# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 06:33:20 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 5-[3-(2-methoxyphenyl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethylpyridine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1c2c[nH]c3ncc(cc23)c4cncc(c4)C(=O)N(C)C
#
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
 P3Y  P3Y  5-[3-(2-methoxyphenyl)-1H-pyrrolo[2,3-b]pyridin-5-yl]-N,N-dimethylpyridine-3-carboxamide  ligand  48  28  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P3Y
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
 P3Y  N1    N  N     0  -0.418  -0.2679  -2.9202  -1.3610
 P3Y  C2    C  CR16  0  -0.125   0.6887  -2.0105  -1.3102
 P3Y  C3    C  CR6   0  -0.021   0.5183  -0.7017  -0.8224
 P3Y  C4    C  CR16  0  -0.303  -0.7388  -0.3130  -0.3739
 P3Y  C5    C  CR56  0   0.029  -1.7729  -1.2383  -0.4323
 P3Y  C6    C  CR56  0   0.472  -1.4521  -2.5236  -0.9243
 P3Y  C9    C  CR5   0  -0.023  -3.1594  -1.2615  -0.0686
 P3Y  C10   C  CR15  0  -0.035  -3.5943  -2.5302  -0.3479
 P3Y  N11   N  NR15  0  -0.667  -2.5771  -3.2832  -0.8604
 P3Y  C14   C  CR6   0  -0.075  -3.9675  -0.1980   0.5360
 P3Y  C15   C  CR6   0   0.337  -3.9937   1.0986  -0.0086
 P3Y  C16   C  CR16  0  -0.381  -4.7711   2.0906   0.5825
 P3Y  C17   C  CR16  0  -0.252  -5.5432   1.7966   1.7005
 P3Y  C18   C  CR16  0  -0.272  -5.5434   0.5208   2.2385
 P3Y  C19   C  CR16  0  -0.302  -4.7517  -0.4604   1.6555
 P3Y  O1    O  O2    0  -0.464  -3.2536   1.2888  -1.1162
 P3Y  C24   C  CR6   0   0.009   1.6545   0.2331  -0.8024
 P3Y  C25   C  CR16  0  -0.095   1.4798   1.5839  -1.1048
 P3Y  N26   N  N     0  -0.394   2.4592   2.4757  -1.1053
 P3Y  C27   C  CR16  0  -0.070   3.6849   2.0615  -0.8204
 P3Y  C28   C  CR6   0  -0.139   3.9825   0.7424  -0.4961
 P3Y  C29   C  CR16  0  -0.204   2.9462  -0.1799  -0.4879
 P3Y  C33   C  C     0   0.512   5.4111   0.3532  -0.2834
 P3Y  O34   O  O     0  -0.488   6.2479   0.7094  -1.1045
 P3Y  N35   N  NT    0  -0.439   5.7084  -0.4004   0.7886
 P3Y  C41   C  CH3   0  -0.525   7.0525  -0.9220   0.9388
 P3Y  C45   C  CH3   0  -0.537   4.8418  -0.5919   1.9356
 P3Y  C1    C  CH3   0  -0.440  -3.1813   2.5833  -1.6768
 P3Y  H11A  H  HCH3  0   0.259  -2.5226   2.5085  -2.5387
 P3Y  H12   H  HCH3  0   0.230  -4.1582   2.9409  -2.0126
 P3Y  H13   H  HCH3  0   0.228  -2.7622   3.3100  -0.9758
 P3Y  H16   H  HCR6  0   0.277  -4.7966   3.0932   0.1781
 P3Y  H17   H  HCR6  0   0.259  -6.1463   2.5775   2.1450
 P3Y  H18   H  HCR6  0   0.252  -6.1404   0.2908   3.1108
 P3Y  H19   H  HCR6  0   0.249  -4.7266  -1.4544   2.0851
 P3Y  H10   H  HCR5  0   0.295  -4.5800  -2.9512  -0.2261
