# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 03:54:39 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 1-(1-benzylpiperidin-4-yl)-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CCC1n2cnc3cnc4[nH]ccc4c23)Cc5ccccc5
#
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
 0NV  0NV  1-(1-benzylpiperidin-4-yl)-1,6-dihydroimidazo[4,5-d]pyrrolo[2,3-b]pyridine  ligand  46  25  .  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_0NV
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
 0NV  C1   C  CH2   0  -0.433  -0.2023   0.2745   1.7310
 0NV  C2   C  CH2   0  -0.287  -1.4170  -0.6312   1.8633
 0NV  N3   N  NT    0  -0.414  -2.4042  -0.3260   0.8445
 0NV  C4   C  CH2   0  -0.283  -1.8572  -0.5148  -0.4865
 0NV  C5   C  CH2   0  -0.432  -0.6563   0.3872  -0.7238
 0NV  C6   C  CH1   0  -0.122   0.4015   0.1265   0.3405
 0NV  N7   N  NR5   0  -0.521   1.5745   0.9704   0.1662
 0NV  C8   C  CR15  0   0.083   1.5922   2.3365   0.1570
 0NV  N9   N  N     0  -0.459   2.7779   2.8432   0.0007
 0NV  C10  C  CR56  0   0.005   3.6114   1.7538  -0.0979
 0NV  C11  C  CR16  0  -0.136   5.0014   1.7020  -0.2751
 0NV  N12  N  N     0  -0.433   5.6514   0.5587  -0.3433
 0NV  C13  C  CR56  0   0.419   4.9183  -0.5525  -0.2360
 0NV  N14  N  NR15  0  -0.655   5.4224  -1.8175  -0.2796
 0NV  C15  C  CR15  0  -0.008   4.4094  -2.7170  -0.1375
 0NV  C16  C  CR15  0  -0.459   3.2187  -2.0576   0.0008
 0NV  C17  C  CR56  0   0.006   3.5211  -0.6661  -0.0596
 0NV  C18  C  CR56  0   0.368   2.8676   0.5709   0.0074
 0NV  C19  C  CH2   0  -0.323  -3.6237  -1.0853   1.0324
 0NV  C20  C  CR6   0   0.088  -4.7677  -0.5510   0.2094
 0NV  C21  C  CR16  0  -0.283  -5.0527   0.8136   0.1984
 0NV  C22  C  CR16  0  -0.243  -6.1255   1.3057  -0.5297
 0NV  C23  C  CR16  0  -0.271  -6.9322   0.4396  -1.2602
 0NV  C24  C  CR16  0  -0.241  -6.6538  -0.9195  -1.2586
 0NV  C25  C  CR16  0  -0.313  -5.5754  -1.4083  -0.5296
 0NV  H1   H  HCH2  0   0.235  -0.5022   1.3127   1.8995
 0NV  H2   H  HCH2  0   0.253   0.5363   0.0174   2.4929
 0NV  H3   H  HCH2  0   0.195  -1.0885  -1.6847   1.8122
 0NV  H4   H  HCH2  0   0.247  -1.8681  -0.4895   2.8475
 0NV  H6   H  HCH2  0   0.198  -1.5659  -1.5681  -0.6506
 0NV  H7   H  HCH2  0   0.252  -2.6267  -0.2866  -1.2258
 0NV  H8   H  HCH2  0   0.255  -0.2469   0.2009  -1.7184
 0NV  H9   H  HCH2  0   0.234  -0.9810   1.4305  -0.6883
 0NV  H10  H  HCH1  0   0.263   0.7486  -0.9022   0.2253
 0NV  H11  H  HCR5  0   0.291   0.6855   2.9122   0.2728
 0NV  H12  H  HCR6  0   0.258   5.5803   2.6155  -0.3591
 0NV  H13  H  HCR5  0   0.288   4.6088  -3.7759  -0.1435
 0NV  H14  H  HCR5  0   0.252   2.2576  -2.5274   0.1290
 0NV  H16  H  HCH2  0   0.214  -3.4834  -2.1565   0.8093
 0NV  H17  H  HCH2  0   0.252  -3.8954  -1.0285   2.0912
 0NV  H18  H  HCR6  0   0.244  -4.4230   1.4917   0.7609
 0NV  H19  H  HCR6  0   0.252  -6.3366   2.3677  -0.5272
 0NV  H20  H  HCR6  0   0.253  -7.7701   0.8246  -1.8275
 0NV  H21  H  HCR6  0   0.253  -7.2705  -1.6011  -1.8304
 0NV  H22  H  HCR6  0   0.247  -5.3569  -2.4700  -0.5407
 0NV  H5   H  HNR5  0   0.411   6.3964  -2.0466  -0.3930

