# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 23:51:59 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 4-[(2~{R})-2-phenylpyrrolidin-1-yl]-1~{H}-pyrrolo[2,3-b]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C[C@@H](N(C1)c2ccnc3[nH]ccc23)c4ccccc4
#
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
 C8Z  C8Z  4-[(2~{R})-2-phenylpyrrolidin-1-yl]-1~{H}-pyrrolo[2,3-b]pyridine  ligand  37  20  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C8Z
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
 C8Z  C1   C  CR56  0   0.435  -2.9828  -0.5820   0.3417
 C8Z  C2   C  CR56  0  -0.065  -1.6102  -0.2614   0.4566
 C8Z  C3   C  CR15  0  -0.431  -0.9952  -1.3767   1.1190
 C8Z  C7   C  CH2   0  -0.484   1.9232   2.8825  -0.2851
 C8Z  C8   C  CH2   0  -0.450   2.0982   2.0388   0.9690
 C8Z  C9   C  CH1   0  -0.163   1.1643   0.8480   0.7133
 C8Z  C10  C  CR6   0   0.115   1.8639  -0.2576  -0.0509
 C8Z  C11  C  CR16  0  -0.286   2.7762  -1.0675   0.6239
 C8Z  C12  C  CR16  0  -0.246   3.4615  -2.0734  -0.0399
 C8Z  C13  C  CR16  0  -0.269   3.2428  -2.2865  -1.3962
 C8Z  C14  C  CR16  0  -0.239   2.3340  -1.4873  -2.0742
 C8Z  C15  C  CR16  0  -0.302   1.6469  -0.4805  -1.4048
 C8Z  C16  C  CR16  0  -0.472  -2.2155   1.7461  -0.6800
 C8Z  N1   N  NR15  0  -0.663  -3.1730  -1.8024   0.9090
 C8Z  C5   C  CR6   0   0.433  -1.1970   0.9878  -0.0726
 C8Z  C4   C  CR15  0  -0.022  -1.9806  -2.2822   1.3737
 C8Z  N2   N  NT    0  -0.529   0.0709   1.4598  -0.0198
 C8Z  C6   C  CH2   0  -0.284   0.4322   2.7598  -0.5719
 C8Z  C17  C  CR16  0  -0.091  -3.5274   1.2881  -0.7194
 C8Z  N3   N  N     0  -0.458  -3.9511   0.1388  -0.2175
 C8Z  H1   H  HCR5  0   0.250   0.0415  -1.5250   1.3651
 C8Z  H2   H  HCH2  0   0.258   2.2260   3.9194  -0.1478
 C8Z  H3   H  HCH2  0   0.242   2.5075   2.4718  -1.1111
 C8Z  H4   H  HCH2  0   0.257   3.1260   1.7286   1.1525
 C8Z  H5   H  HCH2  0   0.248   1.7510   2.5869   1.8477
 C8Z  H6   H  HCH1  0   0.270   0.8073   0.4542   1.6682
 C8Z  H7   H  HCR6  0   0.252   2.9499  -0.9112   1.6831
 C8Z  H8   H  HCR6  0   0.254   4.1644  -2.6929   0.5023
 C8Z  H9   H  HCR6  0   0.254   3.7739  -3.0715  -1.9186
 C8Z  H10  H  HCR6  0   0.254   2.1536  -1.6474  -3.1296
 C8Z  H11  H  HCR6  0   0.249   0.9346   0.1277  -1.9478
 C8Z  H12  H  HCR6  0   0.268  -2.0018   2.7070  -1.1238
 C8Z  H13  H  HNR5  0   0.405  -4.0603  -2.2730   0.9756
 C8Z  H14  H  HCR5  0   0.280  -1.9216  -3.2450   1.8542
 C8Z  H15  H  HCH2  0   0.239  -0.1330   3.5589  -0.0791
