# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 20:59:05 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (6~{S})-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
 8XN  8XN  (6~{S})-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_8XN
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
 8XN  C1   C  CR6   0   0.002  -1.7161  -2.5569  -0.7321
 8XN  C2   C  CR16  0  -0.038  -3.0992  -2.6091  -0.7971
 8XN  C3   C  CR6   0   0.596  -3.3107  -0.4723  -0.1722
 8XN  N6   N  NR5   0  -0.343  -6.0447   1.8259   0.5954
 8XN  C7   C  CR5   0  -0.136   2.1662   0.0156   0.2603
 8XN  C8   C  CR5   0   0.369   2.4356  -1.1900  -0.3503
 8XN  C9   C  CH2   0  -0.511   3.8142  -1.6505  -0.6310
 8XN  C10  C  CH1   0  -0.137   4.7284  -1.0326   0.4300
 8XN  C11  C  C     0   0.514   3.2331   0.9342   0.6531
 8XN  C13  C  CH2   0  -0.129   6.3887   1.6534  -0.3645
 8XN  C14  C  CH3   0  -0.393   6.1661   2.8127  -2.3766
 8XN  C15  C  CH3   0  -0.640   4.6189  -1.7497   1.7720
 8XN  C16  C  CR5   0   0.662  -5.4451   0.7113   0.1220
 8XN  O    O  O     0  -0.500   3.0022   2.0900   0.9914
 8XN  C6   C  CR15  0  -0.372   0.7670   0.1549   0.3290
 8XN  N3   N  NT    0  -0.478   4.4838   0.4073   0.5852
 8XN  O1   O  O2    0  -0.475   5.5577   2.4487  -1.1652
 8XN  N2   N  NR15  0  -0.726   1.2689  -1.7834  -0.6369
 8XN  C5   C  CR5   0   0.276   0.2188  -0.9828  -0.2295
 8XN  C4   C  CR6   0   0.232  -1.1927  -1.3020  -0.3641
 8XN  C    C  CH3   0  -0.803  -0.9197  -3.7920  -1.0222
 8XN  N1   N  N     0  -0.499  -2.0035  -0.2822  -0.0852
 8XN  N    N  N     0  -0.455  -3.9124  -1.5971  -0.5325
 8XN  N4   N  NH1   0  -0.782  -4.0731   0.6179   0.1460
 8XN  N5   N  N     0  -0.297  -7.3795   1.7670   0.4845
 8XN  C18  C  CR15  0  -0.067  -7.6259   0.5941  -0.0591
 8XN  C17  C  CR15  0  -0.523  -6.4520  -0.1302  -0.3173
 8XN  H1   H  HCR6  0   0.266  -3.5791  -3.5411  -1.0807
 8XN  H2   H  HCH2  0   0.274   3.9037  -2.7375  -0.6060
 8XN  H3   H  HCH2  0   0.279   4.1209  -1.3248  -1.6300
 8XN  H4   H  HCH1  0   0.268   5.7545  -1.1359   0.0738
 8XN  H5   H  HCH2  0   0.254   6.3258   0.6712   1.5232
 8XN  H6   H  HCH2  0   0.261   5.3234   2.1060   1.4472
 8XN  H7   H  HCH2  0   0.208   7.2941   2.1992  -0.0612
 8XN  H8   H  HCH2  0   0.197   6.7312   0.7666  -0.9191
 8XN  H9   H  HCH3  0   0.202   6.4570   1.9367  -2.9697
 8XN  H10  H  HCH3  0   0.232   5.4490   3.3957  -2.9534
 8XN  H11  H  HCH3  0   0.203   7.0643   3.4233  -2.2230
 8XN  H12  H  HCH3  0   0.235   4.9102  -2.7953   1.6690
 8XN  H13  H  HCH3  0   0.241   5.2786  -1.2918   2.5097
 8XN  H14  H  HCH3  0   0.231   3.6013  -1.7167   2.1632