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
 0NV  N14  C15  aromatic  1.362  0.020  1.362
 0NV  N14  C13  aromatic  1.362  0.020  1.362
 0NV  N12  C13  aromatic  1.336  0.020  1.336
 0NV  N12  C11  aromatic  1.317  0.020  1.317
 0NV  C15  C16  aromatic  1.368  0.020  1.368
 0NV  C13  C17  aromatic  1.413  0.020  1.413
 0NV  C11  C10  aromatic  1.402  0.020  1.402
 0NV  C16  C17  aromatic  1.425  0.020  1.425
 0NV  C17  C18  aromatic  1.401  0.020  1.401
 0NV  C10  C18  aromatic  1.401  0.020  1.401
 0NV  C10  N9   aromatic  1.375  0.020  1.375
 0NV  C18  N7   aromatic  1.363  0.020  1.363
 0NV  N9   C8   aromatic  1.299  0.020  1.299
 0NV  N7   C8   aromatic  1.366  0.020  1.366
 0NV  N7   C6   single    1.456  0.020  1.456
 0NV  C6   C1   single    1.523  0.020  1.523
 0NV  C6   C5   single    1.523  0.020  1.523
 0NV  C1   C2   single    1.521  0.020  1.521
 0NV  C2   N3   single    1.451  0.020  1.451
 0NV  C5   C4   single    1.521  0.020  1.521
 0NV  C4   N3   single    1.451  0.020  1.451
 0NV  C21  C22  aromatic  1.387  0.020  1.387
 0NV  C21  C20  aromatic  1.394  0.020  1.394
 0NV  N3   C19  single    1.449  0.020  1.449
 0NV  C22  C23  aromatic  1.391  0.020  1.391
 0NV  C19  C20  single    1.507  0.020  1.507
 0NV  C20  C25  aromatic  1.390  0.020  1.390
 0NV  C23  C24  aromatic  1.387  0.020  1.387
 0NV  C25  C24  aromatic  1.390  0.020  1.390
 0NV  C1   H1   single    0.970  0.020  1.090
 0NV  C1   H2   single    0.970  0.020  1.090
 0NV  C2   H3   single    0.970  0.020  1.090
 0NV  C2   H4   single    0.970  0.020  1.090
 0NV  C4   H6   single    0.970  0.020  1.090
 0NV  C4   H7   single    0.970  0.020  1.090
 0NV  C5   H8   single    0.970  0.020  1.090
 0NV  C5   H9   single    0.970  0.020  1.090
 0NV  C6   H10  single    0.970  0.020  1.090
 0NV  C8   H11  single    0.930  0.020  1.080
 0NV  C11  H12  single    0.930  0.020  1.080
 0NV  C15  H13  single    0.930  0.020  1.080
 0NV  C16  H14  single    0.930  0.020  1.080
 0NV  C19  H16  single    0.970  0.020  1.090
 0NV  C19  H17  single    0.970  0.020  1.090
 0NV  C21  H18  single    0.930  0.020  1.080
 0NV  C22  H19  single    0.930  0.020  1.080
 0NV  C23  H20  single    0.930  0.020  1.080
 0NV  C24  H21  single    0.930  0.020  1.080
 0NV  C25  H22  single    0.930  0.020  1.080
 0NV  N14  H5   single    0.860  0.020  1.020

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
 0NV  H2   C1   H1   107.55  3.000
 0NV  H2   C1   C6   110.24  3.000
 0NV  H1   C1   C6   109.97  3.000
 0NV  H2   C1   C2   109.84  3.000
 0NV  H1   C1   C2   109.44  3.000
 0NV  C6   C1   C2   109.76  3.000
 0NV  H4   C2   H3   106.75  3.000
 0NV  H4   C2   N3   108.93  3.000
 0NV  H3   C2   N3   111.74  3.000
 0NV  H4   C2   C1   109.34  3.000
 0NV  H3   C2   C1   109.05  3.000
 0NV  N3   C2   C1   110.92  3.000
 0NV  C19  N3   C4   111.59  3.000
 0NV  C19  N3   C2   111.80  3.000
 0NV  C4   N3   C2   111.11  3.000
 0NV  H7   C4   H6   106.54  3.000
 0NV  H7   C4   C5   109.10  3.000
 0NV  H6   C4   C5   109.51  3.000
 0NV  H7   C4   N3   109.17  3.000
 0NV  H6   C4   N3   111.06  3.000