 C8Z  H16  H  HCH2  0   0.247   0.2120   2.8151  -1.6409
 C8Z  H17  H  HCR6  0   0.245  -4.2785   1.9133  -1.1914

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
 C8Z  C7   C6   single    1.523  0.020  1.523
 C8Z  C7   C8   single    1.522  0.020  1.522
 C8Z  C6   N2   single    1.458  0.020  1.458
 C8Z  C8   C9   single    1.535  0.020  1.535
 C8Z  C16  C17  aromatic  1.390  0.020  1.390
 C8Z  C16  C5   aromatic  1.408  0.020  1.408
 C8Z  N2   C9   single    1.452  0.020  1.452
 C8Z  N2   C5   single    1.354  0.020  1.354
 C8Z  C17  N3   aromatic  1.324  0.020  1.324
 C8Z  C9   C10  single    1.515  0.020  1.515
 C8Z  C5   C2   aromatic  1.418  0.020  1.418
 C8Z  N3   C1   aromatic  1.330  0.020  1.330
 C8Z  C2   C1   aromatic  1.414  0.020  1.414
 C8Z  C2   C3   aromatic  1.436  0.020  1.436
 C8Z  C10  C11  aromatic  1.394  0.020  1.394
 C8Z  C10  C15  aromatic  1.389  0.020  1.389
 C8Z  C1   N1   aromatic  1.359  0.020  1.359
 C8Z  C11  C12  aromatic  1.386  0.020  1.386
 C8Z  C15  C14  aromatic  1.391  0.020  1.391
 C8Z  C3   C4   aromatic  1.362  0.020  1.362
 C8Z  N1   C4   aromatic  1.367  0.020  1.367
 C8Z  C12  C13  aromatic  1.390  0.020  1.390
 C8Z  C14  C13  aromatic  1.387  0.020  1.387
 C8Z  C3   H1   single    0.930  0.020  1.080
 C8Z  C7   H2   single    0.970  0.020  1.090
 C8Z  C7   H3   single    0.970  0.020  1.090
 C8Z  C8   H4   single    0.970  0.020  1.090
 C8Z  C8   H5   single    0.970  0.020  1.090
 C8Z  C9   H6   single    0.970  0.020  1.090
 C8Z  C11  H7   single    0.930  0.020  1.080
 C8Z  C12  H8   single    0.930  0.020  1.080
 C8Z  C13  H9   single    0.930  0.020  1.080
 C8Z  C14  H10  single    0.930  0.020  1.080
 C8Z  C15  H11  single    0.930  0.020  1.080
 C8Z  C16  H12  single    0.930  0.020  1.080
 C8Z  N1   H13  single    0.860  0.020  1.020
 C8Z  C4   H14  single    0.930  0.020  1.080
 C8Z  C6   H15  single    0.970  0.020  1.090
 C8Z  C6   H16  single    0.970  0.020  1.090
 C8Z  C17  H17  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
 C8Z  N3   C1   N1   124.06  3.000
 C8Z  N1   C1   C2   107.79  3.000
 C8Z  N3   C1   C2   128.15  3.000
 C8Z  C5   C2   C3   137.02  3.000
 C8Z  C3   C2   C1   106.09  3.000
 C8Z  C5   C2   C1   116.88  3.000
 C8Z  H1   C3   C4   124.24  3.000
 C8Z  H1   C3   C2   128.72  3.000
 C8Z  C4   C3   C2   107.02  3.000
 C8Z  H3   C7   H2   107.74  3.000
 C8Z  H3   C7   C6   110.55  3.000
 C8Z  H2   C7   C6   111.88  3.000
 C8Z  H3   C7   C8   110.69  3.000
