# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 00:29:39 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: N-[2-(methylamino)-1H-benzimidazol-6-yl]guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1[nH]c2cc(NC(N)=N)ccc2n1
#
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
 6H8  6H8  N-[2-(methylamino)-1H-benzimidazol-6-yl]guanidine  ligand  27  15  .  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_6H8
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
 6H8  C2   C  CR56  0   0.380  -0.7362   0.0837  -0.0117
 6H8  C4   C  CR6   0   0.347   1.5513  -0.5194   0.0799
 6H8  C5   C  C     0   0.561   3.6225   0.8944   0.0379
 6H8  C6   C  CR16  0  -0.376   1.1506  -1.8684   0.1338
 6H8  C1   C  CR5   0   0.652  -2.9347  -0.0894  -0.0583
 6H8  C3   C  CR16  0  -0.412   0.5884   0.4888   0.0069
 6H8  C8   C  CR56  0   0.137  -1.1541  -1.2534   0.0436
 6H8  N4   N  N     0  -0.703   3.0391   2.0342   0.0333
 6H8  N3   N  NH2   0  -0.846   4.9888   0.6909   0.0486
 6H8  N2   N  NH1   0  -0.753   2.9264  -0.2858   0.0994
 6H8  C7   C  CR16  0  -0.340  -0.1822  -2.2447   0.1179
 6H8  N1   N  NR15  0  -0.741  -1.9049   0.8076  -0.0757
 6H8  N5   N  N     0  -0.535  -2.5298  -1.3337   0.0155
 6H8  N    N  NH1   0  -0.674  -4.2244   0.3042  -0.1508
 6H8  C    C  CH3   0  -0.547  -4.6268   1.6683   0.1022
 6H8  H1   H  HCR6  0   0.255   1.9104  -2.6397   0.1872
 6H8  H2   H  HCR6  0   0.292   0.8755   1.5276  -0.0283
 6H8  H3   H  H     0   0.327   3.7212   2.7792  -0.0481
 6H8  H4   H  HNH2  0   0.389   5.5345   1.4966  -0.2122
 6H8  H5   H  HNH2  0   0.387   5.3265  -0.1437  -0.4067
 6H8  H6   H  HNH1  0   0.400   3.4857  -1.1158   0.2108
 6H8  H7   H  HCR6  0   0.246  -0.4523  -3.2923   0.1621
 6H8  H8   H  HNR5  0   0.419  -1.9804   1.8110  -0.1206
 6H8  H10  H  HNH1  0   0.396  -4.8915  -0.4143   0.0776
 6H8  H11  H  HCH3  0   0.234  -4.3730   2.0159   1.1080
 6H8  H12  H  HCH3  0   0.242  -4.1769   2.3497  -0.6210
 6H8  H13  H  HCH3  0   0.265  -5.7041   1.7365  -0.0190

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
 6H8  C   N    single    1.445  0.020  1.445
 6H8  N   C1   single    1.352  0.020  1.352
 6H8  C1  N1   aromatic  1.366  0.020  1.366
 6H8  C1  N5   aromatic  1.311  0.020  1.311
 6H8  N1  C2   aromatic  1.376  0.020  1.376
 6H8  N5  C8   aromatic  1.378  0.020  1.378
 6H8  C2  C8   aromatic  1.402  0.020  1.402
 6H8  C2  C3   aromatic  1.385  0.020  1.385
 6H8  C8  C7   aromatic  1.390  0.020  1.390
 6H8  C3  C4   aromatic  1.396  0.020  1.396
 6H8  C7  C6   aromatic  1.385  0.020  1.385
 6H8  C4  C6   aromatic  1.408  0.020  1.408
 6H8  C4  N2   single    1.395  0.020  1.395
 6H8  N2  C5   single    1.372  0.020  1.372
 6H8  C5  N4   double    1.280  0.020  1.280
 6H8  C5  N3   single    1.381  0.020  1.381
 6H8  C6  H1   single    0.930  0.020  1.080
 6H8  C3  H2   single    0.930  0.020  1.080
 6H8  N4  H3   single    0.890  0.020  1.040
 6H8  N3  H4   single    0.890  0.020  1.040
 6H8  N3  H5   single    0.890  0.020  1.040
 6H8  N2  H6   single    0.860  0.020  1.020
 6H8  C7  H7   single    0.930  0.020  1.080
 6H8  N1  H8   single    0.860  0.020  1.020
 6H8  N   H10  single    0.890  0.020  1.040
 6H8  C   H11  single    0.970  0.020  1.090
 6H8  C   H12  single    0.970  0.020  1.090
 6H8  C   H13  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
 6H8  N1   C2  C8   104.50  3.000
 6H8  C8   C2  C3   124.30  3.000
 6H8  N1   C2  C3   131.20  3.000
 6H8  N2   C4  C3   124.04  3.000
 6H8  N2   C4  C6   116.12  3.000
 6H8  C3   C4  C6   119.84  3.000
 6H8  N2   C5  N3   112.02  3.000
 6H8  N3   C5  N4   125.57  3.000