 8XN  H15  H  HCH3  0   0.260  -4.7660   2.7233   1.9955
 8XN  H16  H  HCH3  0   0.261  -4.8086   3.5170   0.4072
 8XN  H17  H  HCH3  0   0.281  -6.1816   3.6595   1.5116
 8XN  H18  H  HCR5  0   0.255   0.2110   0.9753   0.7521
 8XN  H19  H  HNR5  0   0.431   1.1897  -2.6609  -1.1242
 8XN  H20  H  HCH3  0   0.255  -0.3560  -3.7187  -1.9552
 8XN  H21  H  HCH3  0   0.257  -0.2249  -4.0371  -0.2174
 8XN  H22  H  HCH3  0   0.274  -1.5856  -4.6469  -1.1338
 8XN  H23  H  HNH1  0   0.421  -3.5431   1.4336   0.4139
 8XN  H24  H  HCR5  0   0.255  -8.6432   0.2892  -0.2543
 8XN  H25  H  HCR5  0   0.269  -6.3493  -1.1066  -0.7508
 8XN  C12  C  CH2   0  -0.355   5.6388   1.2302   0.8826
 8XN  C19  C  CH3   0  -0.559  -5.4048   2.9915   1.1539

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
 8XN  C14  O1   single    1.404  0.020  1.404
 8XN  O1   C13  single    1.402  0.020  1.402
 8XN  O    C11  double    1.226  0.020  1.226
 8XN  C    C1   single    1.498  0.020  1.498
 8XN  C13  C12  single    1.515  0.020  1.515
 8XN  C6   C7   aromatic  1.408  0.020  1.408
 8XN  C6   C5   aromatic  1.381  0.020  1.381
 8XN  C11  C7   single    1.462  0.020  1.462
 8XN  C11  N3   single    1.359  0.020  1.359
 8XN  C1   C2   aromatic  1.386  0.020  1.386
 8XN  C1   C4   aromatic  1.409  0.020  1.409
 8XN  C2   N    aromatic  1.325  0.020  1.325
 8XN  C12  N3   single    1.449  0.020  1.449
 8XN  C7   C8   aromatic  1.378  0.020  1.378
 8XN  N3   C10  single    1.469  0.020  1.469
 8XN  C15  C10  single    1.526  0.020  1.526
 8XN  C5   C4   single    1.453  0.020  1.453
 8XN  C5   N2   aromatic  1.382  0.020  1.382
 8XN  C4   N1   aromatic  1.332  0.020  1.332
 8XN  N    C3   aromatic  1.326  0.020  1.326
 8XN  C10  C9   single    1.531  0.020  1.531
 8XN  N1   C3   aromatic  1.324  0.020  1.324
 8XN  C8   N2   aromatic  1.340  0.020  1.340
 8XN  C8   C9   single    1.480  0.020  1.480
 8XN  C3   N4   single    1.368  0.020  1.368
 8XN  N4   C16  single    1.375  0.020  1.375
 8XN  C19  N6   single    1.442  0.020  1.442
 8XN  C16  N6   aromatic  1.351  0.020  1.351
 8XN  C16  C17  aromatic  1.384  0.020  1.384
 8XN  N6   N5   aromatic  1.341  0.020  1.341
 8XN  C17  C18  aromatic  1.403  0.020  1.403
 8XN  N5   C18  aromatic  1.316  0.020  1.316
 8XN  C2   H1   single    0.930  0.020  1.080
 8XN  C9   H2   single    0.970  0.020  1.090
 8XN  C9   H3   single    0.970  0.020  1.090
 8XN  C10  H4   single    0.970  0.020  1.090
 8XN  C12  H5   single    0.970  0.020  1.090
 8XN  C12  H6   single    0.970  0.020  1.090
 8XN  C13  H7   single    0.970  0.020  1.090
 8XN  C13  H8   single    0.970  0.020  1.090
 8XN  C14  H9   single    0.970  0.020  1.090
