# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 12:22:27 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: [(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1n[nH]c2ncc(cc12)C(=O)N3CCC[C@H]3c4ccc(Cl)cc4
#
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
 6A7  6A7  '[(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](3-methyl-1H-pyrazolo[3,4-b]pyridin-5-yl)methanone'  ligand  41  24  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6A7
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
 6A7  C2   C   CR6   0  -0.058  -4.6321  -1.1864  -0.3978
 6A7  C3   C   CR16  0  -0.197  -4.6146  -0.7192   0.9056
 6A7  C4   C   CR16  0  -0.331  -3.6464   0.2037   1.2763
 6A7  C5   C   CR6   0   0.182  -2.7078   0.6682   0.3642
 6A7  C6   C   CR16  0  -0.307  -2.7502   0.1845  -0.9400
 6A7  C7   C   CR16  0  -0.198  -3.7037  -0.7433  -1.3283
 6A7  C8   C   CR15  0  -0.119  -1.7024   1.7111   0.7738
 6A7  C11  C   CH2   0  -0.470  -0.6545   3.7639   0.1096
 6A7  C12  C   CH2   0  -0.286   0.2056   2.6248  -0.4198
 6A7  N13  N   NR5   0  -0.498  -0.3633   1.4495   0.2445
 6A7  C16  C   CR6   0  -0.161   1.6551   0.1070   0.0797
 6A7  C17  C   CR16  0  -0.237   2.6730  -0.3598   0.8955
 6A7  C18  C   CR56  0  -0.119   3.8883  -0.6496   0.2902
 6A7  C19  C   CR56  0   0.539   3.9831  -0.4853  -1.1034
 6A7  C21  C   CR16  0  -0.060   1.8806   0.2180  -1.3082
 6A7  N22  N   NR15  0  -0.523   5.2381  -0.8386  -1.4343
 6A7  C24  C   CR5   0   0.217   5.1752  -1.1187   0.6881
 6A7  CL1  CL  CL    0  -0.134  -5.8294  -2.3482  -0.8750
 6A7  C10  C   CH2   0  -0.472  -2.0233   3.1095   0.2328
 6A7  C14  C   C     0   0.536   0.3158   0.3703   0.6786
 6A7  O15  O   O     0  -0.479  -0.1395  -0.3884   1.5248
 6A7  N20  N   N     0  -0.423   3.0138  -0.0747  -1.9142
 6A7  N23  N   N     0  -0.247   5.9504  -1.2184  -0.3613
 6A7  C25  C   CH3   0  -0.742   5.6332  -1.4646   2.0585
 6A7  H1   H   HCR6  0   0.278  -5.3373  -1.0727   1.6284
 6A7  H2   H   HCR6  0   0.259  -3.6257   0.5610   2.2988
 6A7  H3   H   HCR6  0   0.256  -2.0281   0.5257  -1.6722
 6A7  H4   H   HCR6  0   0.278  -3.7222  -1.1143  -2.3440
 6A7  H5   H   HCR5  0   0.268  -1.6598   1.7461   1.8674
 6A7  H6   H   HCH2  0   0.244  -0.2915   4.0880   1.0871
 6A7  H7   H   HCH2  0   0.258  -0.6489   4.6252  -0.5572
 6A7  H8   H   HCH2  0   0.246   0.1081   2.5485  -1.5056
 6A7  H9   H   HCH2  0   0.267   1.2615   2.7414  -0.1802
 6A7  H10  H   HCR6  0   0.274   2.5244  -0.4817   1.9613
 6A7  H11  H   HCR6  0   0.271   1.0720   0.5397  -1.9559
 6A7  H12  H   HNR5  0   0.418   5.6565  -0.8537  -2.3506
 6A7  H13  H   HCH2  0   0.246  -2.4929   3.0353  -0.7509
 6A7  H14  H   HCH2  0   0.264  -2.7093   3.6418   0.8901
 6A7  H15  H   HCH3  0   0.254   5.0254  -2.2656   2.4814
