# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 02:56:56 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: N-[(5-chlorothiophen-2-yl)methyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCc1sc(Cl)cc1
#
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
 J64  J64  N-[(5-chlorothiophen-2-yl)methyl]acetamide  ligand  19  11  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_J64
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
 J64  N1   N   NH1   0  -0.609  -2.6793   0.6551  -0.3627
 J64  C4   C   CR5   0  -0.141  -0.3048   0.8574   0.2754
 J64  C5   C   CR15  0  -0.227   0.7023   1.6767  -0.1337
 J64  C6   C   CR15  0  -0.136   1.9520   1.0165  -0.2901
 J64  C7   C   CR5   0  -0.257   1.8509  -0.3024   0.0125
 J64  C1   C   CH3   0  -0.770  -4.1080  -1.0770  -1.2559
 J64  C2   C   C     0   0.532  -3.0884  -0.6178  -0.2472
 J64  O1   O   O     0  -0.507  -2.6696  -1.3527   0.6402
 J64  C3   C   CH2   0  -0.378  -1.7258   1.2381   0.5538
 J64  CL1  CL  CL    0  -0.088   3.1015  -1.4686  -0.0476
 J64  S1   S   S2    0   0.273   0.2597  -0.7636   0.4804
 J64  H1   H   HNH1  0   0.408  -2.9883   1.2105  -1.1427
 J64  H2   H   HCR5  0   0.273   0.5590   2.7329  -0.3169
 J64  H3   H   HCR5  0   0.285   2.8641   1.4980  -0.6099
 J64  H4   H   HCH3  0   0.251  -4.2639  -0.3677  -2.0662
 J64  H5   H   HCH3  0   0.265  -3.8003  -2.0321  -1.6787
 J64  H6   H   HCH3  0   0.271  -5.0626  -1.2347  -0.7529
 J64  H7   H   HCH2  0   0.285  -1.8072   2.3211   0.4733
 J64  H8   H   HCH2  0   0.273  -2.0009   0.9731   1.5758

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
 J64  O1  C2   double    1.226  0.020  1.226
 J64  C1  C2   single    1.506  0.020  1.506
 J64  C2  N1   single    1.342  0.020  1.342
 J64  N1  C3   single    1.445  0.020  1.445
 J64  C3  C4   single    1.497  0.020  1.497
 J64  C4  C5   aromatic  1.361  0.020  1.361
 J64  C4  S1   aromatic  1.729  0.020  1.729
 J64  C5  C6   aromatic  1.422  0.020  1.422
 J64  S1  C7   aromatic  1.722  0.020  1.722
 J64  C6  C7   aromatic  1.357  0.020  1.357
 J64  C7  CL1  single    1.711  0.020  1.711
 J64  N1  H1   single    0.860  0.020  1.020
 J64  C5  H2   single    0.930  0.020  1.080
 J64  C6  H3   single    0.930  0.020  1.080
 J64  C1  H4   single    0.970  0.020  1.090
 J64  C1  H5   single    0.970  0.020  1.090
 J64  C1  H6   single    0.970  0.020  1.090
 J64  C3  H7   single    0.970  0.020  1.090
 J64  C3  H8   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
 J64  H1   N1  C3   118.13  3.000
 J64  H1   N1  C2   119.78  3.000
 J64  C3   N1  C2   121.95  3.000
 J64  S1   C4  C3   121.76  3.000
 J64  S1   C4  C5   111.01  3.000
 J64  C3   C4  C5   127.23  3.000
 J64  H2   C5  C6   123.45  3.000
 J64  H2   C5  C4   122.73  3.000
 J64  C6   C5  C4   113.82  3.000
 J64  H3   C6  C7   124.21  3.000
 J64  H3   C6  C5   124.61  3.000
 J64  C7   C6  C5   111.18  3.000
 J64  S1   C7  CL1  120.17  3.000
 J64  CL1  C7  C6   126.89  3.000
 J64  S1   C7  C6   112.94  3.000
 J64  H6   C1  H5   107.43  3.000
 J64  H6   C1  H4   108.21  3.000
 J64  H5   C1  H4   108.85  3.000
 J64  H6   C1  C2   109.13  3.000
 J64  H5   C1  C2   109.64  3.000
 J64  H4   C1  C2   113.40  3.000
 J64  O1   C2  C1   122.24  3.000
 J64  C1   C2  N1   115.97  3.000
 J64  O1   C2  N1   121.79  3.000
 J64  H8   C3  H7   106.97  3.000
 J64  H8   C3  C4   110.59  3.000
 J64  H7   C3  C4   108.06  3.000
 J64  H8   C3  N1   109.25  3.000
 J64  H7   C3  N1   107.76  3.000
 J64  C4   C3  N1   113.93  3.000
 J64  C7   S1  C4    91.05  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
 J64  CONST_01  C7   C6  C5  C4    0.00   0.0  0
 J64  CONST_02  C6   C7  S1  C4    0.00   0.0  0
 J64  CONST_03  C7   S1  C4  C5    0.00   0.0  0
 J64  CONST_04  S1   C7  C6  C5    0.00   0.0  0
 J64  CONST_05  S1   C4  C5  C6    0.00   0.0  0
 J64  CONST_06  CL1  C7  S1  C4  180.00   0.0  0
 J64  CONST_07  CL1  C7  C6  C5  180.00   0.0  0
 J64  CONST_08  C3   C4  C5  C6  180.00   0.0  0
 J64  CONST_09  C3   C4  S1  C7  180.00   0.0  0
 J64  CONST_10  H3   C6  C5  C4  180.00   0.0  0
 J64  CONST_11  H2   C5  C6  C7  180.00   0.0  0
 J64  CONST_12  C3   N1  C2  C1  180.00   0.0  0
 J64  CONST_13  C3   N1  C2  O1    0.00   0.0  0
 J64  CONST_14  H1   N1  C2  C1    0.00   0.0  0
 J64  Var_01    C5   C4  C3  N1  113.90  30.0  2
 J64  Var_02    C2   N1  C3  C4   78.81  30.0  1
 J64  Var_03    H4   C1  C2  N1    9.99  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
 J64  plan-1  C4   0.020
 J64  plan-1  C5   0.020
 J64  plan-1  C6   0.020
 J64  plan-1  C7   0.020
 J64  plan-1  C3   0.020
 J64  plan-1  CL1  0.020
 J64  plan-1  S1   0.020
 J64  plan-1  H2   0.020
 J64  plan-1  H3   0.020
 J64  plan-2  N1   0.020
 J64  plan-2  C1   0.020
 J64  plan-2  C2   0.020
 J64  plan-2  O1   0.020
 J64  plan-2  C3   0.020
 J64  plan-2  H1   0.020

