# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 26 14:38:12 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 3,3'-benzene-1,4-diylbis(4-cyano-5-ethylthiophene-2-carboxylic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1sc(C(O)=O)c(c2ccc(cc2)c3c(sc(CC)c3C#N)C(O)=O)c1C#N
#
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
 RN8  RN8  '3,3'-benzene-1,4-diylbis(4-cyano-5-ethylthiophene-2-carboxylic acid)'  ligand  46  30  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RN8
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
 RN8  C4    C  CR16  0  -0.254  -0.6551  -0.6270   1.1545
 RN8  C5    C  CR16  0  -0.253   0.6275   0.6270  -0.9626
 RN8  C6    C  CR16  0  -0.277   0.7209  -0.4773   1.1686
 RN8  C10   C  CSP   0  -0.015   3.2060  -2.2153   0.1084
 RN8  C13   C  CR5   0  -0.143  -5.0601   0.6089   0.1355
 RN8  C15   C  CR5   0   0.064  -3.7128   0.8929   0.1024
 RN8  C17   C  CR5   0   0.330  -2.8695  -0.2573   0.0805
 RN8  C20   C  CR5   0  -0.454   3.5834   1.4158   0.1060
 RN8  C22   C  C     0   0.505   3.1046   2.8015   0.1698
 RN8  O28   O  O     0  -0.412   1.9496   3.1241   0.2768
 RN8  O26   O  OH1   0  -0.602   4.1199   3.6542   0.1040
 RN8  S30   S  S2    0   0.345   5.2778   1.0886   0.1046
 RN8  C14   C  CR5   0  -0.142   5.0358  -0.5924   0.1260
 RN8  C2    C  CH3   0  -0.655   6.5633  -1.8786  -1.3808
 RN8  C18   C  CR5   0   0.331   2.8410   0.2653   0.1199
 RN8  C16   C  CR5   0   0.061   3.6894  -0.8815   0.1305
 RN8  N24   N  NS    0  -0.235   2.8306  -3.3048   0.0857
 RN8  C12   C  CR6   0   0.025   1.3729   0.1538   0.1118
 RN8  C11   C  CR6   0   0.025  -1.4007  -0.1521   0.0808
 RN8  C3    C  CR16  0  -0.277  -0.7487   0.4775  -0.9766
 RN8  C9    C  CSP   0  -0.015  -3.2232   2.2243   0.1194
 RN8  N23   N  NS    0  -0.235  -2.8418   3.3119   0.1325
 RN8  C19   C  CR5   0  -0.454  -3.6162  -1.4048   0.0893
 RN8  S29   S  S2    0   0.346  -5.3087  -1.0713   0.1328
 RN8  H4    H  HCR6  0   0.260  -1.1504  -1.1019   1.9906
 RN8  H5    H  HCR6  0   0.260   1.1227   1.1017  -1.7988
 RN8  H6    H  HCR6  0   0.266   1.2863  -0.8430   2.0164
 RN8  H7    H  HCH2  0   0.277  -7.0450   1.1582   0.6626
 RN8  H7A   H  HCH2  0   0.270  -5.8975   2.4771   0.6521
 RN8  H8    H  HCH2  0   0.277   7.0338  -1.1444   0.5960
 RN8  H8A   H  HCH2  0   0.270   5.8902  -2.4666   0.5868
 RN8  HO26  H  HOH1  0   0.496   3.8000   4.5679   0.1539
 RN8  H2    H  HCH3  0   0.236   6.8938  -0.9860  -1.9113
 RN8  H2A   H  HCH3  0   0.250   7.3798  -2.5993  -1.3930
 RN8  H2B   H  HCH3  0   0.238   5.7247  -2.3071  -1.9289
 RN8  H3    H  HCR6  0   0.266  -1.3146   0.8442  -1.8237
 RN8  HO25  H  HOH1  0   0.496  -3.8424  -4.5564   0.0297
 RN8  H1    H  HCH3  0   0.250  -7.4323   2.6496  -1.2900
 RN8  H1A   H  HCH3  0   0.237  -5.7903   2.3656  -1.8683
 RN8  H1B   H  HCH3  0   0.235  -6.9603   1.0457  -1.8501
 RN8  C21   C  C     0   0.505  -3.1423  -2.7913   0.0104
 RN8  C7    C  CH2   0  -0.516  -6.1969   1.5739   0.1171
 RN8  C8    C  CH2   0  -0.516   6.1748  -1.5530   0.0619
 RN8  O27   O  O     0  -0.413  -1.9899  -3.1151  -0.1193
