# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 14:14:05 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 2-(4'-carbamimidoylbiphenyl-3-yl)-1H-benzimidazole-6-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(cc1)c2cccc(c2)c3[nH]c4cc(ccc4n3)C(N)=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
 DB9  DB9  2-(4'-carbamimidoylbiphenyl-3-yl)-1H-benzimidazole-6-carboximidamide  ligand  45  27  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DB9
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
 DB9  C1    C  CR16  0  -0.273   2.0557   1.8446  10.6500
 DB9  C2    C  CR6   0  -0.006   2.9350   1.6258  11.7080
 DB9  C3    C  CR16  0  -0.265   3.6239   0.4160  11.7643
 DB9  C4    C  CR16  0  -0.293   3.4337  -0.5499  10.7899
 DB9  C5    C  CR6   0   0.082   2.5619  -0.3304   9.7235
 DB9  C6    C  CR16  0  -0.297   1.8761   0.8839   9.6703
 DB9  C7    C  CR6   0   0.116   2.3760  -1.3523   8.6751
 DB9  C8    C  CR16  0  -0.308   2.3443  -2.7101   8.9925
 DB9  C9    C  CR16  0  -0.224   2.1796  -3.6623   7.9969
 DB9  C10   C  CR16  0  -0.297   2.0419  -3.2790   6.6739
 DB9  C11   C  CR6   0   0.046   2.0666  -1.9257   6.3376
 DB9  C12   C  CR16  0  -0.376   2.2377  -0.9754   7.3410
 DB9  C13   C  C     0   0.330   3.1117   2.6661  12.7595
 DB9  N14   N  NH2   0  -0.803   4.3673   2.7395  13.2852
 DB9  N15   N  N     0  -0.640   2.1785   3.4223  13.1959
 DB9  C16   C  CR5   0   0.475   1.9300  -1.5338   4.9363
 DB9  N17   N  NR15  0  -0.729   1.6374  -0.2633   4.5473
 DB9  C18   C  CR56  0   0.361   1.5879  -0.2536   3.1816
 DB9  C19   C  CR56  0   0.153   1.8651  -1.5796   2.8069
 DB9  N20   N  N     0  -0.477   2.0736  -2.3473   3.9205
 DB9  C21   C  CR16  0  -0.327   1.8897  -1.9209   1.4550
 DB9  C22   C  CR16  0  -0.292   1.6264  -0.9302   0.5298
 DB9  C23   C  CR6   0  -0.017   1.3493   0.3960   0.9179
 DB9  C24   C  CR16  0  -0.359   1.3284   0.7491   2.2612
 DB9  C25   C  C     0   0.332   1.0887   1.4460  -0.1068
 DB9  N26   N  NH2   0  -0.805   0.4535   1.0086  -1.2310
 DB9  N27   N  N     0  -0.645   1.4455   2.6696  -0.0022
 DB9  H1    H  HCR6  0   0.265   1.5140   2.7795  10.5767
 DB9  H3    H  HCR6  0   0.266   4.3087   0.2158  12.5782
 DB9  H4    H  HCR6  0   0.261   3.9881  -1.4779  10.8525
 DB9  H6    H  HCR6  0   0.261   1.1793   1.0792   8.8650
 DB9  H8    H  HCR6  0   0.265   2.4309  -3.0277  10.0240
 DB9  H9    H  HCR6  0   0.267   2.1499  -4.7119   8.2572
 DB9  H10   H  HCR6  0   0.262   1.9106  -4.0232   5.9003
 DB9  H12   H  HCR6  0   0.252   2.3083   0.0762   7.0905
 DB9  H141  H  HNH2  0   0.385   4.5446   3.5156  13.9036
 DB9  H142  H  HNH2  0   0.393   5.1458   2.4976  12.6946
 DB9  HN15  H  H     0   0.333   1.2886   3.1719  12.7812
 DB9  HN17  H  HNR5  0   0.426   1.4369   0.5194   5.1494
 DB9  H21   H  HCR6  0   0.261   2.1131  -2.9318   1.1402
 DB9  H22   H  HCR6  0   0.261   1.6563  -1.1764  -0.5234
 DB9  H24   H  HCR6  0   0.275   1.0955   1.7578   2.5784
 DB9  H261  H  HNH2  0   0.384   0.1424   1.7225  -1.8705
 DB9  H262  H  HNH2  0   0.392  -0.1700   0.2226  -1.1529
 DB9  HN27  H  H     0   0.332   1.9993   2.8092   0.8347

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
 DB9  C1   C2    aromatic  1.393  0.020  1.393
