# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 18:26:59 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 2-[(2S)-2-methylpyrrolidin-2-yl]-1H-benzimidazole-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(CCCN1)c2[nH]c3c(cccc3C(N)=O)n2
#
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
 3GN  3GN  2-[(2S)-2-methylpyrrolidin-2-yl]-1H-benzimidazole-7-carboxamide  ligand  34  18  .  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_3GN
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
 3GN  C4    C  CR56  0   0.332  -1.1443   0.2667   0.0168
 3GN  C5    C  CR6   0  -0.091  -2.4627  -0.1918  -0.0620
 3GN  C6    C  CR16  0  -0.331  -3.4392   0.7880  -0.2224
 3GN  C8    C  CR5   0   0.522   1.0215   0.5861   0.1886
 3GN  C10   C  C     0   0.517  -2.7313  -1.6528   0.0313
 3GN  C13   C  CR5   0  -0.021   2.4702   0.2236   0.3498
 3GN  C15   C  CH2   0  -0.292   3.4954  -1.6783  -0.6611
 3GN  C17   C  CH2   0  -0.457   3.2836   0.6543  -0.8970
 3GN  C1    C  CR16  0  -0.259  -3.1221   2.1459  -0.2990
 3GN  C2    C  CR16  0  -0.341  -1.8117   2.5870  -0.2168
 3GN  C3    C  CR56  0   0.142  -0.8114   1.6345  -0.0567
 3GN  N7    N  N     0  -0.474   0.5482   1.7957   0.0542
 3GN  N9    N  NR15  0  -0.680   0.0558  -0.3620   0.1720
 3GN  N11   N  NH2   0  -0.825  -4.0063  -2.0580  -0.0346
 3GN  O12   O  O     0  -0.493  -1.8025  -2.4451   0.1657
 3GN  N14   N  NR15  0  -0.617   2.6085  -1.2382   0.4170
 3GN  C16   C  CH2   0  -0.467   4.3213  -0.4525  -1.0345
 3GN  C18   C  CH3   0  -0.674   3.0146   0.8902   1.6143
 3GN  H6    H  HCR6  0   0.247  -4.4847   0.5197  -0.2937
 3GN  H15   H  HCH2  0   0.240   4.0924  -2.5306  -0.3366
 3GN  H15A  H  HCH2  0   0.218   2.9073  -2.0066  -1.5238
 3GN  H17   H  HCH2  0   0.243   2.6474   0.6760  -1.7854
 3GN  H17A  H  HCH2  0   0.252   3.7071   1.6515  -0.7760
 3GN  H1    H  HCR6  0   0.260  -3.9222   2.8630  -0.4234
 3GN  H2    H  HCR6  0   0.260  -1.5713   3.6409  -0.2745
 3GN  HN9   H  HNR5  0   0.408   0.2252  -1.3520   0.2570
 3GN  HN11  H  HNH2  0   0.416  -4.7860  -1.4346  -0.1409
 3GN  HN1A  H  HNH2  0   0.407  -4.2152  -3.0409   0.0268
 3GN  HN14  H  HNR5  0   0.363   2.9944  -1.5043   1.3121
 3GN  H16   H  HCH2  0   0.228   5.1374  -0.3115  -0.3210
 3GN  H16A  H  HCH2  0   0.242   4.7547  -0.5092  -2.0335
 3GN  H18   H  HCH3  0   0.240   2.5349   0.4856   2.5076
 3GN  H18A  H  HCH3  0   0.241   4.0893   0.7188   1.6982
 3GN  H18B  H  HCH3  0   0.242   2.8414   1.9651   1.5958

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
 3GN  C4   C5    aromatic  1.398  0.020  1.398
 3GN  C4   C3    aromatic  1.410  0.020  1.410
 3GN  C4   N9    aromatic  1.364  0.020  1.364
 3GN  C5   C6    aromatic  1.393  0.020  1.393
 3GN  C5   C10   single    1.488  0.020  1.488
 3GN  C6   C1    aromatic  1.397  0.020  1.397
 3GN  C8   C13   single    1.502  0.020  1.502
 3GN  C8   N7    aromatic  1.306  0.020  1.306
 3GN  C8   N9    aromatic  1.353  0.020  1.353
 3GN  C10  N11   single    1.339  0.020  1.339
