# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:35:22 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: 6-(4,5-dihydro-1H-imidazol-2-yl)-2-{5-[4-(4,5-dihydro-1H-imidazol-2-yl)phenyl]thiophen-2-yl}-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN=C(N1)c2ccc(cc2)c3sc(cc3)c4[nH]c5cc(ccc5n4)C6=NCCN6
#
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
 DBN  DBN  6-(4,5-dihydro-1H-imidazol-2-yl)-2-{5-[4-(4,5-dihydro-1H-imidazol-2-yl)phenyl]thiophen-2-yl}-1H-benzimidazole  ligand  50  30  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DBN
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
 DBN  C27   C  CH2   0  -0.309    9.3607  -1.5957   0.6165
 DBN  C28   C  CH2   0  -0.346    8.5498  -2.7599   0.0172
 DBN  C29   C  CH2   0  -0.310   -9.7597  -0.8506   0.0524
 DBN  C30   C  CH2   0  -0.347   -9.2066  -2.2839  -0.0567
 DBN  C1    C  CR5   0  -0.204   -2.1287   1.1307  -0.1487
 DBN  S2    S  S2    0   0.262   -0.7671   0.0735  -0.1202
 DBN  C3    C  CR5   0  -0.305    0.3413   1.3901  -0.1510
 DBN  C4    C  CR15  0  -0.188   -0.3202   2.5893  -0.1914
 DBN  C5    C  CR15  0  -0.216   -1.7212   2.4398  -0.1903
 DBN  C6    C  CR5   0   0.523    1.7719   1.1998  -0.1442
 DBN  N7    N  N     0  -0.476    2.6376   2.1759  -0.2689
 DBN  C8    C  CR56  0   0.153    3.8650   1.5768  -0.2106
 DBN  C9    C  CR56  0   0.375    3.7194   0.1865  -0.0473
 DBN  N10   N  NR15  0  -0.739    2.3668  -0.0169  -0.0091
 DBN  C11   C  CR16  0  -0.329    5.1428   2.1293  -0.2907
 DBN  C12   C  CR16  0  -0.304    6.2253   1.2770  -0.1993
 DBN  C13   C  CR6   0   0.016    6.0653  -0.1125  -0.0309
 DBN  C14   C  CR16  0  -0.355    4.7969  -0.6769   0.0414
 DBN  C15   C  CR6   0   0.151   -3.4889   0.6044  -0.1348
 DBN  C16   C  CR16  0  -0.311   -4.5490   1.3894  -0.5933
 DBN  C17   C  CR16  0  -0.274   -5.8462   0.9086  -0.5754
 DBN  C18   C  CR6   0   0.030   -6.1227  -0.3747  -0.1071
 DBN  C19   C  CR16  0  -0.260   -5.0661  -1.1655   0.3415
 DBN  C20   C  CR16  0  -0.308   -3.7721  -0.6827   0.3339
 DBN  C21   C  CR5   0   0.430    7.2403  -0.9939   0.0592
 DBN  N22   N  NR15  0  -0.672    8.4862  -0.4685   0.3171
 DBN  N23   N  N     0  -0.459    7.1896  -2.2570  -0.1286
 DBN  C24   C  CR5   0   0.431   -7.4929  -0.9090  -0.0956
 DBN  N25   N  NR15  0  -0.671   -8.5700  -0.0712  -0.2695
 DBN  N26   N  N     0  -0.453   -7.7570  -2.1532   0.0236
 DBN  H271  H  HCH2  0   0.235    9.5003  -1.7101   1.6956
 DBN  H272  H  HCH2  0   0.240   10.3433  -1.4799   0.1595
 DBN  H281  H  HCH2  0   0.234    8.5766  -3.6550   0.6411
 DBN  H282  H  HCH2  0   0.231    8.9394  -3.0479  -0.9646
 DBN  H292  H  HCH2  0   0.236  -10.1156  -0.6271   1.0624
 DBN  H301  H  HCH2  0   0.236   -9.5885  -2.9438   0.7239
 DBN  H302  H  HCH2  0   0.234   -9.4764  -2.7402  -1.0148
 DBN  H4    H  HCR5  0   0.272    0.1886   3.5420  -0.2120
 DBN  H5    H  HCR5  0   0.275   -2.4076   3.2743  -0.1976
 DBN  H10   H  HNR5  0   0.426    1.9101  -0.9059   0.1279