 DB9  C1   C6    aromatic  1.384  0.020  1.384
 DB9  C1   H1    single    0.930  0.020  1.080
 DB9  C2   C13   single    1.490  0.020  1.490
 DB9  C2   C3    aromatic  1.393  0.020  1.393
 DB9  C3   C4    aromatic  1.385  0.020  1.385
 DB9  C3   H3    single    0.930  0.020  1.080
 DB9  C4   C5    aromatic  1.395  0.020  1.395
 DB9  C4   H4    single    0.930  0.020  1.080
 DB9  C5   C6    aromatic  1.396  0.020  1.396
 DB9  C5   C7    single    1.476  0.020  1.476
 DB9  C6   H6    single    0.930  0.020  1.080
 DB9  C7   C8    aromatic  1.395  0.020  1.395
 DB9  C7   C12   aromatic  1.393  0.020  1.393
 DB9  C8   C9    aromatic  1.387  0.020  1.387
 DB9  C8   H8    single    0.930  0.020  1.080
 DB9  C9   C10   aromatic  1.384  0.020  1.384
 DB9  C9   H9    single    0.930  0.020  1.080
 DB9  C10  C11   aromatic  1.395  0.020  1.395
 DB9  C10  H10   single    0.930  0.020  1.080
 DB9  C11  C12   aromatic  1.393  0.020  1.393
 DB9  C11  C16   single    1.461  0.020  1.461
 DB9  C12  H12   single    0.930  0.020  1.080
 DB9  C13  N14   single    1.363  0.020  1.363
 DB9  C13  N15   double    1.278  0.020  1.278
 DB9  N14  H141  single    0.890  0.020  1.040
 DB9  N14  H142  single    0.890  0.020  1.040
 DB9  N15  HN15  single    0.890  0.020  1.040
 DB9  C16  N17   aromatic  1.361  0.020  1.361
 DB9  C16  N20   aromatic  1.309  0.020  1.309
 DB9  N17  C18   aromatic  1.367  0.020  1.367
 DB9  N17  HN17  single    0.860  0.020  1.020
 DB9  C18  C19   aromatic  1.406  0.020  1.406
 DB9  C18  C24   aromatic  1.386  0.020  1.386
 DB9  C19  N20   aromatic  1.369  0.020  1.369
 DB9  C19  C21   aromatic  1.395  0.020  1.395
 DB9  C21  C22   aromatic  1.381  0.020  1.381
 DB9  C21  H21   single    0.930  0.020  1.080
 DB9  C22  C23   aromatic  1.409  0.020  1.409
 DB9  C22  H22   single    0.930  0.020  1.080
 DB9  C23  C24   aromatic  1.389  0.020  1.389
 DB9  C23  C25   single    1.490  0.020  1.490
 DB9  C24  H24   single    0.930  0.020  1.080
 DB9  C25  N26   single    1.363  0.020  1.363
 DB9  C25  N27   double    1.279  0.020  1.279
 DB9  N26  H261  single    0.890  0.020  1.040
 DB9  N26  H262  single    0.890  0.020  1.040
 DB9  N27  HN27  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
 DB9  H1    C1   C6    119.11  3.000
 DB9  H1    C1   C2    120.18  3.000
 DB9  C6    C1   C2    120.70  3.000
 DB9  C13   C2   C3    121.28  3.000
 DB9  C3    C2   C1    118.63  3.000
 DB9  C13   C2   C1    120.09  3.000
 DB9  H3    C3   C4    119.13  3.000
 DB9  H3    C3   C2    120.25  3.000
 DB9  C4    C3   C2    120.61  3.000
 DB9  H4    C4   C5    119.93  3.000
 DB9  H4    C4   C3    119.13  3.000
 DB9  C5    C4   C3    120.93  3.000
 DB9  C7    C5   C6    120.90  3.000
 DB9  C7    C5   C4    120.86  3.000
 DB9  C6    C5   C4    118.24  3.000
 DB9  H6    C6   C5    120.11  3.000
 DB9  H6    C6   C1    119.00  3.000
 DB9  C5    C6   C1    120.89  3.000
 DB9  C12   C7   C8    118.62  3.000
 DB9  C12   C7   C5    120.36  3.000
 DB9  C8    C7   C5    121.02  3.000
 DB9  H8    C8   C9    119.46  3.000
 DB9  H8    C8   C7    120.03  3.000
 DB9  C9    C8   C7    120.50  3.000
 DB9  H9    C9   C10   119.72  3.000
 DB9  H9    C9   C8    119.77  3.000
 DB9  C10   C9   C8    120.51  3.000
