# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 05:33:13 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2,6-dichloro-N-{2-[(2-{[(2S)-1-hydroxypropan-2-yl]amino}-6-methylpyrimidin-4-yl)amino]pyridin-4-yl}benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CO)Nc1nc(C)cc(Nc2cc(NC(=O)c3c(Cl)cccc3Cl)ccn2)n1
#
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
 3R1  3R1  2,6-dichloro-N-{2-[(2-{[(2S)-1-hydroxypropan-2-yl]amino}-6-methylpyrimidin-4-yl)amino]pyridin-4-yl}benzamide  ligand  50  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3R1
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
 3R1  C4   C   CR6   0   0.552   3.3030   1.4915  -0.1050
 3R1  C6   C   CR6   0   0.572   5.1900   0.2506  -0.1664
 3R1  C11  C   CH3   0  -0.655   4.5688  -2.7947  -1.0780
 3R1  C9   C   CH1   0  -0.110   5.0707  -2.1870   0.2297
 3R1  C12  C   CH2   0  -0.160   5.9541  -3.1369   1.0185
 3R1  C3   C   CR16  0  -0.501   4.0383   2.6330  -0.4596
 3R1  C2   C   CR6   0   0.287   5.3942   2.4548  -0.6572
 3R1  N5   N   N     0  -0.475   3.8713   0.3092   0.0280
 3R1  N7   N   N     0  -0.511   5.9844   1.2692  -0.5097
 3R1  N8   N   NH1   0  -0.657   5.7860  -0.9453   0.0130
 3R1  O13  O   OH1   0  -0.674   7.1179  -3.4122   0.2696
 3R1  N14  N   NH1   0  -0.766   1.9504   1.6175   0.0704
 3R1  C15  C   CR6   0   0.526   1.0326   0.6859   0.5292
 3R1  C16  C   CR16  0  -0.515  -0.2921   0.8312   0.1176
 3R1  C17  C   CR6   0   0.493  -1.2523  -0.0480   0.6010
 3R1  C18  C   CR16  0  -0.394  -0.8423  -1.0657   1.4657
 3R1  C19  C   CR16  0  -0.067   0.4996  -1.1082   1.7981
 3R1  N20  N   N     0  -0.416   1.4251  -0.2615   1.3677
 3R1  N21  N   NH1   0  -0.715  -2.5613   0.1542   0.1760
 3R1  C22  C   C     0   0.477  -3.6744  -0.5525   0.4864
 3R1  O23  O   O     0  -0.410  -3.7197  -1.5319   1.1967
 3R1  C24  C   CR6   0   0.084  -4.9165   0.0079  -0.1494
 3R1  C25  C   CR6   0  -0.083  -5.3659  -0.4612  -1.3770
 3R1  C26  C   CR16  0  -0.190  -6.5410   0.0029  -1.9437
 3R1  C27  C   CR16  0  -0.273  -7.2838   0.9549  -1.2622
 3R1  C28  C   CR16  0  -0.191  -6.8619   1.4435  -0.0351
 3R1  C29  C   CR6   0  -0.082  -5.6824   0.9624   0.5074
 3R1  CL1  CL  CL    0  -0.097  -5.1381   1.5647   2.0336
 3R1  CL2  CL  CL    0  -0.098  -4.4197  -1.6398  -2.2155
 3R1  H2   H   HCH3  0   0.233   3.8894  -2.1041  -1.5774
 3R1  H3   H   HCH3  0   0.223   5.3906  -3.0175  -1.7590
 3R1  H4   H   HCH1  0   0.261   4.2066  -1.9618   0.8575
 3R1  H5   H   HCH2  0   0.211   6.1983  -2.6759   1.9835
 3R1  H6   H   HCH2  0   0.204   5.3821  -4.0492   1.2295
