# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 08:39:14 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: 4-[2-methyl-3-[(2~{R})-2-phenoxypropyl]imidazo[4,5-b]pyridin-5-yl]pyridine-2,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Cn1c(C)nc2ccc(nc12)c3cc(N)nc(N)c3)Oc4ccccc4
#
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
 RKZ  RKZ  4-[2-methyl-3-[(2~{R})-2-phenoxypropyl]imidazo[4,5-b]pyridin-5-yl]pyridine-2,6-diamine  ligand  50  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RKZ
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
 RKZ  C1   C  CH3   0  -0.682  -5.1483   2.1855  28.9227
 RKZ  N1   N  NR5   0  -0.531  -6.7082  -0.4294  29.2663
 RKZ  O1   O  O2    0  -0.482  -3.8534   0.2713  29.3692
 RKZ  C2   C  CH1   0  -0.001  -4.7295   0.8265  28.4002
 RKZ  N2   N  N     0  -0.473  -8.3354  -0.3360  30.7953
 RKZ  C3   C  CH2   0  -0.355  -5.8992  -0.1157  28.1093
 RKZ  N3   N  N     0  -0.452  -5.5417  -2.3829  30.0675
 RKZ  C4   C  CR5   0   0.442  -7.8494   0.1931  29.7026
 RKZ  N4   N  NH2   0  -0.841  -1.3081  -5.1097  29.4353
 RKZ  C5   C  CH3   0  -0.767  -8.4984   1.3093  28.9716
 RKZ  N5   N  N     0  -0.503  -2.6653  -6.4234  30.7315
 RKZ  C6   C  CR56  0   0.108  -7.4980  -1.3745  31.0968
 RKZ  N6   N  NH2   0  -0.838  -3.9484  -7.8325  32.0064
 RKZ  C7   C  CR16  0  -0.223  -7.4998  -2.3191  32.1114
 RKZ  C8   C  CR16  0  -0.343  -6.5146  -3.2908  32.0631
 RKZ  C9   C  CR6   0   0.193  -5.5703  -3.3130  31.0231
 RKZ  C10  C  CR56  0   0.466  -6.4756  -1.4627  30.1397
 RKZ  C11  C  CR6   0   0.191  -4.5583  -4.3921  30.9339
 RKZ  C12  C  CR16  0  -0.475  -3.4051  -4.2064  30.1821
 RKZ  C13  C  CR6   0   0.459  -2.4821  -5.2571  30.1151
 RKZ  C14  C  CR6   0   0.462  -3.7756  -6.5992  31.4430
 RKZ  C15  C  CR16  0  -0.510  -4.7559  -5.6095  31.5779
 RKZ  C16  C  CR6   0   0.406  -2.7858  -0.4655  29.0010
 RKZ  C17  C  CR16  0  -0.351  -1.8444  -0.7074  30.0040
 RKZ  C18  C  CR16  0  -0.235  -0.6972  -1.4283  29.7253
 RKZ  C19  C  CR16  0  -0.302  -0.4641  -1.9200  28.4446
 RKZ  C20  C  CR16  0  -0.240  -1.4087  -1.6940  27.4563
 RKZ  C21  C  CR16  0  -0.373  -2.5707  -0.9770  27.7232
 RKZ  H1   H  HCH3  0   0.258  -4.2736   2.8216  29.0549
 RKZ  H2   H  HCH3  0   0.240  -5.8087   2.6776  28.2094
 RKZ  H3   H  HCH3  0   0.238  -5.6627   2.1151  29.8817
 RKZ  H4   H  HCH1  0   0.250  -4.2059   0.9744  27.4494
 RKZ  H5   H  HCH2  0   0.285  -6.5294   0.3395  27.3445
 RKZ  H6   H  HCH2  0   0.286  -5.5343  -1.0576  27.6979
 RKZ  H7   H  HNH2  0   0.376  -0.8302  -5.9567  29.1751
 RKZ  H8   H  HNH2  0   0.394  -1.2560  -4.3728  28.7516
