# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 07:34:05 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-[4-(4-carbamimidoylphenoxy)phenyl]-1H-benzimidazole-5-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc(Oc2ccc(cc2)c3[nH]c4ccc(cc4n3)C(N)=N)cc1
#
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
 HXL  HXL  2-[4-(4-carbamimidoylphenoxy)phenyl]-1H-benzimidazole-5-carboximidamide  ligand  46  28  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HXL
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
 HXL  N1    N  N     0  -0.655  41.8563  63.0067  10.4305
 HXL  N2    N  NH2   0  -0.823  40.1459  63.2458   8.8291
 HXL  C1    C  C     0   0.333  41.0519  63.7188   9.7378
 HXL  C2    C  CR6   0   0.030  41.1076  65.2010   9.8677
 HXL  C3    C  CR16  0  -0.378  41.5650  65.7506  11.0573
 HXL  C4    C  CR56  0   0.187  41.6021  67.1356  11.1769
 HXL  N3    N  N     0  -0.485  41.9850  67.9188  12.2348
 HXL  C5    C  CR5   0   0.489  41.8247  69.1535  11.8333
 HXL  N4    N  NR15  0  -0.737  41.3534  69.2250  10.5556
 HXL  C6    C  CR56  0   0.339  41.1971  67.9466  10.1029
 HXL  C7    C  CR16  0  -0.300  40.7514  67.4153   8.9003
 HXL  C8    C  CR16  0  -0.310  40.7107  66.0364   8.8047
 HXL  C9    C  CR6   0   0.004  42.1047  70.3296  12.6506
 HXL  C10   C  CR16  0  -0.281  42.5595  70.1583  13.9589
 HXL  C11   C  CR16  0  -0.308  42.8246  71.2433  14.7735
 HXL  C12   C  CR6   0   0.347  42.6395  72.5311  14.2792
 HXL  C13   C  CR16  0  -0.315  42.1920  72.7223  12.9784
 HXL  C14   C  CR16  0  -0.294  41.9234  71.6282  12.1757
 HXL  O1    O  O2    0  -0.502  42.8221  73.6465  15.0355
 HXL  C15   C  CR6   0   0.329  43.7751  73.6730  16.0149
 HXL  C16   C  CR16  0  -0.300  45.0812  73.2587  15.7776
 HXL  C17   C  CR16  0  -0.267  46.0221  73.3755  16.7845
 HXL  C18   C  CR6   0   0.040  45.6834  73.8964  18.0325
 HXL  C19   C  CR16  0  -0.286  44.3712  74.3115  18.2458
 HXL  C20   C  CR16  0  -0.314  43.4167  74.1981  17.2460
 HXL  C21   C  C     0   0.335  46.7314  74.0216  19.0818
 HXL  N5    N  N     0  -0.651  47.9529  74.1033  18.7160
 HXL  N6    N  NH2   0  -0.823  46.2679  74.0939  20.3644
 HXL  HN1   H  H     0   0.321  41.6865  62.0154  10.2826
 HXL  HN21  H  HNH2  0   0.389  39.9713  62.2531   8.8329
 HXL  HN22  H  HNH2  0   0.393  39.3192  63.7934   8.6545
 HXL  H3    H  HCR6  0   0.253  41.8724  65.1128  11.8753
 HXL  HN4   H  HNR5  0   0.426  41.1515  70.0605  10.0303
 HXL  H7    H  HCR6  0   0.270  40.4502  68.0416   8.0713
 HXL  H8    H  HCR6  0   0.258  40.3813  65.5990   7.8717
 HXL  H10   H  HCR6  0   0.266  42.7006  69.1592  14.3480
 HXL  H11   H  HCR6  0   0.288  43.1620  71.0769  15.7881
