# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 12:16:29 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 3-[(2S)-pyrrolidin-2-ylethynyl]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN[C@@H](C1)C#Cc2cccnc2
#
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
 TI9  TI9  3-[(2S)-pyrrolidin-2-ylethynyl]pyridine  ligand  25  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TI9
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
 TI9  C13   C  CH2   0  -0.457  -2.9876  -1.0132   0.7285
 TI9  C12   C  CH2   0  -0.457  -4.3696  -0.8960   0.0569
 TI9  C11   C  CH2   0  -0.303  -4.3365   0.4560  -0.6649
 TI9  N10   N  NH1   0  -0.609  -2.9154   0.6890  -0.8799
 TI9  C9    C  CH1   0  -0.268  -2.2888   0.3161   0.3819
 TI9  C8    C  CSP   0   0.148  -0.8400   0.2010   0.2625
 TI9  C7    C  CSP   0   0.117   0.3585   0.1004   0.1848
 TI9  C5    C  CR6   0  -0.213   1.7733  -0.0172   0.0791
 TI9  C6    C  CR16  0  -0.194   2.3726  -1.0687  -0.6158
 TI9  C1    C  CR16  0  -0.317   3.7532  -1.1245  -0.6820
 TI9  C4    C  CR16  0  -0.095   2.6141   0.9277   0.6753
 TI9  N3    N  N     0  -0.394   3.9344   0.8745   0.6133
 TI9  C2    C  CR16  0  -0.065   4.4907  -0.1319  -0.0529
 TI9  H131  H  HCH2  0   0.248  -3.0435  -1.1498   1.8071
 TI9  H132  H  HCH2  0   0.243  -2.4252  -1.8522   0.3190
 TI9  H121  H  HCH2  0   0.240  -4.5176  -1.7105  -0.6519
 TI9  H122  H  HCH2  0   0.239  -5.1852  -0.9393   0.7772
 TI9  H112  H  HCH2  0   0.235  -4.8758   0.4441  -1.6132
 TI9  H111  H  HCH2  0   0.204  -4.7983   1.2277  -0.0334
 TI9  HN10  H  HNH1  0   0.355  -2.7255   1.6570  -1.1076
 TI9  H14   H  HCH1  0   0.253  -2.5032   1.0435   1.1810
 TI9  H6    H  HCR6  0   0.275   1.7636  -1.8252  -1.0925
 TI9  H1    H  HCR6  0   0.279   4.2539  -1.9234  -1.2106
 TI9  H4    H  HCR6  0   0.266   2.1817   1.7583   1.2225
 TI9  H2    H  HCR6  0   0.271   5.5739  -0.1502  -0.0890

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
 TI9  C13  C12   single    1.541  0.020  1.541
 TI9  C13  C9    single    1.541  0.020  1.541
 TI9  C12  C11   single    1.533  0.020  1.533
 TI9  C9   N10   single    1.457  0.020  1.457
 TI9  C9   C8    single    1.458  0.020  1.458
 TI9  C11  N10   single    1.456  0.020  1.456
 TI9  C8   C7    triple    1.205  0.020  1.205
 TI9  C7   C5    single    1.424  0.020  1.424
 TI9  C5   C4    aromatic  1.398  0.020  1.398
 TI9  C5   C6    aromatic  1.396  0.020  1.396
 TI9  C4   N3    aromatic  1.323  0.020  1.323
 TI9  C6   C1    aromatic  1.383  0.020  1.383
 TI9  N3   C2    aromatic  1.329  0.020  1.329
 TI9  C1   C2    aromatic  1.387  0.020  1.387
 TI9  C13  H131  single    0.970  0.020  1.090
 TI9  C13  H132  single    0.970  0.020  1.090
 TI9  C12  H121  single    0.970  0.020  1.090
 TI9  C12  H122  single    0.970  0.020  1.090
 TI9  C11  H112  single    0.970  0.020  1.090
 TI9  C11  H111  single    0.970  0.020  1.090
 TI9  N10  HN10  single    0.890  0.020  1.040
 TI9  C9   H14   single    0.970  0.020  1.090
 TI9  C6   H6    single    0.930  0.020  1.080
