# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:44:50 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-6-(cyclopentyloxy)phenolate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(nc2c1)c3cccc(OC4CCCC4)c3[O-]
#
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
 655  655  2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-6-(cyclopentyloxy)phenolate  ligand  45  25  .  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_655
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
 655  C1    C  CR6    0  -0.005   5.0072   0.4635  -0.1777
 655  C2    C  CR16   0  -0.295   5.1653  -0.8849  -0.5433
 655  C3    C  CR16   0  -0.303   4.0872  -1.7502  -0.5664
 655  C4    C  CR56   0   0.358   2.8482  -1.2241  -0.2283
 655  C5    C  CR56   0   0.159   2.6653   0.1293   0.1237
 655  C6    C  CR16   0  -0.375   3.7577   0.9834   0.1596
 655  C7    C  C      0   0.578   6.1835   1.3358  -0.1341
 655  N1    N  NH2    0  -0.766   6.2702   2.2571   0.7975
 655  N2    N  NC2    1  -0.769   7.1387   1.1851  -1.0227
 655  N3    N  NR15   0  -0.726   1.6053  -1.7630  -0.1464
 655  N4    N  N      0  -0.477   1.3490   0.3775   0.3929
 655  C8    C  CR5    0   0.480   0.7254  -0.7704   0.2294
 655  C1'   C  CR6    0  -0.248  -0.6788  -1.0580   0.4244
 655  C2'   C  CR16   0  -0.307  -1.0662  -2.3802   0.7361
 655  C3'   C  CR16   0  -0.310  -2.3797  -2.7139   0.9281
 655  C4'   C  CR16   0  -0.375  -3.3711  -1.7176   0.8053
 655  C5'   C  CR6    0   0.218  -3.0300  -0.4244   0.5022
 655  O5'   O  O2     0  -0.480  -3.9061   0.6019   0.3825
 655  C6'   C  CR6    0   0.217  -1.6487  -0.0093   0.2885
 655  O6'   O  OC    -1  -0.556  -1.3859   1.1782  -0.0048
 655  C1B   C  CH2    0  -0.457  -5.9667   1.7278   0.6490
 655  C2B   C  CR15   0   0.002  -5.2844   0.3646   0.6215
 655  C3B   C  CH2    0  -0.473  -5.9593  -0.3782  -0.5524
 655  C4B   C  CH2    0  -0.452  -6.7316   0.6895  -1.3563
 655  C5B   C  CH2    0  -0.444  -6.2366   2.0347  -0.8202
 655  HC2   H  HCR6   0   0.272   6.1483  -1.2722  -0.7765
 655  HC3   H  HCR6   0   0.276   4.2177  -2.7916  -0.8270
 655  HC6   H  HCR6   0   0.272   3.6248   2.0277   0.4143
 655  HH11  H  HNH2   0   0.443   5.6190   2.2746   1.5651
 655  HH12  H  HNH2   0   0.435   7.0328   2.9160   0.8316
 655  HH21  H  HNC2   0   0.435   7.9955   1.7157  -0.9855
 655  HH22  H  HNC2   0   0.443   7.0064   0.5888  -1.8228
 655  HN3   H  HNR5   0   0.419   1.3566  -2.7057  -0.3998
 655  HC2'  H  HCR6   0   0.227  -0.3122  -3.1487   0.8646
 655  HC3'  H  HCR6   0   0.229  -2.6644  -3.7260   1.1817
 655  HC4'  H  HCR6   0   0.257  -4.4054  -2.0010   0.9565
 655  H1A   H  HCH2   0   0.230  -6.9154   1.6314   1.1845
 655  H1B   H  HCH2   0   0.239  -5.3744   2.4808   1.1715
 655  H2A   H  HCR5   0   0.232  -5.4044  -0.1667   1.5732
 655  H3A   H  HCH2   0   0.245  -5.2124  -0.8825  -1.1673
 655  H3B   H  HCH2   0   0.236  -6.6271  -1.1569  -0.1812
 655  H4A   H  HCH2   0   0.226  -7.8037   0.5958  -1.1693
 655  H4B   H  HCH2   0   0.232  -6.5871   0.5848  -2.4321
 655  H5A   H  HCH2   0   0.230  -6.9602   2.8385  -0.9622
 655  H5B   H  HCH2   0   0.223  -5.3126   2.3360  -1.3197

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
 655  C1   C2    aromatic  1.406  0.020  1.406
 655  C1   C6    aromatic  1.395  0.020  1.395
 655  C1   C7    single    1.465  0.020  1.465
 655  C2   C3    aromatic  1.383  0.020  1.383
 655  C2   HC2   single    0.930  0.020  1.080
 655  C3   C4    aromatic  1.388  0.020  1.388
 655  C3   HC3   single    0.930  0.020  1.080
 655  C4   C5    aromatic  1.410  0.020  1.410
 655  C4   N3    aromatic  1.357  0.020  1.357
 655  C5   C6    aromatic  1.387  0.020  1.387
 655  C5   N4    aromatic  1.366  0.020  1.366
 655  C6   HC6   single    0.930  0.020  1.080
 655  C7   N1    single    1.313  0.020  1.313