 RKZ  H9   H  HCH3  0   0.275  -9.4531   1.5284  29.4422
 RKZ  H10  H  HCH3  0   0.271  -7.8992   2.2184  28.9813
 RKZ  H11  H  HCH3  0   0.266  -8.6815   1.0480  27.9284
 RKZ  H12  H  HNH2  0   0.377  -3.1164  -8.3900  32.1104
 RKZ  H13  H  HNH2  0   0.385  -4.5851  -7.9002  32.7829
 RKZ  H14  H  HCR6  0   0.267  -8.2379  -2.3087  32.9029
 RKZ  H15  H  HCR6  0   0.265  -6.4752  -4.0366  32.8435
 RKZ  H16  H  HCR6  0   0.260  -3.2118  -3.2743  29.6697
 RKZ  H17  H  HCR6  0   0.248  -5.6505  -5.8231  32.1464
 RKZ  H18  H  HCR6  0   0.260  -2.0181  -0.3156  30.9986
 RKZ  H19  H  HCR6  0   0.256   0.0247  -1.6014  30.5131
 RKZ  H20  H  HCR6  0   0.259   0.4395  -2.4736  28.2249
 RKZ  H21  H  HCR6  0   0.259  -1.2506  -2.0790  26.4570
 RKZ  H22  H  HCR6  0   0.276  -3.2839  -0.8306  26.9233

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
 RKZ  C20  C21  aromatic  1.391  0.020  1.391
 RKZ  C20  C19  aromatic  1.386  0.020  1.386
 RKZ  C21  C16  aromatic  1.393  0.020  1.393
 RKZ  C19  C18  aromatic  1.392  0.020  1.392
 RKZ  C3   C2   single    1.530  0.020  1.530
 RKZ  C3   N1   single    1.446  0.020  1.446
 RKZ  C2   C1   single    1.515  0.020  1.515
 RKZ  C2   O1   single    1.419  0.020  1.419
 RKZ  C5   C4   single    1.484  0.020  1.484
 RKZ  C16  O1   single    1.348  0.020  1.348
 RKZ  C16  C17  aromatic  1.397  0.020  1.397
 RKZ  N1   C4   aromatic  1.371  0.020  1.371
 RKZ  N1   C10  aromatic  1.373  0.020  1.373
 RKZ  N4   C13  single    1.365  0.020  1.365
 RKZ  C18  C17  aromatic  1.383  0.020  1.383
 RKZ  C4   N2   aromatic  1.308  0.020  1.308
 RKZ  N3   C10  aromatic  1.313  0.020  1.313
 RKZ  N3   C9   aromatic  1.334  0.020  1.334
 RKZ  C10  C6   aromatic  1.403  0.020  1.403
 RKZ  C12  C13  aromatic  1.400  0.020  1.400
 RKZ  C12  C11  aromatic  1.389  0.020  1.389
 RKZ  C13  N5   aromatic  1.332  0.020  1.332
 RKZ  N2   C6   aromatic  1.368  0.020  1.368
 RKZ  C6   C7   aromatic  1.386  0.020  1.386
 RKZ  C9   C11  single    1.482  0.020  1.482
 RKZ  C9   C8   aromatic  1.405  0.020  1.405
 RKZ  C11  C15  aromatic  1.391  0.020  1.391
 RKZ  N5   C14  aromatic  1.330  0.020  1.330
 RKZ  C7   C8   aromatic  1.385  0.020  1.385
 RKZ  C15  C14  aromatic  1.400  0.020  1.400
 RKZ  C14  N6   single    1.367  0.020  1.367
 RKZ  C1   H1   single    0.970  0.020  1.090
 RKZ  C1   H2   single    0.970  0.020  1.090
 RKZ  C1   H3   single    0.970  0.020  1.090
 RKZ  C2   H4   single    0.970  0.020  1.090
 RKZ  C3   H5   single    0.970  0.020  1.090
 RKZ  C3   H6   single    0.970  0.020  1.090
 RKZ  N4   H7   single    0.890  0.020  1.040
 RKZ  N4   H8   single    0.890  0.020  1.040
 RKZ  C5   H9   single    0.970  0.020  1.090
