# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 08:55:26 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2S)-(4-chlorophenyl)(6-chloropyridin-2-yl)ethanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(cc1)[C@H](C#N)c2cccc(Cl)n2
#
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
 A08  A08  (2S)-(4-chlorophenyl)(6-chloropyridin-2-yl)ethanenitrile  ligand  25  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A08
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
 A08  CL1  CL  CL    0  -0.121   4.7400   1.7054  -0.2781
 A08  C1   C   CR6   0  -0.049   3.3101   0.7830   0.0423
 A08  C2   C   CR16  0  -0.195   2.6801   0.9066   1.2696
 A08  C3   C   CR16  0  -0.311   1.5359   0.1620   1.5185
 A08  C4   C   CR6   0   0.173   1.0280  -0.6958   0.5535
 A08  C5   C   CR16  0  -0.284   1.6725  -0.8036  -0.6737
 A08  C6   C   CR16  0  -0.193   2.8165  -0.0682  -0.9358
 A08  C7   C   CH1   0  -0.504  -0.2531  -1.4633   0.8249
 A08  C8   C   CR6   0   0.302  -1.4014  -0.8655   0.0320
 A08  C9   C   CR16  0  -0.343  -1.9077  -1.4321  -1.1245
 A08  C10  C   CR16  0  -0.136  -2.9221  -0.7588  -1.7945
 A08  C11  C   CR16  0  -0.268  -3.3919   0.4413  -1.2955
 A08  C12  C   CR6   0   0.155  -2.8037   0.9037  -0.1264
 A08  N14  N   N     0  -0.387  -1.8483   0.2873   0.5201
 A08  CL2  CL  CL    0  -0.099  -3.3521   2.4014   0.5523
 A08  C16  C   CSP   0   0.143  -0.0716  -2.8858   0.5569
 A08  N17  N   NS    0  -0.244   0.0823  -4.0060   0.3491
 A08  H1   H   HCR6  0   0.286   3.0716   1.5714   2.0269
 A08  H2   H   HCR6  0   0.275   1.0434   0.2544   2.4779
 A08  H3   H   HCR6  0   0.270   1.2880  -1.4627  -1.4433
 A08  H4   H   HCR6  0   0.287   3.3131  -0.1571  -1.8920
 A08  H5   H   HCH1  0   0.363  -0.4999  -1.3757   1.8868
 A08  H6   H   HCR6  0   0.286  -1.5327  -2.3725  -1.5042
 A08  H7   H   HCR6  0   0.294  -3.3430  -1.1703  -2.7016
 A08  H8   H   HCR6  0   0.298  -4.1776   0.9951  -1.7881

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
 A08  C10  C9   aromatic  1.390  0.020  1.390
 A08  C10  C11  aromatic  1.382  0.020  1.382
 A08  C9   C8   aromatic  1.384  0.020  1.384
 A08  C11  C12  aromatic  1.388  0.020  1.388
 A08  C8   C7   single    1.518  0.020  1.518
 A08  C8   N14  aromatic  1.329  0.020  1.329
 A08  C7   C16  single    1.459  0.020  1.459
 A08  C7   C4   single    1.518  0.020  1.518
 A08  C16  N17  triple    1.150  0.020  1.150
 A08  C12  N14  aromatic  1.308  0.020  1.308
 A08  C12  CL2  single    1.733  0.020  1.733
 A08  C5   C4   aromatic  1.390  0.020  1.390
 A08  C5   C6   aromatic  1.385  0.020  1.385
 A08  C4   C3   aromatic  1.387  0.020  1.387
 A08  C6   C1   aromatic  1.387  0.020  1.387
 A08  C3   C2   aromatic  1.388  0.020  1.388
 A08  C1   C2   aromatic  1.385  0.020  1.385
 A08  C1   CL1  single    1.731  0.020  1.731
 A08  C2   H1   single    0.930  0.020  1.080
 A08  C3   H2   single    0.930  0.020  1.080
 A08  C5   H3   single    0.930  0.020  1.080
 A08  C6   H4   single    0.930  0.020  1.080
 A08  C7   H5   single    0.970  0.020  1.090
 A08  C9   H6   single    0.930  0.020  1.080
 A08  C10  H7   single    0.930  0.020  1.080
 A08  C11  H8   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
 A08  C6   C1   C2   121.17  3.000
 A08  C2   C1   CL1  119.48  3.000
 A08  C6   C1   CL1  119.35  3.000
 A08  H1   C2   C3   120.19  3.000
 A08  H1   C2   C1   120.72  3.000
