# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:44:41 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-6-(2-methylpropoxy)phenolate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)COc1cccc(c1[O-])c2[nH]c3ccc(cc3n2)C(N)=[NH2+]
#
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
 656  656  2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-6-(2-methylpropoxy)phenolate  ligand  44  24  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_656
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
 656  C1    C  CR6    0  -0.001   4.8518  -0.4713   0.0435
 656  C2    C  CR16   0  -0.297   5.0343   0.8200   0.5686
 656  C3    C  CR16   0  -0.303   3.9636   1.6740   0.7569
 656  C4    C  CR56   0   0.358   2.7093   1.2022   0.3953
 656  C5    C  CR56   0   0.160   2.5034  -0.0912  -0.1277
 656  C6    C  CR16   0  -0.376   3.5852  -0.9409  -0.3046
 656  C7    C  C      0   0.581   6.0165  -1.3401  -0.1424
 656  N1    N  NH2    0  -0.770   7.1700  -0.8148  -0.4871
 656  N2    N  NC2    1  -0.769   5.8952  -2.6354   0.0367
 656  N3    N  NR15   0  -0.727   1.4698   1.7535   0.4242
 656  N4    N  N      0  -0.477   1.1792  -0.2899  -0.3999
 656  C8    C  CR5    0   0.481   0.5706   0.8276  -0.0615
 656  C1'   C  CR6    0  -0.246  -0.8360   1.1458  -0.1730
 656  C2'   C  CR16   0  -0.307  -1.2240   2.5018  -0.2541
 656  C3'   C  CR16   0  -0.309  -2.5398   2.8671  -0.3487
 656  C4'   C  CR16   0  -0.384  -3.5356   1.8672  -0.3565
 656  C5'   C  CR6    0   0.225  -3.1926   0.5424  -0.2746
 656  C6'   C  CR6    0   0.220  -1.8096   0.0913  -0.1835
 656  O6'   O  OC    -1  -0.553  -1.5507  -1.1295  -0.1016
 656  O5'   O  O2     0  -0.469  -4.0792  -0.4823  -0.2664
 656  C10   C  CH2    0  -0.143  -5.4546  -0.1815  -0.3020
 656  C20   C  CH1    0  -0.276  -6.2516  -1.4692  -0.1715
 656  C30   C  CH3    0  -0.650  -5.9535  -2.1934   1.1368
 656  C40   C  CH3    0  -0.660  -7.7377  -1.1488  -0.2951
 656  HC2   H  HCR6   0   0.272   6.0217   1.1509   0.8618
 656  HC3   H  HCR6   0   0.276   4.1083   2.6617   1.1731
 656  HC6   H  HCR6   0   0.271   3.4394  -1.9245  -0.7338
 656  HH11  H  HNH2   0   0.443   7.2346   0.1520  -0.7604
 656  HH12  H  HNH2   0   0.435   8.0109  -1.3672  -0.5604
 656  HH21  H  HNC2   0   0.435   6.6490  -3.2767  -0.1578
 656  HH22  H  HNC2   0   0.444   5.0572  -3.0230   0.4375
 656  HN3   H  HNR5   0   0.420   1.2390   2.6561   0.8069
 656  HC2'  H  HCR6   0   0.227  -0.4698   3.2798  -0.2811
 656  HC3'  H  HCR6   0   0.229  -2.8212   3.9083  -0.4308
 656  HC4'  H  HCR6   0   0.257  -4.5727   2.1707  -0.4334
 656  H10A  H  HCH2   0   0.212  -5.7147   0.3254  -1.2415
 656  H10B  H  HCH2   0   0.198  -5.7243   0.5002   0.5176
 656  H20   H  HCH1   0   0.225  -5.9769  -2.1256  -1.0049
 656  H30A  H  HCH3   0   0.211  -6.2034  -1.5653   1.9958
 656  H30B  H  HCH3   0   0.225  -6.5455  -3.1067   1.2146
 656  H30C  H  HCH3   0   0.232  -4.9031  -2.4713   1.2189
 656  H40A  H  HCH3   0   0.217  -8.0642  -0.4733   0.4990
