# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 00:12:49 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: 4-(3-methylbenzimidazol-5-yl)pyridine-2,6-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc2ccc(cc12)c3cc(N)nc(N)c3
#
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
 RHT  RHT  4-(3-methylbenzimidazol-5-yl)pyridine-2,6-diamine  ligand  31  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_RHT
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
 RHT  C1   C  CH3   0  -0.529  43.7474  2.4004  16.2579
 RHT  N1   N  NR5   0  -0.503  44.0056  3.8120  16.4075
 RHT  C2   C  CR15  0   0.101  44.5786  4.4304  17.4690
 RHT  N2   N  N     0  -0.463  44.6963  5.7215  17.3323
 RHT  C3   C  CR56  0   0.122  44.1661  5.9862  16.0935
 RHT  N3   N  NH2   0  -0.838  42.1878  4.0037   9.1434
 RHT  C4   C  CR16  0  -0.307  44.0163  7.1904  15.4071
 RHT  N4   N  N     0  -0.505  41.2278  6.0150   9.6800
 RHT  C5   C  CR16  0  -0.318  43.4339  7.1591  14.1556
 RHT  N5   N  NH2   0  -0.838  40.2195  8.0308  10.0994
 RHT  C6   C  CR6   0   0.059  42.9974  5.9578  13.5580
 RHT  C7   C  CR16  0  -0.366  43.1466  4.7522  14.2342
 RHT  C8   C  CR56  0   0.371  43.7275  4.7942  15.4939
 RHT  C9   C  CR6   0   0.202  42.3861  5.9806  12.2123
 RHT  C10  C  CR16  0  -0.489  42.6321  4.9525  11.3085
 RHT  C11  C  CR6   0   0.458  42.0227  5.0130  10.0502
 RHT  C12  C  CR6   0   0.460  41.0006  7.0018  10.5445
 RHT  C13  C  CR16  0  -0.490  41.5539  7.0271  11.8304
 RHT  H1   H  HCH3  0   0.270  44.0742  1.8823  17.1554
 RHT  H2   H  HCH3  0   0.260  42.6831  2.2191  16.1162
 RHT  H3   H  HCH3  0   0.260  44.2916  1.9990  15.4043
 RHT  H4   H  HCR5  0   0.286  44.8968  3.8644  18.3336
 RHT  H5   H  HNH2  0   0.377  41.9921  4.2368   8.1835
 RHT  H6   H  HNH2  0   0.385  42.9876  3.4041   9.2620
 RHT  H7   H  HCR6  0   0.254  44.3524  8.1239  15.8398
 RHT  H8   H  HCR6  0   0.250  43.3290  8.0851  13.6051
 RHT  H9   H  HNH2  0   0.377  39.6230  7.8270   9.3142
 RHT  H10  H  HNH2  0   0.385  39.7937  8.6223  10.7936
 RHT  H11  H  HCR6  0   0.270  42.8025  3.8212  13.8013
 RHT  H12  H  HCR6  0   0.250  43.2974  4.1344  11.5517
 RHT  H13  H  HCR6  0   0.250  41.3158  7.8353  12.5094

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
 RHT  N3   C11  single    1.367  0.020  1.367
 RHT  N4   C11  aromatic  1.331  0.020  1.331
 RHT  N4   C12  aromatic  1.331  0.020  1.331
 RHT  N5   C12  single    1.366  0.020  1.366
 RHT  C11  C10  aromatic  1.399  0.020  1.399
 RHT  C12  C13  aromatic  1.400  0.020  1.400
 RHT  C10  C9   aromatic  1.391  0.020  1.391
 RHT  C13  C9   aromatic  1.391  0.020  1.391
 RHT  C9   C6   single    1.478  0.020  1.478
 RHT  C6   C7   aromatic  1.390  0.020  1.390
 RHT  C6   C5   aromatic  1.411  0.020  1.411
 RHT  C7   C8   aromatic  1.388  0.020  1.388
 RHT  C5   C4   aromatic  1.381  0.020  1.381
 RHT  C8   C3   aromatic  1.405  0.020  1.405
