# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:04:09 2021
#   Inital geometry file: a 67 line input string
#   Ligand name: 2-[(3S)-pyrrolidin-3-yl]-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C[C@@H](CN1)c2[nH]c3ccccc3n2
#
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
 D6V  D6V  2-[(3S)-pyrrolidin-3-yl]-1H-benzimidazole  ligand  27  14  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D6V
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
 D6V  C4   C  CR56  0   0.336  -1.9417   8.9548   7.3857
 D6V  C5   C  CR16  0  -0.311  -2.8765   9.9815   7.4362
 D6V  C6   C  CR5   0   0.467  -0.2428   7.5619   7.5862
 D6V  N1   N  N     0  -0.481  -1.0246   6.9802   6.7159
 D6V  C7   C  CH1   0  -0.389   1.0460   7.0210   8.0905
 D6V  C8   C  CH2   0  -0.475   2.2388   8.0057   7.9830
 D6V  N2   N  NH1   0  -0.578   2.3139   6.9776  10.1495
 D6V  C9   C  CH2   0  -0.324   2.7146   8.1809   9.4356
 D6V  C10  C  CH2   0  -0.312   1.0052   6.6670   9.6073
 D6V  C3   C  CR56  0   0.134  -2.1001   7.8253   6.5651
 D6V  C2   C  CR16  0  -0.337  -3.2329   7.7063   5.7613
 D6V  C1   C  CR16  0  -0.273  -4.1707   8.7241   5.8049
 D6V  N    N  NR15  0  -0.698  -0.7473   8.7497   8.0227
 D6V  C    C  CR16  0  -0.279  -3.9944   9.8447   6.6296
 D6V  H1   H  HCR6  0   0.264  -2.7414  10.8464   8.0725
 D6V  H3   H  HCH1  0   0.276   1.2546   6.1187   7.5155
 D6V  H4   H  HCH2  0   0.253   3.0261   7.5635   7.3719
 D6V  H5   H  HCH2  0   0.247   1.9691   8.9536   7.5152
 D6V  H6   H  HNH1  0   0.349   2.9538   6.2290   9.9099
 D6V  H8   H  HCH2  0   0.246   3.7889   8.3441   9.5184
 D6V  H9   H  HCH2  0   0.227   2.2176   9.0431   9.8917
 D6V  H10  H  HCH2  0   0.231   0.2552   7.2812  10.1151
 D6V  H11  H  HCH2  0   0.257   0.7401   5.6248   9.7807
 D6V  H12  H  HCR6  0   0.252  -3.3725   6.8424   5.1238
 D6V  H13  H  HCR6  0   0.251  -5.0600   8.6572   5.1916
 D6V  H14  H  HNR5  0   0.414  -0.3175   9.3694   8.6913
 D6V  H15  H  HCR6  0   0.254  -4.7491  10.6199   6.6363

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
 D6V  C1   C2   aromatic  1.385  0.020  1.385
 D6V  C1   C    aromatic  1.403  0.020  1.403
 D6V  C2   C3   aromatic  1.394  0.020  1.394
 D6V  C    C5   aromatic  1.385  0.020  1.385
 D6V  C3   N1   aromatic  1.376  0.020  1.376
 D6V  C3   C4   aromatic  1.405  0.020  1.405
 D6V  N1   C6   aromatic  1.307  0.020  1.307
 D6V  C5   C4   aromatic  1.389  0.020  1.389
 D6V  C4   N    aromatic  1.369  0.020  1.369
 D6V  C6   N    aromatic  1.362  0.020  1.362
 D6V  C6   C7   single    1.486  0.020  1.486
 D6V  C8   C7   single    1.551  0.020  1.551
 D6V  C8   C9   single    1.539  0.020  1.539
 D6V  C7   C10  single    1.558  0.020  1.558
 D6V  C9   N2   single    1.455  0.020  1.455
 D6V  C10  N2   single    1.450  0.020  1.450
 D6V  C5   H1   single    0.930  0.020  1.080
 D6V  C7   H3   single    0.970  0.020  1.090
 D6V  C8   H4   single    0.970  0.020  1.090
 D6V  C8   H5   single    0.970  0.020  1.090
 D6V  N2   H6   single    0.890  0.020  1.040
 D6V  C9   H8   single    0.970  0.020  1.090
 D6V  C9   H9   single    0.970  0.020  1.090
 D6V  C10  H10  single    0.970  0.020  1.090
 D6V  C10  H11  single    0.970  0.020  1.090
 D6V  C2   H12  single    0.930  0.020  1.080
 D6V  C1   H13  single    0.930  0.020  1.080
 D6V  N    H14  single    0.860  0.020  1.020
 D6V  C    H15  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
 D6V  N    C4   C3   104.46  3.000
 D6V  N    C4   C5   132.90  3.000
 D6V  C3   C4   C5   122.64  3.000
 D6V  H1   C5   C    121.47  3.000
