# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 23:44:24 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}phenolate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(nc2c1)c3ccccc3[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
 CR4  CR4  2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}phenolate  ligand  31  19  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CR4
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
 CR4  C1    C  CR6    0  -0.001   3.3131   0.0393   0.0174
 CR4  C2    C  CR16   0  -0.298   3.0950  -1.3348   0.2278
 CR4  C3    C  CR16   0  -0.305   1.8162  -1.8469   0.3373
 CR4  C4    C  CR56   0   0.360   0.7616  -0.9512   0.2201
 CR4  C5    C  CR56   0   0.170   0.9599   0.4327   0.0052
 CR4  C6    C  CR16   0  -0.379   2.2498   0.9348  -0.0924
 CR4  C7    C  C      0   0.581   4.6864   0.5390  -0.0869
 CR4  N1    N  NH2    0  -0.769   4.9803   1.7306   0.3811
 CR4  N2    N  NC2    1  -0.771   5.6101  -0.2074  -0.6480
 CR4  N3    N  NR15   0  -0.728  -0.5854  -1.0978   0.2619
 CR4  N4    N  N      0  -0.504  -0.2414   1.0759  -0.0815
 CR4  C8    C  CR5    0   0.490  -1.1490   0.1313   0.0777
 CR4  C1'   C  CR6    0  -0.248  -2.5844   0.2987   0.0657
 CR4  C2'   C  CR16   0  -0.281  -3.1173   1.5774  -0.1431
 CR4  C3'   C  CR16   0  -0.316  -4.4763   1.8036  -0.1680
 CR4  C4'   C  CR16   0  -0.234  -5.3361   0.7122   0.0225
 CR4  C5'   C  CR16   0  -0.410  -4.8452  -0.5552   0.2286
 CR4  C6'   C  CR6    0   0.337  -3.4433  -0.8412   0.2623
 CR4  O6'   O  OC    -1  -0.612  -3.0103  -2.0207   0.4528
 CR4  HC2   H  HCR6   0   0.271   3.9352  -2.0068   0.3413
 CR4  HC3   H  HCR6   0   0.274   1.6535  -2.9019   0.5113
 CR4  HC6   H  HCR6   0   0.271   2.4105   1.9888  -0.2811
 CR4  HH11  H  HNH2   0   0.444   4.3152   2.2440   0.9356
 CR4  HH12  H  HNH2   0   0.435   5.8973   2.1374   0.2759
 CR4  HH21  H  HNC2   0   0.435   6.5795   0.0700  -0.6759
 CR4  HH22  H  HNC2   0   0.443   5.3660  -1.0577  -1.1280
 CR4  HN3   H  HNR5   0   0.419  -1.1927  -1.9090   0.4028
 CR4  HC2'  H  HCR6   0   0.237  -2.4311   2.4036  -0.2885
 CR4  HC3'  H  HCR6   0   0.232  -4.8693   2.7980  -0.3318
 CR4  HC4'  H  HCR6   0   0.239  -6.4092   0.8670   0.0073
 CR4  HC5'  H  HCR6   0   0.222  -5.5308  -1.3834   0.3715

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
 CR4  C1   C2    aromatic  1.407  0.020  1.407
 CR4  C1   C6    aromatic  1.394  0.020  1.394
 CR4  C1   C7    single    1.465  0.020  1.465
 CR4  C2   C3    aromatic  1.382  0.020  1.382
 CR4  C2   HC2   single    0.930  0.020  1.080
 CR4  C3   C4    aromatic  1.389  0.020  1.389
 CR4  C3   HC3   single    0.930  0.020  1.080
 CR4  C4   C5    aromatic  1.414  0.020  1.414
 CR4  C4   N3    aromatic  1.356  0.020  1.356
 CR4  C5   C6    aromatic  1.388  0.020  1.388
 CR4  C5   N4    aromatic  1.365  0.020  1.365
 CR4  C6   HC6   single    0.930  0.020  1.080
 CR4  C7   N1    single    1.314  0.020  1.314
 CR4  C7   N2    double    1.313  0.020  1.313
 CR4  N1   HH11  single    0.860  0.020  1.020
 CR4  N1   HH12  single    0.860  0.020  1.020
 CR4  N2   HH21  single    0.860  0.020  1.020
 CR4  N2   HH22  single    0.860  0.020  1.020
