# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 00:39:31 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 5-(2-methoxyethyl)-1-methyl-2-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]-6,7-dihydropyrrolo[3,2-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCN1CCc2n(C)c(cc2C1=O)c3ccnc(Nc4ccnn4C)n3
#
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
 8XK  8XK  5-(2-methoxyethyl)-1-methyl-2-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]-6,7-dihydropyrrolo[3,2-c]pyridin-4-one  ligand  51  28  .  2021-08-06  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8XK
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
 8XK  C1   C  CR5   0   0.664   5.5382   0.0104  -0.3195
 8XK  C2   C  CR15  0  -0.523   6.3438  -1.0765  -0.0309
 8XK  C3   C  CR15  0  -0.066   7.6355  -0.6222  -0.3385
 8XK  N6   N  NT    0  -0.485  -4.8031   0.6457   0.5336
 8XK  C7   C  CR6   0   0.268   0.9955  -0.9009   0.5876
 8XK  C8   C  CR5   0   0.327  -0.3598  -0.3852   0.5803
 8XK  C9   C  CR15  0  -0.413  -1.5214  -1.1112   0.7489
 8XK  C10  C  CR5   0  -0.137  -2.5926  -0.2127   0.6264
 8XK  C11  C  CR5   0   0.376  -2.0551   1.0378   0.3984
 8XK  C13  C  CH2   0  -0.531  -2.9100   2.2444   0.2811
 8XK  C14  C  CH2   0  -0.294  -4.2737   1.7801  -0.2151
 8XK  C15  C  C     0   0.522  -4.0256  -0.4346   0.8147
 8XK  C16  C  CH2   0  -0.353  -6.2440   0.5540   0.6404
 8XK  O    O  O     0  -0.499  -4.4655  -1.4927   1.2496
 8XK  C17  C  CH2   0  -0.145  -6.9395   0.3109  -0.6863
 8XK  O1   O  O2    0  -0.475  -6.4753  -0.8846  -1.2511
 8XK  C18  C  CH3   0  -0.392  -7.0423  -1.1417  -2.5096
 8XK  N5   N  NR5   0  -0.547  -0.7135   0.9419   0.3740
 8XK  C6   C  CR16  0  -0.403   1.2549  -2.2106   1.0223
 8XK  C5   C  CR16  0  -0.004   2.5660  -2.6212   0.9868
 8XK  N3   N  N     0  -0.464   3.5688  -1.8461   0.5764
 8XK  N4   N  N     0  -0.500   1.9868  -0.1247   0.1713
 8XK  C4   C  CR6   0   0.605   3.2198  -0.6289   0.1918
 8XK  N2   N  NH1   0  -0.779   4.1839   0.2369  -0.2393
 8XK  N1   N  N     0  -0.296   7.6377   0.6199  -0.7731
 8XK  N    N  NR5   0  -0.344   6.3514   0.9968  -0.7580
 8XK  C    C  CH3   0  -0.562   5.9688   2.3255  -1.1694
 8XK  H1   H  HCR5  0   0.270   6.0413  -2.0364   0.3410
 8XK  H2   H  HCR5  0   0.256   8.5628  -1.1688  -0.2520
 8XK  H3   H  HCR5  0   0.261  -1.5889  -2.1744   0.9166
 8XK  H4   H  HCH3  0   0.260   0.7077   2.0417  -0.7229
 8XK  H5   H  HCH3  0   0.262  -0.4286   2.9898   0.2449
 8XK  H6   H  HCH3  0   0.261   0.8902   2.1265   1.0308
 8XK  H7   H  HCH2  0   0.275  -2.9963   2.7449   1.2509
 8XK  H8   H  HCH2  0   0.276  -2.5178   2.9764  -0.4254
