# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 16:44:07 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 4-(3-methylphenyl)-6-[(1-methylpyrazol-3-yl)amino]-1~{H}-pyrrolo[2,3-b]pyridine-3-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ccc(Nc2cc(c3cccc(C)c3)c4c([nH]cc4C#N)n2)n1
#
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
 A3H  A3H  4-(3-methylphenyl)-6-[(1-methylpyrazol-3-yl)amino]-1~{H}-pyrrolo[2,3-b]pyridine-3-carbonitrile  ligand  41  25  .  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_A3H
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
 A3H  N    N  N     0  -0.494  -1.4193   1.1846   0.1333
 A3H  C    C  CR16  0  -0.500  -0.0157  -0.7513  -0.1442
 A3H  C1   C  CR6   0   0.560  -1.2800  -0.1203  -0.0215
 A3H  N1   N  NR15  0  -0.662  -0.2109   3.2214   0.3718
 A3H  C2   C  CR6   0   0.160   1.1482  -0.0152  -0.1109
 A3H  C3   C  CR15  0   0.038   1.0829   3.6080   0.4097
 A3H  N3   N  NH1   0  -0.770  -2.3921  -0.9076  -0.0753
 A3H  C4   C  CR5   0  -0.201   1.8877   2.5058   0.2330
 A3H  N4   N  NR5   0  -0.259  -5.8064  -0.8489  -0.0428
 A3H  C5   C  CR56  0   0.045   1.0170   1.3728   0.0735
 A3H  N5   N  N     0  -0.351  -4.6323  -1.4731  -0.1527
 A3H  C6   C  CR56  0   0.503  -0.2882   1.8720   0.1808
 A3H  C7   C  CSP   0  -0.056   3.2955   2.5562   0.2740
 A3H  C8   C  CR6   0   0.047   2.4590  -0.6729  -0.2725
 A3H  C9   C  CR16  0  -0.306   3.3570  -0.2262  -1.2383
 A3H  C10  C  CR16  0  -0.225   4.5742  -0.8703  -1.3987
 A3H  C11  C  CR16  0  -0.304   4.9053  -1.9533  -0.5977
 A3H  C12  C  CR6   0   0.116   4.0220  -2.4158   0.3761
 A3H  C13  C  CR16  0  -0.349   2.7992  -1.7679   0.5202
 A3H  C14  C  CR5   0   0.484  -3.7183  -0.5262  -0.0093
 A3H  C15  C  CR15  0  -0.535  -4.3116   0.7353   0.1971
 A3H  C16  C  CR15  0   0.047  -5.6626   0.4655   0.1653
 A3H  C18  C  CH3   0  -0.724   4.3906  -3.5674   1.2652
 A3H  H1   H  HCR6  0   0.274   0.0289  -1.8228  -0.2933
 A3H  H2   H  HNR5  0   0.424  -1.0018   3.8364   0.4858
 A3H  H3   H  HCR5  0   0.317   1.3606   4.6373   0.5643
 A3H  H4   H  HNH1  0   0.408  -2.2423  -1.8957  -0.2070
 A3H  H5   H  HCR6  0   0.257   3.1003   0.6076  -1.8797
 A3H  H6   H  HCR6  0   0.256   5.2666  -0.5274  -2.1564
 A3H  H7   H  HCR6  0   0.250   5.8614  -2.4455  -0.7311
 A3H  H8   H  HCR6  0   0.248   2.1019  -2.1160   1.2741
 A3H  H9   H  HCR5  0   0.272  -3.8336   1.6846   0.3463
 A3H  H10  H  HCR5  0   0.289  -6.5121   1.1198   0.2768
 A3H  H11  H  HCH3  0   0.257  -7.0842  -2.0992  -1.1197
 A3H  H12  H  HCH3  0   0.256  -7.0970  -2.3451   0.6369
 A3H  H13  H  HCH3  0   0.257  -7.8712  -0.9167  -0.0646
 A3H  H14  H  HCH3  0   0.250   4.9975  -3.2298   2.1081
 A3H  H15  H  HCH3  0   0.245   3.5077  -4.0561   1.6755
 A3H  H16  H  HCH3  0   0.245   4.9739  -4.3152   0.7284
 A3H  C17  C  CH3   0  -0.504  -7.0311  -1.5995  -0.1540