 6A7  H16  H   HCH3  0   0.257   6.6711  -1.7919   2.0503
 6A7  H17  H   HCH3  0   0.253   5.5495  -0.6078   2.7279

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
 6A7  O15  C14  double    1.224  0.020  1.224
 6A7  C21  N20  aromatic  1.318  0.020  1.318
 6A7  C21  C16  aromatic  1.410  0.020  1.410
 6A7  N20  C19  aromatic  1.329  0.020  1.329
 6A7  C12  N13  single    1.465  0.020  1.465
 6A7  C12  C11  single    1.522  0.020  1.522
 6A7  C14  N13  single    1.347  0.020  1.347
 6A7  C14  C16  single    1.491  0.020  1.491
 6A7  N13  C8   single    1.464  0.020  1.464
 6A7  C16  C17  aromatic  1.385  0.020  1.385
 6A7  C11  C10  single    1.522  0.020  1.522
 6A7  C10  C8   single    1.533  0.020  1.533
 6A7  C19  N22  aromatic  1.345  0.020  1.345
 6A7  C19  C18  aromatic  1.406  0.020  1.406
 6A7  C8   C5   single    1.505  0.020  1.505
 6A7  N22  N23  aromatic  1.343  0.020  1.343
 6A7  C17  C18  aromatic  1.388  0.020  1.388
 6A7  C18  C24  aromatic  1.426  0.020  1.426
 6A7  C5   C4   aromatic  1.389  0.020  1.389
 6A7  C5   C6   aromatic  1.392  0.020  1.392
 6A7  N23  C24  aromatic  1.308  0.020  1.308
 6A7  C24  C25  single    1.486  0.020  1.486
 6A7  C4   C3   aromatic  1.388  0.020  1.388
 6A7  C6   C7   aromatic  1.386  0.020  1.386
 6A7  C3   C2   aromatic  1.385  0.020  1.385
 6A7  C7   C2   aromatic  1.387  0.020  1.387
 6A7  C2   CL1  single    1.735  0.020  1.735
 6A7  C3   H1   single    0.930  0.020  1.080
 6A7  C4   H2   single    0.930  0.020  1.080
 6A7  C6   H3   single    0.930  0.020  1.080
 6A7  C7   H4   single    0.930  0.020  1.080
 6A7  C8   H5   single    0.970  0.020  1.090
 6A7  C11  H6   single    0.970  0.020  1.090
 6A7  C11  H7   single    0.970  0.020  1.090
 6A7  C12  H8   single    0.970  0.020  1.090
 6A7  C12  H9   single    0.970  0.020  1.090
 6A7  C17  H10  single    0.930  0.020  1.080
 6A7  C21  H11  single    0.930  0.020  1.080
 6A7  N22  H12  single    0.860  0.020  1.020
 6A7  C10  H13  single    0.970  0.020  1.090
 6A7  C10  H14  single    0.970  0.020  1.090
 6A7  C25  H15  single    0.970  0.020  1.090
 6A7  C25  H16  single    0.970  0.020  1.090
 6A7  C25  H17  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
 6A7  CL1  C2   C7   119.43  3.000
 6A7  CL1  C2   C3   119.57  3.000
 6A7  C7   C2   C3   121.01  3.000
 6A7  H1   C3   C4   120.33  3.000
 6A7  H1   C3   C2   120.69  3.000
 6A7  C4   C3   C2   118.98  3.000
 6A7  H2   C4   C5   119.79  3.000
 6A7  H2   C4   C3   118.99  3.000
 6A7  C5   C4   C3   121.22  3.000
 6A7  C8   C5   C6   121.07  3.000
 6A7  C6   C5   C4   118.60  3.000
 6A7  C8   C5   C4   120.29  3.000
 6A7  H3   C6   C7   118.69  3.000
 6A7  H3   C6   C5   120.24  3.000
 6A7  C7   C6   C5   121.07  3.000