 8XK  H9   H  HCH2  0   0.247  -4.1962   1.5315  -1.2790
 8XK  H10  H  HCH2  0   0.265  -4.9865   2.5989  -0.1267
 8XK  H11  H  HCH2  0   0.260  -6.4944  -0.2359   1.3457
 8XK  H12  H  HCH2  0   0.257  -6.6258   1.4909   1.0544
 8XK  H13  H  HCH2  0   0.213  -8.0235   0.2768  -0.5036
 8XK  H14  H  HCH2  0   0.202  -6.7671   1.1551  -1.3705
 8XK  H15  H  HCH3  0   0.232  -6.6093  -2.0652  -2.8924
 8XK  H16  H  HCH3  0   0.203  -8.1305  -1.2668  -2.4561
 8XK  H17  H  HCH3  0   0.203  -6.8327  -0.3383  -3.2266
 8XK  H18  H  HCR6  0   0.270   0.4784  -2.8704   1.3785
 8XK  H19  H  HCR6  0   0.274   2.8349  -3.6208   1.3087
 8XK  H20  H  HNH1  0   0.420   3.8324   1.1364  -0.5313
 8XK  H21  H  HCH3  0   0.261   5.5030   2.8758  -0.3514
 8XK  H22  H  HCH3  0   0.282   6.8676   2.8531  -1.4718
 8XK  H23  H  HCH3  0   0.261   5.2843   2.2979  -2.0176
 8XK  C12  C  CH3   0  -0.521   0.1699   2.0840   0.2194

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
 8XK  C18  O1   single    1.404  0.020  1.404
 8XK  O1   C17  single    1.401  0.020  1.401
 8XK  C17  C16  single    1.518  0.020  1.518
 8XK  O    C15  double    1.226  0.020  1.226
 8XK  C16  N6   single    1.448  0.020  1.448
 8XK  C15  C10  single    1.462  0.020  1.462
 8XK  C15  N6   single    1.360  0.020  1.360
 8XK  C6   C5   aromatic  1.374  0.020  1.374
 8XK  C6   C7   aromatic  1.404  0.020  1.404
 8XK  C5   N3   aromatic  1.332  0.020  1.332
 8XK  C9   C10  aromatic  1.404  0.020  1.404
 8XK  C9   C8   aromatic  1.380  0.020  1.380
 8XK  C10  C11  aromatic  1.380  0.020  1.380
 8XK  N6   C14  single    1.459  0.020  1.459
 8XK  C8   C7   single    1.450  0.020  1.450
 8XK  C8   N5   aromatic  1.389  0.020  1.389
 8XK  C7   N4   aromatic  1.326  0.020  1.326
 8XK  C11  N5   aromatic  1.345  0.020  1.345
 8XK  C11  C13  single    1.483  0.020  1.483
 8XK  N3   C4   aromatic  1.323  0.020  1.323
 8XK  N5   C12  single    1.452  0.020  1.452
 8XK  C13  C14  single    1.524  0.020  1.524
 8XK  N4   C4   aromatic  1.332  0.020  1.332
 8XK  C4   N2   single    1.366  0.020  1.366
 8XK  N2   C1   single    1.375  0.020  1.375
 8XK  C    N    single    1.443  0.020  1.443
 8XK  C1   N    aromatic  1.351  0.020  1.351
 8XK  C1   C2   aromatic  1.383  0.020  1.383
 8XK  N    N1   aromatic  1.341  0.020  1.341
 8XK  C2   C3   aromatic  1.403  0.020  1.403
 8XK  N1   C3   aromatic  1.316  0.020  1.316
 8XK  C2   H1   single    0.930  0.020  1.080
 8XK  C3   H2   single    0.930  0.020  1.080
 8XK  C9   H3   single    0.930  0.020  1.080
 8XK  C12  H4   single    0.970  0.020  1.090
 8XK  C12  H5   single    0.970  0.020  1.090
