# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 13:11:32 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (6~{R})-5-(2-methoxyethyl)-6-methyl-2-[5-methyl-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: COCCN1[C@H](C)Cc2[nH]c(cc2C1=O)c3nc(Nc4ccnn4C)ncc3C
#
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
 8XB  8XB  (6~{R})-5-(2-methoxyethyl)-6-methyl-2-[5-methyl-2-[(2-methylpyrazol-3-yl)amino]pyrimidin-4-yl]-6,7-dihydro-1~{H}-pyrrolo[3,2-c]pyridin-4-one  ligand  54  29  .  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_8XB
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
 8XB  C1   C  C     0   0.512   3.1293  -1.3098   0.0683
 8XB  C2   C  CR5   0  -0.126   2.0858  -0.3044   0.2570
 8XB  C3   C  CR15  0  -0.372   0.6923  -0.3792   0.0760
 8XB  N6   N  NR5   0  -0.344  -6.1304  -1.7491  -0.6408
 8XB  C7   C  CH1   0  -0.128   4.5924   0.2585   1.3208
 8XB  C8   C  CH3   0  -0.642   4.3230  -0.0372   2.7923
 8XB  C9   C  CH2   0  -0.515   3.7832   1.4544   0.8151
 8XB  C10  C  CR5   0   0.367   2.3930   0.9954   0.5976
 8XB  C11  C  CR5   0   0.275   0.1832   0.8818   0.3198
 8XB  C12  C  CR6   0   0.233  -1.2116   1.2877   0.2725
 8XB  C13  C  CR6   0   0.006  -1.6940   2.5983   0.4585
 8XB  C14  C  CH3   0  -0.809  -0.8624   3.8160   0.7227
 8XB  C15  C  CR6   0   0.597  -3.3486   0.5448  -0.0394
 8XB  C16  C  CR16  0  -0.038  -3.0712   2.7249   0.3717
 8XB  C19  C  CR15  0  -0.066  -7.6800  -0.3209  -0.5693
 8XB  C20  C  CR15  0  -0.524  -6.4935   0.4000  -0.3645
 8XB  O1   O  O     0  -0.505   2.9090  -2.3904  -0.4711
 8XB  N1   N  NT    0  -0.477   4.3622  -0.9371   0.4971
 8XB  C4   C  CH2   0  -0.351   5.4849  -1.8327   0.2925
 8XB  C5   C  CH2   0  -0.132   6.1661  -1.6175  -1.0440
 8XB  O2   O  O2    0  -0.479   6.6826  -0.3131  -1.0984
 8XB  C6   C  CH3   0  -0.393   7.2702  -0.0138  -2.3379
 8XB  N2   N  NR15  0  -0.729   1.2534   1.6985   0.6320
 8XB  N3   N  N     0  -0.502  -2.0523   0.2845   0.0234
 8XB  N4   N  N     0  -0.456  -3.9144   1.7316   0.1298
 8XB  N5   N  NH1   0  -0.783  -4.1382  -0.5407  -0.3017
 8XB  C17  C  CR5   0   0.664  -5.5078  -0.5701  -0.4201
 8XB  N7   N  N     0  -0.297  -7.4603  -1.6075  -0.7362
 8XB  H1   H  HCR5  0   0.255   0.1128  -1.2469  -0.1933
 8XB  H2   H  HCH1  0   0.268   5.6453   0.5117   1.2065
 8XB  H3   H  HCH3  0   0.230   3.2754  -0.2835   2.9697
 8XB  H4   H  HCH3  0   0.240   4.9277  -0.8776   3.1342
 8XB  H5   H  HCH3  0   0.234   4.5790   0.8265   3.4069
 8XB  H6   H  HCH2  0   0.273   3.8448   2.2724   1.5348
 8XB  H7   H  HCH2  0   0.279   4.2054   1.8194  -0.1268
 8XB  H8   H  HCH3  0   0.256  -0.3413   3.7687   1.6816
 8XB  H9   H  HCH3  0   0.255  -0.1262   3.9971  -0.0632
