# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 22:48:30 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 4-(4-methoxyphenyl)-6,7-dihydrothieno[3,2-c]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)C2=NCCc3sccc23
#
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
 JLY  JLY  4-(4-methoxyphenyl)-6,7-dihydrothieno[3,2-c]pyridine  ligand  30  17  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JLY
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
 JLY  C13   C  CR56  0  -0.212   2.8964   0.0505   0.1971
 JLY  C15   C  CR15  0  -0.482   2.6153  -2.2200  -0.7217
 JLY  C17   C  CR56  0   0.109   1.6104  -0.2044  -0.1951
 JLY  C01   C  CH3   0  -0.438  -5.4694  -1.3137   0.4596
 JLY  C03   C  CR6   0   0.380  -3.5798   0.0183  -0.0738
 JLY  C04   C  CR16  0  -0.331  -3.0841   1.1997  -0.6356
 JLY  C05   C  CR16  0  -0.269  -1.7303   1.4606  -0.6235
 JLY  C06   C  CR6   0   0.039  -0.8225   0.5528  -0.0702
 JLY  C07   C  CR16  0  -0.292  -1.3275  -0.6181   0.4844
 JLY  C08   C  CR16  0  -0.373  -2.6898  -0.8898   0.4938
 JLY  C09   C  CR6   0   0.175   0.6205   0.8726  -0.0397
 JLY  N10   N  N     0  -0.390   0.9674   2.0915   0.1132
 JLY  C11   C  C     0  -0.327   2.3814   2.4145   0.1034
 JLY  C12   C  C     0  -0.518   3.2782   1.3719   0.7670
 JLY  S14   S  S2    0   0.239   3.9083  -1.3006  -0.0551
 JLY  C16   C  CR15  0  -0.220   1.4538  -1.5159  -0.7367
 JLY  H151  H  HCR5  0   0.299   2.7881  -3.2255  -1.0719
 JLY  H011  H  HCH3  0   0.230  -5.1100  -2.2286  -0.0185
 JLY  H012  H  HCH3  0   0.231  -5.2603  -1.3686   1.5309
 JLY  H013  H  HCH3  0   0.261  -6.5445  -1.2446   0.3152
 JLY  H041  H  HCR6  0   0.264  -3.7726   1.9078  -1.0803
 JLY  H051  H  HCR6  0   0.253  -1.3626   2.3805  -1.0588
 JLY  H071  H  HCR6  0   0.266  -0.6616  -1.3350   0.9481
 JLY  H081  H  HCR6  0   0.282  -3.0317  -1.8099   0.9468
 JLY  H111  H  H     0   0.240   2.6959   2.5477  -0.9396
 JLY  H112  H  H     0   0.245   2.5174   3.3800   0.5918
 JLY  H122  H  H     0   0.263   3.1325   1.3704   1.8524
 JLY  H121  H  H     0   0.268   4.3258   1.6134   0.5863
 JLY  H161  H  HCR5  0   0.274   0.5306  -1.9096  -1.1362
 JLY  O02   O  O2    0  -0.467  -4.9105  -0.1543  -0.1277

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
 JLY  C13  C17   aromatic  1.368  0.020  1.368
 JLY  C13  C12   single    1.489  0.020  1.489
 JLY  C13  S14   aromatic  1.707  0.020  1.707
 JLY  C15  S14   aromatic  1.721  0.020  1.721
 JLY  C15  C16   aromatic  1.358  0.020  1.358
 JLY  C17  C09   single    1.471  0.020  1.471
 JLY  C17  C16   aromatic  1.428  0.020  1.428
 JLY  C01  O02   single    1.415  0.020  1.415
 JLY  O02  C03   single    1.343  0.020  1.343
 JLY  C03  C04   aromatic  1.399  0.020  1.399
 JLY  C03  C08   aromatic  1.392  0.020  1.392
 JLY  C04  C05   aromatic  1.379  0.020  1.379
 JLY  C05  C06   aromatic  1.398  0.020  1.398
 JLY  C06  C07   aromatic  1.391  0.020  1.391
 JLY  C06  C09   single    1.478  0.020  1.478
 JLY  C07  C08   aromatic  1.389  0.020  1.389
 JLY  C09  N10   double    1.276  0.020  1.276
 JLY  N10  C11   single    1.450  0.020  1.450
 JLY  C11  C12   single    1.527  0.020  1.527
 JLY  C15  H151  single    0.930  0.020  1.080
 JLY  C01  H011  single    0.970  0.020  1.090
 JLY  C01  H012  single    0.970  0.020  1.090
 JLY  C01  H013  single    0.970  0.020  1.090
 JLY  C04  H041  single    0.930  0.020  1.080
 JLY  C05  H051  single    0.930  0.020  1.080
 JLY  C07  H071  single    0.930  0.020  1.080
 JLY  C08  H081  single    0.930  0.020  1.080
 JLY  C11  H111  single    0.970  0.020  1.090
 JLY  C11  H112  single    0.970  0.020  1.090
 JLY  C12  H122  single    0.970  0.020  1.090
 JLY  C12  H121  single    0.970  0.020  1.090
 JLY  C16  H161  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
 JLY  S14   C13  C12   127.38  3.000
 JLY  S14   C13  C17   111.55  3.000
 JLY  C12   C13  C17   121.07  3.000
 JLY  H151  C15  C16   128.07  3.000
 JLY  H151  C15  S14   120.22  3.000
