# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 17:36:11 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 2-(3'-carbamimidoylbiphenyl-4-yl)-1H-benzimidazole-5-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1cccc(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
 M1B  M1B  2-(3'-carbamimidoylbiphenyl-4-yl)-1H-benzimidazole-5-carboximidamide  ligand  45  27  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_M1B
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
 M1B  C1    C  CR16  0  -0.293  2.5516  -3.5654  13.2009
 M1B  C2    C  CR16  0  -0.225  1.6522  -4.2502  12.3967
 M1B  C3    C  CR16  0  -0.310  1.5485  -3.9511  11.0479
 M1B  C4    C  CR6   0   0.115  2.3448  -2.9554  10.4794
 M1B  C5    C  CR16  0  -0.367  3.2384  -2.2686  11.2987
 M1B  C6    C  CR6   0   0.033  3.3492  -2.5630  12.6538
 M1B  C7    C  CR6   0   0.086  2.2473  -2.6347   9.0425
 M1B  C8    C  CR16  0  -0.293  2.0079  -3.6332   8.0981
 M1B  C9    C  CR16  0  -0.286  1.9149  -3.3328   6.7502
 M1B  C10   C  CR6   0   0.005  2.0584  -2.0195   6.3051
 M1B  C11   C  CR16  0  -0.271  2.3022  -1.0171   7.2445
 M1B  C12   C  CR16  0  -0.294  2.3933  -1.3215   8.5892
 M1B  C13   C  CR5   0   0.481  1.9686  -1.6675   4.8914
 M1B  C14   C  C     0   0.330  4.3076  -1.7922  13.4971
 M1B  N15   N  N     0  -0.639  4.5758  -0.5521  13.3411
 M1B  N16   N  NH2   0  -0.804  4.8697  -2.4985  14.5173
 M1B  N17   N  NR15  0  -0.729  1.4727  -2.5128   3.9439
 M1B  C18   C  CR56  0   0.342  1.5332  -1.8652   2.7441
 M1B  C19   C  CR56  0   0.175  2.0933  -0.6115   3.0443
 M1B  N20   N  N     0  -0.478  2.3491  -0.5220   4.3871
 M1B  C21   C  CR16  0  -0.390  2.3044   0.3180   2.0306
 M1B  C22   C  CR16  0  -0.297  1.1628  -2.2233   1.4542
 M1B  C23   C  CR16  0  -0.300  1.3685  -1.2826   0.4631
 M1B  C24   C  CR6   0  -0.008  1.9373  -0.0226   0.7363
 M1B  C25   C  C     0   0.331  2.1703   0.9534  -0.3651
 M1B  N26   N  NH2   0  -0.805  1.2462   0.9240  -1.3677
 M1B  N27   N  N     0  -0.645  3.1660   1.7533  -0.4296
 M1B  H1    H  HCR6  0   0.267  2.6141  -3.8010  14.2552
 M1B  H2    H  HCR6  0   0.266  1.0208  -5.0157  12.8281
 M1B  H3    H  HCR6  0   0.262  0.8287  -4.4816  10.4378
 M1B  H5    H  HCR6  0   0.265  3.8891  -1.5192  10.8636
 M1B  H8    H  HCR6  0   0.264  1.9155  -4.6655   8.4107
 M1B  H9    H  HCR6  0   0.253  1.7539  -4.1460   6.0542
 M1B  H11   H  HCR6  0   0.261  2.4075   0.0085   6.9171
 M1B  H12   H  HCR6  0   0.261  2.5552  -0.5187   9.2971
 M1B  HN15  H  H     0   0.332  3.9996  -0.1478  12.6124
 M1B  H161  H  HNH2  0   0.386  5.6086  -2.0370  15.0242
 M1B  H162  H  HNH2  0   0.393  5.0043  -3.4887  14.3981
 M1B  HN17  H  HNR5  0   0.426  1.0756  -3.4257   4.1000
 M1B  H21   H  HCR6  0   0.263  2.7245   1.2896   2.2607
 M1B  H22   H  HCR6  0   0.273  0.7374  -3.1913   1.2260
 M1B  H23   H  HCR6  0   0.263  1.1042  -1.5359  -0.5547
 M1B  H261  H  HNH2  0   0.383  1.3164   1.6576  -2.0549
 M1B  H262  H  HNH2  0   0.391  0.3025   0.6593  -1.1399
 M1B  HN27  H  H     0   0.331  3.8164   1.5752   0.3266

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
 M1B  C1   C2    aromatic  1.387  0.020  1.387
 M1B  C1   C6    aromatic  1.393  0.020  1.393
 M1B  C1   H1    single    0.930  0.020  1.080