 656  H40B  H  HCH3   0   0.228  -7.9701  -0.6762  -1.2510
 656  H40C  H  HCH3   0   0.233  -8.3382  -2.0560  -0.2224

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
 656  C1   C2    aromatic  1.406  0.020  1.406
 656  C1   C6    aromatic  1.395  0.020  1.395
 656  C1   C7    single    1.465  0.020  1.465
 656  C2   C3    aromatic  1.382  0.020  1.382
 656  C2   HC2   single    0.930  0.020  1.080
 656  C3   C4    aromatic  1.388  0.020  1.388
 656  C3   HC3   single    0.930  0.020  1.080
 656  C4   C5    aromatic  1.410  0.020  1.410
 656  C4   N3    aromatic  1.357  0.020  1.357
 656  C5   C6    aromatic  1.387  0.020  1.387
 656  C5   N4    aromatic  1.366  0.020  1.366
 656  C6   HC6   single    0.930  0.020  1.080
 656  C7   N1    single    1.313  0.020  1.313
 656  C7   N2    double    1.313  0.020  1.313
 656  N1   HH11  single    0.860  0.020  1.020
 656  N1   HH12  single    0.860  0.020  1.020
 656  N2   HH21  single    0.860  0.020  1.020
 656  N2   HH22  single    0.860  0.020  1.020
 656  N3   C8    aromatic  1.379  0.020  1.379
 656  N3   HN3   single    0.860  0.020  1.020
 656  N4   C8    aromatic  1.317  0.020  1.317
 656  C8   C1'   single    1.446  0.020  1.446
 656  C1'  C2'   aromatic  1.413  0.020  1.413
 656  C1'  C6'   aromatic  1.435  0.020  1.435
 656  C2'  C3'   aromatic  1.369  0.020  1.369
 656  C2'  HC2'  single    0.930  0.020  1.080
 656  C3'  C4'   aromatic  1.411  0.020  1.411
 656  C3'  HC3'  single    0.930  0.020  1.080
 656  C4'  C5'   aromatic  1.371  0.020  1.371
 656  C4'  HC4'  single    0.930  0.020  1.080
 656  C5'  C6'   aromatic  1.458  0.020  1.458
 656  C5'  O5'   single    1.355  0.020  1.355
 656  C6'  O6'   single    1.251  0.020  1.251
 656  O5'  C10   single    1.408  0.020  1.408
 656  C10  C20   single    1.520  0.020  1.520
 656  C10  H10A  single    0.970  0.020  1.090
 656  C10  H10B  single    0.970  0.020  1.090
 656  C20  C30   single    1.525  0.020  1.525
 656  C20  C40   single    1.525  0.020  1.525
 656  C20  H20   single    0.970  0.020  1.090
 656  C30  H30A  single    0.970  0.020  1.090
 656  C30  H30B  single    0.970  0.020  1.090
 656  C30  H30C  single    0.970  0.020  1.090
 656  C40  H40A  single    0.970  0.020  1.090
 656  C40  H40B  single    0.970  0.020  1.090
 656  C40  H40C  single    0.970  0.020  1.090

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
 656  C7    C1   C6    119.38  3.000
 656  C7    C1   C2    119.27  3.000
 656  C6    C1   C2    121.35  3.000
 656  HC2   C2   C3    118.75  3.000
 656  HC2   C2   C1    120.04  3.000
 656  C3    C2   C1    121.18  3.000
 656  HC3   C3   C4    122.11  3.000
 656  HC3   C3   C2    120.86  3.000
 656  C4    C3   C2    117.03  3.000
 656  N3    C4   C5    104.31  3.000
 656  N3    C4   C3    132.99  3.000
 656  C5    C4   C3    122.70  3.000
 656  N4    C5   C6    129.90  3.000
 656  N4    C5   C4    110.41  3.000
 656  C6    C5   C4    119.69  3.000
 656  HC6   C6   C5    120.13  3.000
 656  HC6   C6   C1    121.79  3.000
