# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 17:02:25 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: N-(1,3-benzodioxol-5-yl)-2-(piperidin-1-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CN1CCCCC1)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
 F41  F41  N-(1,3-benzodioxol-5-yl)-2-(piperidin-1-yl)acetamide  ligand  37  19  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F41
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
 F41  C1    C  CH2   0  -0.440  -5.8407   0.9570  -0.6194
 F41  C2    C  CH2   0  -0.438  -5.7018   0.2280   0.7113
 F41  C3    C  CH2   0  -0.280  -4.5648  -0.7807   0.6606
 F41  N4    N  NT    0  -0.408  -3.3136  -0.1374   0.2949
 F41  C5    C  CH2   0  -0.284  -3.4068   0.5024  -1.0077
 F41  C6    C  CH2   0  -0.437  -4.5015   1.5569  -1.0265
 F41  C7    C  CH2   0  -0.406  -2.2062  -1.0492   0.3577
 F41  C8    C  C     0   0.518  -0.8707  -0.3220   0.4515
 F41  O9    O  O     0  -0.462  -0.7529   0.7664   0.9817
 F41  N10   N  NH1   0  -0.741   0.1566  -1.0336  -0.0734
 F41  C11   C  CR6   0   0.365   1.5296  -0.7571  -0.0635
 F41  C12   C  CR16  0  -0.423   2.0568   0.4922   0.3100
 F41  C13   C  CR56  0   0.330   3.4228   0.6202   0.2546
 F41  C14   C  CR56  0   0.282   4.2646  -0.4028  -0.1432
 F41  C15   C  CR16  0  -0.331   3.7647  -1.6250  -0.5141
 F41  C16   C  CR16  0  -0.367   2.3783  -1.7867  -0.4658
 F41  O17   O  O     0  -0.487   4.1588   1.7230   0.5335
 F41  C18   C  CH2   0   0.069   5.5182   1.3049   0.5107
 F41  O19   O  O     0  -0.488   5.5507   0.0340  -0.1226
 F41  H1    H  HCH2  0   0.210  -6.1733   0.2507  -1.3874
 F41  H1A   H  HCH2  0   0.232  -6.6073   1.7322  -0.5553
 F41  H2    H  HCH2  0   0.216  -5.5044   0.9511   1.5084
 F41  H2A   H  HCH2  0   0.231  -6.6292  -0.2875   0.9699
 F41  H3    H  HCH2  0   0.236  -4.4411  -1.2514   1.6392
 F41  H3A   H  HCH2  0   0.186  -4.8284  -1.5873  -0.0473
 F41  H5    H  HCH2  0   0.238  -2.4487   0.9681  -1.2486
 F41  H5A   H  HCH2  0   0.188  -3.6004  -0.2457  -1.7978
 F41  H6    H  HCH2  0   0.231  -4.5590   1.9984  -2.0239
 F41  H6A   H  HCH2  0   0.216  -4.2315   2.3617  -0.3361
 F41  H7    H  HCH2  0   0.285  -2.2901  -1.6543   1.2676
 F41  H7A   H  HCH2  0   0.226  -2.1924  -1.7658  -0.4815
 F41  HN10  H  HNH1  0   0.414  -0.0902  -1.9193  -0.4885
 F41  H12   H  HCR6  0   0.293   1.4321   1.3150   0.6159
 F41  H15   H  HCR6  0   0.276   4.4047  -2.4357  -0.8343
 F41  H16   H  HCR6  0   0.273   1.9576  -2.7428  -0.7512
 F41  H18   H  HCH2  0   0.246   6.1135   2.0182  -0.0589
 F41  H18A  H  HCH2  0   0.232   5.8966   1.2218   1.5356

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
 F41  C1   C2    single    1.524  0.020  1.524
 F41  C1   C6    single    1.523  0.020  1.523
 F41  C2   C3    single    1.521  0.020  1.521
 F41  C3   N4    single    1.454  0.020  1.454
 F41  N4   C5    single    1.454  0.020  1.454
 F41  N4   C7    single    1.436  0.020  1.436
 F41  C5   C6    single    1.520  0.020  1.520
 F41  C7   C8    single    1.524  0.020  1.524
