# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 14:58:41 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 3-[4-(piperidin-1-ylmethyl)phenyl]-9H-pyrrolo[2,3-b:5,4-c']dipyridine-6-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1cc2c([nH]c3ncc(cc23)c4ccc(CN5CCCCC5)cc4)cn1
#
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
 3X7  3X7  3-[4-(piperidin-1-ylmethyl)phenyl]-9H-pyrrolo[2,3-b:5,4-c']dipyridine-6-carbonitrile  ligand  49  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3X7
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
 3X7  N5   N  NS    0  -0.248  -6.9098  -3.9631   0.0313
 3X7  C18  C  CSP   0   0.050  -6.4875  -2.8938  -0.0373
 3X7  C6   C  CR6   0   0.173  -5.9559  -1.5647  -0.1224
 3X7  N2   N  N     0  -0.411  -6.8516  -0.5997  -0.3756
 3X7  C7   C  CR16  0  -0.096  -6.4395   0.6449  -0.4700
 3X7  C3   C  CR56  0   0.288  -5.0909   0.9637  -0.3085
 3X7  C5   C  CR16  0  -0.386  -4.5963  -1.3595   0.0549
 3X7  C2   C  CR56  0   0.144  -4.1494  -0.0509  -0.0405
 3X7  C1   C  CR56  0   0.025  -2.8759   0.6002   0.0669
 3X7  C10  C  CR16  0  -0.287  -1.5735   0.2015   0.3214
 3X7  C9   C  CR6   0  -0.013  -0.5845   1.1794   0.3506
 3X7  C8   C  CR16  0  -0.103  -0.9667   2.5123   0.1123
 3X7  N3   N  N     0  -0.420  -2.2025   2.9213  -0.1267
 3X7  C4   C  CR56  0   0.476  -3.1190   1.9722  -0.1415
 3X7  N1   N  NR15  0  -0.756  -4.4544   2.1656  -0.3647
 3X7  C14  C  CR6   0   0.072   0.8280   0.8466   0.6099
 3X7  C13  C  CR16  0  -0.301   1.3895  -0.3333   0.1158
 3X7  C12  C  CR16  0  -0.266   2.7177  -0.6452   0.3521
 3X7  C15  C  CR16  0  -0.298   1.6450   1.7013   1.3484
 3X7  C16  C  CR16  0  -0.297   2.9786   1.3911   1.5717
 3X7  C11  C  CR6   0   0.069   3.5350   0.2154   1.0821
 3X7  C17  C  CH2   0  -0.313   4.9735  -0.1302   1.3647
 3X7  N4   N  NT    0  -0.413   5.6563  -0.6999   0.2230
 3X7  C23  C  CH2   0  -0.275   5.7947   0.2641  -0.8567
 3X7  C22  C  CH2   0  -0.437   6.4389  -0.3652  -2.0814
 3X7  C21  C  CH2   0  -0.440   7.7919  -0.9694  -1.7306
 3X7  C20  C  CH2   0  -0.439   7.6406  -1.9276  -0.5564
 3X7  C19  C  CH2   0  -0.276   6.9460  -1.2470   0.6126
 3X7  H1   H  HCR6  0   0.292  -7.1815   1.4075  -0.6762
 3X7  H2   H  HCR6  0   0.291  -3.9287  -2.1864   0.2561
 3X7  H3   H  HCR6  0   0.272  -1.3364  -0.8384   0.5104
 3X7  H4   H  HCR6  0   0.268  -0.2074   3.2862   0.1011
 3X7  H5   H  HNR5  0   0.424  -4.8876   3.0586  -0.5425
 3X7  H6   H  HCR6  0   0.253   0.7881  -1.0089  -0.4801
 3X7  H7   H  HCR6  0   0.247   3.1353  -1.5576  -0.0550
 3X7  H8   H  HCR6  0   0.253   1.2419   2.6150   1.7674
