# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 08:00:34 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 1-(3H-imidazo[4,5-c]pyridin-2-yl)-3,4-dihydropyrido[2,1-a]isoindol-6(2H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N2CCCC(=C2c3ccccc13)c4[nH]c5cnccc5n4
#
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
 YJX  YJX  1-(3H-imidazo[4,5-c]pyridin-2-yl)-3,4-dihydropyrido[2,1-a]isoindol-6(2H)-one  ligand  37  23  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YJX
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
 YJX  C15   C  CR16  0  -0.233  -1.1295  -3.4465   0.1450
 YJX  C19   C  CR16  0  -0.257  -2.4982  -3.6923   0.0786
 YJX  C8    C  CR16  0  -0.368  -0.6153  -2.1544   0.1603
 YJX  C14   C  CR16  0  -0.292  -3.3908  -2.6309   0.0203
 YJX  C20   C  CR16  0  -0.398   4.0238  -1.0102   0.8658
 YJX  C22   C  CR16  0  -0.099   5.2862  -0.6682   0.4200
 YJX  C21   C  CR16  0  -0.110   4.5775   1.1742  -0.7626
 YJX  C3    C  CR56  0  -0.009  -1.5021  -1.0868   0.0952
 YJX  C7    C  CR56  0  -0.041  -2.8701  -1.3518   0.0287
 YJX  C17   C  CR56  0   0.251   2.9769  -0.1884   0.4526
 YJX  C18   C  CR56  0   0.251   3.2736   0.9101  -0.3677
 YJX  C5    C  CR5   0   0.423   1.1188   0.7804   0.0521
 YJX  C1    C  CR5   0   0.547  -1.3387   0.3800   0.0542
 YJX  C9    C  CR5   0   0.541  -3.5963  -0.0773  -0.0506
 YJX  C2    C  C     0  -0.136  -0.2710   1.2080   0.0151
 YJX  C6    C  CH2   0  -0.503  -0.4836   2.7017  -0.0910
 YJX  C13   C  CH2   0  -0.477  -1.8346   3.1216   0.4617
 YJX  C10   C  CH2   0  -0.284  -2.9401   2.3039  -0.1685
 YJX  N23   N  N     0  -0.414   5.5609   0.3843  -0.3658
 YJX  N11   N  N     0  -0.495   1.6363  -0.2373   0.7028
 YJX  N12   N  NR15  0  -0.707   2.0696   1.5094  -0.5973
 YJX  N4    N  NR5   0  -0.636  -2.6379   0.8948  -0.0158
 YJX  O16   O  O     0  -0.449  -4.7942   0.1106  -0.1400
 YJX  H15   H  HCR6  0   0.268  -0.4421  -4.2809   0.1933
 YJX  H19   H  HCR6  0   0.269  -2.8633  -4.7107   0.0726
 YJX  H8    H  HCR6  0   0.287   0.4474  -1.9945   0.2417
 YJX  H14   H  HCR6  0   0.266  -4.4594  -2.7953  -0.0299
 YJX  H22   H  HCR6  0   0.261   6.1364  -1.2758   0.7078
 YJX  H21   H  HCR6  0   0.273   4.8241   2.0195  -1.3958
 YJX  H12   H  HNR5  0   0.431   1.9105   2.3207  -1.1750
 YJX  H61C  H  HCH2  0   0.272   0.3054   3.2228   0.4542
 YJX  H62C  H  HCH2  0   0.265  -0.3966   3.0178  -1.1370
 YJX  H131  H  HCH2  0   0.251  -1.8496   2.9885   1.5458
 YJX  H132  H  HCH2  0   0.264  -2.0089   4.1781   0.2610
 YJX  H101  H  HCH2  0   0.269  -3.8978   2.5077   0.3079
 YJX  H102  H  HCH2  0   0.256  -3.0391   2.5446  -1.2307
 YJX  H20   H  HCR6  0   0.269   3.8676  -1.8724   1.4996

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
 YJX  C15  C19   aromatic  1.392  0.020  1.392
 YJX  C15  C8    aromatic  1.391  0.020  1.391
 YJX  C19  C14   aromatic  1.388  0.020  1.388
 YJX  C8   C3    aromatic  1.389  0.020  1.389
 YJX  C14  C7    aromatic  1.381  0.020  1.381
 YJX  C20  C22   aromatic  1.382  0.020  1.382
 YJX  C20  C17   aromatic  1.394  0.020  1.394
 YJX  C22  N23   aromatic  1.342  0.020  1.342
 YJX  C21  C18   aromatic  1.388  0.020  1.388
 YJX  C21  N23   aromatic  1.322  0.020  1.322
 YJX  C3   C7    aromatic  1.395  0.020  1.395
 YJX  C3   C1    single    1.476  0.020  1.476
 YJX  C7   C9    single    1.469  0.020  1.469
 YJX  C17  C18   aromatic  1.403  0.020  1.403
 YJX  C17  N11   aromatic  1.365  0.020  1.365
 YJX  C18  N12   aromatic  1.364  0.020  1.364
