# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:13:10 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: 6-[2,3-bis(chloranyl)phenoxy]-5-chloranyl-2-methylsulfanyl-1~{H}-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1[nH]c2cc(Oc3cccc(Cl)c3Cl)c(Cl)cc2n1
#
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
 JA9  JA9  "6-[2,3-bis(chloranyl)phenoxy]-5-chloranyl-2-methylsulfanyl-1H-benzimidazole"
  ligand  30  21  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JA9
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
 JA9  CAA  C   CR16  0  -0.334  -21.4707  -1.2932   -8.3375
 JA9  CAB  C   CR6   0   0.449  -21.8961   0.0238   -8.4290
 JA9  CAC  C   CR16  0  -0.248  -21.2817  -2.0333   -9.4944
 JA9  CAD  C   CR6   0  -0.105  -22.1323   0.5948   -9.6800
 JA9  CAE  C   CR16  0  -0.240  -21.5130  -1.4812  -10.7427
 JA9  CAF  C   CR6   0   0.001  -21.9417  -0.1650  -10.8273
 JA9  CAH  C   CR6   0   0.359  -21.6619   0.4476   -6.1287
 JA9  CAI  C   CR6   0  -0.112  -20.2979   0.5823   -5.8254
 JA9  CAJ  C   CR16  0  -0.367  -22.5695   0.0012   -5.1868
 JA9  CAK  C   CR16  0  -0.304  -19.8008   0.2789   -4.5727
 JA9  CAL  C   CR56  0   0.354  -22.0646  -0.2919   -3.9301
 JA9  CAM  C   CR56  0   0.149  -20.7034  -0.1633   -3.6113
 JA9  CAO  C   CR5   0   0.292  -21.6643  -0.8398   -1.8460
 JA9  CAT  C   CH3   0  -0.761  -20.3932  -1.2922    0.5132
 JA9  NAN  N   N     0  -0.458  -20.4871  -0.5139   -2.3011
 JA9  NAP  N   NR15  0  -0.699  -22.6527  -0.7303   -2.7752
 JA9  OAG  O   O2    0  -0.491  -22.1235   0.8233   -7.3606
 JA9  SAS  S   S2    0   0.063  -22.0349  -1.3681   -0.2334
 JA9  CLQ  CL  CL    0  -0.100  -19.2286   1.1614   -7.0535
 JA9  CLR  CL  CL    0  -0.092  -22.2310   0.5325  -12.3747
 JA9  CLU  CL  CL    0  -0.073  -22.6513   2.2291   -9.7668
 JA9  H1   H   HCR6  0   0.297  -21.2882  -1.7467   -7.3721
 JA9  H2   H   HCR6  0   0.279  -20.9500  -3.0598   -9.4194
 JA9  H3   H   HCR6  0   0.285  -21.3664  -2.0618  -11.6426
 JA9  H4   H   HCR6  0   0.292  -23.6184  -0.0974   -5.4339
 JA9  H5   H   HCR6  0   0.284  -18.7488   0.3885   -4.3466
 JA9  H6   H   HCH3  0   0.288  -20.5239  -1.6056    1.5465
 JA9  H7   H   HCH3  0   0.282  -19.7064  -1.9709    0.0147
 JA9  H8   H   HCH3  0   0.282  -20.0028  -0.2785    0.4907
 JA9  H10  H   HNR5  0   0.429  -23.6336  -0.9243   -2.6373

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
