# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 20:10:27 2021
#   Inital geometry file: a 85 line input string
#   Ligand name: (3~{a}~{R},7~{a}~{R})-4-(4-methoxyphenyl)-2,3,3~{a},6,7,7~{a}-hexahydrothieno[3,2-c]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)C2=NCC[C@H]3SCC[C@H]23
#
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
 S64  S64  (3~{a}~{R},7~{a}~{R})-4-(4-methoxyphenyl)-2,3,3~{a},6,7,7~{a}-hexahydrothieno[3,2-c]pyridine  ligand  34  17  .  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_S64
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
 S64  C10  C  CH2   0  -0.453  -27.5660   98.6120  139.4118
 S64  C13  C  CH2   0  -0.542  -26.2543  102.3698  139.1012
 S64  C15  C  CH1   0  -0.303  -26.8219  100.3703  137.8485
 S64  C17  C  CR16  0  -0.331  -27.1379  101.4151  133.4420
 S64  C01  C  CH3   0  -0.438  -25.4860  100.0285  130.5194
 S64  C03  C  CR6   0   0.377  -26.4508  100.5070  132.6333
 S64  C04  C  CR16  0  -0.371  -26.0613   99.2809  133.1675
 S64  C05  C  CR16  0  -0.274  -26.3615   98.9805  134.4898
 S64  C06  C  CR6   0   0.049  -27.0252   99.8840  135.3122
 S64  C07  C  C     0   0.204  -27.3317   99.5061  136.7151
 S64  C09  C  CH2   0  -0.325  -28.2004   97.8827  138.2242
 S64  C11  C  CH1   0  -0.373  -27.6240  100.0892  139.1073
 S64  C14  C  CH2   0  -0.449  -26.7579  101.8887  137.7385
 S64  C16  C  CR16  0  -0.269  -27.4095  101.1078  134.7613
 S64  N08  N  N     0  -0.366  -27.9080   98.3904  136.8998
 S64  S12  S  S2    0  -0.020  -26.9072  101.1995  140.3613
 S64  H1   H  HCH2  0   0.253  -28.1060   98.3527  140.3241
 S64  H2   H  HCH2  0   0.236  -26.5252   98.3078  139.5507
 S64  H3   H  HCH2  0   0.268  -25.1657  102.3548  139.1429
 S64  H4   H  HCH2  0   0.274  -26.5910  103.3796  139.3272
 S64  H5   H  HCH1  0   0.278  -25.7907  100.0266  138.0203
 S64  H6   H  HCR6  0   0.264  -27.4587  102.3625  133.0273
 S64  H7   H  HCH3  0   0.260  -25.3799  100.5448  129.5686
 S64  H8   H  HCH3  0   0.230  -24.4902   99.8107  130.9135
 S64  H9   H  HCH3  0   0.230  -26.0124   99.0857  130.3501
 S64  H10  H  HCR6  0   0.280  -25.5245   98.5501  132.5779
 S64  H11  H  HCR6  0   0.254  -26.0558   98.0223  134.8899
 S64  H13  H  HCH2  0   0.241  -29.2901   97.8924  138.3298
 S64  H14  H  HCH1  0   0.272  -28.6660  100.3841  138.9433
 S64  H15  H  HCH2  0   0.266  -26.0862  102.2316  136.9516
 S64  H16  H  HCH2  0   0.246  -27.7494  102.3016  137.5400
 S64  H17  H  HCR6  0   0.256  -27.9556  101.8280  135.3554
 S64  H12  H  HCH2  0   0.247  -27.9191   96.8271  138.2393
 S64  O02  O  O2    0  -0.469  -26.2114  100.8959  131.3685

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
 S64  C01  O02  single    1.414  0.020  1.414
 S64  O02  C03  single    1.345  0.020  1.345