 P3Y  H11   H  HNR5  0   0.415  -2.6546  -4.2418  -1.1591
 P3Y  H2    H  HCR6  0   0.259   1.6583  -2.3171  -1.6880
 P3Y  H4    H  HCR6  0   0.256  -0.8956   0.6774   0.0338
 P3Y  H25   H  HCR6  0   0.259   0.4964   1.9529  -1.3783
 P3Y  H27   H  HCR6  0   0.272   4.4688   2.8100  -0.8381
 P3Y  H29   H  HCR6  0   0.279   3.1378  -1.2160  -0.2347
 P3Y  H411  H  HCH3  0   0.243   7.6861  -0.2398   1.5102
 P3Y  H412  H  HCH3  0   0.249   7.0038  -1.8699   1.4729
 P3Y  H413  H  HCH3  0   0.255   7.5119  -1.0961  -0.0298
 P3Y  H451  H  HCH3  0   0.248   4.4574  -1.6123   1.9809
 P3Y  H452  H  HCH3  0   0.261   5.4103  -0.4031   2.8469
 P3Y  H453  H  HCH3  0   0.265   4.0028   0.0971   1.9253

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
 P3Y  N1   C6    aromatic  1.323  0.020  1.323
 P3Y  N1   C2    aromatic  1.321  0.020  1.321
 P3Y  C2   C3    aromatic  1.407  0.020  1.407
 P3Y  C2   H2    single    0.930  0.020  1.080
 P3Y  C3   C4    aromatic  1.390  0.020  1.390
 P3Y  C3   C24   single    1.471  0.020  1.471
 P3Y  C4   C5    aromatic  1.389  0.020  1.389
 P3Y  C4   H4    single    0.930  0.020  1.080
 P3Y  C5   C9    aromatic  1.434  0.020  1.434
 P3Y  C5   C6    aromatic  1.413  0.020  1.413
 P3Y  C6   N11   aromatic  1.359  0.020  1.359
 P3Y  C9   C14   single    1.466  0.020  1.466
 P3Y  C9   C10   aromatic  1.370  0.020  1.370
 P3Y  C10  N11   aromatic  1.365  0.020  1.365
 P3Y  C10  H10   single    0.930  0.020  1.080
 P3Y  N11  H11   single    0.860  0.020  1.020
 P3Y  C14  C19   aromatic  1.392  0.020  1.392
 P3Y  C14  C15   aromatic  1.407  0.020  1.407
 P3Y  C15  O1    single    1.346  0.020  1.346
 P3Y  C15  C16   aromatic  1.392  0.020  1.392
 P3Y  C16  C17   aromatic  1.390  0.020  1.390
 P3Y  C16  H16   single    0.930  0.020  1.080
 P3Y  C17  C18   aromatic  1.385  0.020  1.385
 P3Y  C17  H17   single    0.930  0.020  1.080
 P3Y  C18  C19   aromatic  1.389  0.020  1.389
 P3Y  C18  H18   single    0.930  0.020  1.080
 P3Y  C19  H19   single    0.930  0.020  1.080
 P3Y  O1   C1    single    1.412  0.020  1.412
 P3Y  C24  C25   aromatic  1.395  0.020  1.395
 P3Y  C24  C29   aromatic  1.392  0.020  1.392
 P3Y  C25  N26   aromatic  1.325  0.020  1.325
 P3Y  C25  H25   single    0.930  0.020  1.080
 P3Y  N26  C27   aromatic  1.325  0.020  1.325
 P3Y  C27  C28   aromatic  1.391  0.020  1.391
 P3Y  C27  H27   single    0.930  0.020  1.080
 P3Y  C28  C29   aromatic  1.387  0.020  1.387
 P3Y  C28  C33   single    1.496  0.020  1.496
 P3Y  C29  H29   single    0.930  0.020  1.080
 P3Y  C33  O34   double    1.225  0.020  1.225
 P3Y  C33  N35   single    1.344  0.020  1.344
 P3Y  N35  C41   single    1.450  0.020  1.450