 RKZ  C5   H10  single    0.970  0.020  1.090
 RKZ  C5   H11  single    0.970  0.020  1.090
 RKZ  N6   H12  single    0.890  0.020  1.040
 RKZ  N6   H13  single    0.890  0.020  1.040
 RKZ  C7   H14  single    0.930  0.020  1.080
 RKZ  C8   H15  single    0.930  0.020  1.080
 RKZ  C12  H16  single    0.930  0.020  1.080
 RKZ  C15  H17  single    0.930  0.020  1.080
 RKZ  C17  H18  single    0.930  0.020  1.080
 RKZ  C18  H19  single    0.930  0.020  1.080
 RKZ  C19  H20  single    0.930  0.020  1.080
 RKZ  C20  H21  single    0.930  0.020  1.080
 RKZ  C21  H22  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
 RKZ  H3   C1   H2   108.59  3.000
 RKZ  H3   C1   H1   108.04  3.000
 RKZ  H2   C1   H1   107.60  3.000
 RKZ  H3   C1   C2   112.07  3.000
 RKZ  H2   C1   C2   110.30  3.000
 RKZ  H1   C1   C2   110.10  3.000
 RKZ  C10  N1   C4   106.28  3.000
 RKZ  C10  N1   C3   125.27  3.000
 RKZ  C4   N1   C3   128.44  3.000
 RKZ  C16  O1   C2   121.06  3.000
 RKZ  H4   C2   C3   106.47  3.000
 RKZ  H4   C2   O1   110.51  3.000
 RKZ  C3   C2   O1   111.15  3.000
 RKZ  H4   C2   C1   108.08  3.000
 RKZ  O1   C2   C1   106.62  3.000
 RKZ  C3   C2   C1   113.99  3.000
 RKZ  C6   N2   C4   105.31  3.000
 RKZ  H6   C3   H5   106.82  3.000
 RKZ  H6   C3   C2   110.35  3.000
 RKZ  H5   C3   C2   108.55  3.000
 RKZ  H6   C3   N1   107.56  3.000
 RKZ  H5   C3   N1   109.17  3.000
 RKZ  C2   C3   N1   114.15  3.000
 RKZ  C10  N3   C9   115.72  3.000
 RKZ  C5   C4   N2   123.61  3.000
 RKZ  N2   C4   N1   113.04  3.000
 RKZ  C5   C4   N1   123.28  3.000
 RKZ  H8   N4   H7   114.57  3.000
 RKZ  H8   N4   C13  117.52  3.000
 RKZ  H7   N4   C13  116.51  3.000
 RKZ  H11  C5   H10  107.51  3.000
 RKZ  H11  C5   H9   108.36  3.000
 RKZ  H10  C5   H9   108.13  3.000
 RKZ  H11  C5   C4   111.37  3.000
 RKZ  H10  C5   C4   112.52  3.000
 RKZ  H9   C5   C4   108.82  3.000
 RKZ  C14  N5   C13  118.56  3.000
 RKZ  C10  C6   C7   117.21  3.000
 RKZ  C7   C6   N2   132.69  3.000
 RKZ  C10  C6   N2   110.09  3.000
 RKZ  H13  N6   H12  113.95  3.000
 RKZ  H13  N6   C14  117.30  3.000
 RKZ  H12  N6   C14  115.96  3.000
 RKZ  H14  C7   C8   121.17  3.000
 RKZ  H14  C7   C6   121.98  3.000
 RKZ  C8   C7   C6   116.86  3.000
 RKZ  H15  C8   C9   119.96  3.000
 RKZ  H15  C8   C7   119.03  3.000
 RKZ  C9   C8   C7   121.01  3.000
 RKZ  C11  C9   C8   121.00  3.000
 RKZ  C8   C9   N3   122.26  3.000
 RKZ  C11  C9   N3   116.74  3.000
 RKZ  C6   C10  N3   126.85  3.000
 RKZ  C6   C10  N1   105.26  3.000
 RKZ  N3   C10  N1   127.81  3.000
 RKZ  C15  C11  C12  119.04  3.000
 RKZ  C15  C11  C9   120.82  3.000