 CR4  N3   C8    aromatic  1.365  0.020  1.365
 CR4  N3   HN3   single    0.860  0.020  1.020
 CR4  N4   C8    aromatic  1.320  0.020  1.320
 CR4  C8   C1'   single    1.445  0.020  1.445
 CR4  C1'  C2'   aromatic  1.401  0.020  1.401
 CR4  C1'  C6'   aromatic  1.441  0.020  1.441
 CR4  C2'  C3'   aromatic  1.378  0.020  1.378
 CR4  C2'  HC2'  single    0.930  0.020  1.080
 CR4  C3'  C4'   aromatic  1.402  0.020  1.402
 CR4  C3'  HC3'  single    0.930  0.020  1.080
 CR4  C4'  C5'   aromatic  1.375  0.020  1.375
 CR4  C4'  HC4'  single    0.930  0.020  1.080
 CR4  C5'  C6'   aromatic  1.431  0.020  1.431
 CR4  C5'  HC5'  single    0.930  0.020  1.080
 CR4  C6'  O6'   single    1.271  0.020  1.271

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
 CR4  C7    C1   C6    119.35  3.000
 CR4  C7    C1   C2    119.28  3.000
 CR4  C6    C1   C2    121.38  3.000
 CR4  HC2   C2   C3    118.70  3.000
 CR4  HC2   C2   C1    120.12  3.000
 CR4  C3    C2   C1    121.15  3.000
 CR4  HC3   C3   C4    121.91  3.000
 CR4  HC3   C3   C2    120.89  3.000
 CR4  C4    C3   C2    117.20  3.000
 CR4  N3    C4   C5    104.47  3.000
 CR4  N3    C4   C3    133.02  3.000
 CR4  C5    C4   C3    122.51  3.000
 CR4  N4    C5   C6    130.02  3.000
 CR4  N4    C5   C4    110.31  3.000
 CR4  C6    C5   C4    119.67  3.000
 CR4  HC6   C6   C5    120.16  3.000
 CR4  HC6   C6   C1    121.72  3.000
 CR4  C5    C6   C1    118.10  3.000
 CR4  N2    C7   N1    120.69  3.000
 CR4  N2    C7   C1    119.72  3.000
 CR4  N1    C7   C1    119.59  3.000
 CR4  HH12  N1   HH11  116.90  3.000
 CR4  HH12  N1   C7    122.14  3.000
 CR4  HH11  N1   C7    120.74  3.000
 CR4  HH22  N2   HH21  116.88  3.000
 CR4  HH22  N2   C7    120.88  3.000
 CR4  HH21  N2   C7    122.10  3.000
 CR4  HN3   N3   C8    119.18  3.000
 CR4  HN3   N3   C4    132.83  3.000
 CR4  C8    N3   C4    107.98  3.000
 CR4  C8    N4   C5    105.09  3.000
 CR4  C1'   C8   N4    126.81  3.000
 CR4  C1'   C8   N3    121.04  3.000
 CR4  N4    C8   N3    112.15  3.000
 CR4  C6'   C1'  C2'   121.05  3.000
 CR4  C6'   C1'  C8    119.95  3.000
 CR4  C2'   C1'  C8    119.00  3.000
 CR4  HC2'  C2'  C3'   119.79  3.000
 CR4  HC2'  C2'  C1'   118.36  3.000
 CR4  C3'   C2'  C1'   121.85  3.000
 CR4  HC3'  C3'  C4'   120.88  3.000
 CR4  HC3'  C3'  C2'   120.80  3.000
 CR4  C4'   C3'  C2'   118.32  3.000
 CR4  HC4'  C4'  C5'   119.15  3.000
 CR4  HC4'  C4'  C3'   119.58  3.000
 CR4  C5'   C4'  C3'   121.26  3.000
 CR4  HC5'  C5'  C6'   117.61  3.000
 CR4  HC5'  C5'  C4'   119.87  3.000
 CR4  C6'   C5'  C4'   122.52  3.000
 CR4  O6'   C6'  C5'   121.52  3.000
 CR4  O6'   C6'  C1'   123.49  3.000
 CR4  C5'   C6'  C1'   115.00  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
 CR4  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 CR4  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 CR4  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 CR4  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 CR4  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 CR4  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 CR4  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 CR4  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 CR4  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 CR4  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 CR4  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 CR4  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 CR4  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 CR4  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 CR4  CONST_15  N3    C8   N4   C5      0.00   0.0  0
