# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 08:57:48 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 2,2-dimethyl-3-[(4-{[2-methyl-1-(propan-2-yl)-1H-imidazo[4,5-c]pyridin-6-yl]amino}pyrimidin-2-yl)amino]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1c(C)nc2cnc(Nc3ccnc(NCC(C)(C)C(N)=O)n3)cc12
#
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
 4Z8  4Z8  2,2-dimethyl-3-[(4-{[2-methyl-1-(propan-2-yl)-1H-imidazo[4,5-c]pyridin-6-yl]amino}pyrimidin-2-yl)amino]propanamide  ligand  54  28  .  2022-07-23  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_4Z8
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
 4Z8  C4   C  CR56  0   0.041   3.2689   1.3709   1.2614
 4Z8  C5   C  CR16  0  -0.137   2.0588   1.2103   1.9220
 4Z8  C11  C  CH1   0  -0.144   5.8509   0.0159  -0.9042
 4Z8  C7   C  CR6   0   0.459   1.8345  -0.9143   1.0915
 4Z8  C8   C  CR16  0  -0.439   3.0253  -0.8710   0.3751
 4Z8  C9   C  CR56  0   0.457   3.7537   0.3048   0.4897
 4Z8  C12  C  CH3   0  -0.652   6.3976  -1.2309  -0.2214
 4Z8  C13  C  CH3   0  -0.652   5.2005  -0.2852  -2.2482
 4Z8  N3   N  N     0  -0.477   4.1421   2.4277   1.2135
 4Z8  C1   C  CH3   0  -0.778   6.3044   2.8471   0.1027
 4Z8  C2   C  CR5   0   0.434   5.1162   2.0267   0.4464
 4Z8  N6   N  N     0  -0.412   1.3728   0.0831   1.8469
 4Z8  N10  N  NR5   0  -0.545   4.9394   0.7473  -0.0252
 4Z8  N14  N  NH1   0  -0.756   1.0948  -2.1028   1.0689
 4Z8  C15  C  CR6   0   0.530  -0.2453  -2.2300   0.8647
 4Z8  C16  C  CR16  0  -0.465  -0.8199  -3.5176   0.8872
 4Z8  C17  C  CR16  0  -0.017  -2.1706  -3.5714   0.6545
 4Z8  N18  N  N     0  -0.497  -2.9315  -2.5006   0.4295
 4Z8  C19  C  CR6   0   0.591  -2.2850  -1.3345   0.4296
 4Z8  N20  N  N     0  -0.491  -0.9730  -1.1543   0.6296
 4Z8  N21  N  NH1   0  -0.672  -2.9981  -0.2158   0.1922
 4Z8  C22  C  CH2   0  -0.194  -4.4345  -0.2029   0.0527
 4Z8  C23  C  CT    0  -0.312  -4.9394   1.1732  -0.4026
 4Z8  C24  C  CH3   0  -0.647  -4.6273   2.2384   0.6591
 4Z8  C25  C  CH3   0  -0.635  -4.3092   1.5530  -1.7497
 4Z8  C26  C  C     0   0.583  -6.4630   1.0686  -0.5721
 4Z8  O27  O  O     0  -0.483  -7.0754   0.0274  -0.3822
 4Z8  N28  N  NH2   0  -0.805  -7.0843   2.1953  -0.9535
 4Z8  H1   H  HCR6  0   0.261   1.6471   2.0042   2.5366
 4Z8  H2   H  HCH1  0   0.279   6.6891   0.6886  -1.0849
 4Z8  H3   H  HCR6  0   0.276   3.3349  -1.7110  -0.2306
 4Z8  H4   H  HCH3  0   0.231   5.6270  -1.9841  -0.0545
 4Z8  H5   H  HCH3  0   0.248   7.1625  -1.6798  -0.8543
 4Z8  H6   H  HCH3  0   0.246   6.8535  -0.9867   0.7379
 4Z8  H7   H  HCH3  0   0.246   4.8261   0.6240  -2.7180
 4Z8  H8   H  HCH3  0   0.247   5.9400  -0.7304  -2.9135