 3X7  H9   H  HCR6  0   0.251   3.5932   2.0776   2.1421
 3X7  H10  H  HCH2  0   0.208   5.4902   0.7650   1.7516
 3X7  H11  H  HCH2  0   0.251   4.9995  -0.8676   2.1740
 3X7  H13  H  HCH2  0   0.238   4.8066   0.6461  -1.1204
 3X7  H14  H  HCH2  0   0.184   6.3930   1.1361  -0.5336
 3X7  H15  H  HCH2  0   0.215   5.7770  -1.1429  -2.4745
 3X7  H16  H  HCH2  0   0.229   6.5415   0.3915  -2.8623
 3X7  H17  H  HCH2  0   0.230   8.2246  -1.4806  -2.5932
 3X7  H18  H  HCH2  0   0.210   8.4877  -0.1676  -1.4601
 3X7  H19  H  HCH2  0   0.215   7.0555  -2.7993  -0.8644
 3X7  H20  H  HCH2  0   0.230   8.6142  -2.2982  -0.2281
 3X7  H21  H  HCH2  0   0.182   7.6073  -0.4600   1.0188
 3X7  H22  H  HCH2  0   0.233   6.7868  -1.9672   1.4194

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
 3X7  N5   C18  triple    1.152  0.020  1.152
 3X7  C18  C6   single    1.434  0.020  1.434
 3X7  C6   C5   aromatic  1.386  0.020  1.386
 3X7  C6   N2   aromatic  1.341  0.020  1.341
 3X7  C5   C2   aromatic  1.386  0.020  1.386
 3X7  N2   C7   aromatic  1.315  0.020  1.315
 3X7  C2   C3   aromatic  1.410  0.020  1.410
 3X7  C2   C1   aromatic  1.434  0.020  1.434
 3X7  C12  C13  aromatic  1.385  0.020  1.385
 3X7  C12  C11  aromatic  1.393  0.020  1.393
 3X7  C7   C3   aromatic  1.395  0.020  1.395
 3X7  C13  C14  aromatic  1.397  0.020  1.397
 3X7  C3   N1   aromatic  1.361  0.020  1.361
 3X7  C10  C1   aromatic  1.386  0.020  1.386
 3X7  C10  C9   aromatic  1.391  0.020  1.391
 3X7  C1   C4   aromatic  1.409  0.020  1.409
 3X7  C23  C22  single    1.520  0.020  1.520
 3X7  C23  N4   single    1.454  0.020  1.454
 3X7  C17  C11  single    1.506  0.020  1.506
 3X7  C17  N4   single    1.447  0.020  1.447
 3X7  C22  C21  single    1.523  0.020  1.523
 3X7  C11  C16  aromatic  1.390  0.020  1.390
 3X7  C14  C9   single    1.474  0.020  1.474
 3X7  C14  C15  aromatic  1.394  0.020  1.394
 3X7  C9   C8   aromatic  1.407  0.020  1.407
 3X7  N1   C4   aromatic  1.368  0.020  1.368
 3X7  C4   N3   aromatic  1.320  0.020  1.320
 3X7  N4   C19  single    1.454  0.020  1.454
 3X7  C8   N3   aromatic  1.323  0.020  1.323
 3X7  C16  C15  aromatic  1.387  0.020  1.387
 3X7  C21  C20  single    1.523  0.020  1.523
 3X7  C19  C20  single    1.521  0.020  1.521
 3X7  C7   H1   single    0.930  0.020  1.080
 3X7  C5   H2   single    0.930  0.020  1.080
 3X7  C10  H3   single    0.930  0.020  1.080
 3X7  C8   H4   single    0.930  0.020  1.080
 3X7  N1   H5   single    0.860  0.020  1.020
 3X7  C13  H6   single    0.930  0.020  1.080
 3X7  C12  H7   single    0.930  0.020  1.080
 3X7  C15  H8   single    0.930  0.020  1.080
 3X7  C16  H9   single    0.930  0.020  1.080
