# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 12:22:23 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: 5-(2-chlorobenzyl)-4,5,6,7-tetrahydrothieno[3,2-c]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccccc1CN2CCc3sccc3C2
#
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
 TIC  TIC  5-(2-chlorobenzyl)-4,5,6,7-tetrahydrothieno[3,2-c]pyridine  ligand  31  17  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TIC
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
 TIC  C1   C   CH2   0  -0.298   1.0903  -1.8763  -1.1890
 TIC  N1   N   NT    0  -0.425   0.0847  -1.0791  -0.5058
 TIC  S1   S   S2    0   0.195   4.2584  -0.1983   0.7861
 TIC  CL1  CL  CL    0  -0.138  -2.7924   1.3464  -2.0679
 TIC  C2   C   CH2   0  -0.302   0.4825   0.3148  -0.4086
 TIC  C3   C   CH2   0  -0.483   2.3474  -1.9943  -0.3343
 TIC  C4   C   CR5   0   0.133   1.8786   0.4363   0.1154
 TIC  C5   C   CR5   0  -0.237   2.7206  -0.6321   0.1441
 TIC  C6   C   CH2   0  -0.342  -1.2227  -1.2123  -1.1214
 TIC  C7   C   CR6   0   0.175  -2.2956  -0.6199  -0.2449
 TIC  C8   C   CR15  0  -0.211   2.4849   1.6283   0.6102
 TIC  C9   C   CR15  0  -0.474   3.7695   1.4342   1.0096
 TIC  C10  C   CR6   0  -0.123  -3.0530   0.5003  -0.5698
 TIC  C11  C   CR16  0  -0.291  -2.5412  -1.2177   0.9918
 TIC  C12  C   CR16  0  -0.198  -4.0281   1.0018   0.2845
 TIC  C13  C   CR16  0  -0.234  -3.5046  -0.7327   1.8589
 TIC  C14  C   CR16  0  -0.277  -4.2534   0.3818   1.5015
 TIC  H1   H   HCH2  0   0.248   0.6824  -2.8722  -1.3695
 TIC  H1A  H   HCH2  0   0.207   1.3503  -1.4530  -2.1730
 TIC  H2   H   HCH2  0   0.214   0.4153   0.8258  -1.3855
 TIC  H2A  H   HCH2  0   0.255  -0.2074   0.8397   0.2578
 TIC  H3   H   HCH2  0   0.252   2.1632  -2.6643   0.5100
 TIC  H3A  H   HCH2  0   0.253   3.1486  -2.4445  -0.9241
 TIC  H6   H   HCH2  0   0.224  -1.2516  -0.7779  -2.1299
 TIC  H6A  H   HCH2  0   0.264  -1.4307  -2.2787  -1.2391
 TIC  H8   H   HCR5  0   0.260   1.9823   2.5846   0.6663
 TIC  H9   H   HCR5  0   0.291   4.4549   2.1589   1.4211
 TIC  H11  H   HCR6  0   0.258  -1.9559  -2.0857   1.2701
 TIC  H12  H   HCR6  0   0.278  -4.6003   1.8747   0.0008
 TIC  H13  H   HCR6  0   0.261  -3.6730  -1.2207   2.8096
 TIC  H14  H   HCR6  0   0.267  -5.0108   0.7736   2.1674

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
 TIC  C1   N1   single    1.454  0.020  1.454
 TIC  C1   C3   single    1.525  0.020  1.525
 TIC  N1   C2   single    1.453  0.020  1.453
 TIC  N1   C6   single    1.451  0.020  1.451
 TIC  S1   C5   aromatic  1.722  0.020  1.722
 TIC  S1   C9   aromatic  1.719  0.020  1.719
 TIC  CL1  C10  single    1.740  0.020  1.740