 0NV  C5   C4   N3   111.32  3.000
 0NV  H9   C5   H8   107.69  3.000
 0NV  H9   C5   C6   110.29  3.000
 0NV  H8   C5   C6   110.31  3.000
 0NV  H9   C5   C4   109.06  3.000
 0NV  H8   C5   C4   109.71  3.000
 0NV  C6   C5   C4   109.75  3.000
 0NV  H10  C6   N7   106.11  3.000
 0NV  H10  C6   C5   107.96  3.000
 0NV  N7   C6   C5   112.14  3.000
 0NV  H10  C6   C1   108.30  3.000
 0NV  C5   C6   C1   110.25  3.000
 0NV  N7   C6   C1   111.87  3.000
 0NV  C18  N7   C8   106.26  3.000
 0NV  C8   N7   C6   126.23  3.000
 0NV  C18  N7   C6   127.50  3.000
 0NV  H11  C8   N9   124.83  3.000
 0NV  H11  C8   N7   121.42  3.000
 0NV  N9   C8   N7   113.75  3.000
 0NV  C10  N9   C8   104.65  3.000
 0NV  C18  C10  C11  120.30  3.000
 0NV  C18  C10  N9   109.97  3.000
 0NV  C11  C10  N9   129.72  3.000
 0NV  H12  C11  N12  117.63  3.000
 0NV  H12  C11  C10  120.51  3.000
 0NV  N12  C11  C10  121.86  3.000
 0NV  C13  N12  C11  116.57  3.000
 0NV  C17  C13  N14  107.17  3.000
 0NV  C17  C13  N12  128.30  3.000
 0NV  N14  C13  N12  124.53  3.000
 0NV  H5   N14  C15  125.51  3.000
 0NV  H5   N14  C13  124.94  3.000
 0NV  C15  N14  C13  109.55  3.000
 0NV  H13  C15  C16  129.44  3.000
 0NV  H13  C15  N14  120.71  3.000
 0NV  C16  C15  N14  109.85  3.000
 0NV  H14  C16  C17  128.32  3.000
 0NV  H14  C16  C15  125.33  3.000
 0NV  C17  C16  C15  106.36  3.000
 0NV  C18  C17  C16  139.57  3.000
 0NV  C18  C17  C13  113.35  3.000
 0NV  C16  C17  C13  107.08  3.000
 0NV  C17  C18  C10  119.62  3.000
 0NV  C10  C18  N7   105.37  3.000
 0NV  C17  C18  N7   135.01  3.000
 0NV  H17  C19  H16  106.12  3.000
 0NV  H17  C19  C20  108.74  3.000
 0NV  H16  C19  C20  109.29  3.000
 0NV  H17  C19  N3   107.88  3.000
 0NV  H16  C19  N3   112.06  3.000
 0NV  C20  C19  N3   112.48  3.000
 0NV  C25  C20  C21  118.72  3.000
 0NV  C25  C20  C19  120.83  3.000
 0NV  C21  C20  C19  120.43  3.000
 0NV  H18  C21  C22  120.02  3.000
 0NV  H18  C21  C20  119.34  3.000
 0NV  C22  C21  C20  120.64  3.000
 0NV  H19  C22  C23  119.93  3.000
 0NV  H19  C22  C21  119.84  3.000
 0NV  C23  C22  C21  120.23  3.000
 0NV  H20  C23  C24  120.29  3.000
 0NV  H20  C23  C22  120.17  3.000
 0NV  C24  C23  C22  119.54  3.000
 0NV  H21  C24  C25  119.83  3.000
 0NV  H21  C24  C23  120.13  3.000
 0NV  C25  C24  C23  120.04  3.000
 0NV  H22  C25  C24  119.69  3.000
 0NV  H22  C25  C20  119.49  3.000
 0NV  C24  C25  C20  120.82  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
 0NV  CONST_01  C13  C17  C18  N7   180.00   0.0  0
 0NV  CONST_02  C16  C17  C18  N7     0.00   0.0  0
 0NV  CONST_03  C11  C10  C18  N7   180.00   0.0  0
 0NV  CONST_04  N9   C10  C18  N7     0.00   0.0  0
 0NV  CONST_05  C10  N9   C8   N7     0.00   0.0  0
 0NV  CONST_06  C11  C10  N9   C8   180.00   0.0  0
 0NV  CONST_07  C18  C10  N9   C8     0.00   0.0  0
 0NV  CONST_08  C17  C18  N7   C8   180.00   0.0  0
 0NV  CONST_09  C10  C18  N7   C8     0.00   0.0  0
 0NV  CONST_10  N12  C11  C10  N9   180.00   0.0  0
 0NV  CONST_11  C17  C18  C10  N9   180.00   0.0  0
 0NV  CONST_12  C18  N7   C8   N9     0.00   0.0  0
 0NV  CONST_13  C13  N12  C11  C10    0.00   0.0  0