 6A7  H4   C7   C6   120.30  3.000
 6A7  H4   C7   C2   120.59  3.000
 6A7  C6   C7   C2   119.11  3.000
 6A7  H5   C8   C10  109.35  3.000
 6A7  H5   C8   N13  109.35  3.000
 6A7  C10  C8   N13  103.11  3.000
 6A7  H5   C8   C5   108.66  3.000
 6A7  C10  C8   C5   113.33  3.000
 6A7  N13  C8   C5   112.88  3.000
 6A7  H7   C11  H6   108.16  3.000
 6A7  H7   C11  C10  113.21  3.000
 6A7  H6   C11  C10  110.74  3.000
 6A7  H7   C11  C12  112.08  3.000
 6A7  H6   C11  C12  110.21  3.000
 6A7  C10  C11  C12  102.39  3.000
 6A7  H9   C12  H8   108.21  3.000
 6A7  H9   C12  N13  111.26  3.000
 6A7  H8   C12  N13  111.09  3.000
 6A7  H9   C12  C11  113.03  3.000
 6A7  H8   C12  C11  110.33  3.000
 6A7  N13  C12  C11  102.90  3.000
 6A7  C14  N13  C12  126.38  3.000
 6A7  C14  N13  C8   119.21  3.000
 6A7  C12  N13  C8   112.08  3.000
 6A7  C14  C16  C21  121.68  3.000
 6A7  C14  C16  C17  118.89  3.000
 6A7  C21  C16  C17  119.24  3.000
 6A7  H10  C17  C18  121.71  3.000
 6A7  H10  C17  C16  121.10  3.000
 6A7  C18  C17  C16  117.18  3.000
 6A7  C24  C18  C19  104.72  3.000
 6A7  C24  C18  C17  137.46  3.000
 6A7  C19  C18  C17  117.81  3.000
 6A7  N20  C19  N22  127.71  3.000
 6A7  N22  C19  C18  106.02  3.000
 6A7  N20  C19  C18  126.27  3.000
 6A7  H11  C21  N20  115.60  3.000
 6A7  H11  C21  C16  119.45  3.000
 6A7  N20  C21  C16  124.92  3.000
 6A7  H12  N22  N23  120.15  3.000
 6A7  H12  N22  C19  127.97  3.000
 6A7  N23  N22  C19  111.88  3.000
 6A7  C25  C24  N23  122.64  3.000
 6A7  C25  C24  C18  127.73  3.000
 6A7  N23  C24  C18  109.62  3.000
 6A7  H14  C10  H13  107.81  3.000
 6A7  H14  C10  C11  113.90  3.000
 6A7  H13  C10  C11  110.05  3.000
 6A7  H14  C10  C8   111.38  3.000
 6A7  H13  C10  C8   110.22  3.000
 6A7  C11  C10  C8   103.44  3.000
 6A7  O15  C14  C16  120.16  3.000
 6A7  C16  C14  N13  117.71  3.000
 6A7  O15  C14  N13  122.13  3.000
 6A7  C21  N20  C19  114.53  3.000
 6A7  C24  N23  N22  107.76  3.000
 6A7  H17  C25  H16  108.31  3.000
 6A7  H17  C25  H15  107.23  3.000
 6A7  H16  C25  H15  108.28  3.000
 6A7  H17  C25  C24  111.07  3.000
 6A7  H16  C25  C24  110.92  3.000
 6A7  H15  C25  C24  110.90  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
 6A7  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 6A7  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 6A7  CONST_03  C6   C5   C4   C3     0.00   0.0  0
 6A7  CONST_04  C6   C7   C2   C3     0.00   0.0  0
 6A7  CONST_05  C7   C6   C5   C4     0.00   0.0  0
 6A7  CONST_06  C7   C2   C3   C4     0.00   0.0  0
 6A7  CONST_07  C19  N20  C21  C16    0.00   0.0  0
 6A7  CONST_08  C19  C18  C17  C16    0.00   0.0  0
 6A7  CONST_09  C24  C18  C17  C16  180.00   0.0  0
 6A7  CONST_10  N20  C21  C16  C17    0.00   0.0  0
 6A7  CONST_11  N20  C19  C18  C17    0.00   0.0  0
