# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 03:58:20 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 1,3-benzodioxol-5-ylmethyl(cyclopentyl)azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCC(C1)[NH2+]Cc2ccc3OCOc3c2
#
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
 8JT  8JT  1,3-benzodioxol-5-ylmethyl(cyclopentyl)azanium  ligand  34  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8JT
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
 8JT  C4   C  CR16  0  -0.373  -1.3833   0.7345  -0.6439
 8JT  C5   C  CR6   0   0.066  -0.5557  -0.4009  -0.5976
 8JT  C6   C  CH2   0  -0.393   0.8725  -0.2792  -1.0284
 8JT  C7   C  CH1   0  -0.091   3.1294   0.5698  -0.3001
 8JT  C8   C  CH2   0  -0.473   3.8724  -0.7132  -0.6763
 8JT  C9   C  CH2   0  -0.451   5.3079  -0.4144  -0.2546
 8JT  C10  C  CH2   0  -0.444   5.1317   0.2963   1.0848
 8JT  C11  C  CH2   0  -0.479   3.9082   1.1988   0.8741
 8JT  C12  C  CH2   0   0.068  -4.8530   0.7973   0.1641
 8JT  O1   O  O     0  -0.480  -4.4591  -0.5050   0.5805
 8JT  C2   C  CR56  0   0.303  -3.1628  -0.6418   0.2266
 8JT  C1   C  CR16  0  -0.329  -2.3713  -1.7613   0.2804
 8JT  O    O  O     0  -0.482  -3.6620   1.5038  -0.1595
 8JT  C3   C  CR56  0   0.318  -2.6779   0.5787  -0.2244
 8JT  C    C  CR16  0  -0.300  -1.0451  -1.6162  -0.1431
 8JT  N    N  NT2   1  -0.671   1.7044   0.3113   0.0669
 8JT  H1   H  HCR6  0   0.282  -1.0174   1.6877  -1.0055
 8JT  H3   H  HCH2  0   0.318   1.3020  -1.2474  -1.2748
 8JT  H2   H  HCH2  0   0.314   0.9828   0.3807  -1.8876
 8JT  H4   H  HCH1  0   0.312   3.0846   1.2537  -1.1472
 8JT  H5   H  HCH2  0   0.248   3.4949  -1.5594  -0.0927
 8JT  H6   H  HCH2  0   0.270   3.7703  -0.9673  -1.7307
 8JT  H8   H  HCH2  0   0.250   5.9183  -1.3147  -0.1892
 8JT  H7   H  HCH2  0   0.235   5.7826   0.2516  -0.9800
 8JT  H10  H  HCH2  0   0.235   4.9304  -0.4388   1.8671
 8JT  H9   H  HCH2  0   0.248   6.0128   0.8602   1.3900
 8JT  H11  H  HCH2  0   0.266   4.2072   2.2107   0.6042
 8JT  H12  H  HCH2  0   0.261   3.2975   1.2807   1.7755
 8JT  H13  H  HCH2  0   0.239  -5.4953   0.7261  -0.7192
 8JT  H14  H  HCH2  0   0.250  -5.3729   1.3032   0.9770
 8JT  H15  H  HCR6  0   0.281  -2.7497  -2.7126   0.6275
 8JT  H16  H  HCR6  0   0.267  -0.3917  -2.4790  -0.1218
 8JT  H18  H  HNT2  0   0.473   1.2745   1.1894   0.3649
 8JT  H17  H  HNT2  0   0.462   1.6647  -0.2977   0.8871

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
 8JT  C12  O    single    1.422  0.020  1.422
 8JT  C12  O1   single    1.423  0.020  1.423
 8JT  O    C3   single    1.352  0.020  1.352
 8JT  O1   C2   single    1.351  0.020  1.351
 8JT  C3   C2   aromatic  1.389  0.020  1.389
 8JT  C3   C4   aromatic  1.370  0.020  1.370
 8JT  C2   C1   aromatic  1.372  0.020  1.372
 8JT  C4   C5   aromatic  1.406  0.020  1.406
 8JT  C1   C    aromatic  1.400  0.020  1.400
 8JT  C5   C    aromatic  1.387  0.020  1.387
 8JT  C5   C6   single    1.497  0.020  1.497
 8JT  C6   N    single    1.497  0.020  1.497
 8JT  C8   C7   single    1.530  0.020  1.530
 8JT  C8   C9   single    1.526  0.020  1.526
 8JT  N    C7   single    1.494  0.020  1.494
 8JT  C7   C11  single    1.543  0.020  1.543
 8JT  C9   C10  single    1.526  0.020  1.526
 8JT  C11  C10  single    1.535  0.020  1.535
 8JT  C4   H1   single    0.930  0.020  1.080
 8JT  C6   H3   single    0.970  0.020  1.090
 8JT  C6   H2   single    0.970  0.020  1.090
 8JT  C7   H4   single    0.970  0.020  1.090
 8JT  C8   H5   single    0.970  0.020  1.090
 8JT  C8   H6   single    0.970  0.020  1.090
 8JT  C9   H8   single    0.970  0.020  1.090
 8JT  C9   H7   single    0.970  0.020  1.090
 8JT  C10  H10  single    0.970  0.020  1.090
 8JT  C10  H9   single    0.970  0.020  1.090
 8JT  C11  H11  single    0.970  0.020  1.090
 8JT  C11  H12  single    0.970  0.020  1.090
 8JT  C12  H13  single    0.970  0.020  1.090
 8JT  C12  H14  single    0.970  0.020  1.090
 8JT  C1   H15  single    0.930  0.020  1.080
 8JT  C    H16  single    0.930  0.020  1.080