 CR4  CONST_16  C1'   C8   N4   C5    180.00   0.0  0
 CR4  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 CR4  CONST_18  C8    N4   C5   C6    180.00   0.0  0
 CR4  CONST_19  N4    C5   C4   N3      0.00   0.0  0
 CR4  CONST_20  C2'   C1'  C8   N3    180.00   0.0  0
 CR4  CONST_21  C6'   C1'  C8   N3      0.00   0.0  0
 CR4  CONST_22  C2'   C1'  C8   N4      0.00   0.0  0
 CR4  CONST_23  C6'   C1'  C8   N4    180.00   0.0  0
 CR4  CONST_24  C3'   C2'  C1'  C8    180.00   0.0  0
 CR4  CONST_25  C5'   C6'  C1'  C8    180.00   0.0  0
 CR4  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 CR4  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 CR4  CONST_28  C5'   C6'  C1'  C2'     0.00   0.0  0
 CR4  CONST_29  C5'   C4'  C3'  C2'     0.00   0.0  0
 CR4  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 CR4  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 CR4  CONST_32  C7    C1   C2   C3    180.00   0.0  0
 CR4  CONST_33  C7    C1   C6   C5    180.00   0.0  0
 CR4  CONST_34  O6'   C6'  C1'  C8      0.00   0.0  0
 CR4  CONST_35  O6'   C6'  C1'  C2'   180.00   0.0  0
 CR4  CONST_36  O6'   C6'  C5'  C4'   180.00   0.0  0
 CR4  CONST_37  HC3   C3   C2   C1    180.00   0.0  0
 CR4  CONST_38  HC6   C6   C1   C2    180.00   0.0  0
 CR4  CONST_39  HN3   N3   C4   C3      0.00   0.0  0
 CR4  CONST_40  HC2   C2   C3   C4    180.00   0.0  0
 CR4  CONST_41  HC2'  C2'  C1'  C8      0.00   0.0  0
 CR4  CONST_42  HC3'  C3'  C2'  C1'   180.00   0.0  0
 CR4  CONST_43  HC5'  C5'  C6'  C1'   180.00   0.0  0
 CR4  CONST_44  HC4'  C4'  C3'  C2'   180.00   0.0  0
 CR4  CONST_45  HH11  N1   C7   C1      0.00   0.0  0
 CR4  CONST_46  HH12  N1   C7   C1    180.00   0.0  0
 CR4  CONST_47  HH21  N2   C7   C1    180.00   0.0  0
 CR4  CONST_48  HH22  N2   C7   C1      0.00   0.0  0
 CR4  Var_01    N1    C7   C1   C2   -145.60  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
 CR4  plan-1  C8    0.020
 CR4  plan-1  C1'   0.020
 CR4  plan-1  C2'   0.020
 CR4  plan-1  C3'   0.020
 CR4  plan-1  C4'   0.020
 CR4  plan-1  C5'   0.020
 CR4  plan-1  C6'   0.020
 CR4  plan-1  O6'   0.020
 CR4  plan-1  HC2'  0.020
 CR4  plan-1  HC3'  0.020
 CR4  plan-1  HC4'  0.020
 CR4  plan-1  HC5'  0.020
 CR4  plan-2  C1    0.020
 CR4  plan-2  C2    0.020
 CR4  plan-2  C3    0.020
 CR4  plan-2  C4    0.020
 CR4  plan-2  C5    0.020
 CR4  plan-2  C6    0.020
 CR4  plan-2  C7    0.020
 CR4  plan-2  N3    0.020
 CR4  plan-2  N4    0.020
 CR4  plan-2  C8    0.020
 CR4  plan-2  C1'   0.020
 CR4  plan-2  HC2   0.020
 CR4  plan-2  HC3   0.020
 CR4  plan-2  HC6   0.020
 CR4  plan-2  HN3   0.020
 CR4  plan-3  C1    0.020
 CR4  plan-3  C7    0.020
 CR4  plan-3  N1    0.020
 CR4  plan-3  N2    0.020
 CR4  plan-3  HH11  0.020
 CR4  plan-3  HH12  0.020
 CR4  plan-3  HH21  0.020
 CR4  plan-3  HH22  0.020