 6A7  CONST_12  N22  C19  C18  C17  180.00   0.0  0
 6A7  CONST_13  N23  C24  C18  C17  180.00   0.0  0
 6A7  CONST_14  C21  N20  C19  C18    0.00   0.0  0
 6A7  CONST_15  N23  N22  C19  C18    0.00   0.0  0
 6A7  CONST_16  C21  C16  C17  C18    0.00   0.0  0
 6A7  CONST_17  N22  N23  C24  C18    0.00   0.0  0
 6A7  CONST_18  C24  N23  N22  C19    0.00   0.0  0
 6A7  CONST_19  N23  C24  C18  C19    0.00   0.0  0
 6A7  CONST_20  N22  C19  N20  C21  180.00   0.0  0
 6A7  CONST_21  C24  C18  C19  N22    0.00   0.0  0
 6A7  CONST_22  N20  C19  C18  C24  180.00   0.0  0
 6A7  CONST_23  N23  N22  C19  N20  180.00   0.0  0
 6A7  CONST_24  C8   C5   C4   C3   180.00   0.0  0
 6A7  CONST_25  C8   C5   C6   C7   180.00   0.0  0
 6A7  CONST_26  CL1  C2   C3   C4   180.00   0.0  0
 6A7  CONST_27  CL1  C2   C7   C6   180.00   0.0  0
 6A7  CONST_28  C25  C24  C18  C17    0.00   0.0  0
 6A7  CONST_29  C14  C16  C17  C18  180.00   0.0  0
 6A7  CONST_30  C25  C24  C18  C19  180.00   0.0  0
 6A7  CONST_31  C25  C24  N23  N22  180.00   0.0  0
 6A7  CONST_32  N20  C21  C16  C14  180.00   0.0  0
 6A7  CONST_33  C16  C14  N13  C8   180.00   0.0  0
 6A7  CONST_35  H2   C4   C3   C2   180.00   0.0  0
 6A7  CONST_36  H3   C6   C7   C2   180.00   0.0  0
 6A7  CONST_37  H4   C7   C2   C3   180.00   0.0  0
 6A7  CONST_38  H1   C3   C4   C5   180.00   0.0  0
 6A7  CONST_39  H11  C21  C16  C17  180.00   0.0  0
 6A7  CONST_40  H12  N22  C19  C18  180.00   0.0  0
 6A7  CONST_41  H10  C17  C18  C19  180.00   0.0  0
 6A7  CONST_42  O15  C14  N13  C8     0.00   0.0  0
 6A7  Var_01    C11  C12  N13  C8    17.73  30.0  1
 6A7  Var_02    C12  C11  C10  C8    39.99  30.0  1
 6A7  Var_03    C10  C11  C12  N13  -35.13  30.0  1
 6A7  Var_04    C21  C16  C14  N13  -43.80  30.0  2
 6A7  Var_05    H15  C25  C24  C18   59.81  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
 6A7  chir_01  C8  N13  C10  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
 6A7  plan-1  C2   0.020
 6A7  plan-1  C3   0.020
 6A7  plan-1  C4   0.020
 6A7  plan-1  C5   0.020
 6A7  plan-1  C6   0.020
 6A7  plan-1  C7   0.020
 6A7  plan-1  C8   0.020
 6A7  plan-1  CL1  0.020
 6A7  plan-1  H1   0.020
 6A7  plan-1  H2   0.020
 6A7  plan-1  H3   0.020
 6A7  plan-1  H4   0.020
 6A7  plan-2  C16  0.020
 6A7  plan-2  C17  0.020
 6A7  plan-2  C18  0.020
 6A7  plan-2  C19  0.020
 6A7  plan-2  C21  0.020
 6A7  plan-2  N22  0.020
 6A7  plan-2  C24  0.020
 6A7  plan-2  C14  0.020
 6A7  plan-2  N20  0.020
 6A7  plan-2  N23  0.020
 6A7  plan-2  C25  0.020
 6A7  plan-2  H10  0.020
 6A7  plan-2  H11  0.020
 6A7  plan-2  H12  0.020
 6A7  plan-3  C8   0.020
 6A7  plan-3  C12  0.020
 6A7  plan-3  N13  0.020
 6A7  plan-3  C16  0.020
 6A7  plan-3  C14  0.020
 6A7  plan-3  O15  0.020