 4Z8  H9   H  HCH3  0   0.232   4.3741  -0.9901  -2.1579
 4Z8  H10  H  HCH3  0   0.268   7.2280   2.3824   0.4506
 4Z8  H11  H  HCH3  0   0.267   6.3944   2.9932  -0.9744
 4Z8  H12  H  HCH3  0   0.279   6.2133   3.8222   0.5735
 4Z8  H13  H  HNH1  0   0.410   1.6295  -2.9548   1.0111
 4Z8  H14  H  HCR6  0   0.268  -0.2362  -4.4068   1.0782
 4Z8  H15  H  HCR6  0   0.261  -2.6806  -4.5293   0.6526
 4Z8  H16  H  HNH1  0   0.385  -2.5014   0.6488   0.3283
 4Z8  H17  H  HCH2  0   0.242  -4.7220  -0.9580  -0.6797
 4Z8  H18  H  HCH2  0   0.234  -4.9184  -0.4767   0.9961
 4Z8  H19  H  HCH3  0   0.247  -5.0861   1.9870   1.6165
 4Z8  H20  H  HCH3  0   0.237  -3.5537   2.3378   0.8239
 4Z8  H21  H  HCH3  0   0.236  -4.9797   3.2269   0.3656
 4Z8  H22  H  HCH3  0   0.232  -4.6509   2.5257  -2.1038
 4Z8  H23  H  HCH3  0   0.242  -3.2237   1.6094  -1.6684
 4Z8  H24  H  HCH3  0   0.242  -4.5457   0.8142  -2.5173
 4Z8  H25  H  HNH2  0   0.399  -6.6052   3.0691  -1.0807
 4Z8  H26  H  HNH2  0   0.402  -8.0856   2.2045  -1.0591

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
 4Z8  C24  C23  single    1.536  0.020  1.536
 4Z8  N18  C17  aromatic  1.333  0.020  1.333
 4Z8  N18  C19  aromatic  1.333  0.020  1.333
 4Z8  C17  C16  aromatic  1.372  0.020  1.372
 4Z8  N28  C26  single    1.342  0.020  1.342
 4Z8  N21  C19  single    1.348  0.020  1.348
 4Z8  N21  C22  single    1.443  0.020  1.443
 4Z8  C19  N20  aromatic  1.339  0.020  1.339
 4Z8  C23  C26  single    1.537  0.020  1.537
 4Z8  C23  C22  single    1.535  0.020  1.535
 4Z8  C23  C25  single    1.535  0.020  1.535
 4Z8  C26  O27  double    1.223  0.020  1.223
 4Z8  C16  C15  aromatic  1.410  0.020  1.410
 4Z8  N20  C15  aromatic  1.320  0.020  1.320
 4Z8  C15  N14  single    1.362  0.020  1.362
 4Z8  N14  C7   single    1.400  0.020  1.400
 4Z8  C7   C8   aromatic  1.390  0.020  1.390
 4Z8  C7   N6   aromatic  1.334  0.020  1.334
 4Z8  C8   C9   aromatic  1.388  0.020  1.388
 4Z8  C13  C11  single    1.523  0.020  1.523
 4Z8  C12  C11  single    1.523  0.020  1.523
 4Z8  N6   C5   aromatic  1.322  0.020  1.322
 4Z8  C9   N10  aromatic  1.366  0.020  1.366
 4Z8  C9   C4   aromatic  1.403  0.020  1.403
 4Z8  C11  N10  single    1.462  0.020  1.462
 4Z8  N10  C2   aromatic  1.375  0.020  1.375
 4Z8  C5   C4   aromatic  1.388  0.020  1.388
 4Z8  C4   N3   aromatic  1.372  0.020  1.372
 4Z8  C2   N3   aromatic  1.303  0.020  1.303
 4Z8  C2   C1   single    1.484  0.020  1.484
 4Z8  C5   H1   single    0.930  0.020  1.080
 4Z8  C11  H2   single    0.970  0.020  1.090
 4Z8  C8   H3   single    0.930  0.020  1.080
 4Z8  C12  H4   single    0.970  0.020  1.090
 4Z8  C12  H5   single    0.970  0.020  1.090
 4Z8  C12  H6   single    0.970  0.020  1.090
