# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 10:02:34 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 5-(1H-benzimidazol-2-yl)pentan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCCc1[nH]c2ccccc2n1
#
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
 JA2  JA2  5-(1H-benzimidazol-2-yl)pentan-1-amine  ligand  32  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JA2
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
 JA2  N1    N  NR15  0  -0.691  -1.2606  -1.0040  -0.3162
 JA2  C2    C  CR56  0   0.333  -2.5157  -0.4638  -0.3954
 JA2  C3    C  CR56  0   0.132  -2.5638   0.4671   0.6566
 JA2  C4    C  CR16  0  -0.339  -3.7234   1.2115   0.8699
 JA2  C5    C  CR16  0  -0.273  -4.7978   0.9988   0.0233
 JA2  C6    C  CR16  0  -0.280  -4.7318   0.0632  -1.0199
 JA2  C7    C  CR16  0  -0.311  -3.5894  -0.6859  -1.2488
 JA2  C8    C  CR5   0   0.437  -0.6215  -0.4149   0.7304
 JA2  N9    N  N     0  -0.477  -1.3674   0.4706   1.3360
 JA2  C10   C  CH2   0  -0.532   0.7887  -0.7425   1.0713
 JA2  C11   C  CH2   0  -0.421   1.7884  -0.0604   0.1321
 JA2  C12   C  CH2   0  -0.424   3.2289  -0.4284   0.4630
 JA2  C13   C  CH2   0  -0.427   4.2374   0.2638  -0.4441
 JA2  C14   C  CH2   0  -0.270   5.6743  -0.1251  -0.1309
 JA2  N15   N  NH2   0  -0.801   6.6065   0.5764  -1.0021
 JA2  HN1   H  HNR5  0   0.417  -0.8786  -1.7227  -0.9107
 JA2  H4    H  HCR6  0   0.252  -3.7778   1.9338   1.6744
 JA2  H5    H  HCR6  0   0.250  -5.7097   1.5640   0.1664
 JA2  H6    H  HCR6  0   0.253  -5.5934  -0.0771  -1.6595
 JA2  H7    H  HCR6  0   0.264  -3.5396  -1.4077  -2.0534
 JA2  H10   H  HCH2  0   0.258   0.9718  -0.4278   2.0995
 JA2  H10A  H  HCH2  0   0.255   0.9316  -1.8263   1.0350
 JA2  H11   H  HCH2  0   0.227   1.5714  -0.3394  -0.9030
 JA2  H11A  H  HCH2  0   0.231   1.6590   1.0238   0.1960
 JA2  H12   H  HCH2  0   0.217   3.4382  -0.1695   1.5062
 JA2  H12A  H  HCH2  0   0.216   3.3491  -1.5145   0.3868
 JA2  H13   H  HCH2  0   0.212   4.0175   0.0150  -1.4885
 JA2  H13A  H  HCH2  0   0.214   4.1323   1.3496  -0.3550
 JA2  H14   H  HCH2  0   0.211   5.9006   0.1500   0.9031
 JA2  H14A  H  HCH2  0   0.186   5.7633  -1.2204  -0.1828
 JA2  HN15  H  HNH2  0   0.345   7.5546   0.3131  -0.7659
 JA2  HN1A  H  HNH2  0   0.336   6.4698   0.2650  -1.9563

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
 JA2  N1   C2    aromatic  1.369  0.020  1.369
 JA2  N1   C8    aromatic  1.360  0.020  1.360
 JA2  C2   C3    aromatic  1.406  0.020  1.406
 JA2  C2   C7    aromatic  1.389  0.020  1.389
 JA2  C3   C4    aromatic  1.394  0.020  1.394
 JA2  C3   N9    aromatic  1.376  0.020  1.376
 JA2  C4   C5    aromatic  1.384  0.020  1.384
 JA2  C5   C6    aromatic  1.403  0.020  1.403
