# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 17:24:33 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 4-[(5R)-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
 0T3  0T3  4-[(5R)-5,6,7,8-tetrahydroimidazo[1,5-a]pyridin-5-yl]benzonitrile  ligand  30  17  .  2022-08-09  2022-08-09
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0T3
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
 0T3  C01  C  CH2   0  -0.463   2.8813  -2.1011  -0.0623
 0T3  C02  C  CH2   0  -0.452   1.3684  -1.9436  -0.1334
 0T3  C03  C  CH1   0  -0.128   0.9054  -0.6999   0.6278
 0T3  N04  N  NR5   0  -0.480   1.7393   0.4380   0.2601
 0T3  C05  C  CR15  0   0.090   1.5120   1.7384   0.5640
 0T3  N06  N  N     0  -0.449   2.5128   2.4994   0.2113
 0T3  C07  C  CR15  0  -0.281   3.4382   1.6531  -0.3343
 0T3  C08  C  CR5   0   0.307   2.9843   0.3639  -0.3125
 0T3  C09  C  CH2   0  -0.500   3.5582  -0.9324  -0.7719
 0T3  C10  C  CR6   0   0.131  -0.5534  -0.4184   0.3749
 0T3  C11  C  CR16  0  -0.307  -1.4910  -0.7063   1.3598
 0T3  C12  C  CR16  0  -0.220  -2.8422  -0.5063   1.1316
 0T3  C13  C  CR6   0  -0.008  -3.2598  -0.0058  -0.0992
 0T3  C14  C  CR16  0  -0.224  -2.3277   0.2886  -1.0957
 0T3  C15  C  CR16  0  -0.274  -0.9837   0.0792  -0.8540
 0T3  C16  C  CSP   0   0.058  -4.6497   0.2075  -0.3433
 0T3  N17  N  NS    0  -0.251  -5.7731   0.3733  -0.5389
 0T3  H1   H  HCH2  0   0.236   3.1998  -2.1491   0.9830
 0T3  H2   H  HCH2  0   0.257   3.1806  -3.0404  -0.5282
 0T3  H3   H  HCH2  0   0.245   1.0524  -1.8762  -1.1790
 0T3  H4   H  HCH2  0   0.268   0.8609  -2.8072   0.2978
 0T3  H5   H  HCH1  0   0.289   1.0444  -0.8842   1.6973
 0T3  H6   H  HCR5  0   0.279   0.6016   2.0709   1.0400
 0T3  H7   H  HCR5  0   0.249   4.3820   2.0088  -0.7203
 0T3  H8   H  HCH2  0   0.263   4.6359  -0.9393  -0.6024
 0T3  H9   H  HCH2  0   0.251   3.4143  -1.0394  -1.8518
 0T3  H10  H  HCR6  0   0.273  -1.1644  -1.0887   2.3185
 0T3  H11  H  HCR6  0   0.284  -3.5652  -0.7309   1.9035
 0T3  H12  H  HCR6  0   0.284  -2.6569   0.6759  -2.0500
 0T3  H13  H  HCR6  0   0.272  -0.2662   0.3054  -1.6327

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
 0T3  N17  C16  triple    1.152  0.020  1.152
 0T3  C16  C13  single    1.427  0.020  1.427
 0T3  C13  C14  aromatic  1.396  0.020  1.396
 0T3  C13  C12  aromatic  1.393  0.020  1.393
 0T3  C14  C15  aromatic  1.382  0.020  1.382
 0T3  C12  C11  aromatic  1.385  0.020  1.385
 0T3  C15  C10  aromatic  1.394  0.020  1.394
 0T3  C11  C10  aromatic  1.390  0.020  1.390
 0T3  C10  C03  single    1.507  0.020  1.507
 0T3  C01  C02  single    1.523  0.020  1.523
 0T3  C01  C09  single    1.526  0.020  1.526
 0T3  C02  C03  single    1.530  0.020  1.530
 0T3  C03  N04  single    1.458  0.020  1.458
 0T3  C09  C08  single    1.490  0.020  1.490
 0T3  N04  C08  aromatic  1.372  0.020  1.372
 0T3  N04  C05  aromatic  1.355  0.020  1.355
 0T3  C08  C07  aromatic  1.367  0.020  1.367
 0T3  C05  N06  aromatic  1.306  0.020  1.306
 0T3  C07  N06  aromatic  1.368  0.020  1.368
 0T3  C01  H1   single    0.970  0.020  1.090
 0T3  C01  H2   single    0.970  0.020  1.090
 0T3  C02  H3   single    0.970  0.020  1.090
 0T3  C02  H4   single    0.970  0.020  1.090
 0T3  C03  H5   single    0.970  0.020  1.090
 0T3  C05  H6   single    0.930  0.020  1.080
 0T3  C07  H7   single    0.930  0.020  1.080
 0T3  C09  H8   single    0.970  0.020  1.090
 0T3  C09  H9   single    0.970  0.020  1.090
 0T3  C11  H10  single    0.930  0.020  1.080
 0T3  C12  H11  single    0.930  0.020  1.080
 0T3  C14  H12  single    0.930  0.020  1.080
 0T3  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
 0T3  H2   C01  H1   106.89  3.000
 0T3  H2   C01  C09  109.84  3.000
 0T3  H1   C01  C09  110.42  3.000
 0T3  H2   C01  C02  109.99  3.000
