# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 15:04:42 2022
#   Inital geometry file: a 119 line input string
#   Ligand name: 4-(2,3-dibutylimidazo[4,5-b]pyridin-5-yl)pyridine-2,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCn1c(CCCC)nc2ccc(nc12)c3cc(N)nc(N)c3
#
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
 RKK  RKK  4-(2,3-dibutylimidazo[4,5-b]pyridin-5-yl)pyridine-2,6-diamine  ligand  51  25  .  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_RKK
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
 RKK  C1   C  CH3   0  -0.671   -4.1811   1.4508  26.2324
 RKK  N1   N  NR5   0  -0.541   -6.4430  -0.4451  29.5553
 RKK  C2   C  CH2   0  -0.433   -4.0395  -0.0214  26.6012
 RKK  N2   N  N     0  -0.478   -8.4160  -0.6214  30.5895
 RKK  C3   C  CH2   0  -0.449   -5.2096  -0.5746  27.4099
 RKK  N3   N  N     0  -0.450   -5.4951  -2.5729  30.1533
 RKK  C4   C  CH2   0  -0.314   -5.3402   0.0862  28.7770
 RKK  N4   N  NH2   0  -0.838   -1.9761  -6.0015  28.7828
 RKK  C5   C  CR5   0   0.477   -7.6444   0.1393  29.8531
 RKK  N5   N  N     0  -0.504   -2.6683  -6.6226  30.8785
 RKK  C6   C  CH2   0  -0.565   -8.0339   1.4930  29.3754
 RKK  N6   N  NH2   0  -0.838   -3.2602  -7.3242  32.9796
 RKK  C7   C  CH2   0  -0.436   -8.5014   1.5042  27.9156
 RKK  C8   C  CH2   0  -0.428   -8.8281   2.9048  27.4079
 RKK  C9   C  CH3   0  -0.669   -9.9902   3.5737  28.1303
 RKK  C10  C  CR56  0   0.108   -7.6982  -1.7666  30.7999
 RKK  C11  C  CR16  0  -0.230   -7.9588  -2.9296  31.5098
 RKK  C12  C  CR16  0  -0.341   -6.9592  -3.8898  31.5274
 RKK  C13  C  CR6   0   0.186   -5.7470  -3.6813  30.8498
 RKK  C14  C  CR56  0   0.453   -6.4543  -1.6748  30.1562
 RKK  C15  C  CR6   0   0.185   -4.6812  -4.7079  30.8652
 RKK  C16  C  CR16  0  -0.475   -3.8474  -4.8552  29.7644
 RKK  C17  C  CR6   0   0.462   -2.8509  -5.8364  29.8189
 RKK  C18  C  CR6   0   0.462   -3.4663  -6.4712  31.9329
 RKK  C19  C  CR16  0  -0.493   -4.4964  -5.5231  31.9749
 RKK  H1   H  HCH3  0   0.233   -3.3753   1.7674  25.5698
 RKK  H2   H  HCH3  0   0.219   -5.1259   1.6370  25.7176
 RKK  H3   H  HCH3  0   0.223   -4.1507   2.1000  27.1083
 RKK  H4   H  HCH2  0   0.232   -3.9483  -0.6131  25.6878
 RKK  H5   H  HCH2  0   0.220   -3.1088  -0.1756  27.1551
 RKK  H6   H  HCH2  0   0.232   -6.1392  -0.4411  26.8492
 RKK  H7   H  HCH2  0   0.246   -5.0775  -1.6501  27.5465
 RKK  H8   H  HCH2  0   0.263   -4.4228  -0.0577  29.3516
 RKK  H9   H  HCH2  0   0.270   -5.4867   1.1607  28.6831
 RKK  H10  H  HNH2  0   0.377   -1.4865  -6.8805  28.7491
 RKK  H11  H  HNH2  0   0.386   -2.2544  -5.6505  27.8817
 RKK  H12  H  HCH2  0   0.258   -7.2035   2.1940  29.4993
 RKK  H13  H  HCH2  0   0.273   -8.8352   1.8389  30.0281
 RKK  H14  H  HNH2  0   0.377   -2.3554  -7.7636  33.0233
 RKK  H15  H  HNH2  0   0.386   -3.6306  -7.0558  33.8760
 RKK  H16  H  HCH2  0   0.231   -9.3787   0.8587  27.8177
 RKK  H17  H  HCH2  0   0.243   -7.7268   1.0708  27.2782
 RKK  H18  H  HCH2  0   0.229   -9.0594   2.8379  26.3420
 RKK  H19  H  HCH2  0   0.218   -7.9343   3.5313  27.4855
 RKK  H20  H  HCH3  0   0.231  -10.2325   4.5339  27.6741
 RKK  H21  H  HCH3  0   0.218  -10.8878   2.9536  28.0891