 0NV  CONST_14  C13  C17  C18  C10    0.00   0.0  0
 0NV  CONST_15  C16  C17  C18  C10  180.00   0.0  0
 0NV  CONST_16  N14  C13  N12  C11  180.00   0.0  0
 0NV  CONST_17  C17  C13  N12  C11    0.00   0.0  0
 0NV  CONST_18  C17  C18  C10  C11    0.00   0.0  0
 0NV  CONST_19  C15  N14  C13  N12  180.00   0.0  0
 0NV  CONST_20  C16  C17  C13  N12  180.00   0.0  0
 0NV  CONST_21  C18  C17  C13  N12    0.00   0.0  0
 0NV  CONST_22  C18  C10  C11  N12    0.00   0.0  0
 0NV  CONST_23  C16  C15  N14  C13    0.00   0.0  0
 0NV  CONST_24  C15  C16  C17  C13    0.00   0.0  0
 0NV  CONST_25  C17  C16  C15  N14    0.00   0.0  0
 0NV  CONST_26  C16  C17  C13  N14    0.00   0.0  0
 0NV  CONST_27  C18  C17  C13  N14  180.00   0.0  0
 0NV  CONST_28  C17  C13  N14  C15    0.00   0.0  0
 0NV  CONST_29  C18  C17  C16  C15  180.00   0.0  0
 0NV  CONST_30  C23  C22  C21  C20    0.00   0.0  0
 0NV  CONST_31  C23  C24  C25  C20    0.00   0.0  0
 0NV  CONST_32  C24  C23  C22  C21    0.00   0.0  0
 0NV  CONST_33  C24  C25  C20  C21    0.00   0.0  0
 0NV  CONST_34  C25  C20  C21  C22    0.00   0.0  0
 0NV  CONST_35  C25  C24  C23  C22    0.00   0.0  0
 0NV  CONST_36  C17  C18  N7   C6     0.00   0.0  0
 0NV  CONST_37  C10  C18  N7   C6   180.00   0.0  0
 0NV  CONST_38  N9   C8   N7   C6   180.00   0.0  0
 0NV  CONST_39  C22  C21  C20  C19  180.00   0.0  0
 0NV  CONST_40  C24  C25  C20  C19  180.00   0.0  0
 0NV  CONST_41  H11  C8   N7   C6     0.00   0.0  0
 0NV  CONST_42  H12  C11  C10  N9     0.00   0.0  0
 0NV  CONST_43  H5   N14  C13  N12    0.00   0.0  0
 0NV  CONST_44  H13  C15  N14  C13  180.00   0.0  0
 0NV  CONST_45  H14  C16  C17  C13  180.00   0.0  0
 0NV  CONST_46  H19  C22  C21  C20  180.00   0.0  0
 0NV  CONST_47  H21  C24  C25  C20  180.00   0.0  0
 0NV  CONST_48  H20  C23  C22  C21  180.00   0.0  0
 0NV  CONST_49  H22  C25  C20  C21  180.00   0.0  0
 0NV  CONST_50  H18  C21  C22  C23  180.00   0.0  0
 0NV  Var_01    C4   N3   C2   C1    60.29  30.0  1
 0NV  Var_02    C5   C4   N3   C2   -60.04  30.0  1
 0NV  Var_03    C6   C1   C2   N3   -57.56  30.0  1
 0NV  Var_04    C6   C5   C4   N3    56.82  30.0  1
 0NV  Var_05    C20  C19  N3   C2   165.96  30.0  3
 0NV  Var_06    C21  C20  C19  N3   -47.75  30.0  2

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
 0NV  chir_01  C6  N7  C1  C5  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
 0NV  plan-1  C19  0.020
 0NV  plan-1  C20  0.020
 0NV  plan-1  C21  0.020
 0NV  plan-1  C22  0.020
 0NV  plan-1  C23  0.020
 0NV  plan-1  C24  0.020
 0NV  plan-1  C25  0.020
 0NV  plan-1  H18  0.020
 0NV  plan-1  H19  0.020
 0NV  plan-1  H20  0.020
 0NV  plan-1  H21  0.020
 0NV  plan-1  H22  0.020
 0NV  plan-2  C6   0.020
 0NV  plan-2  N7   0.020
 0NV  plan-2  C8   0.020
 0NV  plan-2  N9   0.020
 0NV  plan-2  C10  0.020
 0NV  plan-2  C11  0.020
 0NV  plan-2  N12  0.020
 0NV  plan-2  C13  0.020
 0NV  plan-2  N14  0.020
 0NV  plan-2  C15  0.020
 0NV  plan-2  C16  0.020
 0NV  plan-2  C17  0.020
 0NV  plan-2  C18  0.020
 0NV  plan-2  H11  0.020
 0NV  plan-2  H12  0.020
 0NV  plan-2  H13  0.020
 0NV  plan-2  H14  0.020
 0NV  plan-2  H5   0.020

