# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:49:46 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-6-fluoro-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]c3cc(F)c(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
 950  950  2-{5-[amino(iminio)methyl]-6-fluoro-1H-benzimidazol-2-yl}-6-(2-methylpropoxy)phenolate  ligand  44  25  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_950
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
 950  C1    C  CR6    0  -0.230  -4.5027  -0.6026   0.0447
 950  C2    C  CR6    0   0.550  -4.6730   0.6980  -0.4494
 950  F2    F  F      0  -0.305  -5.9100   1.1065  -0.7707
 950  C3    C  CR16   0  -0.463  -3.6385   1.5948  -0.5912
 950  C4    C  CR56   0   0.376  -2.3827   1.1318  -0.2261
 950  C5    C  CR56   0   0.153  -2.1585  -0.1711   0.2658
 950  C6    C  CR16   0  -0.352  -3.2274  -1.0375   0.4154
 950  C7    C  C      0   0.591  -5.6378  -1.5197   0.2027
 950  N1    N  NH2    0  -0.755  -5.7241  -2.2137   1.3132
 950  N2    N  NC2    1  -0.756  -6.5231  -1.6592  -0.7537
 950  N3    N  NR15   0  -0.728  -1.1559   1.7040  -0.2377
 950  N4    N  N      0  -0.474  -0.8291  -0.3582   0.5270
 950  C8    C  CR5    0   0.479  -0.2393   0.7759   0.2201
 950  C1'   C  CR6    0  -0.248   1.1623   1.1131   0.3278
 950  C2'   C  CR16   0  -0.306   1.5297   2.4710   0.4577
 950  C3'   C  CR16   0  -0.309   2.8413   2.8535   0.5412
 950  C4'   C  CR16   0  -0.384   3.8526   1.8708   0.4839
 950  C5'   C  CR6    0   0.225   3.5291   0.5452   0.3524
 950  C6'   C  CR6    0   0.221   2.1519   0.0749   0.2767
 950  O6'   O  OC    -1  -0.552   1.9095  -1.1455   0.1517
 950  O5'   O  O2     0  -0.469   4.4318  -0.4630   0.2780
 950  C10   C  CH2    0  -0.143   5.8019  -0.1366   0.2502
 950  C20   C  CH1    0  -0.276   6.6132  -1.3999   0.0129
 950  C30   C  CH3    0  -0.652   6.2509  -2.0612  -1.3125
 950  C40   C  CH3    0  -0.660   8.0979  -1.0534   0.0650
 950  HC3   H  HCR6   0   0.297  -3.8162   2.5966  -0.9586
 950  HC6   H  HCR6   0   0.286  -3.0703  -2.0443   0.7807
 950  HH11  H  HNH2   0   0.447  -5.1218  -2.0070   2.0933
 950  HH12  H  HNH2   0   0.437  -6.4320  -2.9188   1.4547
 950  HH21  H  HNC2   0   0.437  -7.3371  -2.2456  -0.6456
 950  HH22  H  HNC2   0   0.443  -6.3939  -1.2255  -1.6525
 950  HN3   H  HNR5   0   0.422  -0.9380   2.6167  -0.6041
 950  HC2'  H  HCR6   0   0.228   0.7639   3.2349   0.5319
 950  HC3'  H  HCR6   0   0.230   3.1081   3.8947   0.6620
 950  HC4'  H  HCR6   0   0.258   4.8863   2.1880   0.5512
 950  H10A  H  HCH2   0   0.213   6.1050   0.3352   1.1950
 950  H10B  H  HCH2   0   0.198   6.0104   0.5858  -0.5521
 950  H20   H  HCH1   0   0.226   6.4001  -2.1020   0.8269
 950  H30A  H  HCH3   0   0.225   6.8624  -2.9485  -1.4837
 950  H30B  H  HCH3   0   0.232   5.2058  -2.3681  -1.3422
 950  H30C  H  HCH3   0   0.212   6.4233  -1.3766  -2.1471
 950  H40A  H  HCH3   0   0.217   8.3624  -0.3340  -0.7135
 950  H40B  H  HCH3   0   0.228   8.3770  -0.6207   1.0272
 950  H40C  H  HCH3   0   0.234   8.7102  -1.9428  -0.0873

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
 950  C1   C2    aromatic  1.402  0.020  1.402
 950  C1   C6    aromatic  1.397  0.020  1.397
 950  C1   C7    single    1.468  0.020  1.468
 950  C2   F2    single    1.342  0.020  1.342
 950  C2   C3    aromatic  1.376  0.020  1.376
 950  C3   C4    aromatic  1.387  0.020  1.387
 950  C3   HC3   single    0.930  0.020  1.080
 950  C4   C5    aromatic  1.411  0.020  1.411
 950  C4   N3    aromatic  1.354  0.020  1.354
 950  C5   C6    aromatic  1.384  0.020  1.384
 950  C5   N4    aromatic  1.368  0.020  1.368
 950  C6   HC6   single    0.930  0.020  1.080
 950  C7   N1    single    1.312  0.020  1.312
 950  C7   N2    double    1.311  0.020  1.311
 950  N1   HH11  single    0.860  0.020  1.020
 950  N1   HH12  single    0.860  0.020  1.020
 950  N2   HH21  single    0.860  0.020  1.020
 950  N2   HH22  single    0.860  0.020  1.020
 950  N3   C8    aromatic  1.382  0.020  1.382