 4Z8  C13  H7   single    0.970  0.020  1.090
 4Z8  C13  H8   single    0.970  0.020  1.090
 4Z8  C13  H9   single    0.970  0.020  1.090
 4Z8  C1   H10  single    0.970  0.020  1.090
 4Z8  C1   H11  single    0.970  0.020  1.090
 4Z8  C1   H12  single    0.970  0.020  1.090
 4Z8  N14  H13  single    0.860  0.020  1.020
 4Z8  C16  H14  single    0.930  0.020  1.080
 4Z8  C17  H15  single    0.930  0.020  1.080
 4Z8  N21  H16  single    0.860  0.020  1.020
 4Z8  C22  H17  single    0.970  0.020  1.090
 4Z8  C22  H18  single    0.970  0.020  1.090
 4Z8  C24  H19  single    0.970  0.020  1.090
 4Z8  C24  H20  single    0.970  0.020  1.090
 4Z8  C24  H21  single    0.970  0.020  1.090
 4Z8  C25  H22  single    0.970  0.020  1.090
 4Z8  C25  H23  single    0.970  0.020  1.090
 4Z8  C25  H24  single    0.970  0.020  1.090
 4Z8  N28  H25  single    0.860  0.020  1.020
 4Z8  N28  H26  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
 4Z8  N3   C4   C9   110.26  3.000
 4Z8  N3   C4   C5   131.36  3.000
 4Z8  C9   C4   C5   118.38  3.000
 4Z8  H1   C5   N6   117.34  3.000
 4Z8  H1   C5   C4   121.05  3.000
 4Z8  N6   C5   C4   121.61  3.000
 4Z8  H2   C11  N10  105.68  3.000
 4Z8  H2   C11  C13  107.71  3.000
 4Z8  N10  C11  C13  111.29  3.000
 4Z8  H2   C11  C12  107.67  3.000
 4Z8  N10  C11  C12  111.33  3.000
 4Z8  C13  C11  C12  112.77  3.000
 4Z8  N14  C7   N6   117.46  3.000
 4Z8  N6   C7   C8   124.41  3.000
 4Z8  N14  C7   C8   118.07  3.000
 4Z8  H3   C8   C9   123.66  3.000
 4Z8  H3   C8   C7   120.66  3.000
 4Z8  C9   C8   C7   115.68  3.000
 4Z8  N10  C9   C8   134.32  3.000
 4Z8  N10  C9   C4   105.14  3.000
 4Z8  C8   C9   C4   120.53  3.000
 4Z8  H6   C12  H5   108.05  3.000
 4Z8  H6   C12  H4   108.40  3.000
 4Z8  H5   C12  H4   107.48  3.000
 4Z8  H6   C12  C11  111.19  3.000
 4Z8  H5   C12  C11  109.20  3.000
 4Z8  H4   C12  C11  112.36  3.000
 4Z8  H9   C13  H8   107.51  3.000
 4Z8  H9   C13  H7   108.34  3.000
 4Z8  H8   C13  H7   108.10  3.000
 4Z8  H9   C13  C11  112.24  3.000
 4Z8  H8   C13  C11  109.25  3.000
 4Z8  H7   C13  C11  111.24  3.000
 4Z8  C2   N3   C4   105.03  3.000
 4Z8  H12  C1   H11  108.34  3.000
 4Z8  H12  C1   H10  108.36  3.000
 4Z8  H11  C1   H10  107.59  3.000
 4Z8  H12  C1   C2   109.18  3.000
 4Z8  H11  C1   C2   111.64  3.000
 4Z8  H10  C1   C2   111.62  3.000
 4Z8  N10  C2   C1   122.54  3.000
 4Z8  C1   C2   N3   124.38  3.000
 4Z8  N10  C2   N3   113.09  3.000
 4Z8  C7   N6   C5   119.36  3.000
 4Z8  C2   N10  C9   106.48  3.000
 4Z8  C2   N10  C11  126.26  3.000
 4Z8  C9   N10  C11  127.26  3.000
 4Z8  H13  N14  C15  115.77  3.000
 4Z8  H13  N14  C7   116.00  3.000
 4Z8  C15  N14  C7   126.99  3.000
 4Z8  N20  C15  C16  121.49  3.000
