  0.020  1.090
 XWW  C11  H111  single    0.970  0.020  1.090
 XWW  C11  H112  single    0.970  0.020  1.090
 XWW  C12  H121  single    0.970  0.020  1.090
 XWW  C12  H122  single    0.970  0.020  1.090
 XWW  C15  H15   single    0.930  0.020  1.080
 XWW  C16  H16   single    0.930  0.020  1.080
 XWW  C17  H171  single    0.970  0.020  1.090
 XWW  C17  H172  single    0.970  0.020  1.090
 XWW  C17  H173  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
 XWW  H13C  C1   H12C  108.55  3.000
 XWW  H13C  C1   H11C  108.31  3.000
 XWW  H12C  C1   H11C  108.66  3.000
 XWW  H13C  C1   C2    110.83  3.000
 XWW  H12C  C1   C2    110.81  3.000
 XWW  H11C  C1   C2    109.62  3.000
 XWW  H2    C2   N3    109.08  3.000
 XWW  H2    C2   C3    107.29  3.000
 XWW  N3    C2   C3    109.39  3.000
 XWW  H2    C2   C1    108.51  3.000
 XWW  N3    C2   C1    112.46  3.000
 XWW  C3    C2   C1    109.96  3.000
 XWW  N2    C3   N1    125.19  3.000
 XWW  N2    C3   C2    118.61  3.000
 XWW  N1    C3   C2    116.17  3.000
 XWW  C4    N1   C3    117.62  3.000
 XWW  H4    C4   C5    121.26  3.000
 XWW  H4    C4   N1    118.23  3.000
 XWW  C5    C4   N1    120.50  3.000
 XWW  F1    C5   C6    120.82  3.000
 XWW  F1    C5   C4    120.65  3.000
 XWW  C6    C5   C4    118.53  3.000
 XWW  H6    C6   N2    118.21  3.000
 XWW  H6    C6   C5    121.61  3.000
 XWW  N2    C6   C5    120.17  3.000
 XWW  C6    N2   C3    117.98  3.000
 XWW  H3    N3   C7    117.42  3.000
 XWW  H3    N3   C2    117.86  3.000
 XWW  C7    N3   C2    124.63  3.000
 XWW  N6    C7   N4    125.51  3.000
 XWW  N6    C7   N3    116.59  3.000
 XWW  N4    C7   N3    117.90  3.000
 XWW  C8    N4   C7    113.93  3.000
 XWW  N8    C8   N5    115.56  3.000
 XWW  N8    C8   N4    118.22  3.000
 XWW  N5    C8   N4    126.22  3.000
 XWW  C9    N5   C8    114.66  3.000
 XWW  N7    C9   N6    117.67  3.000
 XWW  N7    C9   N5    117.73  3.000
 XWW  N6    C9   N5    124.61  3.000
 XWW  C9    N6   C7    115.07  3.000
 XWW  C13   N7   C10   113.84  3.000
 XWW  C13   N7   C9    122.89  3.000
 XWW  C10   N7   C9    123.10  3.000
 XWW  H102  C10  H101  107.75  3.000
 XWW  H102  C10  C11   109.86  3.000
 XWW  H101  C10  C11   109.83  3.000
 XWW  H102  C10  N7    109.96  3.000
 XWW  H101  C10  N7    109.69  3.000
 XWW  C11   C10  N7    109.72  3.000
 XWW  H112  C11  H111  107.95  3.000
 XWW  H112  C11  O1    110.46  3.000
 XWW  H111  C11  O1    107.48  3.000
 XWW  H112  C11  C10   109.35  3.000
 XWW  H111  C11  C10   109.77  3.000
 XWW  O1    C11  C10   111.74  3.000
 XWW  C12   O1   C11   111.06  3.000
 XWW  H122  C12  H121  108.05  3.000
 XWW  H122  C12  C13   109.28  3.000
 XWW  H121  C12  C13   109.73  3.000
 XWW  H122  C12  O1    110.47  3.000
 XWW  H121  C12  O1    107.44  3.000
 XWW  C13   C12  O1    111.78  3.000
 XWW  H132  C13  H131  107.86  3.000
 XWW  H132  C13  C12   109.95  3.000
 XWW  H131  C13  C12   109.90  3.000
 XWW  H132  C13  N7    109.62  3.000
 XWW  H131  C13  N7    109.86  3.000
 XWW  C12   C13  N7    109.62  3.000
 XWW  H8    N8   C14   115.75  3.000
 XWW  H8    N8   C8    116.26  3.000
 XWW  C14   N8   C8    127.99  3.000
 XWW  N10   C14  C15   110.61  3.000
 XWW  N10   C14  N8    117.75  3.000
 XWW  C15   C14  N8    131.64  3.000
 XWW  H15   C15  N9    122.78  3.000
 XWW  H15   C15  C14   132.53  3.000
 XWW  N9    C15  C14   104.69  3.000
 XWW  C17   N9   C16   126.81  3.000
 XWW  C17   N9   C15   125.73  3.000
 XWW  C16   N9   C15   107.46  3.000
 XWW  H16   C16  N10   125.59  3.000
 XWW  H16   C16  N9    122.42  3.000
 XWW  N10   C16  N9    111.99  3.000
 XWW  C16   N10  C14   105.26  3.000
 XWW  H173  C17  H172  108.70  3.000
 XWW  H173  C17  H171  109.04  3.000