 C8Z  H2   C7   C8   113.09  3.000
 C8Z  C6   C7   C8   102.89  3.000
 C8Z  H5   C8   H4   107.90  3.000
 C8Z  H5   C8   C9   109.27  3.000
 C8Z  H4   C8   C9   112.42  3.000
 C8Z  H5   C8   C7   110.38  3.000
 C8Z  H4   C8   C7   113.91  3.000
 C8Z  C9   C8   C7   102.88  3.000
 C8Z  H6   C9   N2   110.31  3.000
 C8Z  H6   C9   C10  109.18  3.000
 C8Z  N2   C9   C10  113.62  3.000
 C8Z  H6   C9   C8   109.43  3.000
 C8Z  C10  C9   C8   111.67  3.000
 C8Z  N2   C9   C8   102.45  3.000
 C8Z  C15  C10  C11  118.73  3.000
 C8Z  C15  C10  C9   122.44  3.000
 C8Z  C11  C10  C9   118.81  3.000
 C8Z  H7   C11  C12  119.54  3.000
 C8Z  H7   C11  C10  119.59  3.000
 C8Z  C12  C11  C10  120.87  3.000
 C8Z  H8   C12  C13  120.21  3.000
 C8Z  H8   C12  C11  119.75  3.000
 C8Z  C13  C12  C11  120.03  3.000
 C8Z  H9   C13  C14  120.23  3.000
 C8Z  H9   C13  C12  120.32  3.000
 C8Z  C14  C13  C12  119.45  3.000
 C8Z  H10  C14  C15  119.60  3.000
 C8Z  H10  C14  C13  120.03  3.000
 C8Z  C15  C14  C13  120.37  3.000
 C8Z  H11  C15  C14  119.36  3.000
 C8Z  H11  C15  C10  120.09  3.000
 C8Z  C14  C15  C10  120.54  3.000
 C8Z  H12  C16  C17  117.93  3.000
 C8Z  H12  C16  C5   120.90  3.000
 C8Z  C17  C16  C5   121.17  3.000
 C8Z  H13  N1   C4   125.62  3.000
 C8Z  H13  N1   C1   124.80  3.000
 C8Z  C4   N1   C1   109.57  3.000
 C8Z  N2   C5   C16  120.44  3.000
 C8Z  N2   C5   C2   124.43  3.000
 C8Z  C16  C5   C2   115.13  3.000
 C8Z  H14  C4   N1   120.86  3.000
 C8Z  H14  C4   C3   129.61  3.000
 C8Z  N1   C4   C3   109.52  3.000
 C8Z  C6   N2   C5   121.88  3.000
 C8Z  C5   N2   C9   125.32  3.000
 C8Z  C6   N2   C9   112.36  3.000
 C8Z  H16  C6   H15  107.41  3.000
 C8Z  H16  C6   N2   111.45  3.000
 C8Z  H15  C6   N2   110.62  3.000
 C8Z  H16  C6   C7   112.16  3.000
 C8Z  H15  C6   C7   111.19  3.000
 C8Z  N2   C6   C7   104.07  3.000
 C8Z  H17  C17  N3   116.33  3.000
 C8Z  H17  C17  C16  118.40  3.000
 C8Z  N3   C17  C16  125.26  3.000
 C8Z  C17  N3   C1   113.38  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
 C8Z  CONST_01  C16  C17  N3   C1      0.00   0.0  0
 C8Z  CONST_02  C16  C5   C2   C1      0.00   0.0  0
 C8Z  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 C8Z  CONST_04  C3   C4   N1   C1      0.00   0.0  0
 C8Z  CONST_05  C17  C16  C5   C2      0.00   0.0  0
 C8Z  CONST_06  C17  N3   C1   C2      0.00   0.0  0
 C8Z  CONST_07  C4   N1   C1   C2      0.00   0.0  0
 C8Z  CONST_08  N1   C4   C3   C2      0.00   0.0  0
 C8Z  CONST_09  C16  C5   C2   C3    180.00   0.0  0
