# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 11:51:59 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 3-[(3R)-3-(imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl)piperidin-1-yl]-3-oxopropanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CC#N)N1CCC[C@H](C1)n2cnc3cnc4[nH]ccc4c23
#
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
 0NU  0NU  3-[(3R)-3-(imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl)piperidin-1-yl]-3-oxopropanenitrile  ligand  39  23  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0NU
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
 0NU  N5   N  NS    0  -0.261  -5.1034  -3.3159  -0.1426
 0NU  C15  C  CSP   0   0.149  -4.7356  -2.2350  -0.2741
 0NU  C14  C  CH2   0  -0.710  -4.3192  -0.8574  -0.4628
 0NU  C13  C  C     0   0.593  -2.9089  -0.6557   0.0865
 0NU  O    O  O     0  -0.472  -2.3006  -1.6044   0.5516
 0NU  N4   N  NT    0  -0.461  -2.4211   0.5967   0.0379
 0NU  C11  C  CH2   0  -0.332  -3.0460   1.7220  -0.6419
 0NU  C10  C  CH2   0  -0.436  -2.2284   2.1109  -1.8665
 0NU  C9   C  CH2   0  -0.476  -0.7797   2.4015  -1.4865
 0NU  C12  C  CH2   0  -0.316  -1.0660   0.8687   0.4774
 0NU  C8   C  CH1   0  -0.089  -0.1934   1.2124  -0.7353
 0NU  N3   N  NR5   0  -0.532   1.1789   1.4396  -0.3145
 0NU  C4   C  CR56  0   0.371   2.0992   0.4687  -0.0420
 0NU  C3   C  CR56  0   0.005   2.0976  -0.9296  -0.0870
 0NU  C    C  CR15  0  -0.457   1.2099  -2.0024  -0.3884
 0NU  C7   C  CR15  0   0.090   1.7995   2.6329  -0.0626
 0NU  N2   N  N     0  -0.458   3.0304   2.5074   0.3305
 0NU  C5   C  CR56  0   0.006   3.2553   1.1507   0.3536
 0NU  C6   C  CR16  0  -0.137   4.4141   0.4372   0.6932
 0NU  N1   N  N     0  -0.431   4.4555  -0.8787   0.6562
 0NU  C2   C  CR56  0   0.420   3.3357  -1.5022   0.2817
 0NU  N    N  NR15  0  -0.655   3.1926  -2.8542   0.1966
 0NU  C1   C  CR15  0  -0.009   1.9241  -3.1542  -0.2010
 0NU  H14  H  HCH2  0   0.347  -4.3695  -0.6296  -1.5306
 0NU  H15  H  HCH2  0   0.350  -5.0429  -0.2079   0.0350
 0NU  H11  H  HCH2  0   0.288  -4.0684   1.4893  -0.9240
 0NU  H10  H  HCH2  0   0.262  -3.0970   2.5594   0.0600
 0NU  H8   H  HCH2  0   0.241  -2.2734   1.3045  -2.6037
 0NU  H9   H  HCH2  0   0.260  -2.6722   2.9938  -2.3284
 0NU  H6   H  HCH2  0   0.272  -0.1865   2.6194  -2.3762
 0NU  H7   H  HCH2  0   0.245  -0.7617   3.2936  -0.8532
 0NU  H13  H  HCH2  0   0.266  -1.0806   1.7195   1.1656
 0NU  H12  H  HCH2  0   0.288  -0.6737   0.0102   1.0169
 0NU  H1   H  HCH1  0   0.277  -0.1767   0.3531  -1.4119
 0NU  H2   H  HCR5  0   0.254   0.1765  -1.9477  -0.6879
 0NU  H5   H  HCR5  0   0.291   1.2912   3.5754  -0.1931