 TIC  C2   C4   single    1.496  0.020  1.496
 TIC  C3   C5   single    1.491  0.020  1.491
 TIC  C4   C5   aromatic  1.361  0.020  1.361
 TIC  C4   C8   aromatic  1.426  0.020  1.426
 TIC  C6   C7   single    1.507  0.020  1.507
 TIC  C7   C10  aromatic  1.391  0.020  1.391
 TIC  C7   C11  aromatic  1.395  0.020  1.395
 TIC  C8   C9   aromatic  1.359  0.020  1.359
 TIC  C10  C12  aromatic  1.390  0.020  1.390
 TIC  C11  C13  aromatic  1.384  0.020  1.384
 TIC  C12  C14  aromatic  1.384  0.020  1.384
 TIC  C13  C14  aromatic  1.389  0.020  1.389
 TIC  C1   H1   single    0.970  0.020  1.090
 TIC  C1   H1A  single    0.970  0.020  1.090
 TIC  C2   H2   single    0.970  0.020  1.090
 TIC  C2   H2A  single    0.970  0.020  1.090
 TIC  C3   H3   single    0.970  0.020  1.090
 TIC  C3   H3A  single    0.970  0.020  1.090
 TIC  C6   H6   single    0.970  0.020  1.090
 TIC  C6   H6A  single    0.970  0.020  1.090
 TIC  C8   H8   single    0.930  0.020  1.080
 TIC  C9   H9   single    0.930  0.020  1.080
 TIC  C11  H11  single    0.930  0.020  1.080
 TIC  C12  H12  single    0.930  0.020  1.080
 TIC  C13  H13  single    0.930  0.020  1.080
 TIC  C14  H14  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
 TIC  H1A  C1   H1   106.92  3.000
 TIC  H1A  C1   C3   109.62  3.000
 TIC  H1   C1   C3   109.29  3.000
 TIC  H1A  C1   N1   111.84  3.000
 TIC  H1   C1   N1   108.64  3.000
 TIC  C3   C1   N1   110.44  3.000
 TIC  C6   N1   C2   111.29  3.000
 TIC  C6   N1   C1   111.93  3.000
 TIC  C2   N1   C1   111.60  3.000
 TIC  C9   S1   C5    91.93  3.000
 TIC  H2A  C2   H2   106.18  3.000
 TIC  H2A  C2   C4   109.65  3.000
 TIC  H2   C2   C4   109.21  3.000
 TIC  H2A  C2   N1   109.18  3.000
 TIC  H2   C2   N1   111.59  3.000
 TIC  C4   C2   N1   110.91  3.000
 TIC  H3A  C3   H3   106.73  3.000
 TIC  H3A  C3   C5   111.48  3.000
 TIC  H3   C3   C5   110.75  3.000
 TIC  H3A  C3   C1   109.51  3.000
 TIC  H3   C3   C1   109.96  3.000
 TIC  C5   C3   C1   108.39  3.000
 TIC  C8   C4   C5   112.71  3.000
 TIC  C8   C4   C2   125.88  3.000
 TIC  C5   C4   C2   121.41  3.000
 TIC  C4   C5   C3   123.75  3.000
 TIC  C4   C5   S1   111.27  3.000
 TIC  C3   C5   S1   124.98  3.000
 TIC  H6A  C6   H6   106.38  3.000
 TIC  H6A  C6   C7   108.11  3.000
 TIC  H6   C6   C7   111.09  3.000
 TIC  H6A  C6   N1   107.86  3.000
 TIC  H6   C6   N1   112.14  3.000
 TIC  C7   C6   N1   111.02  3.000
 TIC  C11  C7   C10  117.14  3.000
 TIC  C11  C7   C6   118.19  3.000
 TIC  C10  C7   C6   124.66  3.000
 TIC  H8   C8   C9   123.37  3.000
 TIC  H8   C8   C4   124.02  3.000
 TIC  C9   C8   C4   112.60  3.000
 TIC  H9   C9   C8   128.06  3.000
 TIC  H9   C9   S1   120.45  3.000