 655  C7   N2    double    1.313  0.020  1.313
 655  N1   HH11  single    0.860  0.020  1.020
 655  N1   HH12  single    0.860  0.020  1.020
 655  N2   HH21  single    0.860  0.020  1.020
 655  N2   HH22  single    0.860  0.020  1.020
 655  N3   C8    aromatic  1.379  0.020  1.379
 655  N3   HN3   single    0.860  0.020  1.020
 655  N4   C8    aromatic  1.317  0.020  1.317
 655  C8   C1'   single    1.447  0.020  1.447
 655  C1'  C2'   aromatic  1.413  0.020  1.413
 655  C1'  C6'   aromatic  1.435  0.020  1.435
 655  C2'  C3'   aromatic  1.369  0.020  1.369
 655  C2'  HC2'  single    0.930  0.020  1.080
 655  C3'  C4'   aromatic  1.411  0.020  1.411
 655  C3'  HC3'  single    0.930  0.020  1.080
 655  C4'  C5'   aromatic  1.371  0.020  1.371
 655  C4'  HC4'  single    0.930  0.020  1.080
 655  C5'  O5'   single    1.355  0.020  1.355
 655  C5'  C6'   aromatic  1.458  0.020  1.458
 655  O5'  C2B   single    1.419  0.020  1.419
 655  C6'  O6'   single    1.251  0.020  1.251
 655  C1B  C2B   single    1.525  0.020  1.525
 655  C1B  C5B   single    1.525  0.020  1.525
 655  C1B  H1A   single    0.970  0.020  1.090
 655  C1B  H1B   single    0.970  0.020  1.090
 655  C2B  C3B   single    1.545  0.020  1.545
 655  C2B  H2A   single    0.970  0.020  1.090
 655  C3B  C4B   single    1.544  0.020  1.544
 655  C3B  H3A   single    0.970  0.020  1.090
 655  C3B  H3B   single    0.970  0.020  1.090
 655  C4B  C5B   single    1.530  0.020  1.530
 655  C4B  H4A   single    0.970  0.020  1.090
 655  C4B  H4B   single    0.970  0.020  1.090
 655  C5B  H5A   single    0.970  0.020  1.090
 655  C5B  H5B   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
 655  C7    C1   C6    119.35  3.000
 655  C7    C1   C2    119.24  3.000
 655  C6    C1   C2    121.41  3.000
 655  HC2   C2   C3    118.74  3.000
 655  HC2   C2   C1    120.10  3.000
 655  C3    C2   C1    121.12  3.000
 655  HC3   C3   C4    122.11  3.000
 655  HC3   C3   C2    120.84  3.000
 655  C4    C3   C2    117.06  3.000
 655  N3    C4   C5    104.31  3.000
 655  N3    C4   C3    132.98  3.000
 655  C5    C4   C3    122.70  3.000
 655  N4    C5   C6    129.92  3.000
 655  N4    C5   C4    110.39  3.000
 655  C6    C5   C4    119.69  3.000
 655  HC6   C6   C5    120.21  3.000
 655  HC6   C6   C1    121.75  3.000
 655  C5    C6   C1    118.01  3.000
 655  N2    C7   N1    120.84  3.000
 655  N2    C7   C1    119.70  3.000
 655  N1    C7   C1    119.46  3.000
 655  HH12  N1   HH11  116.87  3.000
 655  HH12  N1   C7    122.16  3.000
 655  HH11  N1   C7    120.70  3.000
 655  HH22  N2   HH21  116.91  3.000
 655  HH22  N2   C7    120.68  3.000
 655  HH21  N2   C7    122.18  3.000
 655  HN3   N3   C8    125.78  3.000
 655  HN3   N3   C4    125.63  3.000
 655  C8    N3   C4    108.37  3.000
 655  C8    N4   C5    105.87  3.000
 655  C1'   C8   N4    128.06  3.000
 655  C1'   C8   N3    120.87  3.000
 655  N4    C8   N3    111.05  3.000
 655  C6'   C1'  C2'   121.31  3.000
 655  C6'   C1'  C8    119.87  3.000
 655  C2'   C1'  C8    118.82  3.000
 655  HC2'  C2'  C3'   118.55  3.000
 655  HC2'  C2'  C1'   119.93  3.000
 655  C3'   C2'  C1'   121.48  3.000
 655  HC3'  C3'  C4'   119.75  3.000
 655  HC3'  C3'  C2'   120.91  3.000
 655  C4'   C3'  C2'   119.34  3.000
 655  HC4'  C4'  C5'   121.01  3.000
 655  HC4'  C4'  C3'   118.31  3.000
 655  C5'   C4'  C3'   120.68  3.000
 655  C6'   C5'  O5'   112.59  3.000
 655  C6'   C5'  C4'   122.45  3.000
 655  O5'   C5'  C4'   124.96  3.000
 655  C2B   O5'  C5'   119.12  3.000
 655  O6'   C6'  C5'   120.23  3.000
 655  O6'   C6'  C1'   125.02  3.000
 655  C5'   C6'  C1'   114.74  3.000
 655  H1B   C1B  H1A   107.29  3.000
 655  H1B   C1B  C5B   114.74  3.000
 655  H1A   C1B  C5B   109.63  3.000
 655  H1B   C1B  C2B   112.50  3.000
 655  H1A   C1B  C2B   108.55  3.000
 655  C5B   C1B  C2B   103.99  3.000
