# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 08:06:50 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: N-[1-(2,3-dihydro-1,4-benzodioxin-6-yl)cyclopentyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NC1(CCCC1)c2ccc3OCCOc3c2
#
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
 H3D  H3D  N-[1-(2,3-dihydro-1,4-benzodioxin-6-yl)cyclopentyl]acetamide  ligand  38  19  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H3D
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
 H3D  C4   C  CH2   0  -0.452  -1.9492   1.5312  -1.4279
 H3D  C5   C  C     0   0.531  -2.4981  -1.4446   0.7186
 H3D  C6   C  CH3   0  -0.777  -3.5239  -2.5325   0.5062
 H3D  C7   C  CR6   0   0.210  -0.1360   0.1825  -0.2992
 H3D  C8   C  CR16  0  -0.470   0.8733   0.7106   0.4920
 H3D  C10  C  CR6   0   0.297   2.5255  -0.6664  -0.6019
 H3D  C13  C  CH2   0  -0.226   4.7789  -0.2491  -0.1937
 H3D  O    O  O     0  -0.497  -1.7360  -1.4598   1.6743
 H3D  C3   C  CR5   0   0.022  -1.5726   0.6607  -0.2172
 H3D  C2   C  CH2   0  -0.432  -1.9168   1.6212   0.9298
 H3D  C1   C  CH2   0  -0.440  -3.2636   2.2238   0.5198
 H3D  C    C  CH2   0  -0.457  -3.2629   2.2169  -1.0266
 H3D  C12  C  CR16  0  -0.314   0.2058  -0.7921  -1.2365
 H3D  C11  C  CR16  0  -0.354   1.5170  -1.2074  -1.3891
 H3D  O1   O  O2    0  -0.482   3.8007  -1.0907  -0.7839
 H3D  C14  C  CH2   0  -0.225   4.3574   0.1421   1.2025
 H3D  O2   O  O2    0  -0.483   3.1270   0.8478   1.1658
 H3D  C9   C  CR6   0   0.347   2.1933   0.2964   0.3513
 H3D  H1   H  HCH2  0   0.249  -1.1581   2.2708  -1.5653
 H3D  H2   H  HCH2  0   0.249  -2.0154   0.9577  -2.3551
 H3D  H3   H  HCH3  0   0.263  -4.1826  -2.5808   1.3732
 H3D  H4   H  HCH3  0   0.247  -4.1364  -2.3957  -0.3833
 H3D  H5   H  HCH3  0   0.264  -3.0181  -3.4952   0.4297
 H3D  H6   H  HCR6  0   0.255   0.6635   1.4547   1.2497
 H3D  H7   H  HCH2  0   0.259   5.7129  -0.8091  -0.1653
 H3D  H8   H  HCH2  0   0.241   4.9306   0.6437  -0.8101
 H3D  H9   H  HNH1  0   0.399  -3.1435  -0.5518  -0.9744
 H3D  H10  H  HCH2  0   0.251  -1.9300   1.1398   1.9062
 H3D  H11  H  HCH2  0   0.232  -1.1650   2.4128   0.9662
 H3D  H12  H  HCH2  0   0.230  -4.0883   1.6230   0.9054
 H3D  H13  H  HCH2  0   0.234  -3.3918   3.2266   0.9277
 H3D  H14  H  HCH2  0   0.239  -3.3226   3.2224  -1.4428
 H3D  H15  H  HCH2  0   0.234  -4.1260   1.6718  -1.4120
 H3D  H16  H  HCR6  0   0.241  -0.5574  -1.2410  -1.8595
 H3D  H17  H  HCR6  0   0.262   1.7699  -1.9586  -2.1275
 H3D  H18  H  HCH2  0   0.242   4.2639  -0.7468   1.8357
 H3D  H19  H  HCH2  0   0.259   5.0963   0.8050   1.6507
 H3D  N    N  NH1   0  -0.646  -2.4866  -0.4770  -0.2150

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
 H3D  C    C4   single    1.535  0.020  1.535
 H3D  C    C1   single    1.546  0.020  1.546
 H3D  O1   C10  single    1.356  0.020  1.356
 H3D  O1   C13  single    1.419  0.020  1.419
 H3D  C11  C10  aromatic  1.389  0.020  1.389
 H3D  C11  C12  aromatic  1.384  0.020  1.384
 H3D  C4   C3   single    1.538  0.020  1.538
 H3D  C10  C9   aromatic  1.395  0.020  1.395
 H3D  C12  C7   aromatic  1.395  0.020  1.395
 H3D  C1   C2   single    1.531  0.020  1.531
 H3D  C13  C14  single    1.510  0.020  1.510
 H3D  C9   O2   single    1.356  0.020  1.356