 RKK  H22  H  HCH3  0   0.223   -9.7679   3.7633  29.1810
 RKK  H23  H  HCR6  0   0.266   -8.8969  -3.0878  32.0261
 RKK  H24  H  HCR6  0   0.265   -7.1226  -4.8195  32.0544
 RKK  H25  H  HCR6  0   0.250   -3.9670  -4.2386  28.8840
 RKK  H26  H  HCR6  0   0.251   -5.1023  -5.4211  32.8654

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
 RKK  C1   C2   single    1.524  0.020  1.524
 RKK  C2   C3   single    1.526  0.020  1.526
 RKK  C3   C4   single    1.524  0.020  1.524
 RKK  C8   C9   single    1.523  0.020  1.523
 RKK  C8   C7   single    1.525  0.020  1.525
 RKK  C7   C6   single    1.533  0.020  1.533
 RKK  C4   N1   single    1.451  0.020  1.451
 RKK  N4   C17  single    1.366  0.020  1.366
 RKK  C6   C5   single    1.487  0.020  1.487
 RKK  N1   C5   aromatic  1.369  0.020  1.369
 RKK  N1   C14  aromatic  1.369  0.020  1.369
 RKK  C16  C17  aromatic  1.400  0.020  1.400
 RKK  C16  C15  aromatic  1.389  0.020  1.389
 RKK  C5   N2   aromatic  1.310  0.020  1.310
 RKK  C17  N5   aromatic  1.332  0.020  1.332
 RKK  N3   C14  aromatic  1.314  0.020  1.314
 RKK  N3   C13  aromatic  1.333  0.020  1.333
 RKK  C14  C10  aromatic  1.404  0.020  1.404
 RKK  N2   C10  aromatic  1.368  0.020  1.368
 RKK  C13  C15  single    1.480  0.020  1.480
 RKK  C13  C12  aromatic  1.404  0.020  1.404
 RKK  C15  C19  aromatic  1.389  0.020  1.389
 RKK  C10  C11  aromatic  1.387  0.020  1.387
 RKK  N5   C18  aromatic  1.331  0.020  1.331
 RKK  C12  C11  aromatic  1.386  0.020  1.386
 RKK  C19  C18  aromatic  1.401  0.020  1.401
 RKK  C18  N6   single    1.366  0.020  1.366
 RKK  C1   H1   single    0.970  0.020  1.090
 RKK  C1   H2   single    0.970  0.020  1.090
 RKK  C1   H3   single    0.970  0.020  1.090
 RKK  C2   H4   single    0.970  0.020  1.090
 RKK  C2   H5   single    0.970  0.020  1.090
 RKK  C3   H6   single    0.970  0.020  1.090
 RKK  C3   H7   single    0.970  0.020  1.090
 RKK  C4   H8   single    0.970  0.020  1.090
 RKK  C4   H9   single    0.970  0.020  1.090
 RKK  N4   H10  single    0.890  0.020  1.040
 RKK  N4   H11  single    0.890  0.020  1.040
 RKK  C6   H12  single    0.970  0.020  1.090
 RKK  C6   H13  single    0.970  0.020  1.090
 RKK  N6   H14  single    0.890  0.020  1.040
 RKK  N6   H15  single    0.890  0.020  1.040
 RKK  C7   H16  single    0.970  0.020  1.090
 RKK  C7   H17  single    0.970  0.020  1.090
 RKK  C8   H18  single    0.970  0.020  1.090
 RKK  C8   H19  single    0.970  0.020  1.090
 RKK  C9   H20  single    0.970  0.020  1.090
 RKK  C9   H21  single    0.970  0.020  1.090
 RKK  C9   H22  single    0.970  0.020  1.090
 RKK  C11  H23  single    0.930  0.020  1.080
 RKK  C12  H24  single    0.930  0.020  1.080
 RKK  C16  H25  single    0.930  0.020  1.080
 RKK  C19  H26  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
 RKK  H3   C1   H2   107.53  3.000
 RKK  H3   C1   H1   107.14  3.000
 RKK  H2   C1   H1   107.67  3.000
 RKK  H3   C1   C2   112.21  3.000
 RKK  H2   C1   C2   111.05  3.000
 RKK  H1   C1   C2   111.03  3.000
 RKK  C14  N1   C5   106.31  3.000
 RKK  C14  N1   C4   124.82  3.000
 RKK  C5   N1   C4   128.87  3.000
 RKK  H5   C2   H4   106.02  3.000