 TI9  C1   H1    single    0.930  0.020  1.080
 TI9  C4   H4    single    0.930  0.020  1.080
 TI9  C2   H2    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
 TI9  H132  C13  H131  107.59  3.000
 TI9  H132  C13  C9    110.21  3.000
 TI9  H131  C13  C9    110.75  3.000
 TI9  H132  C13  C12   110.95  3.000
 TI9  H131  C13  C12   113.29  3.000
 TI9  C9    C13  C12   104.06  3.000
 TI9  H122  C12  H121  107.39  3.000
 TI9  H122  C12  C11   111.27  3.000
 TI9  H121  C12  C11   110.85  3.000
 TI9  H122  C12  C13   112.35  3.000
 TI9  H121  C12  C13   110.39  3.000
 TI9  C11   C12  C13   104.65  3.000
 TI9  H111  C11  H112  107.43  3.000
 TI9  H111  C11  N10   112.50  3.000
 TI9  H112  C11  N10   110.85  3.000
 TI9  H111  C11  C12   109.85  3.000
 TI9  H112  C11  C12   112.88  3.000
 TI9  N10   C11  C12   103.40  3.000
 TI9  HN10  N10  C9    111.02  3.000
 TI9  HN10  N10  C11   111.67  3.000
 TI9  C9    N10  C11   104.53  3.000
 TI9  H14   C9   C8    107.75  3.000
 TI9  H14   C9   N10   112.05  3.000
 TI9  C8    C9   N10   112.12  3.000
 TI9  H14   C9   C13   108.55  3.000
 TI9  C8    C9   C13   113.63  3.000
 TI9  N10   C9   C13   102.74  3.000
 TI9  C7    C8   C9    180.00  3.000
 TI9  C5    C7   C8    180.00  3.000
 TI9  C4    C5   C6    117.60  3.000
 TI9  C6    C5   C7    121.74  3.000
 TI9  C4    C5   C7    120.66  3.000
 TI9  H6    C6   C1    120.83  3.000
 TI9  H6    C6   C5    120.30  3.000
 TI9  C1    C6   C5    118.87  3.000
 TI9  H1    C1   C2    120.29  3.000
 TI9  H1    C1   C6    121.03  3.000
 TI9  C2    C1   C6    118.68  3.000
 TI9  H4    C4   N3    116.89  3.000
 TI9  H4    C4   C5    119.54  3.000
 TI9  N3    C4   C5    123.57  3.000
 TI9  C2    N3   C4    118.14  3.000
 TI9  H2    C2   N3    116.60  3.000
 TI9  H2    C2   C1    120.26  3.000
 TI9  N3    C2   C1    123.14  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
 TI9  CONST_01  C2   N3   C4   C5     0.00   0.0  0
 TI9  CONST_02  C2   C1   C6   C5     0.00   0.0  0
 TI9  CONST_03  N3   C4   C5   C6     0.00   0.0  0
 TI9  CONST_04  N3   C2   C1   C6     0.00   0.0  0
 TI9  CONST_05  C4   C5   C6   C1     0.00   0.0  0
 TI9  CONST_06  C4   N3   C2   C1     0.00   0.0  0
 TI9  CONST_07  N3   C4   C5   C7   180.00   0.0  0
 TI9  CONST_08  C1   C6   C5   C7   180.00   0.0  0
 TI9  CONST_09  H1   C1   C6   C5   180.00   0.0  0
 TI9  CONST_10  H4   C4   C5   C6   180.00   0.0  0
 TI9  CONST_11  H2   C2   C1   C6   180.00   0.0  0
 TI9  CONST_12  H6   C6   C5   C4   180.00   0.0  0
 TI9  Var_01    N10  C11  C12  C13   24.36  30.0  1
 TI9  Var_02    C9   N10  C11  C12  -43.58  30.0  1
 TI9  Var_03    C9   C13  C12  C11    2.20  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
 TI9  chir_01  C9  C13  N10  C8  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
 TI9  plan-1  C8  0.020
 TI9  plan-1  C7  0.020
 TI9  plan-1  C5  0.020
 TI9  plan-1  C6  0.020
 TI9  plan-1  C1  0.020
 TI9  plan-1  C4  0.020
 TI9  plan-1  N3  0.020
 TI9  plan-1  C2  0.020
 TI9  plan-1  H6  0.020
 TI9  plan-1  H1  0.020
 TI9  plan-1  H4  0.020
 TI9  plan-1  H2  0.020