 A3H  N2   N  NS    0  -0.263   4.4473   2.6259   0.3116

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
 A3H  C18  C12  single    1.501  0.020  1.501
 A3H  C12  C11  aromatic  1.394  0.020  1.394
 A3H  C12  C13  aromatic  1.391  0.020  1.391
 A3H  C11  C10  aromatic  1.387  0.020  1.387
 A3H  C13  C8   aromatic  1.394  0.020  1.394
 A3H  N2   C7   triple    1.155  0.020  1.155
 A3H  C10  C9   aromatic  1.386  0.020  1.386
 A3H  C7   C4   single    1.409  0.020  1.409
 A3H  C8   C9   aromatic  1.392  0.020  1.392
 A3H  C8   C2   single    1.475  0.020  1.475
 A3H  C4   C5   aromatic  1.438  0.020  1.438
 A3H  C4   C3   aromatic  1.376  0.020  1.376
 A3H  C2   C5   aromatic  1.406  0.020  1.406
 A3H  C2   C    aromatic  1.378  0.020  1.378
 A3H  C5   C6   aromatic  1.401  0.020  1.401
 A3H  C3   N1   aromatic  1.351  0.020  1.351
 A3H  C    C1   aromatic  1.418  0.020  1.418
 A3H  C6   N1   aromatic  1.365  0.020  1.365
 A3H  C6   N    aromatic  1.324  0.020  1.324
 A3H  C1   N    aromatic  1.321  0.020  1.321
 A3H  C1   N3   single    1.364  0.020  1.364
 A3H  N5   N4   aromatic  1.334  0.020  1.334
 A3H  N5   C14  aromatic  1.324  0.020  1.324
 A3H  C17  N4   single    1.441  0.020  1.441
 A3H  N4   C16  aromatic  1.338  0.020  1.338
 A3H  N3   C14  single    1.382  0.020  1.382
 A3H  C14  C15  aromatic  1.409  0.020  1.409
 A3H  C16  C15  aromatic  1.378  0.020  1.378
 A3H  C    H1   single    0.930  0.020  1.080
 A3H  N1   H2   single    0.860  0.020  1.020
 A3H  C3   H3   single    0.930  0.020  1.080
 A3H  N3   H4   single    0.860  0.020  1.020
 A3H  C9   H5   single    0.930  0.020  1.080
 A3H  C10  H6   single    0.930  0.020  1.080
 A3H  C11  H7   single    0.930  0.020  1.080
 A3H  C13  H8   single    0.930  0.020  1.080
 A3H  C15  H9   single    0.930  0.020  1.080
 A3H  C16  H10  single    0.930  0.020  1.080
 A3H  C17  H11  single    0.970  0.020  1.090
 A3H  C17  H12  single    0.970  0.020  1.090
 A3H  C17  H13  single    0.970  0.020  1.090
 A3H  C18  H14  single    0.970  0.020  1.090
 A3H  C18  H15  single    0.970  0.020  1.090
 A3H  C18  H16  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
 A3H  C6   N    C1   115.25  3.000
 A3H  H1   C    C2   119.82  3.000
 A3H  H1   C    C1   119.27  3.000
 A3H  C2   C    C1   120.89  3.000
 A3H  N3   C1   C    117.82  3.000
 A3H  N3   C1   N    119.26  3.000
 A3H  C    C1   N    122.92  3.000
 A3H  H2   N1   C6   125.05  3.000
 A3H  H2   N1   C3   124.99  3.000
 A3H  C6   N1   C3   109.94  3.000
 A3H  C8   C2   C5   122.49  3.000
 A3H  C5   C2   C    116.85  3.000
 A3H  C8   C2   C    120.66  3.000
 A3H  H3   C3   C4   129.27  3.000
 A3H  H3   C3   N1   121.63  3.000
 A3H  C4   C3   N1   109.10  3.000
 A3H  H4   N3   C14  114.80  3.000
 A3H  H4   N3   C1   116.74  3.000
 A3H  C14  N3   C1   128.43  3.000
 A3H  C7   C4   C5   129.52  3.000
 A3H  C5   C4   C3   106.93  3.000