 DBN  H11   H  HCR6  0   0.261    5.2822   3.1938  -0.4244
 DBN  H12   H  HCR6  0   0.255    7.2208   1.6934  -0.2796
 DBN  H14   H  HCR6  0   0.266    4.6712  -1.7439   0.1674
 DBN  H16   H  HCR6  0   0.264   -4.3615   2.3793  -0.9881
 DBN  H17   H  HCR6  0   0.262   -6.6398   1.5399  -0.9541
 DBN  H19   H  HCR6  0   0.261   -5.2656  -2.1622   0.7108
 DBN  H20   H  HCR6  0   0.260   -2.9793  -1.3153   0.7152
 DBN  H22   H  HNR5  0   0.387    8.5447   0.3377   0.9208
 DBN  H25   H  HNR5  0   0.389   -8.5106   0.8623   0.1078
 DBN  H291  H  HCH2  0   0.241  -10.5740  -0.6551  -0.6445

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
 DBN  C27  C28   single    1.540  0.020  1.540
 DBN  C27  N22   single    1.458  0.020  1.458
 DBN  C27  H271  single    0.970  0.020  1.090
 DBN  C27  H272  single    0.970  0.020  1.090
 DBN  C28  N23   single    1.457  0.020  1.457
 DBN  C28  H281  single    0.970  0.020  1.090
 DBN  C28  H282  single    0.970  0.020  1.090
 DBN  C29  C30   single    1.540  0.020  1.540
 DBN  C29  N25   single    1.458  0.020  1.458
 DBN  C29  H291  single    0.970  0.020  1.090
 DBN  C29  H292  single    0.970  0.020  1.090
 DBN  C30  N26   single    1.458  0.020  1.458
 DBN  C30  H301  single    0.970  0.020  1.090
 DBN  C30  H302  single    0.970  0.020  1.090
 DBN  C1   S2    aromatic  1.724  0.020  1.724
 DBN  C1   C5    aromatic  1.372  0.020  1.372
 DBN  C1   C15   single    1.459  0.020  1.459
 DBN  S2   C3    aromatic  1.721  0.020  1.721
 DBN  C3   C4    aromatic  1.370  0.020  1.370
 DBN  C3   C6    single    1.443  0.020  1.443
 DBN  C4   C5    aromatic  1.409  0.020  1.409
 DBN  C4   H4    single    0.930  0.020  1.080
 DBN  C5   H5    single    0.930  0.020  1.080
 DBN  C6   N7    aromatic  1.311  0.020  1.311
 DBN  C6   N10   aromatic  1.361  0.020  1.361
 DBN  N7   C8    aromatic  1.367  0.020  1.367
 DBN  C8   C9    aromatic  1.407  0.020  1.407
 DBN  C8   C11   aromatic  1.394  0.020  1.394
 DBN  C9   N10   aromatic  1.368  0.020  1.368
 DBN  C9   C14   aromatic  1.384  0.020  1.384
 DBN  N10  H10   single    0.860  0.020  1.020
 DBN  C11  C12   aromatic  1.381  0.020  1.381
 DBN  C11  H11   single    0.930  0.020  1.080
 DBN  C12  C13   aromatic  1.409  0.020  1.409
 DBN  C12  H12   single    0.930  0.020  1.080
 DBN  C13  C14   aromatic  1.390  0.020  1.390
 DBN  C13  C21   single    1.472  0.020  1.472
 DBN  C14  H14   single    0.930  0.020  1.080
 DBN  C15  C16   aromatic  1.397  0.020  1.397
 DBN  C15  C20   aromatic  1.399  0.020  1.399
 DBN  C16  C17   aromatic  1.384  0.020  1.384
 DBN  C16  H16   single    0.930  0.020  1.080
 DBN  C17  C18   aromatic  1.394  0.020  1.394
 DBN  C17  H17   single    0.930  0.020  1.080
 DBN  C18  C19   aromatic  1.394  0.020  1.394
 DBN  C18  C24   single    1.471  0.020  1.471
 DBN  C19  C20   aromatic  1.381  0.020  1.381
 DBN  C19  H19   single    0.930  0.020  1.080
 DBN  C20  H20   single    0.930  0.020  1.080