 JA9  CLR  CAF  single    1.722  0.020  1.722
 JA9  CAF  CAE  aromatic  1.387  0.020  1.387
 JA9  CAF  CAD  aromatic  1.389  0.020  1.389
 JA9  CAE  CAC  aromatic  1.384  0.020  1.384
 JA9  CLU  CAD  single    1.717  0.020  1.717
 JA9  CAD  CAB  aromatic  1.395  0.020  1.395
 JA9  CAC  CAA  aromatic  1.386  0.020  1.386
 JA9  CAB  CAA  aromatic  1.387  0.020  1.387
 JA9  CAB  OAG  single    1.354  0.020  1.354
 JA9  OAG  CAH  single    1.368  0.020  1.368
 JA9  CLQ  CAI  single    1.728  0.020  1.728
 JA9  CAH  CAI  aromatic  1.404  0.020  1.404
 JA9  CAH  CAJ  aromatic  1.382  0.020  1.382
 JA9  CAI  CAK  aromatic  1.381  0.020  1.381
 JA9  CAJ  CAL  aromatic  1.386  0.020  1.386
 JA9  CAK  CAM  aromatic  1.391  0.020  1.391
 JA9  CAL  CAM  aromatic  1.404  0.020  1.404
 JA9  CAL  NAP  aromatic  1.368  0.020  1.368
 JA9  CAM  NAN  aromatic  1.373  0.020  1.373
 JA9  NAP  CAO  aromatic  1.361  0.020  1.361
 JA9  NAN  CAO  aromatic  1.304  0.020  1.304
 JA9  CAO  SAS  single    1.737  0.020  1.737
 JA9  CAT  SAS  single    1.805  0.020  1.805
 JA9  CAA  H1   single    0.930  0.020  1.080
 JA9  CAC  H2   single    0.930  0.020  1.080
 JA9  CAE  H3   single    0.930  0.020  1.080
 JA9  CAJ  H4   single    0.930  0.020  1.080
 JA9  CAK  H5   single    0.930  0.020  1.080
 JA9  CAT  H6   single    0.970  0.020  1.090
 JA9  CAT  H7   single    0.970  0.020  1.090
 JA9  CAT  H8   single    0.970  0.020  1.090
 JA9  NAP  H10  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
 JA9  H1   CAA  CAC  119.85  3.000
 JA9  H1   CAA  CAB  120.56  3.000
 JA9  CAC  CAA  CAB  119.59  3.000
 JA9  OAG  CAB  CAD  115.94  3.000
 JA9  OAG  CAB  CAA  124.08  3.000
 JA9  CAD  CAB  CAA  119.98  3.000
 JA9  H2   CAC  CAE  119.50  3.000
 JA9  H2   CAC  CAA  119.39  3.000
 JA9  CAE  CAC  CAA  121.11  3.000
 JA9  CLU  CAD  CAF  121.36  3.000
 JA9  CLU  CAD  CAB  119.08  3.000
 JA9  CAF  CAD  CAB  119.56  3.000
 JA9  H3   CAE  CAF  120.06  3.000
 JA9  H3   CAE  CAC  120.92  3.000
 JA9  CAF  CAE  CAC  119.02  3.000
 JA9  CLR  CAF  CAE  119.42  3.000
 JA9  CAE  CAF  CAD  120.74  3.000
 JA9  CLR  CAF  CAD  119.84  3.000
 JA9  OAG  CAH  CAJ  118.74  3.000
 JA9  CAJ  CAH  CAI  121.45  3.000
 JA9  OAG  CAH  CAI  119.74  3.000
 JA9  CLQ  CAI  CAK  119.69  3.000
 JA9  CAK  CAI  CAH  121.63  3.000
 JA9  CLQ  CAI  CAH  118.67  3.000
 JA9  H4   CAJ  CAL  122.75  3.000
 JA9  H4   CAJ  CAH  120.69  3.000
