# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 02:06:57 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 3-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-5-(2-ammonioethyl)biphenyl-2-olate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(nc2c1)c3cc(CC[NH3+])cc(c3[O-])c4ccccc4
#
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
 653  653  3-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-5-(2-ammonioethyl)biphenyl-2-olate  ligand  50  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_653
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
 653  C1    C  CR6    0  -0.001   5.3959   0.3404   0.0294
 653  C2    C  CR16   0  -0.298   5.0618   1.6995   0.1731
 653  C3    C  CR16   0  -0.305   3.7437   2.1129   0.1998
 653  C4    C  CR56   0   0.358   2.7691   1.1324   0.0690
 653  C5    C  CR56   0   0.172   3.0842  -0.2377  -0.0792
 653  C6    C  CR16   0  -0.378   4.4123  -0.6400  -0.0945
 653  C7    C  C      0   0.581   6.8075  -0.0529   0.0127
 653  N1    N  NH2    0  -0.769   7.1660  -1.2004   0.5418
 653  N2    N  NC2    1  -0.770   7.6994   0.7439  -0.5297
 653  N3    N  NR15   0  -0.729   1.4143   1.1734   0.0437
 653  N4    N  N      0  -0.505   1.9414  -0.9763  -0.1934
 653  C8    C  CR5    0   0.487   0.9566  -0.1020  -0.1144
 653  C1'   C  CR6    0  -0.213  -0.4590  -0.3958  -0.1771
 653  C2'   C  CR16   0  -0.359  -0.8576  -1.7246  -0.3483
 653  C3'   C  CR6    0   0.103  -2.1869  -2.0824  -0.4292
 653  CV'   C  CH2    0  -0.542  -2.6139  -3.5169  -0.5734
 653  CW'   C  CH2    0  -0.300  -3.0467  -4.0833   0.7696
 653  NX'   N  NT3    1  -0.779  -3.4855  -5.4995   0.6369
 653  C4'   C  CR16   0  -0.332  -3.1396  -1.0599  -0.3211
 653  C5'   C  CR6    0  -0.108  -2.8032   0.2668  -0.1395
 653  C6'   C  CR6    0   0.309  -1.4193   0.6706  -0.0677
 653  O6'   O  OC    -1  -0.583  -1.0878   1.8850   0.0672
 653  C1B   C  CR6    0   0.106  -3.8757   1.2781  -0.0461
 653  C2B   C  CR16   0  -0.295  -3.8785   2.2628   0.9473
 653  C3B   C  CR16   0  -0.245  -4.9253   3.1667   1.0520
 653  C4B   C  CR16   0  -0.276  -5.9915   3.1187   0.1613
 653  C5B   C  CR16   0  -0.243  -5.9998   2.1522  -0.8344
 653  C6B   C  CR16   0  -0.320  -4.9522   1.2463  -0.9360
 653  HC2   H  HCR6   0   0.272   5.8408   2.4391   0.3003
 653  HC3   H  HCR6   0   0.275   3.4916   3.1571   0.3258
 653  HC6   H  HCR6   0   0.271   4.6629  -1.6847  -0.2314
 653  HH11  H  HNH2   0   0.435   8.1158  -1.5376   0.5012
 653  HH12  H  HNH2   0   0.444   6.5133  -1.7423   1.0835
 653  HH21  H  HNC2   0   0.443   7.4160   1.5513  -1.0599
 653  HH22  H  HNC2   0   0.435   8.6866   0.5383  -0.5061
 653  HN3   H  HNR5   0   0.420   0.7473   1.9424   0.1168
 653  HC2'  H  HCR6   0   0.236  -0.0908  -2.4887  -0.4168
 653  H31A  H  HCH2   0   0.262  -3.4420  -3.6015  -1.2830
 653  H31B  H  HCH2   0   0.264  -1.7922  -4.1173  -0.9716
