# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 10:56:29 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 5-(2-methoxyethyl)-2-[2-(oxan-4-ylamino)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(NC4CCOCC4)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
 8XH  8XH  5-(2-methoxyethyl)-2-[2-(oxan-4-ylamino)pyrimidin-4-yl]-6,7-dihydro-1~{H}-pyrrolo[3,2-c]pyridin-4-one  ligand  52  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8XH
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
 8XH  C1   C  CH2   0  -0.147   6.6478  -1.5751  -0.4369
 8XH  C2   C  CH2   0  -0.356   5.9462  -1.4022   0.8950
 8XH  C3   C  CH2   0  -0.274   4.9189   0.8465   1.2147
 8XH  C7   C  CR15  0  -0.371   1.0827  -0.3448   0.2672
 8XH  C8   C  CR5   0   0.310   0.5097   0.8984   0.1139
 8XH  C9   C  CR6   0   0.259  -0.8860   1.2525  -0.0569
 8XH  C10  C  CR16  0  -0.369  -1.3229   2.5781  -0.1446
 8XH  C11  C  CR16  0   0.005  -2.6824   2.7588  -0.3073
 8XH  C12  C  CR6   0   0.602  -3.0360   0.5319  -0.2896
 8XH  C13  C  CH1   0  -0.063  -5.3168  -0.4182  -0.4093
 8XH  C14  C  CH2   0  -0.444  -5.9168  -0.1939   0.9789
 8XH  C15  C  CH2   0  -0.171  -7.4358  -0.2229   0.9092
 8XH  C16  C  CH2   0  -0.169  -7.4343  -1.6138  -0.9701
 8XH  C18  C  C     0   0.505   3.5672  -1.0988   0.5291
 8XH  N    N  NT    0  -0.488   4.7773  -0.5485   0.8037
 8XH  O    O  O2    0  -0.478   7.0831  -0.3224  -0.8976
 8XH  C    C  CH3   0  -0.370   7.6511  -0.3824  -2.1798
 8XH  C6   C  CR5   0  -0.131   2.4703  -0.1383   0.4194
 8XH  N1   N  NR15  0  -0.713   1.5234   1.8323   0.1575
 8XH  C5   C  CR5   0   0.368   2.7015   1.2193   0.3403
 8XH  C4   C  CH2   0  -0.509   4.0619   1.8018   0.3955
 8XH  N3   N  N     0  -0.501  -1.7422   0.2403  -0.1283
 8XH  N2   N  N     0  -0.467  -3.5525   1.7636  -0.3797
 8XH  N4   N  NH1   0  -0.663  -3.8752  -0.5179  -0.3877
 8XH  C17  C  CH2   0  -0.453  -5.9152  -1.6794  -1.0211
 8XH  O1   O  O2    0  -0.483  -7.9155  -1.4227   0.3418
 8XH  H1   H  HCH2  0   0.210   7.4923  -2.2674  -0.3064
 8XH  H2   H  HCH2  0   0.218   5.9621  -2.0409  -1.1584
 8XH  H3   H  HCH2  0   0.272   5.6662  -2.3854   1.2723
 8XH  H4   H  HCH2  0   0.254   6.6327  -0.9679   1.6238
 8XH  H5   H  HCH2  0   0.234   4.6568   0.9484   2.2734
 8XH  H6   H  HCH2  0   0.257   5.9650   1.1237   1.1128
 8XH  H7   H  HCR5  0   0.248   0.5522  -1.2831   0.2774
 8XH  H8   H  HCR6  0   0.214  -0.6609   3.4291  -0.0834
 8XH  H9   H  HCR6  0   0.247  -3.0910   3.7613  -0.3798
 8XH  H10  H  HCH1  0   0.239  -5.5836   0.4314  -1.0439
 8XH  H12  H  HCH2  0   0.242  -5.5917   0.7670   1.3848
 8XH  H13  H  HCH2  0   0.233  -7.8677  -0.1463   1.9085
 8XH  H14  H  HCH2  0   0.189  -7.7935   0.6422   0.3308
 8XH  H15  H  HCH2  0   0.190  -7.7850  -0.8037  -1.6273
 8XH  H16  H  HCH2  0   0.233  -7.8691  -2.5440  -1.3387
 8XH  H17  H  HCH3  0   0.193   8.5373  -1.0282  -2.2104
 8XH  H18  H  HCH3  0   0.197   6.9396  -0.7565  -2.9262
 8XH  H19  H  HCH3  0   0.218   7.9504   0.6258  -2.4644
 8XH  H20  H  HNR5  0   0.385   1.4099   2.8295   0.0634
 8XH  H21  H  HCH2  0   0.250   4.0731   2.7873   0.8626
 8XH  H22  H  HCH2  0   0.262   4.4681   1.9157  -0.6146
