# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 10:06:38 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (3R)-3-methyl-1-(4-{[2-methyl-1-(propan-2-yl)-1H-imidazo[4,5-c]pyridin-6-yl]amino}pyrimidin-2-yl)pyrrolidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1c(C)nc2cnc(Nc3ccnc(n3)N4CC[C@](C)(C4)C(N)=O)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
 4ZB  4ZB  (3R)-3-methyl-1-(4-{[2-methyl-1-(propan-2-yl)-1H-imidazo[4,5-c]pyridin-6-yl]amino}pyrimidin-2-yl)pyrrolidine-3-carboxamide  ligand  55  29  .  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_4ZB
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
 4ZB  C4   C  CR56  0   0.041   3.1827   1.3506   1.1288
 4ZB  C5   C  CR16  0  -0.135   1.9920   1.2210   1.8315
 4ZB  C11  C  CH1   0  -0.142   5.7257  -0.1138  -1.0107
 4ZB  C7   C  CR6   0   0.453   1.7805  -0.9597   1.1581
 4ZB  C8   C  CR16  0  -0.433   2.9509  -0.9516   0.4096
 4ZB  C9   C  CR56  0   0.454   3.6651   0.2394   0.4227
 4ZB  C12  C  CH3   0  -0.653   6.3064  -1.3111  -0.2692
 4ZB  C13  C  CH3   0  -0.653   5.0424  -0.5020  -2.3152
 4ZB  N3   N  N     0  -0.478   4.0363   2.4142   0.9817
 4ZB  C1   C  CH3   0  -0.778   6.1584   2.7874  -0.2189
 4ZB  C2   C  CR5   0   0.435   4.9968   1.9738   0.2188
 4ZB  N6   N  N     0  -0.411   1.3234   0.0822   1.8543
 4ZB  N10  N  NR5   0  -0.544   4.8306   0.6612  -0.1533
 4ZB  N14  N  NH1   0  -0.755   1.0490  -2.1534   1.2375
 4ZB  C15  C  CR6   0   0.531  -0.2790  -2.2944   0.9728
 4ZB  C16  C  CR16  0  -0.468  -0.8790  -3.5625   1.0914
 4ZB  C17  C  CR16  0  -0.022  -2.2168  -3.6183   0.7817
 4ZB  N18  N  N     0  -0.500  -2.9386  -2.5686   0.3992
 4ZB  C19  C  CR6   0   0.616  -2.2690  -1.4123   0.3295
 4ZB  N20  N  N     0  -0.493  -0.9705  -1.2348   0.5927
 4ZB  N21  N  NT    0  -0.499  -2.9561  -0.3188  -0.0469
 4ZB  C22  C  CH2   0  -0.262  -2.3482   0.9917  -0.2041
 4ZB  C23  C  CH2   0  -0.453  -3.4552   1.8090  -0.8594
 4ZB  C24  C  CT    0  -0.274  -4.7420   1.1601  -0.3438
 4ZB  C25  C  CH2   0  -0.231  -4.3697  -0.3332  -0.3551
 4ZB  C26  C  CH3   0  -0.644  -5.0518   1.6275   1.0848
 4ZB  C27  C  C     0   0.555  -5.9391   1.4745  -1.2290
 4ZB  O28  O  O     0  -0.482  -5.9321   2.3995  -2.0279
 4ZB  N29  N  NH2   0  -0.804  -7.0092   0.6839  -1.0506
 4ZB  H1   H  HCR6  0   0.259   1.5837   2.0511   2.3986
 4ZB  H2   H  HCH1  0   0.280   6.5522   0.5531  -1.2557
 4ZB  H3   H  HCR6  0   0.279   3.2558  -1.8270  -0.1461
 4ZB  H4   H  HCH3  0   0.247   7.0531  -1.7942  -0.8987
 4ZB  H5   H  HCH3  0   0.246   6.7931  -1.0030   0.6559
 4ZB  H6   H  HCH3  0   0.232   5.5492  -2.0572  -0.0277
 4ZB  H7   H  HCH3  0   0.246   4.6408   0.3729  -2.8260
 4ZB  H8   H  HCH3  0   0.247   5.7688  -0.9757  -2.9752
