# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 11:11:38 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 5-(2-methoxyethyl)-2-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]-6,7-dihydro-1~{H}-pyrrolo[3,2-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCN1CCc2[nH]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
 8XE  8XE  5-(2-methoxyethyl)-2-[2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]-6,7-dihydro-1~{H}-pyrrolo[3,2-c]pyridin-4-one  ligand  48  27  .  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_8XE
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
 8XE  C1   C  CR5   0   0.662   5.3291  -0.5696  -0.0187
 8XE  C2   C  CR15  0  -0.521   6.3008   0.2681  -0.5367
 8XE  C3   C  CR15  0  -0.066   7.4926  -0.4466  -0.3418
 8XE  N6   N  NT    0  -0.485  -4.7121   0.0055   0.7115
 8XE  C7   C  CR6   0   0.258   1.0464   1.4015  -0.2435
 8XE  C8   C  CR5   0   0.308  -0.3614   1.1533  -0.0190
 8XE  C9   C  CR15  0  -0.380  -0.9911  -0.0131   0.3576
 8XE  C10  C  CR5   0  -0.140  -2.3703   0.2714   0.4221
 8XE  C11  C  CR5   0   0.369  -2.5382   1.6017   0.0959
 8XE  C12  C  CH2   0  -0.526  -3.8588   2.2706   0.1282
 8XE  C13  C  CH2   0  -0.298  -4.9081   1.1929  -0.1157
 8XE  C14  C  C     0   0.523  -3.4870  -0.5712   0.8492
 8XE  C16  C  CH2   0  -0.147  -6.5967  -1.3306  -0.1881
 8XE  O    O  O     0  -0.498  -3.3108  -1.6786   1.3431
 8XE  O1   O  O2    0  -0.475  -5.6960  -2.1365  -0.8966
 8XE  C17  C  CH3   0  -0.392  -6.2453  -2.6497  -2.0823
 8XE  N5   N  NR15  0  -0.718  -1.3317   2.1222  -0.1671
 8XE  C6   C  CR16  0  -0.389   1.5409   2.6309  -0.6936
 8XE  C5   C  CR16  0  -0.001   2.9068   2.7179  -0.8584
 8XE  N3   N  N     0  -0.460   3.7393   1.7133  -0.6129
 8XE  N4   N  N     0  -0.500   1.8700   0.3875   0.0037
 8XE  C4   C  CR6   0   0.598   3.1691   0.5916  -0.1890
 8XE  N2   N  NH1   0  -0.779   3.9601  -0.4844   0.0936
 8XE  N1   N  N     0  -0.296   7.2874  -1.6108   0.2369
 8XE  N    N  NR5   0  -0.342   5.9636  -1.6734   0.4343
 8XE  C    C  CH3   0  -0.559   5.3652  -2.8315   1.0519
 8XE  H1   H  HCR5  0   0.269   6.1648   1.2364  -0.9792
 8XE  H2   H  HCR5  0   0.256   8.4937  -0.1418  -0.6077
 8XE  H3   H  HCR5  0   0.257  -0.5051  -0.9553   0.5536
 8XE  H4   H  HCH2  0   0.272  -4.0137   2.7483   1.1005
 8XE  H5   H  HCH2  0   0.277  -3.9525   3.0454  -0.6335
 8XE  H6   H  HCH2  0   0.247  -4.9008   0.9200  -1.1765
 8XE  H7   H  HCH2  0   0.266  -5.8965   1.5914   0.1088
 8XE  H8   H  HCH2  0   0.262  -5.6451  -1.5396   1.7327
 8XE  H9   H  HCH2  0   0.257  -6.6145  -0.0881   1.5397
 8XE  H10  H  HCH2  0   0.216  -7.4731  -1.9025   0.1494
 8XE  H11  H  HCH2  0   0.202  -6.9823  -0.5230  -0.8281
 8XE  H12  H  HCH3  0   0.203  -7.0961  -3.3152  -1.8920
 8XE  H13  H  HCH3  0   0.203  -6.5870  -1.8529  -2.7544
 8XE  H14  H  HCH3  0   0.232  -5.4710  -3.2211  -2.5933
 8XE  H15  H  HNR5  0   0.422  -1.1707   3.0848  -0.4198
 8XE  H16  H  HCR6  0   0.265   0.9105   3.4793  -0.9145
 8XE  H17  H  HCR6  0   0.277   3.3563   3.6410  -1.2062
 8XE  H18  H  HNH1  0   0.423   3.4571  -1.2999   0.4111
