# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 21:36:40 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-{[3-(2H-1,2,3-triazol-2-yl)phenyl]amino}pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCCC[C@H]1Nc2ncc(C(N)=O)c(Nc3cccc(c3)n4nccn4)n2
#
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
 3YT  3YT  2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-{[3-(2H-1,2,3-triazol-2-yl)phenyl]amino}pyrimidine-5-carboxamide  ligand  52  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_3YT
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
 3YT  C2   C  CH1   0  -0.104   5.0930  -1.8909   0.9471
 3YT  C3   C  CH2   0  -0.438   4.8092  -3.1575   0.1418
 3YT  C11  C  CR16  0  -0.019   2.1636   2.5991  -0.5894
 3YT  C12  C  CR6   0  -0.304   0.7833   2.5617  -0.4588
 3YT  C13  C  C     0   0.542  -0.0719   3.7419  -0.6821
 3YT  C16  C  CR6   0   0.574   0.2585   1.2743  -0.1213
 3YT  C18  C  CR6   0   0.414  -1.8490  -0.0103   0.2598
 3YT  C19  C  CR16  0  -0.321  -1.3614  -1.2331   0.7278
 3YT  C20  C  CR16  0  -0.234  -2.2542  -2.2596   0.9996
 3YT  C21  C  CR16  0  -0.338  -3.6194  -2.1167   0.8231
 3YT  C22  C  CR6   0   0.439  -4.0927  -0.8957   0.3580
 3YT  C23  C  CR16  0  -0.464  -3.2270   0.1468   0.0789
 3YT  C26  C  CR15  0  -0.139  -7.5180  -1.1152   0.1067
 3YT  C27  C  CR15  0  -0.134  -7.2854   0.1934  -0.3315
 3YT  N1   N  NH2   0  -0.800   4.4606  -1.9920   2.2527
 3YT  C4   C  CH2   0  -0.435   5.3757  -3.0762  -1.2709
 3YT  C5   C  CH2   0  -0.432   4.8696  -1.8319  -1.9913
 3YT  C6   C  CH2   0  -0.443   5.1794  -0.5741  -1.1909
 3YT  C7   C  CH1   0  -0.074   4.5992  -0.6300   0.2243
 3YT  N8   N  NH1   0  -0.642   3.1489  -0.6294   0.2261
 3YT  C9   C  CR6   0   0.628   2.3800   0.4341  -0.0233
 3YT  N10  N  N     0  -0.482   2.9744   1.5781  -0.3914
 3YT  N14  N  NH2   0  -0.818   0.5261   4.9407  -0.7420
 3YT  O15  O  O     0  -0.518  -1.2968   3.6409  -0.8164
 3YT  N24  N  NR5   0  -0.226  -5.4784  -0.7113   0.1615
 3YT  N25  N  N     0  -0.236  -6.3553  -1.6580   0.4099
 3YT  N28  N  N     0  -0.240  -5.9867   0.4157  -0.2845
 3YT  N29  N  N     0  -0.530   1.0612   0.2544   0.1103
 3YT  H1   H  HCH1  0   0.219   6.1867  -1.7794   1.0117
 3YT  H2   H  HCH2  0   0.236   5.2346  -4.0155   0.6706
 3YT  H3   H  HCH2  0   0.215   3.7291  -3.3358   0.0965
 3YT  H4   H  HCR6  0   0.261   2.6578   3.5160  -0.8943
 3YT  H5   H  HCR6  0   0.293  -0.3058  -1.3836   0.8741
 3YT  H6   H  HCR6  0   0.266  -1.8682  -3.2028   1.3629
 3YT  H7   H  HCR6  0   0.280  -4.2940  -2.9310   1.0411
 3YT  H8   H  HCR6  0   0.289  -3.6177   1.0875  -0.2859
 3YT  H10  H  HCR5  0   0.289  -7.9798   0.9472  -0.6633