 653  H32A  H  HCH2   0   0.296  -2.2303  -4.0715   1.4879
 653  H32B  H  HCH2   0   0.294  -3.8871  -3.5316   1.1851
 653  H33A  H  HNT3   0   0.469  -4.2805  -5.5945   0.0056
 653  H33B  H  HNT3   0   0.469  -2.7400  -6.0941   0.2760
 653  H33C  H  HNT3   0   0.478  -3.7699  -5.8927   1.5331
 653  HC4'  H  HCR6   0   0.239  -4.1919  -1.3261  -0.3684
 653  H2B   H  HCR6   0   0.239  -3.0654   2.3111   1.6574
 653  H3B   H  HCR6   0   0.249  -4.9100   3.9121   1.8371
 653  H4B   H  HCR6   0   0.250  -6.8059   3.8267   0.2445
 653  H5B   H  HCR6   0   0.250  -6.8201   2.1043  -1.5393
 653  H6B   H  HCR6   0   0.244  -4.9668   0.5085  -1.7293

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
 653  C1   C2    aromatic  1.407  0.020  1.407
 653  C1   C6    aromatic  1.394  0.020  1.394
 653  C1   C7    single    1.465  0.020  1.465
 653  C2   C3    aromatic  1.382  0.020  1.382
 653  C2   HC2   single    0.930  0.020  1.080
 653  C3   C4    aromatic  1.389  0.020  1.389
 653  C3   HC3   single    0.930  0.020  1.080
 653  C4   C5    aromatic  1.414  0.020  1.414
 653  C4   N3    aromatic  1.356  0.020  1.356
 653  C5   C6    aromatic  1.388  0.020  1.388
 653  C5   N4    aromatic  1.366  0.020  1.366
 653  C6   HC6   single    0.930  0.020  1.080
 653  C7   N1    single    1.313  0.020  1.313
 653  C7   N2    double    1.313  0.020  1.313
 653  N1   HH11  single    0.860  0.020  1.020
 653  N1   HH12  single    0.860  0.020  1.020
 653  N2   HH21  single    0.860  0.020  1.020
 653  N2   HH22  single    0.860  0.020  1.020
 653  N3   C8    aromatic  1.364  0.020  1.364
 653  N3   HN3   single    0.860  0.020  1.020
 653  N4   C8    aromatic  1.319  0.020  1.319
 653  C8   C1'   single    1.447  0.020  1.447
 653  C1'  C2'   aromatic  1.398  0.020  1.398
 653  C1'  C6'   aromatic  1.439  0.020  1.439
 653  C2'  C3'   aromatic  1.379  0.020  1.379
 653  C2'  HC2'  single    0.930  0.020  1.080
 653  C3'  CV'   single    1.504  0.020  1.504
 653  C3'  C4'   aromatic  1.402  0.020  1.402
 653  CV'  CW'   single    1.520  0.020  1.520
 653  CV'  H31A  single    0.970  0.020  1.090
 653  CV'  H31B  single    0.970  0.020  1.090
 653  CW'  NX'   single    1.489  0.020  1.489
 653  CW'  H32A  single    0.970  0.020  1.090
 653  CW'  H32B  single    0.970  0.020  1.090
 653  NX'  H33A  single    0.890  0.020  1.040
 653  NX'  H33B  single    0.890  0.020  1.040
 653  NX'  H33C  single    0.890  0.020  1.040
 653  C4'  C5'   aromatic  1.381  0.020  1.381
 653  C4'  HC4'  single    0.930  0.020  1.080
 653  C5'  C6'   aromatic  1.443  0.020  1.443
 653  C5'  C1B   single    1.477  0.020  1.477
 653  C6'  O6'   single    1.266  0.020  1.266
 653  C1B  C2B   aromatic  1.399  0.020  1.399
 653  C1B  C6B   aromatic  1.397  0.020  1.397
 653  C2B  C3B   aromatic  1.387  0.020  1.387
 653  C2B  H2B   single    0.930  0.020  1.080
