# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 13:39:00 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 2,5-dichloro-N-(pyridin-3-yl)thiophene-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1sc(Cl)c(c1)C(=O)Nc2cccnc2
#
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
 DJ6  DJ6  2,5-dichloro-N-(pyridin-3-yl)thiophene-3-carboxamide  ligand  22  16  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DJ6
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
 DJ6  C    C   CR16  0  -0.312   4.9545   0.3850   0.5605
 DJ6  N    N   N     0  -0.387   4.7632  -1.7246  -0.5175
 DJ6  O    O   O     0  -0.441   0.8719   1.5942   0.7704
 DJ6  S    S   S2    0   0.374  -3.4222   0.3876  -0.3266
 DJ6  CL   CL  CL    0  -0.039  -1.7210   2.7829  -0.3317
 DJ6  C1   C   CR16  0  -0.210   3.5794   0.5624   0.5406
 DJ6  CL1  CL  CL    0  -0.053  -3.7702  -2.5452  -0.0489
 DJ6  C2   C   CR6   0   0.292   2.7958  -0.4408  -0.0254
 DJ6  C3   C   CR16  0  -0.146   3.4535  -1.5636  -0.5391
 DJ6  C4   C   CR16  0  -0.083   5.5067  -0.7656   0.0245
 DJ6  C5   C   C     0   0.540   0.5382   0.5318   0.2843
 DJ6  C6   C   CR5   0   0.102  -0.8902   0.1776   0.0810
 DJ6  C7   C   CR15  0  -0.164  -1.4182  -1.1483   0.1363
 DJ6  C8   C   CR5   0  -0.251  -2.7568  -1.1775  -0.0630
 DJ6  C9   C   CR5   0  -0.314  -1.8701   1.1000  -0.1528
 DJ6  H    H   HCR6  0   0.276   5.5915   1.1450   0.9919
 DJ6  H1   H   HCR6  0   0.297   3.1452   1.4570   0.9539
 DJ6  HN1  H   HNH1  0   0.427   1.0124  -1.2290  -0.5988
 DJ6  H3   H   HCR6  0   0.275   2.8723  -2.3649  -0.9875
 DJ6  H4   H   HCR6  0   0.266   6.5790  -0.9213   0.0308
 DJ6  H7   H   HCR5  0   0.307  -0.8350  -2.0328   0.3504
 DJ6  N1   N   NH1   0  -0.754   1.4051  -0.4305  -0.1229

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
 DJ6  C    C1   aromatic  1.387  0.020  1.387
 DJ6  C    C4   aromatic  1.384  0.020  1.384
 DJ6  N    C3   aromatic  1.320  0.020  1.320
 DJ6  N    C4   aromatic  1.329  0.020  1.329
 DJ6  O    C5   double    1.215  0.020  1.215
 DJ6  S    C8   aromatic  1.721  0.020  1.721
 DJ6  S    C9   aromatic  1.717  0.020  1.717
 DJ6  CL   C9   single    1.699  0.020  1.699
 DJ6  C1   C2   aromatic  1.393  0.020  1.393
 DJ6  N1   C2   single    1.394  0.020  1.394
 DJ6  N1   C5   single    1.358  0.020  1.358
 DJ6  CL1  C8   single    1.702  0.020  1.702
 DJ6  C2   C3   aromatic  1.399  0.020  1.399
 DJ6  C5   C6   single    1.486  0.020  1.486
 DJ6  C6   C7   aromatic  1.428  0.020  1.428
 DJ6  C6   C9   aromatic  1.366  0.020  1.366
 DJ6  C7   C8   aromatic  1.354  0.020  1.354
 DJ6  C    H    single    0.930  0.020  1.080
 DJ6  C1   H1   single    0.930  0.020  1.080
 DJ6  N1   HN1  single    0.860  0.020  1.020
 DJ6  C3   H3   single    0.930  0.020  1.080
 DJ6  C4   H4   single    0.930  0.020  1.080
 DJ6  C7   H7   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
 DJ6  H    C   C4   120.24  3.000
 DJ6  H    C   C1   120.00  3.000
 DJ6  C4   C   C1   119.76  3.000
 DJ6  C4   N   C3   118.29  3.000
 DJ6  C9   S   C8    90.71  3.000
 DJ6  H1   C1  C2   121.83  3.000
 DJ6  H1   C1  C    120.04  3.000
 DJ6  C2   C1  C    118.13  3.000