 JA2  C6   C7    aromatic  1.385  0.020  1.385
 JA2  C8   N9    aromatic  1.307  0.020  1.307
 JA2  C8   C10   single    1.487  0.020  1.487
 JA2  C10  C11   single    1.532  0.020  1.532
 JA2  C11  C12   single    1.523  0.020  1.523
 JA2  C12  C13   single    1.523  0.020  1.523
 JA2  C13  C14   single    1.521  0.020  1.521
 JA2  C14  N15   single    1.456  0.020  1.456
 JA2  N1   HN1   single    0.860  0.020  1.020
 JA2  C4   H4    single    0.930  0.020  1.080
 JA2  C5   H5    single    0.930  0.020  1.080
 JA2  C6   H6    single    0.930  0.020  1.080
 JA2  C7   H7    single    0.930  0.020  1.080
 JA2  C10  H10   single    0.970  0.020  1.090
 JA2  C10  H10A  single    0.970  0.020  1.090
 JA2  C11  H11   single    0.970  0.020  1.090
 JA2  C11  H11A  single    0.970  0.020  1.090
 JA2  C12  H12   single    0.970  0.020  1.090
 JA2  C12  H12A  single    0.970  0.020  1.090
 JA2  C13  H13   single    0.970  0.020  1.090
 JA2  C13  H13A  single    0.970  0.020  1.090
 JA2  C14  H14   single    0.970  0.020  1.090
 JA2  C14  H14A  single    0.970  0.020  1.090
 JA2  N15  HN15  single    0.890  0.020  1.040
 JA2  N15  HN1A  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
 JA2  HN1   N1   C8    125.77  3.000
 JA2  HN1   N1   C2    126.50  3.000
 JA2  C8    N1   C2    107.72  3.000
 JA2  C7    C2   C3    122.63  3.000
 JA2  C7    C2   N1    132.93  3.000
 JA2  C3    C2   N1    104.45  3.000
 JA2  N9    C3   C4    130.26  3.000
 JA2  N9    C3   C2    109.97  3.000
 JA2  C4    C3   C2    119.77  3.000
 JA2  H4    C4   C5    121.20  3.000
 JA2  H4    C4   C3    120.77  3.000
 JA2  C5    C4   C3    118.03  3.000
 JA2  H5    C5   C6    119.10  3.000
 JA2  H5    C5   C4    119.52  3.000
 JA2  C6    C5   C4    121.38  3.000
 JA2  H6    C6   C7    119.27  3.000
 JA2  H6    C6   C5    119.24  3.000
 JA2  C7    C6   C5    121.49  3.000
 JA2  H7    C7   C6    121.44  3.000
 JA2  H7    C7   C2    121.86  3.000
 JA2  C6    C7   C2    116.70  3.000
 JA2  C10   C8   N9    125.75  3.000
 JA2  C10   C8   N1    121.76  3.000
 JA2  N9    C8   N1    112.45  3.000
 JA2  C8    N9   C3    105.41  3.000
 JA2  H10A  C10  H10   107.17  3.000
 JA2  H10A  C10  C11   109.61  3.000
 JA2  H10   C10  C11   109.87  3.000
 JA2  H10A  C10  C8    109.54  3.000
 JA2  H10   C10  C8    108.16  3.000
 JA2  C11   C10  C8    112.34  3.000
 JA2  H11A  C11  H11   106.54  3.000
 JA2  H11A  C11  C12   109.80  3.000
 JA2  H11   C11  C12   109.37  3.000
 JA2  H11A  C11  C10   109.17  3.000
 JA2  H11   C11  C10   109.70  3.000
 JA2  C12   C11  C10   112.11  3.000
 JA2  H12A  C12  H12   106.25  3.000
 JA2  H12A  C12  C13   109.67  3.000
 JA2  H12   C12  C13   109.48  3.000
 JA2  H12A  C12  C11   109.16  3.000