 653  C3B  C4B   aromatic  1.390  0.020  1.390
 653  C3B  H3B   single    0.930  0.020  1.080
 653  C4B  C5B   aromatic  1.388  0.020  1.388
 653  C4B  H4B   single    0.930  0.020  1.080
 653  C5B  C6B   aromatic  1.389  0.020  1.389
 653  C5B  H5B   single    0.930  0.020  1.080
 653  C6B  H6B   single    0.930  0.020  1.080

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
 653  C7    C1   C6    119.33  3.000
 653  C7    C1   C2    119.29  3.000
 653  C6    C1   C2    121.39  3.000
 653  HC2   C2   C3    118.70  3.000
 653  HC2   C2   C1    120.10  3.000
 653  C3    C2   C1    121.17  3.000
 653  HC3   C3   C4    121.95  3.000
 653  HC3   C3   C2    120.89  3.000
 653  C4    C3   C2    117.16  3.000
 653  N3    C4   C5    104.49  3.000
 653  N3    C4   C3    132.98  3.000
 653  C5    C4   C3    122.53  3.000
 653  N4    C5   C6    130.03  3.000
 653  N4    C5   C4    110.27  3.000
 653  C6    C5   C4    119.70  3.000
 653  HC6   C6   C5    120.16  3.000
 653  HC6   C6   C1    121.75  3.000
 653  C5    C6   C1    118.05  3.000
 653  N2    C7   N1    120.74  3.000
 653  N2    C7   C1    119.74  3.000
 653  N1    C7   C1    119.53  3.000
 653  HH12  N1   HH11  116.88  3.000
 653  HH12  N1   C7    120.68  3.000
 653  HH11  N1   C7    122.20  3.000
 653  HH22  N2   HH21  116.83  3.000
 653  HH22  N2   C7    122.09  3.000
 653  HH21  N2   C7    120.86  3.000
 653  HN3   N3   C8    119.57  3.000
 653  HN3   N3   C4    132.43  3.000
 653  C8    N3   C4    108.01  3.000
 653  C8    N4   C5    105.15  3.000
 653  C1'   C8   N4    126.37  3.000
 653  C1'   C8   N3    121.53  3.000
 653  N4    C8   N3    112.09  3.000
 653  C6'   C1'  C2'   121.56  3.000
 653  C6'   C1'  C8    119.93  3.000
 653  C2'   C1'  C8    118.51  3.000
 653  HC2'  C2'  C3'   119.67  3.000
 653  HC2'  C2'  C1'   118.41  3.000
 653  C3'   C2'  C1'   121.92  3.000
 653  C4'   C3'  CV'   120.68  3.000
 653  C4'   C3'  C2'   117.48  3.000
 653  CV'   C3'  C2'   121.80  3.000
 653  H31B  CV'  H31A  106.89  3.000
 653  H31B  CV'  CW'   109.34  3.000
 653  H31A  CV'  CW'   109.20  3.000
 653  H31B  CV'  C3'   110.21  3.000
 653  H31A  CV'  C3'   110.55  3.000
 653  CW'   CV'  C3'   110.58  3.000
 653  H32B  CW'  H32A  108.79  3.000
 653  H32B  CW'  NX'   106.79  3.000
 653  H32A  CW'  NX'   106.89  3.000
 653  H32B  CW'  CV'   111.62  3.000
 653  H32A  CW'  CV'   111.45  3.000
 653  NX'   CW'  CV'   111.07  3.000
 653  H33C  NX'  H33B  106.87  3.000
 653  H33C  NX'  H33A  106.91  3.000
 653  H33B  NX'  H33A  107.26  3.000
 653  H33C  NX'  CW'   111.77  3.000
 653  H33B  NX'  CW'   111.77  3.000
 653  H33A  NX'  CW'   111.94  3.000
 653  HC4'  C4'  C5'   118.49  3.000
 653  HC4'  C4'  C3'   118.44  3.000
 653  C5'   C4'  C3'   123.06  3.000
 653  C1B   C5'  C6'   120.10  3.000
 653  C1B   C5'  C4'   119.30  3.000
 653  C6'   C5'  C4'   120.59  3.000
 653  O6'   C6'  C5'   121.65  3.000
