# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 12:09:12 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2-(4'-carbamimidoyl-2'-hydroxybiphenyl-4-yl)-1H-benzimidazole-5-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(c(O)c1)c2ccc(cc2)c3[nH]c4ccc(cc4n3)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
 D98  D98  2-(4'-carbamimidoyl-2'-hydroxybiphenyl-4-yl)-1H-benzimidazole-5-carboximidamide  ligand  46  28  .  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_D98
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
 D98  C1    C  CR16  0  -0.362   5.8029  -0.6228   0.7875
 D98  C2    C  CR6   0   0.334   4.4180  -0.7336   0.7623
 D98  C3    C  CR6   0  -0.048   3.6540   0.1655   0.0052
 D98  C4    C  CR16  0  -0.271   4.3168   1.1717  -0.6919
 D98  C5    C  CR16  0  -0.306   5.6971   1.2775  -0.6786
 D98  C6    C  CR6   0   0.052   6.4506   0.3677   0.0612
 D98  C7    C  CR6   0   0.011   2.1803   0.0641  -0.0504
 D98  C8    C  CR16  0  -0.266   1.3788   1.1370   0.3434
 D98  C9    C  CR16  0  -0.273   0.0007   1.0544   0.2798
 D98  C10   C  CR6   0   0.012  -0.6208  -0.1076  -0.1808
 D98  C11   C  CR16  0  -0.285   0.1753  -1.1802  -0.5776
 D98  C12   C  CR16  0  -0.290   1.5566  -1.0946  -0.5132
 D98  C13   C  CR5   0   0.483  -2.0793  -0.1657  -0.2275
 D98  N14   N  NR15  0  -0.732  -2.7669  -1.1842  -0.8172
 D98  C15   C  CR56  0   0.341  -4.0976  -0.9192  -0.6716
 D98  C16   C  CR56  0   0.184  -4.1445   0.2983   0.0290
 D98  N17   N  N     0  -0.479  -2.8721   0.7375   0.2879
 D98  C18   C  CR16  0  -0.377  -5.3705   0.8668   0.3590
 D98  C19   C  CR16  0  -0.298  -5.2466  -1.5933  -1.0641
 D98  C20   C  CR16  0  -0.309  -6.4547  -1.0171  -0.7191
 D98  C21   C  CR6   0   0.030  -6.5292   0.1988  -0.0101
 D98  C22   C  C     0   0.334  -7.8455   0.7957   0.3484
 D98  N24   N  NH2   0  -0.823  -8.8788  -0.0923   0.4574
 D98  N23   N  N     0  -0.655  -7.9304   2.0635   0.4872
 D98  C25   C  C     0   0.332   7.9379   0.4463   0.1133
 D98  N26   N  N     0  -0.649   8.5378   0.0193   1.1571
 D98  N27   N  NH2   0  -0.821   8.5233   1.0311  -0.9725
 D98  OAE   O  OH1   0  -0.618   3.8702  -1.7196   1.4997
 D98  H1    H  HCR6  0   0.264   6.3814  -1.3214   1.3783
 D98  HAE   H  HOH1  0   0.477   2.9075  -1.6537   1.5080
 D98  H4    H  HCR6  0   0.263   3.7341   1.8799  -1.2679
 D98  H5    H  HCR6  0   0.258   6.1723   2.0784  -1.2289
 D98  H8    H  HCR6  0   0.265   1.8406   2.0433   0.7136
 D98  H12   H  HCR6  0   0.279   2.1485  -1.9342  -0.8565
 D98  H9    H  HCR6  0   0.263  -0.6022   1.8959   0.5931
 D98  H11   H  HCR6  0   0.254  -0.2608  -2.1014  -0.9414
 D98  H14   H  HNR5  0   0.426  -2.3757  -1.9793  -1.2958
 D98  H19   H  HCR6  0   0.271  -5.2076  -2.5221  -1.6172
 D98  H18   H  HCR6  0   0.254  -5.4232   1.8014   0.9014
 D98  H20   H  HCR6  0   0.259  -7.3650  -1.5140  -1.0274
 D98  H23   H  H     0   0.321  -8.8660   2.3388   0.7737
 D98  H241  H  HNH2  0   0.393  -8.6674  -1.0385   0.7291
 D98  H242  H  HNH2  0   0.390  -9.7426   0.2523   0.8456
 D98  H26   H  H     0   0.324   9.5464   0.1018   1.0606
 D98  H271  H  HNH2  0   0.396   8.0533   0.9687  -1.8609
 D98  H272  H  HNH2  0   0.392   9.5270   0.9749  -1.0432

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
 D98  C1   C2    aromatic  1.390  0.020  1.390
