# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 12:16:21 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: [4-(imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl)piperidin-1-yl][(2S)-1-(propan-2-yl)pyrrolidin-2-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)N1CCC[C@H]1C(=O)N2CC[C@@H](CC2)n3cnc4cnc5[nH]ccc5c34
#
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
 0NT  0NT  '[4-(imidazo[4,5-d]pyrrolo[2,3-b]pyridin-1(6H)-yl)piperidin-1-yl][(2S)-1-(propan-2-yl)pyrrolidin-2-yl]methanone'  ligand  56  28  .  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_0NT
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
 0NT  C7   C  CH2   0  -0.477  -4.2455   2.1240  -0.8812
 0NT  C2   C  CH1   0  -0.062  -5.1637  -1.3904  -0.6636
 0NT  C10  C  C     0   0.562  -3.0171   0.6992   0.8018
 0NT  C6   C  CH2   0  -0.449  -5.7114   2.2432  -0.4847
 0NT  C1   C  CH3   0  -0.670  -4.0603  -2.1995   0.0103
 0NT  C3   C  CH3   0  -0.676  -6.5141  -2.0295  -0.3618
 0NT  N4   N  NR5   0  -0.406  -5.1381  -0.0018  -0.2305
 0NT  C5   C  CH2   0  -0.271  -6.2158   0.8354  -0.7345
 0NT  C8   C  CR15  0  -0.226  -3.8770   0.6805  -0.4637
 0NT  O11  O  O     0  -0.488  -3.5169   0.5404   1.9037
 0NT  N12  N  NT    0  -0.456  -1.6917   0.9380   0.6446
 0NT  C13  C  CH2   0  -0.331  -1.0129   1.2206  -0.6060
 0NT  C14  C  CH2   0  -0.420   0.0656   0.1799  -0.8821
 0NT  C15  C  CH1   0  -0.127   1.0362   0.1135   0.2923
 0NT  C16  C  CH2   0  -0.429   0.2909  -0.1270   1.6008
 0NT  C17  C  CH2   0  -0.318  -0.7931   0.9290   1.7849
 0NT  N18  N  NR5   0  -0.523   2.0766  -0.8799   0.0720
 0NT  C19  C  CR15  0   0.085   1.8910  -2.2264  -0.0749
 0NT  N20  N  N     0  -0.457   2.9911  -2.8864  -0.2743
 0NT  C21  C  CR56  0   0.005   3.9792  -1.9294  -0.2614
 0NT  C22  C  CR56  0   0.369   3.4176  -0.6646  -0.0437
 0NT  C23  C  CR56  0   0.007   4.2474   0.4618   0.0116
 0NT  C24  C  CR15  0  -0.459   4.1522   1.8706   0.2046
 0NT  C25  C  CR15  0  -0.006   5.4294   2.3559   0.1339
 0NT  N26  N  NR15  0  -0.654   6.3010   1.3337  -0.0909
 0NT  C28  C  CR56  0   0.420   5.6153   0.1589  -0.1711
 0NT  N29  N  N     0  -0.432   6.1776  -1.0337  -0.3832
 0NT  C30  C  CR16  0  -0.136   5.3647  -2.0686  -0.4276
 0NT  H1   H  HCH2  0   0.248  -4.1365   2.2281  -1.9622
 0NT  H2   H  HCH2  0   0.255  -3.6113   2.8829  -0.4209
 0NT  H3   H  HCH1  0   0.184  -5.0021  -1.4462  -1.7573
 0NT  H4   H  HCH2  0   0.232  -5.8089   2.4981   0.5727
 0NT  H5   H  HCH2  0   0.241  -6.2481   2.9940  -1.0638
 0NT  H6   H  HCH3  0   0.225  -4.1619  -2.1611   1.0952
 0NT  H7   H  HCH3  0   0.233  -4.1228  -3.2423  -0.3020
 0NT  H8   H  HCH3  0   0.221  -3.0595  -1.8495  -0.2491
 0NT  H10  H  HCH3  0   0.220  -6.7391  -1.9663   0.7048
 0NT  H11  H  HCH3  0   0.236  -7.3315  -1.5628  -0.9109