 656  C5    C6   C1    118.05  3.000
 656  N2    C7   N1    120.75  3.000
 656  N2    C7   C1    119.62  3.000
 656  N1    C7   C1    119.63  3.000
 656  HH12  N1   HH11  116.92  3.000
 656  HH12  N1   C7    122.15  3.000
 656  HH11  N1   C7    120.77  3.000
 656  HH22  N2   HH21  117.01  3.000
 656  HH22  N2   C7    120.73  3.000
 656  HH21  N2   C7    122.13  3.000
 656  HN3   N3   C8    125.88  3.000
 656  HN3   N3   C4    125.56  3.000
 656  C8    N3   C4    108.38  3.000
 656  C8    N4   C5    105.87  3.000
 656  C1'   C8   N4    128.05  3.000
 656  C1'   C8   N3    120.90  3.000
 656  N4    C8   N3    111.03  3.000
 656  C6'   C1'  C2'   121.23  3.000
 656  C6'   C1'  C8    119.91  3.000
 656  C2'   C1'  C8    118.86  3.000
 656  HC2'  C2'  C3'   118.40  3.000
 656  HC2'  C2'  C1'   119.95  3.000
 656  C3'   C2'  C1'   121.61  3.000
 656  HC3'  C3'  C4'   119.87  3.000
 656  HC3'  C3'  C2'   120.81  3.000
 656  C4'   C3'  C2'   119.31  3.000
 656  HC4'  C4'  C5'   120.97  3.000
 656  HC4'  C4'  C3'   118.51  3.000
 656  C5'   C4'  C3'   120.52  3.000
 656  O5'   C5'  C6'   112.73  3.000
 656  O5'   C5'  C4'   124.57  3.000
 656  C6'   C5'  C4'   122.70  3.000
 656  O6'   C6'  C5'   120.18  3.000
 656  O6'   C6'  C1'   125.19  3.000
 656  C5'   C6'  C1'   114.62  3.000
 656  C10   O5'  C5'   118.51  3.000
 656  H10B  C10  H10A  107.05  3.000
 656  H10B  C10  C20   109.43  3.000
 656  H10A  C10  C20   109.88  3.000
 656  H10B  C10  O5'   110.68  3.000
 656  H10A  C10  O5'   110.57  3.000
 656  C20   C10  O5'   109.21  3.000
 656  H20   C20  C40   107.97  3.000
 656  H20   C20  C30   108.60  3.000
 656  C40   C20  C30   111.09  3.000
 656  H20   C20  C10   108.10  3.000
 656  C40   C20  C10   109.02  3.000
 656  C30   C20  C10   111.93  3.000
 656  H30C  C30  H30B  107.71  3.000
 656  H30C  C30  H30A  107.92  3.000
 656  H30B  C30  H30A  107.51  3.000
 656  H30C  C30  C20   111.98  3.000
 656  H30B  C30  C20   110.65  3.000
 656  H30A  C30  C20   110.90  3.000
 656  H40C  C40  H40B  107.54  3.000
 656  H40C  C40  H40A  107.54  3.000
 656  H40B  C40  H40A  107.77  3.000
 656  H40C  C40  C20   110.88  3.000
 656  H40B  C40  C20   111.68  3.000
 656  H40A  C40  C20   111.24  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
 656  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 656  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 656  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 656  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 656  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 656  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 656  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 656  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 656  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 656  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 656  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 656  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 656  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 656  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 656  CONST_15  N3    C8   N4   C5      0.00   0.0  0