 0T3  H1   C01  C02  109.79  3.000
 0T3  C09  C01  C02  109.87  3.000
 0T3  H4   C02  H3   106.99  3.000
 0T3  H4   C02  C03  107.83  3.000
 0T3  H3   C02  C03  109.75  3.000
 0T3  H4   C02  C01  111.22  3.000
 0T3  H3   C02  C01  109.75  3.000
 0T3  C03  C02  C01  111.19  3.000
 0T3  H5   C03  C10  108.57  3.000
 0T3  H5   C03  N04  107.78  3.000
 0T3  C10  C03  N04  111.44  3.000
 0T3  H5   C03  C02  108.12  3.000
 0T3  N04  C03  C02  109.63  3.000
 0T3  C10  C03  C02  111.18  3.000
 0T3  C08  N04  C05  107.32  3.000
 0T3  C05  N04  C03  126.64  3.000
 0T3  C08  N04  C03  125.59  3.000
 0T3  H6   C05  N06  125.86  3.000
 0T3  H6   C05  N04  122.41  3.000
 0T3  N06  C05  N04  111.73  3.000
 0T3  C07  N06  C05  105.41  3.000
 0T3  H7   C07  C08  127.34  3.000
 0T3  H7   C07  N06  122.02  3.000
 0T3  C08  C07  N06  110.64  3.000
 0T3  C09  C08  C07  133.44  3.000
 0T3  C07  C08  N04  104.89  3.000
 0T3  C09  C08  N04  121.67  3.000
 0T3  H9   C09  H8   106.41  3.000
 0T3  H9   C09  C08  109.79  3.000
 0T3  H8   C09  C08  109.76  3.000
 0T3  H9   C09  C01  109.00  3.000
 0T3  H8   C09  C01  111.18  3.000
 0T3  C08  C09  C01  110.61  3.000
 0T3  C15  C10  C11  119.37  3.000
 0T3  C11  C10  C03  119.69  3.000
 0T3  C15  C10  C03  120.89  3.000
 0T3  H10  C11  C12  119.42  3.000
 0T3  H10  C11  C10  119.81  3.000
 0T3  C12  C11  C10  120.77  3.000
 0T3  H11  C12  C13  120.33  3.000
 0T3  H11  C12  C11  120.32  3.000
 0T3  C13  C12  C11  119.34  3.000
 0T3  C16  C13  C14  119.78  3.000
 0T3  C14  C13  C12  120.42  3.000
 0T3  C16  C13  C12  119.79  3.000
 0T3  H12  C14  C15  120.33  3.000
 0T3  H12  C14  C13  120.15  3.000
 0T3  C15  C14  C13  119.52  3.000
 0T3  H13  C15  C14  119.16  3.000
 0T3  H13  C15  C10  120.27  3.000
 0T3  C14  C15  C10  120.57  3.000
 0T3  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
 0T3  CONST_01  N06  C07  C08  N04    0.00   0.0  0
 0T3  CONST_02  C07  N06  C05  N04    0.00   0.0  0
 0T3  CONST_03  C07  C08  N04  C05    0.00   0.0  0
 0T3  CONST_04  C08  C07  N06  C05    0.00   0.0  0
 0T3  CONST_05  C08  N04  C05  N06    0.00   0.0  0
 0T3  CONST_06  C13  C14  C15  C10    0.00   0.0  0
 0T3  CONST_07  C13  C12  C11  C10    0.00   0.0  0
 0T3  CONST_08  C14  C13  C12  C11    0.00   0.0  0
 0T3  CONST_09  C14  C15  C10  C11    0.00   0.0  0
 0T3  CONST_10  C15  C14  C13  C12    0.00   0.0  0
 0T3  CONST_11  C15  C10  C11  C12    0.00   0.0  0
 0T3  CONST_12  C14  C15  C10  C03  180.00   0.0  0
 0T3  CONST_13  C12  C11  C10  C03  180.00   0.0  0
 0T3  CONST_14  C16  C13  C12  C11  180.00   0.0  0
 0T3  CONST_15  C16  C13  C14  C15  180.00   0.0  0
 0T3  CONST_16  H13  C15  C10  C03    0.00   0.0  0
 0T3  CONST_17  H10  C11  C10  C03    0.00   0.0  0
 0T3  CONST_18  H6   C05  N04  C03    0.00   0.0  0
 0T3  CONST_19  H7   C07  C08  N04  180.00   0.0  0
 0T3  CONST_20  H12  C14  C15  C10  180.00   0.0  0
 0T3  CONST_21  H11  C12  C11  C10  180.00   0.0  0
 0T3  Var_01    N04  C08  C09  C01  -21.73  30.0  1
 0T3  Var_02    C08  C09  C01  C02   48.97  30.0  1
 0T3  Var_03    C09  C01  C02  C03  -64.33  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
 0T3  chir_01  C03  C10  C02  N04  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
 0T3  plan-1  C03  0.020
 0T3  plan-1  C10  0.020
 0T3  plan-1  C11  0.020
 0T3  plan-1  C12  0.020
 0T3  plan-1  C13  0.020
 0T3  plan-1  C14  0.020
 0T3  plan-1  C15  0.020
 0T3  plan-1  C16  0.020
 0T3  plan-1  N17  0.020
 0T3  plan-1  H10  0.020
 0T3  plan-1  H11  0.020
 0T3  plan-1  H12  0.020
 0T3  plan-1  H13  0.020
 0T3  plan-2  C03  0.020
 0T3  plan-2  N04  0.020
 0T3  plan-2  C05  0.020
 0T3  plan-2  N06  0.020
 0T3  plan-2  C07  0.020
 0T3  plan-2  C08  0.020
 0T3  plan-2  C09  0.020
 0T3  plan-2  H6   0.020
 0T3  plan-2  H7   0.020