 0NT  H12  H  HCH3  0   0.231  -6.4966  -3.0837  -0.6397
 0NT  H14  H  HCH2  0   0.234  -7.1545   0.6280  -0.2175
 0NT  H15  H  HCH2  0   0.188  -6.3956   0.6864  -1.8129
 0NT  H9   H  HCR5  0   0.254  -3.3267   0.1955  -1.2797
 0NT  H16  H  HCH2  0   0.281  -1.7068   1.2610  -1.4389
 0NT  H17  H  HCH2  0   0.253  -0.5584   2.2156  -0.5404
 0NT  H18  H  HCH2  0   0.239  -0.4081  -0.7936  -1.0400
 0NT  H19  H  HCH2  0   0.264   0.5976   0.4402  -1.7986
 0NT  H20  H  HCH1  0   0.270   1.5477   1.0754   0.3632
 0NT  H21  H  HCH2  0   0.239  -0.1689  -1.1198   1.5963
 0NT  H22  H  HCH2  0   0.263   0.9852  -0.0897   2.4421
 0NT  H23  H  HCH2  0   0.244  -0.3325   1.9182   1.8851
 0NT  H24  H  HCH2  0   0.274  -1.3574   0.7407   2.6929
 0NT  H25  H  HCR5  0   0.290   0.9067  -2.6688  -0.0221
 0NT  H26  H  HCR5  0   0.252   3.2699   2.4649   0.3758
 0NT  H28  H  HCR5  0   0.288   5.7823   3.3696   0.2295
 0NT  H27  H  HNR5  0   0.411   7.2997   1.4266  -0.1789
 0NT  H29  H  HCR6  0   0.259   5.8022  -3.0462  -0.6003

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
 0NT  N20  C21  aromatic  1.376  0.020  1.376
 0NT  N20  C19  aromatic  1.298  0.020  1.298
 0NT  C30  C21  aromatic  1.402  0.020  1.402
 0NT  C30  N29  aromatic  1.317  0.020  1.317
 0NT  C21  C22  aromatic  1.401  0.020  1.401
 0NT  C19  N18  aromatic  1.367  0.020  1.367
 0NT  N29  C28  aromatic  1.335  0.020  1.335
 0NT  C14  C15  single    1.525  0.020  1.525
 0NT  C14  C13  single    1.524  0.020  1.524
 0NT  C22  N18  aromatic  1.363  0.020  1.363
 0NT  C22  C23  aromatic  1.400  0.020  1.400
 0NT  N18  C15  single    1.455  0.020  1.455
 0NT  C28  C23  aromatic  1.413  0.020  1.413
 0NT  C28  N26  aromatic  1.363  0.020  1.363
 0NT  C23  C24  aromatic  1.425  0.020  1.425
 0NT  C6   C7   single    1.523  0.020  1.523
 0NT  C6   C5   single    1.516  0.020  1.516
 0NT  O11  C10  double    1.220  0.020  1.220
 0NT  N26  C25  aromatic  1.362  0.020  1.362
 0NT  C15  C16  single    1.525  0.020  1.525
 0NT  C13  N12  single    1.451  0.020  1.451
 0NT  C7   C8   single    1.547  0.020  1.547
 0NT  C24  C25  aromatic  1.368  0.020  1.368
 0NT  C10  N12  single    1.356  0.020  1.356
 0NT  C10  C8   single    1.530  0.020  1.530
 0NT  N12  C17  single    1.452  0.020  1.452
 0NT  C16  C17  single    1.524  0.020  1.524
 0NT  C5   N4   single    1.455  0.020  1.455
 0NT  C8   N4   single    1.453  0.020  1.453
 0NT  N4   C2   single    1.455  0.020  1.455
 0NT  C1   C2   single    1.525  0.020  1.525
 0NT  C2   C3   single    1.524  0.020  1.524
 0NT  C7   H1   single    0.970  0.020  1.090
 0NT  C7   H2   single    0.970  0.020  1.090
 0NT  C2   H3   single    0.970  0.020  1.090
 0NT  C6   H4   single    0.970  0.020  1.090
 0NT  C6   H5   single    0.970  0.020  1.090
 0NT  C1   H6   single    0.970  0.020  1.090
 0NT  C1   H7   single    0.970  0.020  1.090