 RKK  H5   C2   C3   109.44  3.000
 RKK  H4   C2   C3   108.11  3.000
 RKK  H5   C2   C1   109.74  3.000
 RKK  H4   C2   C1   109.19  3.000
 RKK  C3   C2   C1   114.03  3.000
 RKK  C10  N2   C5   105.28  3.000
 RKK  H7   C3   H6   106.68  3.000
 RKK  H7   C3   C4   108.98  3.000
 RKK  H6   C3   C4   109.52  3.000
 RKK  H7   C3   C2   109.30  3.000
 RKK  H6   C3   C2   109.61  3.000
 RKK  C4   C3   C2   112.57  3.000
 RKK  C14  N3   C13  115.42  3.000
 RKK  H9   C4   H8   106.77  3.000
 RKK  H9   C4   C3   111.24  3.000
 RKK  H8   C4   C3   110.05  3.000
 RKK  H9   C4   N1   107.79  3.000
 RKK  H8   C4   N1   107.94  3.000
 RKK  C3   C4   N1   112.80  3.000
 RKK  H11  N4   H10  114.14  3.000
 RKK  H11  N4   C17  117.39  3.000
 RKK  H10  N4   C17  116.25  3.000
 RKK  C6   C5   N2   123.70  3.000
 RKK  N2   C5   N1   113.04  3.000
 RKK  C6   C5   N1   123.27  3.000
 RKK  C18  N5   C17  118.75  3.000
 RKK  H13  C6   H12  106.67  3.000
 RKK  H13  C6   C7   110.11  3.000
 RKK  H12  C6   C7   109.56  3.000
 RKK  H13  C6   C5   106.80  3.000
 RKK  H12  C6   C5   110.37  3.000
 RKK  C7   C6   C5   113.11  3.000
 RKK  H15  N6   H14  114.11  3.000
 RKK  H15  N6   C18  117.42  3.000
 RKK  H14  N6   C18  116.20  3.000
 RKK  H17  C7   H16  106.40  3.000
 RKK  H17  C7   C8   108.78  3.000
 RKK  H16  C7   C8   109.91  3.000
 RKK  H17  C7   C6   109.65  3.000
 RKK  H16  C7   C6   109.00  3.000
 RKK  C8   C7   C6   112.90  3.000
 RKK  H19  C8   H18  106.09  3.000
 RKK  H19  C8   C9   109.76  3.000
 RKK  H18  C8   C9   109.14  3.000
 RKK  H19  C8   C7   109.10  3.000
 RKK  H18  C8   C7   108.29  3.000
 RKK  C9   C8   C7   114.13  3.000
 RKK  H22  C9   H21  107.62  3.000
 RKK  H22  C9   H20  107.17  3.000
 RKK  H21  C9   H20  107.56  3.000
 RKK  H22  C9   C8   112.20  3.000
 RKK  H21  C9   C8   111.10  3.000
 RKK  H20  C9   C8   110.97  3.000
 RKK  C14  C10  C11  117.13  3.000
 RKK  C11  C10  N2   133.01  3.000
 RKK  C14  C10  N2   109.86  3.000
 RKK  H23  C11  C12  121.18  3.000
 RKK  H23  C11  C10  121.97  3.000
 RKK  C12  C11  C10  116.86  3.000
 RKK  H24  C12  C13  119.57  3.000
 RKK  H24  C12  C11  119.53  3.000
 RKK  C13  C12  C11  120.89  3.000
 RKK  C15  C13  C12  120.91  3.000
 RKK  C12  C13  N3   122.60  3.000
 RKK  C15  C13  N3   116.49  3.000
 RKK  C10  C14  N3   127.10  3.000
 RKK  C10  C14  N1   105.51  3.000
 RKK  N3   C14  N1   127.38  3.000
 RKK  C19  C15  C16  119.41  3.000
 RKK  C19  C15  C13  120.74  3.000
 RKK  C16  C15  C13  119.85  3.000
 RKK  H25  C16  C17  120.68  3.000
 RKK  H25  C16  C15  121.22  3.000
 RKK  C17  C16  C15  118.10  3.000
 RKK  C16  C17  N5   122.84  3.000
 RKK  N5   C17  N4   116.38  3.000
 RKK  C16  C17  N4   120.74  3.000
 RKK  C19  C18  N6   120.72  3.000
 RKK  N6   C18  N5   116.46  3.000
 RKK  C19  C18  N5   122.80  3.000
 RKK  H26  C19  C18  120.02  3.000
 RKK  H26  C19  C15  121.85  3.000
 RKK  C18  C19  C15  118.11  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
 RKK  CONST_01  C10  N2   C5   N1      0.00   0.0  0
 RKK  CONST_02  C13  N3   C14  N1    180.00   0.0  0
 RKK  CONST_03  N2   C10  C14  N1      0.00   0.0  0
 RKK  CONST_04  C11  C10  C14  N1    180.00   0.0  0