 F41  C8   O9    double    1.216  0.020  1.216
 F41  C8   N10   single    1.355  0.020  1.355
 F41  N10  C11   single    1.401  0.020  1.401
 F41  C11  C12   aromatic  1.406  0.020  1.406
 F41  C11  C16   aromatic  1.394  0.020  1.394
 F41  C12  C13   aromatic  1.373  0.020  1.373
 F41  C13  C14   aromatic  1.383  0.020  1.383
 F41  C13  O17   single    1.355  0.020  1.355
 F41  C14  C15   aromatic  1.372  0.020  1.372
 F41  C14  O19   single    1.358  0.020  1.358
 F41  C15  C16   aromatic  1.397  0.020  1.397
 F41  O17  C18   single    1.422  0.020  1.422
 F41  C18  O19   single    1.420  0.020  1.420
 F41  C1   H1    single    0.970  0.020  1.090
 F41  C1   H1A   single    0.970  0.020  1.090
 F41  C2   H2    single    0.970  0.020  1.090
 F41  C2   H2A   single    0.970  0.020  1.090
 F41  C3   H3    single    0.970  0.020  1.090
 F41  C3   H3A   single    0.970  0.020  1.090
 F41  C5   H5    single    0.970  0.020  1.090
 F41  C5   H5A   single    0.970  0.020  1.090
 F41  C6   H6    single    0.970  0.020  1.090
 F41  C6   H6A   single    0.970  0.020  1.090
 F41  C7   H7    single    0.970  0.020  1.090
 F41  C7   H7A   single    0.970  0.020  1.090
 F41  N10  HN10  single    0.860  0.020  1.020
 F41  C12  H12   single    0.930  0.020  1.080
 F41  C15  H15   single    0.930  0.020  1.080
 F41  C16  H16   single    0.930  0.020  1.080
 F41  C18  H18   single    0.970  0.020  1.090
 F41  C18  H18A  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
 F41  H1A   C1   H1   106.60  3.000
 F41  H1A   C1   C6   110.69  3.000
 F41  H1    C1   C6   109.49  3.000
 F41  H1A   C1   C2   110.63  3.000
 F41  H1    C1   C2   109.37  3.000
 F41  C6    C1   C2   109.99  3.000
 F41  H2A   C2   H2   107.02  3.000
 F41  H2A   C2   C3   109.25  3.000
 F41  H2    C2   C3   109.14  3.000
 F41  H2A   C2   C1   110.80  3.000
 F41  H2    C2   C1   109.67  3.000
 F41  C3    C2   C1   110.88  3.000
 F41  H3A   C3   H3   106.63  3.000
 F41  H3A   C3   N4   111.54  3.000
 F41  H3    C3   N4   108.56  3.000
 F41  H3A   C3   C2   109.10  3.000
 F41  H3    C3   C2   109.90  3.000
 F41  N4    C3   C2   111.00  3.000
 F41  C7    N4   C5   111.59  3.000
 F41  C7    N4   C3   111.83  3.000
 F41  C5    N4   C3   111.40  3.000
 F41  H5A   C5   H5   106.53  3.000
 F41  H5A   C5   C6   109.55  3.000
 F41  H5    C5   C6   109.46  3.000
 F41  H5A   C5   N4   110.72  3.000
 F41  H5    C5   N4   109.21  3.000
 F41  C6    C5   N4   111.25  3.000
 F41  H6A   C6   H6   106.97  3.000
 F41  H6A   C6   C5   108.94  3.000
 F41  H6    C6   C5   109.25  3.000
 F41  H6A   C6   C1   109.76  3.000
 F41  H6    C6   C1   110.92  3.000
 F41  C5    C6   C1   110.90  3.000
 F41  H7A   C7   H7   105.89  3.000
 F41  H7A   C7   C8   110.23  3.000
 F41  H7    C7   C8   106.23  3.000
 F41  H7A   C7   N4   112.87  3.000
 F41  H7    C7   N4   109.14  3.000
 F41  C8    C7   N4   112.06  3.000
 F41  N10   C8   O9   124.41  3.000
 F41  N10   C8   C7   112.95  3.000
 F41  O9    C8   C7   122.60  3.000