 HXL  H13   H  HCR6  0   0.279  42.0482  73.7249  12.5976
 HXL  H14   H  HCR6  0   0.253  41.5767  71.8174  11.1683
 HXL  H16   H  HCR6  0   0.284  45.3695  72.8561  14.8147
 HXL  H17   H  HCR6  0   0.264  47.0400  73.0609  16.6000
 HXL  H19   H  HCR6  0   0.265  44.0741  74.7444  19.1920
 HXL  H20   H  HCR6  0   0.275  42.4004  74.5268  17.4203
 HXL  HN5   H  H     0   0.324  48.5759  74.1561  19.5173
 HXL  HN61  H  HNH2  0   0.391  46.9493  74.0488  21.1052
 HXL  HN62  H  HNH2  0   0.395  45.4032  73.6293  20.5881

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
 HXL  N1   C1    double    1.278  0.020  1.278
 HXL  N1   HN1   single    0.890  0.020  1.040
 HXL  N2   C1    single    1.368  0.020  1.368
 HXL  N2   HN21  single    0.890  0.020  1.040
 HXL  N2   HN22  single    0.890  0.020  1.040
 HXL  C1   C2    single    1.489  0.020  1.489
 HXL  C2   C3    aromatic  1.388  0.020  1.388
 HXL  C2   C8    aromatic  1.409  0.020  1.409
 HXL  C3   C4    aromatic  1.391  0.020  1.391
 HXL  C3   H3    single    0.930  0.020  1.080
 HXL  C4   N3    aromatic  1.371  0.020  1.371
 HXL  C4   C6    aromatic  1.405  0.020  1.405
 HXL  N3   C5    aromatic  1.308  0.020  1.308
 HXL  C5   N4    aromatic  1.364  0.020  1.364
 HXL  C5   C9    single    1.459  0.020  1.459
 HXL  N4   C6    aromatic  1.365  0.020  1.365
 HXL  N4   HN4   single    0.860  0.020  1.020
 HXL  C6   C7    aromatic  1.388  0.020  1.388
 HXL  C7   C8    aromatic  1.383  0.020  1.383
 HXL  C7   H7    single    0.930  0.020  1.080
 HXL  C8   H8    single    0.930  0.020  1.080
 HXL  C9   C10   aromatic  1.396  0.020  1.396
 HXL  C9   C14   aromatic  1.395  0.020  1.395
 HXL  C10  C11   aromatic  1.382  0.020  1.382
 HXL  C10  H10   single    0.930  0.020  1.080
 HXL  C11  C12   aromatic  1.392  0.020  1.392
 HXL  C11  H11   single    0.930  0.020  1.080
 HXL  C12  C13   aromatic  1.389  0.020  1.389
 HXL  C12  O1    single    1.360  0.020  1.360
 HXL  C13  C14   aromatic  1.383  0.020  1.383
 HXL  C13  H13   single    0.930  0.020  1.080
 HXL  C14  H14   single    0.930  0.020  1.080
 HXL  O1   C15   single    1.367  0.020  1.367
 HXL  C15  C16   aromatic  1.391  0.020  1.391
 HXL  C15  C20   aromatic  1.386  0.020  1.386
 HXL  C16  C17   aromatic  1.383  0.020  1.383
 HXL  C16  H16   single    0.930  0.020  1.080
 HXL  C17  C18   aromatic  1.394  0.020  1.394
 HXL  C17  H17   single    0.930  0.020  1.080
 HXL  C18  C19   aromatic  1.393  0.020  1.393
 HXL  C18  C21   single    1.488  0.020  1.488
 HXL  C19  C20   aromatic  1.387  0.020  1.387
 HXL  C19  H19   single    0.930  0.020  1.080
 HXL  C20  H20   single    0.930  0.020  1.080