 YJX  C5   C2    single    1.455  0.020  1.455
 YJX  C5   N11   aromatic  1.314  0.020  1.314
 YJX  C5   N12   aromatic  1.363  0.020  1.363
 YJX  C1   C2    double    1.352  0.020  1.352
 YJX  C1   N4    single    1.399  0.020  1.399
 YJX  C9   N4    single    1.366  0.020  1.366
 YJX  C9   O16   double    1.216  0.020  1.216
 YJX  C2   C6    single    1.512  0.020  1.512
 YJX  C6   C13   single    1.519  0.020  1.519
 YJX  C13  C10   single    1.513  0.020  1.513
 YJX  C10  N4    single    1.449  0.020  1.449
 YJX  C15  H15   single    0.930  0.020  1.080
 YJX  C19  H19   single    0.930  0.020  1.080
 YJX  C8   H8    single    0.930  0.020  1.080
 YJX  C14  H14   single    0.930  0.020  1.080
 YJX  C20  H20   single    0.930  0.020  1.080
 YJX  C22  H22   single    0.930  0.020  1.080
 YJX  C21  H21   single    0.930  0.020  1.080
 YJX  N12  H12   single    0.860  0.020  1.020
 YJX  C6   H61C  single    0.970  0.020  1.090
 YJX  C6   H62C  single    0.970  0.020  1.090
 YJX  C13  H131  single    0.970  0.020  1.090
 YJX  C13  H132  single    0.970  0.020  1.090
 YJX  C10  H101  single    0.970  0.020  1.090
 YJX  C10  H102  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
 YJX  H15   C15  C8    118.75  3.000
 YJX  H15   C15  C19   119.37  3.000
 YJX  C8    C15  C19   121.88  3.000
 YJX  H19   C19  C14   120.17  3.000
 YJX  H19   C19  C15   119.88  3.000
 YJX  C14   C19  C15   119.94  3.000
 YJX  H8    C8   C3    121.25  3.000
 YJX  H8    C8   C15   120.22  3.000
 YJX  C3    C8   C15   118.52  3.000
 YJX  H14   C14  C7    120.87  3.000
 YJX  H14   C14  C19   121.38  3.000
 YJX  C7    C14  C19   117.75  3.000
 YJX  H20   C20  C17   122.37  3.000
 YJX  H20   C20  C22   121.22  3.000
 YJX  C17   C20  C22   116.41  3.000
 YJX  H22   C22  N23   115.76  3.000
 YJX  H22   C22  C20   119.49  3.000
 YJX  N23   C22  C20   124.76  3.000
 YJX  H21   C21  N23   118.14  3.000
 YJX  H21   C21  C18   121.88  3.000
 YJX  N23   C21  C18   119.98  3.000
 YJX  C1    C3   C7    107.21  3.000
 YJX  C1    C3   C8    133.95  3.000
 YJX  C7    C3   C8    118.83  3.000
 YJX  C9    C7   C3    108.82  3.000
 YJX  C9    C7   C14   128.09  3.000
 YJX  C3    C7   C14   123.09  3.000
 YJX  N11   C17  C18   110.07  3.000
 YJX  N11   C17  C20   131.49  3.000
 YJX  C18   C17  C20   118.44  3.000
 YJX  N12   C18  C17   104.82  3.000
 YJX  N12   C18  C21   134.24  3.000
 YJX  C17   C18  C21   120.95  3.000
 YJX  N12   C5   N11   112.06  3.000
 YJX  N12   C5   C2    119.82  3.000
 YJX  N11   C5   C2    128.06  3.000
 YJX  N4    C1   C2    120.43  3.000
 YJX  N4    C1   C3    105.32  3.000
 YJX  C2    C1   C3    134.17  3.000
 YJX  O16   C9   N4    125.68  3.000
 YJX  O16   C9   C7    128.69  3.000
 YJX  N4    C9   C7    105.62  3.000
 YJX  C6    C2   C1    119.74  3.000
 YJX  C6    C2   C5    115.24  3.000
 YJX  C1    C2   C5    125.02  3.000
 YJX  H62C  C6   H61C  106.36  3.000
 YJX  H62C  C6   C13   109.76  3.000
 YJX  H61C  C6   C13   109.22  3.000
 YJX  H62C  C6   C2    109.91  3.000
 YJX  H61C  C6   C2    109.56  3.000
 YJX  C13   C6   C2    111.87  3.000
 YJX  H132  C13  H131  107.39  3.000
 YJX  H132  C13  C10   109.30  3.000
 YJX  H131  C13  C10   109.73  3.000
 YJX  H132  C13  C6    110.08  3.000
 YJX  H131  C13  C6    109.86  3.000
 YJX  C10   C13  C6    110.43  3.000
 YJX  H102  C10  H101  107.71  3.000
 YJX  H102  C10  N4    109.59  3.000
 YJX  H101  C10  N4    108.62  3.000
 YJX  H102  C10  C13   110.61  3.000