 8XH  H23  H  HNH1  0   0.362  -3.4694  -1.4218  -0.2010
 8XH  H24  H  HCH2  0   0.245  -5.5956  -1.7917  -2.0599
 8XH  H25  H  HCH2  0   0.215  -5.5658  -2.5626  -0.4752
 8XH  O2   O  O     0  -0.452   3.4055  -2.3027   0.3521
 8XH  H11  H  HCH2  0   0.215  -5.5603  -0.9744   1.6583

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
 8XH  C    O    single    1.404  0.020  1.404
 8XH  O    C1   single    1.404  0.020  1.404
 8XH  C1   C2   single    1.515  0.020  1.515
 8XH  O2   C18  double    1.228  0.020  1.228
 8XH  C7   C6   aromatic  1.411  0.020  1.411
 8XH  C7   C8   aromatic  1.377  0.020  1.377
 8XH  C18  C6   single    1.462  0.020  1.462
 8XH  C18  N    single    1.357  0.020  1.357
 8XH  C10  C11  aromatic  1.381  0.020  1.381
 8XH  C10  C9   aromatic  1.398  0.020  1.398
 8XH  C2   N    single    1.450  0.020  1.450
 8XH  C11  N2   aromatic  1.324  0.020  1.324
 8XH  C6   C5   aromatic  1.379  0.020  1.379
 8XH  N    C3   single    1.461  0.020  1.461
 8XH  C8   C9   single    1.450  0.020  1.450
 8XH  C8   N1   aromatic  1.379  0.020  1.379
 8XH  C9   N3   aromatic  1.328  0.020  1.328
 8XH  N2   C12  aromatic  1.339  0.020  1.339
 8XH  C3   C4   single    1.523  0.020  1.523
 8XH  C5   N1   aromatic  1.341  0.020  1.341
 8XH  C5   C4   single    1.481  0.020  1.481
 8XH  N3   C12  aromatic  1.336  0.020  1.336
 8XH  C12  N4   single    1.348  0.020  1.348
 8XH  N4   C13  single    1.445  0.020  1.445
 8XH  C13  C17  single    1.524  0.020  1.524
 8XH  C13  C14  single    1.529  0.020  1.529
 8XH  C17  C16  single    1.521  0.020  1.521
 8XH  C16  O1   single    1.410  0.020  1.410
 8XH  C14  C15  single    1.521  0.020  1.521
 8XH  C15  O1   single    1.411  0.020  1.411
 8XH  C1   H1   single    0.970  0.020  1.090
 8XH  C1   H2   single    0.970  0.020  1.090
 8XH  C2   H3   single    0.970  0.020  1.090
 8XH  C2   H4   single    0.970  0.020  1.090
 8XH  C3   H5   single    0.970  0.020  1.090
 8XH  C3   H6   single    0.970  0.020  1.090
 8XH  C7   H7   single    0.930  0.020  1.080
 8XH  C10  H8   single    0.930  0.020  1.080
 8XH  C11  H9   single    0.930  0.020  1.080
 8XH  C13  H10  single    0.970  0.020  1.090
 8XH  C14  H11  single    0.970  0.020  1.090
 8XH  C14  H12  single    0.970  0.020  1.090
 8XH  C15  H13  single    0.970  0.020  1.090
 8XH  C15  H14  single    0.970  0.020  1.090
 8XH  C16  H15  single    0.970  0.020  1.090
 8XH  C16  H16  single    0.970  0.020  1.090
 8XH  C    H17  single    0.970  0.020  1.090
 8XH  C    H18  single    0.970  0.020  1.090
 8XH  C    H19  single    0.970  0.020  1.090
 8XH  N1   H20  single    0.860  0.020  1.020
 8XH  C4   H21  single    0.970  0.020  1.090
 8XH  C4   H22  single    0.970  0.020  1.090
 8XH  N4   H23  single    0.860  0.020  1.020
 8XH  C17  H24  single    0.970  0.020  1.090
 8XH  C17  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
 8XH  H2   C1   H1   106.87  3.000
 8XH  H2   C1   O    110.87  3.000
 8XH  H1   C1   O    111.26  3.000
 8XH  H2   C1   C2   109.67  3.000
 8XH  H1   C1   C2   108.85  3.000
 8XH  O    C1   C2   109.28  3.000
 8XH  H4   C2   H3   106.83  3.000
 8XH  H4   C2   N    108.35  3.000