 DB9  H10   C10  C11   119.83  3.000
 DB9  H10   C10  C9    120.35  3.000
 DB9  C11   C10  C9    119.82  3.000
 DB9  C16   C11  C12   121.29  3.000
 DB9  C16   C11  C10   119.32  3.000
 DB9  C12   C11  C10   119.38  3.000
 DB9  H12   C12  C11   120.25  3.000
 DB9  H12   C12  C7    118.53  3.000
 DB9  C11   C12  C7    121.17  3.000
 DB9  N15   C13  N14   120.60  3.000
 DB9  N15   C13  C2    124.59  3.000
 DB9  N14   C13  C2    114.78  3.000
 DB9  H142  N14  H141  114.14  3.000
 DB9  H142  N14  C13   118.24  3.000
 DB9  H141  N14  C13   116.10  3.000
 DB9  HN15  N15  C13   110.81  3.000
 DB9  N20   C16  N17   112.45  3.000
 DB9  N20   C16  C11   124.55  3.000
 DB9  N17   C16  C11   123.00  3.000
 DB9  HN17  N17  C18   125.76  3.000
 DB9  HN17  N17  C16   126.68  3.000
 DB9  C18   N17  C16   107.47  3.000
 DB9  C24   C18  C19   122.86  3.000
 DB9  C24   C18  N17   132.51  3.000
 DB9  C19   C18  N17   104.63  3.000
 DB9  C21   C19  N20   130.46  3.000
 DB9  C21   C19  C18   119.52  3.000
 DB9  N20   C19  C18   110.02  3.000
 DB9  C19   N20  C16   105.43  3.000
 DB9  H21   C21  C22   120.98  3.000
 DB9  H21   C21  C19   120.95  3.000
 DB9  C22   C21  C19   118.07  3.000
 DB9  H22   C22  C23   119.18  3.000
 DB9  H22   C22  C21   118.93  3.000
 DB9  C23   C22  C21   121.88  3.000
 DB9  C25   C23  C24   118.90  3.000
 DB9  C25   C23  C22   120.54  3.000
 DB9  C24   C23  C22   120.56  3.000
 DB9  H24   C24  C23   121.56  3.000
 DB9  H24   C24  C18   121.33  3.000
 DB9  C23   C24  C18   117.10  3.000
 DB9  N27   C25  N26   120.30  3.000
 DB9  N27   C25  C23   124.69  3.000
 DB9  N26   C25  C23   114.99  3.000
 DB9  H262  N26  H261  114.29  3.000
 DB9  H262  N26  C25   118.38  3.000
 DB9  H261  N26  C25   116.09  3.000
 DB9  HN27  N27  C25   110.61  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
 DB9  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 DB9  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 DB9  CONST_03  C7    C5   C6   C1    180.00   0.0  0
 DB9  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 DB9  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 DB9  CONST_06  C6    C1   C2   C3      0.00   0.0  0
 DB9  CONST_07  C6    C5   C4   C3      0.00   0.0  0
 DB9  CONST_08  C7    C5   C4   C3    180.00   0.0  0
 DB9  CONST_11  C9    C8   C7   C5    180.00   0.0  0
 DB9  CONST_12  C11   C12  C7   C5    180.00   0.0  0
 DB9  CONST_15  C10   C9   C8   C7      0.00   0.0  0
 DB9  CONST_16  C10   C11  C12  C7      0.00   0.0  0
 DB9  CONST_17  C16   C11  C12  C7    180.00   0.0  0
 DB9  CONST_18  C11   C12  C7   C8      0.00   0.0  0
 DB9  CONST_19  C11   C10  C9   C8      0.00   0.0  0
 DB9  CONST_20  C12   C7   C8   C9      0.00   0.0  0
 DB9  CONST_21  C12   C11  C10  C9      0.00   0.0  0
 DB9  CONST_22  C16   C11  C10  C9    180.00   0.0  0
 DB9  CONST_25  C18   N17  C16  C11   180.00   0.0  0
 DB9  CONST_26  C19   N20  C16  C11   180.00   0.0  0
 DB9  CONST_29  C19   C18  N17  C16     0.00   0.0  0
 DB9  CONST_30  C24   C18  N17  C16   180.00   0.0  0
 DB9  CONST_31  C18   C19  N20  C16     0.00   0.0  0
 DB9  CONST_32  C21   C19  N20  C16   180.00   0.0  0
 DB9  CONST_33  C19   N20  C16  N17     0.00   0.0  0
 DB9  CONST_34  N20   C19  C18  N17     0.00   0.0  0