 RKZ  C12  C11  C9   120.14  3.000
 RKZ  H16  C12  C13  120.43  3.000
 RKZ  H16  C12  C11  121.35  3.000
 RKZ  C13  C12  C11  118.22  3.000
 RKZ  C12  C13  N5   122.98  3.000
 RKZ  N5   C13  N4   116.33  3.000
 RKZ  C12  C13  N4   120.66  3.000
 RKZ  C15  C14  N6   120.65  3.000
 RKZ  N6   C14  N5   116.44  3.000
 RKZ  C15  C14  N5   122.87  3.000
 RKZ  H17  C15  C14  119.38  3.000
 RKZ  H17  C15  C11  122.25  3.000
 RKZ  C14  C15  C11  118.34  3.000
 RKZ  C21  C16  C17  119.41  3.000
 RKZ  C17  C16  O1   115.61  3.000
 RKZ  C21  C16  O1   124.98  3.000
 RKZ  H18  C17  C18  120.44  3.000
 RKZ  H18  C17  C16  119.25  3.000
 RKZ  C18  C17  C16  120.31  3.000
 RKZ  H19  C18  C19  120.10  3.000
 RKZ  H19  C18  C17  119.33  3.000
 RKZ  C19  C18  C17  120.56  3.000
 RKZ  H20  C19  C20  120.51  3.000
 RKZ  H20  C19  C18  120.50  3.000
 RKZ  C20  C19  C18  118.98  3.000
 RKZ  H21  C20  C21  118.84  3.000
 RKZ  H21  C20  C19  120.06  3.000
 RKZ  C21  C20  C19  121.10  3.000
 RKZ  H22  C21  C20  118.59  3.000
 RKZ  H22  C21  C16  121.80  3.000
 RKZ  C20  C21  C16  119.61  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
 RKZ  CONST_01  C6   N2   C4   N1     0.00   0.0  0
 RKZ  CONST_02  C9   N3   C10  N1   180.00   0.0  0
 RKZ  CONST_03  N2   C6   C10  N1     0.00   0.0  0
 RKZ  CONST_04  C7   C6   C10  N1   180.00   0.0  0
 RKZ  CONST_05  C10  N1   C4   N2     0.00   0.0  0
 RKZ  CONST_06  N3   C10  C6   N2   180.00   0.0  0
 RKZ  CONST_07  C8   C7   C6   N2   180.00   0.0  0
 RKZ  CONST_08  C4   N1   C10  N3   180.00   0.0  0
 RKZ  CONST_09  C7   C6   C10  N3     0.00   0.0  0
 RKZ  CONST_12  C7   C8   C9   N3     0.00   0.0  0
 RKZ  CONST_13  C6   C10  N1   C4     0.00   0.0  0
 RKZ  CONST_14  C10  C6   N2   C4     0.00   0.0  0
 RKZ  CONST_15  C7   C6   N2   C4   180.00   0.0  0
 RKZ  CONST_16  C11  C12  C13  N5     0.00   0.0  0
 RKZ  CONST_17  C11  C15  C14  N5     0.00   0.0  0
 RKZ  CONST_18  C9   N3   C10  C6     0.00   0.0  0
 RKZ  CONST_19  C9   C8   C7   C6     0.00   0.0  0
 RKZ  CONST_20  C11  C9   C8   C7   180.00   0.0  0
 RKZ  CONST_21  C10  N3   C9   C8     0.00   0.0  0
 RKZ  CONST_24  C10  C6   C7   C8     0.00   0.0  0
 RKZ  CONST_25  C13  C12  C11  C9   180.00   0.0  0
 RKZ  CONST_26  C14  C15  C11  C9   180.00   0.0  0
 RKZ  CONST_27  C11  C9   N3   C10  180.00   0.0  0
 RKZ  CONST_28  C14  N5   C13  C12    0.00   0.0  0
 RKZ  CONST_29  C14  C15  C11  C12    0.00   0.0  0
 RKZ  CONST_30  C15  C11  C12  C13    0.00   0.0  0
 RKZ  CONST_31  C15  C14  N5   C13    0.00   0.0  0
 RKZ  CONST_32  C19  C20  C21  C16    0.00   0.0  0
 RKZ  CONST_33  C19  C18  C17  C16    0.00   0.0  0
