# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 13:44:38 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 4-[(5S)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-5-yl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#Cc1ccc(cc1)[C@@H]2CCCc3cncn23
#
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
 JD7  JD7  4-[(5S)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-5-yl]benzonitrile  ligand  30  17  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JD7
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
 JD7  C01  C  CH2   0  -0.463   2.8751   2.1117  -0.0736
 JD7  C02  C  CH2   0  -0.452   1.3622   1.9560  -0.1495
 JD7  C03  C  CH1   0  -0.128   0.8957   0.7090   0.6039
 JD7  N04  N  NR5   0  -0.480   1.7282  -0.4279   0.2306
 JD7  C05  C  CR15  0   0.090   1.4982  -1.7298   0.5257
 JD7  N06  N  N     0  -0.449   2.4988  -2.4900   0.1713
 JD7  C07  C  CR15  0  -0.281   3.4274  -1.6417  -0.3660
 JD7  C08  C  CR5   0   0.306   2.9750  -0.3520  -0.3374
 JD7  C09  C  CH2   0  -0.500   3.5527   0.9460  -0.7873
 JD7  C10  C  CR6   0   0.131  -0.5634   0.4323   0.3483
 JD7  C11  C  CR16  0  -0.307  -1.5006   0.7162   1.3347
 JD7  C12  C  CR16  0  -0.220  -2.8522   0.5209   1.1048
 JD7  C13  C  CR6   0  -0.008  -3.2707   0.0289  -0.1291
 JD7  C14  C  CR16  0  -0.224  -2.3390  -0.2611  -1.1274
 JD7  C15  C  CR16  0  -0.274  -0.9945  -0.0567  -0.8839
 JD7  C16  C  CSP   0   0.058  -4.6609  -0.1812  -0.3740
 JD7  N17  N  NS    0  -0.251  -5.7830  -0.3533  -0.5713
 JD7  H2   H  HCH2  0   0.257   3.1760   3.0532  -0.5337
 JD7  H1   H  HCH2  0   0.236   3.1914   2.1534   0.9727
 JD7  H3   H  HCH2  0   0.268   0.8545   2.8185   0.2840
 JD7  H4   H  HCH2  0   0.246   1.0497   1.8938  -1.1966
 JD7  H5   H  HCH1  0   0.289   1.0340   0.8870   1.6745
 JD7  H6   H  HCR5  0   0.279   0.5858  -2.0641   0.9966
 JD7  H7   H  HCR5  0   0.249   4.3721  -1.9958  -0.7510
 JD7  H9   H  HCH2  0   0.251   3.4132   1.0592  -1.8671
 JD7  H8   H  HCH2  0   0.263   4.6297   0.9497  -0.6135
 JD7  H10  H  HCR6  0   0.273  -1.1735   1.0924   2.2957
 JD7  H11  H  HCR6  0   0.284  -3.5749   0.7418   1.8782
 JD7  H12  H  HCR6  0   0.284  -2.6687  -0.6414  -2.0844
 JD7  H13  H  HCR6  0   0.272  -0.2775  -0.2797  -1.6638

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
 JD7  N17  C16  triple    1.152  0.020  1.152
 JD7  C16  C13  single    1.427  0.020  1.427
 JD7  C13  C12  aromatic  1.393  0.020  1.393
 JD7  C13  C14  aromatic  1.396  0.020  1.396
 JD7  C12  C11  aromatic  1.385  0.020  1.385
 JD7  C14  C15  aromatic  1.381  0.020  1.381
 JD7  C11  C10  aromatic  1.390  0.020  1.390
 JD7  C15  C10  aromatic  1.394  0.020  1.394
 JD7  C10  C03  single    1.507  0.020  1.507
 JD7  C03  C02  single    1.530  0.020  1.530
 JD7  C03  N04  single    1.458  0.020  1.458
 JD7  C02  C01  single    1.523  0.020  1.523
 JD7  C01  C09  single    1.526  0.020  1.526
 JD7  N04  C05  aromatic  1.355  0.020  1.355
 JD7  N04  C08  aromatic  1.372  0.020  1.372
 JD7  C09  C08  single    1.490  0.020  1.490
 JD7  C05  N06  aromatic  1.306  0.020  1.306
 JD7  C08  C07  aromatic  1.367  0.020  1.367
 JD7  N06  C07  aromatic  1.368  0.020  1.368
 JD7  C01  H2   single    0.970  0.020  1.090
 JD7  C01  H1   single    0.970  0.020  1.090
 JD7  C02  H3   single    0.970  0.020  1.090
 JD7  C02  H4   single    0.970  0.020  1.090
 JD7  C03  H5   single    0.970  0.020  1.090
 JD7  C05  H6   single    0.930  0.020  1.080
 JD7  C07  H7   single    0.930  0.020  1.080
 JD7  C09  H9   single    0.970  0.020  1.090
 JD7  C09  H8   single    0.970  0.020  1.090
 JD7  C11  H10  single    0.930  0.020  1.080
 JD7  C12  H11  single    0.930  0.020  1.080
 JD7  C14  H12  single    0.930  0.020  1.080
 JD7  C15  H13  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
 JD7  H1   C01  H2   106.91  3.000
 JD7  H1   C01  C09  110.38  3.000