 YJX  H101  C10  C13   111.06  3.000
 YJX  N4    C10  C13   109.23  3.000
 YJX  C21   N23  C22   119.47  3.000
 YJX  C5    N11  C17   105.56  3.000
 YJX  H12   N12  C5    126.38  3.000
 YJX  H12   N12  C18   126.08  3.000
 YJX  C5    N12  C18   107.49  3.000
 YJX  C10   N4   C9    122.90  3.000
 YJX  C10   N4   C1    123.82  3.000
 YJX  C9    N4   C1    113.01  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
 YJX  CONST_01  C7   C14  C19  C15     0.00   0.0  0
 YJX  CONST_02  C7   C3   C8   C15     0.00   0.0  0
 YJX  CONST_03  C3   C8   C15  C19     0.00   0.0  0
 YJX  CONST_04  C3   C7   C14  C19     0.00   0.0  0
 YJX  CONST_05  C14  C19  C15  C8      0.00   0.0  0
 YJX  CONST_06  C14  C7   C3   C8      0.00   0.0  0
 YJX  CONST_07  C21  N23  C22  C20     0.00   0.0  0
 YJX  CONST_08  C21  C18  C17  C20     0.00   0.0  0
 YJX  CONST_09  N12  C18  C17  C20   180.00   0.0  0
 YJX  CONST_10  C5   N11  C17  C20   180.00   0.0  0
 YJX  CONST_11  C18  C17  C20  C22     0.00   0.0  0
 YJX  CONST_12  N11  C17  C20  C22   180.00   0.0  0
 YJX  CONST_13  C18  C21  N23  C22     0.00   0.0  0
 YJX  CONST_14  N11  C17  C18  C21   180.00   0.0  0
 YJX  CONST_15  C5   N12  C18  C21   180.00   0.0  0
 YJX  CONST_16  N23  C22  C20  C17     0.00   0.0  0
 YJX  CONST_17  N23  C21  C18  C17     0.00   0.0  0
 YJX  CONST_18  C5   N12  C18  C17     0.00   0.0  0
 YJX  CONST_19  N12  C5   N11  C17     0.00   0.0  0
 YJX  CONST_20  C5   N11  C17  C18     0.00   0.0  0
 YJX  CONST_21  N11  C5   N12  C18     0.00   0.0  0
 YJX  CONST_22  N12  C18  C21  N23   180.00   0.0  0
 YJX  CONST_23  N12  C18  C17  N11     0.00   0.0  0
 YJX  CONST_24  C2   C5   N11  C17   180.00   0.0  0
 YJX  CONST_25  C2   C5   N12  C18   180.00   0.0  0
 YJX  CONST_26  C1   N4   C9   C7      0.00   0.0  0
 YJX  CONST_27  C10  N4   C9   C7    180.00   0.0  0
 YJX  CONST_28  O16  C9   N4   C1    180.00   0.0  0
 YJX  CONST_29  O16  C9   N4   C10     0.00   0.0  0
 YJX  CONST_30  H14  C14  C19  C15   180.00   0.0  0
 YJX  CONST_31  H8   C8   C15  C19   180.00   0.0  0
 YJX  CONST_32  H19  C19  C15  C8    180.00   0.0  0
 YJX  CONST_33  H15  C15  C19  C14   180.00   0.0  0
 YJX  CONST_34  H21  C21  N23  C22   180.00   0.0  0
 YJX  CONST_35  H12  N12  C18  C21     0.00   0.0  0
 YJX  CONST_36  H22  C22  N23  C21   180.00   0.0  0
 YJX  CONST_37  H20  C20  C17  C18   180.00   0.0  0
 YJX  Var_01    C5   C2   C1   C3     -2.33  30.0  1
 YJX  Var_02    C13  C6   C2   C5   -155.37  30.0  1
 YJX  Var_03    N11  C5   C2   C1    -34.49  30.0  3
 YJX  Var_04    C13  C10  N4   C1    -29.34  30.0  1
 YJX  Var_05    C10  C13  C6   C2    -52.29  30.0  1
 YJX  Var_06    N4   C10  C13  C6     53.14  30.0  1

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
 YJX  plan-1  C20  0.020
 YJX  plan-1  C22  0.020
 YJX  plan-1  C21  0.020
 YJX  plan-1  C17  0.020
 YJX  plan-1  C18  0.020
 YJX  plan-1  C5   0.020
 YJX  plan-1  C2   0.020
 YJX  plan-1  N23  0.020
 YJX  plan-1  N11  0.020
 YJX  plan-1  N12  0.020
 YJX  plan-1  H22  0.020
 YJX  plan-1  H21  0.020
 YJX  plan-1  H12  0.020
 YJX  plan-1  H20  0.020
 YJX  plan-2  C15  0.020
 YJX  plan-2  C19  0.020
 YJX  plan-2  C8   0.020
 YJX  plan-2  C14  0.020
 YJX  plan-2  C3   0.020
 YJX  plan-2  C7   0.020
 YJX  plan-2  C1   0.020
 YJX  plan-2  C9   0.020
 YJX  plan-2  C2   0.020
 YJX  plan-2  C10  0.020
 YJX  plan-2  N4   0.020
 YJX  plan-2  O16  0.020
 YJX  plan-2  H15  0.020
 YJX  plan-2  H19  0.020
 YJX  plan-2  H8   0.020
 YJX  plan-2  H14  0.020