 D98  C1   C6    aromatic  1.389  0.020  1.389
 D98  C2   C3    aromatic  1.402  0.020  1.402
 D98  C2   OAE   single    1.348  0.020  1.348
 D98  C3   C4    aromatic  1.392  0.020  1.392
 D98  C3   C7    single    1.478  0.020  1.478
 D98  C4   C5    aromatic  1.384  0.020  1.384
 D98  C5   C6    aromatic  1.394  0.020  1.394
 D98  C6   C25   single    1.490  0.020  1.490
 D98  C7   C8    aromatic  1.396  0.020  1.396
 D98  C7   C12   aromatic  1.395  0.020  1.395
 D98  C8   C9    aromatic  1.382  0.020  1.382
 D98  C9   C10   aromatic  1.396  0.020  1.396
 D98  C10  C11   aromatic  1.393  0.020  1.393
 D98  C10  C13   single    1.460  0.020  1.460
 D98  C11  C12   aromatic  1.385  0.020  1.385
 D98  C13  N14   aromatic  1.363  0.020  1.363
 D98  C13  N17   aromatic  1.308  0.020  1.308
 D98  N14  C15   aromatic  1.365  0.020  1.365
 D98  C15  C16   aromatic  1.405  0.020  1.405
 D98  C15  C19   aromatic  1.389  0.020  1.389
 D98  C16  N17   aromatic  1.371  0.020  1.371
 D98  C16  C18   aromatic  1.391  0.020  1.391
 D98  C18  C21   aromatic  1.387  0.020  1.387
 D98  C19  C20   aromatic  1.382  0.020  1.382
 D98  C20  C21   aromatic  1.409  0.020  1.409
 D98  C21  C22   single    1.489  0.020  1.489
 D98  C22  N23   double    1.278  0.020  1.278
 D98  C22  N24   single    1.367  0.020  1.367
 D98  C25  N26   double    1.277  0.020  1.277
 D98  C25  N27   single    1.365  0.020  1.365
 D98  C1   H1    single    0.930  0.020  1.080
 D98  OAE  HAE   single    0.850  0.020  0.980
 D98  C4   H4    single    0.930  0.020  1.080
 D98  C5   H5    single    0.930  0.020  1.080
 D98  C8   H8    single    0.930  0.020  1.080
 D98  C12  H12   single    0.930  0.020  1.080
 D98  C9   H9    single    0.930  0.020  1.080
 D98  C11  H11   single    0.930  0.020  1.080
 D98  N14  H14   single    0.860  0.020  1.020
 D98  C19  H19   single    0.930  0.020  1.080
 D98  C18  H18   single    0.930  0.020  1.080
 D98  C20  H20   single    0.930  0.020  1.080
 D98  N23  H23   single    0.890  0.020  1.040
 D98  N24  H241  single    0.890  0.020  1.040
 D98  N24  H242  single    0.890  0.020  1.040
 D98  N26  H26   single    0.890  0.020  1.040
 D98  N27  H271  single    0.890  0.020  1.040
 D98  N27  H272  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
 D98  H1    C1   C6    119.77  3.000
 D98  H1    C1   C2    119.42  3.000
 D98  C6    C1   C2    120.81  3.000
 D98  OAE   C2   C3    122.91  3.000
 D98  OAE   C2   C1    116.97  3.000
 D98  C3    C2   C1    120.12  3.000
 D98  C7    C3   C4    120.36  3.000
 D98  C7    C3   C2    121.31  3.000
 D98  C4    C3   C2    118.33  3.000
 D98  H4    C4   C5    119.44  3.000
 D98  H4    C4   C3    118.87  3.000
 D98  C5    C4   C3    121.68  3.000
 D98  H5    C5   C6    121.06  3.000
 D98  H5    C5   C4    119.32  3.000
 D98  C6    C5   C4    119.61  3.000
 D98  C25   C6   C5    121.58  3.000
 D98  C25   C6   C1    119.00  3.000
 D98  C5    C6   C1    119.41  3.000
 D98  C12   C7   C8    118.38  3.000
 D98  C12   C7   C3    121.01  3.000
 D98  C8    C7   C3    120.60  3.000
 D98  H8    C8   C9    119.42  3.000
 D98  H8    C8   C7    119.67  3.000
 D98  C9    C8   C7    120.91  3.000
 D98  H9    C9   C10   119.67  3.000
 D98  H9    C9   C8    119.74  3.000
 D98  C10   C9   C8    120.59  3.000
 D98  C13   C10  C11   122.06  3.000
 D98  C13   C10  C9    119.23  3.000