 DJ6  C3   C2  N1   116.70  3.000
 DJ6  C3   C2  C1   117.56  3.000
 DJ6  N1   C2  C1   125.74  3.000
 DJ6  H3   C3  C2   119.46  3.000
 DJ6  H3   C3  N    116.59  3.000
 DJ6  C2   C3  N    123.95  3.000
 DJ6  H4   C4  N    116.89  3.000
 DJ6  H4   C4  C    120.79  3.000
 DJ6  N    C4  C    122.31  3.000
 DJ6  C6   C5  N1   113.82  3.000
 DJ6  C6   C5  O    121.82  3.000
 DJ6  N1   C5  O    124.36  3.000
 DJ6  C9   C6  C7   111.61  3.000
 DJ6  C9   C6  C5   123.52  3.000
 DJ6  C7   C6  C5   124.86  3.000
 DJ6  H7   C7  C8   123.03  3.000
 DJ6  H7   C7  C6   124.60  3.000
 DJ6  C8   C7  C6   112.33  3.000
 DJ6  C7   C8  CL1  127.21  3.000
 DJ6  C7   C8  S    112.66  3.000
 DJ6  CL1  C8  S    120.12  3.000
 DJ6  C6   C9  CL   128.61  3.000
 DJ6  C6   C9  S    112.69  3.000
 DJ6  CL   C9  S    118.67  3.000
 DJ6  HN1  N1  C5   116.99  3.000
 DJ6  HN1  N1  C2   114.54  3.000
 DJ6  C5   N1  C2   128.40  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
 DJ6  CONST_01  C3   C2  C1  C       0.00   0.0  0
 DJ6  CONST_02  C3   N   C4  C       0.00   0.0  0
 DJ6  CONST_03  C1   C2  C3  N       0.00   0.0  0
 DJ6  CONST_04  C1   C   C4  N       0.00   0.0  0
 DJ6  CONST_05  C6   C7  C8  S       0.00   0.0  0
 DJ6  CONST_06  C7   C6  C9  S       0.00   0.0  0
 DJ6  CONST_07  C4   C   C1  C2      0.00   0.0  0
 DJ6  CONST_08  C4   N   C3  C2      0.00   0.0  0
 DJ6  CONST_09  C8   S   C9  C6      0.00   0.0  0
 DJ6  CONST_10  C9   S   C8  C7      0.00   0.0  0
 DJ6  CONST_11  C9   C6  C7  C8      0.00   0.0  0
 DJ6  CONST_12  N1   C2  C1  C     180.00   0.0  0
 DJ6  CONST_13  N1   C2  C3  N     180.00   0.0  0
 DJ6  CONST_14  C5   C6  C9  S     180.00   0.0  0
 DJ6  CONST_15  C8   S   C9  CL    180.00   0.0  0
 DJ6  CONST_16  C7   C6  C9  CL    180.00   0.0  0
 DJ6  CONST_17  C9   S   C8  CL1   180.00   0.0  0
 DJ6  CONST_18  C6   C7  C8  CL1   180.00   0.0  0
 DJ6  CONST_19  C8   C7  C6  C5    180.00   0.0  0
 DJ6  CONST_20  H    C   C4  N     180.00   0.0  0
 DJ6  CONST_21  H7   C7  C8  S     180.00   0.0  0
 DJ6  CONST_22  H4   C4  C   C1    180.00   0.0  0
 DJ6  CONST_23  H3   C3  C2  C1    180.00   0.0  0
 DJ6  CONST_24  H1   C1  C2  C3    180.00   0.0  0
 DJ6  CONST_25  C6   C5  N1  C2    180.00   0.0  0
 DJ6  CONST_26  C5   N1  C2  C1      0.00   0.0  0
 DJ6  CONST_27  C5   N1  C2  C3    180.00   0.0  0
 DJ6  CONST_28  HN1  N1  C2  C1    180.00   0.0  0
 DJ6  CONST_29  C2   N1  C5  O       0.00   0.0  0
 DJ6  Var_01    C7   C6  C5  O    -148.80  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
 DJ6  plan-1  S    0.020
 DJ6  plan-1  CL   0.020
 DJ6  plan-1  CL1  0.020
 DJ6  plan-1  C5   0.020
 DJ6  plan-1  C6   0.020
 DJ6  plan-1  C7   0.020
 DJ6  plan-1  C8   0.020
 DJ6  plan-1  C9   0.020
 DJ6  plan-1  H7   0.020
 DJ6  plan-2  C    0.020
 DJ6  plan-2  N    0.020
 DJ6  plan-2  C1   0.020
 DJ6  plan-2  C2   0.020
 DJ6  plan-2  C3   0.020
 DJ6  plan-2  C4   0.020
 DJ6  plan-2  H    0.020
 DJ6  plan-2  H1   0.020
 DJ6  plan-2  H3   0.020
 DJ6  plan-2  H4   0.020
 DJ6  plan-2  N1   0.020
 DJ6  plan-3  O    0.020
 DJ6  plan-3  C2   0.020
 DJ6  plan-3  C5   0.020
 DJ6  plan-3  C6   0.020
 DJ6  plan-3  HN1  0.020
 DJ6  plan-3  N1   0.020