 M1B  C2   C3    aromatic  1.385  0.020  1.385
 M1B  C2   H2    single    0.930  0.020  1.080
 M1B  C3   C4    aromatic  1.396  0.020  1.396
 M1B  C3   H3    single    0.930  0.020  1.080
 M1B  C4   C7    single    1.476  0.020  1.476
 M1B  C4   C5    aromatic  1.393  0.020  1.393
 M1B  C5   C6    aromatic  1.391  0.020  1.391
 M1B  C5   H5    single    0.930  0.020  1.080
 M1B  C6   C14   single    1.491  0.020  1.491
 M1B  C7   C8    aromatic  1.395  0.020  1.395
 M1B  C7   C12   aromatic  1.397  0.020  1.397
 M1B  C8   C9    aromatic  1.384  0.020  1.384
 M1B  C8   H8    single    0.930  0.020  1.080
 M1B  C9   C10   aromatic  1.394  0.020  1.394
 M1B  C9   H9    single    0.930  0.020  1.080
 M1B  C10  C13   single    1.460  0.020  1.460
 M1B  C10  C11   aromatic  1.395  0.020  1.395
 M1B  C11  C12   aromatic  1.382  0.020  1.382
 M1B  C11  H11   single    0.930  0.020  1.080
 M1B  C12  H12   single    0.930  0.020  1.080
 M1B  C13  N20   aromatic  1.308  0.020  1.308
 M1B  C13  N17   aromatic  1.363  0.020  1.363
 M1B  C14  N16   single    1.362  0.020  1.362
 M1B  C14  N15   double    1.278  0.020  1.278
 M1B  N15  HN15  single    0.890  0.020  1.040
 M1B  N16  H161  single    0.890  0.020  1.040
 M1B  N16  H162  single    0.890  0.020  1.040
 M1B  N17  C18   aromatic  1.365  0.020  1.365
 M1B  N17  HN17  single    0.860  0.020  1.020
 M1B  C18  C22   aromatic  1.389  0.020  1.389
 M1B  C18  C19   aromatic  1.406  0.020  1.406
 M1B  C19  C21   aromatic  1.391  0.020  1.391
 M1B  C19  N20   aromatic  1.370  0.020  1.370
 M1B  C21  C24   aromatic  1.388  0.020  1.388
 M1B  C21  H21   single    0.930  0.020  1.080
 M1B  C22  C23   aromatic  1.382  0.020  1.382
 M1B  C22  H22   single    0.930  0.020  1.080
 M1B  C23  C24   aromatic  1.409  0.020  1.409
 M1B  C23  H23   single    0.930  0.020  1.080
 M1B  C24  C25   single    1.490  0.020  1.490
 M1B  C25  N26   single    1.364  0.020  1.364
 M1B  C25  N27   double    1.279  0.020  1.279
 M1B  N26  H261  single    0.890  0.020  1.040
 M1B  N26  H262  single    0.890  0.020  1.040
 M1B  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
 M1B  H1    C1   C6    120.41  3.000
 M1B  H1    C1   C2    119.65  3.000
 M1B  C6    C1   C2    119.92  3.000
 M1B  H2    C2   C3    119.81  3.000
 M1B  H2    C2   C1    119.77  3.000
 M1B  C3    C2   C1    120.42  3.000
 M1B  H3    C3   C4    119.96  3.000
 M1B  H3    C3   C2    119.51  3.000
 M1B  C4    C3   C2    120.51  3.000
 M1B  C7    C4   C5    120.52  3.000
 M1B  C5    C4   C3    118.55  3.000
 M1B  C7    C4   C3    120.92  3.000
 M1B  H5    C5   C6    119.31  3.000
 M1B  H5    C5   C4    119.33  3.000
 M1B  C6    C5   C4    121.30  3.000
 M1B  C14   C6   C5    119.52  3.000
 M1B  C14   C6   C1    121.19  3.000
 M1B  C5    C6   C1    119.29  3.000
 M1B  C12   C7   C8    118.11  3.000
 M1B  C12   C7   C4    120.89  3.000
 M1B  C8    C7   C4    121.00  3.000
 M1B  H8    C8   C9    118.85  3.000
 M1B  H8    C8   C7    120.11  3.000
 M1B  C9    C8   C7    121.02  3.000
 M1B  H9    C9   C10   121.18  3.000
 M1B  H9    C9   C8    118.24  3.000
 M1B  C10   C9   C8    120.57  3.000
 M1B  C13   C10  C11   119.31  3.000
 M1B  C11   C10  C9    118.67  3.000
 M1B  C13   C10  C9    122.01  3.000
 M1B  H11   C11  C12   119.80  3.000