 3R1  H7   H   HCR6  0   0.264   3.5702   3.6012  -0.5737
 3R1  H11  H   HNH1  0   0.378   6.7531  -1.0043  -0.2640
 3R1  H12  H   HOH1  0   0.459   7.7069  -3.9485   0.8075
 3R1  H13  H   HNH1  0   0.416   1.5549   2.4784  -0.2739
 3R1  H14  H   HCR6  0   0.291  -0.5662   1.6225  -0.5700
 3R1  H15  H   HCR6  0   0.289  -1.5190  -1.7925   1.8799
 3R1  H16  H   HCR6  0   0.262   0.8440  -1.8806   2.4771
 3R1  H17  H   HNH1  0   0.433  -2.6968   0.9445  -0.4389
 3R1  H18  H   HCR6  0   0.294  -6.8708  -0.3728  -2.9020
 3R1  H19  H   HCR6  0   0.287  -8.2039   1.3232  -1.6946
 3R1  H20  H   HCR6  0   0.294  -7.4429   2.1865   0.4928
 3R1  C1   C   CH3   0  -0.722   6.2762   3.5990  -1.0456
 3R1  H1   H   HCH3  0   0.221   4.0248  -3.7216  -0.8891
 3R1  H8   H   HCH3  0   0.253   7.0774   3.7265  -0.3168
 3R1  H9   H   HCH3  0   0.253   6.7477   3.4048  -2.0100
 3R1  H10  H   HCH3  0   0.244   5.7218   4.5327  -1.1165

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
 3R1  C26  C27  aromatic  1.387  0.020  1.387
 3R1  C26  C25  aromatic  1.385  0.020  1.385
 3R1  CL2  C25  single    1.728  0.020  1.728
 3R1  C27  C28  aromatic  1.387  0.020  1.387
 3R1  C25  C24  aromatic  1.389  0.020  1.389
 3R1  O23  C22  double    1.211  0.020  1.211
 3R1  C28  C29  aromatic  1.385  0.020  1.385
 3R1  C24  C29  aromatic  1.389  0.020  1.389
 3R1  C24  C22  single    1.504  0.020  1.504
 3R1  C29  CL1  single    1.729  0.020  1.729
 3R1  C22  N21  single    1.354  0.020  1.354
 3R1  C18  C19  aromatic  1.383  0.020  1.383
 3R1  C18  C17  aromatic  1.397  0.020  1.397
 3R1  N21  C17  single    1.391  0.020  1.391
 3R1  C19  N20  aromatic  1.326  0.020  1.326
 3R1  C17  C16  aromatic  1.389  0.020  1.389
 3R1  O13  C12  single    1.411  0.020  1.411
 3R1  N20  C15  aromatic  1.325  0.020  1.325
 3R1  C16  C15  aromatic  1.395  0.020  1.395
 3R1  C15  N14  single    1.386  0.020  1.386
 3R1  C12  C9   single    1.518  0.020  1.518
 3R1  C11  C9   single    1.527  0.020  1.527
 3R1  C9   N8   single    1.449  0.020  1.449
 3R1  N14  C4   single    1.370  0.020  1.370
 3R1  N5   C4   aromatic  1.319  0.020  1.319
 3R1  N5   C6   aromatic  1.334  0.020  1.334
 3R1  C4   C3   aromatic  1.403  0.020  1.403
 3R1  N8   C6   single    1.348  0.020  1.348
 3R1  C6   N7   aromatic  1.337  0.020  1.337
 3R1  C3   C2   aromatic  1.382  0.020  1.382
 3R1  N7   C2   aromatic  1.333  0.020  1.333
 3R1  C2   C1   single    1.496  0.020  1.496
 3R1  C11  H1   single    0.970  0.020  1.090
 3R1  C11  H2   single    0.970  0.020  1.090
 3R1  C11  H3   single    0.970  0.020  1.090
 3R1  C9   H4   single    0.970  0.020  1.090