 8XH  H3   C2   N    110.23  3.000
 8XH  H4   C2   C1   109.94  3.000
 8XH  H3   C2   C1   108.68  3.000
 8XH  N    C2   C1   112.64  3.000
 8XH  H6   C3   H5   107.29  3.000
 8XH  H6   C3   C4   109.34  3.000
 8XH  H5   C3   C4   109.08  3.000
 8XH  H6   C3   N    108.09  3.000
 8XH  H5   C3   N    109.73  3.000
 8XH  C4   C3   N    113.15  3.000
 8XH  H7   C7   C6   127.61  3.000
 8XH  H7   C7   C8   125.59  3.000
 8XH  C6   C7   C8   106.80  3.000
 8XH  N1   C8   C9   123.09  3.000
 8XH  N1   C8   C7   107.58  3.000
 8XH  C9   C8   C7   129.34  3.000
 8XH  N3   C9   C10  121.19  3.000
 8XH  N3   C9   C8   116.16  3.000
 8XH  C10  C9   C8   122.65  3.000
 8XH  H8   C10  C11  120.47  3.000
 8XH  H8   C10  C9   123.50  3.000
 8XH  C11  C10  C9   116.03  3.000
 8XH  H9   C11  N2   116.32  3.000
 8XH  H9   C11  C10  119.96  3.000
 8XH  N2   C11  C10  123.72  3.000
 8XH  N4   C12  N2   118.14  3.000
 8XH  N4   C12  N3   116.22  3.000
 8XH  N2   C12  N3   125.63  3.000
 8XH  H10  C13  C17  108.32  3.000
 8XH  H10  C13  N4   107.79  3.000
 8XH  C17  C13  N4   109.91  3.000
 8XH  H10  C13  C14  108.50  3.000
 8XH  C17  C13  C14  109.38  3.000
 8XH  N4   C13  C14  112.83  3.000
 8XH  H12  C14  H11  107.44  3.000
 8XH  H12  C14  C15  109.32  3.000
 8XH  H11  C14  C15  109.89  3.000
 8XH  H12  C14  C13  110.46  3.000
 8XH  H11  C14  C13  109.34  3.000
 8XH  C15  C14  C13  110.34  3.000
 8XH  H14  C15  H13  107.31  3.000
 8XH  H14  C15  O1   110.27  3.000
 8XH  H13  C15  O1   107.06  3.000
 8XH  H14  C15  C14  109.50  3.000
 8XH  H13  C15  C14  110.61  3.000
 8XH  O1   C15  C14  111.97  3.000
 8XH  H16  C16  H15  107.39  3.000
 8XH  H16  C16  O1   107.09  3.000
 8XH  H15  C16  O1   110.31  3.000
 8XH  H16  C16  C17  110.48  3.000
 8XH  H15  C16  C17  109.26  3.000
 8XH  O1   C16  C17  112.19  3.000
 8XH  C6   C18  N    114.68  3.000
 8XH  N    C18  O2   122.97  3.000
 8XH  C6   C18  O2   122.32  3.000
 8XH  C18  N    C3   122.03  3.000
 8XH  C3   N    C2   117.78  3.000
 8XH  C18  N    C2   119.51  3.000
 8XH  C    O    C1   112.77  3.000
 8XH  H19  C    H18  108.42  3.000
 8XH  H19  C    H17  108.39  3.000
 8XH  H18  C    H17  107.70  3.000
 8XH  H19  C    O    108.08  3.000
 8XH  H18  C    O    111.94  3.000
 8XH  H17  C    O    112.18  3.000
 8XH  C5   C6   C18  121.68  3.000
 8XH  C5   C6   C7   107.62  3.000
 8XH  C18  C6   C7   130.52  3.000
 8XH  H20  N1   C5   124.33  3.000
 8XH  H20  N1   C8   125.75  3.000
 8XH  C5   N1   C8   109.91  3.000
 8XH  C4   C5   N1   129.24  3.000
 8XH  C4   C5   C6   122.61  3.000
 8XH  N1   C5   C6   108.09  3.000
 8XH  H22  C4   H21  107.30  3.000
 8XH  H22  C4   C5   110.33  3.000
 8XH  H21  C4   C5   112.38  3.000
 8XH  H22  C4   C3   110.66  3.000
 8XH  H21  C4   C3   109.32  3.000
 8XH  C5   C4   C3   106.88  3.000
 8XH  C12  N3   C9   117.68  3.000
 8XH  C12  N2   C11  115.75  3.000
 8XH  H23  N4   C13  117.78  3.000
 8XH  H23  N4   C12  115.74  3.000
 8XH  C13  N4   C12  124.65  3.000
 8XH  H25  C17  H24  107.32  3.000
 8XH  H25  C17  C16  109.67  3.000
 8XH  H24  C17  C16  109.17  3.000
 8XH  H25  C17  C13  109.99  3.000
 8XH  H24  C17  C13  110.60  3.000
 8XH  C16  C17  C13  110.05  3.000