 XWW  H172  C17  H171  108.70  3.000
 XWW  H173  C17  N9    110.67  3.000
 XWW  H172  C17  N9    109.11  3.000
 XWW  H171  C17  N9    110.57  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
 XWW  CONST_01  C5    C4   N1   C3      0.00   0.0  0
 XWW  CONST_02  C5    C6   N2   C3      0.00   0.0  0
 XWW  CONST_03  C6    N2   C3   N1      0.00   0.0  0
 XWW  CONST_04  C6    C5   C4   N1      0.00   0.0  0
 XWW  CONST_05  N2    C3   N1   C4      0.00   0.0  0
 XWW  CONST_06  N2    C6   C5   C4      0.00   0.0  0
 XWW  CONST_07  N5    C8   N4   C7      0.00   0.0  0
 XWW  CONST_08  N5    C9   N6   C7      0.00   0.0  0
 XWW  CONST_09  C9    N6   C7   N4      0.00   0.0  0
 XWW  CONST_10  C9    N5   C8   N4      0.00   0.0  0
 XWW  CONST_11  N6    C7   N4   C8      0.00   0.0  0
 XWW  CONST_12  N6    C9   N5   C8      0.00   0.0  0
 XWW  CONST_13  C16   N9   C15  C14     0.00   0.0  0
 XWW  CONST_14  N9    C16  N10  C14     0.00   0.0  0
 XWW  CONST_15  C16   N10  C14  C15     0.00   0.0  0
 XWW  CONST_16  N10   C16  N9   C15     0.00   0.0  0
 XWW  CONST_17  N10   C14  C15  N9      0.00   0.0  0
 XWW  CONST_18  N7    C9   N6   C7    180.00   0.0  0
 XWW  CONST_19  N7    C9   N5   C8    180.00   0.0  0
 XWW  CONST_20  C4    N1   C3   C2    180.00   0.0  0
 XWW  CONST_21  C6    N2   C3   C2    180.00   0.0  0
 XWW  CONST_22  F1    C5   C4   N1    180.00   0.0  0
 XWW  CONST_23  F1    C5   C6   N2    180.00   0.0  0
 XWW  CONST_24  C8    N4   C7   N3    180.00   0.0  0
 XWW  CONST_25  C9    N6   C7   N3    180.00   0.0  0
 XWW  CONST_26  N8    C8   N4   C7    180.00   0.0  0
 XWW  CONST_27  N8    C8   N5   C9    180.00   0.0  0
 XWW  CONST_28  N9    C15  C14  N8    180.00   0.0  0
 XWW  CONST_29  C16   N10  C14  N8    180.00   0.0  0
 XWW  CONST_30  C17   N9   C15  C14   180.00   0.0  0
 XWW  CONST_31  C17   N9   C16  N10   180.00   0.0  0
 XWW  CONST_32  H4    C4   N1   C3    180.00   0.0  0
 XWW  CONST_33  H6    C6   N2   C3    180.00   0.0  0
 XWW  CONST_34  H16   C16  N10  C14   180.00   0.0  0
 XWW  CONST_35  H15   C15  N9   C16   180.00   0.0  0
 XWW  CONST_36  N4    C7   N3   C2      0.00   0.0  0
 XWW  CONST_37  N6    C7   N3   C2    180.00   0.0  0
 XWW  CONST_38  H3    N3   C7   N4    180.00   0.0  0
 XWW  Var_01    C10   N7   C9   N5     -2.70  30.0  2
 XWW  Var_02    C11   C10  N7   C9    132.53  30.0  1
 XWW  Var_03    C12   C13  N7   C9   -132.49  30.0  1
 XWW  Var_04    O1    C11  C10  N7     54.45  30.0  1
 XWW  Var_05    O1    C12  C13  N7    -54.58  30.0  1
 XWW  Var_06    C13   C12  O1   C11    58.89  30.0  1
 XWW  Var_07    C14   N8   C8   N4     -1.30  30.0  2
 XWW  Var_08    C15   C14  N8   C8     -1.33  30.0  2
 XWW  Var_09    H171  C17  N9   C15    59.46  30.0  2

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
 XWW  chir_01  C2  C1  C3  N3  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
 XWW  plan-1  N8   0.020
 XWW  plan-1  C14  0.020
 XWW  plan-1  C15  0.020
 XWW  plan-1  N9   0.020
 XWW  plan-1  C16  0.020
 XWW  plan-1  N10  0.020
 XWW  plan-1  C17  0.020
 XWW  plan-1  H15  0.020
 XWW  plan-1  H16  0.020
 XWW  plan-2  C2   0.020
 XWW  plan-2  C3   0.020
 XWW  plan-2  N1   0.020
 XWW  plan-2  C4   0.020
 XWW  plan-2  C5   0.020
 XWW  plan-2  C6   0.020
 XWW  plan-2  N2   0.020
 XWW  plan-2  F1   0.020
 XWW  plan-2  H4   0.020
 XWW  plan-2  H6   0.020
 XWW  plan-3  N3   0.020
 XWW  plan-3  C7   0.020
 XWW  plan-3  N4   0.020
 XWW  plan-3  C8   0.020
 XWW  plan-3  N5   0.020
 XWW  plan-3  C9   0.020
 XWW  plan-3  N6   0.020
 XWW  plan-3  N7   0.020
 XWW  plan-3  N8   0.020
 XWW  plan-4  C2   0.020
 XWW  plan-4  N3   0.020
 XWW  plan-4  C7   0.020
 XWW  plan-4  H3   0.020