 F41  HN10  N10  C11  114.58  3.000
 F41  HN10  N10  C8   115.78  3.000
 F41  C11   N10  C8   129.54  3.000
 F41  C16   C11  C12  120.30  3.000
 F41  C16   C11  N10  116.69  3.000
 F41  C12   C11  N10  123.00  3.000
 F41  H12   C12  C13  121.14  3.000
 F41  H12   C12  C11  122.43  3.000
 F41  C13   C12  C11  116.42  3.000
 F41  O17   C13  C14  109.31  3.000
 F41  O17   C13  C12  127.44  3.000
 F41  C14   C13  C12  123.24  3.000
 F41  O19   C14  C15  129.47  3.000
 F41  O19   C14  C13  109.51  3.000
 F41  C15   C14  C13  121.00  3.000
 F41  H15   C15  C16  120.73  3.000
 F41  H15   C15  C14  122.17  3.000
 F41  C16   C15  C14  117.10  3.000
 F41  H16   C16  C15  118.61  3.000
 F41  H16   C16  C11  119.45  3.000
 F41  C15   C16  C11  121.94  3.000
 F41  C18   O17  C13  106.06  3.000
 F41  H18A  C18  H18  110.48  3.000
 F41  H18A  C18  O19  109.95  3.000
 F41  H18   C18  O19  109.88  3.000
 F41  H18A  C18  O17  109.72  3.000
 F41  H18   C18  O17  109.76  3.000
 F41  O19   C18  O17  106.98  3.000
 F41  C18   O19  C14  105.83  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
 F41  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 F41  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 F41  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 F41  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 F41  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 F41  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 F41  CONST_07  C13   C12  C11  N10   180.00   0.0  0
 F41  CONST_08  C15   C16  C11  N10   180.00   0.0  0
 F41  CONST_09  H15   C15  C16  C11   180.00   0.0  0
 F41  CONST_10  H16   C16  C11  C12   180.00   0.0  0
 F41  CONST_11  H12   C12  C13  C14   180.00   0.0  0
 F41  CONST_12  C12   C11  N10  C8      0.00   0.0  0
 F41  CONST_13  C16   C11  N10  C8    180.00   0.0  0
 F41  CONST_14  HN10  N10  C11  C12   180.00   0.0  0
 F41  CONST_15  C11   N10  C8   C7    180.00   0.0  0
 F41  CONST_16  C11   N10  C8   O9      0.00   0.0  0
 F41  Var_01    N4    C3   C2   C1     56.56  30.0  1
 F41  Var_02    N4    C5   C6   C1    -56.09  30.0  1
 F41  Var_03    C5    C6   C1   C2     52.84  30.0  1
 F41  Var_04    C5    N4   C3   C2    -59.54  30.0  1
 F41  Var_05    C6    C1   C2   C3    -53.13  30.0  1
 F41  Var_06    C6    C5   N4   C3     59.38  30.0  1
 F41  Var_07    O19   C18  O17  C13    14.83  30.0  1
 F41  Var_08    O17   C18  O19  C14   -14.77  30.0  1
 F41  Var_09    C8    C7   N4   C3   -160.42  30.0  3
 F41  Var_10    O9    C8   C7   N4     29.89  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
 F41  plan-1  C7    0.020
 F41  plan-1  C8    0.020
 F41  plan-1  O9    0.020
 F41  plan-1  N10   0.020
 F41  plan-1  C11   0.020
 F41  plan-1  HN10  0.020
 F41  plan-2  N10   0.020
 F41  plan-2  C11   0.020
 F41  plan-2  C12   0.020
 F41  plan-2  C13   0.020
 F41  plan-2  C14   0.020
 F41  plan-2  C15   0.020
 F41  plan-2  C16   0.020
 F41  plan-2  O17   0.020
 F41  plan-2  O19   0.020
 F41  plan-2  H12   0.020
 F41  plan-2  H15   0.020
 F41  plan-2  H16   0.020