 8XB  H10  H  HCH3  0   0.277  -1.4983   4.6996   0.7621
 8XB  H11  H  HCR6  0   0.266  -3.5189   3.7047   0.5080
 8XB  H12  H  HCR5  0   0.255  -8.6877   0.0656  -0.5992
 8XB  H13  H  HCR5  0   0.269  -6.3706   1.4538  -0.2036
 8XB  H14  H  HCH2  0   0.254   6.1994  -1.6825   1.1040
 8XB  H15  H  HCH2  0   0.259   5.1561  -2.8699   0.3520
 8XB  H16  H  HCH2  0   0.206   6.9644  -2.3647  -1.1608
 8XB  H17  H  HCH2  0   0.203   5.4454  -1.7884  -1.8559
 8XB  H18  H  HCH3  0   0.233   7.6488   1.0069  -2.2945
 8XB  H19  H  HCH3  0   0.203   8.1073  -0.6831  -2.5708
 8XB  H20  H  HCH3  0   0.204   6.5495  -0.0809  -3.1615
 8XB  H21  H  HNR5  0   0.432   1.2063   2.6782   0.8567
 8XB  H22  H  HNH1  0   0.421  -3.6278  -1.4009  -0.4339
 8XB  H23  H  HCH3  0   0.260  -4.8554  -3.0815  -1.6488
 8XB  H24  H  HCH3  0   0.260  -4.9533  -3.3179   0.1095
 8XB  H25  H  HCH3  0   0.281  -6.3091  -3.7752  -0.9250
 8XB  C18  C  CH3   0  -0.559  -5.5173  -3.0470  -0.7830

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
 8XB  C6   O2   single    1.404  0.020  1.404
 8XB  O2   C5   single    1.404  0.020  1.404
 8XB  O1   C1   double    1.228  0.020  1.228
 8XB  C5   C4   single    1.515  0.020  1.515
 8XB  C14  C13  single    1.498  0.020  1.498
 8XB  C1   C2   single    1.461  0.020  1.461
 8XB  C1   N1   single    1.357  0.020  1.357
 8XB  C3   C2   aromatic  1.407  0.020  1.407
 8XB  C3   C11  aromatic  1.382  0.020  1.382
 8XB  C4   N1   single    1.451  0.020  1.451
 8XB  C13  C16  aromatic  1.386  0.020  1.386
 8XB  C13  C12  aromatic  1.409  0.020  1.409
 8XB  C2   C10  aromatic  1.378  0.020  1.378
 8XB  C16  N4   aromatic  1.325  0.020  1.325
 8XB  N1   C7   single    1.470  0.020  1.470
 8XB  C11  C12  single    1.453  0.020  1.453
 8XB  C11  N2   aromatic  1.382  0.020  1.382
 8XB  C12  N3   aromatic  1.332  0.020  1.332
 8XB  C10  N2   aromatic  1.339  0.020  1.339
 8XB  C10  C9   single    1.480  0.020  1.480
 8XB  N4   C15  aromatic  1.326  0.020  1.326
 8XB  N3   C15  aromatic  1.324  0.020  1.324
 8XB  C15  N5   single    1.368  0.020  1.368
 8XB  C9   C7   single    1.530  0.020  1.530
 8XB  C7   C8   single    1.525  0.020  1.525
 8XB  N5   C17  single    1.375  0.020  1.375
 8XB  C18  N6   single    1.442  0.020  1.442
 8XB  C17  N6   aromatic  1.351  0.020  1.351
 8XB  C17  C20  aromatic  1.384  0.020  1.384
 8XB  N6   N7   aromatic  1.341  0.020  1.341
 8XB  C20  C19  aromatic  1.403  0.020  1.403
 8XB  N7   C19  aromatic  1.316  0.020  1.316
 8XB  C3   H1   single    0.930  0.020  1.080
 8XB  C7   H2   single    0.970  0.020  1.090
 8XB  C8   H3   single    0.970  0.020  1.090
 8XB  C8   H4   single    0.970  0.020  1.090
 8XB  C8   H5   single    0.970  0.020  1.090