 4ZB  H9   H  HCH3  0   0.233   4.2298  -1.2114  -2.1602
 4ZB  H10  H  HCH3  0   0.268   7.1028   2.3570   0.1167
 4ZB  H11  H  HCH3  0   0.268   6.2022   2.8724  -1.3056
 4ZB  H12  H  HCH3  0   0.278   6.0707   3.7873   0.1974
 4ZB  H13  H  HNH1  0   0.410   1.5849  -3.0051   1.2900
 4ZB  H14  H  HCR6  0   0.267  -0.3268  -4.4383   1.4008
 4ZB  H15  H  HCR6  0   0.259  -2.7449  -4.5645   0.8440
 4ZB  H16  H  HCH2  0   0.231  -2.0494   1.4044   0.7637
 4ZB  H17  H  HCH2  0   0.246  -1.4499   0.9433  -0.8205
 4ZB  H18  H  HCH2  0   0.254  -3.3840   2.8686  -0.6148
 4ZB  H19  H  HCH2  0   0.250  -3.3934   1.7159  -1.9452
 4ZB  H20  H  HCH2  0   0.243  -4.5605  -0.7821  -1.3368
 4ZB  H21  H  HCH2  0   0.246  -4.9295  -0.9121   0.3825
 4ZB  H22  H  HCH3  0   0.237  -5.8821   1.0696   1.5189
 4ZB  H23  H  HCH3  0   0.251  -4.1873   1.4879   1.7352
 4ZB  H24  H  HCH3  0   0.245  -5.3093   2.6875   1.1019
 4ZB  H25  H  HNH2  0   0.407  -7.0256  -0.0644  -0.3796
 4ZB  H26  H  HNH2  0   0.402  -7.8571   0.8518  -1.5681

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
 4ZB  C26  C24  single    1.535  0.020  1.535
 4ZB  C25  C24  single    1.539  0.020  1.539
 4ZB  C25  N21  single    1.447  0.020  1.447
 4ZB  C24  C27  single    1.522  0.020  1.522
 4ZB  C24  C23  single    1.531  0.020  1.531
 4ZB  N18  C17  aromatic  1.330  0.020  1.330
 4ZB  N18  C19  aromatic  1.338  0.020  1.338
 4ZB  C17  C16  aromatic  1.374  0.020  1.374
 4ZB  N29  C27  single    1.342  0.020  1.342
 4ZB  N21  C19  single    1.345  0.020  1.345
 4ZB  N21  C22  single    1.453  0.020  1.453
 4ZB  C27  O28  double    1.222  0.020  1.222
 4ZB  C19  N20  aromatic  1.337  0.020  1.337
 4ZB  C23  C22  single    1.524  0.020  1.524
 4ZB  C16  C15  aromatic  1.408  0.020  1.408
 4ZB  N20  C15  aromatic  1.321  0.020  1.321
 4ZB  C15  N14  single    1.361  0.020  1.361
 4ZB  N14  C7   single    1.402  0.020  1.402
 4ZB  C7   C8   aromatic  1.389  0.020  1.389
 4ZB  C7   N6   aromatic  1.334  0.020  1.334
 4ZB  C8   C9   aromatic  1.389  0.020  1.389
 4ZB  C12  C11  single    1.523  0.020  1.523
 4ZB  C11  C13  single    1.523  0.020  1.523
 4ZB  C11  N10  single    1.462  0.020  1.462
 4ZB  N6   C5   aromatic  1.321  0.020  1.321
 4ZB  C9   N10  aromatic  1.367  0.020  1.367
 4ZB  C9   C4   aromatic  1.402  0.020  1.402
 4ZB  N10  C2   aromatic  1.374  0.020  1.374
 4ZB  C5   C4   aromatic  1.389  0.020  1.389
 4ZB  C4   N3   aromatic  1.372  0.020  1.372
 4ZB  C2   N3   aromatic  1.303  0.020  1.303
 4ZB  C2   C1   single    1.484  0.020  1.484
 4ZB  C5   H1   single    0.930  0.020  1.080
 4ZB  C11  H2   single    0.970  0.020  1.090
 4ZB  C8   H3   single    0.930  0.020  1.080
 4ZB  C12  H4   single    0.970  0.020  1.090