 DB9  CONST_35  C21   C19  C18  N17   180.00   0.0  0
 DB9  CONST_36  C23   C24  C18  N17   180.00   0.0  0
 DB9  CONST_37  N20   C16  N17  C18     0.00   0.0  0
 DB9  CONST_38  C22   C21  C19  C18     0.00   0.0  0
 DB9  CONST_39  C22   C23  C24  C18     0.00   0.0  0
 DB9  CONST_40  C23   C24  C18  C19     0.00   0.0  0
 DB9  CONST_41  C23   C22  C21  C19     0.00   0.0  0
 DB9  CONST_42  C24   C18  C19  N20   180.00   0.0  0
 DB9  CONST_43  C22   C21  C19  N20   180.00   0.0  0
 DB9  CONST_44  C24   C18  C19  C21     0.00   0.0  0
 DB9  CONST_45  C24   C23  C22  C21     0.00   0.0  0
 DB9  CONST_46  C13   C2   C3   C4    180.00   0.0  0
 DB9  CONST_47  C13   C2   C1   C6    180.00   0.0  0
 DB9  CONST_48  C25   C23  C24  C18   180.00   0.0  0
 DB9  CONST_49  C25   C23  C22  C21   180.00   0.0  0
 DB9  CONST_50  H3    C3   C2   C1    180.00   0.0  0
 DB9  CONST_51  H6    C6   C1   C2    180.00   0.0  0
 DB9  CONST_52  H4    C4   C3   C2    180.00   0.0  0
 DB9  CONST_53  H1    C1   C2   C3    180.00   0.0  0
 DB9  CONST_54  H8    C8   C7   C5      0.00   0.0  0
 DB9  CONST_55  H12   C12  C7   C5      0.00   0.0  0
 DB9  CONST_56  H9    C9   C8   C7    180.00   0.0  0
 DB9  CONST_57  H10   C10  C9   C8    180.00   0.0  0
 DB9  CONST_58  HN17  N17  C16  C11     0.00   0.0  0
 DB9  CONST_59  H24   C24  C18  N17     0.00   0.0  0
 DB9  CONST_60  H21   C21  C19  C18   180.00   0.0  0
 DB9  CONST_61  H22   C22  C21  C19   180.00   0.0  0
 DB9  CONST_62  H141  N14  C13  C2    180.00   0.0  0
 DB9  CONST_64  HN15  N15  C13  C2      0.00   0.0  0
 DB9  CONST_65  H261  N26  C25  C23   180.00   0.0  0
 DB9  CONST_67  HN27  N27  C25  C23     0.00   0.0  0
 DB9  Var_01    N14   C13  C2   C1   -146.59  30.0  2
 DB9  Var_02    N26   C25  C23  C22    33.37  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
 DB9  plan-1  C1    0.020
 DB9  plan-1  C2    0.020
 DB9  plan-1  C3    0.020
 DB9  plan-1  C4    0.020
 DB9  plan-1  C5    0.020
 DB9  plan-1  C6    0.020
 DB9  plan-1  C7    0.020
 DB9  plan-1  C13   0.020
 DB9  plan-1  H1    0.020
 DB9  plan-1  H3    0.020
 DB9  plan-1  H4    0.020
 DB9  plan-1  H6    0.020
 DB9  plan-2  C5    0.020
 DB9  plan-2  C7    0.020
 DB9  plan-2  C8    0.020
 DB9  plan-2  C9    0.020
 DB9  plan-2  C10   0.020
 DB9  plan-2  C11   0.020
 DB9  plan-2  C12   0.020
 DB9  plan-2  C16   0.020
 DB9  plan-2  H8    0.020
 DB9  plan-2  H9    0.020
 DB9  plan-2  H10   0.020
 DB9  plan-2  H12   0.020
 DB9  plan-3  C11   0.020
 DB9  plan-3  C16   0.020
 DB9  plan-3  N17   0.020
 DB9  plan-3  C18   0.020
 DB9  plan-3  C19   0.020
 DB9  plan-3  N20   0.020
 DB9  plan-3  C21   0.020
 DB9  plan-3  C22   0.020
 DB9  plan-3  C23   0.020
 DB9  plan-3  C24   0.020
 DB9  plan-3  C25   0.020
 DB9  plan-3  HN17  0.020
 DB9  plan-3  H21   0.020
 DB9  plan-3  H22   0.020
 DB9  plan-3  H24   0.020
 DB9  plan-4  C2    0.020
 DB9  plan-4  C13   0.020
 DB9  plan-4  N14   0.020
 DB9  plan-4  N15   0.020
 DB9  plan-4  H141  0.020
 DB9  plan-4  H142  0.020
 DB9  plan-4  HN15  0.020
 DB9  plan-5  C23   0.020
 DB9  plan-5  C25   0.020
 DB9  plan-5  N26   0.020
 DB9  plan-5  N27   0.020
 DB9  plan-5  H261  0.020
 DB9  plan-5  H262  0.020
 DB9  plan-5  HN27  0.020