 3YT  H11  H  HNH2  0   0.349   4.8049  -2.8147   2.7324
 3YT  H12  H  HNH2  0   0.346   4.7294  -1.2022   2.8277
 3YT  H14  H  HCH2  0   0.212   6.4697  -3.0513  -1.2275
 3YT  H15  H  HCH2  0   0.231   5.1086  -3.9768  -1.8283
 3YT  H16  H  HCH2  0   0.230   5.3175  -1.7574  -2.9848
 3YT  H17  H  HCH2  0   0.214   3.7887  -1.9117  -2.1445
 3YT  H18  H  HCH2  0   0.221   6.2638  -0.4501  -1.1044
 3YT  H19  H  HCH2  0   0.244   4.8077   0.3161  -1.6996
 3YT  H20  H  HCH1  0   0.248   4.9541   0.2460   0.7794
 3YT  H21  H  HNH1  0   0.392   2.6885  -1.4067   0.6747
 3YT  H22  H  HNH2  0   0.414   1.4845   5.0958  -0.4851
 3YT  H23  H  HNH2  0   0.408  -0.0413   5.7605  -0.8826
 3YT  N17  N  NH1   0  -0.805  -1.0804   1.1076  -0.0394
 3YT  H9   H  HCR5  0   0.289  -8.4428  -1.6579   0.2098
 3YT  H24  H  HNH1  0   0.437  -1.5895   1.9482  -0.3116

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
 3YT  C5   C6   single    1.523  0.020  1.523
 3YT  C5   C4   single    1.524  0.020  1.524
 3YT  C6   C7   single    1.531  0.020  1.531
 3YT  C27  N28  aromatic  1.318  0.020  1.318
 3YT  C27  C26  aromatic  1.399  0.020  1.399
 3YT  C4   C3   single    1.524  0.020  1.524
 3YT  N28  N24  aromatic  1.314  0.020  1.314
 3YT  C26  N25  aromatic  1.319  0.020  1.319
 3YT  C7   N8   single    1.450  0.020  1.450
 3YT  C7   C2   single    1.535  0.020  1.535
 3YT  N24  N25  aromatic  1.314  0.020  1.314
 3YT  N24  C22  single    1.412  0.020  1.412
 3YT  N8   C9   single    1.336  0.020  1.336
 3YT  C3   C2   single    1.528  0.020  1.528
 3YT  C2   N1   single    1.454  0.020  1.454
 3YT  C9   N29  aromatic  1.338  0.020  1.338
 3YT  C9   N10  aromatic  1.341  0.020  1.341
 3YT  C22  C23  aromatic  1.384  0.020  1.384
 3YT  C22  C21  aromatic  1.390  0.020  1.390
 3YT  C23  C18  aromatic  1.399  0.020  1.399
 3YT  N29  C16  aromatic  1.318  0.020  1.318
 3YT  N10  C11  aromatic  1.319  0.020  1.319
 3YT  C21  C20  aromatic  1.384  0.020  1.384
 3YT  C16  N17  single    1.352  0.020  1.352
 3YT  C16  C12  aromatic  1.431  0.020  1.431
 3YT  C18  N17  single    1.389  0.020  1.389
 3YT  C18  C19  aromatic  1.397  0.020  1.397
 3YT  C11  C12  aromatic  1.387  0.020  1.387
 3YT  C12  C13  single    1.474  0.020  1.474
 3YT  C20  C19  aromatic  1.387  0.020  1.387
 3YT  C13  N14  single    1.341  0.020  1.341
 3YT  C13  O15  double    1.236  0.020  1.236
 3YT  C2   H1   single    0.970  0.020  1.090
 3YT  C3   H2   single    0.970  0.020  1.090
 3YT  C3   H3   single    0.970  0.020  1.090
 3YT  C11  H4   single    0.930  0.020  1.080
 3YT  C19  H5   single    0.930  0.020  1.080
 3YT  C20  H6   single    0.930  0.020  1.080