 653  O6'   C6'  C1'   122.96  3.000
 653  C5'   C6'  C1'   115.38  3.000
 653  C6B   C1B  C2B   117.83  3.000
 653  C6B   C1B  C5'   120.24  3.000
 653  C2B   C1B  C5'   121.89  3.000
 653  H2B   C2B  C3B   119.28  3.000
 653  H2B   C2B  C1B   119.78  3.000
 653  C3B   C2B  C1B   120.93  3.000
 653  H3B   C3B  C4B   119.95  3.000
 653  H3B   C3B  C2B   119.52  3.000
 653  C4B   C3B  C2B   120.53  3.000
 653  H4B   C4B  C5B   120.41  3.000
 653  H4B   C4B  C3B   120.35  3.000
 653  C5B   C4B  C3B   119.24  3.000
 653  H5B   C5B  C6B   119.67  3.000
 653  H5B   C5B  C4B   120.17  3.000
 653  C6B   C5B  C4B   120.15  3.000
 653  H6B   C6B  C5B   119.19  3.000
 653  H6B   C6B  C1B   119.49  3.000
 653  C5B   C6B  C1B   121.32  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
 653  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 653  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 653  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 653  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 653  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 653  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 653  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 653  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 653  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 653  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 653  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 653  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 653  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 653  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 653  CONST_15  N3    C8   N4   C5     0.00   0.0  0
 653  CONST_16  C1'   C8   N4   C5   180.00   0.0  0
 653  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 653  CONST_18  C8    N4   C5   C6   180.00   0.0  0
 653  CONST_19  N4    C5   C4   N3     0.00   0.0  0
 653  CONST_20  C2'   C1'  C8   N3   180.00   0.0  0
 653  CONST_21  C6'   C1'  C8   N3     0.00   0.0  0
 653  CONST_22  C2'   C1'  C8   N4     0.00   0.0  0
 653  CONST_23  C6'   C1'  C8   N4   180.00   0.0  0
 653  CONST_24  C3'   C2'  C1'  C8   180.00   0.0  0
 653  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 653  CONST_26  C4'   C3'  C2'  C1'    0.00   0.0  0
 653  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 653  CONST_28  C1B   C5'  C6'  C1'  180.00   0.0  0
 653  CONST_29  C5'   C6'  C1'  C2'    0.00   0.0  0
 653  CONST_30  C5'   C4'  C3'  C2'    0.00   0.0  0
 653  CONST_31  C6'   C1'  C2'  C3'    0.00   0.0  0
 653  CONST_32  C6'   C5'  C4'  C3'    0.00   0.0  0
 653  CONST_33  C1B   C5'  C4'  C3'  180.00   0.0  0
 653  CONST_36  C3B   C2B  C1B  C5'  180.00   0.0  0
 653  CONST_37  C5B   C6B  C1B  C5'  180.00   0.0  0
 653  CONST_40  C4B   C3B  C2B  C1B    0.00   0.0  0
 653  CONST_41  C4B   C5B  C6B  C1B    0.00   0.0  0
 653  CONST_42  C5B   C6B  C1B  C2B    0.00   0.0  0