 RKZ  CONST_34  C20  C21  C16  C17    0.00   0.0  0
 RKZ  CONST_35  C20  C19  C18  C17    0.00   0.0  0
 RKZ  CONST_36  C21  C20  C19  C18    0.00   0.0  0
 RKZ  CONST_37  C21  C16  C17  C18    0.00   0.0  0
 RKZ  CONST_38  C20  C21  C16  O1   180.00   0.0  0
 RKZ  CONST_39  C18  C17  C16  O1   180.00   0.0  0
 RKZ  CONST_40  C3   N1   C4   N2   180.00   0.0  0
 RKZ  CONST_41  N3   C10  N1   C3     0.00   0.0  0
 RKZ  CONST_42  C6   C10  N1   C3   180.00   0.0  0
 RKZ  CONST_43  C11  C12  C13  N4   180.00   0.0  0
 RKZ  CONST_44  C14  N5   C13  N4   180.00   0.0  0
 RKZ  CONST_45  C10  N1   C4   C5   180.00   0.0  0
 RKZ  CONST_46  C6   N2   C4   C5   180.00   0.0  0
 RKZ  CONST_47  C13  N5   C14  N6   180.00   0.0  0
 RKZ  CONST_48  C11  C15  C14  N6   180.00   0.0  0
 RKZ  CONST_49  H14  C7   C6   N2     0.00   0.0  0
 RKZ  CONST_50  H15  C8   C9   N3   180.00   0.0  0
 RKZ  CONST_51  H16  C12  C13  N5   180.00   0.0  0
 RKZ  CONST_52  H17  C15  C14  N5   180.00   0.0  0
 RKZ  CONST_53  H21  C20  C21  C16  180.00   0.0  0
 RKZ  CONST_54  H19  C18  C17  C16  180.00   0.0  0
 RKZ  CONST_55  H22  C21  C16  C17  180.00   0.0  0
 RKZ  CONST_56  H20  C19  C18  C17  180.00   0.0  0
 RKZ  CONST_57  H18  C17  C18  C19  180.00   0.0  0
 RKZ  Var_01    C4   N1   C3   C2    93.36  30.0  2
 RKZ  Var_02    C21  C16  O1   C2   -13.25  30.0  2
 RKZ  Var_03    H9   C5   C4   N1   171.94  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
 RKZ  chir_01  C2  C3  C1  O1  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
 RKZ  plan-1  N4   0.020
 RKZ  plan-1  N5   0.020
 RKZ  plan-1  N6   0.020
 RKZ  plan-1  C9   0.020
 RKZ  plan-1  C11  0.020
 RKZ  plan-1  C12  0.020
 RKZ  plan-1  C13  0.020
 RKZ  plan-1  C14  0.020
 RKZ  plan-1  C15  0.020
 RKZ  plan-1  H16  0.020
 RKZ  plan-1  H17  0.020
 RKZ  plan-2  O1   0.020
 RKZ  plan-2  C16  0.020
 RKZ  plan-2  C17  0.020
 RKZ  plan-2  C18  0.020
 RKZ  plan-2  C19  0.020
 RKZ  plan-2  C20  0.020
 RKZ  plan-2  C21  0.020
 RKZ  plan-2  H18  0.020
 RKZ  plan-2  H19  0.020
 RKZ  plan-2  H20  0.020
 RKZ  plan-2  H21  0.020
 RKZ  plan-2  H22  0.020
 RKZ  plan-3  N1   0.020
 RKZ  plan-3  N2   0.020
 RKZ  plan-3  C3   0.020
 RKZ  plan-3  N3   0.020
 RKZ  plan-3  C4   0.020
 RKZ  plan-3  C5   0.020
 RKZ  plan-3  C6   0.020
 RKZ  plan-3  C7   0.020
 RKZ  plan-3  C8   0.020
 RKZ  plan-3  C9   0.020
 RKZ  plan-3  C10  0.020
 RKZ  plan-3  C11  0.020
 RKZ  plan-3  H14  0.020
 RKZ  plan-3  H15  0.020
 RKZ  plan-4  N4   0.020
 RKZ  plan-4  C13  0.020
 RKZ  plan-4  H7   0.020
 RKZ  plan-4  H8   0.020
 RKZ  plan-5  N6   0.020
 RKZ  plan-5  C14  0.020
 RKZ  plan-5  H12  0.020
 RKZ  plan-5  H13  0.020

