# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 13:12:04 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (5R)-5-(3-aminopropyl)-1-propyl-4,5,6,7-tetrahydro-1H-benzimidazole-5-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCn1cnc2C[C@@](CCCN)(CCc12)C(O)=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
 2B8  2B8  '(5R)-5-(3-aminopropyl)-1-propyl-4,5,6,7-tetrahydro-1H-benzimidazole-5-carboxylic acid'  ligand  41  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2B8
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
 2B8  C1   C  CH3    0  -0.668   5.2695   1.0029  -1.7111
 2B8  C2   C  CH2    0  -0.437   3.9894   0.9413  -0.8910
 2B8  C3   C  CH2    0  -0.296   3.9125  -0.3366  -0.0657
 2B8  N6   N  N      0  -0.481   1.3340  -0.2524   2.4484
 2B8  C7   C  CR5    0   0.093   0.6188  -0.6253   1.3425
 2B8  C8   C  CH2    0  -0.496  -0.8487  -0.8878   1.2903
 2B8  C9   C  CT     0  -0.233  -1.3553  -0.8380  -0.1628
 2B8  C10  C  CH2    0  -0.396  -1.3929   0.6146  -0.6771
 2B8  C11  C  CH2    0  -0.436  -2.4761   1.5035  -0.0763
 2B8  C12  C  CH2    0  -0.268  -2.3329   2.9528  -0.5164
 2B8  C14  C  CH2    0  -0.421  -0.3978  -1.6619  -1.0487
 2B8  C15  C  CH2    0  -0.525   1.0285  -1.1037  -1.1131
 2B8  C16  C  CR5    0   0.298   1.4460  -0.7379   0.2629
 2B8  N4   N  NR5    0  -0.463   2.6999  -0.4262   0.7194
 2B8  C5   C  CR15   0   0.054   2.5725  -0.1413   2.0350
 2B8  N13  N  NH2    0  -0.801  -3.3960   3.7776   0.0427
 2B8  H1   H  HCH3   0   0.224   6.1545   0.9751  -1.0733
 2B8  H2   H  HCH3   0   0.224   5.3358   0.1648  -2.4068
 2B8  H3   H  HCH3   0   0.237   5.3132   1.9215  -2.2957
 2B8  H4   H  HCH2   0   0.231   3.9295   1.8027  -0.2213
 2B8  H5   H  HCH2   0   0.233   3.1235   0.9997  -1.5553
 2B8  H6   H  HCH2   0   0.251   3.9725  -1.2128  -0.7154
 2B8  H7   H  HCH2   0   0.260   4.7578  -0.3934   0.6219
 2B8  H8   H  HCH2   0   0.228  -1.0707  -1.8719   1.7135
 2B8  H9   H  HCH2   0   0.224  -1.3837  -0.1720   1.9198
 2B8  H10  H  HCH2   0   0.213  -0.4190   1.0784  -0.4910
 2B8  H11  H  HCH2   0   0.212  -1.5182   0.5985  -1.7644
 2B8  H12  H  HCH2   0   0.214  -3.4665   1.1462  -0.3700
 2B8  H13  H  HCH2   0   0.210  -2.4409   1.4605   1.0171
 2B8  H14  H  HCH2   0   0.184  -1.3241   3.3065  -0.2554
 2B8  H15  H  HCH2   0   0.207  -2.4004   3.0046  -1.6074
 2B8  H16  H  HCH2   0   0.222  -0.3522  -2.6859  -0.6616
 2B8  H17  H  HCH2   0   0.229  -0.8056  -1.7270  -2.0574
 2B8  H18  H  HCH2   0   0.251   1.6963  -1.8497  -1.5549
 2B8  H19  H  HCH2   0   0.239   1.0667  -0.2332  -1.7771
 2B8  H20  H  HCR5   0   0.267   3.4229   0.1363   2.6412
 2B8  H21  H  HNH2   0   0.335  -3.2958   3.8053   1.0504
 2B8  H22  H  HNH2   0   0.343  -3.2773   4.7345  -0.2651
 2B8  C17  C  C      0   0.451  -2.7855  -1.4259  -0.2869
 2B8  O18  O  O      0  -0.616  -3.2214  -1.5793  -1.4476
 2B8  O19  O  OC    -1  -0.597  -3.4090  -1.6790   0.7630

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
 2B8  C1   C2   single    1.522  0.020  1.522
 2B8  C2   C3   single    1.523  0.020  1.523