 3X7  C17  H10  single    0.970  0.020  1.090
 3X7  C17  H11  single    0.970  0.020  1.090
 3X7  C23  H13  single    0.970  0.020  1.090
 3X7  C23  H14  single    0.970  0.020  1.090
 3X7  C22  H15  single    0.970  0.020  1.090
 3X7  C22  H16  single    0.970  0.020  1.090
 3X7  C21  H17  single    0.970  0.020  1.090
 3X7  C21  H18  single    0.970  0.020  1.090
 3X7  C20  H19  single    0.970  0.020  1.090
 3X7  C20  H20  single    0.970  0.020  1.090
 3X7  C19  H21  single    0.970  0.020  1.090
 3X7  C19  H22  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
 3X7  C6   C18  N5   180.00  3.000
 3X7  C5   C6   N2   124.94  3.000
 3X7  N2   C6   C18  115.51  3.000
 3X7  C5   C6   C18  119.55  3.000
 3X7  C7   N2   C6   119.05  3.000
 3X7  H1   C7   C3   121.54  3.000
 3X7  H1   C7   N2   117.73  3.000
 3X7  C3   C7   N2   120.74  3.000
 3X7  N1   C3   C2   109.33  3.000
 3X7  N1   C3   C7   130.46  3.000
 3X7  C2   C3   C7   120.20  3.000
 3X7  H2   C5   C2   122.39  3.000
 3X7  H2   C5   C6   121.06  3.000
 3X7  C2   C5   C6   116.56  3.000
 3X7  C1   C2   C5   135.20  3.000
 3X7  C1   C2   C3   106.29  3.000
 3X7  C5   C2   C3   118.51  3.000
 3X7  C4   C1   C10  118.00  3.000
 3X7  C4   C1   C2   106.13  3.000
 3X7  C10  C1   C2   135.87  3.000
 3X7  H3   C10  C9   121.03  3.000
 3X7  H3   C10  C1   120.93  3.000
 3X7  C9   C10  C1   118.02  3.000
 3X7  C14  C9   C8   120.26  3.000
 3X7  C8   C9   C10  117.98  3.000
 3X7  C14  C9   C10  121.75  3.000
 3X7  H4   C8   N3   115.56  3.000
 3X7  H4   C8   C9   119.19  3.000
 3X7  N3   C8   C9   125.25  3.000
 3X7  C4   N3   C8   115.35  3.000
 3X7  N1   C4   N3   125.33  3.000
 3X7  N3   C4   C1   125.38  3.000
 3X7  N1   C4   C1   109.29  3.000
 3X7  H5   N1   C4   125.00  3.000
 3X7  H5   N1   C3   126.04  3.000
 3X7  C4   N1   C3   108.96  3.000
 3X7  C15  C14  C13  118.01  3.000
 3X7  C15  C14  C9   121.09  3.000
 3X7  C13  C14  C9   120.90  3.000
 3X7  H6   C13  C12  119.08  3.000
 3X7  H6   C13  C14  119.88  3.000
 3X7  C12  C13  C14  121.03  3.000
 3X7  H7   C12  C11  119.42  3.000
 3X7  H7   C12  C13  119.70  3.000
 3X7  C11  C12  C13  120.86  3.000
 3X7  H8   C15  C16  118.96  3.000
 3X7  H8   C15  C14  120.27  3.000
 3X7  C16  C15  C14  120.77  3.000
 3X7  H9   C16  C11  119.62  3.000
 3X7  H9   C16  C15  119.23  3.000
 3X7  C11  C16  C15  121.15  3.000
 3X7  C17  C11  C16  120.68  3.000
 3X7  C16  C11  C12  118.18  3.000
 3X7  C17  C11  C12  121.12  3.000
 3X7  H11  C17  H10  106.02  3.000
 3X7  H11  C17  N4   107.86  3.000
 3X7  H10  C17  N4   112.03  3.000
 3X7  H11  C17  C11  108.41  3.000
 3X7  H10  C17  C11  109.08  3.000