 8XB  C9   H6   single    0.970  0.020  1.090
 8XB  C9   H7   single    0.970  0.020  1.090
 8XB  C14  H8   single    0.970  0.020  1.090
 8XB  C14  H9   single    0.970  0.020  1.090
 8XB  C14  H10  single    0.970  0.020  1.090
 8XB  C16  H11  single    0.930  0.020  1.080
 8XB  C19  H12  single    0.930  0.020  1.080
 8XB  C20  H13  single    0.930  0.020  1.080
 8XB  C4   H14  single    0.970  0.020  1.090
 8XB  C4   H15  single    0.970  0.020  1.090
 8XB  C5   H16  single    0.970  0.020  1.090
 8XB  C5   H17  single    0.970  0.020  1.090
 8XB  C6   H18  single    0.970  0.020  1.090
 8XB  C6   H19  single    0.970  0.020  1.090
 8XB  C6   H20  single    0.970  0.020  1.090
 8XB  N2   H21  single    0.860  0.020  1.020
 8XB  N5   H22  single    0.860  0.020  1.020
 8XB  C18  H23  single    0.970  0.020  1.090
 8XB  C18  H24  single    0.970  0.020  1.090
 8XB  C18  H25  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
 8XB  N1   C1   O1   122.92  3.000
 8XB  N1   C1   C2   114.76  3.000
 8XB  O1   C1   C2   122.29  3.000
 8XB  C10  C2   C3   107.62  3.000
 8XB  C10  C2   C1   121.44  3.000
 8XB  C3   C2   C1   130.84  3.000
 8XB  H1   C3   C11  125.51  3.000
 8XB  H1   C3   C2   127.41  3.000
 8XB  C11  C3   C2   107.08  3.000
 8XB  N7   N6   C18  120.63  3.000
 8XB  N7   N6   C17  112.11  3.000
 8XB  C18  N6   C17  127.25  3.000
 8XB  H2   C7   N1   106.36  3.000
 8XB  H2   C7   C9   107.16  3.000
 8XB  N1   C7   C9   111.58  3.000
 8XB  H2   C7   C8   108.49  3.000
 8XB  C9   C7   C8   112.15  3.000
 8XB  N1   C7   C8   110.81  3.000
 8XB  H5   C8   H4   107.67  3.000
 8XB  H5   C8   H3   108.22  3.000
 8XB  H4   C8   H3   107.92  3.000
 8XB  H5   C8   C7   110.41  3.000
 8XB  H4   C8   C7   110.73  3.000
 8XB  H3   C8   C7   111.74  3.000
 8XB  H7   C9   H6   107.20  3.000
 8XB  H7   C9   C10  109.83  3.000
 8XB  H6   C9   C10  112.48  3.000
 8XB  H7   C9   C7   109.94  3.000
 8XB  H6   C9   C7   109.76  3.000
 8XB  C10  C9   C7   107.63  3.000
 8XB  N2   C10  C9   129.24  3.000
 8XB  C9   C10  C2   122.55  3.000
 8XB  N2   C10  C2   108.16  3.000
 8XB  N2   C11  C12  125.84  3.000
 8XB  N2   C11  C3   107.09  3.000
 8XB  C12  C11  C3   127.07  3.000
 8XB  N3   C12  C13  120.60  3.000
 8XB  N3   C12  C11  113.67  3.000
 8XB  C13  C12  C11  125.74  3.000
 8XB  C16  C13  C14  119.24  3.000
 8XB  C16  C13  C12  114.65  3.000
 8XB  C14  C13  C12  126.11  3.000
 8XB  H10  C14  H9   106.57  3.000
 8XB  H10  C14  H8   106.37  3.000
 8XB  H9   C14  H8   108.51  3.000
 8XB  H10  C14  C13  109.97  3.000
 8XB  H9   C14  C13  112.47  3.000
 8XB  H8   C14  C13  112.60  3.000
 8XB  N5   C15  N4   119.25  3.000
 8XB  N5   C15  N3   114.74  3.000
 8XB  N4   C15  N3   126.01  3.000