 3YT  C21  H7   single    0.930  0.020  1.080
 3YT  C23  H8   single    0.930  0.020  1.080
 3YT  C26  H9   single    0.930  0.020  1.080
 3YT  C27  H10  single    0.930  0.020  1.080
 3YT  N1   H11  single    0.890  0.020  1.040
 3YT  N1   H12  single    0.890  0.020  1.040
 3YT  C4   H14  single    0.970  0.020  1.090
 3YT  C4   H15  single    0.970  0.020  1.090
 3YT  C5   H16  single    0.970  0.020  1.090
 3YT  C5   H17  single    0.970  0.020  1.090
 3YT  C6   H18  single    0.970  0.020  1.090
 3YT  C6   H19  single    0.970  0.020  1.090
 3YT  C7   H20  single    0.970  0.020  1.090
 3YT  N8   H21  single    0.860  0.020  1.020
 3YT  N14  H22  single    0.860  0.020  1.020
 3YT  N14  H23  single    0.860  0.020  1.020
 3YT  N17  H24  single    0.860  0.020  1.020

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
 3YT  H1   C2   C7   105.30  3.000
 3YT  H1   C2   N1   112.72  3.000
 3YT  C7   C2   N1   109.87  3.000
 3YT  H1   C2   C3   107.42  3.000
 3YT  N1   C2   C3   109.57  3.000
 3YT  C7   C2   C3   111.91  3.000
 3YT  H3   C3   H2   106.01  3.000
 3YT  H3   C3   C4   109.68  3.000
 3YT  H2   C3   C4   110.20  3.000
 3YT  H3   C3   C2   109.87  3.000
 3YT  H2   C3   C2   108.86  3.000
 3YT  C4   C3   C2   112.04  3.000
 3YT  H4   C11  N10  114.60  3.000
 3YT  H4   C11  C12  120.16  3.000
 3YT  N10  C11  C12  125.23  3.000
 3YT  C16  C12  C13  122.90  3.000
 3YT  C13  C12  C11  122.77  3.000
 3YT  C16  C12  C11  114.31  3.000
 3YT  O15  C13  N14  120.66  3.000
 3YT  O15  C13  C12  121.71  3.000
 3YT  N14  C13  C12  117.63  3.000
 3YT  N29  C16  N17  119.81  3.000
 3YT  N17  C16  C12  119.25  3.000
 3YT  N29  C16  C12  120.94  3.000
 3YT  N17  C18  C23  115.26  3.000
 3YT  N17  C18  C19  125.69  3.000
 3YT  C23  C18  C19  119.04  3.000
 3YT  H5   C19  C20  120.07  3.000
 3YT  H5   C19  C18  120.68  3.000
 3YT  C20  C19  C18  119.25  3.000
 3YT  H6   C20  C21  119.00  3.000
 3YT  H6   C20  C19  118.76  3.000
 3YT  C21  C20  C19  122.24  3.000
 3YT  H7   C21  C22  121.16  3.000
 3YT  H7   C21  C20  120.84  3.000
 3YT  C22  C21  C20  117.99  3.000
 3YT  N24  C22  C23  119.19  3.000
 3YT  C23  C22  C21  121.10  3.000
 3YT  N24  C22  C21  119.71  3.000
 3YT  H8   C23  C22  119.82  3.000
 3YT  H8   C23  C18  119.80  3.000
 3YT  C22  C23  C18  120.38  3.000
 3YT  H9   C26  N25  121.84  3.000
 3YT  H9   C26  C27  130.07  3.000
 3YT  N25  C26  C27  108.08  3.000
 3YT  H10  C27  N28  121.87  3.000
 3YT  H10  C27  C26  130.06  3.000
 3YT  N28  C27  C26  108.07  3.000
 3YT  H12  N1   H11  105.91  3.000
 3YT  H12  N1   C2   109.87  3.000
 3YT  H11  N1   C2   109.50  3.000
 3YT  H15  C4   H14  106.45  3.000
 3YT  H15  C4   C5   110.53  3.000