 C8Z  CONST_10  N3   C1   C2   C3    180.00   0.0  0
 C8Z  CONST_11  N1   C1   C2   C3      0.00   0.0  0
 C8Z  CONST_12  C13  C12  C11  C10     0.00   0.0  0
 C8Z  CONST_13  C13  C14  C15  C10     0.00   0.0  0
 C8Z  CONST_14  C14  C15  C10  C11     0.00   0.0  0
 C8Z  CONST_15  C14  C13  C12  C11     0.00   0.0  0
 C8Z  CONST_16  C15  C10  C11  C12     0.00   0.0  0
 C8Z  CONST_17  C15  C14  C13  C12     0.00   0.0  0
 C8Z  CONST_18  C17  N3   C1   N1    180.00   0.0  0
 C8Z  CONST_19  C5   C2   C1   N1    180.00   0.0  0
 C8Z  CONST_20  N3   C17  C16  C5      0.00   0.0  0
 C8Z  CONST_21  N3   C1   C2   C5      0.00   0.0  0
 C8Z  CONST_22  C4   C3   C2   C5    180.00   0.0  0
 C8Z  CONST_23  N3   C1   N1   C4    180.00   0.0  0
 C8Z  CONST_24  N2   C5   C2   C1    180.00   0.0  0
 C8Z  CONST_25  N2   C5   C2   C3      0.00   0.0  0
 C8Z  CONST_26  C12  C11  C10  C9    180.00   0.0  0
 C8Z  CONST_27  C14  C15  C10  C9    180.00   0.0  0
 C8Z  CONST_28  C17  C16  C5   N2    180.00   0.0  0
 C8Z  CONST_29  H17  C17  N3   C1    180.00   0.0  0
 C8Z  CONST_30  H1   C3   C2   C1    180.00   0.0  0
 C8Z  CONST_31  H14  C4   N1   C1    180.00   0.0  0
 C8Z  CONST_32  H12  C16  C5   C2    180.00   0.0  0
 C8Z  CONST_33  H13  N1   C1   C2    180.00   0.0  0
 C8Z  CONST_34  H7   C11  C10  C9      0.00   0.0  0
 C8Z  CONST_35  H11  C15  C10  C9      0.00   0.0  0
 C8Z  CONST_36  H8   C12  C11  C10   180.00   0.0  0
 C8Z  CONST_37  H10  C14  C15  C10   180.00   0.0  0
 C8Z  CONST_38  H9   C13  C12  C11   180.00   0.0  0
 C8Z  Var_01    C6   N2   C5   C2   -179.42  30.0  2
 C8Z  Var_02    N2   C6   C7   C8    -28.33  30.0  1
 C8Z  Var_03    C6   C7   C8   C9     38.93  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
 C8Z  chir_01  C9  C8  N2  C10  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
 C8Z  plan-1  C9   0.020
 C8Z  plan-1  C10  0.020
 C8Z  plan-1  C11  0.020
 C8Z  plan-1  C12  0.020
 C8Z  plan-1  C13  0.020
 C8Z  plan-1  C14  0.020
 C8Z  plan-1  C15  0.020
 C8Z  plan-1  H7   0.020
 C8Z  plan-1  H8   0.020
 C8Z  plan-1  H9   0.020
 C8Z  plan-1  H10  0.020
 C8Z  plan-1  H11  0.020
 C8Z  plan-2  C1   0.020
 C8Z  plan-2  C2   0.020
 C8Z  plan-2  C3   0.020
 C8Z  plan-2  C16  0.020
 C8Z  plan-2  N1   0.020
 C8Z  plan-2  C5   0.020
 C8Z  plan-2  C4   0.020
 C8Z  plan-2  N2   0.020
 C8Z  plan-2  C17  0.020
 C8Z  plan-2  N3   0.020
 C8Z  plan-2  H1   0.020
 C8Z  plan-2  H12  0.020
 C8Z  plan-2  H13  0.020
 C8Z  plan-2  H14  0.020
 C8Z  plan-2  H17  0.020