 4Z8  N20  C15  N14  119.56  3.000
 4Z8  C16  C15  N14  118.94  3.000
 4Z8  H14  C16  C17  121.98  3.000
 4Z8  H14  C16  C15  122.28  3.000
 4Z8  C17  C16  C15  115.74  3.000
 4Z8  H15  C17  N18  116.15  3.000
 4Z8  H15  C17  C16  119.84  3.000
 4Z8  N18  C17  C16  124.01  3.000
 4Z8  C19  N18  C17  115.21  3.000
 4Z8  N21  C19  N20  115.66  3.000
 4Z8  N20  C19  N18  126.34  3.000
 4Z8  N21  C19  N18  117.99  3.000
 4Z8  C19  N20  C15  117.20  3.000
 4Z8  H16  N21  C22  119.78  3.000
 4Z8  H16  N21  C19  115.35  3.000
 4Z8  C22  N21  C19  123.44  3.000
 4Z8  H18  C22  H17  106.80  3.000
 4Z8  H18  C22  C23  109.53  3.000
 4Z8  H17  C22  C23  109.56  3.000
 4Z8  H18  C22  N21  110.75  3.000
 4Z8  H17  C22  N21  108.73  3.000
 4Z8  C23  C22  N21  111.35  3.000
 4Z8  C26  C23  C25  109.09  3.000
 4Z8  C25  C23  C24  110.58  3.000
 4Z8  C26  C23  C24  108.96  3.000
 4Z8  C25  C23  C22  110.31  3.000
 4Z8  C26  C23  C22  107.33  3.000
 4Z8  C24  C23  C22  110.48  3.000
 4Z8  H21  C24  H20  106.04  3.000
 4Z8  H21  C24  H19  108.02  3.000
 4Z8  H20  C24  H19  107.60  3.000
 4Z8  H21  C24  C23  112.16  3.000
 4Z8  H20  C24  C23  111.57  3.000
 4Z8  H19  C24  C23  111.18  3.000
 4Z8  H24  C25  H23  107.66  3.000
 4Z8  H24  C25  H22  107.92  3.000
 4Z8  H23  C25  H22  106.88  3.000
 4Z8  H24  C25  C23  111.15  3.000
 4Z8  H23  C25  C23  110.87  3.000
 4Z8  H22  C25  C23  112.16  3.000
 4Z8  N28  C26  O27  121.81  3.000
 4Z8  O27  C26  C23  122.51  3.000
 4Z8  N28  C26  C23  115.68  3.000
 4Z8  H26  N28  H25  116.94  3.000
 4Z8  H26  N28  C26  119.86  3.000
 4Z8  H25  N28  C26  123.06  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
 4Z8  CONST_01  C7   C8   C9   C4      0.00   0.0  0
 4Z8  CONST_02  C2   N10  C9   C4      0.00   0.0  0
 4Z8  CONST_03  C7   N6   C5   C4      0.00   0.0  0
 4Z8  CONST_04  N10  C2   N3   C4      0.00   0.0  0
 4Z8  CONST_05  C8   C7   N6   C5      0.00   0.0  0
 4Z8  CONST_06  C8   C9   C4   C5      0.00   0.0  0
 4Z8  CONST_07  N10  C9   C4   C5    180.00   0.0  0
 4Z8  CONST_08  C2   N3   C4   C5    180.00   0.0  0
 4Z8  CONST_09  N10  C9   C8   C7    180.00   0.0  0
 4Z8  CONST_10  C2   N10  C9   C8    180.00   0.0  0
 4Z8  CONST_11  N3   C4   C9   C8    180.00   0.0  0
 4Z8  CONST_12  N6   C7   C8   C9      0.00   0.0  0
 4Z8  CONST_13  N3   C2   N10  C9      0.00   0.0  0
 4Z8  CONST_14  N6   C5   C4   C9      0.00   0.0  0
 4Z8  CONST_15  C2   N3   C4   C9      0.00   0.0  0
 4Z8  CONST_16  N10  C9   C4   N3      0.00   0.0  0
 4Z8  CONST_17  N6   C5   C4   N3    180.00   0.0  0
 4Z8  CONST_18  N18  C17  C16  C15     0.00   0.0  0
 4Z8  CONST_19  N18  C19  N20  C15     0.00   0.0  0
 4Z8  CONST_20  C19  N18  C17  C16     0.00   0.0  0