 8XE  H19  H  HCH3  0   0.261   4.7017  -3.3522   0.3606
 8XE  H20  H  HCH3  0   0.281   6.1646  -3.5065   1.3396
 8XE  H21  H  HCH3  0   0.261   4.8049  -2.5552   1.9451
 8XE  C15  C  CH2   0  -0.355  -5.9061  -0.7486   1.0330

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
 8XE  C17  O1   single    1.404  0.020  1.404
 8XE  O1   C16  single    1.401  0.020  1.401
 8XE  C16  C15  single    1.519  0.020  1.519
 8XE  O    C14  double    1.225  0.020  1.225
 8XE  C9   C10  aromatic  1.410  0.020  1.410
 8XE  C9   C8   aromatic  1.378  0.020  1.378
 8XE  C14  C10  single    1.463  0.020  1.463
 8XE  C14  N6   single    1.361  0.020  1.361
 8XE  C6   C5   aromatic  1.379  0.020  1.379
 8XE  C6   C7   aromatic  1.399  0.020  1.399
 8XE  C15  N6   single    1.448  0.020  1.448
 8XE  C5   N3   aromatic  1.328  0.020  1.328
 8XE  C10  C11  aromatic  1.380  0.020  1.380
 8XE  N6   C13  single    1.460  0.020  1.460
 8XE  C8   C7   single    1.447  0.020  1.447
 8XE  C8   N5   aromatic  1.379  0.020  1.379
 8XE  C7   N4   aromatic  1.329  0.020  1.329
 8XE  N3   C4   aromatic  1.328  0.020  1.328
 8XE  C13  C12  single    1.524  0.020  1.524
 8XE  C11  N5   aromatic  1.340  0.020  1.340
 8XE  C11  C12  single    1.481  0.020  1.481
 8XE  N4   C4   aromatic  1.329  0.020  1.329
 8XE  C4   N2   single    1.365  0.020  1.365
 8XE  N2   C1   single    1.376  0.020  1.376
 8XE  C    N    single    1.442  0.020  1.442
 8XE  C1   N    aromatic  1.351  0.020  1.351
 8XE  C1   C2   aromatic  1.384  0.020  1.384
 8XE  N    N1   aromatic  1.340  0.020  1.340
 8XE  C2   C3   aromatic  1.403  0.020  1.403
 8XE  N1   C3   aromatic  1.316  0.020  1.316
 8XE  C2   H1   single    0.930  0.020  1.080
 8XE  C3   H2   single    0.930  0.020  1.080
 8XE  C9   H3   single    0.930  0.020  1.080
 8XE  C12  H4   single    0.970  0.020  1.090
 8XE  C12  H5   single    0.970  0.020  1.090
 8XE  C13  H6   single    0.970  0.020  1.090
 8XE  C13  H7   single    0.970  0.020  1.090
 8XE  C15  H8   single    0.970  0.020  1.090
 8XE  C15  H9   single    0.970  0.020  1.090
 8XE  C16  H10  single    0.970  0.020  1.090
 8XE  C16  H11  single    0.970  0.020  1.090
 8XE  C17  H12  single    0.970  0.020  1.090
 8XE  C17  H13  single    0.970  0.020  1.090
 8XE  C17  H14  single    0.970  0.020  1.090
 8XE  N5   H15  single    0.860  0.020  1.020
 8XE  C6   H16  single    0.930  0.020  1.080
 8XE  C5   H17  single    0.930  0.020  1.080
 8XE  N2   H18  single    0.860  0.020  1.020
 8XE  C    H19  single    0.970  0.020  1.090
 8XE  C    H20  single    0.970  0.020  1.090
 8XE  C    H21  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
 8XE  N    C1   N2   119.36  3.000
 8XE  N    C1   C2   106.88  3.000
 8XE  N2   C1   C2   133.76  3.000
 8XE  H1   C2   C3   128.63  3.000
 8XE  H1   C2   C1   127.71  3.000
 8XE  C3   C2   C1   103.66  3.000
 8XE  H2   C3   N1   120.17  3.000
 8XE  H2   C3   C2   127.55  3.000
 8XE  N1   C3   C2   112.28  3.000
 8XE  C15  N6   C14  119.93  3.000
 8XE  C15  N6   C13  116.01  3.000
 8XE  C14  N6   C13  121.51  3.000
 8XE  N4   C7   C6   120.73  3.000