 RN8  O25   O  OH1   0  -0.602  -4.1581  -3.6420   0.0893
 RN8  C1    C  CH3   0  -0.654  -6.6171   1.9276  -1.3101

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
 RN8  C6   C4    aromatic  1.384  0.020  1.384
 RN8  C11  C4    aromatic  1.391  0.020  1.391
 RN8  C4   H4    single    0.930  0.020  1.080
 RN8  C12  C5    aromatic  1.391  0.020  1.391
 RN8  C5   C3    aromatic  1.384  0.020  1.384
 RN8  C5   H5    single    0.930  0.020  1.080
 RN8  C12  C6    aromatic  1.393  0.020  1.393
 RN8  C6   H6    single    0.930  0.020  1.080
 RN8  C13  C7    single    1.491  0.020  1.491
 RN8  C7   C1    single    1.529  0.020  1.529
 RN8  C7   H7    single    0.970  0.020  1.090
 RN8  C7   H7A   single    0.970  0.020  1.090
 RN8  C14  C8    single    1.491  0.020  1.491
 RN8  C8   C2    single    1.529  0.020  1.529
 RN8  C8   H8    single    0.970  0.020  1.090
 RN8  C8   H8A   single    0.970  0.020  1.090
 RN8  C16  C10   single    1.419  0.020  1.419
 RN8  C10  N24   triple    1.153  0.020  1.153
 RN8  S29  C13   aromatic  1.699  0.020  1.699
 RN8  C15  C13   aromatic  1.377  0.020  1.377
 RN8  C17  C15   aromatic  1.426  0.020  1.426
 RN8  C15  C9    single    1.419  0.020  1.419
 RN8  C19  C17   aromatic  1.369  0.020  1.369
 RN8  C11  C17   single    1.473  0.020  1.473
 RN8  C22  C20   single    1.467  0.020  1.467
 RN8  C20  S30   aromatic  1.726  0.020  1.726
 RN8  C20  C18   aromatic  1.369  0.020  1.369
 RN8  O27  C21   double    1.204  0.020  1.204
 RN8  O25  C21   single    1.327  0.020  1.327
 RN8  C21  C19   single    1.467  0.020  1.467
 RN8  O28  C22   double    1.204  0.020  1.204
 RN8  O26  C22   single    1.328  0.020  1.328
 RN8  O26  HO26  single    0.850  0.020  0.980
 RN8  S30  C14   aromatic  1.699  0.020  1.699
 RN8  C16  C14   aromatic  1.377  0.020  1.377
 RN8  C2   H2    single    0.970  0.020  1.090
 RN8  C2   H2A   single    0.970  0.020  1.090
 RN8  C2   H2B   single    0.970  0.020  1.090
 RN8  C12  C18   single    1.472  0.020  1.472
 RN8  C18  C16   aromatic  1.427  0.020  1.427
 RN8  C3   C11   aromatic  1.393  0.020  1.393
 RN8  C3   H3    single    0.930  0.020  1.080
 RN8  C9   N23   triple    1.153  0.020  1.153
 RN8  C19  S29   aromatic  1.726  0.020  1.726
 RN8  O25  HO25  single    0.850  0.020  0.980
 RN8  C1   H1    single    0.970  0.020  1.090
 RN8  C1   H1A   single    0.970  0.020  1.090
 RN8  C1   H1B   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
 RN8  H4    C4   C11  120.08  3.000
 RN8  H4    C4   C6   119.65  3.000
 RN8  C11   C4   C6   120.26  3.000
 RN8  H5    C5   C3   119.66  3.000
 RN8  H5    C5   C12  120.08  3.000
 RN8  C3    C5   C12  120.26  3.000
 RN8  H6    C6   C12  120.18  3.000
 RN8  H6    C6   C4   119.38  3.000
 RN8  C12   C6   C4   120.44  3.000
 RN8  N24   C10  C16  180.00  3.000
 RN8  S29   C13  C15  110.31  3.000
 RN8  C15   C13  C7   127.73  3.000
 RN8  S29   C13  C7   121.91  3.000
 RN8  C9    C15  C17  123.57  3.000
 RN8  C9    C15  C13  122.06  3.000
 RN8  C17   C15  C13  114.36  3.000
 RN8  C19   C17  C11  127.15  3.000