 8XN  C14  H10  single    0.970  0.020  1.090
 8XN  C14  H11  single    0.970  0.020  1.090
 8XN  C15  H12  single    0.970  0.020  1.090
 8XN  C15  H13  single    0.970  0.020  1.090
 8XN  C15  H14  single    0.970  0.020  1.090
 8XN  C19  H15  single    0.970  0.020  1.090
 8XN  C19  H16  single    0.970  0.020  1.090
 8XN  C19  H17  single    0.970  0.020  1.090
 8XN  C6   H18  single    0.930  0.020  1.080
 8XN  N2   H19  single    0.860  0.020  1.020
 8XN  C    H20  single    0.970  0.020  1.090
 8XN  C    H21  single    0.970  0.020  1.090
 8XN  C    H22  single    0.970  0.020  1.090
 8XN  N4   H23  single    0.860  0.020  1.020
 8XN  C18  H24  single    0.930  0.020  1.080
 8XN  C17  H25  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
 8XN  C    C1   C4   125.98  3.000
 8XN  C4   C1   C2   114.63  3.000
 8XN  C    C1   C2   119.37  3.000
 8XN  H1   C2   N    115.88  3.000
 8XN  H1   C2   C1   119.06  3.000
 8XN  N    C2   C1   125.06  3.000
 8XN  N4   C3   N    119.11  3.000
 8XN  N4   C3   N1   114.88  3.000
 8XN  N    C3   N1   126.01  3.000
 8XN  N5   N6   C19  120.62  3.000
 8XN  N5   N6   C16  112.12  3.000
 8XN  C19  N6   C16  127.26  3.000
 8XN  C6   C7   C11  130.55  3.000
 8XN  C11  C7   C8   121.75  3.000
 8XN  C6   C7   C8   107.61  3.000
 8XN  N2   C8   C9   129.24  3.000
 8XN  C9   C8   C7   122.56  3.000
 8XN  N2   C8   C7   108.18  3.000
 8XN  H3   C9   H2   107.12  3.000
 8XN  H3   C9   C10  110.19  3.000
 8XN  H2   C9   C10  109.71  3.000
 8XN  H3   C9   C8   109.97  3.000
 8XN  H2   C9   C8   112.45  3.000
 8XN  C10  C9   C8   107.41  3.000
 8XN  H4   C10  N3   106.50  3.000
 8XN  H4   C10  C15  108.07  3.000
 8XN  N3   C10  C15  110.85  3.000
 8XN  H4   C10  C9   107.29  3.000
 8XN  C15  C10  C9   112.15  3.000
 8XN  N3   C10  C9   111.68  3.000
 8XN  N3   C11  O    123.54  3.000
 8XN  N3   C11  C7   114.50  3.000
 8XN  O    C11  C7   121.95  3.000
 8XN  H8   C13  H7   106.42  3.000
 8XN  H8   C13  O1   110.73  3.000
 8XN  H7   C13  O1   111.35  3.000
 8XN  H8   C13  C12  110.10  3.000
 8XN  H7   C13  C12  108.60  3.000
 8XN  O1   C13  C12  109.59  3.000
 8XN  H11  C14  H10  108.37  3.000
 8XN  H11  C14  H9   107.64  3.000
 8XN  H10  C14  H9   108.40  3.000
 8XN  H11  C14  O1   112.23  3.000
 8XN  H10  C14  O1   108.08  3.000
 8XN  H9   C14  O1   111.99  3.000
 8XN  H14  C15  H13  108.01  3.000
 8XN  H14  C15  H12  108.19  3.000
 8XN  H13  C15  H12  107.76  3.000
 8XN  H14  C15  C10  111.61  3.000
 8XN  H13  C15  C10  110.75  3.000
 8XN  H12  C15  C10  110.39  3.000
 8XN  C17  C16  N4   133.64  3.000
 8XN  C17  C16  N6   106.85  3.000
 8XN  N4   C16  N6   119.51  3.000