 3GN  C10  O12   double    1.228  0.020  1.228
 3GN  C13  C17   single    1.550  0.020  1.550
 3GN  C13  N14   single    1.470  0.020  1.470
 3GN  C13  C18   single    1.530  0.020  1.530
 3GN  C15  N14   single    1.464  0.020  1.464
 3GN  C15  C16   single    1.525  0.020  1.525
 3GN  C17  C16   single    1.523  0.020  1.523
 3GN  C1   C2    aromatic  1.385  0.020  1.385
 3GN  C2   C3    aromatic  1.391  0.020  1.391
 3GN  C3   N7    aromatic  1.374  0.020  1.374
 3GN  C6   H6    single    0.930  0.020  1.080
 3GN  C15  H15   single    0.970  0.020  1.090
 3GN  C15  H15A  single    0.970  0.020  1.090
 3GN  C17  H17   single    0.970  0.020  1.090
 3GN  C17  H17A  single    0.970  0.020  1.090
 3GN  C1   H1    single    0.930  0.020  1.080
 3GN  C2   H2    single    0.930  0.020  1.080
 3GN  N9   HN9   single    0.860  0.020  1.020
 3GN  N11  HN11  single    0.860  0.020  1.020
 3GN  N11  HN1A  single    0.860  0.020  1.020
 3GN  N14  HN14  single    0.890  0.020  1.040
 3GN  C16  H16   single    0.970  0.020  1.090
 3GN  C16  H16A  single    0.970  0.020  1.090
 3GN  C18  H18   single    0.970  0.020  1.090
 3GN  C18  H18A  single    0.970  0.020  1.090
 3GN  C18  H18B  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
 3GN  N9    C4   C3    104.20  3.000
 3GN  N9    C4   C5    133.25  3.000
 3GN  C3    C4   C5    122.55  3.000
 3GN  C10   C5   C6    124.84  3.000
 3GN  C10   C5   C4    119.25  3.000
 3GN  C6    C5   C4    115.91  3.000
 3GN  H6    C6   C1    117.20  3.000
 3GN  H6    C6   C5    120.72  3.000
 3GN  C1    C6   C5    122.08  3.000
 3GN  N9    C8   N7    112.89  3.000
 3GN  N9    C8   C13   121.36  3.000
 3GN  N7    C8   C13   125.74  3.000
 3GN  O12   C10  N11   122.01  3.000
 3GN  O12   C10  C5    120.24  3.000
 3GN  N11   C10  C5    117.75  3.000
 3GN  C18   C13  N14   111.23  3.000
 3GN  C18   C13  C17   110.93  3.000
 3GN  N14   C13  C17   105.29  3.000
 3GN  C18   C13  C8    109.08  3.000
 3GN  N14   C13  C8    109.61  3.000
 3GN  C17   C13  C8    110.66  3.000
 3GN  H15A  C15  H15   107.12  3.000
 3GN  H15A  C15  C16   109.83  3.000
 3GN  H15   C15  C16   113.89  3.000
 3GN  H15A  C15  N14   110.19  3.000
 3GN  H15   C15  N14   110.35  3.000
 3GN  C16   C15  N14   105.48  3.000
 3GN  H17A  C17  H17   107.35  3.000
 3GN  H17A  C17  C16   114.21  3.000
 3GN  H17   C17  C16   109.72  3.000
 3GN  H17A  C17  C13   111.64  3.000
 3GN  H17   C17  C13   110.73  3.000
 3GN  C16   C17  C13   103.19  3.000
 3GN  H1    C1   C2    119.70  3.000
 3GN  H1    C1   C6    118.88  3.000
 3GN  C2    C1   C6    121.42  3.000
 3GN  H2    C2   C3    120.88  3.000
 3GN  H2    C2   C1    121.13  3.000
 3GN  C3    C2   C1    117.99  3.000
 3GN  N7    C3   C2    129.87  3.000
 3GN  N7    C3   C4    110.08  3.000
 3GN  C2    C3   C4    120.05  3.000
 3GN  C3    N7   C8    104.98  3.000
 3GN  HN9   N9   C8    124.55  3.000
 3GN  HN9   N9   C4    127.61  3.000
 3GN  C8    N9   C4    107.84  3.000
 3GN  HN1A  N11  HN11  116.84  3.000
 3GN  HN1A  N11  C10   119.33  3.000