 8XE  N4   C7   C8   116.30  3.000
 8XE  C6   C7   C8   122.98  3.000
 8XE  N5   C8   C9   107.61  3.000
 8XE  N5   C8   C7   123.18  3.000
 8XE  C9   C8   C7   129.21  3.000
 8XE  H3   C9   C10  127.53  3.000
 8XE  H3   C9   C8   125.69  3.000
 8XE  C10  C9   C8   106.78  3.000
 8XE  C14  C10  C11  122.10  3.000
 8XE  C11  C10  C9   107.63  3.000
 8XE  C14  C10  C9   130.09  3.000
 8XE  N5   C11  C12  129.18  3.000
 8XE  C12  C11  C10  122.61  3.000
 8XE  N5   C11  C10  108.14  3.000
 8XE  H5   C12  H4   107.36  3.000
 8XE  H5   C12  C13  109.36  3.000
 8XE  H4   C12  C13  110.70  3.000
 8XE  H5   C12  C11  112.48  3.000
 8XE  H4   C12  C11  110.05  3.000
 8XE  C13  C12  C11  106.92  3.000
 8XE  H7   C13  H6   107.27  3.000
 8XE  H7   C13  C12  109.46  3.000
 8XE  H6   C13  C12  109.06  3.000
 8XE  H7   C13  N6   107.61  3.000
 8XE  H6   C13  N6   110.19  3.000
 8XE  C12  C13  N6   113.08  3.000
 8XE  O    C14  C10  121.91  3.000
 8XE  C10  C14  N6   114.43  3.000
 8XE  O    C14  N6   123.58  3.000
 8XE  H11  C16  H10  106.32  3.000
 8XE  H11  C16  O1   110.69  3.000
 8XE  H10  C16  O1   111.62  3.000
 8XE  H11  C16  C15  110.23  3.000
 8XE  H10  C16  C15  108.36  3.000
 8XE  O1   C16  C15  109.55  3.000
 8XE  C17  O1   C16  112.70  3.000
 8XE  H14  C17  H13  108.36  3.000
 8XE  H14  C17  H12  108.33  3.000
 8XE  H13  C17  H12  107.78  3.000
 8XE  H14  C17  O1   108.05  3.000
 8XE  H13  C17  O1   111.95  3.000
 8XE  H12  C17  O1   112.26  3.000
 8XE  H15  N5   C11  124.32  3.000
 8XE  H15  N5   C8   125.83  3.000
 8XE  C11  N5   C8   109.84  3.000
 8XE  H16  C6   C5   120.29  3.000
 8XE  H16  C6   C7   123.35  3.000
 8XE  C5   C6   C7   116.35  3.000
 8XE  H17  C5   N3   116.34  3.000
 8XE  H17  C5   C6   120.19  3.000
 8XE  N3   C5   C6   123.47  3.000
 8XE  C4   N3   C5   115.40  3.000
 8XE  C4   N4   C7   117.48  3.000
 8XE  N2   C4   N4   114.55  3.000
 8XE  N2   C4   N3   118.89  3.000
 8XE  N4   C4   N3   126.57  3.000
 8XE  H18  N2   C4   114.41  3.000
 8XE  H18  N2   C1   118.12  3.000
 8XE  C4   N2   C1   127.47  3.000
 8XE  N    N1   C3   105.08  3.000
 8XE  C    N    N1   120.69  3.000
 8XE  N1   N    C1   112.11  3.000
 8XE  C    N    C1   127.20  3.000
 8XE  H21  C    H20  108.61  3.000
 8XE  H21  C    H19  109.13  3.000
 8XE  H20  C    H19  108.63  3.000
 8XE  H21  C    N    111.13  3.000
 8XE  H20  C    N    107.90  3.000
 8XE  H19  C    N    111.37  3.000
 8XE  H9   C15  H8   107.26  3.000
 8XE  H9   C15  C16  108.03  3.000
 8XE  H8   C15  C16  110.34  3.000
 8XE  H9   C15  N6   108.82  3.000
 8XE  H8   C15  N6   108.88  3.000
 8XE  C16  C15  N6   113.33  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
 8XE  CONST_01  C3   N1   N    C1      0.00   0.0  0
 8XE  CONST_02  N1   C3   C2   C1      0.00   0.0  0
 8XE  CONST_03  N1   N    C1   C2      0.00   0.0  0
 8XE  CONST_04  N    N1   C3   C2      0.00   0.0  0
 8XE  CONST_05  N    C1   C2   C3      0.00   0.0  0
 8XE  CONST_06  N3   C5   C6   C7      0.00   0.0  0
 8XE  CONST_07  C10  C9   C8   C7    180.00   0.0  0
 8XE  CONST_08  C11  N5   C8   C7    180.00   0.0  0