 8XB  H11  C16  N4   115.91  3.000
 8XB  H11  C16  C13  118.97  3.000
 8XB  N4   C16  C13  125.12  3.000
 8XB  H12  C19  N7   120.15  3.000
 8XB  H12  C19  C20  127.53  3.000
 8XB  N7   C19  C20  112.31  3.000
 8XB  H13  C20  C17  127.79  3.000
 8XB  H13  C20  C19  128.55  3.000
 8XB  C17  C20  C19  103.66  3.000
 8XB  C4   N1   C7   117.38  3.000
 8XB  C7   N1   C1   122.86  3.000
 8XB  C4   N1   C1   119.26  3.000
 8XB  H15  C4   H14  106.73  3.000
 8XB  H15  C4   C5   108.60  3.000
 8XB  H14  C4   C5   109.99  3.000
 8XB  H15  C4   N1   110.26  3.000
 8XB  H14  C4   N1   108.47  3.000
 8XB  C5   C4   N1   112.62  3.000
 8XB  H17  C5   H16  106.97  3.000
 8XB  H17  C5   O2   110.92  3.000
 8XB  H16  C5   O2   111.11  3.000
 8XB  H17  C5   C4   109.55  3.000
 8XB  H16  C5   C4   108.87  3.000
 8XB  O2   C5   C4   109.36  3.000
 8XB  C6   O2   C5   112.72  3.000
 8XB  H20  C6   H19  107.75  3.000
 8XB  H20  C6   H18  108.40  3.000
 8XB  H19  C6   H18  108.36  3.000
 8XB  H20  C6   O2   112.02  3.000
 8XB  H19  C6   O2   112.14  3.000
 8XB  H18  C6   O2   108.06  3.000
 8XB  H21  N2   C11  126.13  3.000
 8XB  H21  N2   C10  123.82  3.000
 8XB  C11  N2   C10  110.05  3.000
 8XB  C15  N3   C12  118.61  3.000
 8XB  C16  N4   C15  115.01  3.000
 8XB  H22  N5   C17  118.32  3.000
 8XB  H22  N5   C15  114.19  3.000
 8XB  C17  N5   C15  127.48  3.000
 8XB  N5   C17  C20  133.70  3.000
 8XB  C20  C17  N6   106.86  3.000
 8XB  N5   C17  N6   119.44  3.000
 8XB  C19  N7   N6   105.06  3.000
 8XB  H25  C18  H24  108.54  3.000
 8XB  H25  C18  H23  108.53  3.000
 8XB  H24  C18  H23  109.16  3.000
 8XB  H25  C18  N6   107.86  3.000
 8XB  H24  C18  N6   111.28  3.000
 8XB  H23  C18  N6   111.39  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
 8XB  CONST_01  C12  C11  C3   C2    180.00   0.0  0
 8XB  CONST_02  N2   C11  C3   C2      0.00   0.0  0
 8XB  CONST_03  C11  N2   C10  C2      0.00   0.0  0
 8XB  CONST_04  N2   C10  C2   C3      0.00   0.0  0
 8XB  CONST_05  C13  C12  C11  C3    180.00   0.0  0
 8XB  CONST_06  N3   C12  C11  C3      0.00   0.0  0
 8XB  CONST_07  C10  N2   C11  C3      0.00   0.0  0
 8XB  CONST_08  C19  C20  C17  N6      0.00   0.0  0
 8XB  CONST_09  C20  C19  N7   N6      0.00   0.0  0
 8XB  CONST_10  C11  C3   C2   C10     0.00   0.0  0
 8XB  CONST_11  C12  C11  N2   C10   180.00   0.0  0
 8XB  CONST_12  C16  C13  C12  C11   180.00   0.0  0
 8XB  CONST_13  C15  N3   C12  C11   180.00   0.0  0
 8XB  CONST_14  N4   C16  C13  C12     0.00   0.0  0
 8XB  CONST_15  N4   C15  N3   C12     0.00   0.0  0
 8XB  CONST_16  C15  N4   C16  C13     0.00   0.0  0
 8XB  CONST_17  N2   C11  C12  C13     0.00   0.0  0
 8XB  CONST_18  C15  N3   C12  C13     0.00   0.0  0