 4Z8  CONST_21  C19  N20  C15  C16     0.00   0.0  0
 4Z8  CONST_22  N20  C19  N18  C17     0.00   0.0  0
 4Z8  CONST_23  N20  C15  C16  C17     0.00   0.0  0
 4Z8  CONST_24  C11  N10  C9   C4    180.00   0.0  0
 4Z8  CONST_25  C1   C2   N3   C4    180.00   0.0  0
 4Z8  CONST_26  N14  C7   N6   C5    180.00   0.0  0
 4Z8  CONST_27  C8   C9   N10  C11     0.00   0.0  0
 4Z8  CONST_28  N3   C2   N10  C11   180.00   0.0  0
 4Z8  CONST_29  N14  C7   C8   C9    180.00   0.0  0
 4Z8  CONST_30  C1   C2   N10  C9    180.00   0.0  0
 4Z8  CONST_31  C17  C16  C15  N14   180.00   0.0  0
 4Z8  CONST_32  C19  N20  C15  N14   180.00   0.0  0
 4Z8  CONST_33  N21  C19  N20  C15   180.00   0.0  0
 4Z8  CONST_34  N21  C19  N18  C17   180.00   0.0  0
 4Z8  CONST_35  H3   C8   C9   C4    180.00   0.0  0
 4Z8  CONST_36  H1   C5   N6   C7    180.00   0.0  0
 4Z8  CONST_37  H15  C17  C16  C15   180.00   0.0  0
 4Z8  CONST_38  H14  C16  C17  N18   180.00   0.0  0
 4Z8  CONST_39  C22  N21  C19  N18     0.00   0.0  0
 4Z8  CONST_40  C22  N21  C19  N20   180.00   0.0  0
 4Z8  CONST_41  H16  N21  C19  N18   180.00   0.0  0
 4Z8  CONST_42  H25  N28  C26  C23     0.00   0.0  0
 4Z8  CONST_43  H26  N28  C26  C23   180.00   0.0  0
 4Z8  Var_01    C16  C15  N14  C7   -179.51  30.0  2
 4Z8  Var_02    C15  N14  C7   C8   -133.54  30.0  2
 4Z8  Var_03    C13  C11  N10  C9     64.28  30.0  2
 4Z8  Var_04    H10  C1   C2   N3    118.67  30.0  2
 4Z8  Var_05    C23  C22  N21  C19  -172.13  30.0  3
 4Z8  Var_06    H7   C13  C11  N10    54.54  30.0  3
 4Z8  Var_07    H4   C12  C11  N10    67.81  30.0  3
 4Z8  Var_08    C24  C23  C22  N21   -63.43  30.0  3
 4Z8  Var_09    N28  C26  C23  C22   179.16  30.0  3
 4Z8  Var_10    H19  C24  C23  C22   -58.62  30.0  3
 4Z8  Var_11    H22  C25  C23  C22   179.78  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
 4Z8  plan-1  N14  0.020
 4Z8  plan-1  C15  0.020
 4Z8  plan-1  C16  0.020
 4Z8  plan-1  C17  0.020
 4Z8  plan-1  N18  0.020
 4Z8  plan-1  C19  0.020
 4Z8  plan-1  N20  0.020
 4Z8  plan-1  N21  0.020
 4Z8  plan-1  H14  0.020
 4Z8  plan-1  H15  0.020
 4Z8  plan-2  C4   0.020
 4Z8  plan-2  C5   0.020
 4Z8  plan-2  C11  0.020
 4Z8  plan-2  C7   0.020
 4Z8  plan-2  C8   0.020
 4Z8  plan-2  C9   0.020
 4Z8  plan-2  N3   0.020
 4Z8  plan-2  C1   0.020
 4Z8  plan-2  C2   0.020
 4Z8  plan-2  N6   0.020
 4Z8  plan-2  N10  0.020
 4Z8  plan-2  N14  0.020
 4Z8  plan-2  H1   0.020
 4Z8  plan-2  H3   0.020
 4Z8  plan-3  C23  0.020
 4Z8  plan-3  C26  0.020
 4Z8  plan-3  O27  0.020
 4Z8  plan-3  N28  0.020
 4Z8  plan-3  H25  0.020
 4Z8  plan-3  H26  0.020
 4Z8  plan-4  C19  0.020
 4Z8  plan-4  N21  0.020
 4Z8  plan-4  C22  0.020
 4Z8  plan-4  H16  0.020