 JLY  C16   C15  S14   111.70  3.000
 JLY  C16   C17  C09   129.71  3.000
 JLY  C16   C17  C13   112.52  3.000
 JLY  C09   C17  C13   117.76  3.000
 JLY  H013  C01  H012  108.82  3.000
 JLY  H013  C01  H011  108.69  3.000
 JLY  H012  C01  H011  108.89  3.000
 JLY  H013  C01  O02   106.46  3.000
 JLY  H012  C01  O02   111.87  3.000
 JLY  H011  C01  O02   112.00  3.000
 JLY  C08   C03  C04   119.21  3.000
 JLY  C08   C03  O02   124.47  3.000
 JLY  C04   C03  O02   116.33  3.000
 JLY  H041  C04  C05   120.27  3.000
 JLY  H041  C04  C03   119.46  3.000
 JLY  C05   C04  C03   120.28  3.000
 JLY  H051  C05  C06   119.38  3.000
 JLY  H051  C05  C04   119.41  3.000
 JLY  C06   C05  C04   121.21  3.000
 JLY  C09   C06  C07   121.90  3.000
 JLY  C09   C06  C05   120.10  3.000
 JLY  C07   C06  C05   117.96  3.000
 JLY  H071  C07  C08   118.08  3.000
 JLY  H071  C07  C06   120.33  3.000
 JLY  C08   C07  C06   121.57  3.000
 JLY  H081  C08  C07   118.65  3.000
 JLY  H081  C08  C03   121.58  3.000
 JLY  C07   C08  C03   119.77  3.000
 JLY  N10   C09  C06   118.32  3.000
 JLY  N10   C09  C17   121.93  3.000
 JLY  C06   C09  C17   119.75  3.000
 JLY  C11   N10  C09   118.48  3.000
 JLY  H112  C11  H111  106.40  3.000
 JLY  H112  C11  C12   109.67  3.000
 JLY  H111  C11  C12   109.12  3.000
 JLY  H112  C11  N10   108.40  3.000
 JLY  H111  C11  N10   108.23  3.000
 JLY  C12   C11  N10   114.68  3.000
 JLY  H121  C12  H122  107.00  3.000
 JLY  H121  C12  C11   109.94  3.000
 JLY  H122  C12  C11   110.70  3.000
 JLY  H121  C12  C13   112.31  3.000
 JLY  H122  C12  C13   110.13  3.000
 JLY  C11   C12  C13   106.80  3.000
 JLY  C15   S14  C13    91.99  3.000
 JLY  H161  C16  C17   124.67  3.000
 JLY  H161  C16  C15   123.09  3.000
 JLY  C17   C16  C15   112.23  3.000
 JLY  C03   O02  C01   118.69  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
 JLY  CONST_01  C15   C16  C17  C13     0.00   0.0  0
 JLY  CONST_02  C16   C15  S14  C13     0.00   0.0  0
 JLY  CONST_03  C17   C13  S14  C15     0.00   0.0  0
 JLY  CONST_04  S14   C15  C16  C17     0.00   0.0  0
 JLY  CONST_05  C06   C05  C04  C03     0.00   0.0  0
 JLY  CONST_06  C06   C07  C08  C03     0.00   0.0  0
 JLY  CONST_07  C07   C08  C03  C04     0.00   0.0  0
 JLY  CONST_08  C07   C06  C05  C04     0.00   0.0  0
 JLY  CONST_09  C08   C03  C04  C05     0.00   0.0  0
 JLY  CONST_10  C08   C07  C06  C05     0.00   0.0  0
 JLY  CONST_11  C16   C17  C13  S14     0.00   0.0  0
 JLY  CONST_12  C09   C06  C05  C04   180.00   0.0  0
 JLY  CONST_13  C09   C06  C07  C08   180.00   0.0  0
 JLY  CONST_14  C05   C04  C03  O02   180.00   0.0  0
 JLY  CONST_15  C07   C08  C03  O02   180.00   0.0  0
 JLY  CONST_16  H161  C16  C17  C13   180.00   0.0  0
 JLY  CONST_17  H151  C15  S14  C13   180.00   0.0  0
 JLY  CONST_18  H051  C05  C04  C03   180.00   0.0  0
 JLY  CONST_19  H071  C07  C08  C03   180.00   0.0  0
 JLY  CONST_20  H081  C08  C03  C04   180.00   0.0  0
 JLY  CONST_21  H041  C04  C05  C06   180.00   0.0  0
 JLY  Var_01    C06   C09  C17  C13  -162.42  30.0  1
 JLY  Var_02    N10   C11  C12  C13    49.43  30.0  1
 JLY  Var_03    C11   C12  C13  C17   -31.59  30.0  1
 JLY  Var_04    C05   C06  C09  C17  -145.87  30.0  3
 JLY  Var_05    C12   C11  N10  C09   -36.82  30.0  1
 JLY  Var_06    C04   C03  O02  C01  -178.22  30.0  2
 JLY  Var_07    H011  C01  O02  C03   -62.10  30.0  3

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
 JLY  plan-1  C03   0.020
 JLY  plan-1  C04   0.020
 JLY  plan-1  C05   0.020
 JLY  plan-1  C06   0.020
 JLY  plan-1  C07   0.020
 JLY  plan-1  C08   0.020
 JLY  plan-1  C09   0.020
 JLY  plan-1  H041  0.020
 JLY  plan-1  H051  0.020
 JLY  plan-1  H071  0.020
 JLY  plan-1  H081  0.020
 JLY  plan-1  O02   0.020
 JLY  plan-2  C13   0.020
 JLY  plan-2  C15   0.020
 JLY  plan-2  C17   0.020
 JLY  plan-2  C09   0.020
 JLY  plan-2  C12   0.020
 JLY  plan-2  S14   0.020
 JLY  plan-2  C16   0.020
 JLY  plan-2  H151  0.020
 JLY  plan-2  H161  0.020