 P3Y  N35  C45   single    1.450  0.020  1.450
 P3Y  C41  H411  single    0.970  0.020  1.090
 P3Y  C41  H412  single    0.970  0.020  1.090
 P3Y  C41  H413  single    0.970  0.020  1.090
 P3Y  C45  H451  single    0.970  0.020  1.090
 P3Y  C45  H452  single    0.970  0.020  1.090
 P3Y  C45  H453  single    0.970  0.020  1.090
 P3Y  C1   H11A  single    0.970  0.020  1.090
 P3Y  C1   H12   single    0.970  0.020  1.090
 P3Y  C1   H13   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
 P3Y  C6    N1   C2    115.41  3.000
 P3Y  H2    C2   C3    119.46  3.000
 P3Y  H2    C2   N1    116.05  3.000
 P3Y  C3    C2   N1    124.48  3.000
 P3Y  C24   C3   C4    121.08  3.000
 P3Y  C24   C3   C2    120.14  3.000
 P3Y  C4    C3   C2    118.78  3.000
 P3Y  H4    C4   C5    121.17  3.000
 P3Y  H4    C4   C3    120.55  3.000
 P3Y  C5    C4   C3    118.25  3.000
 P3Y  C9    C5   C6    107.05  3.000
 P3Y  C6    C5   C4    116.85  3.000
 P3Y  C9    C5   C4    136.07  3.000
 P3Y  N11   C6   C5    107.70  3.000
 P3Y  N11   C6   N1    126.08  3.000
 P3Y  C5    C6   N1    126.21  3.000
 P3Y  C14   C9   C10   125.51  3.000
 P3Y  C10   C9   C5    105.68  3.000
 P3Y  C14   C9   C5    128.76  3.000
 P3Y  H10   C10  N11   120.52  3.000
 P3Y  H10   C10  C9    128.94  3.000
 P3Y  N11   C10  C9    110.53  3.000
 P3Y  H11   N11  C10   125.38  3.000
 P3Y  H11   N11  C6    125.58  3.000
 P3Y  C10   N11  C6    109.04  3.000
 P3Y  C19   C14  C15   118.34  3.000
 P3Y  C15   C14  C9    121.28  3.000
 P3Y  C19   C14  C9    120.36  3.000
 P3Y  O1    C15  C16   123.78  3.000
 P3Y  C16   C15  C14   120.19  3.000
 P3Y  O1    C15  C14   116.02  3.000
 P3Y  H16   C16  C17   118.93  3.000
 P3Y  H16   C16  C15   121.00  3.000
 P3Y  C17   C16  C15   120.07  3.000
 P3Y  H17   C17  C18   120.34  3.000
 P3Y  H17   C17  C16   119.16  3.000
 P3Y  C18   C17  C16   120.50  3.000
 P3Y  H18   C18  C19   120.19  3.000
 P3Y  H18   C18  C17   120.62  3.000
 P3Y  C19   C18  C17   119.19  3.000
 P3Y  H19   C19  C18   119.67  3.000
 P3Y  H19   C19  C14   118.62  3.000
 P3Y  C18   C19  C14   121.71  3.000
 P3Y  C1    O1   C15   118.97  3.000
 P3Y  C29   C24  C25   116.90  3.000
 P3Y  C29   C24  C3    122.08  3.000
 P3Y  C25   C24  C3    121.02  3.000
 P3Y  H25   C25  N26   116.16  3.000
 P3Y  H25   C25  C24   119.82  3.000
 P3Y  N26   C25  C24   124.01  3.000
 P3Y  C27   N26  C25   118.26  3.000
 P3Y  H27   C27  C28   120.26  3.000
 P3Y  H27   C27  N26   116.72  3.000
 P3Y  C28   C27  N26   123.01  3.000
 P3Y  C33   C28  C29   122.65  3.000
 P3Y  C33   C28  C27   118.98  3.000
 P3Y  C29   C28  C27   118.17  3.000
 P3Y  H29   C29  C28   120.33  3.000
 P3Y  H29   C29  C24   120.03  3.000