 3X7  N4   C17  C11  113.13  3.000
 3X7  C19  N4   C23  111.34  3.000
 3X7  C19  N4   C17  110.81  3.000
 3X7  C23  N4   C17  111.70  3.000
 3X7  H14  C23  H13  106.52  3.000
 3X7  H14  C23  C22  109.43  3.000
 3X7  H13  C23  C22  109.50  3.000
 3X7  H14  C23  N4   110.94  3.000
 3X7  H13  C23  N4   108.97  3.000
 3X7  C22  C23  N4   111.36  3.000
 3X7  H16  C22  H15  107.00  3.000
 3X7  H16  C22  C21  110.86  3.000
 3X7  H15  C22  C21  109.77  3.000
 3X7  H16  C22  C23  109.21  3.000
 3X7  H15  C22  C23  109.11  3.000
 3X7  C21  C22  C23  110.80  3.000
 3X7  H18  C21  H17  106.62  3.000
 3X7  H18  C21  C20  109.46  3.000
 3X7  H17  C21  C20  110.71  3.000
 3X7  H18  C21  C22  109.32  3.000
 3X7  H17  C21  C22  110.85  3.000
 3X7  C20  C21  C22  109.82  3.000
 3X7  H20  C20  H19  106.92  3.000
 3X7  H20  C20  C19  109.14  3.000
 3X7  H19  C20  C19  109.19  3.000
 3X7  H20  C20  C21  110.90  3.000
 3X7  H19  C20  C21  109.72  3.000
 3X7  C19  C20  C21  110.88  3.000
 3X7  H22  C19  H21  106.56  3.000
 3X7  H22  C19  C20  109.82  3.000
 3X7  H21  C19  C20  109.14  3.000
 3X7  H22  C19  N4   108.45  3.000
 3X7  H21  C19  N4   111.18  3.000
 3X7  C20  C19  N4   111.57  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
 3X7  CONST_01  C3   C2   C5   C6     0.00   0.0  0
 3X7  CONST_02  C1   C2   C5   C6   180.00   0.0  0
 3X7  CONST_03  C3   C7   N2   C6     0.00   0.0  0
 3X7  CONST_04  C2   C5   C6   N2     0.00   0.0  0
 3X7  CONST_05  C2   C3   C7   N2     0.00   0.0  0
 3X7  CONST_06  N1   C3   C7   N2   180.00   0.0  0
 3X7  CONST_07  C5   C6   N2   C7     0.00   0.0  0
 3X7  CONST_08  C5   C2   C3   C7     0.00   0.0  0
 3X7  CONST_09  C1   C2   C3   C7   180.00   0.0  0
 3X7  CONST_10  C4   N1   C3   C7   180.00   0.0  0
 3X7  CONST_11  C10  C1   C2   C3   180.00   0.0  0
 3X7  CONST_12  C4   C1   C2   C3     0.00   0.0  0
 3X7  CONST_13  C1   C4   N1   C3     0.00   0.0  0
 3X7  CONST_14  N3   C4   N1   C3   180.00   0.0  0
 3X7  CONST_15  N1   C3   C2   C5   180.00   0.0  0
 3X7  CONST_16  C10  C1   C2   C5     0.00   0.0  0
 3X7  CONST_17  C4   C1   C2   C5   180.00   0.0  0
 3X7  CONST_18  C4   N1   C3   C2     0.00   0.0  0
 3X7  CONST_19  C9   C10  C1   C2   180.00   0.0  0
 3X7  CONST_20  N1   C4   C1   C2     0.00   0.0  0
 3X7  CONST_21  N3   C4   C1   C2   180.00   0.0  0
 3X7  CONST_22  N1   C3   C2   C1     0.00   0.0  0
 3X7  CONST_23  C14  C9   C10  C1   180.00   0.0  0
 3X7  CONST_24  C8   C9   C10  C1     0.00   0.0  0
 3X7  CONST_25  C8   N3   C4   C1     0.00   0.0  0
 3X7  CONST_26  N1   C4   C1   C10  180.00   0.0  0
 3X7  CONST_27  N3   C4   C1   C10    0.00   0.0  0