 950  N3   HN3   single    0.860  0.020  1.020
 950  N4   C8    aromatic  1.315  0.020  1.315
 950  C8   C1'   single    1.446  0.020  1.446
 950  C1'  C2'   aromatic  1.413  0.020  1.413
 950  C1'  C6'   aromatic  1.435  0.020  1.435
 950  C2'  C3'   aromatic  1.369  0.020  1.369
 950  C2'  HC2'  single    0.930  0.020  1.080
 950  C3'  C4'   aromatic  1.411  0.020  1.411
 950  C3'  HC3'  single    0.930  0.020  1.080
 950  C4'  C5'   aromatic  1.371  0.020  1.371
 950  C4'  HC4'  single    0.930  0.020  1.080
 950  C5'  C6'   aromatic  1.457  0.020  1.457
 950  C5'  O5'   single    1.355  0.020  1.355
 950  C6'  O6'   single    1.251  0.020  1.251
 950  O5'  C10   single    1.409  0.020  1.409
 950  C10  C20   single    1.520  0.020  1.520
 950  C10  H10A  single    0.970  0.020  1.090
 950  C10  H10B  single    0.970  0.020  1.090
 950  C20  C30   single    1.525  0.020  1.525
 950  C20  C40   single    1.525  0.020  1.525
 950  C20  H20   single    0.970  0.020  1.090
 950  C30  H30A  single    0.970  0.020  1.090
 950  C30  H30B  single    0.970  0.020  1.090
 950  C30  H30C  single    0.970  0.020  1.090
 950  C40  H40A  single    0.970  0.020  1.090
 950  C40  H40B  single    0.970  0.020  1.090
 950  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
 950  C7    C1   C6    118.87  3.000
 950  C7    C1   C2    121.58  3.000
 950  C6    C1   C2    119.55  3.000
 950  C3    C2   F2    118.03  3.000
 950  C3    C2   C1    123.34  3.000
 950  F2    C2   C1    118.61  3.000
 950  HC3   C3   C4    123.17  3.000
 950  HC3   C3   C2    120.99  3.000
 950  C4    C3   C2    115.84  3.000
 950  N3    C4   C5    104.44  3.000
 950  N3    C4   C3    132.61  3.000
 950  C5    C4   C3    122.95  3.000
 950  N4    C5   C6    130.12  3.000
 950  N4    C5   C4    110.33  3.000
 950  C6    C5   C4    119.55  3.000
 950  HC6   C6   C5    120.44  3.000
 950  HC6   C6   C1    120.76  3.000
 950  C5    C6   C1    118.77  3.000
 950  N2    C7   N1    121.11  3.000
 950  N2    C7   C1    120.68  3.000
 950  N1    C7   C1    118.19  3.000
 950  HH12  N1   HH11  117.02  3.000
 950  HH12  N1   C7    122.30  3.000
 950  HH11  N1   C7    120.51  3.000
 950  HH22  N2   HH21  116.73  3.000
 950  HH22  N2   C7    121.27  3.000
 950  HH21  N2   C7    121.91  3.000
 950  HN3   N3   C8    125.83  3.000
 950  HN3   N3   C4    125.60  3.000
 950  C8    N3   C4    108.31  3.000
 950  C8    N4   C5    105.87  3.000
 950  C1'   C8   N4    128.23  3.000
 950  C1'   C8   N3    120.72  3.000
 950  N4    C8   N3    111.04  3.000
 950  C6'   C1'  C2'   121.28  3.000
 950  C6'   C1'  C8    119.81  3.000
 950  C2'   C1'  C8    118.90  3.000
 950  HC2'  C2'  C3'   118.41  3.000
 950  HC2'  C2'  C1'   119.99  3.000
 950  C3'   C2'  C1'   121.56  3.000
 950  HC3'  C3'  C4'   119.87  3.000
 950  HC3'  C3'  C2'   120.81  3.000
 950  C4'   C3'  C2'   119.32  3.000
 950  HC4'  C4'  C5'   120.95  3.000
 950  HC4'  C4'  C3'   118.51  3.000
 950  C5'   C4'  C3'   120.54  3.000
 950  O5'   C5'  C6'   112.74  3.000
 950  O5'   C5'  C4'   124.57  3.000
 950  C6'   C5'  C4'   122.69  3.000
 950  O6'   C6'  C5'   120.22  3.000
 950  O6'   C6'  C1'   125.16  3.000
 950  C5'   C6'  C1'   114.61  3.000
 950  C10   O5'  C5'   118.46  3.000
 950  H10B  C10  H10A  107.04  3.000
 950  H10B  C10  C20   109.32  3.000
 950  H10A  C10  C20   110.11  3.000
 950  H10B  C10  O5'   110.55  3.000
 950  H10A  C10  O5'   110.54  3.000
 950  C20   C10  O5'   109.25  3.000
 950  H20   C20  C40   108.02  3.000
 950  H20   C20  C30   108.76  3.000
 950  C40   C20  C30   111.07  3.000
 950  H20   C20  C10   108.22  3.000
 950  C40   C20  C10   108.99  3.000
 950  C30   C20  C10   111.67  3.000
 950  H30C  C30  H30B  107.87  3.000
 950  H30C  C30  H30A  107.53  3.000
 950  H30B  C30  H30A  107.71  3.000
 950  H30C  C30  C20   110.76  3.000
 950  H30B  C30  C20   111.94  3.000
 950  H30A  C30  C20   110.85  3.000
 950  H40C  C40  H40B  107.64  3.000
 950  H40C  C40  H40A  107.55  3.000
