# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 09:19:31 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: ~{N}-(1,3-benzodioxol-5-yl)-2-piperidin-1-ium-1-yl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(C[NH+]1CCCCC1)Nc2ccc3OCOc3c2
#
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
 9NT  9NT  ~{N}-(1,3-benzodioxol-5-yl)-2-piperidin-1-ium-1-yl-ethanamide  ligand  38  19  .  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_9NT
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
 9NT  C3    C  CH2   0  -0.313   4.6385   1.0877  -0.4951
 9NT  N4    N  NT1   1  -0.531   3.3962   0.2831  -0.2691
 9NT  C7    C  CH2   0  -0.420   2.1823   1.1267  -0.3052
 9NT  C8    C  C     0   0.542   0.9696   0.2470  -0.5764
 9NT  O9    O  O     0  -0.459   1.1040  -0.7959  -1.1928
 9NT  N10   N  NH1   0  -0.742  -0.1817   0.7547  -0.1143
 9NT  C11   C  CR6   0   0.367  -1.4886   0.2509  -0.2407
 9NT  C12   C  CR16  0  -0.445  -2.4958   1.0348   0.3537
 9NT  C13   C  CR56  0   0.320  -3.7826   0.5774   0.2613
 9NT  C14   C  CR56  0   0.296  -4.1007  -0.6049  -0.3874
 9NT  C15   C  CR16  0  -0.337  -3.1317  -1.3770  -0.9706
 9NT  C16   C  CR16  0  -0.329  -1.8039  -0.9358  -0.8919
 9NT  O17   O  O     0  -0.484  -4.9067   1.1355   0.7615
 9NT  C18   C  CH2   0   0.071  -5.9940   0.3418   0.2959
 9NT  O19   O  O     0  -0.486  -5.4366  -0.8177  -0.3079
 9NT  H3    H  HCH2  0   0.306   4.5120   1.6124  -1.4403
 9NT  H1    H  HCH2  0   0.294   4.6879   1.8236   0.3079
 9NT  H7A   H  HCH2  0   0.325   2.1169   1.6851   0.6275
 9NT  H7    H  HCH2  0   0.347   2.2852   1.8405  -1.1245
 9NT  HN10  H  HNH1  0   0.432  -0.1112   1.6185   0.4038
 9NT  H12   H  HCR6  0   0.292  -2.2612   1.9602   0.8649
 9NT  H4    H  HCR6  0   0.279  -3.3690  -2.3033  -1.4754
 9NT  H16   H  HCR6  0   0.287  -1.0359  -1.5386  -1.3454
 9NT  H18A  H  HCH2  0   0.246  -6.6255   0.0542   1.1372
 9NT  H18   H  HCH2  0   0.237  -6.5722   0.9057  -0.4424
 9NT  C1    C  CH2   0  -0.470   5.8623   0.1935  -0.5135
 9NT  C2    C  CH2   0  -0.447   5.9718  -0.6383   0.7571
 9NT  C4    C  CH2   0  -0.468   4.6887  -1.4277   0.9758
 9NT  C6    C  CH2   0  -0.326   3.4846  -0.5087   1.0014
 9NT  H2    H  HCH2  0   0.253   5.8222  -0.4585  -1.3906
 9NT  H5    H  HCH2  0   0.276   6.7346   0.8362  -0.6386
 9NT  H6    H  HCH2  0   0.259   6.8258  -1.3128   0.6921
 9NT  H8    H  HCH2  0   0.237   6.1453   0.0191   1.6140
 9NT  H9    H  HCH2  0   0.252   4.5617  -2.1777   0.1897
 9NT  H10   H  HCH2  0   0.277   4.7121  -1.9662   1.9238
 9NT  H11   H  HCH2  0   0.295   3.5575   0.2179   1.8109
 9NT  H13   H  HCH2  0   0.309   2.5567  -1.0650   1.1151
 9NT  HN4   H  HNT1  0   0.454   3.3066  -0.3838  -1.0443

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
 9NT  N4   C7    single    1.479  0.020  1.479
 9NT  N4   C3    single    1.497  0.020  1.497
 9NT  C7   C8    single    1.523  0.020  1.523
 9NT  C8   O9    double    1.219  0.020  1.219
 9NT  C8   N10   single    1.341  0.020  1.341
 9NT  N10  C11   single    1.406  0.020  1.406
 9NT  C11  C16   aromatic  1.390  0.020  1.390