 8XB  CONST_19  N3   C12  C13  C16     0.00   0.0  0
 8XB  CONST_20  N3   C15  N4   C16     0.00   0.0  0
 8XB  CONST_21  C17  N6   N7   C19     0.00   0.0  0
 8XB  CONST_22  N7   N6   C17  C20     0.00   0.0  0
 8XB  CONST_23  N3   C12  C11  N2    180.00   0.0  0
 8XB  CONST_24  N7   C19  C20  C17     0.00   0.0  0
 8XB  CONST_25  C7   N1   C1   C2      0.00   0.0  0
 8XB  CONST_26  C14  C13  C12  C11     0.00   0.0  0
 8XB  CONST_27  N5   C15  N3   C12   180.00   0.0  0
 8XB  CONST_28  N4   C16  C13  C14   180.00   0.0  0
 8XB  CONST_29  N3   C12  C13  C14   180.00   0.0  0
 8XB  CONST_30  N5   C15  N4   C16   180.00   0.0  0
 8XB  CONST_31  N5   C17  C20  C19   180.00   0.0  0
 8XB  CONST_32  C18  N6   N7   C19   180.00   0.0  0
 8XB  CONST_33  C18  N6   C17  C20   180.00   0.0  0
 8XB  CONST_34  N7   N6   C17  N5    180.00   0.0  0
 8XB  CONST_35  C4   N1   C1   C2    180.00   0.0  0
 8XB  CONST_36  O1   C1   N1   C7    180.00   0.0  0
 8XB  CONST_37  H1   C3   C2   C1      0.00   0.0  0
 8XB  CONST_38  H21  N2   C10  C2    180.00   0.0  0
 8XB  CONST_39  H13  C20  C17  N6    180.00   0.0  0
 8XB  CONST_40  H12  C19  N7   N6    180.00   0.0  0
 8XB  CONST_41  H11  C16  C13  C12   180.00   0.0  0
 8XB  CONST_42  C4   N1   C1   O1      0.00   0.0  0
 8XB  Var_01    C7   C9   C10  C2    -29.29  30.0  1
 8XB  Var_02    N1   C1   C2   C3   -172.24  30.0  1
 8XB  Var_03    C15  N5   C17  N6   -177.86  30.0  2
 8XB  Var_04    C17  N5   C15  N3    179.86  30.0  2
 8XB  Var_05    C5   C4   N1   C1     88.62  30.0  2
 8XB  Var_06    H8   C14  C13  C12   -65.08  30.0  2
 8XB  Var_07    H23  C18  N6   C17   -62.42  30.0  2
 8XB  Var_08    O2   C5   C4   N1     61.85  30.0  2
 8XB  Var_09    H18  C6   O2   C5   -179.65  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
 8XB  chir_01  C7  N1  C9  C8  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
 8XB  plan-1  N6   0.020
 8XB  plan-1  C19  0.020
 8XB  plan-1  C20  0.020
 8XB  plan-1  N5   0.020
 8XB  plan-1  C17  0.020
 8XB  plan-1  N7   0.020
 8XB  plan-1  H12  0.020
 8XB  plan-1  H13  0.020
 8XB  plan-1  C18  0.020
 8XB  plan-2  C11  0.020
 8XB  plan-2  C12  0.020
 8XB  plan-2  C13  0.020
 8XB  plan-2  C14  0.020
 8XB  plan-2  C15  0.020
 8XB  plan-2  C16  0.020
 8XB  plan-2  N3   0.020
 8XB  plan-2  N4   0.020
 8XB  plan-2  N5   0.020
 8XB  plan-2  H11  0.020
 8XB  plan-3  C1   0.020
 8XB  plan-3  C2   0.020
 8XB  plan-3  C3   0.020
 8XB  plan-3  C9   0.020
 8XB  plan-3  C10  0.020
 8XB  plan-3  C11  0.020
 8XB  plan-3  C12  0.020
 8XB  plan-3  N2   0.020
 8XB  plan-3  H1   0.020
 8XB  plan-3  H21  0.020
 8XB  plan-4  C1   0.020
 8XB  plan-4  C2   0.020
 8XB  plan-4  C7   0.020
 8XB  plan-4  O1   0.020
 8XB  plan-4  N1   0.020
 8XB  plan-4  C4   0.020