 P3Y  C28   C29  C24   119.64  3.000
 P3Y  N35   C33  O34   123.14  3.000
 P3Y  N35   C33  C28   118.08  3.000
 P3Y  O34   C33  C28   118.77  3.000
 P3Y  C45   N35  C41   115.13  3.000
 P3Y  C45   N35  C33   124.95  3.000
 P3Y  C41   N35  C33   119.31  3.000
 P3Y  H413  C41  H412  108.47  3.000
 P3Y  H413  C41  H411  108.74  3.000
 P3Y  H412  C41  H411  108.23  3.000
 P3Y  H413  C41  N35   110.95  3.000
 P3Y  H412  C41  N35   108.81  3.000
 P3Y  H411  C41  N35   111.55  3.000
 P3Y  H453  C45  H452  107.51  3.000
 P3Y  H453  C45  H451  108.75  3.000
 P3Y  H452  C45  H451  108.11  3.000
 P3Y  H453  C45  N35   111.75  3.000
 P3Y  H452  C45  N35   109.06  3.000
 P3Y  H451  C45  N35   111.51  3.000
 P3Y  H13   C1   H12   108.79  3.000
 P3Y  H13   C1   H11A  108.76  3.000
 P3Y  H12   C1   H11A  108.69  3.000
 P3Y  H13   C1   O1    111.98  3.000
 P3Y  H12   C1   O1    112.09  3.000
 P3Y  H11A  C1   O1    106.42  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
 P3Y  CONST_01  C4    C5   C6   N1     0.00   0.0  0
 P3Y  CONST_02  C9    C5   C6   N1   180.00   0.0  0
 P3Y  CONST_03  C10   N11  C6   N1   180.00   0.0  0
 P3Y  CONST_04  C4    C3   C2   N1     0.00   0.0  0
 P3Y  CONST_05  C24   C3   C2   N1   180.00   0.0  0
 P3Y  CONST_06  C5    C6   N1   C2     0.00   0.0  0
 P3Y  CONST_07  N11   C6   N1   C2   180.00   0.0  0
 P3Y  CONST_08  C5    C4   C3   C2     0.00   0.0  0
 P3Y  CONST_11  C6    N1   C2   C3     0.00   0.0  0
 P3Y  CONST_12  C9    C5   C4   C3   180.00   0.0  0
 P3Y  CONST_13  C6    C5   C4   C3     0.00   0.0  0
 P3Y  CONST_14  N26   C25  C24  C3   180.00   0.0  0
 P3Y  CONST_15  C28   C29  C24  C3   180.00   0.0  0
 P3Y  CONST_18  C14   C9   C5   C4     0.00   0.0  0
 P3Y  CONST_19  C10   C9   C5   C4   180.00   0.0  0
 P3Y  CONST_20  N11   C6   C5   C4   180.00   0.0  0
 P3Y  CONST_21  C24   C3   C4   C5   180.00   0.0  0
 P3Y  CONST_24  N11   C10  C9   C5     0.00   0.0  0
 P3Y  CONST_25  C10   N11  C6   C5     0.00   0.0  0
 P3Y  CONST_26  C14   C9   C5   C6   180.00   0.0  0
 P3Y  CONST_27  C10   C9   C5   C6     0.00   0.0  0
 P3Y  CONST_28  C9    C10  N11  C6     0.00   0.0  0
 P3Y  CONST_29  N11   C6   C5   C9     0.00   0.0  0
 P3Y  CONST_30  C18   C19  C14  C9   180.00   0.0  0
 P3Y  CONST_31  C16   C15  C14  C9   180.00   0.0  0
 P3Y  CONST_34  C14   C9   C10  N11  180.00   0.0  0
 P3Y  CONST_35  C17   C18  C19  C14    0.00   0.0  0
 P3Y  CONST_36  C17   C16  C15  C14    0.00   0.0  0
 P3Y  CONST_37  C18   C19  C14  C15    0.00   0.0  0
 P3Y  CONST_38  C18   C17  C16  C15    0.00   0.0  0
 P3Y  CONST_39  C19   C14  C15  C16    0.00   0.0  0
 P3Y  CONST_40  C19   C18  C17  C16    0.00   0.0  0