 9NT  C11  C12   aromatic  1.408  0.020  1.408
 9NT  C16  C15   aromatic  1.401  0.020  1.401
 9NT  C12  C13   aromatic  1.369  0.020  1.369
 9NT  C15  C14   aromatic  1.369  0.020  1.369
 9NT  C13  C14   aromatic  1.385  0.020  1.385
 9NT  C13  O17   single    1.351  0.020  1.351
 9NT  C14  O19   single    1.355  0.020  1.355
 9NT  O17  C18   single    1.424  0.020  1.424
 9NT  O19  C18   single    1.421  0.020  1.421
 9NT  C3   H3    single    0.970  0.020  1.090
 9NT  C3   H1    single    0.970  0.020  1.090
 9NT  C7   H7A   single    0.970  0.020  1.090
 9NT  C7   H7    single    0.970  0.020  1.090
 9NT  N10  HN10  single    0.860  0.020  1.020
 9NT  C12  H12   single    0.930  0.020  1.080
 9NT  C15  H4    single    0.930  0.020  1.080
 9NT  C16  H16   single    0.930  0.020  1.080
 9NT  C18  H18A  single    0.970  0.020  1.090
 9NT  C18  H18   single    0.970  0.020  1.090
 9NT  C3   C1    single    1.516  0.020  1.516
 9NT  C1   C2    single    1.523  0.020  1.523
 9NT  C2   C4    single    1.522  0.020  1.522
 9NT  C4   C6    single    1.515  0.020  1.515
 9NT  N4   C6    single    1.500  0.020  1.500
 9NT  C1   H2    single    0.970  0.020  1.090
 9NT  C1   H5    single    0.970  0.020  1.090
 9NT  C2   H6    single    0.970  0.020  1.090
 9NT  C2   H8    single    0.970  0.020  1.090
 9NT  C4   H9    single    0.970  0.020  1.090
 9NT  C4   H10   single    0.970  0.020  1.090
 9NT  C6   H11   single    0.970  0.020  1.090
 9NT  C6   H13   single    0.970  0.020  1.090
 9NT  N4   HN4   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
 9NT  C1    C3   H1    111.75  3.000
 9NT  C1    C3   H3    111.57  3.000
 9NT  H1    C3   H3    108.64  3.000
 9NT  C1    C3   N4    110.78  3.000
 9NT  H1    C3   N4    106.81  3.000
 9NT  H3    C3   N4    107.08  3.000
 9NT  HN4   N4   C6    107.57  3.000
 9NT  HN4   N4   C7    106.30  3.000
 9NT  C6    N4   C7    111.74  3.000
 9NT  HN4   N4   C3    107.91  3.000
 9NT  C6    N4   C3    111.27  3.000
 9NT  C7    N4   C3    111.77  3.000
 9NT  H7    C7   H7A   108.25  3.000
 9NT  H7    C7   C8    108.62  3.000
 9NT  H7A   C7   C8    113.64  3.000
 9NT  H7    C7   N4    108.30  3.000
 9NT  H7A   C7   N4    108.72  3.000
 9NT  C8    C7   N4    109.18  3.000
 9NT  N10   C8   O9    126.38  3.000
 9NT  N10   C8   C7    113.82  3.000
 9NT  O9    C8   C7    119.78  3.000
 9NT  HN10  N10  C11   114.68  3.000
 9NT  HN10  N10  C8    116.16  3.000
 9NT  C11   N10  C8    129.16  3.000
 9NT  C16   C11  C12   120.73  3.000
 9NT  C12   C11  N10   115.30  3.000
 9NT  C16   C11  N10   123.97  3.000
 9NT  H12   C12  C13   121.41  3.000
 9NT  H12   C12  C11   121.34  3.000
 9NT  C13   C12  C11   117.25  3.000
 9NT  O17   C13  C14   109.56  3.000
 9NT  O17   C13  C12   128.25  3.000
 9NT  C14   C13  C12   122.18  3.000
 9NT  O19   C14  C15   129.35  3.000
 9NT  O19   C14  C13   109.44  3.000
 9NT  C15   C14  C13   121.20  3.000
 9NT  H4    C15  C16   120.26  3.000
 9NT  H4    C15  C14   121.77  3.000
 9NT  C16   C15  C14   117.97  3.000
 9NT  H16   C16  C15   118.42  3.000
 9NT  H16   C16  C11   120.91  3.000