 DBN  C21  N22   single    1.377  0.020  1.377
 DBN  C21  N23   double    1.278  0.020  1.278
 DBN  N22  H22   single    0.890  0.020  1.040
 DBN  C24  N25   single    1.376  0.020  1.376
 DBN  C24  N26   double    1.277  0.020  1.277
 DBN  N25  H25   single    0.890  0.020  1.040

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
 DBN  H272  C27  H271  108.04  3.000
 DBN  H272  C27  N22   111.87  3.000
 DBN  H271  C27  N22   111.10  3.000
 DBN  H272  C27  C28   113.07  3.000
 DBN  H271  C27  C28   111.83  3.000
 DBN  N22   C27  C28   100.88  3.000
 DBN  H282  C28  H281  106.75  3.000
 DBN  H282  C28  N23   109.46  3.000
 DBN  H281  C28  N23   111.29  3.000
 DBN  H282  C28  C27   111.12  3.000
 DBN  H281  C28  C27   112.62  3.000
 DBN  N23   C28  C27   105.64  3.000
 DBN  H292  C29  H291  108.10  3.000
 DBN  H292  C29  N25   111.10  3.000
 DBN  H291  C29  N25   111.88  3.000
 DBN  H292  C29  C30   111.86  3.000
 DBN  H291  C29  C30   112.96  3.000
 DBN  N25   C29  C30   100.88  3.000
 DBN  H302  C30  H301  106.72  3.000
 DBN  H302  C30  N26   109.31  3.000
 DBN  H301  C30  N26   111.27  3.000
 DBN  H302  C30  C29   111.18  3.000
 DBN  H301  C30  C29   112.73  3.000
 DBN  N26   C30  C29   105.65  3.000
 DBN  C15   C1   C5    128.44  3.000
 DBN  C15   C1   S2    121.00  3.000
 DBN  C5    C1   S2    110.55  3.000
 DBN  C3    S2   C1     92.25  3.000
 DBN  C6    C3   C4    126.45  3.000
 DBN  C6    C3   S2    122.50  3.000
 DBN  C4    C3   S2    111.05  3.000
 DBN  H4    C4   C5    124.19  3.000
 DBN  H4    C4   C3    123.03  3.000
 DBN  C5    C4   C3    112.78  3.000
 DBN  H5    C5   C4    123.35  3.000
 DBN  H5    C5   C1    123.26  3.000
 DBN  C4    C5   C1    113.37  3.000
 DBN  N10   C6   N7    112.74  3.000
 DBN  N10   C6   C3    123.47  3.000
 DBN  N7    C6   C3    123.78  3.000
 DBN  C8    N7   C6    105.22  3.000
 DBN  C11   C8   C9    119.52  3.000
 DBN  C11   C8   N7    130.29  3.000
 DBN  C9    C8   N7    110.18  3.000
 DBN  C14   C9   N10   132.47  3.000
 DBN  C14   C9   C8    122.92  3.000
 DBN  N10   C9   C8    104.61  3.000
 DBN  H10   N10  C9    125.61  3.000
 DBN  H10   N10  C6    127.12  3.000
 DBN  C9    N10  C6    107.24  3.000
 DBN  H11   C11  C12   120.96  3.000
 DBN  H11   C11  C8    121.00  3.000
 DBN  C12   C11  C8    118.04  3.000
 DBN  H12   C12  C13   119.52  3.000
 DBN  H12   C12  C11   118.62  3.000
 DBN  C13   C12  C11   121.85  3.000
 DBN  C21   C13  C14   118.83  3.000
 DBN  C21   C13  C12   120.49  3.000
 DBN  C14   C13  C12   120.68  3.000
 DBN  H14   C14  C13   120.83  3.000
 DBN  H14   C14  C9    122.18  3.000
 DBN  C13   C14  C9    116.99  3.000
 DBN  C20   C15  C16   118.27  3.000
 DBN  C20   C15  C1    121.60  3.000
 DBN  C16   C15  C1    120.13  3.000
 DBN  H16   C16  C17   119.02  3.000
 DBN  H16   C16  C15   120.17  3.000
 DBN  C17   C16  C15   120.80  3.000
 DBN  H17   C17  C18   120.60  3.000
 DBN  H17   C17  C16   118.69  3.000
 DBN  C18   C17  C16   120.69  3.000
 DBN  C24   C18  C19   119.84  3.000