 3R1  C12  H5   single    0.970  0.020  1.090
 3R1  C12  H6   single    0.970  0.020  1.090
 3R1  C3   H7   single    0.930  0.020  1.080
 3R1  C1   H8   single    0.970  0.020  1.090
 3R1  C1   H9   single    0.970  0.020  1.090
 3R1  C1   H10  single    0.970  0.020  1.090
 3R1  N8   H11  single    0.860  0.020  1.020
 3R1  O13  H12  single    0.850  0.020  0.980
 3R1  N14  H13  single    0.860  0.020  1.020
 3R1  C16  H14  single    0.930  0.020  1.080
 3R1  C18  H15  single    0.930  0.020  1.080
 3R1  C19  H16  single    0.930  0.020  1.080
 3R1  N21  H17  single    0.860  0.020  1.020
 3R1  C26  H18  single    0.930  0.020  1.080
 3R1  C27  H19  single    0.930  0.020  1.080
 3R1  C28  H20  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
 3R1  N14  C4   N5   119.68  3.000
 3R1  N5   C4   C3   121.94  3.000
 3R1  N14  C4   C3   118.35  3.000
 3R1  N8   C6   N7   116.58  3.000
 3R1  N7   C6   N5   126.26  3.000
 3R1  N8   C6   N5   117.16  3.000
 3R1  H3   C11  H2   108.25  3.000
 3R1  H3   C11  H1   108.08  3.000
 3R1  H2   C11  H1   107.87  3.000
 3R1  H3   C11  C9   111.62  3.000
 3R1  H2   C11  C9   110.19  3.000
 3R1  H1   C11  C9   110.71  3.000
 3R1  H4   C9   N8   107.46  3.000
 3R1  H4   C9   C12  106.91  3.000
 3R1  N8   C9   C12  109.06  3.000
 3R1  H4   C9   C11  108.33  3.000
 3R1  N8   C9   C11  112.04  3.000
 3R1  C12  C9   C11  112.78  3.000
 3R1  H6   C12  H5   107.23  3.000
 3R1  H6   C12  O13  111.71  3.000
 3R1  H5   C12  O13  111.42  3.000
 3R1  H6   C12  C9   108.47  3.000
 3R1  H5   C12  C9   108.88  3.000
 3R1  O13  C12  C9   109.04  3.000
 3R1  H7   C3   C2   121.68  3.000
 3R1  H7   C3   C4   121.88  3.000
 3R1  C2   C3   C4   116.44  3.000
 3R1  N7   C2   C1   116.63  3.000
 3R1  C1   C2   C3   121.13  3.000
 3R1  N7   C2   C3   122.25  3.000
 3R1  C6   N5   C4   116.78  3.000
 3R1  C2   N7   C6   116.31  3.000
 3R1  H11  N8   C9   117.68  3.000
 3R1  H11  N8   C6   116.08  3.000
 3R1  C9   N8   C6   124.17  3.000
 3R1  H12  O13  C12  108.50  3.000
 3R1  H13  N14  C15  115.30  3.000
 3R1  H13  N14  C4   114.98  3.000
 3R1  C15  N14  C4   129.38  3.000
 3R1  N20  C15  C16  122.87  3.000
 3R1  C16  C15  N14  117.47  3.000
 3R1  N20  C15  N14  119.61  3.000
 3R1  H14  C16  C17  120.55  3.000
 3R1  H14  C16  C15  120.24  3.000
 3R1  C17  C16  C15  119.21  3.000
 3R1  N21  C17  C18  124.83  3.000
 3R1  N21  C17  C16  116.89  3.000
 3R1  C18  C17  C16  118.28  3.000
 3R1  H15  C18  C19  119.80  3.000
 3R1  H15  C18  C17  123.07  3.000
 3R1  C19  C18  C17  117.12  3.000
 3R1  H16  C19  N20  115.87  3.000
