# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 21:05:16 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-6-chloro-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(Cl)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
 972  972  2-{5-[amino(iminio)methyl]-6-chloro-1H-benzimidazol-2-yl}-6-(2-methylpropoxy)phenolate  ligand  44  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_972
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
 972  C1    C   CR6    0   0.035  -4.1882  -0.7181   0.1514
 972  C2    C   CR6    0  -0.091  -4.4204   0.6038  -0.2656
 972  CL2   CL  CL     0  -0.107  -6.0211   1.1236  -0.6821
 972  C3    C   CR16   0  -0.263  -3.3889   1.5137  -0.4143
 972  C4    C   CR56   0   0.359  -2.1124   1.0612  -0.1210
 972  C5    C   CR56   0   0.166  -1.8434  -0.2600   0.2867
 972  C6    C   CR16   0  -0.362  -2.8921  -1.1572   0.4163
 972  C7    C   C      0   0.545  -5.2774  -1.6959   0.3252
 972  N1    N   NH2    0  -0.740  -6.2752  -1.4305   1.1294
 972  N2    N   NC2    1  -0.742  -5.1880  -2.8394  -0.3071
 972  N3    N   NR15   0  -0.731  -0.8962   1.6610  -0.1432
 972  N4    N   N      0  -0.474  -0.5066  -0.4323   0.4977
 972  C8    C   CR5    0   0.485   0.0519   0.7315   0.2337
 972  C1'   C   CR6    0  -0.247   1.4495   1.0876   0.3187
 972  C2'   C   CR16   0  -0.306   1.8017   2.4490   0.4616
 972  C3'   C   CR16   0  -0.308   3.1085   2.8486   0.5287
 972  C4'   C   CR16   0  -0.384   4.1332   1.8812   0.4446
 972  C5'   C   CR6    0   0.226   3.8262   0.5531   0.3036
 972  C6'   C   CR6    0   0.221   2.4539   0.0646   0.2383
 972  O6'   O   OC    -1  -0.550   2.2291  -1.1573   0.1010
 972  O5'   O   O2     0  -0.469   4.7409  -0.4421   0.2111
 972  C10   C   CH2    0  -0.144   6.1068  -0.0981   0.1907
 972  C20   C   CH1    0  -0.276   6.9360  -1.3505  -0.0418
 972  C30   C   CH3    0  -0.652   6.5851  -2.0230  -1.3647
 972  C40   C   CH3    0  -0.661   8.4155  -0.9826   0.0103
 972  HC3   H   HCR6   0   0.297  -3.5800   2.5233  -0.7508
 972  HC6   H   HCR6   0   0.283  -2.7100  -2.1740   0.7404
 972  HH11  H   HNH2   0   0.442  -6.2856  -0.5855   1.6766
 972  HH12  H   HNH2   0   0.439  -7.0537  -2.0619   1.2500
 972  HH21  H   HNC2   0   0.438  -5.8493  -3.5882  -0.1635
 972  HH22  H   HNC2   0   0.448  -4.4605  -2.9926  -0.9870
 972  HN3   H   HNR5   0   0.422  -0.7106   2.5978  -0.4634
 972  HC2'  H   HCR6   0   0.227   1.0284   3.2024   0.5586
 972  HC3'  H   HCR6   0   0.230   3.3628   3.8919   0.6576
 972  HC4'  H   HCR6   0   0.258   5.1631   2.2124   0.5013
 972  H10A  H   HCH2   0   0.213   6.3988   0.3766   1.1375
 972  H10B  H   HCH2   0   0.198   6.3098   0.6278  -0.6098
 972  H20   H   HCH1   0   0.226   6.7324  -2.0524   0.7748
 972  H30A  H   HCH3   0   0.225   7.2110  -2.9010  -1.5311
 972  H30B  H   HCH3   0   0.232   5.5451  -2.3465  -1.3948
 972  H30C  H   HCH3   0   0.212   6.7478  -1.3394  -2.2021
 972  H40A  H   HCH3   0   0.217   8.6710  -0.2620  -0.7703
 972  H40B  H   HCH3   0   0.228   8.6877  -0.5432   0.9715
 972  H40C  H   HCH3   0   0.234   9.0401  -1.8639  -0.1385

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
 972  C1   C2    aromatic  1.405  0.020  1.405
 972  C1   C6    aromatic  1.394  0.020  1.394
 972  C1   C7    single    1.474  0.020  1.474
 972  C2   CL2   single    1.734  0.020  1.734
 972  C2   C3    aromatic  1.384  0.020  1.384
 972  C3   C4    aromatic  1.386  0.020  1.386
 972  C3   HC3   single    0.930  0.020  1.080
 972  C4   C5    aromatic  1.409  0.020  1.409
 972  C4   N3    aromatic  1.356  0.020  1.356
 972  C5   C6    aromatic  1.386  0.020  1.386
 972  C5   N4    aromatic  1.364  0.020  1.364
 972  C6   HC6   single    0.930  0.020  1.080
 972  C7   N1    single    1.309  0.020  1.309
 972  C7   N2    double    1.310  0.020  1.310
 972  N1   HH11  single    0.860  0.020  1.020
 972  N1   HH12  single    0.860  0.020  1.020
 972  N2   HH21  single    0.860  0.020  1.020
 972  N2   HH22  single    0.860  0.020  1.020