 8XH  C16  O1   C15  111.92  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
 8XH  CONST_01  N1   C5   C6   C7      0.00   0.0  0
 8XH  CONST_02  C10  C9   C8   C7    180.00   0.0  0
 8XH  CONST_03  N3   C9   C8   C7      0.00   0.0  0
 8XH  CONST_04  C5   N1   C8   C7      0.00   0.0  0
 8XH  CONST_05  C5   C6   C7   C8      0.00   0.0  0
 8XH  CONST_06  C11  C10  C9   C8    180.00   0.0  0
 8XH  CONST_07  C12  N3   C9   C8    180.00   0.0  0
 8XH  CONST_08  C6   C5   N1   C8      0.00   0.0  0
 8XH  CONST_09  N2   C11  C10  C9      0.00   0.0  0
 8XH  CONST_10  C6   C7   C8   C9    180.00   0.0  0
 8XH  CONST_11  C5   N1   C8   C9    180.00   0.0  0
 8XH  CONST_12  N2   C12  N3   C9      0.00   0.0  0
 8XH  CONST_13  C12  N2   C11  C10     0.00   0.0  0
 8XH  CONST_14  N1   C8   C9   C10     0.00   0.0  0
 8XH  CONST_15  C12  N3   C9   C10     0.00   0.0  0
 8XH  CONST_16  N3   C9   C10  C11     0.00   0.0  0
 8XH  CONST_17  N3   C12  N2   C11     0.00   0.0  0
 8XH  CONST_18  N1   C8   C7   C6      0.00   0.0  0
 8XH  CONST_19  N3   C9   C8   N1    180.00   0.0  0
 8XH  CONST_20  C6   C18  N    C3      0.00   0.0  0
 8XH  CONST_21  N4   C12  N3   C9    180.00   0.0  0
 8XH  CONST_22  N4   C12  N2   C11   180.00   0.0  0
 8XH  CONST_23  N2   C12  N4   C13     0.00   0.0  0
 8XH  CONST_24  N3   C12  N4   C13   180.00   0.0  0
 8XH  CONST_25  C6   C18  N    C2    180.00   0.0  0
 8XH  CONST_26  O2   C18  N    C3    180.00   0.0  0
 8XH  CONST_27  H20  N1   C8   C7    180.00   0.0  0
 8XH  CONST_28  H8   C10  C9   C8      0.00   0.0  0
 8XH  CONST_29  H9   C11  C10  C9    180.00   0.0  0
 8XH  CONST_30  H7   C7   C8   C9      0.00   0.0  0
 8XH  CONST_31  O2   C18  N    C2      0.00   0.0  0
 8XH  CONST_32  H23  N4   C12  N3      0.00   0.0  0
 8XH  Var_01    C6   C5   C4   C3    -28.17  30.0  1
 8XH  Var_02    N    C18  C6   C7   -173.60  30.0  1
 8XH  Var_03    O1   C16  C17  C13   -56.42  30.0  1
 8XH  Var_04    O1   C15  C14  C13    55.99  30.0  1
 8XH  Var_05    C17  C16  O1   C15    59.94  30.0  1
 8XH  Var_06    C4   C3   N    C18   -43.58  30.0  1
 8XH  Var_07    C5   C4   C3   N      47.96  30.0  1
 8XH  Var_08    C18  N    C2   C1     89.94  30.0  3
 8XH  Var_09    O    C1   C2   N      60.94  30.0  2
 8XH  Var_10    H17  C    O    C1    -61.16  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
 8XH  chir_01  C13  N4  C17  C14  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
 8XH  plan-1  C8   0.020
 8XH  plan-1  C9   0.020
 8XH  plan-1  C10  0.020
 8XH  plan-1  C11  0.020
 8XH  plan-1  C12  0.020
 8XH  plan-1  N3   0.020
 8XH  plan-1  N2   0.020
 8XH  plan-1  N4   0.020
 8XH  plan-1  H8   0.020
 8XH  plan-1  H9   0.020
 8XH  plan-2  C7   0.020
 8XH  plan-2  C8   0.020
 8XH  plan-2  C9   0.020
 8XH  plan-2  C18  0.020
 8XH  plan-2  C6   0.020
 8XH  plan-2  N1   0.020
 8XH  plan-2  C5   0.020
 8XH  plan-2  C4   0.020
 8XH  plan-2  H7   0.020
 8XH  plan-2  H20  0.020
 8XH  plan-3  C12  0.020
 8XH  plan-3  C13  0.020
 8XH  plan-3  N4   0.020
 8XH  plan-3  H23  0.020
 8XH  plan-4  C2   0.020
 8XH  plan-4  C3   0.020
 8XH  plan-4  C18  0.020
 8XH  plan-4  N    0.020
 8XH  plan-4  C6   0.020
 8XH  plan-4  O2   0.020