 3YT  H14  C4   C5   109.38  3.000
 3YT  H15  C4   C3   109.76  3.000
 3YT  H14  C4   C3   109.62  3.000
 3YT  C5   C4   C3   110.99  3.000
 3YT  H17  C5   H16  106.41  3.000
 3YT  H17  C5   C6   109.55  3.000
 3YT  H16  C5   C6   109.77  3.000
 3YT  H17  C5   C4   109.54  3.000
 3YT  H16  C5   C4   110.45  3.000
 3YT  C6   C5   C4   111.00  3.000
 3YT  H19  C6   H18  106.38  3.000
 3YT  H19  C6   C7   109.39  3.000
 3YT  H18  C6   C7   107.85  3.000
 3YT  H19  C6   C5   111.09  3.000
 3YT  H18  C6   C5   109.67  3.000
 3YT  C7   C6   C5   112.25  3.000
 3YT  H20  C7   N8   108.83  3.000
 3YT  H20  C7   C6   108.44  3.000
 3YT  N8   C7   C6   112.34  3.000
 3YT  H20  C7   C2   108.30  3.000
 3YT  N8   C7   C2   108.75  3.000
 3YT  C6   C7   C2   110.09  3.000
 3YT  H21  N8   C9   115.71  3.000
 3YT  H21  N8   C7   117.17  3.000
 3YT  C9   N8   C7   125.15  3.000
 3YT  N29  C9   N10  125.38  3.000
 3YT  N10  C9   N8   118.38  3.000
 3YT  N29  C9   N8   116.23  3.000
 3YT  C9   N10  C11  115.42  3.000
 3YT  H23  N14  H22  116.60  3.000
 3YT  H23  N14  C13  118.87  3.000
 3YT  H22  N14  C13  123.52  3.000
 3YT  N28  N24  N25  115.08  3.000
 3YT  N25  N24  C22  122.31  3.000
 3YT  N28  N24  C22  122.61  3.000
 3YT  N24  N25  C26  104.38  3.000
 3YT  N24  N28  C27  104.39  3.000
 3YT  C9   N29  C16  118.61  3.000
 3YT  H24  N17  C18  116.40  3.000
 3YT  H24  N17  C16  112.13  3.000
 3YT  C18  N17  C16  131.32  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
 3YT  CONST_01  N29  C9   N10  C11     0.00   0.0  0
 3YT  CONST_02  N29  C16  C12  C11     0.00   0.0  0
 3YT  CONST_03  C9   N29  C16  C12     0.00   0.0  0
 3YT  CONST_04  C9   N10  C11  C12     0.00   0.0  0
 3YT  CONST_05  N10  C9   N29  C16     0.00   0.0  0
 3YT  CONST_06  N10  C11  C12  C16     0.00   0.0  0
 3YT  CONST_07  N24  C22  C23  C18   180.00   0.0  0
 3YT  CONST_08  C21  C22  C23  C18     0.00   0.0  0
 3YT  CONST_09  C21  C20  C19  C18     0.00   0.0  0
 3YT  CONST_10  C22  C23  C18  C19     0.00   0.0  0
 3YT  CONST_11  C22  C21  C20  C19     0.00   0.0  0
 3YT  CONST_12  N24  C22  C21  C20   180.00   0.0  0
 3YT  CONST_13  C23  C22  C21  C20     0.00   0.0  0
 3YT  CONST_14  C23  C18  C19  C20     0.00   0.0  0
 3YT  CONST_15  N28  N24  C22  C21   180.00   0.0  0
 3YT  CONST_16  N25  N24  C22  C21     0.00   0.0  0
 3YT  CONST_17  C27  N28  N24  C22   180.00   0.0  0
 3YT  CONST_18  C26  N25  N24  C22   180.00   0.0  0
 3YT  CONST_19  N28  N24  C22  C23     0.00   0.0  0
 3YT  CONST_20  N25  N24  C22  C23   180.00   0.0  0
 3YT  CONST_21  N24  N28  C27  C26     0.00   0.0  0
 3YT  CONST_22  N28  N24  N25  C26     0.00   0.0  0
 3YT  CONST_23  N25  N24  N28  C27     0.00   0.0  0