 972  N3   C8    aromatic  1.380  0.020  1.380
 972  N3   HN3   single    0.860  0.020  1.020
 972  N4   C8    aromatic  1.318  0.020  1.318
 972  C8   C1'   single    1.445  0.020  1.445
 972  C1'  C2'   aromatic  1.413  0.020  1.413
 972  C1'  C6'   aromatic  1.436  0.020  1.436
 972  C2'  C3'   aromatic  1.368  0.020  1.368
 972  C2'  HC2'  single    0.930  0.020  1.080
 972  C3'  C4'   aromatic  1.412  0.020  1.412
 972  C3'  HC3'  single    0.930  0.020  1.080
 972  C4'  C5'   aromatic  1.370  0.020  1.370
 972  C4'  HC4'  single    0.930  0.020  1.080
 972  C5'  C6'   aromatic  1.458  0.020  1.458
 972  C5'  O5'   single    1.355  0.020  1.355
 972  C6'  O6'   single    1.250  0.020  1.250
 972  O5'  C10   single    1.409  0.020  1.409
 972  C10  C20   single    1.520  0.020  1.520
 972  C10  H10A  single    0.970  0.020  1.090
 972  C10  H10B  single    0.970  0.020  1.090
 972  C20  C30   single    1.525  0.020  1.525
 972  C20  C40   single    1.525  0.020  1.525
 972  C20  H20   single    0.970  0.020  1.090
 972  C30  H30A  single    0.970  0.020  1.090
 972  C30  H30B  single    0.970  0.020  1.090
 972  C30  H30C  single    0.970  0.020  1.090
 972  C40  H40A  single    0.970  0.020  1.090
 972  C40  H40B  single    0.970  0.020  1.090
 972  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
 972  C7    C1   C6    117.11  3.000
 972  C7    C1   C2    122.47  3.000
 972  C6    C1   C2    120.42  3.000
 972  C3    C2   CL2   117.73  3.000
 972  C3    C2   C1    121.82  3.000
 972  CL2   C2   C1    120.39  3.000
 972  HC3   C3   C4    122.26  3.000
 972  HC3   C3   C2    121.04  3.000
 972  C4    C3   C2    116.70  3.000
 972  N3    C4   C5    104.38  3.000
 972  N3    C4   C3    132.70  3.000
 972  C5    C4   C3    122.92  3.000
 972  N4    C5   C6    130.18  3.000
 972  N4    C5   C4    110.51  3.000
 972  C6    C5   C4    119.32  3.000
 972  HC6   C6   C5    120.57  3.000
 972  HC6   C6   C1    120.61  3.000
 972  C5    C6   C1    118.81  3.000
 972  N2    C7   N1    121.72  3.000
 972  N2    C7   C1    118.15  3.000
 972  N1    C7   C1    120.09  3.000
 972  HH12  N1   HH11  116.88  3.000
 972  HH12  N1   C7    122.31  3.000
 972  HH11  N1   C7    120.80  3.000
 972  HH22  N2   HH21  117.15  3.000
 972  HH22  N2   C7    120.52  3.000
 972  HH21  N2   C7    122.30  3.000
 972  HN3   N3   C8    125.91  3.000
 972  HN3   N3   C4    125.58  3.000
 972  C8    N3   C4    108.28  3.000
 972  C8    N4   C5    105.83  3.000
 972  C1'   C8   N4    128.02  3.000
 972  C1'   C8   N3    120.97  3.000
 972  N4    C8   N3    111.00  3.000
 972  C6'   C1'  C2'   121.17  3.000
 972  C6'   C1'  C8    119.85  3.000
 972  C2'   C1'  C8    118.97  3.000
 972  HC2'  C2'  C3'   118.30  3.000
 972  HC2'  C2'  C1'   120.04  3.000
 972  C3'   C2'  C1'   121.62  3.000
 972  HC3'  C3'  C4'   119.83  3.000
 972  HC3'  C3'  C2'   120.81  3.000
 972  C4'   C3'  C2'   119.36  3.000
 972  HC4'  C4'  C5'   120.98  3.000
 972  HC4'  C4'  C3'   118.52  3.000
 972  C5'   C4'  C3'   120.50  3.000
 972  O5'   C5'  C6'   112.72  3.000
 972  O5'   C5'  C4'   124.59  3.000
 972  C6'   C5'  C4'   122.70  3.000
 972  O6'   C6'  C5'   120.11  3.000
 972  O6'   C6'  C1'   125.23  3.000
 972  C5'   C6'  C1'   114.65  3.000
 972  C10   O5'  C5'   118.44  3.000
 972  H10B  C10  H10A  107.05  3.000
 972  H10B  C10  C20   109.38  3.000
 972  H10A  C10  C20   110.05  3.000
 972  H10B  C10  O5'   110.54  3.000
 972  H10A  C10  O5'   110.53  3.000
 972  C20   C10  O5'   109.27  3.000
 972  H20   C20  C40   108.01  3.000
 972  H20   C20  C30   108.74  3.000
 972  C40   C20  C30   111.05  3.000
 972  H20   C20  C10   108.20  3.000
 972  C40   C20  C10   108.98  3.000
 972  C30   C20  C10   111.75  3.000
 972  H30C  C30  H30B  107.86  3.000
 972  H30C  C30  H30A  107.52  3.000
 972  H30B  C30  H30A  107.72  3.000
 972  H30C  C30  C20   110.76  3.000
 972  H30B  C30  C20   112.00  3.000
 972  H30A  C30  C20   110.80  3.000
 972  H40C  C40  H40B  107.62  3.000