 2B8  C3   N4   single    1.447  0.020  1.447
 2B8  N4   C5   aromatic  1.352  0.020  1.352
 2B8  N4   C16  aromatic  1.370  0.020  1.370
 2B8  C5   N6   aromatic  1.310  0.020  1.310
 2B8  C15  C16  single    1.484  0.020  1.484
 2B8  C15  C14  single    1.533  0.020  1.533
 2B8  C16  C7   aromatic  1.365  0.020  1.365
 2B8  O18  C17  deloc     1.249  0.020  1.249
 2B8  N6   C7   aromatic  1.369  0.020  1.369
 2B8  C7   C8   single    1.492  0.020  1.492
 2B8  C17  O19  deloc     1.247  0.020  1.247
 2B8  C17  C9   single    1.551  0.020  1.551
 2B8  C14  C9   single    1.543  0.020  1.543
 2B8  C9   C8   single    1.540  0.020  1.540
 2B8  C9   C10  single    1.541  0.020  1.541
 2B8  C11  C10  single    1.525  0.020  1.525
 2B8  C11  C12  single    1.521  0.020  1.521
 2B8  C12  N13  single    1.457  0.020  1.457
 2B8  C1   H1   single    0.970  0.020  1.090
 2B8  C1   H2   single    0.970  0.020  1.090
 2B8  C1   H3   single    0.970  0.020  1.090
 2B8  C2   H4   single    0.970  0.020  1.090
 2B8  C2   H5   single    0.970  0.020  1.090
 2B8  C3   H6   single    0.970  0.020  1.090
 2B8  C3   H7   single    0.970  0.020  1.090
 2B8  C8   H8   single    0.970  0.020  1.090
 2B8  C8   H9   single    0.970  0.020  1.090
 2B8  C10  H10  single    0.970  0.020  1.090
 2B8  C10  H11  single    0.970  0.020  1.090
 2B8  C11  H12  single    0.970  0.020  1.090
 2B8  C11  H13  single    0.970  0.020  1.090
 2B8  C12  H14  single    0.970  0.020  1.090
 2B8  C12  H15  single    0.970  0.020  1.090
 2B8  C14  H16  single    0.970  0.020  1.090
 2B8  C14  H17  single    0.970  0.020  1.090
 2B8  C15  H18  single    0.970  0.020  1.090
 2B8  C15  H19  single    0.970  0.020  1.090
 2B8  C5   H20  single    0.930  0.020  1.080
 2B8  N13  H21  single    0.890  0.020  1.040
 2B8  N13  H22  single    0.890  0.020  1.040

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
 2B8  H3   C1   H2   107.63  3.000
 2B8  H3   C1   H1   107.61  3.000
 2B8  H2   C1   H1   107.68  3.000
 2B8  H3   C1   C2   110.92  3.000
 2B8  H2   C1   C2   111.33  3.000
 2B8  H1   C1   C2   111.48  3.000
 2B8  H5   C2   H4   106.68  3.000
 2B8  H5   C2   C3   109.53  3.000
 2B8  H4   C2   C3   109.06  3.000
 2B8  H5   C2   C1   109.68  3.000
 2B8  H4   C2   C1   110.15  3.000
 2B8  C3   C2   C1   111.62  3.000
 2B8  H7   C3   H6   106.89  3.000
 2B8  H7   C3   N4   107.70  3.000
 2B8  H6   C3   N4   108.60  3.000
 2B8  H7   C3   C2   110.25  3.000
 2B8  H6   C3   C2   110.35  3.000
 2B8  N4   C3   C2   112.84  3.000
 2B8  C5   N6   C7   105.19  3.000
 2B8  C16  C7   C8   123.65  3.000
 2B8  C8   C7   N6   126.17  3.000
 2B8  C16  C7   N6   110.18  3.000
 2B8  H9   C8   H8   105.48  3.000
 2B8  H9   C8   C9   111.18  3.000
 2B8  H8   C8   C9   109.11  3.000
 2B8  H9   C8   C7   110.25  3.000
 2B8  H8   C8   C7   110.15  3.000
 2B8  C9   C8   C7   110.55  3.000
 2B8  C17  C9   C14  108.90  3.000
 2B8  C14  C9   C10  109.08  3.000
 2B8  C17  C9   C10  107.94  3.000
 2B8  C10  C9   C8   110.69  3.000
 2B8  C14  C9   C8   108.69  3.000