 JD7  H2   C01  C09  109.87  3.000
 JD7  H1   C01  C02  109.81  3.000
 JD7  H2   C01  C02  109.97  3.000
 JD7  C09  C01  C02  109.87  3.000
 JD7  H4   C02  H3   106.99  3.000
 JD7  H4   C02  C03  109.74  3.000
 JD7  H3   C02  C03  107.87  3.000
 JD7  H4   C02  C01  109.71  3.000
 JD7  H3   C02  C01  111.22  3.000
 JD7  C03  C02  C01  111.21  3.000
 JD7  H5   C03  C10  108.55  3.000
 JD7  H5   C03  N04  107.78  3.000
 JD7  C10  C03  N04  111.49  3.000
 JD7  H5   C03  C02  108.11  3.000
 JD7  N04  C03  C02  109.60  3.000
 JD7  C10  C03  C02  111.19  3.000
 JD7  C08  N04  C05  107.32  3.000
 JD7  C08  N04  C03  125.58  3.000
 JD7  C05  N04  C03  126.64  3.000
 JD7  H6   C05  N06  125.85  3.000
 JD7  H6   C05  N04  122.41  3.000
 JD7  N06  C05  N04  111.74  3.000
 JD7  C07  N06  C05  105.42  3.000
 JD7  H7   C07  C08  127.32  3.000
 JD7  H7   C07  N06  122.05  3.000
 JD7  C08  C07  N06  110.63  3.000
 JD7  C09  C08  C07  133.40  3.000
 JD7  C07  C08  N04  104.90  3.000
 JD7  C09  C08  N04  121.69  3.000
 JD7  H8   C09  H9   106.42  3.000
 JD7  H8   C09  C08  109.73  3.000
 JD7  H9   C09  C08  109.78  3.000
 JD7  H8   C09  C01  111.18  3.000
 JD7  H9   C09  C01  109.02  3.000
 JD7  C08  C09  C01  110.61  3.000
 JD7  C15  C10  C11  119.37  3.000
 JD7  C15  C10  C03  120.92  3.000
 JD7  C11  C10  C03  119.67  3.000
 JD7  H10  C11  C12  119.42  3.000
 JD7  H10  C11  C10  119.81  3.000
 JD7  C12  C11  C10  120.77  3.000
 JD7  H11  C12  C13  120.33  3.000
 JD7  H11  C12  C11  120.32  3.000
 JD7  C13  C12  C11  119.35  3.000
 JD7  C16  C13  C14  119.79  3.000
 JD7  C14  C13  C12  120.42  3.000
 JD7  C16  C13  C12  119.79  3.000
 JD7  H12  C14  C15  120.32  3.000
 JD7  H12  C14  C13  120.16  3.000
 JD7  C15  C14  C13  119.52  3.000
 JD7  H13  C15  C14  119.15  3.000
 JD7  H13  C15  C10  120.27  3.000
 JD7  C14  C15  C10  120.57  3.000
 JD7  N17  C16  C13  180.00  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
 JD7  CONST_01  C07  N06  C05  N04    0.00   0.0  0
 JD7  CONST_02  N06  C07  C08  N04    0.00   0.0  0
 JD7  CONST_03  C07  C08  N04  C05    0.00   0.0  0
 JD7  CONST_04  C08  C07  N06  C05    0.00   0.0  0
 JD7  CONST_05  C08  N04  C05  N06    0.00   0.0  0
 JD7  CONST_06  C13  C12  C11  C10    0.00   0.0  0
 JD7  CONST_07  C13  C14  C15  C10    0.00   0.0  0
 JD7  CONST_08  C14  C13  C12  C11    0.00   0.0  0
 JD7  CONST_09  C14  C15  C10  C11    0.00   0.0  0
 JD7  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 JD7  CONST_11  C15  C10  C11  C12    0.00   0.0  0
 JD7  CONST_12  C12  C11  C10  C03  180.00   0.0  0
 JD7  CONST_13  C14  C15  C10  C03  180.00   0.0  0
 JD7  CONST_14  C16  C13  C12  C11  180.00   0.0  0
 JD7  CONST_15  C16  C13  C14  C15  180.00   0.0  0
 JD7  CONST_16  H10  C11  C10  C03    0.00   0.0  0
 JD7  CONST_17  H13  C15  C10  C03    0.00   0.0  0
 JD7  CONST_18  H6   C05  N04  C03    0.00   0.0  0
 JD7  CONST_19  H7   C07  C08  N04  180.00   0.0  0
 JD7  CONST_20  H11  C12  C11  C10  180.00   0.0  0
 JD7  CONST_21  H12  C14  C15  C10  180.00   0.0  0
 JD7  Var_01    N04  C08  C09  C01   21.70  30.0  1
 JD7  Var_02    C08  C09  C01  C02  -48.89  30.0  1
 JD7  Var_03    C09  C01  C02  C03   64.32  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
 JD7  chir_01  C03  C10  C02  N04  positiv

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
 JD7  plan-1  C03  0.020
 JD7  plan-1  C10  0.020
 JD7  plan-1  C11  0.020
 JD7  plan-1  C12  0.020
 JD7  plan-1  C13  0.020
 JD7  plan-1  C14  0.020
 JD7  plan-1  C15  0.020
 JD7  plan-1  C16  0.020
 JD7  plan-1  N17  0.020
 JD7  plan-1  H10  0.020
 JD7  plan-1  H11  0.020
 JD7  plan-1  H12  0.020
 JD7  plan-1  H13  0.020
 JD7  plan-2  C03  0.020
 JD7  plan-2  N04  0.020
 JD7  plan-2  C05  0.020
 JD7  plan-2  N06  0.020
 JD7  plan-2  C07  0.020
 JD7  plan-2  C08  0.020
 JD7  plan-2  C09  0.020
 JD7  plan-2  H6   0.020
 JD7  plan-2  H7   0.020