 JA9  CAL  CAJ  CAH  116.56  3.000
 JA9  H5   CAK  CAM  121.27  3.000
 JA9  H5   CAK  CAI  121.15  3.000
 JA9  CAM  CAK  CAI  117.59  3.000
 JA9  NAP  CAL  CAM  104.73  3.000
 JA9  NAP  CAL  CAJ  132.59  3.000
 JA9  CAM  CAL  CAJ  122.67  3.000
 JA9  NAN  CAM  CAL  110.24  3.000
 JA9  NAN  CAM  CAK  129.67  3.000
 JA9  CAL  CAM  CAK  120.09  3.000
 JA9  SAS  CAO  NAP  120.23  3.000
 JA9  SAS  CAO  NAN  126.36  3.000
 JA9  NAP  CAO  NAN  113.41  3.000
 JA9  H8   CAT  H7   110.25  3.000
 JA9  H8   CAT  H6   109.37  3.000
 JA9  H7   CAT  H6   109.38  3.000
 JA9  H8   CAT  SAS  110.94  3.000
 JA9  H7   CAT  SAS  111.03  3.000
 JA9  H6   CAT  SAS  105.75  3.000
 JA9  CAO  NAN  CAM  104.75  3.000
 JA9  H10  NAP  CAO  126.66  3.000
 JA9  H10  NAP  CAL  126.48  3.000
 JA9  CAO  NAP  CAL  106.86  3.000
 JA9  CAH  OAG  CAB  119.46  3.000
 JA9  CAT  SAS  CAO  100.21  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
 JA9  CONST_01  CAF  CAE  CAC  CAA     0.00   0.0  0
 JA9  CONST_02  CAF  CAD  CAB  CAA     0.00   0.0  0
 JA9  CONST_03  CAE  CAF  CAD  CAB     0.00   0.0  0
 JA9  CONST_04  CAE  CAC  CAA  CAB     0.00   0.0  0
 JA9  CONST_05  CAD  CAF  CAE  CAC     0.00   0.0  0
 JA9  CONST_06  CAD  CAB  CAA  CAC     0.00   0.0  0
 JA9  CONST_07  CAM  CAK  CAI  CAH     0.00   0.0  0
 JA9  CONST_08  CAM  CAL  CAJ  CAH     0.00   0.0  0
 JA9  CONST_09  NAP  CAL  CAJ  CAH   180.00   0.0  0
 JA9  CONST_10  CAL  CAJ  CAH  CAI     0.00   0.0  0
 JA9  CONST_11  CAL  CAM  CAK  CAI     0.00   0.0  0
 JA9  CONST_12  NAN  CAM  CAK  CAI   180.00   0.0  0
 JA9  CONST_13  CAK  CAI  CAH  CAJ     0.00   0.0  0
 JA9  CONST_14  CAK  CAM  CAL  CAJ     0.00   0.0  0
 JA9  CONST_15  NAN  CAM  CAL  CAJ   180.00   0.0  0
 JA9  CONST_16  CAO  NAP  CAL  CAJ   180.00   0.0  0
 JA9  CONST_17  NAP  CAL  CAM  CAK   180.00   0.0  0
 JA9  CONST_18  CAO  NAN  CAM  CAK   180.00   0.0  0
 JA9  CONST_19  CAO  NAN  CAM  CAL     0.00   0.0  0
 JA9  CONST_20  NAN  CAO  NAP  CAL     0.00   0.0  0
 JA9  CONST_21  CAO  NAP  CAL  CAM     0.00   0.0  0
 JA9  CONST_22  NAP  CAO  NAN  CAM     0.00   0.0  0
 JA9  CONST_23  NAP  CAL  CAM  NAN     0.00   0.0  0
 JA9  CONST_24  CLU  CAD  CAB  CAA   180.00   0.0  0
 JA9  CONST_25  CLR  CAF  CAD  CAB   180.00   0.0  0
 JA9  CONST_26  CLR  CAF  CAE  CAC   180.00   0.0  0
 JA9  CONST_27  OAG  CAB  CAA  CAC   180.00   0.0  0