 DBN  C24   C18  C17   121.46  3.000
 DBN  C19   C18  C17   118.69  3.000
 DBN  H19   C19  C20   119.79  3.000
 DBN  H19   C19  C18   119.53  3.000
 DBN  C20   C19  C18   120.67  3.000
 DBN  H20   C20  C19   118.65  3.000
 DBN  H20   C20  C15   120.46  3.000
 DBN  C19   C20  C15   120.87  3.000
 DBN  N23   C21  N22   116.15  3.000
 DBN  N23   C21  C13   123.46  3.000
 DBN  N22   C21  C13   120.37  3.000
 DBN  H22   N22  C21   118.01  3.000
 DBN  H22   N22  C27   117.40  3.000
 DBN  C21   N22  C27   106.64  3.000
 DBN  C21   N23  C28   106.81  3.000
 DBN  N26   C24  N25   116.30  3.000
 DBN  N26   C24  C18   123.17  3.000
 DBN  N25   C24  C18   120.48  3.000
 DBN  H25   N25  C24   118.06  3.000
 DBN  H25   N25  C29   117.40  3.000
 DBN  C24   N25  C29   106.58  3.000
 DBN  C24   N26  C30   106.72  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
 DBN  CONST_01  C4    C3   S2   C1      0.00   0.0  0
 DBN  CONST_02  C6    C3   S2   C1    180.00   0.0  0
 DBN  CONST_03  C3    C4   C5   C1      0.00   0.0  0
 DBN  CONST_04  C17   C16  C15  C1    180.00   0.0  0
 DBN  CONST_05  C19   C20  C15  C1    180.00   0.0  0
 DBN  CONST_06  C4    C5   C1   S2      0.00   0.0  0
 DBN  CONST_09  C5    C4   C3   S2      0.00   0.0  0
 DBN  CONST_10  N7    C6   C3   S2    180.00   0.0  0
 DBN  CONST_11  N10   C6   C3   S2      0.00   0.0  0
 DBN  CONST_12  C5    C1   S2   C3      0.00   0.0  0
 DBN  CONST_13  C15   C1   S2   C3    180.00   0.0  0
 DBN  CONST_14  C8    N7   C6   C3    180.00   0.0  0
 DBN  CONST_15  C9    N10  C6   C3    180.00   0.0  0
 DBN  CONST_16  N7    C6   C3   C4      0.00   0.0  0
 DBN  CONST_17  N10   C6   C3   C4    180.00   0.0  0
 DBN  CONST_18  C15   C1   C5   C4    180.00   0.0  0
 DBN  CONST_21  C6    C3   C4   C5    180.00   0.0  0
 DBN  CONST_22  C9    C8   N7   C6      0.00   0.0  0
 DBN  CONST_23  C11   C8   N7   C6    180.00   0.0  0
 DBN  CONST_24  C8    C9   N10  C6      0.00   0.0  0
 DBN  CONST_25  C14   C9   N10  C6    180.00   0.0  0
 DBN  CONST_26  C9    N10  C6   N7      0.00   0.0  0
 DBN  CONST_27  N10   C9   C8   N7      0.00   0.0  0
 DBN  CONST_28  C14   C9   C8   N7    180.00   0.0  0
 DBN  CONST_29  C12   C11  C8   N7    180.00   0.0  0
 DBN  CONST_30  N10   C6   N7   C8      0.00   0.0  0
 DBN  CONST_31  C13   C14  C9   C8      0.00   0.0  0
 DBN  CONST_32  C13   C12  C11  C8      0.00   0.0  0
 DBN  CONST_33  C12   C11  C8   C9      0.00   0.0  0
 DBN  CONST_34  C12   C13  C14  C9      0.00   0.0  0
 DBN  CONST_35  C11   C8   C9   N10   180.00   0.0  0
 DBN  CONST_36  C13   C14  C9   N10   180.00   0.0  0
 DBN  CONST_37  C14   C9   C8   C11     0.00   0.0  0
 DBN  CONST_38  C14   C13  C12  C11     0.00   0.0  0
 DBN  CONST_39  C18   C17  C16  C15     0.00   0.0  0
 DBN  CONST_40  C18   C19  C20  C15     0.00   0.0  0
 DBN  CONST_41  C19   C20  C15  C16     0.00   0.0  0
 DBN  CONST_42  C19   C18  C17  C16     0.00   0.0  0
 DBN  CONST_43  C20   C15  C16  C17     0.00   0.0  0