 4ZB  C12  H5   single    0.970  0.020  1.090
 4ZB  C12  H6   single    0.970  0.020  1.090
 4ZB  C13  H7   single    0.970  0.020  1.090
 4ZB  C13  H8   single    0.970  0.020  1.090
 4ZB  C13  H9   single    0.970  0.020  1.090
 4ZB  C1   H10  single    0.970  0.020  1.090
 4ZB  C1   H11  single    0.970  0.020  1.090
 4ZB  C1   H12  single    0.970  0.020  1.090
 4ZB  N14  H13  single    0.860  0.020  1.020
 4ZB  C16  H14  single    0.930  0.020  1.080
 4ZB  C17  H15  single    0.930  0.020  1.080
 4ZB  C22  H16  single    0.970  0.020  1.090
 4ZB  C22  H17  single    0.970  0.020  1.090
 4ZB  C23  H18  single    0.970  0.020  1.090
 4ZB  C23  H19  single    0.970  0.020  1.090
 4ZB  C25  H20  single    0.970  0.020  1.090
 4ZB  C25  H21  single    0.970  0.020  1.090
 4ZB  C26  H22  single    0.970  0.020  1.090
 4ZB  C26  H23  single    0.970  0.020  1.090
 4ZB  C26  H24  single    0.970  0.020  1.090
 4ZB  N29  H25  single    0.860  0.020  1.020
 4ZB  N29  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
 4ZB  N3   C4   C9   110.27  3.000
 4ZB  N3   C4   C5   131.32  3.000
 4ZB  C9   C4   C5   118.41  3.000
 4ZB  H1   C5   N6   117.40  3.000
 4ZB  H1   C5   C4   121.04  3.000
 4ZB  N6   C5   C4   121.56  3.000
 4ZB  H2   C11  N10  105.77  3.000
 4ZB  H2   C11  C13  107.68  3.000
 4ZB  N10  C11  C13  111.27  3.000
 4ZB  H2   C11  C12  107.53  3.000
 4ZB  N10  C11  C12  111.38  3.000
 4ZB  C13  C11  C12  112.81  3.000
 4ZB  N14  C7   N6   117.17  3.000
 4ZB  N6   C7   C8   124.43  3.000
 4ZB  N14  C7   C8   118.35  3.000
 4ZB  H3   C8   C9   123.67  3.000
 4ZB  H3   C8   C7   120.66  3.000
 4ZB  C9   C8   C7   115.67  3.000
 4ZB  N10  C9   C8   134.36  3.000
 4ZB  N10  C9   C4   105.13  3.000
 4ZB  C8   C9   C4   120.49  3.000
 4ZB  H6   C12  H5   108.40  3.000
 4ZB  H6   C12  H4   107.49  3.000
 4ZB  H5   C12  H4   108.05  3.000
 4ZB  H6   C12  C11  112.39  3.000
 4ZB  H5   C12  C11  111.18  3.000
 4ZB  H4   C12  C11  109.18  3.000
 4ZB  H9   C13  H8   107.47  3.000
 4ZB  H9   C13  H7   108.33  3.000
 4ZB  H8   C13  H7   108.10  3.000
 4ZB  H9   C13  C11  112.25  3.000
 4ZB  H8   C13  C11  109.30  3.000
 4ZB  H7   C13  C11  111.24  3.000
 4ZB  C2   N3   C4   105.03  3.000
 4ZB  H12  C1   H11  108.25  3.000
 4ZB  H12  C1   H10  108.37  3.000
 4ZB  H11  C1   H10  107.61  3.000
 4ZB  H12  C1   C2   109.16  3.000
 4ZB  H11  C1   C2   111.59  3.000
 4ZB  H10  C1   C2   111.75  3.000
 4ZB  N10  C2   C1   122.57  3.000
 4ZB  C1   C2   N3   124.35  3.000
 4ZB  N10  C2   N3   113.08  3.000
 4ZB  C7   N6   C5   119.40  3.000
 4ZB  C2   N10  C9   106.48  3.000
 4ZB  C2   N10  C11  126.23  3.000
 4ZB  C9   N10  C11  127.28  3.000
 4ZB  H13  N14  C15  116.18  3.000
 4ZB  H13  N14  C7   116.43  3.000