 0NU  H4   H  HCR6  0   0.259   5.3140   0.9608   0.9976
 0NU  H    H  HNR5  0   0.411   3.9131  -3.5260   0.4054
 0NU  H3   H  HCR5  0   0.288   1.6139  -4.1791  -0.3213

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
 0NU  N2   C5   aromatic  1.375  0.020  1.375
 0NU  N2   C7   aromatic  1.298  0.020  1.298
 0NU  C6   C5   aromatic  1.403  0.020  1.403
 0NU  C6   N1   aromatic  1.317  0.020  1.317
 0NU  C5   C4   aromatic  1.399  0.020  1.399
 0NU  C7   N3   aromatic  1.368  0.020  1.368
 0NU  N1   C2   aromatic  1.335  0.020  1.335
 0NU  C4   N3   aromatic  1.365  0.020  1.365
 0NU  C4   C3   aromatic  1.399  0.020  1.399
 0NU  N3   C8   single    1.453  0.020  1.453
 0NU  C2   C3   aromatic  1.413  0.020  1.413
 0NU  C2   N    aromatic  1.362  0.020  1.362
 0NU  C3   C    aromatic  1.425  0.020  1.425
 0NU  C12  C8   single    1.533  0.020  1.533
 0NU  C12  N4   single    1.450  0.020  1.450
 0NU  N    C1   aromatic  1.363  0.020  1.363
 0NU  C8   C9   single    1.524  0.020  1.524
 0NU  O    C13  double    1.219  0.020  1.219
 0NU  C    C1   aromatic  1.368  0.020  1.368
 0NU  N4   C13  single    1.345  0.020  1.345
 0NU  N4   C11  single    1.456  0.020  1.456
 0NU  C9   C10  single    1.526  0.020  1.526
 0NU  C13  C14  single    1.527  0.020  1.527
 0NU  C11  C10  single    1.523  0.020  1.523
 0NU  C14  C15  single    1.452  0.020  1.452
 0NU  C15  N5   triple    1.149  0.020  1.149
 0NU  C14  H14  single    0.970  0.020  1.090
 0NU  C14  H15  single    0.970  0.020  1.090
 0NU  C11  H11  single    0.970  0.020  1.090
 0NU  C11  H10  single    0.970  0.020  1.090
 0NU  C10  H8   single    0.970  0.020  1.090
 0NU  C10  H9   single    0.970  0.020  1.090
 0NU  C9   H6   single    0.970  0.020  1.090
 0NU  C9   H7   single    0.970  0.020  1.090
 0NU  C12  H13  single    0.970  0.020  1.090
 0NU  C12  H12  single    0.970  0.020  1.090
 0NU  C8   H1   single    0.970  0.020  1.090
 0NU  C    H2   single    0.930  0.020  1.080
 0NU  C7   H5   single    0.930  0.020  1.080
 0NU  C6   H4   single    0.930  0.020  1.080
 0NU  N    H    single    0.860  0.020  1.020
 0NU  C1   H3   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
 0NU  C14  C15  N5   180.00  3.000
 0NU  H15  C14  H14  106.91  3.000
 0NU  H15  C14  C13  111.68  3.000
 0NU  H14  C14  C13  111.49  3.000
 0NU  H15  C14  C15  108.36  3.000
 0NU  H14  C14  C15  108.16  3.000
 0NU  C13  C14  C15  110.10  3.000
 0NU  N4   C13  O    123.88  3.000
 0NU  N4   C13  C14  116.43  3.000
 0NU  O    C13  C14  119.69  3.000
 0NU  C12  N4   C11  113.43  3.000
 0NU  C11  N4   C13  125.52  3.000
 0NU  C12  N4   C13  120.17  3.000
 0NU  H10  C11  H11  106.68  3.000
 0NU  H10  C11  C10  110.22  3.000