 9NT  C15   C16  C11   120.67  3.000
 9NT  C18   O17  C13   106.49  3.000
 9NT  H18   C18  H18A  110.52  3.000
 9NT  H18   C18  O19   109.94  3.000
 9NT  H18A  C18  O19   109.85  3.000
 9NT  H18   C18  O17   109.68  3.000
 9NT  H18A  C18  O17   109.68  3.000
 9NT  O19   C18  O17   107.10  3.000
 9NT  C18   O19  C14   106.47  3.000
 9NT  H5    C1   H2    106.78  3.000
 9NT  H5    C1   C2    111.11  3.000
 9NT  H2    C1   C2    110.26  3.000
 9NT  H5    C1   C3    107.43  3.000
 9NT  H2    C1   C3    109.38  3.000
 9NT  C2    C1   C3    111.73  3.000
 9NT  H8    C2   H6    107.12  3.000
 9NT  H8    C2   C4    109.44  3.000
 9NT  H6    C2   C4    110.37  3.000
 9NT  H8    C2   C1    109.68  3.000
 9NT  H6    C2   C1    110.16  3.000
 9NT  C4    C2   C1    110.03  3.000
 9NT  H10   C4   H9    106.77  3.000
 9NT  H10   C4   C6    107.57  3.000
 9NT  H9    C4   C6    109.62  3.000
 9NT  H10   C4   C2    111.28  3.000
 9NT  H9    C4   C2    110.50  3.000
 9NT  C6    C4   C2    110.97  3.000
 9NT  H13   C6   H11   108.68  3.000
 9NT  H13   C6   C4    111.69  3.000
 9NT  H11   C6   C4    111.32  3.000
 9NT  H13   C6   N4    107.96  3.000
 9NT  H11   C6   N4    106.32  3.000
 9NT  C4    C6   N4    110.66  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
 9NT  CONST_01  C14   C15  C16  C11    0.00   0.0  0
 9NT  CONST_02  C14   C13  C12  C11    0.00   0.0  0
 9NT  CONST_03  C15   C16  C11  C12    0.00   0.0  0
 9NT  CONST_04  C15   C14  C13  C12    0.00   0.0  0
 9NT  CONST_05  C16   C11  C12  C13    0.00   0.0  0
 9NT  CONST_06  C16   C15  C14  C13    0.00   0.0  0
 9NT  CONST_07  C15   C16  C11  N10  180.00   0.0  0
 9NT  CONST_08  C13   C12  C11  N10  180.00   0.0  0
 9NT  CONST_09  H4    C15  C16  C11  180.00   0.0  0
 9NT  CONST_10  H16   C16  C11  C12  180.00   0.0  0
 9NT  CONST_11  H12   C12  C13  C14  180.00   0.0  0
 9NT  CONST_12  C16   C11  N10  C8     0.00   0.0  0
 9NT  CONST_13  C12   C11  N10  C8   180.00   0.0  0
 9NT  CONST_14  HN10  N10  C11  C12    0.00   0.0  0
 9NT  CONST_15  C11   N10  C8   C7   180.00   0.0  0
 9NT  CONST_16  C11   N10  C8   O9     0.00   0.0  0
 9NT  Var_01    C4    C2   C1   C3    54.79  30.0  1
 9NT  Var_02    C2    C1   C3   N4   -55.56  30.0  1
 9NT  Var_03    C2    C4   C6   N4    57.30  30.0  1
 9NT  Var_04    O19   C18  O17  C13    9.39  30.0  1
 9NT  Var_05    O17   C18  O19  C14   -9.42  30.0  1
 9NT  Var_06    C6    C4   C2   C1   -55.49  30.0  1
 9NT  Var_07    O9    C8   C7   N4   -27.14  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
 9NT  chir_01  N4  C7  C3  C6  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
 9NT  plan-1  C7    0.020
 9NT  plan-1  C8    0.020
 9NT  plan-1  O9    0.020
 9NT  plan-1  N10   0.020
 9NT  plan-1  C11   0.020
 9NT  plan-1  HN10  0.020
 9NT  plan-2  N10   0.020
 9NT  plan-2  C11   0.020
 9NT  plan-2  C12   0.020
 9NT  plan-2  C13   0.020
 9NT  plan-2  C14   0.020
 9NT  plan-2  C15   0.020
 9NT  plan-2  C16   0.020
 9NT  plan-2  O17   0.020
 9NT  plan-2  O19   0.020
 9NT  plan-2  H12   0.020
 9NT  plan-2  H4    0.020
 9NT  plan-2  H16   0.020