 RN8  C11   C17  C15  122.15  3.000
 RN8  C19   C17  C15  110.69  3.000
 RN8  C18   C20  S30  111.90  3.000
 RN8  C18   C20  C22  128.03  3.000
 RN8  S30   C20  C22  119.96  3.000
 RN8  O26   C22  O28  124.47  3.000
 RN8  O26   C22  C20  110.78  3.000
 RN8  O28   C22  C20  124.75  3.000
 RN8  HO26  O26  C22  110.52  3.000
 RN8  C14   S30  C20   92.74  3.000
 RN8  C16   C14  S30  110.31  3.000
 RN8  C16   C14  C8   127.71  3.000
 RN8  S30   C14  C8   121.88  3.000
 RN8  H2B   C2   H2A  108.13  3.000
 RN8  H2B   C2   H2   108.10  3.000
 RN8  H2A   C2   H2   108.01  3.000
 RN8  H2B   C2   C8   111.27  3.000
 RN8  H2A   C2   C8   110.00  3.000
 RN8  H2    C2   C8   111.22  3.000
 RN8  C12   C18  C16  122.15  3.000
 RN8  C16   C18  C20  110.68  3.000
 RN8  C12   C18  C20  127.17  3.000
 RN8  C18   C16  C14  114.38  3.000
 RN8  C18   C16  C10  123.57  3.000
 RN8  C14   C16  C10  122.03  3.000
 RN8  C18   C12  C6   119.79  3.000
 RN8  C18   C12  C5   120.86  3.000
 RN8  C6    C12  C5   119.30  3.000
 RN8  C3    C11  C17  119.94  3.000
 RN8  C3    C11  C4   119.31  3.000
 RN8  C17   C11  C4   120.70  3.000
 RN8  H3    C3   C11  120.17  3.000
 RN8  H3    C3   C5   119.40  3.000
 RN8  C11   C3   C5   120.43  3.000
 RN8  N23   C9   C15  180.00  3.000
 RN8  S29   C19  C21  120.05  3.000
 RN8  S29   C19  C17  111.90  3.000
 RN8  C21   C19  C17  127.99  3.000
 RN8  C19   S29  C13   92.73  3.000
 RN8  O25   C21  O27  124.51  3.000
 RN8  O25   C21  C19  110.81  3.000
 RN8  O27   C21  C19  124.68  3.000
 RN8  H7A   C7   H7   106.47  3.000
 RN8  H7A   C7   C1   109.97  3.000
 RN8  H7    C7   C1   109.95  3.000
 RN8  H7A   C7   C13  108.68  3.000
 RN8  H7    C7   C13  109.87  3.000
 RN8  C1    C7   C13  111.75  3.000
 RN8  H8A   C8   H8   106.46  3.000
 RN8  H8A   C8   C2   109.98  3.000
 RN8  H8    C8   C2   109.98  3.000
 RN8  H8A   C8   C14  108.62  3.000
 RN8  H8    C8   C14  109.82  3.000
 RN8  C2    C8   C14  111.83  3.000
 RN8  HO25  O25  C21  110.59  3.000
 RN8  H1B   C1   H1A  108.09  3.000
 RN8  H1B   C1   H1   108.05  3.000
 RN8  H1A   C1   H1   108.12  3.000
 RN8  H1B   C1   C7   111.22  3.000
 RN8  H1A   C1   C7   111.26  3.000
 RN8  H1    C1   C7   109.98  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
 RN8  CONST_01  C5    C12  C6   C4      0.00   0.0  0
 RN8  CONST_02  C18   C12  C6   C4    180.00   0.0  0
 RN8  CONST_05  C5    C3   C11  C4      0.00   0.0  0
 RN8  CONST_08  C17   C11  C3   C5    180.00   0.0  0
 RN8  CONST_09  C17   C11  C4   C6    180.00   0.0  0
 RN8  CONST_10  C3    C11  C4   C6      0.00   0.0  0
 RN8  CONST_11  C3    C5   C12  C6      0.00   0.0  0
 RN8  CONST_14  C17   C19  S29  C13     0.00   0.0  0
 RN8  CONST_15  C19   C17  C15  C13     0.00   0.0  0
 RN8  CONST_16  C11   C17  C15  C13   180.00   0.0  0
 RN8  CONST_17  C19   S29  C13  C15     0.00   0.0  0
 RN8  CONST_18  S29   C19  C17  C15     0.00   0.0  0
 RN8  CONST_20  S29   C13  C15  C17     0.00   0.0  0
 RN8  CONST_21  C16   C14  S30  C20     0.00   0.0  0
 RN8  CONST_22  C14   C16  C18  C20     0.00   0.0  0
 RN8  CONST_23  C12   C18  C20  S30   180.00   0.0  0
