# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 09:58:31 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: N-(1,3-benzodioxol-5-ylmethyl)cyclopentanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCC(C1)NCc2ccc3OCOc3c2
#
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
 45N  45N  N-(1,3-benzodioxol-5-ylmethyl)cyclopentanamine  ligand  33  16  .  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_45N
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
 45N  C4   C  CR16  0  -0.374  -1.0799   0.5585   0.0356
 45N  C5   C  CR6   0   0.071  -0.5303  -0.5507  -0.6317
 45N  C6   C  CH2   0  -0.321   0.9472  -0.5771  -0.9187
 45N  C7   C  CR15  0  -0.049   3.1540  -0.3189   0.0672
 45N  C8   C  CH2   0  -0.453   3.9257  -0.1214   1.3693
 45N  C9   C  CH2   0  -0.448   5.3394   0.2730   0.9241
 45N  C10  C  CH2   0  -0.449   5.1763   0.8738  -0.4931
 45N  C11  C  CH2   0  -0.450   3.6726   0.8314  -0.7932
 45N  C12  C  CH2   0   0.069  -4.4855   0.9354   1.0075
 45N  O1   O  O     0  -0.487  -4.5321  -0.2194   0.1814
 45N  C2   C  CR56  0   0.283  -3.2445  -0.4956  -0.1473
 45N  C1   C  CR16  0  -0.331  -2.7332  -1.5905  -0.7942
 45N  O    O  O     0  -0.488  -3.1955   1.5082   0.8474
 45N  C3   C  CR56  0   0.314  -2.4321   0.5540   0.2571
 45N  C    C  CR16  0  -0.335  -1.3499  -1.5977  -1.0260
 45N  N    N  NH1   0  -0.595   1.7199  -0.2964   0.2770
 45N  H1   H  HCR6  0   0.262  -0.4531   1.3792   0.3589
 45N  H2   H  HCH2  0   0.211   1.2082  -1.5403  -1.3840
 45N  H3   H  HCH2  0   0.239   1.1760   0.1914  -1.6630
 45N  H4   H  HCR5  0   0.188   3.4832  -1.2678  -0.3940
 45N  H5   H  HCH2  0   0.216   3.4530   0.6948   1.9238
 45N  H6   H  HCH2  0   0.232   3.9102  -1.0041   2.0118
 45N  H7   H  HCH2  0   0.229   5.7969   0.9773   1.6192
 45N  H8   H  HCH2  0   0.226   5.9916  -0.6012   0.8957
 45N  H9   H  HCH2  0   0.230   5.5708   1.8879  -0.5621
 45N  H10  H  HCH2  0   0.226   5.7256   0.2776  -1.2237
 45N  H11  H  HCH2  0   0.233   3.4664   0.7129  -1.8581
 45N  H12  H  HCH2  0   0.216   3.1824   1.7531  -0.4643
 45N  H13  H  HCH2  0   0.245  -5.2478   1.6469   0.6907
 45N  H14  H  HCH2  0   0.230  -4.6389   0.6507   2.0545
 45N  H15  H  HCR6  0   0.270  -3.3598  -2.4130  -1.1116
 45N  H16  H  HCR6  0   0.252  -0.9116  -2.4536  -1.5240
 45N  H17  H  HNH1  0   0.341   1.4846  -0.9910   0.9770

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
 45N  C9   C10  single    1.548  0.020  1.548
 45N  C9   C8   single    1.534  0.020  1.534
 45N  C10  C11  single    1.534  0.020  1.534
 45N  C8   C7   single    1.526  0.020  1.526
 45N  C11  C7   single    1.527  0.020  1.527
 45N  C7   N    single    1.449  0.020  1.449
 45N  N    C6   single    1.451  0.020  1.451
 45N  O    C12  single    1.421  0.020  1.421
 45N  O    C3   single    1.357  0.020  1.357
 45N  C12  O1   single    1.421  0.020  1.421
 45N  C3   C4   aromatic  1.370  0.020  1.370
 45N  C3   C2   aromatic  1.387  0.020  1.387
 45N  C4   C5   aromatic  1.406  0.020  1.406
 45N  O1   C2   single    1.357  0.020  1.357
 45N  C2   C1   aromatic  1.371  0.020  1.371
 45N  C6   C5   single    1.505  0.020  1.505
 45N  C5   C    aromatic  1.387  0.020  1.387
 45N  C1   C    aromatic  1.403  0.020  1.403
 45N  C4   H1   single    0.930  0.020  1.080
 45N  C6   H2   single    0.970  0.020  1.090
 45N  C6   H3   single    0.970  0.020  1.090
 45N  C7   H4   single    0.970  0.020  1.090
 45N  C8   H5   single    0.970  0.020  1.090
 45N  C8   H6   single    0.970  0.020  1.090
 45N  C9   H7   single    0.970  0.020  1.090
 45N  C9   H8   single    0.970  0.020  1.090
 45N  C10  H9   single    0.970  0.020  1.090
 45N  C10  H10  single    0.970  0.020  1.090
 45N  C11  H11  single    0.970  0.020  1.090
 45N  C11  H12  single    0.970  0.020  1.090
 45N  C12  H13  single    0.970  0.020  1.090
 45N  C12  H14  single    0.970  0.020  1.090