 0NU  H11  C11  C10  110.57  3.000
 0NU  H10  C11  N4   108.18  3.000
 0NU  H11  C11  N4   111.09  3.000
 0NU  C10  C11  N4   110.03  3.000
 0NU  H9   C10  H8   107.14  3.000
 0NU  H9   C10  C9   109.73  3.000
 0NU  H8   C10  C9   110.33  3.000
 0NU  H9   C10  C11  109.19  3.000
 0NU  H8   C10  C11  109.37  3.000
 0NU  C9   C10  C11  110.99  3.000
 0NU  H7   C9   H6   107.47  3.000
 0NU  H7   C9   C8   110.15  3.000
 0NU  H6   C9   C8   110.40  3.000
 0NU  H7   C9   C10  108.36  3.000
 0NU  H6   C9   C10  110.56  3.000
 0NU  C8   C9   C10  109.85  3.000
 0NU  H12  C12  H13  107.86  3.000
 0NU  H12  C12  C8   111.35  3.000
 0NU  H13  C12  C8   109.31  3.000
 0NU  H12  C12  N4   109.84  3.000
 0NU  H13  C12  N4   108.90  3.000
 0NU  C8   C12  N4   109.52  3.000
 0NU  H1   C8   N3   106.71  3.000
 0NU  H1   C8   C12  108.78  3.000
 0NU  N3   C8   C12  110.09  3.000
 0NU  H1   C8   C9   108.30  3.000
 0NU  C12  C8   C9   110.23  3.000
 0NU  N3   C8   C9   112.58  3.000
 0NU  C7   N3   C4   106.12  3.000
 0NU  C4   N3   C8   125.67  3.000
 0NU  C7   N3   C8   128.17  3.000
 0NU  C5   C4   C3   119.81  3.000
 0NU  C3   C4   N3   134.72  3.000
 0NU  C5   C4   N3   105.47  3.000
 0NU  C2   C3   C    107.22  3.000
 0NU  C    C3   C4   139.47  3.000
 0NU  C2   C3   C4   113.31  3.000
 0NU  H2   C    C1   125.56  3.000
 0NU  H2   C    C3   128.19  3.000
 0NU  C1   C    C3   106.24  3.000
 0NU  H5   C7   N2   124.60  3.000
 0NU  H5   C7   N3   121.73  3.000
 0NU  N2   C7   N3   113.67  3.000
 0NU  C5   N2   C7   104.80  3.000
 0NU  C6   C5   N2   129.86  3.000
 0NU  C6   C5   C4   120.21  3.000
 0NU  N2   C5   C4   109.93  3.000
 0NU  H4   C6   N1   117.65  3.000
 0NU  H4   C6   C5   120.52  3.000
 0NU  N1   C6   C5   121.83  3.000
 0NU  C2   N1   C6   116.62  3.000
 0NU  N    C2   N1   124.69  3.000
 0NU  N    C2   C3   107.09  3.000
 0NU  N1   C2   C3   128.22  3.000
 0NU  H    N    C1   125.43  3.000
 0NU  H    N    C2   125.03  3.000
 0NU  C1   N    C2   109.54  3.000
 0NU  H3   C1   N    120.65  3.000
 0NU  H3   C1   C    129.44  3.000
 0NU  N    C1   C    109.91  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
 0NU  CONST_01  C5   N2   C7   N3      0.00   0.0  0
 0NU  CONST_02  N2   C5   C4   N3      0.00   0.0  0
 0NU  CONST_03  C6   C5   C4   N3    180.00   0.0  0
 0NU  CONST_04  C2   C3   C4   N3    180.00   0.0  0
 0NU  CONST_05  C    C3   C4   N3      0.00   0.0  0
 0NU  CONST_06  C7   N2   C5   C4      0.00   0.0  0
 0NU  CONST_07  N1   C6   C5   C4      0.00   0.0  0
 0NU  CONST_08  N2   C7   N3   C4      0.00   0.0  0
 0NU  CONST_09  N1   C2   C3   C4      0.00   0.0  0
 0NU  CONST_10  N    C2   C3   C4    180.00   0.0  0