 A3H  C7   C4   C3   123.49  3.000
 A3H  C17  N4   C16  127.95  3.000
 A3H  C16  N4   N5   112.19  3.000
 A3H  C17  N4   N5   119.86  3.000
 A3H  C6   C5   C4   105.95  3.000
 A3H  C6   C5   C2   116.65  3.000
 A3H  C4   C5   C2   137.37  3.000
 A3H  C14  N5   N4   105.31  3.000
 A3H  C5   C6   N1   108.06  3.000
 A3H  N1   C6   N    124.50  3.000
 A3H  C5   C6   N    127.43  3.000
 A3H  C4   C7   N2   180.00  3.000
 A3H  C13  C8   C9   119.28  3.000
 A3H  C9   C8   C2   120.39  3.000
 A3H  C13  C8   C2   120.31  3.000
 A3H  H5   C9   C10  119.82  3.000
 A3H  H5   C9   C8   120.33  3.000
 A3H  C10  C9   C8   119.83  3.000
 A3H  H6   C10  C11  119.93  3.000
 A3H  H6   C10  C9   119.70  3.000
 A3H  C11  C10  C9   120.37  3.000
 A3H  H7   C11  C12  119.64  3.000
 A3H  H7   C11  C10  119.62  3.000
 A3H  C12  C11  C10  120.75  3.000
 A3H  C18  C12  C13  120.79  3.000
 A3H  C13  C12  C11  118.35  3.000
 A3H  C18  C12  C11  120.85  3.000
 A3H  H8   C13  C12  119.18  3.000
 A3H  H8   C13  C8   119.39  3.000
 A3H  C12  C13  C8   121.43  3.000
 A3H  C15  C14  N5   111.43  3.000
 A3H  C15  C14  N3   131.17  3.000
 A3H  N5   C14  N3   117.40  3.000
 A3H  H9   C15  C16  127.80  3.000
 A3H  H9   C15  C14  128.65  3.000
 A3H  C16  C15  C14  103.54  3.000
 A3H  H10  C16  C15  130.65  3.000
 A3H  H10  C16  N4   121.83  3.000
 A3H  C15  C16  N4   107.53  3.000
 A3H  H16  C18  H15  108.15  3.000
 A3H  H16  C18  H14  107.15  3.000
 A3H  H15  C18  H14  107.35  3.000
 A3H  H16  C18  C12  111.49  3.000
 A3H  H15  C18  C12  111.61  3.000
 A3H  H14  C18  C12  110.89  3.000
 A3H  H13  C17  H12  108.89  3.000
 A3H  H13  C17  H11  108.89  3.000
 A3H  H12  C17  H11  109.09  3.000
 A3H  H13  C17  N4   108.88  3.000
 A3H  H12  C17  N4   110.62  3.000
 A3H  H11  C17  N4   110.43  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
 A3H  CONST_01  C4   C5   C6   N    180.00   0.0  0
 A3H  CONST_02  C2   C5   C6   N      0.00   0.0  0
 A3H  CONST_03  C3   N1   C6   N    180.00   0.0  0
 A3H  CONST_04  C2   C    C1   N      0.00   0.0  0
 A3H  CONST_07  C4   C5   C2   C    180.00   0.0  0
 A3H  CONST_08  C6   C5   C2   C      0.00   0.0  0
 A3H  CONST_09  C6   N    C1   C      0.00   0.0  0
 A3H  CONST_10  C8   C2   C    C1   180.00   0.0  0
 A3H  CONST_11  C5   C2   C    C1     0.00   0.0  0
 A3H  CONST_12  C5   C6   N    C1     0.00   0.0  0
 A3H  CONST_13  N1   C6   N    C1   180.00   0.0  0
 A3H  CONST_14  C5   C4   C3   N1     0.00   0.0  0
 A3H  CONST_15  C4   C5   C6   N1     0.00   0.0  0
 A3H  CONST_16  C2   C5   C6   N1   180.00   0.0  0
 A3H  CONST_17  C12  C13  C8   C2   180.00   0.0  0
 A3H  CONST_18  C10  C9   C8   C2   180.00   0.0  0
 A3H  CONST_19  C3   C4   C5   C2   180.00   0.0  0
 A3H  CONST_20  C6   C5   C4   C3     0.00   0.0  0
 A3H  CONST_21  C5   C6   N1   C3     0.00   0.0  0
 A3H  CONST_22  C8   C2   C5   C4     0.00   0.0  0