 JA9  CONST_28  CLU  CAD  CAF  CAE   180.00   0.0  0
 JA9  CONST_29  OAG  CAB  CAD  CAF   180.00   0.0  0
 JA9  CONST_30  CLQ  CAI  CAH  CAJ   180.00   0.0  0
 JA9  CONST_31  OAG  CAH  CAI  CAK   180.00   0.0  0
 JA9  CONST_32  OAG  CAH  CAJ  CAL   180.00   0.0  0
 JA9  CONST_33  SAS  CAO  NAP  CAL   180.00   0.0  0
 JA9  CONST_34  CLQ  CAI  CAK  CAM   180.00   0.0  0
 JA9  CONST_35  SAS  CAO  NAN  CAM   180.00   0.0  0
 JA9  CONST_36  H3   CAE  CAC  CAA   180.00   0.0  0
 JA9  CONST_37  H2   CAC  CAA  CAB   180.00   0.0  0
 JA9  CONST_38  H3   CAE  CAF  CAD   180.00   0.0  0
 JA9  CONST_39  H1   CAA  CAB  CAD   180.00   0.0  0
 JA9  CONST_40  H1   CAA  CAC  CAE   180.00   0.0  0
 JA9  CONST_41  H2   CAC  CAE  CAF   180.00   0.0  0
 JA9  CONST_42  H5   CAK  CAI  CAH   180.00   0.0  0
 JA9  CONST_43  H4   CAJ  CAH  CAI   180.00   0.0  0
 JA9  CONST_44  H10  NAP  CAL  CAJ     0.00   0.0  0
 JA9  CONST_45  H5   CAK  CAM  CAL   180.00   0.0  0
 JA9  CONST_46  H4   CAJ  CAL  CAM   180.00   0.0  0
 JA9  CONST_47  H10  NAP  CAL  CAM   180.00   0.0  0
 JA9  CONST_48  H5   CAK  CAM  NAN     0.00   0.0  0
 JA9  CONST_49  H10  NAP  CAO  NAN   180.00   0.0  0
 JA9  CONST_50  H4   CAJ  CAL  NAP     0.00   0.0  0
 JA9  Var_01    CAH  OAG  CAB  CAA    14.20  30.0  2
 JA9  Var_02    CAI  CAH  OAG  CAB    76.23  30.0  2
 JA9  Var_03    CAJ  CAH  OAG  CAB  -106.82  30.0  2
 JA9  Var_04    CAH  OAG  CAB  CAD  -166.60  30.0  2
 JA9  Var_05    NAP  CAO  SAS  CAT  -179.19  30.0  1
 JA9  Var_06    NAN  CAO  SAS  CAT     0.66  30.0  1
 JA9  Var_07    H6   CAT  SAS  CAO   179.67  30.0  3
 JA9  Var_08    H7   CAT  SAS  CAO   -61.78  30.0  3
 JA9  Var_09    H8   CAT  SAS  CAO    61.18  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
 JA9  plan-1  CAA  0.020
 JA9  plan-1  CAB  0.020
 JA9  plan-1  CAC  0.020
 JA9  plan-1  CAD  0.020
 JA9  plan-1  CAE  0.020
 JA9  plan-1  CAF  0.020
 JA9  plan-1  OAG  0.020
 JA9  plan-1  CLR  0.020
 JA9  plan-1  CLU  0.020
 JA9  plan-1  H1   0.020
 JA9  plan-1  H2   0.020
 JA9  plan-1  H3   0.020
 JA9  plan-2  CAH  0.020
 JA9  plan-2  CAI  0.020
 JA9  plan-2  CAJ  0.020
 JA9  plan-2  CAK  0.020
 JA9  plan-2  CAL  0.020
 JA9  plan-2  CAM  0.020
 JA9  plan-2  CAO  0.020
 JA9  plan-2  NAN  0.020
 JA9  plan-2  NAP  0.020
 JA9  plan-2  OAG  0.020
 JA9  plan-2  SAS  0.020
 JA9  plan-2  CLQ  0.020
 JA9  plan-2  H4   0.020
 JA9  plan-2  H5   0.020
 JA9  plan-2  H10  0.020