 0NU  CONST_11  C1   C    C3   C4    180.00   0.0  0
 0NU  CONST_12  N2   C5   C4   C3    180.00   0.0  0
 0NU  CONST_13  C6   C5   C4   C3      0.00   0.0  0
 0NU  CONST_14  C7   N3   C4   C3    180.00   0.0  0
 0NU  CONST_15  C6   N1   C2   C3      0.00   0.0  0
 0NU  CONST_16  C1   N    C2   C3      0.00   0.0  0
 0NU  CONST_17  N    C1   C    C3      0.00   0.0  0
 0NU  CONST_18  C5   C4   C3   C     180.00   0.0  0
 0NU  CONST_19  N1   C2   C3   C     180.00   0.0  0
 0NU  CONST_20  N    C2   C3   C       0.00   0.0  0
 0NU  CONST_21  C2   N    C1   C       0.00   0.0  0
 0NU  CONST_22  C6   C5   N2   C7    180.00   0.0  0
 0NU  CONST_23  C5   C4   N3   C7      0.00   0.0  0
 0NU  CONST_24  N1   C6   C5   N2    180.00   0.0  0
 0NU  CONST_25  C2   N1   C6   C5      0.00   0.0  0
 0NU  CONST_26  C2   C3   C4   C5      0.00   0.0  0
 0NU  CONST_27  N    C2   N1   C6    180.00   0.0  0
 0NU  CONST_28  C1   N    C2   N1    180.00   0.0  0
 0NU  CONST_29  C1   C    C3   C2      0.00   0.0  0
 0NU  CONST_30  N2   C7   N3   C8    180.00   0.0  0
 0NU  CONST_31  C5   C4   N3   C8    180.00   0.0  0
 0NU  CONST_32  C3   C4   N3   C8      0.00   0.0  0
 0NU  CONST_33  H5   C7   N3   C8      0.00   0.0  0
 0NU  CONST_34  H4   C6   C5   C4    180.00   0.0  0
 0NU  CONST_35  H2   C    C3   C4      0.00   0.0  0
 0NU  CONST_36  H    N    C2   C3    180.00   0.0  0
 0NU  CONST_37  H3   C1   C    C3    180.00   0.0  0
 0NU  CONST_38  C12  N4   C13  C14   180.00   0.0  0
 0NU  CONST_39  C11  N4   C13  C14     0.00   0.0  0
 0NU  CONST_40  C12  N4   C13  O       0.00   0.0  0
 0NU  CONST_41  C11  N4   C13  O     180.00   0.0  0
 0NU  Var_01    C9   C10  C11  N4    -55.30  30.0  1
 0NU  Var_02    C8   C12  N4   C11   -60.09  30.0  1
 0NU  Var_03    C8   C9   C10  C11    54.44  30.0  1
 0NU  Var_04    C12  N4   C11  C10    59.16  30.0  1
 0NU  Var_05    N4   C13  C14  C15  -176.76  30.0  1
 0NU  Var_06    C13  C14  C15  N5    178.82  30.0  1

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
 0NU  chir_01  C8  N3  C12  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
 0NU  plan-1  C8   0.020
 0NU  plan-1  N3   0.020
 0NU  plan-1  C4   0.020
 0NU  plan-1  C3   0.020
 0NU  plan-1  C    0.020
 0NU  plan-1  C7   0.020
 0NU  plan-1  N2   0.020
 0NU  plan-1  C5   0.020
 0NU  plan-1  C6   0.020
 0NU  plan-1  N1   0.020
 0NU  plan-1  C2   0.020
 0NU  plan-1  N    0.020
 0NU  plan-1  C1   0.020
 0NU  plan-1  H2   0.020
 0NU  plan-1  H5   0.020
 0NU  plan-1  H4   0.020
 0NU  plan-1  H    0.020
 0NU  plan-1  H3   0.020
 0NU  plan-2  C14  0.020
 0NU  plan-2  C13  0.020
 0NU  plan-2  O    0.020
 0NU  plan-2  N4   0.020
 0NU  plan-2  C11  0.020
 0NU  plan-2  C12  0.020