 RHT  C8   N1   aromatic  1.370  0.020  1.370
 RHT  C4   C3   aromatic  1.394  0.020  1.394
 RHT  C1   N1   single    1.443  0.020  1.443
 RHT  C3   N2   aromatic  1.373  0.020  1.373
 RHT  N1   C2   aromatic  1.356  0.020  1.356
 RHT  N2   C2   aromatic  1.304  0.020  1.304
 RHT  C1   H1   single    0.970  0.020  1.090
 RHT  C1   H2   single    0.970  0.020  1.090
 RHT  C1   H3   single    0.970  0.020  1.090
 RHT  C2   H4   single    0.930  0.020  1.080
 RHT  N3   H5   single    0.890  0.020  1.040
 RHT  N3   H6   single    0.890  0.020  1.040
 RHT  C4   H7   single    0.930  0.020  1.080
 RHT  C5   H8   single    0.930  0.020  1.080
 RHT  N5   H9   single    0.890  0.020  1.040
 RHT  N5   H10  single    0.890  0.020  1.040
 RHT  C7   H11  single    0.930  0.020  1.080
 RHT  C10  H12  single    0.930  0.020  1.080
 RHT  C13  H13  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
 RHT  H3   C1   H2   108.97  3.000
 RHT  H3   C1   H1   108.74  3.000
 RHT  H2   C1   H1   108.79  3.000
 RHT  H3   C1   N1   110.64  3.000
 RHT  H2   C1   N1   110.57  3.000
 RHT  H1   C1   N1   109.08  3.000
 RHT  C8   N1   C2   106.31  3.000
 RHT  C2   N1   C1   127.10  3.000
 RHT  C8   N1   C1   126.58  3.000
 RHT  H4   C2   N2   125.15  3.000
 RHT  H4   C2   N1   120.78  3.000
 RHT  N2   C2   N1   114.07  3.000
 RHT  C3   N2   C2   104.51  3.000
 RHT  C8   C3   C4   119.29  3.000
 RHT  C4   C3   N2   130.70  3.000
 RHT  C8   C3   N2   110.01  3.000
 RHT  H6   N3   H5   113.86  3.000
 RHT  H6   N3   C11  117.24  3.000
 RHT  H5   N3   C11  115.97  3.000
 RHT  H7   C4   C5   120.85  3.000
 RHT  H7   C4   C3   120.98  3.000
 RHT  C5   C4   C3   118.16  3.000
 RHT  C12  N4   C11  118.63  3.000
 RHT  H8   C5   C6   118.88  3.000
 RHT  H8   C5   C4   118.85  3.000
 RHT  C6   C5   C4   122.25  3.000
 RHT  H10  N5   H9   113.96  3.000
 RHT  H10  N5   C12  117.37  3.000
 RHT  H9   N5   C12  116.11  3.000
 RHT  C9   C6   C7   120.04  3.000
 RHT  C7   C6   C5   119.95  3.000
 RHT  C9   C6   C5   120.02  3.000
 RHT  H11  C7   C8   121.46  3.000
 RHT  H11  C7   C6   121.13  3.000
 RHT  C8   C7   C6   117.39  3.000
 RHT  C7   C8   C3   122.95  3.000
 RHT  C3   C8   N1   105.09  3.000
 RHT  C7   C8   N1   131.96  3.000
 RHT  C13  C9   C10  118.93  3.000
 RHT  C13  C9   C6   120.61  3.000
 RHT  C10  C9   C6   120.46  3.000
 RHT  H12  C10  C11  120.16  3.000
 RHT  H12  C10  C9   121.44  3.000
 RHT  C11  C10  C9   118.38  3.000
 RHT  C10  C11  N4   122.85  3.000
 RHT  C10  C11  N3   120.80  3.000
 RHT  N4   C11  N3   116.32  3.000
 RHT  C13  C12  N5   120.76  3.000
 RHT  C13  C12  N4   122.84  3.000
 RHT  N5   C12  N4   116.37  3.000
 RHT  H13  C13  C12  120.19  3.000
 RHT  H13  C13  C9   121.43  3.000
 RHT  C12  C13  C9   118.36  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
 RHT  CONST_01  C6   C7   C8   N1   180.00   0.0  0
 RHT  CONST_02  C4   C3   C8   N1   180.00   0.0  0