 8XK  C12  H6   single    0.970  0.020  1.090
 8XK  C13  H7   single    0.970  0.020  1.090
 8XK  C13  H8   single    0.970  0.020  1.090
 8XK  C14  H9   single    0.970  0.020  1.090
 8XK  C14  H10  single    0.970  0.020  1.090
 8XK  C16  H11  single    0.970  0.020  1.090
 8XK  C16  H12  single    0.970  0.020  1.090
 8XK  C17  H13  single    0.970  0.020  1.090
 8XK  C17  H14  single    0.970  0.020  1.090
 8XK  C18  H15  single    0.970  0.020  1.090
 8XK  C18  H16  single    0.970  0.020  1.090
 8XK  C18  H17  single    0.970  0.020  1.090
 8XK  C6   H18  single    0.930  0.020  1.080
 8XK  C5   H19  single    0.930  0.020  1.080
 8XK  N2   H20  single    0.860  0.020  1.020
 8XK  C    H21  single    0.970  0.020  1.090
 8XK  C    H22  single    0.970  0.020  1.090
 8XK  C    H23  single    0.970  0.020  1.090

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
 8XK  N    C1   N2   119.42  3.000
 8XK  N    C1   C2   106.90  3.000
 8XK  N2   C1   C2   133.68  3.000
 8XK  H1   C2   C3   128.69  3.000
 8XK  H1   C2   C1   127.66  3.000
 8XK  C3   C2   C1   103.65  3.000
 8XK  H2   C3   N1   120.18  3.000
 8XK  H2   C3   C2   127.52  3.000
 8XK  N1   C3   C2   112.30  3.000
 8XK  C16  N6   C15  120.22  3.000
 8XK  C15  N6   C14  121.07  3.000
 8XK  C16  N6   C14  116.64  3.000
 8XK  N4   C7   C6   120.34  3.000
 8XK  N4   C7   C8   119.27  3.000
 8XK  C6   C7   C8   120.39  3.000
 8XK  N5   C8   C9   107.85  3.000
 8XK  N5   C8   C7   125.35  3.000
 8XK  C9   C8   C7   126.79  3.000
 8XK  H3   C9   C10  126.65  3.000
 8XK  H3   C9   C8   126.18  3.000
 8XK  C10  C9   C8   107.15  3.000
 8XK  C15  C10  C11  122.72  3.000
 8XK  C11  C10  C9   107.29  3.000
 8XK  C15  C10  C9   129.76  3.000
 8XK  N5   C11  C13  129.14  3.000
 8XK  C13  C11  C10  121.71  3.000
 8XK  N5   C11  C10  109.08  3.000
 8XK  H8   C13  H7   107.19  3.000
 8XK  H8   C13  C14  108.39  3.000
 8XK  H7   C13  C14  110.93  3.000
 8XK  H8   C13  C11  112.95  3.000
 8XK  H7   C13  C11  110.32  3.000
 8XK  C14  C13  C11  107.08  3.000
 8XK  H10  C14  H9   107.20  3.000
 8XK  H10  C14  C13  109.28  3.000
 8XK  H9   C14  C13  108.80  3.000
 8XK  H10  C14  N6   107.78  3.000
 8XK  H9   C14  N6   110.35  3.000
 8XK  C13  C14  N6   113.25  3.000
 8XK  O    C15  C10  121.90  3.000
 8XK  C10  C15  N6   114.39  3.000
 8XK  O    C15  N6   123.62  3.000
 8XK  H12  C16  H11  107.24  3.000
 8XK  H12  C16  C17  107.96  3.000
 8XK  H11  C16  C17  110.18  3.000
 8XK  H12  C16  N6   108.74  3.000
 8XK  H11  C16  N6   108.83  3.000
 8XK  C17  C16  N6   113.69  3.000
 8XK  H14  C17  H13  106.36  3.000
 8XK  H14  C17  O1   110.61  3.000
 8XK  H13  C17  O1   111.53  3.000