 D6V  H1   C5   C4   121.87  3.000
 D6V  C    C5   C4   116.67  3.000
 D6V  N    C6   C7   121.99  3.000
 D6V  C7   C6   N1   125.66  3.000
 D6V  N    C6   N1   112.34  3.000
 D6V  C3   N1   C6   105.50  3.000
 D6V  H3   C7   C10  109.30  3.000
 D6V  H3   C7   C8   109.99  3.000
 D6V  C10  C7   C8   103.41  3.000
 D6V  H3   C7   C6   106.76  3.000
 D6V  C10  C7   C6   112.98  3.000
 D6V  C8   C7   C6   114.37  3.000
 D6V  H5   C8   H4   106.89  3.000
 D6V  H5   C8   C9   112.48  3.000
 D6V  H4   C8   C9   110.61  3.000
 D6V  H5   C8   C7   113.04  3.000
 D6V  H4   C8   C7   109.68  3.000
 D6V  C9   C8   C7   104.17  3.000
 D6V  H6   N2   C10  108.85  3.000
 D6V  H6   N2   C9   108.71  3.000
 D6V  C10  N2   C9   104.01  3.000
 D6V  H9   C9   H8   107.34  3.000
 D6V  H9   C9   N2   108.77  3.000
 D6V  H8   C9   N2   110.98  3.000
 D6V  H9   C9   C8   110.04  3.000
 D6V  H8   C9   C8   113.18  3.000
 D6V  N2   C9   C8   106.49  3.000
 D6V  H11  C10  H10  107.24  3.000
 D6V  H11  C10  N2   111.41  3.000
 D6V  H10  C10  N2   108.95  3.000
 D6V  H11  C10  C7   112.25  3.000
 D6V  H10  C10  C7   110.01  3.000
 D6V  N2   C10  C7   106.96  3.000
 D6V  C2   C3   N1   130.23  3.000
 D6V  N1   C3   C4   109.97  3.000
 D6V  C2   C3   C4   119.80  3.000
 D6V  H12  C2   C1   121.18  3.000
 D6V  H12  C2   C3   120.82  3.000
 D6V  C1   C2   C3   118.00  3.000
 D6V  H13  C1   C    119.07  3.000
 D6V  H13  C1   C2   119.55  3.000
 D6V  C    C1   C2   121.38  3.000
 D6V  H14  N    C6   126.20  3.000
 D6V  H14  N    C4   126.06  3.000
 D6V  C6   N    C4   107.73  3.000
 D6V  H15  C    C1   119.24  3.000
 D6V  H15  C    C5   119.25  3.000
 D6V  C1   C    C5   121.52  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
 D6V  CONST_01  C1   C2  C3   C4    0.00   0.0  0
 D6V  CONST_02  C6   N1  C3   C4    0.00   0.0  0
 D6V  CONST_03  C1   C   C5   C4    0.00   0.0  0
 D6V  CONST_04  N1   C6  N    C4    0.00   0.0  0
 D6V  CONST_05  C2   C1  C    C5    0.00   0.0  0
 D6V  CONST_06  C2   C3  C4   C5    0.00   0.0  0
 D6V  CONST_07  N1   C3  C4   C5  180.00   0.0  0
 D6V  CONST_08  C6   N   C4   C5  180.00   0.0  0
 D6V  CONST_09  C2   C3  N1   C6  180.00   0.0  0
 D6V  CONST_10  C3   C4  N    C6    0.00   0.0  0
 D6V  CONST_11  C1   C2  C3   N1  180.00   0.0  0
 D6V  CONST_12  N    C4  C3   N1    0.00   0.0  0
 D6V  CONST_13  C    C1  C2   C3    0.00   0.0  0
 D6V  CONST_14  N    C6  N1   C3    0.00   0.0  0
 D6V  CONST_15  C    C5  C4   C3    0.00   0.0  0
 D6V  CONST_16  N    C4  C3   C2  180.00   0.0  0
 D6V  CONST_17  C    C5  C4   N   180.00   0.0  0
 D6V  CONST_18  C7   C6  N    C4  180.00   0.0  0
 D6V  CONST_19  C3   N1  C6   C7  180.00   0.0  0
 D6V  CONST_20  H12  C2  C3   C4  180.00   0.0  0
 D6V  CONST_21  H15  C   C5   C4  180.00   0.0  0
 D6V  CONST_22  H13  C1  C    C5  180.00   0.0  0
 D6V  CONST_23  H14  N   C4   C5    0.00   0.0  0
 D6V  CONST_24  H1   C5  C4   C3  180.00   0.0  0
 D6V  Var_01    N2   C9  C8   C7   25.32  30.0  1
 D6V  Var_02    C9   N2  C10  C7   36.79  30.0  1
 D6V  Var_03    C10  N2  C9   C8  -38.79  30.0  1

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
 D6V  chir_01  C7  C6  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
 D6V  plan-1  C4   0.020
 D6V  plan-1  C5   0.020
 D6V  plan-1  C6   0.020
 D6V  plan-1  N1   0.020
 D6V  plan-1  C7   0.020
 D6V  plan-1  C3   0.020
 D6V  plan-1  C2   0.020
 D6V  plan-1  C1   0.020
 D6V  plan-1  N    0.020
 D6V  plan-1  C    0.020
 D6V  plan-1  H1   0.020
 D6V  plan-1  H12  0.020
 D6V  plan-1  H13  0.020
 D6V  plan-1  H14  0.020
 D6V  plan-1  H15  0.020