 HXL  C21  N5    double    1.278  0.020  1.278
 HXL  C21  N6    single    1.366  0.020  1.366
 HXL  N5   HN5   single    0.890  0.020  1.040
 HXL  N6   HN61  single    0.890  0.020  1.040
 HXL  N6   HN62  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
 HXL  HN1   N1   C1    111.06  3.000
 HXL  HN22  N2   HN21  113.21  3.000
 HXL  HN22  N2   C1    118.10  3.000
 HXL  HN21  N2   C1    116.93  3.000
 HXL  C2    C1   N2    115.28  3.000
 HXL  C2    C1   N1    118.93  3.000
 HXL  N2    C1   N1    125.75  3.000
 HXL  C8    C2   C3    120.31  3.000
 HXL  C8    C2   C1    120.92  3.000
 HXL  C3    C2   C1    118.77  3.000
 HXL  H3    C3   C4    120.97  3.000
 HXL  H3    C3   C2    120.55  3.000
 HXL  C4    C3   C2    118.48  3.000
 HXL  C6    C4   N3    109.91  3.000
 HXL  C6    C4   C3    120.09  3.000
 HXL  N3    C4   C3    130.00  3.000
 HXL  C5    N3   C4    105.55  3.000
 HXL  C9    C5   N4    123.29  3.000
 HXL  C9    C5   N3    124.42  3.000
 HXL  N4    C5   N3    112.30  3.000
 HXL  HN4   N4   C6    125.50  3.000
 HXL  HN4   N4   C5    126.97  3.000
 HXL  C6    N4   C5    107.53  3.000
 HXL  C7    C6   N4    133.04  3.000
 HXL  C7    C6   C4    122.25  3.000
 HXL  N4    C6   C4    104.71  3.000
 HXL  H7    C7   C8    121.08  3.000
 HXL  H7    C7   C6    122.12  3.000
 HXL  C8    C7   C6    116.80  3.000
 HXL  H8    C8   C7    118.15  3.000
 HXL  H8    C8   C2    119.78  3.000
 HXL  C7    C8   C2    122.06  3.000
 HXL  C14   C9   C10   118.42  3.000
 HXL  C14   C9   C5    122.33  3.000
 HXL  C10   C9   C5    119.25  3.000
 HXL  H10   C10  C11   119.21  3.000
 HXL  H10   C10  C9    119.55  3.000
 HXL  C11   C10  C9    121.23  3.000
 HXL  H11   C11  C12   121.11  3.000
 HXL  H11   C11  C10   119.44  3.000
 HXL  C12   C11  C10   119.44  3.000
 HXL  O1    C12  C13   116.82  3.000
 HXL  O1    C12  C11   122.93  3.000
 HXL  C13   C12  C11   120.18  3.000
 HXL  H13   C13  C14   120.19  3.000
 HXL  H13   C13  C12   119.99  3.000
 HXL  C14   C13  C12   119.82  3.000
 HXL  H14   C14  C13   117.66  3.000
 HXL  H14   C14  C9    121.43  3.000
 HXL  C13   C14  C9    120.91  3.000
 HXL  C15   O1   C12   120.53  3.000
 HXL  C20   C15  C16   120.50  3.000
 HXL  C20   C15  O1    117.62  3.000
 HXL  C16   C15  O1    121.79  3.000
 HXL  H16   C16  C17   119.84  3.000
 HXL  H16   C16  C15   120.84  3.000
 HXL  C17   C16  C15   119.31  3.000
 HXL  H17   C17  C18   119.35  3.000
 HXL  H17   C17  C16   119.45  3.000
 HXL  C18   C17  C16   121.20  3.000
 HXL  C21   C18  C19   122.03  3.000
 HXL  C21   C18  C17   119.44  3.000
 HXL  C19   C18  C17   118.51  3.000
 HXL  H19   C19  C20   118.30  3.000