 656  CONST_16  C1'   C8   N4   C5    180.00   0.0  0
 656  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 656  CONST_18  C8    N4   C5   C6    180.00   0.0  0
 656  CONST_19  N4    C5   C4   N3      0.00   0.0  0
 656  CONST_24  C3'   C2'  C1'  C8    180.00   0.0  0
 656  CONST_25  C5'   C6'  C1'  C8    180.00   0.0  0
 656  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 656  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 656  CONST_28  C5'   C6'  C1'  C2'     0.00   0.0  0
 656  CONST_29  C5'   C4'  C3'  C2'     0.00   0.0  0
 656  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 656  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 656  CONST_32  C7    C1   C2   C3    180.00   0.0  0
 656  CONST_33  C7    C1   C6   C5    180.00   0.0  0
 656  CONST_34  O6'   C6'  C1'  C8      0.00   0.0  0
 656  CONST_35  O5'   C5'  C6'  C1'   180.00   0.0  0
 656  CONST_36  O6'   C6'  C1'  C2'   180.00   0.0  0
 656  CONST_37  O5'   C5'  C4'  C3'   180.00   0.0  0
 656  CONST_38  O6'   C6'  C5'  C4'   180.00   0.0  0
 656  CONST_39  HC3   C3   C2   C1    180.00   0.0  0
 656  CONST_40  HC6   C6   C1   C2    180.00   0.0  0
 656  CONST_41  HN3   N3   C4   C3      0.00   0.0  0
 656  CONST_42  HC2   C2   C3   C4    180.00   0.0  0
 656  CONST_43  HC2'  C2'  C1'  C8      0.00   0.0  0
 656  CONST_44  HC3'  C3'  C2'  C1'   180.00   0.0  0
 656  CONST_45  HC4'  C4'  C3'  C2'   180.00   0.0  0
 656  CONST_46  HH11  N1   C7   C1      0.00   0.0  0
 656  CONST_47  HH12  N1   C7   C1    180.00   0.0  0
 656  CONST_48  HH21  N2   C7   C1    180.00   0.0  0
 656  CONST_49  HH22  N2   C7   C1      0.00   0.0  0
 656  Var_01    N1    C7   C1   C2    -34.49  30.0  2
 656  Var_02    C20   C10  O5'  C5'  -175.46  30.0  3
 656  Var_03    C30   C20  C10  O5'    60.08  30.0  3
 656  Var_04    H30A  C30  C20  C10    60.05  30.0  3
 656  Var_05    H40A  C40  C20  C10   -61.33  30.0  3

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
 656  plan-1  C8    0.020
 656  plan-1  C1'   0.020
 656  plan-1  C2'   0.020
 656  plan-1  C3'   0.020
 656  plan-1  C4'   0.020
 656  plan-1  C5'   0.020
 656  plan-1  C6'   0.020
 656  plan-1  O6'   0.020
 656  plan-1  O5'   0.020
 656  plan-1  HC2'  0.020
 656  plan-1  HC3'  0.020
 656  plan-1  HC4'  0.020
 656  plan-2  C1    0.020
 656  plan-2  C2    0.020
 656  plan-2  C3    0.020
 656  plan-2  C4    0.020
 656  plan-2  C5    0.020
 656  plan-2  C6    0.020
 656  plan-2  C7    0.020
 656  plan-2  N3    0.020
 656  plan-2  N4    0.020
 656  plan-2  C8    0.020
 656  plan-2  C1'   0.020
 656  plan-2  HC2   0.020
 656  plan-2  HC3   0.020
 656  plan-2  HC6   0.020
 656  plan-2  HN3   0.020
 656  plan-3  C1    0.020
 656  plan-3  C7    0.020
 656  plan-3  N1    0.020
 656  plan-3  N2    0.020
 656  plan-3  HH11  0.020
 656  plan-3  HH12  0.020
 656  plan-3  HH21  0.020
 656  plan-3  HH22  0.020