 A08  C3   C2   C1   119.09  3.000
 A08  H2   C3   C4   120.18  3.000
 A08  H2   C3   C2   119.23  3.000
 A08  C4   C3   C2   120.59  3.000
 A08  C7   C4   C5   120.66  3.000
 A08  C5   C4   C3   119.48  3.000
 A08  C7   C4   C3   119.82  3.000
 A08  H3   C5   C6   118.79  3.000
 A08  H3   C5   C4   120.63  3.000
 A08  C6   C5   C4   120.58  3.000
 A08  H4   C6   C5   120.21  3.000
 A08  H4   C6   C1   120.70  3.000
 A08  C5   C6   C1   119.09  3.000
 A08  H5   C7   C16  106.53  3.000
 A08  H5   C7   C8   107.75  3.000
 A08  C16  C7   C8   112.46  3.000
 A08  H5   C7   C4   108.88  3.000
 A08  C16  C7   C4   110.81  3.000
 A08  C8   C7   C4   110.24  3.000
 A08  N14  C8   C9   122.61  3.000
 A08  N14  C8   C7   113.83  3.000
 A08  C9   C8   C7   123.51  3.000
 A08  H6   C9   C10  120.35  3.000
 A08  H6   C9   C8   121.51  3.000
 A08  C10  C9   C8   118.14  3.000
 A08  H7   C10  C11  120.06  3.000
 A08  H7   C10  C9   120.28  3.000
 A08  C11  C10  C9   119.66  3.000
 A08  H8   C11  C12  121.44  3.000
 A08  H8   C11  C10  121.86  3.000
 A08  C12  C11  C10  116.70  3.000
 A08  CL2  C12  N14  116.41  3.000
 A08  CL2  C12  C11  118.92  3.000
 A08  N14  C12  C11  124.67  3.000
 A08  C12  N14  C8   118.22  3.000
 A08  N17  C16  C7   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
 A08  CONST_01  C4   C5   C6   C1     0.00  0.0  0
 A08  CONST_02  C4   C3   C2   C1     0.00  0.0  0
 A08  CONST_03  C5   C4   C3   C2     0.00  0.0  0
 A08  CONST_04  C5   C6   C1   C2     0.00  0.0  0
 A08  CONST_05  C6   C5   C4   C3     0.00  0.0  0
 A08  CONST_06  C6   C1   C2   C3     0.00  0.0  0
 A08  CONST_07  C11  C10  C9   C8     0.00  0.0  0
 A08  CONST_08  C11  C12  N14  C8     0.00  0.0  0
 A08  CONST_09  C12  C11  C10  C9     0.00  0.0  0
 A08  CONST_10  C12  N14  C8   C9     0.00  0.0  0
 A08  CONST_11  N14  C8   C9   C10    0.00  0.0  0
 A08  CONST_12  N14  C12  C11  C10    0.00  0.0  0
 A08  CONST_13  C5   C6   C1   CL1  180.00  0.0  0
 A08  CONST_14  C3   C2   C1   CL1  180.00  0.0  0
 A08  CONST_15  C7   C4   C3   C2   180.00  0.0  0
 A08  CONST_16  C7   C4   C5   C6   180.00  0.0  0
 A08  CONST_17  C10  C9   C8   C7   180.00  0.0  0
 A08  CONST_18  C12  N14  C8   C7   180.00  0.0  0
 A08  CONST_19  CL2  C12  N14  C8   180.00  0.0  0
 A08  CONST_20  CL2  C12  C11  C10  180.00  0.0  0
 A08  CONST_21  H3   C5   C6   C1   180.00  0.0  0
 A08  CONST_22  H2   C3   C2   C1   180.00  0.0  0
 A08  CONST_23  H4   C6   C1   C2   180.00  0.0  0
 A08  CONST_24  H1   C2   C3   C4   180.00  0.0  0
 A08  CONST_25  H7   C10  C9   C8   180.00  0.0  0
 A08  CONST_26  H8   C11  C10  C9   180.00  0.0  0
 A08  CONST_27  H6   C9   C10  C11  180.00  0.0  0

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
 A08  chir_01  C7  C8  C16  C4  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
 A08  plan-1  CL1  0.020
 A08  plan-1  C1   0.020
 A08  plan-1  C2   0.020
 A08  plan-1  C3   0.020
 A08  plan-1  C4   0.020
 A08  plan-1  C5   0.020
 A08  plan-1  C6   0.020
 A08  plan-1  C7   0.020
 A08  plan-1  H1   0.020
 A08  plan-1  H2   0.020
 A08  plan-1  H3   0.020
 A08  plan-1  H4   0.020
 A08  plan-2  C7   0.020
 A08  plan-2  C8   0.020
 A08  plan-2  C9   0.020
 A08  plan-2  C10  0.020
 A08  plan-2  C11  0.020
 A08  plan-2  C12  0.020
 A08  plan-2  N14  0.020
 A08  plan-2  CL2  0.020
 A08  plan-2  H6   0.020
 A08  plan-2  H7   0.020
 A08  plan-2  H8   0.020