 D98  C11   C10  C9    118.71  3.000
 D98  H11   C11  C12   118.03  3.000
 D98  H11   C11  C10   121.39  3.000
 D98  C12   C11  C10   120.59  3.000
 D98  H12   C12  C11   118.84  3.000
 D98  H12   C12  C7    120.31  3.000
 D98  C11   C12  C7    120.83  3.000
 D98  N17   C13  N14   112.39  3.000
 D98  N17   C13  C10   124.43  3.000
 D98  N14   C13  C10   123.19  3.000
 D98  H14   N14  C15   125.64  3.000
 D98  H14   N14  C13   126.84  3.000
 D98  C15   N14  C13   107.50  3.000
 D98  C19   C15  C16   122.26  3.000
 D98  C19   C15  N14   133.03  3.000
 D98  C16   C15  N14   104.71  3.000
 D98  C18   C16  N17   129.97  3.000
 D98  C18   C16  C15   120.11  3.000
 D98  N17   C16  C15   109.92  3.000
 D98  C16   N17  C13   105.49  3.000
 D98  H18   C18  C21   120.57  3.000
 D98  H18   C18  C16   120.99  3.000
 D98  C21   C18  C16   118.43  3.000
 D98  H19   C19  C20   121.13  3.000
 D98  H19   C19  C15   122.11  3.000
 D98  C20   C19  C15   116.76  3.000
 D98  H20   C20  C21   119.68  3.000
 D98  H20   C20  C19   118.21  3.000
 D98  C21   C20  C19   122.10  3.000
 D98  C22   C21  C20   120.91  3.000
 D98  C22   C21  C18   118.76  3.000
 D98  C20   C21  C18   120.33  3.000
 D98  N23   C22  N24   125.84  3.000
 D98  N24   C22  C21   115.28  3.000
 D98  N23   C22  C21   118.84  3.000
 D98  H242  N24  H241  113.42  3.000
 D98  H242  N24  C22   117.16  3.000
 D98  H241  N24  C22   118.25  3.000
 D98  H23   N23  C22   111.12  3.000
 D98  N27   C25  N26   126.28  3.000
 D98  N27   C25  C6    115.01  3.000
 D98  N26   C25  C6    118.66  3.000
 D98  H26   N26  C25   111.17  3.000
 D98  H272  N27  H271  113.55  3.000
 D98  H272  N27  C25   117.32  3.000
 D98  H271  N27  C25   118.36  3.000
 D98  HAE   OAE  C2    111.12  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
 D98  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 D98  CONST_02  C7    C3   C2   C1   180.00   0.0  0
 D98  CONST_03  C4    C5   C6   C1     0.00   0.0  0
 D98  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 D98  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 D98  CONST_08  C6    C1   C2   C3     0.00   0.0  0
 D98  CONST_09  C6    C5   C4   C3     0.00   0.0  0
 D98  CONST_10  C9    C8   C7   C3   180.00   0.0  0
 D98  CONST_11  C11   C12  C7   C3   180.00   0.0  0
 D98  CONST_14  C7    C3   C4   C5   180.00   0.0  0
 D98  CONST_15  C10   C9   C8   C7     0.00   0.0  0
 D98  CONST_16  C10   C11  C12  C7     0.00   0.0  0
 D98  CONST_17  C11   C12  C7   C8     0.00   0.0  0
 D98  CONST_18  C11   C10  C9   C8     0.00   0.0  0
 D98  CONST_19  C13   C10  C9   C8   180.00   0.0  0
 D98  CONST_20  C12   C7   C8   C9     0.00   0.0  0
 D98  CONST_21  C12   C11  C10  C9     0.00   0.0  0
 D98  CONST_22  N14   C13  C10  C9   180.00   0.0  0
 D98  CONST_23  N17   C13  C10  C9     0.00   0.0  0
 D98  CONST_24  C15   N14  C13  C10  180.00   0.0  0
 D98  CONST_25  C16   N17  C13  C10  180.00   0.0  0
 D98  CONST_26  N14   C13  C10  C11    0.00   0.0  0
 D98  CONST_27  N17   C13  C10  C11  180.00   0.0  0
 D98  CONST_28  C13   C10  C11  C12  180.00   0.0  0
 D98  CONST_29  C16   C15  N14  C13    0.00   0.0  0
 D98  CONST_30  C19   C15  N14  C13  180.00   0.0  0
 D98  CONST_31  C15   C16  N17  C13    0.00   0.0  0
 D98  CONST_32  C18   C16  N17  C13  180.00   0.0  0
 D98  CONST_33  C16   N17  C13  N14    0.00   0.0  0