 8XN  H18  C6   C5   125.54  3.000
 8XN  H18  C6   C7   127.39  3.000
 8XN  C5   C6   C7   107.05  3.000
 8XN  C12  N3   C11  120.21  3.000
 8XN  C12  N3   C10  116.46  3.000
 8XN  C11  N3   C10  122.60  3.000
 8XN  C14  O1   C13  112.54  3.000
 8XN  H19  N2   C5   126.01  3.000
 8XN  H19  N2   C8   123.91  3.000
 8XN  C5   N2   C8   110.00  3.000
 8XN  C4   C5   N2   125.69  3.000
 8XN  N2   C5   C6   107.15  3.000
 8XN  C4   C5   C6   127.15  3.000
 8XN  N1   C4   C5   113.80  3.000
 8XN  N1   C4   C1   120.69  3.000
 8XN  C5   C4   C1   125.51  3.000
 8XN  H22  C    H21  106.77  3.000
 8XN  H22  C    H20  106.30  3.000
 8XN  H21  C    H20  108.44  3.000
 8XN  H22  C    C1   109.99  3.000
 8XN  H21  C    C1   112.39  3.000
 8XN  H20  C    C1   112.61  3.000
 8XN  C4   N1   C3   118.51  3.000
 8XN  C3   N    C2   115.08  3.000
 8XN  H23  N4   C16  118.27  3.000
 8XN  H23  N4   C3   114.42  3.000
 8XN  C16  N4   C3   127.31  3.000
 8XN  C18  N5   N6   105.06  3.000
 8XN  H24  C18  C17  127.52  3.000
 8XN  H24  C18  N5   120.18  3.000
 8XN  C17  C18  N5   112.29  3.000
 8XN  H25  C17  C18  128.61  3.000
 8XN  H25  C17  C16  127.72  3.000
 8XN  C18  C17  C16  103.68  3.000
 8XN  H6   C12  H5   106.84  3.000
 8XN  H6   C12  N3   109.41  3.000
 8XN  H5   C12  N3   109.32  3.000
 8XN  H6   C12  C13  110.21  3.000
 8XN  H5   C12  C13  108.30  3.000
 8XN  N3   C12  C13  112.59  3.000
 8XN  H17  C19  H16  108.69  3.000
 8XN  H17  C19  H15  108.45  3.000
 8XN  H16  C19  H15  109.08  3.000
 8XN  H17  C19  N6   107.91  3.000
 8XN  H16  C19  N6   111.52  3.000
 8XN  H15  C19  N6   111.11  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
 8XN  CONST_01  C3   N    C2   C1     0.00   0.0  0
 8XN  CONST_02  C6   C5   C4   C1   180.00   0.0  0
 8XN  CONST_03  N2   C5   C4   C1     0.00   0.0  0
 8XN  CONST_04  C3   N1   C4   C1     0.00   0.0  0
 8XN  CONST_05  C5   C4   C1   C2   180.00   0.0  0
 8XN  CONST_06  N1   C4   C1   C2     0.00   0.0  0
 8XN  CONST_07  N1   C3   N    C2     0.00   0.0  0
 8XN  CONST_08  C5   C4   N1   C3   180.00   0.0  0
 8XN  CONST_09  C18  C17  C16  N6     0.00   0.0  0
 8XN  CONST_10  C17  C18  N5   N6     0.00   0.0  0
 8XN  CONST_11  C4   C5   C6   C7   180.00   0.0  0
 8XN  CONST_12  N2   C5   C6   C7     0.00   0.0  0
 8XN  CONST_13  C5   N2   C8   C7     0.00   0.0  0
 8XN  CONST_14  C5   C6   C7   C8     0.00   0.0  0
 8XN  CONST_15  C6   C5   N2   C8     0.00   0.0  0
 8XN  CONST_16  C4   C5   N2   C8   180.00   0.0  0
 8XN  CONST_17  C18  N5   N6   C16    0.00   0.0  0
 8XN  CONST_18  N5   C18  C17  C16    0.00   0.0  0
 8XN  CONST_19  N2   C8   C7   C6     0.00   0.0  0