 P3Y  CONST_41  C27   N26  C25  C24    0.00   0.0  0
 P3Y  CONST_42  C27   C28  C29  C24    0.00   0.0  0
 P3Y  CONST_43  C28   C29  C24  C25    0.00   0.0  0
 P3Y  CONST_44  C28   C27  N26  C25    0.00   0.0  0
 P3Y  CONST_45  C29   C24  C25  N26    0.00   0.0  0
 P3Y  CONST_46  C29   C28  C27  N26    0.00   0.0  0
 P3Y  CONST_47  O1    C15  C14  C9     0.00   0.0  0
 P3Y  CONST_48  O1    C15  C16  C17  180.00   0.0  0
 P3Y  CONST_49  O1    C15  C14  C19  180.00   0.0  0
 P3Y  CONST_50  C33   C28  C29  C24  180.00   0.0  0
 P3Y  CONST_51  C33   C28  C27  N26  180.00   0.0  0
 P3Y  CONST_52  H11   N11  C6   N1     0.00   0.0  0
 P3Y  CONST_53  H4    C4   C3   C2   180.00   0.0  0
 P3Y  CONST_54  H25   C25  C24  C3     0.00   0.0  0
 P3Y  CONST_55  H29   C29  C24  C3     0.00   0.0  0
 P3Y  CONST_56  H2    C2   C3   C4   180.00   0.0  0
 P3Y  CONST_57  H10   C10  C9   C5   180.00   0.0  0
 P3Y  CONST_58  H19   C19  C14  C9     0.00   0.0  0
 P3Y  CONST_59  H18   C18  C19  C14  180.00   0.0  0
 P3Y  CONST_60  H16   C16  C15  C14  180.00   0.0  0
 P3Y  CONST_61  H17   C17  C16  C15  180.00   0.0  0
 P3Y  CONST_62  H27   C27  N26  C25  180.00   0.0  0
 P3Y  CONST_63  C41   N35  C33  C28  180.00   0.0  0
 P3Y  CONST_65  C41   N35  C33  O34    0.00   0.0  0
 P3Y  CONST_66  C45   N35  C33  O34  180.00   0.0  0
 P3Y  Var_01    O34   C33  C28  C27  -47.41  30.0  2
 P3Y  Var_02    H11A  C1   O1   C15  178.84  30.0  3
 P3Y  Var_03    H411  C41  N35  C33   91.10  30.0  3
 P3Y  Var_04    H451  C45  N35  C33  110.69  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
 P3Y  plan-1  C9   0.020
 P3Y  plan-1  C14  0.020
 P3Y  plan-1  C15  0.020
 P3Y  plan-1  C16  0.020
 P3Y  plan-1  C17  0.020
 P3Y  plan-1  C18  0.020
 P3Y  plan-1  C19  0.020
 P3Y  plan-1  O1   0.020
 P3Y  plan-1  H16  0.020
 P3Y  plan-1  H17  0.020
 P3Y  plan-1  H18  0.020
 P3Y  plan-1  H19  0.020
 P3Y  plan-2  C3   0.020
 P3Y  plan-2  C24  0.020
 P3Y  plan-2  C25  0.020
 P3Y  plan-2  N26  0.020
 P3Y  plan-2  C27  0.020
 P3Y  plan-2  C28  0.020
 P3Y  plan-2  C29  0.020
 P3Y  plan-2  C33  0.020
 P3Y  plan-2  H25  0.020
 P3Y  plan-2  H27  0.020
 P3Y  plan-2  H29  0.020
 P3Y  plan-3  N1   0.020
 P3Y  plan-3  C2   0.020
 P3Y  plan-3  C3   0.020
 P3Y  plan-3  C4   0.020
 P3Y  plan-3  C5   0.020
 P3Y  plan-3  C6   0.020
 P3Y  plan-3  C9   0.020
 P3Y  plan-3  C10  0.020
 P3Y  plan-3  N11  0.020
 P3Y  plan-3  C14  0.020
 P3Y  plan-3  C24  0.020
 P3Y  plan-3  H10  0.020
 P3Y  plan-3  H11  0.020
 P3Y  plan-3  H2   0.020
 P3Y  plan-3  H4   0.020
 P3Y  plan-4  C28  0.020
 P3Y  plan-4  C33  0.020
 P3Y  plan-4  O34  0.020
 P3Y  plan-4  N35  0.020
 P3Y  plan-4  C41  0.020
 P3Y  plan-4  C45  0.020