 3X7  CONST_30  N3   C8   C9   C10    0.00   0.0  0
 3X7  CONST_31  C4   C1   C10  C9     0.00   0.0  0
 3X7  CONST_32  C12  C13  C14  C9   180.00   0.0  0
 3X7  CONST_33  C16  C15  C14  C9   180.00   0.0  0
 3X7  CONST_34  C4   N3   C8   C9     0.00   0.0  0
 3X7  CONST_37  N1   C4   N3   C8   180.00   0.0  0
 3X7  CONST_38  C14  C9   C8   N3   180.00   0.0  0
 3X7  CONST_39  C11  C12  C13  C14    0.00   0.0  0
 3X7  CONST_40  C11  C16  C15  C14    0.00   0.0  0
 3X7  CONST_41  C16  C11  C12  C13    0.00   0.0  0
 3X7  CONST_42  C16  C15  C14  C13    0.00   0.0  0
 3X7  CONST_43  C15  C14  C13  C12    0.00   0.0  0
 3X7  CONST_44  C15  C16  C11  C12    0.00   0.0  0
 3X7  CONST_45  C2   C5   C6   C18  180.00   0.0  0
 3X7  CONST_46  C7   N2   C6   C18  180.00   0.0  0
 3X7  CONST_47  C17  C11  C12  C13  180.00   0.0  0
 3X7  CONST_48  C17  C11  C16  C15  180.00   0.0  0
 3X7  CONST_49  H1   C7   N2   C6   180.00   0.0  0
 3X7  CONST_50  H2   C5   C6   N2   180.00   0.0  0
 3X7  CONST_51  H5   N1   C3   C7     0.00   0.0  0
 3X7  CONST_52  H3   C10  C1   C2     0.00   0.0  0
 3X7  CONST_53  H4   C8   C9   C10  180.00   0.0  0
 3X7  CONST_54  H6   C13  C14  C9     0.00   0.0  0
 3X7  CONST_55  H8   C15  C14  C9     0.00   0.0  0
 3X7  CONST_56  H7   C12  C13  C14  180.00   0.0  0
 3X7  CONST_57  H9   C16  C15  C14  180.00   0.0  0
 3X7  Var_01    C21  C22  C23  N4   -56.63  30.0  1
 3X7  Var_02    C21  C20  C19  N4    55.97  30.0  1
 3X7  Var_03    C20  C21  C22  C23   53.50  30.0  1
 3X7  Var_04    C20  C19  N4   C23  -58.59  30.0  1
 3X7  Var_05    C19  N4   C23  C22   58.89  30.0  1
 3X7  Var_06    C19  C20  C21  C22  -53.15  30.0  1
 3X7  Var_07    N4   C17  C11  C12   42.25  30.0  2
 3X7  Var_08    C23  N4   C17  C11   66.13  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
 3X7  plan-1  C9   0.020
 3X7  plan-1  C14  0.020
 3X7  plan-1  C13  0.020
 3X7  plan-1  C12  0.020
 3X7  plan-1  C15  0.020
 3X7  plan-1  C16  0.020
 3X7  plan-1  C11  0.020
 3X7  plan-1  C17  0.020
 3X7  plan-1  H6   0.020
 3X7  plan-1  H7   0.020
 3X7  plan-1  H8   0.020
 3X7  plan-1  H9   0.020
 3X7  plan-2  N5   0.020
 3X7  plan-2  C18  0.020
 3X7  plan-2  C6   0.020
 3X7  plan-2  N2   0.020
 3X7  plan-2  C7   0.020
 3X7  plan-2  C3   0.020
 3X7  plan-2  C5   0.020
 3X7  plan-2  C2   0.020
 3X7  plan-2  C1   0.020
 3X7  plan-2  C10  0.020
 3X7  plan-2  C9   0.020
 3X7  plan-2  C8   0.020
 3X7  plan-2  N3   0.020
 3X7  plan-2  C4   0.020
 3X7  plan-2  N1   0.020
 3X7  plan-2  C14  0.020
 3X7  plan-2  H1   0.020
 3X7  plan-2  H2   0.020
 3X7  plan-2  H3   0.020
 3X7  plan-2  H4   0.020
 3X7  plan-2  H5   0.020