 45N  C1   H15  single    0.930  0.020  1.080
 45N  C    H16  single    0.930  0.020  1.080
 45N  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
 45N  H1   C4   C3   121.73  3.000
 45N  H1   C4   C5   120.90  3.000
 45N  C3   C4   C5   117.37  3.000
 45N  C    C5   C6   120.84  3.000
 45N  C    C5   C4   119.96  3.000
 45N  C6   C5   C4   119.20  3.000
 45N  H3   C6   H2   106.11  3.000
 45N  H3   C6   N    108.26  3.000
 45N  H2   C6   N    113.03  3.000
 45N  H3   C6   C5   108.82  3.000
 45N  H2   C6   C5   109.18  3.000
 45N  N    C6   C5   111.24  3.000
 45N  H4   C7   N    111.62  3.000
 45N  H4   C7   C11  108.08  3.000
 45N  N    C7   C11  113.94  3.000
 45N  H4   C7   C8   108.45  3.000
 45N  N    C7   C8   112.00  3.000
 45N  C11  C7   C8   102.20  3.000
 45N  H6   C8   H5   107.38  3.000
 45N  H6   C8   C9   113.06  3.000
 45N  H5   C8   C9   110.70  3.000
 45N  H6   C8   C7   112.96  3.000
 45N  H5   C8   C7   108.09  3.000
 45N  C9   C8   C7   104.58  3.000
 45N  H8   C9   H7   106.46  3.000
 45N  H8   C9   C10  110.49  3.000
 45N  H7   C9   C10  112.16  3.000
 45N  H8   C9   C8   110.65  3.000
 45N  H7   C9   C8   111.59  3.000
 45N  C10  C9   C8   105.57  3.000
 45N  H10  C10  H9   106.48  3.000
 45N  H10  C10  C11  110.32  3.000
 45N  H9   C10  C11  111.59  3.000
 45N  H10  C10  C9   110.35  3.000
 45N  H9   C10  C9   112.39  3.000
 45N  C11  C10  C9   105.76  3.000
 45N  H12  C11  H11  107.46  3.000
 45N  H12  C11  C10  110.91  3.000
 45N  H11  C11  C10  112.29  3.000
 45N  H12  C11  C7   108.23  3.000
 45N  H11  C11  C7   113.82  3.000
 45N  C10  C11  C7   104.09  3.000
 45N  H14  C12  H13  110.45  3.000
 45N  H14  C12  O    109.85  3.000
 45N  H13  C12  O    109.83  3.000
 45N  H14  C12  O1   109.87  3.000
 45N  H13  C12  O1   109.79  3.000
 45N  O    C12  O1   106.97  3.000
 45N  C2   O1   C12  105.97  3.000
 45N  C3   C2   C1   121.56  3.000
 45N  C1   C2   O1   129.10  3.000
 45N  C3   C2   O1   109.33  3.000
 45N  H15  C1   C    121.26  3.000
 45N  H15  C1   C2   121.99  3.000
 45N  C    C1   C2   116.74  3.000
 45N  C3   O    C12  106.05  3.000
 45N  O    C3   C2   109.22  3.000
 45N  C2   C3   C4   122.23  3.000
 45N  O    C3   C4   128.54  3.000
 45N  H16  C    C1   118.63  3.000
 45N  H16  C    C5   119.23  3.000
 45N  C1   C    C5   122.14  3.000
 45N  H17  N    C7   108.60  3.000
 45N  H17  N    C6   108.23  3.000
 45N  C7   N    C6   113.86  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
 45N  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 45N  CONST_02  C1   C    C5   C4     0.00   0.0  0
 45N  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 45N  CONST_04  C2   C1   C    C5     0.00   0.0  0
 45N  CONST_05  C    C5   C4   C3     0.00   0.0  0
 45N  CONST_06  C    C1   C2   C3     0.00   0.0  0
 45N  CONST_07  C3   C4   C5   C6   180.00   0.0  0
 45N  CONST_08  C1   C    C5   C6   180.00   0.0  0
 45N  CONST_09  H16  C    C5   C4   180.00   0.0  0
 45N  CONST_10  H15  C1   C    C5   180.00   0.0  0
 45N  CONST_11  H1   C4   C3   C2   180.00   0.0  0
 45N  Var_01    C10  C9   C8   C7    24.02  30.0  1
 45N  Var_02    C9   C10  C11  C7   -26.06  30.0  1
 45N  Var_03    C11  C10  C9   C8     1.29  30.0  1
 45N  Var_04    C2   C3   O    C12    9.55  30.0  1
 45N  Var_05    C3   C2   O1   C12   -9.56  30.0  1
 45N  Var_06    O    C12  O1   C2    15.26  30.0  1
 45N  Var_07    N    C6   C5   C4    50.99  30.0  2
 45N  Var_08    C7   N    C6   C5   179.50  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
 45N  chir_01  C7  C8  C11  N  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
 45N  plan-1  C4   0.020
 45N  plan-1  C5   0.020
 45N  plan-1  C6   0.020
 45N  plan-1  O1   0.020
 45N  plan-1  C2   0.020
 45N  plan-1  C1   0.020
 45N  plan-1  O    0.020
 45N  plan-1  C3   0.020
 45N  plan-1  C    0.020
 45N  plan-1  H1   0.020
 45N  plan-1  H15  0.020
 45N  plan-1  H16  0.020