 S64  C03  C04  aromatic  1.393  0.020  1.393
 S64  C03  C17  aromatic  1.397  0.020  1.397
 S64  C04  C05  aromatic  1.389  0.020  1.389
 S64  C17  C16  aromatic  1.382  0.020  1.382
 S64  C05  C06  aromatic  1.390  0.020  1.390
 S64  C16  C06  aromatic  1.396  0.020  1.396
 S64  C06  C07  single    1.485  0.020  1.485
 S64  C07  N08  double    1.269  0.020  1.269
 S64  C07  C15  single    1.514  0.020  1.514
 S64  N08  C09  single    1.448  0.020  1.448
 S64  C14  C15  single    1.524  0.020  1.524
 S64  C14  C13  single    1.530  0.020  1.530
 S64  C15  C11  single    1.519  0.020  1.519
 S64  C09  C10  single    1.531  0.020  1.531
 S64  C13  S12  single    1.839  0.020  1.839
 S64  C11  C10  single    1.509  0.020  1.509
 S64  C11  S12  single    1.822  0.020  1.822
 S64  C10  H1   single    0.970  0.020  1.090
 S64  C10  H2   single    0.970  0.020  1.090
 S64  C13  H3   single    0.970  0.020  1.090
 S64  C13  H4   single    0.970  0.020  1.090
 S64  C15  H5   single    0.970  0.020  1.090
 S64  C17  H6   single    0.930  0.020  1.080
 S64  C01  H7   single    0.970  0.020  1.090
 S64  C01  H8   single    0.970  0.020  1.090
 S64  C01  H9   single    0.970  0.020  1.090
 S64  C04  H10  single    0.930  0.020  1.080
 S64  C05  H11  single    0.930  0.020  1.080
 S64  C09  H13  single    0.970  0.020  1.090
 S64  C11  H14  single    0.970  0.020  1.090
 S64  C14  H15  single    0.970  0.020  1.090
 S64  C14  H16  single    0.970  0.020  1.090
 S64  C16  H17  single    0.930  0.020  1.080
 S64  C09  H12  single    0.970  0.020  1.090

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
 S64  H2   C10  H1   107.38  3.000
 S64  H2   C10  C11  109.54  3.000
 S64  H1   C10  C11  112.46  3.000
 S64  H2   C10  C09  111.13  3.000
 S64  H1   C10  C09  109.28  3.000
 S64  C11  C10  C09  107.08  3.000
 S64  H4   C13  H3   108.30  3.000
 S64  H4   C13  S12  109.77  3.000
 S64  H3   C13  S12  108.64  3.000
 S64  H4   C13  C14  112.01  3.000
 S64  H3   C13  C14  111.02  3.000
 S64  S12  C13  C14  107.05  3.000
 S64  H5   C15  C14  106.45  3.000
 S64  H5   C15  C11  107.92  3.000
 S64  C14  C15  C11  105.46  3.000
 S64  H5   C15  C07  104.72  3.000
 S64  C11  C15  C07  109.70  3.000
 S64  C14  C15  C07  121.94  3.000
 S64  H6   C17  C16  120.14  3.000
 S64  H6   C17  C03  119.53  3.000
 S64  C16  C17  C03  120.33  3.000
 S64  H9   C01  H8   108.83  3.000
 S64  H9   C01  H7   108.73  3.000
 S64  H8   C01  H7   108.73  3.000
 S64  H9   C01  O02  112.03  3.000
 S64  H8   C01  O02  111.91  3.000
 S64  H7   C01  O02  106.50  3.000
 S64  O02  C03  C04  124.44  3.000
 S64  C04  C03  C17  119.19  3.000
 S64  O02  C03  C17  116.37  3.000
 S64  H10  C04  C05  118.70  3.000
 S64  H10  C04  C03  121.63  3.000
 S64  C05  C04  C03  119.67  3.000
 S64  H11  C05  C06  119.43  3.000