 0NT  C1   H8   single    0.970  0.020  1.090
 0NT  C3   H10  single    0.970  0.020  1.090
 0NT  C3   H11  single    0.970  0.020  1.090
 0NT  C3   H12  single    0.970  0.020  1.090
 0NT  C5   H14  single    0.970  0.020  1.090
 0NT  C5   H15  single    0.970  0.020  1.090
 0NT  C8   H9   single    0.970  0.020  1.090
 0NT  C13  H16  single    0.970  0.020  1.090
 0NT  C13  H17  single    0.970  0.020  1.090
 0NT  C14  H18  single    0.970  0.020  1.090
 0NT  C14  H19  single    0.970  0.020  1.090
 0NT  C15  H20  single    0.970  0.020  1.090
 0NT  C16  H21  single    0.970  0.020  1.090
 0NT  C16  H22  single    0.970  0.020  1.090
 0NT  C17  H23  single    0.970  0.020  1.090
 0NT  C17  H24  single    0.970  0.020  1.090
 0NT  C19  H25  single    0.930  0.020  1.080
 0NT  C24  H26  single    0.930  0.020  1.080
 0NT  C25  H28  single    0.930  0.020  1.080
 0NT  N26  H27  single    0.860  0.020  1.020
 0NT  C30  H29  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
 0NT  H2   C7   H1   107.07  3.000
 0NT  H2   C7   C8   113.37  3.000
 0NT  H1   C7   C8   109.41  3.000
 0NT  H2   C7   C6   113.28  3.000
 0NT  H1   C7   C6   110.27  3.000
 0NT  C8   C7   C6   103.41  3.000
 0NT  H3   C2   N4   109.85  3.000
 0NT  H3   C2   C3   107.69  3.000
 0NT  N4   C2   C3   110.91  3.000
 0NT  H3   C2   C1   107.72  3.000
 0NT  C3   C2   C1   109.33  3.000
 0NT  N4   C2   C1   111.23  3.000
 0NT  N12  C10  O11  121.86  3.000
 0NT  N12  C10  C8   117.10  3.000
 0NT  O11  C10  C8   121.01  3.000
 0NT  H5   C6   H4   108.05  3.000
 0NT  H5   C6   C5   112.86  3.000
 0NT  H4   C6   C5   110.28  3.000
 0NT  H5   C6   C7   112.93  3.000
 0NT  H4   C6   C7   110.87  3.000
 0NT  C5   C6   C7   101.81  3.000
 0NT  H8   C1   H7   106.93  3.000
 0NT  H8   C1   H6   108.10  3.000
 0NT  H7   C1   H6   108.26  3.000
 0NT  H8   C1   C2   112.84  3.000
 0NT  H7   C1   C2   109.83  3.000
 0NT  H6   C1   C2   110.70  3.000
 0NT  H12  C3   H11  107.32  3.000
 0NT  H12  C3   H10  107.96  3.000
 0NT  H11  C3   H10  108.23  3.000
 0NT  H12  C3   C2   109.92  3.000
 0NT  H11  C3   C2   112.66  3.000
 0NT  H10  C3   C2   110.59  3.000
 0NT  C8   N4   C5   108.50  3.000
 0NT  C8   N4   C2   114.57  3.000
 0NT  C5   N4   C2   115.67  3.000
 0NT  H15  C5   H14  107.28  3.000
 0NT  H15  C5   N4   112.43  3.000
 0NT  H14  C5   N4   111.32  3.000
 0NT  H15  C5   C6   109.92  3.000
 0NT  H14  C5   C6   112.62  3.000
 0NT  N4   C5   C6   103.35  3.000
 0NT  H9   C8   N4   110.32  3.000
 0NT  H9   C8   C10  109.80  3.000
 0NT  N4   C8   C10  111.15  3.000
 0NT  H9   C8   C7   109.34  3.000
 0NT  N4   C8   C7   105.94  3.000
 0NT  C10  C8   C7   110.22  3.000
 0NT  C17  N12  C13  112.87  3.000
 0NT  C17  N12  C10  120.86  3.000
 0NT  C13  N12  C10  126.27  3.000
 0NT  H17  C13  H16  106.10  3.000