 3R1  H16  C19  C18  118.71  3.000
 3R1  N20  C19  C18  125.42  3.000
 3R1  C19  N20  C15  117.08  3.000
 3R1  H17  N21  C22  115.93  3.000
 3R1  H17  N21  C17  115.20  3.000
 3R1  C22  N21  C17  128.86  3.000
 3R1  C24  C22  O23  121.24  3.000
 3R1  C24  C22  N21  112.80  3.000
 3R1  O23  C22  N21  125.96  3.000
 3R1  C29  C24  C25  118.14  3.000
 3R1  C29  C24  C22  120.78  3.000
 3R1  C25  C24  C22  121.00  3.000
 3R1  CL2  C25  C26  119.64  3.000
 3R1  CL2  C25  C24  118.82  3.000
 3R1  C26  C25  C24  121.54  3.000
 3R1  H18  C26  C27  120.73  3.000
 3R1  H18  C26  C25  120.35  3.000
 3R1  C27  C26  C25  118.92  3.000
 3R1  H19  C27  C28  119.52  3.000
 3R1  H19  C27  C26  119.55  3.000
 3R1  C28  C27  C26  120.92  3.000
 3R1  H20  C28  C29  120.36  3.000
 3R1  H20  C28  C27  120.73  3.000
 3R1  C29  C28  C27  118.92  3.000
 3R1  CL1  C29  C28  119.55  3.000
 3R1  CL1  C29  C24  118.90  3.000
 3R1  C28  C29  C24  121.55  3.000
 3R1  H10  C1   H9   108.39  3.000
 3R1  H10  C1   H8   108.51  3.000
 3R1  H9   C1   H8   107.10  3.000
 3R1  H10  C1   C2   111.89  3.000
 3R1  H9   C1   C2   110.38  3.000
 3R1  H8   C1   C2   110.42  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
 3R1  CONST_01  N7   C6   N5   C4      0.00   0.0  0
 3R1  CONST_02  N7   C2   C3   C4      0.00   0.0  0
 3R1  CONST_03  C3   C4   N5   C6      0.00   0.0  0
 3R1  CONST_04  C3   C2   N7   C6      0.00   0.0  0
 3R1  CONST_05  N5   C4   C3   C2      0.00   0.0  0
 3R1  CONST_06  N5   C6   N7   C2      0.00   0.0  0
 3R1  CONST_07  C18  C19  N20  C15     0.00   0.0  0
 3R1  CONST_08  C18  C17  C16  C15     0.00   0.0  0
 3R1  CONST_09  C19  C18  C17  C16     0.00   0.0  0
 3R1  CONST_10  C19  N20  C15  C16     0.00   0.0  0
 3R1  CONST_11  N20  C19  C18  C17     0.00   0.0  0
 3R1  CONST_12  N20  C15  C16  C17     0.00   0.0  0
 3R1  CONST_13  C27  C26  C25  C24     0.00   0.0  0
 3R1  CONST_14  C27  C28  C29  C24     0.00   0.0  0
 3R1  CONST_15  C28  C27  C26  C25     0.00   0.0  0
 3R1  CONST_16  C28  C29  C24  C25     0.00   0.0  0
 3R1  CONST_17  C29  C28  C27  C26     0.00   0.0  0
 3R1  CONST_18  C29  C24  C25  C26     0.00   0.0  0
 3R1  CONST_19  N8   C6   N5   C4    180.00   0.0  0
 3R1  CONST_20  C1   C2   C3   C4    180.00   0.0  0
 3R1  CONST_21  N14  C4   N5   C6    180.00   0.0  0
 3R1  CONST_22  C1   C2   N7   C6    180.00   0.0  0
 3R1  CONST_23  N14  C4   C3   C2    180.00   0.0  0
 3R1  CONST_24  N8   C6   N7   C2    180.00   0.0  0
 3R1  CONST_25  C19  N20  C15  N14   180.00   0.0  0
 3R1  CONST_26  C17  C16  C15  N14   180.00   0.0  0
 3R1  CONST_27  N21  C17  C16  C15   180.00   0.0  0