 S64  H11  C05  C04  118.84  3.000
 S64  C06  C05  C04  121.73  3.000
 S64  C16  C06  C07  122.62  3.000
 S64  C07  C06  C05  119.47  3.000
 S64  C16  C06  C05  117.88  3.000
 S64  N08  C07  C06  117.06  3.000
 S64  N08  C07  C15  123.08  3.000
 S64  C06  C07  C15  119.51  3.000
 S64  H12  C09  H13  105.28  3.000
 S64  H12  C09  N08  107.41  3.000
 S64  H13  C09  N08  106.62  3.000
 S64  H12  C09  C10  110.05  3.000
 S64  H13  C09  C10  109.48  3.000
 S64  N08  C09  C10  117.30  3.000
 S64  H14  C11  S12  108.26  3.000
 S64  H14  C11  C15  109.17  3.000
 S64  S12  C11  C15  104.47  3.000
 S64  H14  C11  C10  109.29  3.000
 S64  S12  C11  C10  116.27  3.000
 S64  C15  C11  C10  109.15  3.000
 S64  H16  C14  H15  108.02  3.000
 S64  H16  C14  C15  110.60  3.000
 S64  H15  C14  C15  113.05  3.000
 S64  H16  C14  C13  109.98  3.000
 S64  H15  C14  C13  109.95  3.000
 S64  C15  C14  C13  105.23  3.000
 S64  H17  C16  C06  120.40  3.000
 S64  H17  C16  C17  118.40  3.000
 S64  C06  C16  C17  121.18  3.000
 S64  C09  N08  C07  122.20  3.000
 S64  C11  S12  C13   93.21  3.000
 S64  C03  O02  C01  118.60  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
 S64  CONST_01  C05  C04  C03  C17     0.00   0.0  0
 S64  CONST_02  C05  C06  C16  C17     0.00   0.0  0
 S64  CONST_03  C06  C05  C04  C03     0.00   0.0  0
 S64  CONST_04  C06  C16  C17  C03     0.00   0.0  0
 S64  CONST_05  C16  C17  C03  C04     0.00   0.0  0
 S64  CONST_06  C16  C06  C05  C04     0.00   0.0  0
 S64  CONST_07  C07  C06  C16  C17   180.00   0.0  0
 S64  CONST_08  C07  C06  C05  C04   180.00   0.0  0
 S64  CONST_09  O02  C03  C04  C05   180.00   0.0  0
 S64  CONST_10  O02  C03  C17  C16   180.00   0.0  0
 S64  CONST_11  H10  C04  C03  C17   180.00   0.0  0
 S64  CONST_12  H11  C05  C04  C03   180.00   0.0  0
 S64  CONST_13  H17  C16  C17  C03   180.00   0.0  0
 S64  CONST_14  H6   C17  C03  C04   180.00   0.0  0
 S64  Var_01    C05  C06  C07  C15   122.83  30.0  2
 S64  Var_02    S12  C13  C14  C15   -32.80  30.0  1
 S64  Var_03    N08  C09  C10  C11    39.60  30.0  1
 S64  Var_04    C14  C13  S12  C11     5.39  30.0  1
 S64  Var_05    H13  C09  N08  C07   112.15  30.0  1
 S64  Var_06    C04  C03  O02  C01    -1.73  30.0  2
 S64  Var_07    H7   C01  O02  C03  -178.21  30.0  3

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
 S64  chir_01  C15  C07  C14  C11  negativ
 S64  chir_02  C11  S12  C10  C15  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
 S64  plan-1  C17  0.020
 S64  plan-1  C03  0.020
 S64  plan-1  C04  0.020
 S64  plan-1  C05  0.020
 S64  plan-1  C06  0.020
 S64  plan-1  C07  0.020
 S64  plan-1  C16  0.020
 S64  plan-1  H6   0.020
 S64  plan-1  H10  0.020
 S64  plan-1  H11  0.020
 S64  plan-1  H17  0.020
 S64  plan-1  O02  0.020