 655  H2A   C2B  C3B   112.26  3.000
 655  H2A   C2B  C1B   111.63  3.000
 655  C3B   C2B  C1B   104.37  3.000
 655  H2A   C2B  O5'   109.49  3.000
 655  C3B   C2B  O5'   112.14  3.000
 655  C1B   C2B  O5'   106.75  3.000
 655  H3B   C3B  H3A   106.32  3.000
 655  H3B   C3B  C4B   111.39  3.000
 655  H3A   C3B  C4B   111.64  3.000
 655  H3B   C3B  C2B   110.62  3.000
 655  H3A   C3B  C2B   110.58  3.000
 655  C4B   C3B  C2B   106.37  3.000
 655  H4B   C4B  H4A   106.90  3.000
 655  H4B   C4B  C5B   112.78  3.000
 655  H4A   C4B  C5B   109.45  3.000
 655  H4B   C4B  C3B   112.40  3.000
 655  H4A   C4B  C3B   110.03  3.000
 655  C5B   C4B  C3B   105.29  3.000
 655  H5B   C5B  H5A   107.35  3.000
 655  H5B   C5B  C4B   110.84  3.000
 655  H5A   C5B  C4B   112.80  3.000
 655  H5B   C5B  C1B   110.26  3.000
 655  H5A   C5B  C1B   113.02  3.000
 655  C4B   C5B  C1B   102.58  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
 655  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 655  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 655  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 655  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 655  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 655  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 655  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 655  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 655  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 655  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 655  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 655  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 655  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 655  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 655  CONST_15  N3    C8   N4   C5      0.00   0.0  0
 655  CONST_16  C1'   C8   N4   C5    180.00   0.0  0
 655  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 655  CONST_18  C8    N4   C5   C6    180.00   0.0  0
 655  CONST_19  N4    C5   C4   N3      0.00   0.0  0
 655  CONST_24  C3'   C2'  C1'  C8    180.00   0.0  0
 655  CONST_25  C5'   C6'  C1'  C8    180.00   0.0  0
 655  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 655  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 655  CONST_28  C5'   C6'  C1'  C2'     0.00   0.0  0
 655  CONST_29  C5'   C4'  C3'  C2'     0.00   0.0  0
 655  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 655  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 655  CONST_32  C7    C1   C2   C3    180.00   0.0  0
 655  CONST_33  C7    C1   C6   C5    180.00   0.0  0
 655  CONST_34  O6'   C6'  C1'  C8      0.00   0.0  0
 655  CONST_35  O5'   C5'  C6'  C1'   180.00   0.0  0
 655  CONST_36  O6'   C6'  C1'  C2'   180.00   0.0  0
 655  CONST_37  O5'   C5'  C4'  C3'   180.00   0.0  0
 655  CONST_38  O6'   C6'  C5'  C4'   180.00   0.0  0
 655  CONST_39  HC3   C3   C2   C1    180.00   0.0  0
 655  CONST_40  HC6   C6   C1   C2    180.00   0.0  0
 655  CONST_41  HN3   N3   C4   C3      0.00   0.0  0
 655  CONST_42  HC2   C2   C3   C4    180.00   0.0  0
 655  CONST_43  HC2'  C2'  C1'  C8      0.00   0.0  0
 655  CONST_44  HC3'  C3'  C2'  C1'   180.00   0.0  0
 655  CONST_45  HC4'  C4'  C3'  C2'   180.00   0.0  0
 655  CONST_46  HH11  N1   C7   C1      0.00   0.0  0
 655  CONST_47  HH12  N1   C7   C1    180.00   0.0  0
 655  CONST_48  HH21  N2   C7   C1    180.00   0.0  0
 655  CONST_49  HH22  N2   C7   C1      0.00   0.0  0
 655  Var_01    C3B   C4B  C5B  C1B   -33.29  30.0  1
 655  Var_02    C4B   C5B  C1B  C2B    42.33  30.0  1
 655  Var_03    C5B   C4B  C3B  C2B    12.17  30.0  1
 655  Var_04    N1    C7   C1   C2   -143.37  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 655  chir_01  C2B  O5'  C1B  C3B  negativ

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