 3R1  CONST_28  N21  C17  C18  C19   180.00   0.0  0
 3R1  CONST_29  C26  C25  C24  C22   180.00   0.0  0
 3R1  CONST_30  C28  C29  C24  C22   180.00   0.0  0
 3R1  CONST_31  CL1  C29  C24  C25   180.00   0.0  0
 3R1  CONST_32  CL2  C25  C26  C27   180.00   0.0  0
 3R1  CONST_33  CL1  C29  C28  C27   180.00   0.0  0
 3R1  CONST_34  CL2  C25  C24  C29   180.00   0.0  0
 3R1  CONST_35  H7   C3   C4   N5    180.00   0.0  0
 3R1  CONST_36  H16  C19  N20  C15   180.00   0.0  0
 3R1  CONST_37  H15  C18  C17  C16   180.00   0.0  0
 3R1  CONST_38  H14  C16  C17  C18   180.00   0.0  0
 3R1  CONST_39  H18  C26  C25  C24   180.00   0.0  0
 3R1  CONST_40  H20  C28  C29  C24   180.00   0.0  0
 3R1  CONST_41  H19  C27  C26  C25   180.00   0.0  0
 3R1  CONST_42  C24  C22  N21  C17   180.00   0.0  0
 3R1  CONST_43  N5   C6   N8   C9      0.00   0.0  0
 3R1  CONST_44  N7   C6   N8   C9    180.00   0.0  0
 3R1  CONST_45  C22  N21  C17  C16   180.00   0.0  0
 3R1  CONST_46  C22  N21  C17  C18     0.00   0.0  0
 3R1  CONST_47  H11  N8   C6   N5    180.00   0.0  0
 3R1  CONST_48  H17  N21  C17  C16     0.00   0.0  0
 3R1  CONST_49  O23  C22  N21  C17     0.00   0.0  0
 3R1  Var_01    N20  C15  N14  C4     28.45  30.0  2
 3R1  Var_02    C15  N14  C4   C3   -173.69  30.0  2
 3R1  Var_03    C25  C24  C22  N21    92.90  30.0  2
 3R1  Var_04    H8   C1   C2   C3    122.40  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
 3R1  chir_01  C9  C12  C11  N8  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
 3R1  plan-1  C4   0.020
 3R1  plan-1  C6   0.020
 3R1  plan-1  C3   0.020
 3R1  plan-1  C2   0.020
 3R1  plan-1  N5   0.020
 3R1  plan-1  N7   0.020
 3R1  plan-1  N8   0.020
 3R1  plan-1  N14  0.020
 3R1  plan-1  H7   0.020
 3R1  plan-1  C1   0.020
 3R1  plan-2  N14  0.020
 3R1  plan-2  C15  0.020
 3R1  plan-2  C16  0.020
 3R1  plan-2  C17  0.020
 3R1  plan-2  C18  0.020
 3R1  plan-2  C19  0.020
 3R1  plan-2  N20  0.020
 3R1  plan-2  N21  0.020
 3R1  plan-2  H14  0.020
 3R1  plan-2  H15  0.020
 3R1  plan-2  H16  0.020
 3R1  plan-3  C22  0.020
 3R1  plan-3  C24  0.020
 3R1  plan-3  C25  0.020
 3R1  plan-3  C26  0.020
 3R1  plan-3  C27  0.020
 3R1  plan-3  C28  0.020
 3R1  plan-3  C29  0.020
 3R1  plan-3  CL1  0.020
 3R1  plan-3  CL2  0.020
 3R1  plan-3  H18  0.020
 3R1  plan-3  H19  0.020
 3R1  plan-3  H20  0.020
 3R1  plan-4  C17  0.020
 3R1  plan-4  N21  0.020
 3R1  plan-4  C22  0.020
 3R1  plan-4  O23  0.020
 3R1  plan-4  C24  0.020
 3R1  plan-4  H17  0.020
 3R1  plan-5  C6   0.020
 3R1  plan-5  C9   0.020
 3R1  plan-5  N8   0.020
 3R1  plan-5  H11  0.020