 RN8  CONST_24  C16   C18  C20  S30     0.00   0.0  0
 RN8  CONST_25  C18   C16  C14  S30     0.00   0.0  0
 RN8  CONST_26  C18   C20  S30  C14     0.00   0.0  0
 RN8  CONST_27  C12   C18  C16  C14   180.00   0.0  0
 RN8  CONST_28  C3    C5   C12  C18   180.00   0.0  0
 RN8  CONST_29  C11   C3   C5   C12     0.00   0.0  0
 RN8  CONST_30  C11   C4   C6   C12     0.00   0.0  0
 RN8  CONST_31  S29   C19  C17  C11   180.00   0.0  0
 RN8  CONST_33  C19   S29  C13  C7    180.00   0.0  0
 RN8  CONST_34  C17   C15  C13  C7    180.00   0.0  0
 RN8  CONST_35  C20   S30  C14  C8    180.00   0.0  0
 RN8  CONST_36  C18   C16  C14  C8    180.00   0.0  0
 RN8  CONST_37  S30   C14  C16  C10   180.00   0.0  0
 RN8  CONST_38  C20   C18  C16  C10   180.00   0.0  0
 RN8  CONST_39  C12   C18  C16  C10     0.00   0.0  0
 RN8  CONST_40  C21   C19  S29  C13   180.00   0.0  0
 RN8  CONST_41  C21   C19  C17  C15   180.00   0.0  0
 RN8  CONST_42  C11   C17  C19  C21     0.00   0.0  0
 RN8  CONST_43  C14   S30  C20  C22   180.00   0.0  0
 RN8  CONST_44  C12   C18  C20  C22     0.00   0.0  0
 RN8  CONST_45  C16   C18  C20  C22   180.00   0.0  0
 RN8  CONST_46  C9    C15  C17  C11     0.00   0.0  0
 RN8  CONST_47  S29   C13  C15  C9    180.00   0.0  0
 RN8  CONST_48  C19   C17  C15  C9    180.00   0.0  0
 RN8  CONST_49  H3    C3   C11  C4    180.00   0.0  0
 RN8  CONST_50  H6    C6   C12  C5    180.00   0.0  0
 RN8  CONST_51  H5    C5   C12  C6    180.00   0.0  0
 RN8  CONST_52  H4    C4   C11  C17     0.00   0.0  0
 RN8  CONST_53  HO26  O26  C22  C20   180.00   0.0  0
 RN8  CONST_54  HO25  O25  C21  C19   180.00   0.0  0
 RN8  Var_01    C1    C7   C13  C15    87.81  30.0  2
 RN8  Var_02    O27   C21  C19  C17    -2.51  30.0  1
 RN8  Var_03    S30   C20  C22  O28  -174.14  30.0  2
 RN8  Var_04    C2    C8   C14  S30   -87.55  30.0  2
 RN8  Var_05    H1    C1   C7   C13  -178.72  30.0  3
 RN8  Var_06    H2    C2   C8   C14    61.75  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
 RN8  plan-1  C10   0.020
 RN8  plan-1  C20   0.020
 RN8  plan-1  C22   0.020
 RN8  plan-1  S30   0.020
 RN8  plan-1  C14   0.020
 RN8  plan-1  C18   0.020
 RN8  plan-1  C16   0.020
 RN8  plan-1  N24   0.020
 RN8  plan-1  C12   0.020
 RN8  plan-1  C8    0.020
 RN8  plan-2  C13   0.020
 RN8  plan-2  C15   0.020
 RN8  plan-2  C17   0.020
 RN8  plan-2  C11   0.020
 RN8  plan-2  C9    0.020
 RN8  plan-2  N23   0.020
 RN8  plan-2  C19   0.020
 RN8  plan-2  S29   0.020
 RN8  plan-2  C21   0.020
 RN8  plan-2  C7    0.020
 RN8  plan-3  C4    0.020
 RN8  plan-3  C5    0.020
 RN8  plan-3  C6    0.020
 RN8  plan-3  C17   0.020
 RN8  plan-3  C18   0.020
 RN8  plan-3  C12   0.020
 RN8  plan-3  C11   0.020
 RN8  plan-3  C3    0.020
 RN8  plan-3  H4    0.020
 RN8  plan-3  H5    0.020
 RN8  plan-3  H6    0.020
 RN8  plan-3  H3    0.020
 RN8  plan-4  C20   0.020
 RN8  plan-4  C22   0.020
 RN8  plan-4  O28   0.020
 RN8  plan-4  O26   0.020
 RN8  plan-4  HO26  0.020
 RN8  plan-5  C19   0.020
 RN8  plan-5  HO25  0.020
 RN8  plan-5  C21   0.020
 RN8  plan-5  O27   0.020
 RN8  plan-5  O25   0.020