 M1B  H11   C11  C10   119.63  3.000
 M1B  C12   C11  C10   120.56  3.000
 M1B  H12   C12  C11   118.87  3.000
 M1B  H12   C12  C7    120.05  3.000
 M1B  C11   C12  C7    121.07  3.000
 M1B  N20   C13  N17   112.39  3.000
 M1B  N17   C13  C10   123.10  3.000
 M1B  N20   C13  C10   124.51  3.000
 M1B  N16   C14  N15   120.52  3.000
 M1B  N15   C14  C6    124.56  3.000
 M1B  N16   C14  C6    114.88  3.000
 M1B  HN15  N15  C14   110.83  3.000
 M1B  H162  N16  H161  114.34  3.000
 M1B  H162  N16  C14   118.46  3.000
 M1B  H161  N16  C14   116.21  3.000
 M1B  HN17  N17  C18   125.70  3.000
 M1B  HN17  N17  C13   126.69  3.000
 M1B  C18   N17  C13   107.50  3.000
 M1B  C22   C18  C19   122.31  3.000
 M1B  C19   C18  N17   104.66  3.000
 M1B  C22   C18  N17   133.02  3.000
 M1B  C21   C19  N20   129.95  3.000
 M1B  N20   C19  C18   110.00  3.000
 M1B  C21   C19  C18   120.05  3.000
 M1B  C19   N20  C13   105.44  3.000
 M1B  H21   C21  C24   121.39  3.000
 M1B  H21   C21  C19   120.22  3.000
 M1B  C24   C21  C19   118.38  3.000
 M1B  H22   C22  C23   121.09  3.000
 M1B  H22   C22  C18   122.11  3.000
 M1B  C23   C22  C18   116.80  3.000
 M1B  H23   C23  C24   119.37  3.000
 M1B  H23   C23  C22   118.63  3.000
 M1B  C24   C23  C22   121.99  3.000
 M1B  C25   C24  C23   120.37  3.000
 M1B  C25   C24  C21   119.16  3.000
 M1B  C23   C24  C21   120.47  3.000
 M1B  N27   C25  N26   120.26  3.000
 M1B  N27   C25  C24   124.67  3.000
 M1B  N26   C25  C24   115.04  3.000
 M1B  H262  N26  H261  114.28  3.000
 M1B  H262  N26  C25   118.34  3.000
 M1B  H261  N26  C25   116.00  3.000
 M1B  HN27  N27  C25   110.62  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
 M1B  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 M1B  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 M1B  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 M1B  CONST_04  C7    C4   C3   C2    180.00   0.0  0
 M1B  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 M1B  CONST_06  C6    C1   C2   C3      0.00   0.0  0
 M1B  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 M1B  CONST_10  C9    C8   C7   C4    180.00   0.0  0
 M1B  CONST_11  C11   C12  C7   C4    180.00   0.0  0
 M1B  CONST_14  C7    C4   C5   C6    180.00   0.0  0
 M1B  CONST_15  C10   C9   C8   C7      0.00   0.0  0
 M1B  CONST_16  C10   C11  C12  C7      0.00   0.0  0
 M1B  CONST_17  C11   C12  C7   C8      0.00   0.0  0
 M1B  CONST_18  C13   C10  C9   C8    180.00   0.0  0
 M1B  CONST_19  C11   C10  C9   C8      0.00   0.0  0
 M1B  CONST_20  C12   C7   C8   C9      0.00   0.0  0
 M1B  CONST_21  N20   C13  C10  C9    180.00   0.0  0
 M1B  CONST_22  N17   C13  C10  C9      0.00   0.0  0
 M1B  CONST_23  C12   C11  C10  C9      0.00   0.0  0
 M1B  CONST_24  C19   N20  C13  C10   180.00   0.0  0
 M1B  CONST_25  C18   N17  C13  C10   180.00   0.0  0
 M1B  CONST_26  N20   C13  C10  C11     0.00   0.0  0
 M1B  CONST_27  N17   C13  C10  C11   180.00   0.0  0
 M1B  CONST_28  C13   C10  C11  C12   180.00   0.0  0
 M1B  CONST_29  C18   C19  N20  C13     0.00   0.0  0
 M1B  CONST_30  C21   C19  N20  C13   180.00   0.0  0
 M1B  CONST_31  C22   C18  N17  C13   180.00   0.0  0
 M1B  CONST_32  C19   C18  N17  C13     0.00   0.0  0
 M1B  CONST_33  C19   N20  C13  N17     0.00   0.0  0