 0NT  H17  C13  C14  109.71  3.000
 0NT  H16  C13  C14  109.82  3.000
 0NT  H17  C13  N12  108.63  3.000
 0NT  H16  C13  N12  111.71  3.000
 0NT  C14  C13  N12  110.75  3.000
 0NT  H19  C14  H18  107.59  3.000
 0NT  H19  C14  C15  110.29  3.000
 0NT  H18  C14  C15  110.36  3.000
 0NT  H19  C14  C13  109.53  3.000
 0NT  H18  C14  C13  109.11  3.000
 0NT  C15  C14  C13  109.91  3.000
 0NT  H20  C15  N18  106.04  3.000
 0NT  H20  C15  C16  108.19  3.000
 0NT  N18  C15  C16  111.82  3.000
 0NT  H20  C15  C14  108.05  3.000
 0NT  C16  C15  C14  110.89  3.000
 0NT  N18  C15  C14  111.60  3.000
 0NT  H22  C16  H21  107.55  3.000
 0NT  H22  C16  C17  109.61  3.000
 0NT  H21  C16  C17  109.28  3.000
 0NT  H22  C16  C15  110.19  3.000
 0NT  H21  C16  C15  110.18  3.000
 0NT  C17  C16  C15  109.99  3.000
 0NT  H24  C17  H23  107.37  3.000
 0NT  H24  C17  C16  110.52  3.000
 0NT  H23  C17  C16  109.72  3.000
 0NT  H24  C17  N12  109.65  3.000
 0NT  H23  C17  N12  109.05  3.000
 0NT  C16  C17  N12  110.47  3.000
 0NT  C22  N18  C19  106.26  3.000
 0NT  C22  N18  C15  127.47  3.000
 0NT  C19  N18  C15  126.27  3.000
 0NT  H25  C19  N20  124.84  3.000
 0NT  H25  C19  N18  121.45  3.000
 0NT  N20  C19  N18  113.71  3.000
 0NT  C21  N20  C19  104.68  3.000
 0NT  C30  C21  C22  120.28  3.000
 0NT  C22  C21  N20  109.97  3.000
 0NT  C30  C21  N20  129.75  3.000
 0NT  C23  C22  C21  119.66  3.000
 0NT  C23  C22  N18  134.97  3.000
 0NT  C21  C22  N18  105.37  3.000
 0NT  C28  C23  C24  107.11  3.000
 0NT  C24  C23  C22  139.55  3.000
 0NT  C28  C23  C22  113.34  3.000
 0NT  H26  C24  C25  125.24  3.000
 0NT  H26  C24  C23  128.42  3.000
 0NT  C25  C24  C23  106.34  3.000
 0NT  H28  C25  N26  120.74  3.000
 0NT  H28  C25  C24  129.41  3.000
 0NT  N26  C25  C24  109.85  3.000
 0NT  H27  N26  C28  125.00  3.000
 0NT  H27  N26  C25  125.44  3.000
 0NT  C28  N26  C25  109.56  3.000
 0NT  N29  C28  N26  124.57  3.000
 0NT  N26  C28  C23  107.14  3.000
 0NT  N29  C28  C23  128.29  3.000
 0NT  C30  N29  C28  116.57  3.000
 0NT  H29  C30  N29  117.68  3.000
 0NT  H29  C30  C21  120.45  3.000
 0NT  N29  C30  C21  121.86  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
 0NT  CONST_01  C21  N20  C19  N18     0.00   0.0  0
 0NT  CONST_02  N20  C21  C22  N18     0.00   0.0  0
 0NT  CONST_03  C30  C21  C22  N18   180.00   0.0  0
 0NT  CONST_04  C28  C23  C22  N18   180.00   0.0  0
 0NT  CONST_05  C24  C23  C22  N18     0.00   0.0  0
 0NT  CONST_06  C30  C21  N20  C19   180.00   0.0  0
 0NT  CONST_07  C22  C21  N20  C19     0.00   0.0  0
 0NT  CONST_08  C21  C22  N18  C19     0.00   0.0  0
 0NT  CONST_09  C23  C22  N18  C19   180.00   0.0  0
 0NT  CONST_10  N29  C30  C21  N20   180.00   0.0  0
 0NT  CONST_11  C23  C22  C21  N20   180.00   0.0  0
 0NT  CONST_12  C22  N18  C19  N20     0.00   0.0  0