 8XK  H14  C17  C16  110.42  3.000
 8XK  H13  C17  C16  108.15  3.000
 8XK  O1   C17  C16  109.70  3.000
 8XK  C18  O1   C17  112.56  3.000
 8XK  H17  C18  H16  107.76  3.000
 8XK  H17  C18  H15  108.37  3.000
 8XK  H16  C18  H15  108.35  3.000
 8XK  H17  C18  O1   112.00  3.000
 8XK  H16  C18  O1   112.20  3.000
 8XK  H15  C18  O1   108.04  3.000
 8XK  C12  N5   C11  123.55  3.000
 8XK  C12  N5   C8   127.77  3.000
 8XK  C11  N5   C8   108.62  3.000
 8XK  H18  C6   C5   120.81  3.000
 8XK  H18  C6   C7   122.64  3.000
 8XK  C5   C6   C7   116.54  3.000
 8XK  H19  C5   N3   116.18  3.000
 8XK  H19  C5   C6   120.30  3.000
 8XK  N3   C5   C6   123.52  3.000
 8XK  C4   N3   C5   115.23  3.000
 8XK  C4   N4   C7   117.74  3.000
 8XK  N2   C4   N4   114.12  3.000
 8XK  N2   C4   N3   119.26  3.000
 8XK  N4   C4   N3   126.63  3.000
 8XK  H20  N2   C4   114.24  3.000
 8XK  H20  N2   C1   118.23  3.000
 8XK  C4   N2   C1   127.53  3.000
 8XK  N    N1   C3   105.08  3.000
 8XK  C    N    N1   120.68  3.000
 8XK  N1   N    C1   112.07  3.000
 8XK  C    N    C1   127.24  3.000
 8XK  H23  C    H22  108.39  3.000
 8XK  H23  C    H21  109.16  3.000
 8XK  H22  C    H21  108.50  3.000
 8XK  H23  C    N    111.41  3.000
 8XK  H22  C    N    107.91  3.000
 8XK  H21  C    N    111.36  3.000
 8XK  H6   C12  H5   108.39  3.000
 8XK  H6   C12  H4   108.76  3.000
 8XK  H5   C12  H4   109.01  3.000
 8XK  H6   C12  N5   110.78  3.000
 8XK  H5   C12  N5   108.55  3.000
 8XK  H4   C12  N5   111.29  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
 8XK  CONST_01  C3   N1   N    C1      0.00   0.0  0
 8XK  CONST_02  N1   C3   C2   C1      0.00   0.0  0
 8XK  CONST_03  N1   N    C1   C2      0.00   0.0  0
 8XK  CONST_04  N    N1   C3   C2      0.00   0.0  0
 8XK  CONST_05  N    C1   C2   C3      0.00   0.0  0
 8XK  CONST_06  N3   C5   C6   C7      0.00   0.0  0
 8XK  CONST_07  C10  C9   C8   C7    180.00   0.0  0
 8XK  CONST_08  C11  N5   C8   C7    180.00   0.0  0
 8XK  CONST_09  N3   C4   N4   C7      0.00   0.0  0
 8XK  CONST_10  C11  C10  C9   C8      0.00   0.0  0
 8XK  CONST_11  C5   C6   C7   C8    180.00   0.0  0
 8XK  CONST_12  C4   N4   C7   C8    180.00   0.0  0
 8XK  CONST_13  C10  C11  N5   C8      0.00   0.0  0
 8XK  CONST_14  N5   C11  C10  C9      0.00   0.0  0
 8XK  CONST_15  C6   C7   C8   C9      0.00   0.0  0
 8XK  CONST_16  N4   C7   C8   C9    180.00   0.0  0
 8XK  CONST_17  C11  N5   C8   C9      0.00   0.0  0
 8XK  CONST_18  N5   C8   C9   C10     0.00   0.0  0
 8XK  CONST_19  C6   C7   C8   N5    180.00   0.0  0
 8XK  CONST_20  N4   C7   C8   N5      0.00   0.0  0