 653  CONST_43  C5B   C4B  C3B  C2B    0.00   0.0  0
 653  CONST_44  C6B   C1B  C2B  C3B    0.00   0.0  0
 653  CONST_45  C6B   C5B  C4B  C3B    0.00   0.0  0
 653  CONST_46  C7    C1   C2   C3   180.00   0.0  0
 653  CONST_47  C7    C1   C6   C5   180.00   0.0  0
 653  CONST_48  O6'   C6'  C1'  C8     0.00   0.0  0
 653  CONST_49  CV'   C3'  C2'  C1'  180.00   0.0  0
 653  CONST_50  O6'   C6'  C1'  C2'  180.00   0.0  0
 653  CONST_51  C5'   C4'  C3'  CV'  180.00   0.0  0
 653  CONST_52  O6'   C6'  C5'  C4'  180.00   0.0  0
 653  CONST_53  C1B   C5'  C6'  O6'    0.00   0.0  0
 653  CONST_54  HC3   C3   C2   C1   180.00   0.0  0
 653  CONST_55  HC6   C6   C1   C2   180.00   0.0  0
 653  CONST_56  HN3   N3   C4   C3     0.00   0.0  0
 653  CONST_57  HC2   C2   C3   C4   180.00   0.0  0
 653  CONST_58  HC2'  C2'  C1'  C8     0.00   0.0  0
 653  CONST_59  HC4'  C4'  C3'  C2'  180.00   0.0  0
 653  CONST_60  H2B   C2B  C1B  C5'    0.00   0.0  0
 653  CONST_61  H6B   C6B  C1B  C5'    0.00   0.0  0
 653  CONST_62  H3B   C3B  C2B  C1B  180.00   0.0  0
 653  CONST_63  H5B   C5B  C6B  C1B  180.00   0.0  0
 653  CONST_64  H4B   C4B  C3B  C2B  180.00   0.0  0
 653  CONST_65  HH11  N1   C7   C1   180.00   0.0  0
 653  CONST_66  HH12  N1   C7   C1     0.00   0.0  0
 653  CONST_67  HH21  N2   C7   C1     0.00   0.0  0
 653  CONST_68  HH22  N2   C7   C1   180.00   0.0  0
 653  Var_01    N1    C7   C1   C2   145.64  30.0  2
 653  Var_02    CW'   CV'  C3'  C2'   99.70  30.0  2
 653  Var_03    NX'   CW'  CV'  C3'  179.41  30.0  3
 653  Var_04    H33A  NX'  CW'  CV'  -60.63  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
 653  plan-1  C8    0.020
 653  plan-1  C1'   0.020
 653  plan-1  C2'   0.020
 653  plan-1  C3'   0.020
 653  plan-1  CV'   0.020
 653  plan-1  C4'   0.020
 653  plan-1  C5'   0.020
 653  plan-1  C6'   0.020
 653  plan-1  O6'   0.020
 653  plan-1  C1B   0.020
 653  plan-1  HC2'  0.020
 653  plan-1  HC4'  0.020
 653  plan-2  C5'   0.020
 653  plan-2  C1B   0.020
 653  plan-2  C2B   0.020
 653  plan-2  C3B   0.020
 653  plan-2  C4B   0.020
 653  plan-2  C5B   0.020
 653  plan-2  C6B   0.020
 653  plan-2  H2B   0.020
 653  plan-2  H3B   0.020
 653  plan-2  H4B   0.020
 653  plan-2  H5B   0.020
 653  plan-2  H6B   0.020
 653  plan-3  C1    0.020
 653  plan-3  C2    0.020
 653  plan-3  C3    0.020
 653  plan-3  C4    0.020
 653  plan-3  C5    0.020
 653  plan-3  C6    0.020
 653  plan-3  C7    0.020
 653  plan-3  N3    0.020
 653  plan-3  N4    0.020
 653  plan-3  C8    0.020
 653  plan-3  C1'   0.020
 653  plan-3  HC2   0.020
 653  plan-3  HC3   0.020
 653  plan-3  HC6   0.020
 653  plan-3  HN3   0.020
 653  plan-4  C1    0.020
 653  plan-4  C7    0.020
 653  plan-4  N1    0.020
 653  plan-4  N2    0.020
 653  plan-4  HH11  0.020
 653  plan-4  HH12  0.020
 653  plan-4  HH21  0.020
 653  plan-4  HH22  0.020