 M1B  CONST_34  C23   C22  C18  N17   180.00   0.0  0
 M1B  CONST_35  C21   C19  C18  N17   180.00   0.0  0
 M1B  CONST_36  N20   C19  C18  N17     0.00   0.0  0
 M1B  CONST_37  N20   C13  N17  C18     0.00   0.0  0
 M1B  CONST_38  C24   C23  C22  C18     0.00   0.0  0
 M1B  CONST_39  C24   C21  C19  C18     0.00   0.0  0
 M1B  CONST_40  C23   C22  C18  C19     0.00   0.0  0
 M1B  CONST_41  C23   C24  C21  C19     0.00   0.0  0
 M1B  CONST_42  C22   C18  C19  N20   180.00   0.0  0
 M1B  CONST_43  C24   C21  C19  N20   180.00   0.0  0
 M1B  CONST_44  C22   C18  C19  C21     0.00   0.0  0
 M1B  CONST_45  C22   C23  C24  C21     0.00   0.0  0
 M1B  CONST_46  C14   C6   C1   C2    180.00   0.0  0
 M1B  CONST_47  C14   C6   C5   C4    180.00   0.0  0
 M1B  CONST_48  C25   C24  C21  C19   180.00   0.0  0
 M1B  CONST_49  C25   C24  C23  C22   180.00   0.0  0
 M1B  CONST_50  H3    C3   C2   C1    180.00   0.0  0
 M1B  CONST_51  H5    C5   C6   C1    180.00   0.0  0
 M1B  CONST_52  H1    C1   C2   C3    180.00   0.0  0
 M1B  CONST_53  H2    C2   C3   C4    180.00   0.0  0
 M1B  CONST_54  H8    C8   C7   C4      0.00   0.0  0
 M1B  CONST_55  H12   C12  C7   C4      0.00   0.0  0
 M1B  CONST_56  H9    C9   C8   C7    180.00   0.0  0
 M1B  CONST_57  H11   C11  C12  C7    180.00   0.0  0
 M1B  CONST_58  HN17  N17  C13  C10     0.00   0.0  0
 M1B  CONST_59  H22   C22  C18  N17     0.00   0.0  0
 M1B  CONST_60  H23   C23  C22  C18   180.00   0.0  0
 M1B  CONST_61  H21   C21  C19  C18   180.00   0.0  0
 M1B  CONST_62  H161  N16  C14  C6    180.00   0.0  0
 M1B  CONST_64  HN15  N15  C14  C6      0.00   0.0  0
 M1B  CONST_65  H261  N26  C25  C24   180.00   0.0  0
 M1B  CONST_67  HN27  N27  C25  C24     0.00   0.0  0
 M1B  Var_01    N16   C14  C6   C1     33.28  30.0  2
 M1B  Var_02    N26   C25  C24  C21  -147.05  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
 M1B  plan-1  C1    0.020
 M1B  plan-1  C2    0.020
 M1B  plan-1  C3    0.020
 M1B  plan-1  C4    0.020
 M1B  plan-1  C5    0.020
 M1B  plan-1  C6    0.020
 M1B  plan-1  C7    0.020
 M1B  plan-1  C14   0.020
 M1B  plan-1  H1    0.020
 M1B  plan-1  H2    0.020
 M1B  plan-1  H3    0.020
 M1B  plan-1  H5    0.020
 M1B  plan-2  C4    0.020
 M1B  plan-2  C7    0.020
 M1B  plan-2  C8    0.020
 M1B  plan-2  C9    0.020
 M1B  plan-2  C10   0.020
 M1B  plan-2  C11   0.020
 M1B  plan-2  C12   0.020
 M1B  plan-2  C13   0.020
 M1B  plan-2  H8    0.020
 M1B  plan-2  H9    0.020
 M1B  plan-2  H11   0.020
 M1B  plan-2  H12   0.020
 M1B  plan-3  C10   0.020
 M1B  plan-3  C13   0.020
 M1B  plan-3  N17   0.020
 M1B  plan-3  C18   0.020
 M1B  plan-3  C19   0.020
 M1B  plan-3  N20   0.020
 M1B  plan-3  C21   0.020
 M1B  plan-3  C22   0.020
 M1B  plan-3  C23   0.020
 M1B  plan-3  C24   0.020
 M1B  plan-3  C25   0.020
 M1B  plan-3  HN17  0.020
 M1B  plan-3  H21   0.020
 M1B  plan-3  H22   0.020
 M1B  plan-3  H23   0.020
 M1B  plan-4  C6    0.020
 M1B  plan-4  C14   0.020
 M1B  plan-4  N15   0.020
 M1B  plan-4  N16   0.020
 M1B  plan-4  HN15  0.020
 M1B  plan-4  H161  0.020
 M1B  plan-4  H162  0.020
 M1B  plan-5  C24   0.020
 M1B  plan-5  C25   0.020
 M1B  plan-5  N26   0.020
 M1B  plan-5  N27   0.020
 M1B  plan-5  H261  0.020
 M1B  plan-5  H262  0.020
 M1B  plan-5  HN27  0.020

