# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 03:03:41 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: N-[(4-bromothiophen-2-yl)methyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCc1scc(Br)c1
#
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
 J5A  J5A  N-[(4-bromothiophen-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 PERFECT
;

data_comp_J5A
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
 J5A  C   C   CH3   0  -0.771   4.7261  -0.7602  -1.5237
 J5A  O   O   O     0  -0.503   3.8865   1.0597  -0.2108
 J5A  C1  C   C     0   0.531   3.8415  -0.1351  -0.4774
 J5A  C2  C   CH2   0  -0.377   2.0577  -0.5014   1.1446
 J5A  C3  C   CR5   0  -0.140   0.8423   0.1626   0.5722
 J5A  C4  C   CR15  0  -0.200  -0.4357  -0.3057   0.6071
 J5A  C5  C   CR5   0  -0.024  -1.3466   0.5836  -0.0243
 J5A  C6  C   CR15  0  -0.473  -0.7627   1.7027  -0.5250
 J5A  BR  BR  BR    0  -0.036  -3.1830   0.2276  -0.1511
 J5A  S   S   S2    0   0.252   0.9257   1.6855  -0.2329
 J5A  N   N   NH1   0  -0.610   2.9899  -0.9675   0.1439
 J5A  H1  H   HCH3  0   0.267   5.7622  -0.4787  -1.3411
 J5A  H2  H   HCH3  0   0.251   4.6592  -1.8458  -1.5542
 J5A  H3  H   HCH3  0   0.269   4.4507  -0.3716  -2.5045
 J5A  H4  H   HCH2  0   0.274   2.5725   0.1700   1.8330
 J5A  H5  H   HCH2  0   0.286   1.7341  -1.3645   1.7239
 J5A  H6  H   HCR5  0   0.285  -0.7171  -1.2429   1.0663
 J5A  H7  H   HCR5  0   0.312  -1.2270   2.5224  -1.0513
 J5A  H8  H   HNH1  0   0.408   2.9202  -1.9257  -0.1560

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
 J5A  O   C1  double    1.225  0.020  1.225
 J5A  C   C1  single    1.506  0.020  1.506
 J5A  C1  N   single    1.343  0.020  1.343
 J5A  N   C2  single    1.445  0.020  1.445
 J5A  C2  C3  single    1.499  0.020  1.499
 J5A  C3  C4  aromatic  1.361  0.020  1.361
 J5A  C3  S   aromatic  1.725  0.020  1.725
 J5A  C4  C5  aromatic  1.421  0.020  1.421
 J5A  S   C6  aromatic  1.714  0.020  1.714
 J5A  C5  C6  aromatic  1.358  0.020  1.358
 J5A  C5  BR  single    1.875  0.020  1.875
 J5A  C   H1  single    0.970  0.020  1.090
 J5A  C   H2  single    0.970  0.020  1.090
 J5A  C   H3  single    0.970  0.020  1.090
 J5A  C2  H4  single    0.970  0.020  1.090
 J5A  C2  H5  single    0.970  0.020  1.090
 J5A  C4  H6  single    0.930  0.020  1.080
 J5A  C6  H7  single    0.930  0.020  1.080
 J5A  N   H8  single    0.860  0.020  1.020

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
 J5A  H3  C   H2  108.35  3.000
 J5A  H3  C   H1  107.40  3.000
 J5A  H2  C   H1  108.73  3.000
 J5A  H3  C   C1  109.19  3.000
 J5A  H2  C   C1  113.42  3.000
 J5A  H1  C   C1  109.58  3.000
 J5A  N   C1  O   121.81  3.000
 J5A  N   C1  C   115.88  3.000
 J5A  O   C1  C   122.31  3.000
 J5A  H5  C2  H4  107.00  3.000
 J5A  H5  C2  N   107.73  3.000
 J5A  H4  C2  N   109.34  3.000
 J5A  H5  C2  C3  108.27  3.000
 J5A  H4  C2  C3  110.56  3.000
 J5A  N   C2  C3  113.68  3.000
 J5A  S   C3  C4  111.17  3.000
 J5A  S   C3  C2  122.03  3.000
 J5A  C4  C3  C2  126.81  3.000
 J5A  H6  C4  C5  124.36  3.000
 J5A  H6  C4  C3  123.61  3.000
 J5A  C5  C4  C3  112.03  3.000
 J5A  BR  C5  C6  123.55  3.000
 J5A  BR  C5  C4  122.62  3.000
 J5A  C6  C5  C4  113.82  3.000
 J5A  H7  C6  S   120.98  3.000
 J5A  H7  C6  C5  128.38  3.000
 J5A  S   C6  C5  110.64  3.000
 J5A  C6  S   C3   92.34  3.000
 J5A  H8  N   C2  117.96  3.000
 J5A  H8  N   C1  119.74  3.000
 J5A  C2  N   C1  121.97  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
 J5A  CONST_01  C6  C5  C4  C3    0.00   0.0  0
 J5A  CONST_02  C5  C6  S   C3    0.00   0.0  0
 J5A  CONST_03  C6  S   C3  C4    0.00   0.0  0
 J5A  CONST_04  S   C6  C5  C4    0.00   0.0  0
 J5A  CONST_05  S   C3  C4  C5    0.00   0.0  0
 J5A  CONST_06  C5  C4  C3  C2  180.00   0.0  0
 J5A  CONST_07  C6  S   C3  C2  180.00   0.0  0
 J5A  CONST_08  BR  C5  C4  C3  180.00   0.0  0
 J5A  CONST_09  S   C6  C5  BR  180.00   0.0  0
 J5A  CONST_10  H7  C6  S   C3  180.00   0.0  0
 J5A  CONST_11  H6  C4  C5  C6  180.00   0.0  0
 J5A  CONST_12  C2  N   C1  C   180.00   0.0  0
 J5A  CONST_13  C2  N   C1  O     0.00   0.0  0
 J5A  CONST_14  H8  N   C1  C     0.00   0.0  0
 J5A  Var_01    N   C2  C3  C4  111.75  30.0  2
 J5A  Var_02    C3  C2  N   C1   78.89  30.0  3
 J5A  Var_03    H1  C   C1  O    50.86  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
 J5A  plan-1  C2  0.020
 J5A  plan-1  C3  0.020
 J5A  plan-1  C4  0.020
 J5A  plan-1  C5  0.020
 J5A  plan-1  C6  0.020
 J5A  plan-1  BR  0.020
 J5A  plan-1  S   0.020
 J5A  plan-1  H6  0.020
 J5A  plan-1  H7  0.020
 J5A  plan-2  C   0.020
 J5A  plan-2  O   0.020
 J5A  plan-2  C1  0.020
 J5A  plan-2  C2  0.020
 J5A  plan-2  N   0.020
 J5A  plan-2  H8  0.020