 4ZB  C15  N14  C7   125.88  3.000
 4ZB  N20  C15  C16  121.57  3.000
 4ZB  N20  C15  N14  118.91  3.000
 4ZB  C16  C15  N14  119.52  3.000
 4ZB  H14  C16  C17  121.94  3.000
 4ZB  H14  C16  C15  122.43  3.000
 4ZB  C17  C16  C15  115.63  3.000
 4ZB  H15  C17  N18  116.13  3.000
 4ZB  H15  C17  C16  119.74  3.000
 4ZB  N18  C17  C16  124.12  3.000
 4ZB  C19  N18  C17  115.18  3.000
 4ZB  N21  C19  N20  116.32  3.000
 4ZB  N20  C19  N18  126.21  3.000
 4ZB  N21  C19  N18  117.48  3.000
 4ZB  C19  N20  C15  117.30  3.000
 4ZB  C25  N21  C22  113.24  3.000
 4ZB  C22  N21  C19  123.34  3.000
 4ZB  C25  N21  C19  123.41  3.000
 4ZB  H17  C22  H16  106.97  3.000
 4ZB  H17  C22  C23  112.27  3.000
 4ZB  H16  C22  C23  112.12  3.000
 4ZB  H17  C22  N21  111.45  3.000
 4ZB  H16  C22  N21  111.03  3.000
 4ZB  C23  C22  N21  103.08  3.000
 4ZB  H19  C23  H18  107.61  3.000
 4ZB  H19  C23  C24  110.28  3.000
 4ZB  H18  C23  C24  113.05  3.000
 4ZB  H19  C23  C22  109.93  3.000
 4ZB  H18  C23  C22  112.18  3.000
 4ZB  C24  C23  C22  103.79  3.000
 4ZB  C27  C24  C26  108.65  3.000
 4ZB  C27  C24  C25  112.73  3.000
 4ZB  C26  C24  C25  110.56  3.000
 4ZB  C27  C24  C23  112.20  3.000
 4ZB  C25  C24  C23  101.86  3.000
 4ZB  C26  C24  C23  110.74  3.000
 4ZB  H21  C25  H20  107.37  3.000
 4ZB  H21  C25  C24  112.67  3.000
 4ZB  H20  C25  C24  111.21  3.000
 4ZB  H21  C25  N21  111.23  3.000
 4ZB  H20  C25  N21  111.40  3.000
 4ZB  C24  C25  N21  103.01  3.000
 4ZB  H24  C26  H23  107.58  3.000
 4ZB  H24  C26  H22  108.12  3.000
 4ZB  H23  C26  H22  107.50  3.000
 4ZB  H24  C26  C24  110.99  3.000
 4ZB  H23  C26  C24  110.86  3.000
 4ZB  H22  C26  C24  111.62  3.000
 4ZB  N29  C27  O28  122.49  3.000
 4ZB  O28  C27  C24  122.15  3.000
 4ZB  N29  C27  C24  115.35  3.000
 4ZB  H26  N29  H25  116.95  3.000
 4ZB  H26  N29  C27  120.30  3.000
 4ZB  H25  N29  C27  122.69  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
 4ZB  CONST_01  C7   C8   C9   C4      0.00   0.0  0
 4ZB  CONST_02  C2   N10  C9   C4      0.00   0.0  0
 4ZB  CONST_03  C7   N6   C5   C4      0.00   0.0  0
 4ZB  CONST_04  N10  C2   N3   C4      0.00   0.0  0
 4ZB  CONST_05  C8   C7   N6   C5      0.00   0.0  0
 4ZB  CONST_06  C8   C9   C4   C5      0.00   0.0  0
 4ZB  CONST_07  N10  C9   C4   C5    180.00   0.0  0
 4ZB  CONST_08  C2   N3   C4   C5    180.00   0.0  0
 4ZB  CONST_09  N10  C9   C8   C7    180.00   0.0  0
 4ZB  CONST_10  C2   N10  C9   C8    180.00   0.0  0
 4ZB  CONST_11  N3   C4   C9   C8    180.00   0.0  0
 4ZB  CONST_12  N6   C7   C8   C9      0.00   0.0  0
 4ZB  CONST_13  N3   C2   N10  C9      0.00   0.0  0
 4ZB  CONST_14  N6   C5   C4   C9      0.00   0.0  0
 4ZB  CONST_15  C2   N3   C4   C9      0.00   0.0  0