 D98  CONST_34  N17   C16  C15  N14    0.00   0.0  0
 D98  CONST_35  C18   C16  C15  N14  180.00   0.0  0
 D98  CONST_36  C20   C19  C15  N14  180.00   0.0  0
 D98  CONST_37  N17   C13  N14  C15    0.00   0.0  0
 D98  CONST_38  C21   C18  C16  C15    0.00   0.0  0
 D98  CONST_39  C21   C20  C19  C15    0.00   0.0  0
 D98  CONST_40  C20   C19  C15  C16    0.00   0.0  0
 D98  CONST_41  C20   C21  C18  C16    0.00   0.0  0
 D98  CONST_42  C19   C15  C16  N17  180.00   0.0  0
 D98  CONST_43  C21   C18  C16  N17  180.00   0.0  0
 D98  CONST_44  C19   C15  C16  C18    0.00   0.0  0
 D98  CONST_45  C19   C20  C21  C18    0.00   0.0  0
 D98  CONST_46  C25   C6   C1   C2   180.00   0.0  0
 D98  CONST_47  OAE   C2   C3   C4   180.00   0.0  0
 D98  CONST_48  C25   C6   C5   C4   180.00   0.0  0
 D98  CONST_49  OAE   C2   C1   C6   180.00   0.0  0
 D98  CONST_50  OAE   C2   C3   C7     0.00   0.0  0
 D98  CONST_51  C22   C21  C18  C16  180.00   0.0  0
 D98  CONST_52  C22   C21  C20  C19  180.00   0.0  0
 D98  CONST_53  H5    C5   C6   C1   180.00   0.0  0
 D98  CONST_54  H4    C4   C3   C2   180.00   0.0  0
 D98  CONST_55  H1    C1   C2   C3   180.00   0.0  0
 D98  CONST_56  H8    C8   C7   C3     0.00   0.0  0
 D98  CONST_57  H12   C12  C7   C3     0.00   0.0  0
 D98  CONST_58  H9    C9   C8   C7   180.00   0.0  0
 D98  CONST_59  H11   C11  C12  C7   180.00   0.0  0
 D98  CONST_60  H14   N14  C13  C10    0.00   0.0  0
 D98  CONST_61  H19   C19  C15  N14    0.00   0.0  0
 D98  CONST_62  H18   C18  C16  C15  180.00   0.0  0
 D98  CONST_63  H20   C20  C19  C15  180.00   0.0  0
 D98  CONST_64  H26   N26  C25  C6   180.00   0.0  0
 D98  CONST_66  H272  N27  C25  C6   180.00   0.0  0
 D98  CONST_67  H23   N23  C22  C21  180.00   0.0  0
 D98  CONST_69  H242  N24  C22  C21  180.00   0.0  0
 D98  Var_01    N26   C25  C6   C1   -27.73  30.0  2
 D98  Var_02    N23   C22  C21  C18   27.19  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
 D98  plan-1  C1    0.020
 D98  plan-1  C2    0.020
 D98  plan-1  C3    0.020
 D98  plan-1  C4    0.020
 D98  plan-1  C5    0.020
 D98  plan-1  C6    0.020
 D98  plan-1  C7    0.020
 D98  plan-1  C25   0.020
 D98  plan-1  OAE   0.020
 D98  plan-1  H1    0.020
 D98  plan-1  H4    0.020
 D98  plan-1  H5    0.020
 D98  plan-2  C3    0.020
 D98  plan-2  C7    0.020
 D98  plan-2  C8    0.020
 D98  plan-2  C9    0.020
 D98  plan-2  C10   0.020
 D98  plan-2  C11   0.020
 D98  plan-2  C12   0.020
 D98  plan-2  C13   0.020
 D98  plan-2  H8    0.020
 D98  plan-2  H12   0.020
 D98  plan-2  H9    0.020
 D98  plan-2  H11   0.020
 D98  plan-3  C10   0.020
 D98  plan-3  C13   0.020
 D98  plan-3  N14   0.020
 D98  plan-3  C15   0.020
 D98  plan-3  C16   0.020
 D98  plan-3  N17   0.020
 D98  plan-3  C18   0.020
 D98  plan-3  C19   0.020
 D98  plan-3  C20   0.020
 D98  plan-3  C21   0.020
 D98  plan-3  C22   0.020
 D98  plan-3  H14   0.020
 D98  plan-3  H19   0.020
 D98  plan-3  H18   0.020
 D98  plan-3  H20   0.020
 D98  plan-4  C21   0.020
 D98  plan-4  C22   0.020
 D98  plan-4  N24   0.020
 D98  plan-4  N23   0.020
 D98  plan-4  H23   0.020
 D98  plan-4  H241  0.020
 D98  plan-4  H242  0.020
 D98  plan-5  C6    0.020
 D98  plan-5  C25   0.020
 D98  plan-5  N26   0.020
 D98  plan-5  N27   0.020
 D98  plan-5  H26   0.020
 D98  plan-5  H271  0.020
 D98  plan-5  H272  0.020