 RHT  CONST_03  N2   C3   C8   N1     0.00   0.0  0
 RHT  CONST_04  C3   N2   C2   N1     0.00   0.0  0
 RHT  CONST_05  C7   C8   N1   C2   180.00   0.0  0
 RHT  CONST_06  C3   C8   N1   C2     0.00   0.0  0
 RHT  CONST_07  C8   C3   N2   C2     0.00   0.0  0
 RHT  CONST_08  C4   C3   N2   C2   180.00   0.0  0
 RHT  CONST_09  C7   C8   C3   N2   180.00   0.0  0
 RHT  CONST_10  C5   C4   C3   N2   180.00   0.0  0
 RHT  CONST_11  C8   N1   C2   N2     0.00   0.0  0
 RHT  CONST_12  C6   C7   C8   C3     0.00   0.0  0
 RHT  CONST_13  C6   C5   C4   C3     0.00   0.0  0
 RHT  CONST_14  C9   C6   C5   C4   180.00   0.0  0
 RHT  CONST_15  C7   C6   C5   C4     0.00   0.0  0
 RHT  CONST_16  C7   C8   C3   C4     0.00   0.0  0
 RHT  CONST_17  C9   C10  C11  N4     0.00   0.0  0
 RHT  CONST_18  C9   C13  C12  N4     0.00   0.0  0
 RHT  CONST_21  C8   C7   C6   C5     0.00   0.0  0
 RHT  CONST_22  C8   C3   C4   C5     0.00   0.0  0
 RHT  CONST_23  C11  C10  C9   C6   180.00   0.0  0
 RHT  CONST_24  C12  C13  C9   C6   180.00   0.0  0
 RHT  CONST_27  C9   C6   C7   C8   180.00   0.0  0
 RHT  CONST_28  C12  N4   C11  C10    0.00   0.0  0
 RHT  CONST_29  C12  C13  C9   C10    0.00   0.0  0
 RHT  CONST_30  C13  C12  N4   C11    0.00   0.0  0
 RHT  CONST_31  C13  C9   C10  C11    0.00   0.0  0
 RHT  CONST_32  C7   C8   N1   C1     0.00   0.0  0
 RHT  CONST_33  C3   C8   N1   C1   180.00   0.0  0
 RHT  CONST_34  N2   C2   N1   C1   180.00   0.0  0
 RHT  CONST_35  C12  N4   C11  N3   180.00   0.0  0
 RHT  CONST_36  C9   C10  C11  N3   180.00   0.0  0
 RHT  CONST_37  C11  N4   C12  N5   180.00   0.0  0
 RHT  CONST_38  C9   C13  C12  N5   180.00   0.0  0
 RHT  CONST_39  H11  C7   C8   N1     0.00   0.0  0
 RHT  CONST_40  H7   C4   C3   N2     0.00   0.0  0
 RHT  CONST_41  H8   C5   C4   C3   180.00   0.0  0
 RHT  CONST_42  H4   C2   N2   C3   180.00   0.0  0
 RHT  CONST_43  H12  C10  C11  N4   180.00   0.0  0
 RHT  CONST_44  H13  C13  C12  N4   180.00   0.0  0
 RHT  Var_01    H1   C1   N1   C2     0.92  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
 RHT  plan-1  N3   0.020
 RHT  plan-1  N4   0.020
 RHT  plan-1  N5   0.020
 RHT  plan-1  C6   0.020
 RHT  plan-1  C9   0.020
 RHT  plan-1  C10  0.020
 RHT  plan-1  C11  0.020
 RHT  plan-1  C12  0.020
 RHT  plan-1  C13  0.020
 RHT  plan-1  H12  0.020
 RHT  plan-1  H13  0.020
 RHT  plan-2  C1   0.020
 RHT  plan-2  N1   0.020
 RHT  plan-2  C2   0.020
 RHT  plan-2  N2   0.020
 RHT  plan-2  C3   0.020
 RHT  plan-2  C4   0.020
 RHT  plan-2  C5   0.020
 RHT  plan-2  C6   0.020
 RHT  plan-2  C7   0.020
 RHT  plan-2  C8   0.020
 RHT  plan-2  C9   0.020
 RHT  plan-2  H4   0.020
 RHT  plan-2  H7   0.020
 RHT  plan-2  H8   0.020
 RHT  plan-2  H11  0.020
 RHT  plan-3  N3   0.020
 RHT  plan-3  C11  0.020
 RHT  plan-3  H5   0.020
 RHT  plan-3  H6   0.020
 RHT  plan-4  N5   0.020
 RHT  plan-4  C12  0.020
 RHT  plan-4  H9   0.020
 RHT  plan-4  H10  0.020