 972  H40C  C40  H40A  107.55  3.000
 972  H40B  C40  H40A  107.78  3.000
 972  H40C  C40  C20   110.86  3.000
 972  H40B  C40  C20   111.66  3.000
 972  H40A  C40  C20   111.19  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
 972  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 972  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 972  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 972  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 972  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 972  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 972  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 972  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 972  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 972  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 972  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 972  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 972  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 972  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 972  CONST_15  N3    C8   N4   C5      0.00   0.0  0
 972  CONST_16  C1'   C8   N4   C5    180.00   0.0  0
 972  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 972  CONST_18  C8    N4   C5   C6    180.00   0.0  0
 972  CONST_19  N4    C5   C4   N3      0.00   0.0  0
 972  CONST_24  C3'   C2'  C1'  C8    180.00   0.0  0
 972  CONST_25  C5'   C6'  C1'  C8    180.00   0.0  0
 972  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 972  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 972  CONST_28  C5'   C6'  C1'  C2'     0.00   0.0  0
 972  CONST_29  C5'   C4'  C3'  C2'     0.00   0.0  0
 972  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 972  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 972  CONST_32  C6    C1   C2   CL2   180.00   0.0  0
 972  CONST_33  C4    C3   C2   CL2   180.00   0.0  0
 972  CONST_34  C7    C1   C2   C3    180.00   0.0  0
 972  CONST_35  C7    C1   C6   C5    180.00   0.0  0
 972  CONST_36  O6'   C6'  C1'  C8      0.00   0.0  0
 972  CONST_37  O5'   C5'  C6'  C1'   180.00   0.0  0
 972  CONST_38  O6'   C6'  C1'  C2'   180.00   0.0  0
 972  CONST_39  O5'   C5'  C4'  C3'   180.00   0.0  0
 972  CONST_40  O6'   C6'  C5'  C4'   180.00   0.0  0
 972  CONST_41  HC3   C3   C2   C1    180.00   0.0  0
 972  CONST_42  HC6   C6   C1   C2    180.00   0.0  0
 972  CONST_43  HN3   N3   C4   C3      0.00   0.0  0
 972  CONST_44  HC2'  C2'  C1'  C8      0.00   0.0  0
 972  CONST_45  HC3'  C3'  C2'  C1'   180.00   0.0  0
 972  CONST_46  HC4'  C4'  C3'  C2'   180.00   0.0  0
 972  CONST_47  HH11  N1   C7   C1      0.00   0.0  0
 972  CONST_48  HH12  N1   C7   C1    180.00   0.0  0
 972  CONST_49  HH21  N2   C7   C1    180.00   0.0  0
 972  CONST_50  HH22  N2   C7   C1      0.00   0.0  0
 972  Var_01    N1    C7   C1   C2    -56.45  30.0  2
 972  Var_02    C20   C10  O5'  C5'  -174.97  30.0  3
 972  Var_03    C30   C20  C10  O5'    59.84  30.0  3
 972  Var_04    H30A  C30  C20  C10   178.17  30.0  3
 972  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
 972  plan-1  C8    0.020
 972  plan-1  C1'   0.020
 972  plan-1  C2'   0.020
 972  plan-1  C3'   0.020
 972  plan-1  C4'   0.020
 972  plan-1  C5'   0.020
 972  plan-1  C6'   0.020
 972  plan-1  O6'   0.020
 972  plan-1  O5'   0.020
 972  plan-1  HC2'  0.020
 972  plan-1  HC3'  0.020
 972  plan-1  HC4'  0.020
 972  plan-2  C1    0.020
 972  plan-2  C2    0.020
 972  plan-2  CL2   0.020
 972  plan-2  C3    0.020
 972  plan-2  C4    0.020
 972  plan-2  C5    0.020
 972  plan-2  C6    0.020
 972  plan-2  C7    0.020
 972  plan-2  N3    0.020
 972  plan-2  N4    0.020
 972  plan-2  C8    0.020
 972  plan-2  C1'   0.020
 972  plan-2  HC3   0.020
 972  plan-2  HC6   0.020
 972  plan-2  HN3   0.020
 972  plan-3  C1    0.020
 972  plan-3  C7    0.020
 972  plan-3  N1    0.020
 972  plan-3  N2    0.020
 972  plan-3  HH11  0.020
 972  plan-3  HH12  0.020
 972  plan-3  HH21  0.020
 972  plan-3  HH22  0.020