 HXL  H19   C19  C18   120.79  3.000
 HXL  C20   C19  C18   120.91  3.000
 HXL  H20   C20  C19   120.35  3.000
 HXL  H20   C20  C15   120.08  3.000
 HXL  C19   C20  C15   119.57  3.000
 HXL  N6    C21  N5    126.16  3.000
 HXL  N6    C21  C18   115.31  3.000
 HXL  N5    C21  C18   118.47  3.000
 HXL  HN5   N5   C21   111.32  3.000
 HXL  HN62  N6   HN61  113.38  3.000
 HXL  HN62  N6   C21   118.41  3.000
 HXL  HN61  N6   C21   117.29  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
 HXL  CONST_01  N3    C4   C3   C2   180.00   0.0  0
 HXL  CONST_02  C6    C4   C3   C2     0.00   0.0  0
 HXL  CONST_03  C6    C7   C8   C2     0.00   0.0  0
 HXL  CONST_04  C7    C8   C2   C3     0.00   0.0  0
 HXL  CONST_05  C5    N3   C4   C3   180.00   0.0  0
 HXL  CONST_06  N4    C6   C4   C3   180.00   0.0  0
 HXL  CONST_07  C7    C6   C4   C3     0.00   0.0  0
 HXL  CONST_08  C8    C2   C3   C4     0.00   0.0  0
 HXL  CONST_09  N4    C5   N3   C4     0.00   0.0  0
 HXL  CONST_10  C9    C5   N3   C4   180.00   0.0  0
 HXL  CONST_11  C5    N4   C6   C4     0.00   0.0  0
 HXL  CONST_12  C8    C7   C6   C4     0.00   0.0  0
 HXL  CONST_13  N4    C6   C4   N3     0.00   0.0  0
 HXL  CONST_14  C7    C6   C4   N3   180.00   0.0  0
 HXL  CONST_15  C6    N4   C5   N3     0.00   0.0  0
 HXL  CONST_16  C10   C9   C5   N3     0.00   0.0  0
 HXL  CONST_17  C14   C9   C5   N3   180.00   0.0  0
 HXL  CONST_18  C6    C4   N3   C5     0.00   0.0  0
 HXL  CONST_19  C7    C6   N4   C5   180.00   0.0  0
 HXL  CONST_20  C11   C10  C9   C5   180.00   0.0  0
 HXL  CONST_21  C13   C14  C9   C5   180.00   0.0  0
 HXL  CONST_22  C10   C9   C5   N4   180.00   0.0  0
 HXL  CONST_23  C14   C9   C5   N4     0.00   0.0  0
 HXL  CONST_24  C8    C7   C6   N4   180.00   0.0  0
 HXL  CONST_25  C9    C5   N4   C6   180.00   0.0  0
 HXL  CONST_26  C12   C11  C10  C9     0.00   0.0  0
 HXL  CONST_27  C12   C13  C14  C9     0.00   0.0  0
 HXL  CONST_28  C13   C14  C9   C10    0.00   0.0  0
 HXL  CONST_29  C13   C12  C11  C10    0.00   0.0  0
 HXL  CONST_30  C14   C9   C10  C11    0.00   0.0  0
 HXL  CONST_31  C14   C13  C12  C11    0.00   0.0  0
 HXL  CONST_32  C18   C17  C16  C15    0.00   0.0  0
 HXL  CONST_33  C18   C19  C20  C15    0.00   0.0  0
 HXL  CONST_34  C19   C20  C15  C16    0.00   0.0  0
 HXL  CONST_35  C19   C18  C17  C16    0.00   0.0  0
 HXL  CONST_36  C20   C15  C16  C17    0.00   0.0  0
 HXL  CONST_37  C20   C19  C18  C17    0.00   0.0  0
 HXL  CONST_38  C4    C3   C2   C1   180.00   0.0  0
 HXL  CONST_39  C7    C8   C2   C1   180.00   0.0  0
 HXL  CONST_40  O1    C12  C11  C10  180.00   0.0  0
 HXL  CONST_41  O1    C12  C13  C14  180.00   0.0  0