 0NT  CONST_13  C28  N29  C30  C21     0.00   0.0  0
 0NT  CONST_14  C28  C23  C22  C21     0.00   0.0  0
 0NT  CONST_15  C24  C23  C22  C21   180.00   0.0  0
 0NT  CONST_16  N29  C30  C21  C22     0.00   0.0  0
 0NT  CONST_17  N29  C28  C23  C22     0.00   0.0  0
 0NT  CONST_18  N26  C28  C23  C22   180.00   0.0  0
 0NT  CONST_19  C25  C24  C23  C22   180.00   0.0  0
 0NT  CONST_20  C30  C21  C22  C23     0.00   0.0  0
 0NT  CONST_21  C30  N29  C28  C23     0.00   0.0  0
 0NT  CONST_22  C25  N26  C28  C23     0.00   0.0  0
 0NT  CONST_23  N26  C25  C24  C23     0.00   0.0  0
 0NT  CONST_24  N29  C28  C23  C24   180.00   0.0  0
 0NT  CONST_25  N26  C28  C23  C24     0.00   0.0  0
 0NT  CONST_26  C28  N26  C25  C24     0.00   0.0  0
 0NT  CONST_27  N29  C28  N26  C25   180.00   0.0  0
 0NT  CONST_28  C28  C23  C24  C25     0.00   0.0  0
 0NT  CONST_29  C30  N29  C28  N26   180.00   0.0  0
 0NT  CONST_30  N20  C19  N18  C15   180.00   0.0  0
 0NT  CONST_31  C21  C22  N18  C15   180.00   0.0  0
 0NT  CONST_32  C23  C22  N18  C15     0.00   0.0  0
 0NT  CONST_33  C13  N12  C10  C8      0.00   0.0  0
 0NT  CONST_34  C17  N12  C10  C8    180.00   0.0  0
 0NT  CONST_35  H25  C19  N18  C15     0.00   0.0  0
 0NT  CONST_36  H29  C30  C21  N20     0.00   0.0  0
 0NT  CONST_37  H26  C24  C23  C22     0.00   0.0  0
 0NT  CONST_38  H27  N26  C28  C23   180.00   0.0  0
 0NT  CONST_39  H28  C25  C24  C23   180.00   0.0  0
 0NT  CONST_40  C13  N12  C10  O11   180.00   0.0  0
 0NT  CONST_41  C17  N12  C10  O11     0.00   0.0  0
 0NT  Var_01    N4   C5   C6   C7     41.34  30.0  1
 0NT  Var_02    C8   N4   C5   C6    -33.25  30.0  1
 0NT  Var_03    C8   C7   C6   C5    -33.92  30.0  1
 0NT  Var_04    C15  C14  C13  N12   -55.72  30.0  1
 0NT  Var_05    C15  C16  C17  N12    56.03  30.0  1
 0NT  Var_06    C16  C17  N12  C13   -59.53  30.0  1
 0NT  Var_07    C17  N12  C13  C14    59.47  30.0  1
 0NT  Var_08    C5   N4   C2   C1   -175.39  30.0  2
 0NT  Var_09    H6   C1   C2   N4     58.45  30.0  3
 0NT  Var_10    H10  C3   C2   N4    -57.65  30.0  3

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
 0NT  chir_01  C8   C7   C10  N4   negativ
 0NT  chir_02  C15  N18  C14  C16  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
 0NT  plan-1  C10  0.020
 0NT  plan-1  C8   0.020
 0NT  plan-1  O11  0.020
 0NT  plan-1  N12  0.020
 0NT  plan-1  C13  0.020
 0NT  plan-1  C17  0.020
 0NT  plan-2  C15  0.020
 0NT  plan-2  N18  0.020
 0NT  plan-2  C19  0.020
 0NT  plan-2  N20  0.020
 0NT  plan-2  C21  0.020
 0NT  plan-2  C22  0.020
 0NT  plan-2  C23  0.020
 0NT  plan-2  C24  0.020
 0NT  plan-2  C25  0.020
 0NT  plan-2  N26  0.020
 0NT  plan-2  C28  0.020
 0NT  plan-2  N29  0.020
 0NT  plan-2  C30  0.020
 0NT  plan-2  H25  0.020
 0NT  plan-2  H26  0.020
 0NT  plan-2  H28  0.020
 0NT  plan-2  H27  0.020
 0NT  plan-2  H29  0.020