 4ZB  CONST_16  N10  C9   C4   N3      0.00   0.0  0
 4ZB  CONST_17  N6   C5   C4   N3    180.00   0.0  0
 4ZB  CONST_18  N18  C17  C16  C15     0.00   0.0  0
 4ZB  CONST_19  N18  C19  N20  C15     0.00   0.0  0
 4ZB  CONST_20  C19  N18  C17  C16     0.00   0.0  0
 4ZB  CONST_21  C19  N20  C15  C16     0.00   0.0  0
 4ZB  CONST_22  N20  C19  N18  C17     0.00   0.0  0
 4ZB  CONST_23  N20  C15  C16  C17     0.00   0.0  0
 4ZB  CONST_24  N21  C19  N20  C15   180.00   0.0  0
 4ZB  CONST_25  N21  C19  N18  C17   180.00   0.0  0
 4ZB  CONST_26  C11  N10  C9   C4    180.00   0.0  0
 4ZB  CONST_27  C1   C2   N3   C4    180.00   0.0  0
 4ZB  CONST_28  N14  C7   N6   C5    180.00   0.0  0
 4ZB  CONST_29  C8   C9   N10  C11     0.00   0.0  0
 4ZB  CONST_30  N3   C2   N10  C11   180.00   0.0  0
 4ZB  CONST_31  N14  C7   C8   C9    180.00   0.0  0
 4ZB  CONST_32  C1   C2   N10  C9    180.00   0.0  0
 4ZB  CONST_33  C17  C16  C15  N14   180.00   0.0  0
 4ZB  CONST_34  C19  N20  C15  N14   180.00   0.0  0
 4ZB  CONST_35  H3   C8   C9   C4    180.00   0.0  0
 4ZB  CONST_36  H1   C5   N6   C7    180.00   0.0  0
 4ZB  CONST_37  H15  C17  C16  C15   180.00   0.0  0
 4ZB  CONST_38  H14  C16  C17  N18   180.00   0.0  0
 4ZB  CONST_39  H25  N29  C27  C24     0.00   0.0  0
 4ZB  CONST_40  H26  N29  C27  C24   180.00   0.0  0
 4ZB  Var_01    C25  N21  C19  N18     0.97  30.0  2
 4ZB  Var_02    C24  C25  N21  C19   165.18  30.0  1
 4ZB  Var_03    C23  C22  N21  C19   170.63  30.0  1
 4ZB  Var_04    C24  C23  C22  N21    29.37  30.0  1
 4ZB  Var_05    C16  C15  N14  C7    179.78  30.0  1
 4ZB  Var_06    C15  N14  C7   C8   -128.03  30.0  1
 4ZB  Var_07    C12  C11  N10  C9    -62.38  30.0  2
 4ZB  Var_08    H10  C1   C2   N3    119.90  30.0  2
 4ZB  Var_09    H4   C12  C11  N10  -173.46  30.0  3
 4ZB  Var_10    H7   C13  C11  N10    54.23  30.0  3

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
 4ZB  chir_01  C24  C25  C27  C23  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
 4ZB  plan-1  N14  0.020
 4ZB  plan-1  C15  0.020
 4ZB  plan-1  C16  0.020
 4ZB  plan-1  C17  0.020
 4ZB  plan-1  N18  0.020
 4ZB  plan-1  C19  0.020
 4ZB  plan-1  N20  0.020
 4ZB  plan-1  N21  0.020
 4ZB  plan-1  H14  0.020
 4ZB  plan-1  H15  0.020
 4ZB  plan-2  C4   0.020
 4ZB  plan-2  C5   0.020
 4ZB  plan-2  C11  0.020
 4ZB  plan-2  C7   0.020
 4ZB  plan-2  C8   0.020
 4ZB  plan-2  C9   0.020
 4ZB  plan-2  N3   0.020
 4ZB  plan-2  C1   0.020
 4ZB  plan-2  C2   0.020
 4ZB  plan-2  N6   0.020
 4ZB  plan-2  N10  0.020
 4ZB  plan-2  N14  0.020
 4ZB  plan-2  H1   0.020
 4ZB  plan-2  H3   0.020
 4ZB  plan-3  C24  0.020
 4ZB  plan-3  C27  0.020
 4ZB  plan-3  O28  0.020
 4ZB  plan-3  N29  0.020
 4ZB  plan-3  H25  0.020
 4ZB  plan-3  H26  0.020