 3YT  CONST_24  N24  N25  C26  C27     0.00   0.0  0
 3YT  CONST_25  N28  C27  C26  N25     0.00   0.0  0
 3YT  CONST_26  N8   C9   N10  C11   180.00   0.0  0
 3YT  CONST_27  N17  C16  C12  C11   180.00   0.0  0
 3YT  CONST_28  N29  C16  C12  C13   180.00   0.0  0
 3YT  CONST_29  N10  C11  C12  C13   180.00   0.0  0
 3YT  CONST_30  N8   C9   N29  C16   180.00   0.0  0
 3YT  CONST_31  N17  C18  C19  C20   180.00   0.0  0
 3YT  CONST_32  N17  C18  C23  C22   180.00   0.0  0
 3YT  CONST_33  N17  C16  N29  C9    180.00   0.0  0
 3YT  CONST_34  N29  C9   N8   C7    180.00   0.0  0
 3YT  CONST_35  N10  C9   N8   C7      0.00   0.0  0
 3YT  CONST_36  H4   C11  C12  C16   180.00   0.0  0
 3YT  CONST_37  H6   C20  C19  C18   180.00   0.0  0
 3YT  CONST_38  H8   C23  C18  C19   180.00   0.0  0
 3YT  CONST_39  H7   C21  C20  C19   180.00   0.0  0
 3YT  CONST_40  H5   C19  C20  C21   180.00   0.0  0
 3YT  CONST_41  H10  C27  N28  N24   180.00   0.0  0
 3YT  CONST_42  H9   C26  N25  N24   180.00   0.0  0
 3YT  CONST_43  H21  N8   C9   N10   180.00   0.0  0
 3YT  CONST_44  H22  N14  C13  C12     0.00   0.0  0
 3YT  CONST_45  H23  N14  C13  C12   180.00   0.0  0
 3YT  Var_01    C5   C4   C3   C2    -54.67  30.0  1
 3YT  Var_02    C6   C5   C4   C3     55.33  30.0  1
 3YT  Var_03    C7   C6   C5   C4    -56.51  30.0  1
 3YT  Var_04    C18  N17  C16  C12   179.83  30.0  2
 3YT  Var_05    C23  C18  N17  C16  -171.88  30.0  3
 3YT  Var_06    N14  C13  C12  C11   -13.91  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
 3YT  chir_01  C2  C7  C3  N1  positiv
 3YT  chir_02  C7  N8  C6  C2  positiv

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
 3YT  plan-1  C22  0.020
 3YT  plan-1  C26  0.020
 3YT  plan-1  C27  0.020
 3YT  plan-1  N24  0.020
 3YT  plan-1  N25  0.020
 3YT  plan-1  N28  0.020
 3YT  plan-1  H10  0.020
 3YT  plan-1  H9   0.020
 3YT  plan-2  C18  0.020
 3YT  plan-2  C19  0.020
 3YT  plan-2  C20  0.020
 3YT  plan-2  C21  0.020
 3YT  plan-2  C22  0.020
 3YT  plan-2  C23  0.020
 3YT  plan-2  N24  0.020
 3YT  plan-2  H5   0.020
 3YT  plan-2  H6   0.020
 3YT  plan-2  H7   0.020
 3YT  plan-2  H8   0.020
 3YT  plan-2  N17  0.020
 3YT  plan-3  C11  0.020
 3YT  plan-3  C12  0.020
 3YT  plan-3  C13  0.020
 3YT  plan-3  C16  0.020
 3YT  plan-3  N8   0.020
 3YT  plan-3  C9   0.020
 3YT  plan-3  N10  0.020
 3YT  plan-3  N29  0.020
 3YT  plan-3  H4   0.020
 3YT  plan-3  N17  0.020
 3YT  plan-4  C7   0.020
 3YT  plan-4  N8   0.020
 3YT  plan-4  C9   0.020
 3YT  plan-4  H21  0.020
 3YT  plan-5  C12  0.020
 3YT  plan-5  C13  0.020
 3YT  plan-5  N14  0.020
 3YT  plan-5  O15  0.020
 3YT  plan-5  H22  0.020
 3YT  plan-5  H23  0.020