 950  H40B  C40  H40A  107.78  3.000
 950  H40C  C40  C20   110.88  3.000
 950  H40B  C40  C20   111.66  3.000
 950  H40A  C40  C20   111.15  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
 950  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 950  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 950  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 950  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 950  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 950  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 950  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 950  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 950  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 950  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 950  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 950  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 950  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 950  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 950  CONST_15  N3    C8   N4   C5      0.00   0.0  0
 950  CONST_16  C1'   C8   N4   C5    180.00   0.0  0
 950  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 950  CONST_18  C8    N4   C5   C6    180.00   0.0  0
 950  CONST_19  N4    C5   C4   N3      0.00   0.0  0
 950  CONST_24  C3'   C2'  C1'  C8    180.00   0.0  0
 950  CONST_25  C5'   C6'  C1'  C8    180.00   0.0  0
 950  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 950  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 950  CONST_28  C5'   C6'  C1'  C2'     0.00   0.0  0
 950  CONST_29  C5'   C4'  C3'  C2'     0.00   0.0  0
 950  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 950  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 950  CONST_32  C6    C1   C2   F2    180.00   0.0  0
 950  CONST_33  C4    C3   C2   F2    180.00   0.0  0
 950  CONST_34  C7    C1   C2   C3    180.00   0.0  0
 950  CONST_35  C7    C1   C6   C5    180.00   0.0  0
 950  CONST_36  O6'   C6'  C1'  C8      0.00   0.0  0
 950  CONST_37  O5'   C5'  C6'  C1'   180.00   0.0  0
 950  CONST_38  O6'   C6'  C1'  C2'   180.00   0.0  0
 950  CONST_39  O5'   C5'  C4'  C3'   180.00   0.0  0
 950  CONST_40  O6'   C6'  C5'  C4'   180.00   0.0  0
 950  CONST_41  HC3   C3   C2   C1    180.00   0.0  0
 950  CONST_42  HC6   C6   C1   C2    180.00   0.0  0
 950  CONST_43  HN3   N3   C4   C3      0.00   0.0  0
 950  CONST_44  HC2'  C2'  C1'  C8      0.00   0.0  0
 950  CONST_45  HC3'  C3'  C2'  C1'   180.00   0.0  0
 950  CONST_46  HC4'  C4'  C3'  C2'   180.00   0.0  0
 950  CONST_47  HH11  N1   C7   C1      0.00   0.0  0
 950  CONST_48  HH12  N1   C7   C1    180.00   0.0  0
 950  CONST_49  HH21  N2   C7   C1    180.00   0.0  0
 950  CONST_50  HH22  N2   C7   C1      0.00   0.0  0
 950  Var_01    N1    C7   C1   C2   -135.29  30.0  2
 950  Var_02    C20   C10  O5'  C5'  -173.85  30.0  3
 950  Var_03    C30   C20  C10  O5'    60.19  30.0  3
 950  Var_04    H30A  C30  C20  C10   178.24  30.0  3
 950  Var_05    H40A  C40  C20  C10   -61.25  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
 950  plan-1  C8    0.020
 950  plan-1  C1'   0.020
 950  plan-1  C2'   0.020
 950  plan-1  C3'   0.020
 950  plan-1  C4'   0.020
 950  plan-1  C5'   0.020
 950  plan-1  C6'   0.020
 950  plan-1  O6'   0.020
 950  plan-1  O5'   0.020
 950  plan-1  HC2'  0.020
 950  plan-1  HC3'  0.020
 950  plan-1  HC4'  0.020
 950  plan-2  C1    0.020
 950  plan-2  C2    0.020
 950  plan-2  F2    0.020
 950  plan-2  C3    0.020
 950  plan-2  C4    0.020
 950  plan-2  C5    0.020
 950  plan-2  C6    0.020
 950  plan-2  C7    0.020
 950  plan-2  N3    0.020
 950  plan-2  N4    0.020
 950  plan-2  C8    0.020
 950  plan-2  C1'   0.020
 950  plan-2  HC3   0.020
 950  plan-2  HC6   0.020
 950  plan-2  HN3   0.020
 950  plan-3  C1    0.020
 950  plan-3  C7    0.020
 950  plan-3  N1    0.020
 950  plan-3  N2    0.020
 950  plan-3  HH11  0.020
 950  plan-3  HH12  0.020
 950  plan-3  HH21  0.020
 950  plan-3  HH22  0.020