 JA2  H12   C12  C11   109.31  3.000
 JA2  C13   C12  C11   112.77  3.000
 JA2  H13A  C13  H13   106.47  3.000
 JA2  H13A  C13  C14   109.11  3.000
 JA2  H13   C13  C14   109.13  3.000
 JA2  H13A  C13  C12   109.81  3.000
 JA2  H13   C13  C12   109.37  3.000
 JA2  C14   C13  C12   112.75  3.000
 JA2  H14A  C14  H14   106.16  3.000
 JA2  H14A  C14  N15   113.55  3.000
 JA2  H14   C14  N15   108.18  3.000
 JA2  H14A  C14  C13   108.73  3.000
 JA2  H14   C14  C13   109.02  3.000
 JA2  N15   C14  C13   111.00  3.000
 JA2  HN1A  N15  HN15  105.44  3.000
 JA2  HN1A  N15  C14   109.22  3.000
 JA2  HN15  N15  C14   109.56  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
 JA2  CONST_01  C4    C3   C2   N1    180.00   0.0  0
 JA2  CONST_02  N9    C3   C2   N1      0.00   0.0  0
 JA2  CONST_03  C6    C7   C2   N1    180.00   0.0  0
 JA2  CONST_04  C3    N9   C8   N1      0.00   0.0  0
 JA2  CONST_05  N9    C8   N1   C2      0.00   0.0  0
 JA2  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 JA2  CONST_07  C8    N9   C3   C2      0.00   0.0  0
 JA2  CONST_08  C5    C6   C7   C2      0.00   0.0  0
 JA2  CONST_09  C8    N1   C2   C3      0.00   0.0  0
 JA2  CONST_10  C6    C7   C2   C3      0.00   0.0  0
 JA2  CONST_11  C6    C5   C4   C3      0.00   0.0  0
 JA2  CONST_12  C7    C2   C3   C4      0.00   0.0  0
 JA2  CONST_13  C8    N9   C3   C4    180.00   0.0  0
 JA2  CONST_14  C7    C6   C5   C4      0.00   0.0  0
 JA2  CONST_15  N9    C3   C4   C5    180.00   0.0  0
 JA2  CONST_16  C8    N1   C2   C7    180.00   0.0  0
 JA2  CONST_17  N9    C3   C2   C7    180.00   0.0  0
 JA2  CONST_18  C10   C8   N1   C2    180.00   0.0  0
 JA2  CONST_19  C10   C8   N9   C3    180.00   0.0  0
 JA2  CONST_20  H7    C7   C2   N1      0.00   0.0  0
 JA2  CONST_21  H4    C4   C3   C2    180.00   0.0  0
 JA2  CONST_22  H6    C6   C7   C2    180.00   0.0  0
 JA2  CONST_23  HN1   N1   C2   C3    180.00   0.0  0
 JA2  CONST_24  H5    C5   C4   C3    180.00   0.0  0
 JA2  Var_01    C11   C10  C8   N1     77.34  30.0  2
 JA2  Var_02    C12   C11  C10  C8   -178.50  30.0  3
 JA2  Var_03    C13   C12  C11  C10  -178.85  30.0  3
 JA2  Var_04    C14   C13  C12  C11  -178.88  30.0  3
 JA2  Var_05    N15   C14  C13  C12  -178.92  30.0  3
 JA2  Var_06    HN15  N15  C14  C13   179.13  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
 JA2  plan-1  N1   0.020
 JA2  plan-1  C2   0.020
 JA2  plan-1  C3   0.020
 JA2  plan-1  C4   0.020
 JA2  plan-1  C5   0.020
 JA2  plan-1  C6   0.020
 JA2  plan-1  C7   0.020
 JA2  plan-1  C8   0.020
 JA2  plan-1  N9   0.020
 JA2  plan-1  C10  0.020
 JA2  plan-1  HN1  0.020
 JA2  plan-1  H4   0.020
 JA2  plan-1  H5   0.020
 JA2  plan-1  H6   0.020
 JA2  plan-1  H7   0.020