 DBN  CONST_44  C20   C19  C18  C17     0.00   0.0  0
 DBN  CONST_45  C21   C13  C14  C9    180.00   0.0  0
 DBN  CONST_46  C21   C13  C12  C11   180.00   0.0  0
 DBN  CONST_47  C24   C18  C17  C16   180.00   0.0  0
 DBN  CONST_48  C24   C18  C19  C20   180.00   0.0  0
 DBN  CONST_49  C21   N23  C28  C27     0.00   0.0  0
 DBN  CONST_50  C13   C21  N22  C27   180.00   0.0  0
 DBN  CONST_51  N23   C21  N22  C27     0.00   0.0  0
 DBN  CONST_53  C13   C21  N23  C28   180.00   0.0  0
 DBN  CONST_54  N22   C21  N23  C28     0.00   0.0  0
 DBN  CONST_55  C24   N26  C30  C29     0.00   0.0  0
 DBN  CONST_56  C18   C24  N25  C29   180.00   0.0  0
 DBN  CONST_57  N26   C24  N25  C29     0.00   0.0  0
 DBN  CONST_59  C18   C24  N26  C30   180.00   0.0  0
 DBN  CONST_60  N25   C24  N26  C30     0.00   0.0  0
 DBN  CONST_63  H4    C4   C5   C1    180.00   0.0  0
 DBN  CONST_64  H16   C16  C15  C1      0.00   0.0  0
 DBN  CONST_65  H20   C20  C15  C1      0.00   0.0  0
 DBN  CONST_66  H5    C5   C1   S2    180.00   0.0  0
 DBN  CONST_67  H10   N10  C6   C3      0.00   0.0  0
 DBN  CONST_68  H11   C11  C8   N7      0.00   0.0  0
 DBN  CONST_69  H14   C14  C9   C8    180.00   0.0  0
 DBN  CONST_70  H12   C12  C11  C8    180.00   0.0  0
 DBN  CONST_71  H17   C17  C16  C15   180.00   0.0  0
 DBN  CONST_72  H19   C19  C20  C15   180.00   0.0  0
 DBN  Var_01    N22   C21  C13  C12    16.36  30.0  2
 DBN  Var_02    N25   C24  C18  C17   -14.20  30.0  2
 DBN  Var_03    H271  C27  N22  C21  -100.13  30.0  1
 DBN  Var_04    H281  C28  N23  C21   134.09  30.0  1
 DBN  Var_05    H291  C29  N25  C24  -138.78  30.0  1
 DBN  Var_06    H301  C30  N26  C24  -134.34  30.0  1

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
 DBN  plan-1  C1   0.020
 DBN  plan-1  S2   0.020
 DBN  plan-1  C3   0.020
 DBN  plan-1  C4   0.020
 DBN  plan-1  C5   0.020
 DBN  plan-1  C6   0.020
 DBN  plan-1  C15  0.020
 DBN  plan-1  H4   0.020
 DBN  plan-1  H5   0.020
 DBN  plan-2  C1   0.020
 DBN  plan-2  C15  0.020
 DBN  plan-2  C16  0.020
 DBN  plan-2  C17  0.020
 DBN  plan-2  C18  0.020
 DBN  plan-2  C19  0.020
 DBN  plan-2  C20  0.020
 DBN  plan-2  C24  0.020
 DBN  plan-2  H16  0.020
 DBN  plan-2  H17  0.020
 DBN  plan-2  H19  0.020
 DBN  plan-2  H20  0.020
 DBN  plan-3  C3   0.020
 DBN  plan-3  C6   0.020
 DBN  plan-3  N7   0.020
 DBN  plan-3  C8   0.020
 DBN  plan-3  C9   0.020
 DBN  plan-3  N10  0.020
 DBN  plan-3  C11  0.020
 DBN  plan-3  C12  0.020
 DBN  plan-3  C13  0.020
 DBN  plan-3  C14  0.020
 DBN  plan-3  C21  0.020
 DBN  plan-3  H10  0.020
 DBN  plan-3  H11  0.020
 DBN  plan-3  H12  0.020
 DBN  plan-3  H14  0.020
 DBN  plan-4  C27  0.020
 DBN  plan-4  C28  0.020
 DBN  plan-4  C13  0.020
 DBN  plan-4  C21  0.020
 DBN  plan-4  N22  0.020
 DBN  plan-4  N23  0.020
 DBN  plan-4  H22  0.020
 DBN  plan-5  C29  0.020
 DBN  plan-5  C30  0.020
 DBN  plan-5  C18  0.020
 DBN  plan-5  C24  0.020
 DBN  plan-5  N25  0.020
 DBN  plan-5  N26  0.020
 DBN  plan-5  H25  0.020