 TIC  C8   C9   S1   111.49  3.000
 TIC  C12  C10  C7   121.95  3.000
 TIC  C12  C10  CL1  117.30  3.000
 TIC  C7   C10  CL1  120.74  3.000
 TIC  H11  C11  C13  119.73  3.000
 TIC  H11  C11  C7   118.42  3.000
 TIC  C13  C11  C7   121.85  3.000
 TIC  H12  C12  C14  120.39  3.000
 TIC  H12  C12  C10  120.07  3.000
 TIC  C14  C12  C10  119.53  3.000
 TIC  H13  C13  C14  120.26  3.000
 TIC  H13  C13  C11  120.06  3.000
 TIC  C14  C13  C11  119.68  3.000
 TIC  H14  C14  C13  120.63  3.000
 TIC  H14  C14  C12  119.53  3.000
 TIC  C13  C14  C12  119.84  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
 TIC  CONST_01  C8   C4   C5   S1      0.00   0.0  0
 TIC  CONST_02  C4   C8   C9   S1      0.00   0.0  0
 TIC  CONST_03  C9   S1   C5   C4      0.00   0.0  0
 TIC  CONST_04  C8   C9   S1   C5      0.00   0.0  0
 TIC  CONST_05  C9   C8   C4   C5      0.00   0.0  0
 TIC  CONST_06  C14  C12  C10  C7      0.00   0.0  0
 TIC  CONST_07  C14  C13  C11  C7      0.00   0.0  0
 TIC  CONST_08  C13  C11  C7   C10     0.00   0.0  0
 TIC  CONST_09  C13  C14  C12  C10     0.00   0.0  0
 TIC  CONST_10  C12  C10  C7   C11     0.00   0.0  0
 TIC  CONST_11  C12  C14  C13  C11     0.00   0.0  0
 TIC  CONST_12  C11  C7   C10  CL1   180.00   0.0  0
 TIC  CONST_13  C14  C12  C10  CL1   180.00   0.0  0
 TIC  CONST_14  C12  C10  C7   C6    180.00   0.0  0
 TIC  CONST_15  C13  C11  C7   C6    180.00   0.0  0
 TIC  CONST_16  H8   C8   C9   S1    180.00   0.0  0
 TIC  CONST_17  H9   C9   C8   C4    180.00   0.0  0
 TIC  CONST_18  H12  C12  C10  C7    180.00   0.0  0
 TIC  CONST_19  H13  C13  C11  C7    180.00   0.0  0
 TIC  CONST_20  H11  C11  C7   C10   180.00   0.0  0
 TIC  CONST_21  H14  C14  C12  C10   180.00   0.0  0
 TIC  Var_01    C4   C2   N1   C1    -49.19  30.0  1
 TIC  Var_02    S1   C5   C3   C1   -163.35  30.0  1
 TIC  Var_03    C5   C3   C1   N1    -48.54  30.0  1
 TIC  Var_04    C5   C4   C2   N1     15.46  30.0  1
 TIC  Var_05    C3   C1   N1   C2     68.62  30.0  1
 TIC  Var_06    C7   C6   N1   C1    168.18  30.0  3
 TIC  Var_07    C10  C7   C6   N1    113.97  30.0  2

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
 TIC  plan-1  CL1  0.020
 TIC  plan-1  C6   0.020
 TIC  plan-1  C7   0.020
 TIC  plan-1  C10  0.020
 TIC  plan-1  C11  0.020
 TIC  plan-1  C12  0.020
 TIC  plan-1  C13  0.020
 TIC  plan-1  C14  0.020
 TIC  plan-1  H11  0.020
 TIC  plan-1  H12  0.020
 TIC  plan-1  H13  0.020
 TIC  plan-1  H14  0.020
 TIC  plan-2  S1   0.020
 TIC  plan-2  C2   0.020
 TIC  plan-2  C3   0.020
 TIC  plan-2  C4   0.020
 TIC  plan-2  C5   0.020
 TIC  plan-2  C8   0.020
 TIC  plan-2  C9   0.020
 TIC  plan-2  H8   0.020
 TIC  plan-2  H9   0.020