 8JT  N    H18  single    0.890  0.020  1.040
 8JT  N    H17  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
 8JT  H1   C4   C3   121.44  3.000
 8JT  H1   C4   C5   121.53  3.000
 8JT  C3   C4   C5   117.03  3.000
 8JT  C    C5   C6   120.16  3.000
 8JT  C6   C5   C4   119.12  3.000
 8JT  C    C5   C4   120.72  3.000
 8JT  H2   C6   H3   108.71  3.000
 8JT  H2   C6   N    106.37  3.000
 8JT  H3   C6   N    107.31  3.000
 8JT  H2   C6   C5   111.90  3.000
 8JT  H3   C6   C5   111.70  3.000
 8JT  N    C6   C5   110.60  3.000
 8JT  H4   C7   N    105.08  3.000
 8JT  H4   C7   C11  110.88  3.000
 8JT  N    C7   C11  111.41  3.000
 8JT  H4   C7   C8   110.81  3.000
 8JT  C11  C7   C8   106.50  3.000
 8JT  N    C7   C8   112.25  3.000
 8JT  H6   C8   H5   107.65  3.000
 8JT  H6   C8   C9   113.67  3.000
 8JT  H5   C8   C9   109.17  3.000
 8JT  H6   C8   C7   112.84  3.000
 8JT  H5   C8   C7   110.46  3.000
 8JT  C9   C8   C7   102.99  3.000
 8JT  H7   C9   H8   107.46  3.000
 8JT  H7   C9   C10  110.41  3.000
 8JT  H8   C9   C10  113.37  3.000
 8JT  H7   C9   C8   110.15  3.000
 8JT  H8   C9   C8   112.44  3.000
 8JT  C10  C9   C8   103.01  3.000
 8JT  H9   C10  H10  107.26  3.000
 8JT  H9   C10  C11  112.25  3.000
 8JT  H10  C10  C11  110.32  3.000
 8JT  H9   C10  C9   113.16  3.000
 8JT  H10  C10  C9   109.66  3.000
 8JT  C11  C10  C9   104.20  3.000
 8JT  H12  C11  H11  106.76  3.000
 8JT  H12  C11  C10  112.12  3.000
 8JT  H11  C11  C10  111.19  3.000
 8JT  H12  C11  C7   112.12  3.000
 8JT  H11  C11  C7   109.20  3.000
 8JT  C10  C11  C7   105.49  3.000
 8JT  H14  C12  H13  110.63  3.000
 8JT  H14  C12  O    109.80  3.000
 8JT  H13  C12  O    109.89  3.000
 8JT  H14  C12  O1   109.80  3.000
 8JT  H13  C12  O1   109.82  3.000
 8JT  O    C12  O1   106.82  3.000
 8JT  C2   O1   C12  106.36  3.000
 8JT  C3   C2   C1   121.90  3.000
 8JT  C1   C2   O1   128.76  3.000
 8JT  C3   C2   O1   109.34  3.000
 8JT  H15  C1   C    121.34  3.000
 8JT  H15  C1   C2   121.91  3.000
 8JT  C    C1   C2   116.75  3.000
 8JT  C3   O    C12  106.29  3.000
 8JT  O    C3   C2   109.37  3.000
 8JT  C2   C3   C4   121.97  3.000
 8JT  O    C3   C4   128.66  3.000
 8JT  H16  C    C1   118.90  3.000
 8JT  H16  C    C5   119.46  3.000
 8JT  C1   C    C5   121.63  3.000
 8JT  H17  N    H18  105.16  3.000
 8JT  H17  N    C7   109.70  3.000
 8JT  H18  N    C7   108.92  3.000
 8JT  H17  N    C6   109.29  3.000
 8JT  H18  N    C6   108.58  3.000
 8JT  C7   N    C6   114.75  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
 8JT  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 8JT  CONST_02  C1   C    C5   C4      0.00   0.0  0
 8JT  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 8JT  CONST_04  C2   C1   C    C5      0.00   0.0  0
 8JT  CONST_05  C    C1   C2   C3      0.00   0.0  0
 8JT  CONST_06  C    C5   C4   C3      0.00   0.0  0
 8JT  CONST_07  C3   C4   C5   C6    180.00   0.0  0
 8JT  CONST_08  C1   C    C5   C6    180.00   0.0  0
 8JT  CONST_09  H16  C    C5   C4    180.00   0.0  0
 8JT  CONST_10  H15  C1   C    C5    180.00   0.0  0
 8JT  CONST_11  H1   C4   C3   C2    180.00   0.0  0
 8JT  Var_01    C10  C9   C8   C7     41.32  30.0  1
 8JT  Var_02    C9   C10  C11  C7     22.24  30.0  1
 8JT  Var_03    C11  C10  C9   C8    -39.58  30.0  1
 8JT  Var_04    C2   C3   O    C12    -8.29  30.0  1
 8JT  Var_05    C3   C2   O1   C12     8.16  30.0  1
 8JT  Var_06    O    C12  O1   C2    -13.07  30.0  1
 8JT  Var_07    N    C6   C5   C4     80.24  30.0  2
 8JT  Var_08    C7   N    C6   C5   -175.63  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
 8JT  chir_01  C7  C8  N  C11  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
 8JT  plan-1  C4   0.020
 8JT  plan-1  C5   0.020
 8JT  plan-1  C6   0.020
 8JT  plan-1  O1   0.020
 8JT  plan-1  C2   0.020
 8JT  plan-1  C1   0.020
 8JT  plan-1  O    0.020
 8JT  plan-1  C3   0.020
 8JT  plan-1  C    0.020
 8JT  plan-1  H1   0.020
 8JT  plan-1  H15  0.020
 8JT  plan-1  H16  0.020