 8XE  CONST_09  N3   C4   N4   C7      0.00   0.0  0
 8XE  CONST_10  C11  C10  C9   C8      0.00   0.0  0
 8XE  CONST_11  C5   C6   C7   C8    180.00   0.0  0
 8XE  CONST_12  C4   N4   C7   C8    180.00   0.0  0
 8XE  CONST_13  C10  C11  N5   C8      0.00   0.0  0
 8XE  CONST_14  N5   C11  C10  C9      0.00   0.0  0
 8XE  CONST_15  C6   C7   C8   C9    180.00   0.0  0
 8XE  CONST_16  N4   C7   C8   C9      0.00   0.0  0
 8XE  CONST_17  C11  N5   C8   C9      0.00   0.0  0
 8XE  CONST_18  N5   C8   C9   C10     0.00   0.0  0
 8XE  CONST_19  C6   C7   C8   N5      0.00   0.0  0
 8XE  CONST_20  N4   C7   C8   N5    180.00   0.0  0
 8XE  CONST_21  C4   N3   C5   C6      0.00   0.0  0
 8XE  CONST_22  C4   N4   C7   C6      0.00   0.0  0
 8XE  CONST_23  N4   C7   C6   C5      0.00   0.0  0
 8XE  CONST_24  N4   C4   N3   C5      0.00   0.0  0
 8XE  CONST_26  C    N    C1   C2    180.00   0.0  0
 8XE  CONST_27  N2   C1   C2   C3    180.00   0.0  0
 8XE  CONST_28  C    N    N1   C3    180.00   0.0  0
 8XE  CONST_29  N2   C4   N4   C7    180.00   0.0  0
 8XE  CONST_30  N2   C4   N3   C5    180.00   0.0  0
 8XE  CONST_31  N1   N    C1   N2    180.00   0.0  0
 8XE  CONST_32  C15  N6   C14  C10   180.00   0.0  0
 8XE  CONST_33  O    C14  N6   C13   180.00   0.0  0
 8XE  CONST_34  H2   C3   C2   C1    180.00   0.0  0
 8XE  CONST_35  H17  C5   C6   C7    180.00   0.0  0
 8XE  CONST_36  H3   C9   C8   C7      0.00   0.0  0
 8XE  CONST_37  H15  N5   C8   C7      0.00   0.0  0
 8XE  CONST_38  H16  C6   C7   C8      0.00   0.0  0
 8XE  CONST_39  H1   C2   C3   N1    180.00   0.0  0
 8XE  CONST_40  O    C14  N6   C15     0.00   0.0  0
 8XE  Var_01    C9   C10  C14  N6   -176.45  30.0  1
 8XE  Var_02    C11  C12  C13  N6     48.01  30.0  1
 8XE  Var_03    C13  C12  C11  C10   -27.15  30.0  1
 8XE  Var_04    C14  N6   C13  C12   -46.37  30.0  1
 8XE  Var_05    N3   C4   N2   C1     -0.67  30.0  2
 8XE  Var_06    C4   N2   C1   C2     -7.28  30.0  2
 8XE  Var_07    C16  C15  N6   C13    62.71  30.0  2
 8XE  Var_08    H19  C    N    C1     63.71  30.0  2
 8XE  Var_09    O1   C16  C15  N6     56.68  30.0  1
 8XE  Var_10    H12  C17  O1   C16   -63.31  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
 8XE  plan-1  C1   0.020
 8XE  plan-1  C2   0.020
 8XE  plan-1  C3   0.020
 8XE  plan-1  N2   0.020
 8XE  plan-1  N1   0.020
 8XE  plan-1  N    0.020
 8XE  plan-1  C    0.020
 8XE  plan-1  H1   0.020
 8XE  plan-1  H2   0.020
 8XE  plan-2  C7   0.020
 8XE  plan-2  C8   0.020
 8XE  plan-2  C6   0.020
 8XE  plan-2  C5   0.020
 8XE  plan-2  N3   0.020
 8XE  plan-2  N4   0.020
 8XE  plan-2  C4   0.020
 8XE  plan-2  N2   0.020
 8XE  plan-2  H16  0.020
 8XE  plan-2  H17  0.020
 8XE  plan-3  C7   0.020
 8XE  plan-3  C8   0.020
 8XE  plan-3  C9   0.020
 8XE  plan-3  C10  0.020
 8XE  plan-3  C11  0.020
 8XE  plan-3  C12  0.020
 8XE  plan-3  C14  0.020
 8XE  plan-3  N5   0.020
 8XE  plan-3  H3   0.020
 8XE  plan-3  H15  0.020
 8XE  plan-4  N6   0.020
 8XE  plan-4  C10  0.020
 8XE  plan-4  C13  0.020
 8XE  plan-4  C14  0.020
 8XE  plan-4  O    0.020
 8XE  plan-4  C15  0.020