 8XK  CONST_21  C4   N3   C5   C6      0.00   0.0  0
 8XK  CONST_22  C4   N4   C7   C6      0.00   0.0  0
 8XK  CONST_23  N4   C7   C6   C5      0.00   0.0  0
 8XK  CONST_24  N4   C4   N3   C5      0.00   0.0  0
 8XK  CONST_26  C    N    C1   C2    180.00   0.0  0
 8XK  CONST_27  N2   C1   C2   C3    180.00   0.0  0
 8XK  CONST_28  C    N    N1   C3    180.00   0.0  0
 8XK  CONST_29  C12  N5   C8   C7      0.00   0.0  0
 8XK  CONST_30  N2   C4   N4   C7    180.00   0.0  0
 8XK  CONST_31  C12  N5   C8   C9    180.00   0.0  0
 8XK  CONST_32  C12  N5   C11  C10   180.00   0.0  0
 8XK  CONST_33  C13  C11  N5   C12     0.00   0.0  0
 8XK  CONST_34  N2   C4   N3   C5    180.00   0.0  0
 8XK  CONST_35  N1   N    C1   N2    180.00   0.0  0
 8XK  CONST_36  C16  N6   C15  C10   180.00   0.0  0
 8XK  CONST_37  O    C15  N6   C14   180.00   0.0  0
 8XK  CONST_38  H2   C3   C2   C1    180.00   0.0  0
 8XK  CONST_39  H19  C5   C6   C7    180.00   0.0  0
 8XK  CONST_40  H3   C9   C8   C7      0.00   0.0  0
 8XK  CONST_41  H18  C6   C7   C8      0.00   0.0  0
 8XK  CONST_42  H1   C2   C3   N1    180.00   0.0  0
 8XK  CONST_43  O    C15  N6   C16     0.00   0.0  0
 8XK  Var_01    C9   C10  C15  N6   -176.14  30.0  1
 8XK  Var_02    C11  C13  C14  N6     48.68  30.0  1
 8XK  Var_03    C14  C13  C11  C10   -26.89  30.0  1
 8XK  Var_04    C15  N6   C14  C13   -46.61  30.0  1
 8XK  Var_05    N3   C4   N2   C1     -0.77  30.0  1
 8XK  Var_06    C4   N2   C1   C2      0.56  30.0  1
 8XK  Var_07    C17  C16  N6   C14    65.61  30.0  1
 8XK  Var_08    H21  C    N    C1     61.62  30.0  2
 8XK  Var_09    H4   C12  N5   C8     69.60  30.0  2
 8XK  Var_10    O1   C17  C16  N6     59.24  30.0  2
 8XK  Var_11    H15  C18  O1   C17   178.22  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
 8XK  plan-1  C1   0.020
 8XK  plan-1  C2   0.020
 8XK  plan-1  C3   0.020
 8XK  plan-1  N2   0.020
 8XK  plan-1  N1   0.020
 8XK  plan-1  N    0.020
 8XK  plan-1  C    0.020
 8XK  plan-1  H1   0.020
 8XK  plan-1  H2   0.020
 8XK  plan-2  C7   0.020
 8XK  plan-2  C8   0.020
 8XK  plan-2  C6   0.020
 8XK  plan-2  C5   0.020
 8XK  plan-2  N3   0.020
 8XK  plan-2  N4   0.020
 8XK  plan-2  C4   0.020
 8XK  plan-2  N2   0.020
 8XK  plan-2  H18  0.020
 8XK  plan-2  H19  0.020
 8XK  plan-3  C7   0.020
 8XK  plan-3  C8   0.020
 8XK  plan-3  C9   0.020
 8XK  plan-3  C10  0.020
 8XK  plan-3  C11  0.020
 8XK  plan-3  C13  0.020
 8XK  plan-3  C15  0.020
 8XK  plan-3  N5   0.020
 8XK  plan-3  H3   0.020
 8XK  plan-3  C12  0.020
 8XK  plan-4  N6   0.020
 8XK  plan-4  C10  0.020
 8XK  plan-4  C14  0.020
 8XK  plan-4  C15  0.020
 8XK  plan-4  C16  0.020
 8XK  plan-4  O    0.020