 2B8  C17  C9   C8   111.51  3.000
 2B8  H11  C10  H10  106.07  3.000
 2B8  H11  C10  C11  108.58  3.000
 2B8  H10  C10  C11  108.55  3.000
 2B8  H11  C10  C9   108.68  3.000
 2B8  H10  C10  C9   108.72  3.000
 2B8  C11  C10  C9   115.81  3.000
 2B8  H13  C11  H12  106.54  3.000
 2B8  H13  C11  C12  108.86  3.000
 2B8  H12  C11  C12  108.60  3.000
 2B8  H13  C11  C10  110.35  3.000
 2B8  H12  C11  C10  110.32  3.000
 2B8  C12  C11  C10  112.00  3.000
 2B8  H15  C12  H14  106.13  3.000
 2B8  H15  C12  N13  108.10  3.000
 2B8  H14  C12  N13  113.32  3.000
 2B8  H15  C12  C11  109.13  3.000
 2B8  H14  C12  C11  108.90  3.000
 2B8  N13  C12  C11  111.07  3.000
 2B8  H17  C14  H16  106.66  3.000
 2B8  H17  C14  C15  109.33  3.000
 2B8  H16  C14  C15  108.44  3.000
 2B8  H17  C14  C9   109.34  3.000
 2B8  H16  C14  C9   108.79  3.000
 2B8  C15  C14  C9   114.02  3.000
 2B8  H19  C15  H18  106.01  3.000
 2B8  H19  C15  C16  110.87  3.000
 2B8  H18  C15  C16  111.76  3.000
 2B8  H19  C15  C14  110.31  3.000
 2B8  H18  C15  C14  109.67  3.000
 2B8  C16  C15  C14  108.21  3.000
 2B8  N4   C16  C15  128.49  3.000
 2B8  C15  C16  C7   125.70  3.000
 2B8  N4   C16  C7   105.80  3.000
 2B8  C5   N4   C16  106.61  3.000
 2B8  C16  N4   C3   126.87  3.000
 2B8  C5   N4   C3   126.42  3.000
 2B8  H20  C5   N4   121.72  3.000
 2B8  H20  C5   N6   126.06  3.000
 2B8  N4   C5   N6   112.22  3.000
 2B8  H22  N13  H21  105.37  3.000
 2B8  H22  N13  C12  109.44  3.000
 2B8  H21  N13  C12  108.96  3.000
 2B8  O19  C17  O18  125.65  3.000
 2B8  O19  C17  C9   118.07  3.000
 2B8  O18  C17  C9   116.26  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
 2B8  CONST_01  C16  N4   C5   N6      0.00   0.0  0
 2B8  CONST_02  N4   C16  C7   N6      0.00   0.0  0
 2B8  CONST_03  C5   N4   C16  C7      0.00   0.0  0
 2B8  CONST_04  N4   C5   N6   C7      0.00   0.0  0
 2B8  CONST_05  C5   N6   C7   C16     0.00   0.0  0
 2B8  CONST_06  N6   C5   N4   C3    180.00   0.0  0
 2B8  CONST_07  C15  C16  N4   C3      0.00   0.0  0
 2B8  CONST_08  C7   C16  N4   C3    180.00   0.0  0
 2B8  CONST_09  H20  C5   N6   C7    180.00   0.0  0
 2B8  Var_01    C9   C8   C7   N6    161.90  30.0  1
 2B8  Var_02    C14  C15  C16  C7    -13.70  30.0  1
 2B8  Var_03    C16  C15  C14  C9     44.69  30.0  1
 2B8  Var_04    C5   N4   C3   C2    -99.69  30.0  2
 2B8  Var_05    N4   C3   C2   C1   -179.65  30.0  3
 2B8  Var_06    C12  C11  C10  C9    173.21  30.0  1
 2B8  Var_07    N13  C12  C11  C10   178.62  30.0  3
 2B8  Var_08    H1   C1   C2   C3    -60.03  30.0  3
 2B8  Var_09    H21  N13  C12  C11    65.27  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2B8  chir_01  C9  C14  C8  C10  negativ

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
 2B8  plan-1  C9   0.020
 2B8  plan-1  C17  0.020
 2B8  plan-1  O18  0.020
 2B8  plan-1  O19  0.020
 2B8  plan-2  C3   0.020
 2B8  plan-2  N6   0.020
 2B8  plan-2  C7   0.020
 2B8  plan-2  C8   0.020
 2B8  plan-2  C15  0.020
 2B8  plan-2  C16  0.020
 2B8  plan-2  N4   0.020
 2B8  plan-2  C5   0.020
 2B8  plan-2  H20  0.020