 HXL  CONST_42  C17   C16  C15  O1   180.00   0.0  0
 HXL  CONST_43  C19   C20  C15  O1   180.00   0.0  0
 HXL  CONST_44  C21   C18  C17  C16  180.00   0.0  0
 HXL  CONST_45  C21   C18  C19  C20  180.00   0.0  0
 HXL  CONST_46  H7    C7   C8   C2   180.00   0.0  0
 HXL  CONST_47  H8    C8   C2   C3   180.00   0.0  0
 HXL  CONST_48  HN4   N4   C6   C4   180.00   0.0  0
 HXL  CONST_49  H3    C3   C4   N3     0.00   0.0  0
 HXL  CONST_50  H10   C10  C9   C5     0.00   0.0  0
 HXL  CONST_51  H14   C14  C9   C5     0.00   0.0  0
 HXL  CONST_52  H11   C11  C10  C9   180.00   0.0  0
 HXL  CONST_53  H13   C13  C14  C9   180.00   0.0  0
 HXL  CONST_54  H17   C17  C16  C15  180.00   0.0  0
 HXL  CONST_55  H19   C19  C20  C15  180.00   0.0  0
 HXL  CONST_56  H20   C20  C15  C16  180.00   0.0  0
 HXL  CONST_57  H16   C16  C17  C18  180.00   0.0  0
 HXL  CONST_58  HN1   N1   C1   C2   180.00   0.0  0
 HXL  CONST_59  HN21  N2   C1   C2   180.00   0.0  0
 HXL  CONST_61  HN5   N5   C21  C18  180.00   0.0  0
 HXL  CONST_62  HN61  N6   C21  C18  180.00   0.0  0
 HXL  Var_01    C16   C15  O1   C12   48.95  30.0  2
 HXL  Var_02    C3    C2   C1   N1   -26.91  30.0  2
 HXL  Var_03    N5    C21  C18  C17   24.06  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
 HXL  plan-1  C5    0.020
 HXL  plan-1  C9    0.020
 HXL  plan-1  C10   0.020
 HXL  plan-1  C11   0.020
 HXL  plan-1  C12   0.020
 HXL  plan-1  C13   0.020
 HXL  plan-1  C14   0.020
 HXL  plan-1  O1    0.020
 HXL  plan-1  H10   0.020
 HXL  plan-1  H11   0.020
 HXL  plan-1  H13   0.020
 HXL  plan-1  H14   0.020
 HXL  plan-2  O1    0.020
 HXL  plan-2  C15   0.020
 HXL  plan-2  C16   0.020
 HXL  plan-2  C17   0.020
 HXL  plan-2  C18   0.020
 HXL  plan-2  C19   0.020
 HXL  plan-2  C20   0.020
 HXL  plan-2  C21   0.020
 HXL  plan-2  H16   0.020
 HXL  plan-2  H17   0.020
 HXL  plan-2  H19   0.020
 HXL  plan-2  H20   0.020
 HXL  plan-3  C1    0.020
 HXL  plan-3  C2    0.020
 HXL  plan-3  C3    0.020
 HXL  plan-3  C4    0.020
 HXL  plan-3  N3    0.020
 HXL  plan-3  C5    0.020
 HXL  plan-3  N4    0.020
 HXL  plan-3  C6    0.020
 HXL  plan-3  C7    0.020
 HXL  plan-3  C8    0.020
 HXL  plan-3  C9    0.020
 HXL  plan-3  H3    0.020
 HXL  plan-3  HN4   0.020
 HXL  plan-3  H7    0.020
 HXL  plan-3  H8    0.020
 HXL  plan-4  N1    0.020
 HXL  plan-4  N2    0.020
 HXL  plan-4  C1    0.020
 HXL  plan-4  C2    0.020
 HXL  plan-4  HN1   0.020
 HXL  plan-4  HN21  0.020
 HXL  plan-4  HN22  0.020
 HXL  plan-5  C18   0.020
 HXL  plan-5  C21   0.020
 HXL  plan-5  N5    0.020
 HXL  plan-5  N6    0.020
 HXL  plan-5  HN5   0.020
 HXL  plan-5  HN61  0.020
 HXL  plan-5  HN62  0.020