 RKK  CONST_05  C14  N1   C5   N2      0.00   0.0  0
 RKK  CONST_06  N3   C14  C10  N2    180.00   0.0  0
 RKK  CONST_07  C12  C11  C10  N2    180.00   0.0  0
 RKK  CONST_08  C5   N1   C14  N3    180.00   0.0  0
 RKK  CONST_09  C11  C10  C14  N3      0.00   0.0  0
 RKK  CONST_12  C11  C12  C13  N3      0.00   0.0  0
 RKK  CONST_13  C10  C14  N1   C5      0.00   0.0  0
 RKK  CONST_14  C14  C10  N2   C5      0.00   0.0  0
 RKK  CONST_15  C11  C10  N2   C5    180.00   0.0  0
 RKK  CONST_16  C15  C16  C17  N5      0.00   0.0  0
 RKK  CONST_17  C15  C19  C18  N5      0.00   0.0  0
 RKK  CONST_18  C13  N3   C14  C10     0.00   0.0  0
 RKK  CONST_19  C13  C12  C11  C10     0.00   0.0  0
 RKK  CONST_20  C15  C13  C12  C11   180.00   0.0  0
 RKK  CONST_21  C14  N3   C13  C12     0.00   0.0  0
 RKK  CONST_24  C14  C10  C11  C12     0.00   0.0  0
 RKK  CONST_25  C17  C16  C15  C13   180.00   0.0  0
 RKK  CONST_26  C18  C19  C15  C13   180.00   0.0  0
 RKK  CONST_27  C15  C13  N3   C14   180.00   0.0  0
 RKK  CONST_28  C18  N5   C17  C16     0.00   0.0  0
 RKK  CONST_29  C18  C19  C15  C16     0.00   0.0  0
 RKK  CONST_30  C19  C15  C16  C17     0.00   0.0  0
 RKK  CONST_31  C19  C18  N5   C17     0.00   0.0  0
 RKK  CONST_32  C4   N1   C5   N2    180.00   0.0  0
 RKK  CONST_33  C4   N1   C14  N3      0.00   0.0  0
 RKK  CONST_34  C10  C14  N1   C4    180.00   0.0  0
 RKK  CONST_35  C15  C16  C17  N4    180.00   0.0  0
 RKK  CONST_36  C18  N5   C17  N4    180.00   0.0  0
 RKK  CONST_37  C14  N1   C5   C6    180.00   0.0  0
 RKK  CONST_38  C10  N2   C5   C6    180.00   0.0  0
 RKK  CONST_39  C17  N5   C18  N6    180.00   0.0  0
 RKK  CONST_40  C15  C19  C18  N6    180.00   0.0  0
 RKK  CONST_41  H23  C11  C10  N2      0.00   0.0  0
 RKK  CONST_42  H24  C12  C13  N3    180.00   0.0  0
 RKK  CONST_43  H25  C16  C17  N5    180.00   0.0  0
 RKK  CONST_44  H26  C19  C18  N5    180.00   0.0  0
 RKK  Var_01    C7   C6   C5   N1     78.63  30.0  3
 RKK  Var_02    C5   N1   C4   C3   -107.20  30.0  2
 RKK  Var_03    C2   C3   C4   N1   -179.44  30.0  1
 RKK  Var_04    C8   C7   C6   C5   -176.91  30.0  1
 RKK  Var_05    C4   C3   C2   C1    -64.28  30.0  3
 RKK  Var_06    C9   C8   C7   C6    -63.52  30.0  1
 RKK  Var_07    H1   C1   C2   C3   -174.02  30.0  3
 RKK  Var_08    H20  C9   C8   C7   -175.29  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
 RKK  plan-1  N4   0.020
 RKK  plan-1  N5   0.020
 RKK  plan-1  N6   0.020
 RKK  plan-1  C13  0.020
 RKK  plan-1  C15  0.020
 RKK  plan-1  C16  0.020
 RKK  plan-1  C17  0.020
 RKK  plan-1  C18  0.020
 RKK  plan-1  C19  0.020
 RKK  plan-1  H25  0.020
 RKK  plan-1  H26  0.020
 RKK  plan-2  N1   0.020
 RKK  plan-2  N2   0.020
 RKK  plan-2  N3   0.020
 RKK  plan-2  C4   0.020
 RKK  plan-2  C5   0.020
 RKK  plan-2  C6   0.020
 RKK  plan-2  C10  0.020
 RKK  plan-2  C11  0.020
 RKK  plan-2  C12  0.020
 RKK  plan-2  C13  0.020
 RKK  plan-2  C14  0.020
 RKK  plan-2  C15  0.020
 RKK  plan-2  H23  0.020
 RKK  plan-2  H24  0.020
 RKK  plan-3  N4   0.020
 RKK  plan-3  C17  0.020
 RKK  plan-3  H10  0.020
 RKK  plan-3  H11  0.020
 RKK  plan-4  N6   0.020
 RKK  plan-4  C18  0.020
 RKK  plan-4  H14  0.020
 RKK  plan-4  H15  0.020