 A3H  CONST_23  C6   N1   C3   C4     0.00   0.0  0
 A3H  CONST_24  C15  C14  N5   N4     0.00   0.0  0
 A3H  CONST_25  C14  C15  C16  N4     0.00   0.0  0
 A3H  CONST_28  C15  C16  N4   N5     0.00   0.0  0
 A3H  CONST_29  C16  C15  C14  N5     0.00   0.0  0
 A3H  CONST_30  C8   C2   C5   C6   180.00   0.0  0
 A3H  CONST_31  C11  C12  C13  C8     0.00   0.0  0
 A3H  CONST_32  C11  C10  C9   C8     0.00   0.0  0
 A3H  CONST_33  C12  C11  C10  C9     0.00   0.0  0
 A3H  CONST_34  C12  C13  C8   C9     0.00   0.0  0
 A3H  CONST_35  C13  C12  C11  C10    0.00   0.0  0
 A3H  CONST_36  C13  C8   C9   C10    0.00   0.0  0
 A3H  CONST_37  C16  N4   N5   C14    0.00   0.0  0
 A3H  CONST_38  C7   C4   C3   N1   180.00   0.0  0
 A3H  CONST_39  C7   C4   C5   C2     0.00   0.0  0
 A3H  CONST_40  N3   C1   C    C2   180.00   0.0  0
 A3H  CONST_41  C6   N    C1   N3   180.00   0.0  0
 A3H  CONST_42  N4   N5   C14  N3   180.00   0.0  0
 A3H  CONST_43  C16  C15  C14  N3   180.00   0.0  0
 A3H  CONST_44  C7   C4   C5   C6   180.00   0.0  0
 A3H  CONST_45  C18  C12  C13  C8   180.00   0.0  0
 A3H  CONST_46  C18  C12  C11  C10  180.00   0.0  0
 A3H  CONST_47  C17  N4   N5   C14  180.00   0.0  0
 A3H  CONST_48  C17  N4   C16  C15  180.00   0.0  0
 A3H  CONST_49  H2   N1   C6   N      0.00   0.0  0
 A3H  CONST_50  H1   C    C1   N    180.00   0.0  0
 A3H  CONST_51  H8   C13  C8   C2     0.00   0.0  0
 A3H  CONST_52  H5   C9   C8   C2     0.00   0.0  0
 A3H  CONST_53  H9   C15  C16  N4   180.00   0.0  0
 A3H  CONST_54  H3   C3   C4   C5   180.00   0.0  0
 A3H  CONST_55  H10  C16  N4   N5   180.00   0.0  0
 A3H  CONST_56  H6   C10  C9   C8   180.00   0.0  0
 A3H  CONST_57  H7   C11  C10  C9   180.00   0.0  0
 A3H  Var_01    C14  N3   C1   N      1.15  30.0  2
 A3H  Var_02    N5   C14  N3   C1   176.62  30.0  2
 A3H  Var_03    H11  C17  N4   N5   -58.99  30.0  2
 A3H  Var_04    H14  C18  C12  C11   82.96  30.0  2

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
 A3H  plan-1  N3   0.020
 A3H  plan-1  N4   0.020
 A3H  plan-1  N5   0.020
 A3H  plan-1  C14  0.020
 A3H  plan-1  C15  0.020
 A3H  plan-1  C16  0.020
 A3H  plan-1  H9   0.020
 A3H  plan-1  H10  0.020
 A3H  plan-1  C17  0.020
 A3H  plan-2  C2   0.020
 A3H  plan-2  C8   0.020
 A3H  plan-2  C9   0.020
 A3H  plan-2  C10  0.020
 A3H  plan-2  C11  0.020
 A3H  plan-2  C12  0.020
 A3H  plan-2  C13  0.020
 A3H  plan-2  C18  0.020
 A3H  plan-2  H5   0.020
 A3H  plan-2  H6   0.020
 A3H  plan-2  H7   0.020
 A3H  plan-2  H8   0.020
 A3H  plan-3  N    0.020
 A3H  plan-3  C    0.020
 A3H  plan-3  C1   0.020
 A3H  plan-3  N1   0.020
 A3H  plan-3  C2   0.020
 A3H  plan-3  C3   0.020
 A3H  plan-3  N3   0.020
 A3H  plan-3  C4   0.020
 A3H  plan-3  C5   0.020
 A3H  plan-3  C6   0.020
 A3H  plan-3  C7   0.020
 A3H  plan-3  C8   0.020
 A3H  plan-3  H1   0.020
 A3H  plan-3  H2   0.020
 A3H  plan-3  H3   0.020
 A3H  plan-3  N2   0.020