 8XN  CONST_20  N1   C4   C5   C6     0.00   0.0  0
 8XN  CONST_21  N1   C4   C5   N2   180.00   0.0  0
 8XN  CONST_22  N    C2   C1   C4     0.00   0.0  0
 8XN  CONST_23  N    C3   N1   C4     0.00   0.0  0
 8XN  CONST_24  C17  C16  N6   N5     0.00   0.0  0
 8XN  CONST_25  C10  N3   C11  C7     0.00   0.0  0
 8XN  CONST_26  N4   C3   N    C2   180.00   0.0  0
 8XN  CONST_27  C17  C16  N6   C19  180.00   0.0  0
 8XN  CONST_28  C18  N5   N6   C19  180.00   0.0  0
 8XN  CONST_29  C    C1   C4   C5     0.00   0.0  0
 8XN  CONST_30  N4   C3   N1   C4   180.00   0.0  0
 8XN  CONST_31  N    C2   C1   C    180.00   0.0  0
 8XN  CONST_32  N1   C4   C1   C    180.00   0.0  0
 8XN  CONST_33  N5   N6   C16  N4   180.00   0.0  0
 8XN  CONST_34  C18  C17  C16  N4   180.00   0.0  0
 8XN  CONST_35  C12  N3   C11  C7   180.00   0.0  0
 8XN  CONST_36  O    C11  N3   C10  180.00   0.0  0
 8XN  CONST_37  H1   C2   N    C3   180.00   0.0  0
 8XN  CONST_38  H25  C17  C16  N6   180.00   0.0  0
 8XN  CONST_39  H24  C18  N5   N6   180.00   0.0  0
 8XN  CONST_40  H19  N2   C8   C7   180.00   0.0  0
 8XN  CONST_41  H18  C6   C7   C8   180.00   0.0  0
 8XN  CONST_42  O    C11  N3   C12    0.00   0.0  0
 8XN  Var_01    C10  C9   C8   C7    28.83  30.0  1
 8XN  Var_02    N3   C11  C7   C8   -11.00  30.0  1
 8XN  Var_03    N6   C16  N4   C3   173.45  30.0  2
 8XN  Var_04    N    C3   N4   C16   -1.06  30.0  1
 8XN  Var_05    C13  C12  N3   C10   85.36  30.0  3
 8XN  Var_06    H20  C    C1   C2   111.05  30.0  2
 8XN  Var_07    H15  C19  N6   C16  -56.43  30.0  2
 8XN  Var_08    O1   C13  C12  N3    62.89  30.0  1
 8XN  Var_09    H9   C14  O1   C13   58.70  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
 8XN  chir_01  C10  N3  C15  C9  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
 8XN  plan-1  N6   0.020
 8XN  plan-1  C16  0.020
 8XN  plan-1  N4   0.020
 8XN  plan-1  N5   0.020
 8XN  plan-1  C18  0.020
 8XN  plan-1  C17  0.020
 8XN  plan-1  H24  0.020
 8XN  plan-1  H25  0.020
 8XN  plan-1  C19  0.020
 8XN  plan-2  C1   0.020
 8XN  plan-2  C2   0.020
 8XN  plan-2  C3   0.020
 8XN  plan-2  C5   0.020
 8XN  plan-2  C4   0.020
 8XN  plan-2  C    0.020
 8XN  plan-2  N1   0.020
 8XN  plan-2  N    0.020
 8XN  plan-2  N4   0.020
 8XN  plan-2  H1   0.020
 8XN  plan-3  C7   0.020
 8XN  plan-3  C8   0.020
 8XN  plan-3  C9   0.020
 8XN  plan-3  C11  0.020
 8XN  plan-3  C6   0.020
 8XN  plan-3  N2   0.020
 8XN  plan-3  C5   0.020
 8XN  plan-3  C4   0.020
 8XN  plan-3  H18  0.020
 8XN  plan-3  H19  0.020
 8XN  plan-4  C7   0.020
 8XN  plan-4  C10  0.020
 8XN  plan-4  C11  0.020
 8XN  plan-4  O    0.020
 8XN  plan-4  N3   0.020
 8XN  plan-4  C12  0.020