 6H8  N2   C5  N4   122.34  3.000
 6H8  H1   C6  C7   118.80  3.000
 6H8  H1   C6  C4   118.95  3.000
 6H8  C7   C6  C4   122.25  3.000
 6H8  N    C1  N5   125.11  3.000
 6H8  N5   C1  N1   113.04  3.000
 6H8  N    C1  N1   121.83  3.000
 6H8  H2   C3  C4   120.92  3.000
 6H8  H2   C3  C2   122.41  3.000
 6H8  C4   C3  C2   116.68  3.000
 6H8  N5   C8  C7   131.09  3.000
 6H8  C7   C8  C2   118.28  3.000
 6H8  N5   C8  C2   110.63  3.000
 6H8  H3   N4  C5   110.37  3.000
 6H8  H5   N3  H4   111.31  3.000
 6H8  H5   N3  C5   116.71  3.000
 6H8  H4   N3  C5   114.58  3.000
 6H8  H6   N2  C5   115.61  3.000
 6H8  H6   N2  C4   114.27  3.000
 6H8  C5   N2  C4   130.07  3.000
 6H8  H7   C7  C8   121.17  3.000
 6H8  H7   C7  C6   120.17  3.000
 6H8  C8   C7  C6   118.66  3.000
 6H8  H8   N1  C1   126.75  3.000
 6H8  H8   N1  C2   126.14  3.000
 6H8  C1   N1  C2   107.11  3.000
 6H8  C8   N5  C1   104.72  3.000
 6H8  H10  N   C    116.72  3.000
 6H8  H10  N   C1   114.14  3.000
 6H8  C    N   C1   121.93  3.000
 6H8  H13  C   H12  107.21  3.000
 6H8  H13  C   H11  108.22  3.000
 6H8  H12  C   H11  108.38  3.000
 6H8  H13  C   N    108.43  3.000
 6H8  H12  C   N    111.04  3.000
 6H8  H11  C   N    113.36  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
 6H8  CONST_01  N5   C1  N1  C2    0.00   0.0  0
 6H8  CONST_02  C1   N5  C8  C2    0.00   0.0  0
 6H8  CONST_03  C6   C7  C8  C2    0.00   0.0  0
 6H8  CONST_04  C6   C4  C3  C2    0.00   0.0  0
 6H8  CONST_05  N1   C2  C3  C4  180.00   0.0  0
 6H8  CONST_06  C8   C2  C3  C4    0.00   0.0  0
 6H8  CONST_07  C8   C7  C6  C4    0.00   0.0  0
 6H8  CONST_08  N5   C8  C7  C6  180.00   0.0  0
 6H8  CONST_09  C8   C2  N1  C1    0.00   0.0  0
 6H8  CONST_10  C3   C2  N1  C1  180.00   0.0  0
 6H8  CONST_11  C7   C8  N5  C1  180.00   0.0  0
 6H8  CONST_12  N5   C8  C2  C3  180.00   0.0  0
 6H8  CONST_13  C7   C8  C2  C3    0.00   0.0  0
 6H8  CONST_14  C7   C6  C4  C3    0.00   0.0  0
 6H8  CONST_15  N1   C1  N5  C8    0.00   0.0  0
 6H8  CONST_16  N1   C2  C8  C7  180.00   0.0  0
 6H8  CONST_17  N5   C8  C2  N1    0.00   0.0  0
 6H8  CONST_18  N    C1  N1  C2  180.00   0.0  0
 6H8  CONST_19  N2   C4  C3  C2  180.00   0.0  0
 6H8  CONST_20  N    C1  N5  C8  180.00   0.0  0
 6H8  CONST_21  C7   C6  C4  N2  180.00   0.0  0
 6H8  CONST_22  H7   C7  C8  C2  180.00   0.0  0
 6H8  CONST_23  H2   C3  C4  C6  180.00   0.0  0
 6H8  CONST_24  H8   N1  C2  C3    0.00   0.0  0
 6H8  CONST_25  H1   C6  C4  C3  180.00   0.0  0
 6H8  CONST_26  C3   C4  N2  C5    0.00   0.0  0
 6H8  CONST_27  C6   C4  N2  C5  180.00   0.0  0
 6H8  CONST_30  H6   N2  C4  C6    0.00   0.0  0
 6H8  CONST_31  H10  N   C1  N1  180.00   0.0  0
 6H8  CONST_32  N4   C5  N2  C4    0.00   0.0  0
 6H8  CONST_33  N3   C5  N2  C4  180.00   0.0  0
 6H8  CONST_36  H3   N4  C5  N3    0.00   0.0  0
 6H8  Var_01    H11  C   N   C1  -58.99  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
 6H8  plan-1  C2   0.020
 6H8  plan-1  C4   0.020
 6H8  plan-1  C6   0.020
 6H8  plan-1  C1   0.020
 6H8  plan-1  C3   0.020
 6H8  plan-1  C8   0.020
 6H8  plan-1  N2   0.020
 6H8  plan-1  C7   0.020
 6H8  plan-1  N1   0.020
 6H8  plan-1  N5   0.020
 6H8  plan-1  N    0.020
 6H8  plan-1  H1   0.020
 6H8  plan-1  H2   0.020
 6H8  plan-1  H7   0.020
 6H8  plan-1  H8   0.020
 6H8  plan-2  C4   0.020
 6H8  plan-2  C5   0.020
 6H8  plan-2  N4   0.020
 6H8  plan-2  N3   0.020
 6H8  plan-2  N2   0.020
 6H8  plan-2  H3   0.020
 6H8  plan-2  H4   0.020
 6H8  plan-2  H5   0.020
 6H8  plan-2  H6   0.020
 6H8  plan-3  C1   0.020
 6H8  plan-3  N    0.020
 6H8  plan-3  C    0.020
 6H8  plan-3  H10  0.020