 3GN  HN11  N11  C10   123.83  3.000
 3GN  HN14  N14  C15   109.99  3.000
 3GN  HN14  N14  C13   109.77  3.000
 3GN  C15   N14  C13   108.81  3.000
 3GN  H16A  C16  H16   107.93  3.000
 3GN  H16A  C16  C17   113.03  3.000
 3GN  H16   C16  C17   110.85  3.000
 3GN  H16A  C16  C15   113.45  3.000
 3GN  H16   C16  C15   110.38  3.000
 3GN  C17   C16  C15   101.13  3.000
 3GN  H18B  C18  H18A  108.23  3.000
 3GN  H18B  C18  H18   108.05  3.000
 3GN  H18A  C18  H18   108.16  3.000
 3GN  H18B  C18  C13   111.07  3.000
 3GN  H18A  C18  C13   110.22  3.000
 3GN  H18   C18  C13   111.01  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
 3GN  CONST_01  C1    C6   C5   C4     0.00   0.0  0
 3GN  CONST_02  C1    C2   C3   C4     0.00   0.0  0
 3GN  CONST_03  C8    N7   C3   C4     0.00   0.0  0
 3GN  CONST_04  N7    C8   N9   C4     0.00   0.0  0
 3GN  CONST_05  C2    C3   C4   C5     0.00   0.0  0
 3GN  CONST_06  N7    C3   C4   C5   180.00   0.0  0
 3GN  CONST_07  C8    N9   C4   C5   180.00   0.0  0
 3GN  CONST_08  C2    C1   C6   C5     0.00   0.0  0
 3GN  CONST_09  C3    C4   C5   C6     0.00   0.0  0
 3GN  CONST_10  N9    C4   C5   C6   180.00   0.0  0
 3GN  CONST_11  C3    C2   C1   C6     0.00   0.0  0
 3GN  CONST_12  C2    C3   N7   C8   180.00   0.0  0
 3GN  CONST_13  C3    C4   N9   C8     0.00   0.0  0
 3GN  CONST_14  N7    C3   C2   C1   180.00   0.0  0
 3GN  CONST_15  N9    C4   C3   C2   180.00   0.0  0
 3GN  CONST_16  N9    C8   N7   C3     0.00   0.0  0
 3GN  CONST_17  N9    C4   C3   N7     0.00   0.0  0
 3GN  CONST_18  C13   C8   N9   C4   180.00   0.0  0
 3GN  CONST_19  C3    N7   C8   C13  180.00   0.0  0
 3GN  CONST_20  C3    C4   C5   C10  180.00   0.0  0
 3GN  CONST_21  N9    C4   C5   C10    0.00   0.0  0
 3GN  CONST_22  C1    C6   C5   C10  180.00   0.0  0
 3GN  CONST_23  H6    C6   C5   C4   180.00   0.0  0
 3GN  CONST_24  H2    C2   C3   C4   180.00   0.0  0
 3GN  CONST_25  HN9   N9   C4   C5     0.00   0.0  0
 3GN  CONST_26  H1    C1   C6   C5   180.00   0.0  0
 3GN  CONST_27  HN11  N11  C10  C5     0.00   0.0  0
 3GN  CONST_28  HN1A  N11  C10  C5   180.00   0.0  0
 3GN  Var_01    C15   C16  C17  C13   38.37  30.0  1
 3GN  Var_02    C16   C15  N14  C13   21.99  30.0  1
 3GN  Var_03    N14   C15  C16  C17  -37.60  30.0  1
 3GN  Var_04    N11   C10  C5   C4   179.35  30.0  2

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
 3GN  chir_01  C13  C17  N14  C8  positiv

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
 3GN  plan-1  C4    0.020
 3GN  plan-1  C5    0.020
 3GN  plan-1  C6    0.020
 3GN  plan-1  C8    0.020
 3GN  plan-1  C10   0.020
 3GN  plan-1  C13   0.020
 3GN  plan-1  C1    0.020
 3GN  plan-1  C2    0.020
 3GN  plan-1  C3    0.020
 3GN  plan-1  N7    0.020
 3GN  plan-1  N9    0.020
 3GN  plan-1  H6    0.020
 3GN  plan-1  H1    0.020
 3GN  plan-1  H2    0.020
 3GN  plan-1  HN9   0.020
 3GN  plan-2  C5    0.020
 3GN  plan-2  C10   0.020
 3GN  plan-2  N11   0.020
 3GN  plan-2  O12   0.020
 3GN  plan-2  HN11  0.020
 3GN  plan-2  HN1A  0.020