 H3D  C9   C8   aromatic  1.391  0.020  1.391
 H3D  C7   C8   aromatic  1.387  0.020  1.387
 H3D  C7   C3   single    1.516  0.020  1.516
 H3D  C14  O2   single    1.419  0.020  1.419
 H3D  C3   C2   single    1.535  0.020  1.535
 H3D  C3   N    single    1.459  0.020  1.459
 H3D  N    C5   single    1.345  0.020  1.345
 H3D  C5   O    double    1.222  0.020  1.222
 H3D  C5   C6   single    1.510  0.020  1.510
 H3D  C4   H1   single    0.970  0.020  1.090
 H3D  C4   H2   single    0.970  0.020  1.090
 H3D  C6   H3   single    0.970  0.020  1.090
 H3D  C6   H4   single    0.970  0.020  1.090
 H3D  C6   H5   single    0.970  0.020  1.090
 H3D  C8   H6   single    0.930  0.020  1.080
 H3D  C13  H7   single    0.970  0.020  1.090
 H3D  C13  H8   single    0.970  0.020  1.090
 H3D  N    H9   single    0.860  0.020  1.020
 H3D  C2   H10  single    0.970  0.020  1.090
 H3D  C2   H11  single    0.970  0.020  1.090
 H3D  C1   H12  single    0.970  0.020  1.090
 H3D  C1   H13  single    0.970  0.020  1.090
 H3D  C    H14  single    0.970  0.020  1.090
 H3D  C    H15  single    0.970  0.020  1.090
 H3D  C12  H16  single    0.930  0.020  1.080
 H3D  C11  H17  single    0.930  0.020  1.080
 H3D  C14  H18  single    0.970  0.020  1.090
 H3D  C14  H19  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
 H3D  H2   C4   H1   107.03  3.000
 H3D  H2   C4   C    113.86  3.000
 H3D  H1   C4   C    110.51  3.000
 H3D  H2   C4   C3   112.70  3.000
 H3D  H1   C4   C3   107.76  3.000
 H3D  C    C4   C3   104.87  3.000
 H3D  N    C5   O    123.12  3.000
 H3D  O    C5   C6   121.63  3.000
 H3D  N    C5   C6   115.25  3.000
 H3D  H5   C6   H4   108.34  3.000
 H3D  H5   C6   H3   107.28  3.000
 H3D  H4   C6   H3   108.39  3.000
 H3D  H5   C6   C5   109.32  3.000
 H3D  H4   C6   C5   113.99  3.000
 H3D  H3   C6   C5   109.30  3.000
 H3D  C12  C7   C3   119.27  3.000
 H3D  C3   C7   C8   122.59  3.000
 H3D  C12  C7   C8   118.11  3.000
 H3D  H6   C8   C9   117.36  3.000
 H3D  H6   C8   C7   121.33  3.000
 H3D  C9   C8   C7   121.31  3.000
 H3D  C9   C10  O1   122.11  3.000
 H3D  C9   C10  C11  118.89  3.000
 H3D  O1   C10  C11  119.00  3.000
 H3D  H8   C13  H7   108.35  3.000
 H3D  H8   C13  C14  110.35  3.000
 H3D  H7   C13  C14  110.39  3.000
 H3D  H8   C13  O1   110.17  3.000
 H3D  H7   C13  O1   107.28  3.000
 H3D  C14  C13  O1   110.23  3.000
 H3D  C2   C3   N    110.26  3.000
 H3D  N    C3   C7   110.34  3.000
 H3D  C2   C3   C7   116.75  3.000
 H3D  N    C3   C4   106.80  3.000
 H3D  C2   C3   C4   100.32  3.000
 H3D  C7   C3   C4   111.59  3.000
 H3D  H11  C2   H10  107.39  3.000
 H3D  H11  C2   C1   109.21  3.000
 H3D  H10  C2   C1   113.79  3.000
 H3D  H11  C2   C3   108.91  3.000
 H3D  H10  C2   C3   113.34  3.000
 H3D  C1   C2   C3   104.09  3.000
 H3D  H13  C1   H12  106.58  3.000
 H3D  H13  C1   C    112.23  3.000
 H3D  H12  C1   C    110.57  3.000
 H3D  H13  C1   C2   111.42  3.000
 H3D  H12  C1   C2   110.70  3.000
 H3D  C    C1   C2   105.40  3.000
 H3D  H15  C    H14  106.42  3.000
 H3D  H15  C    C1   110.80  3.000
 H3D  H14  C    C1   112.19  3.000
 H3D  H15  C    C4   111.18  3.000
 H3D  H14  C    C4   111.05  3.000
 H3D  C1   C    C4   105.30  3.000
 H3D  H16  C12  C11  118.69  3.000
 H3D  H16  C12  C7   120.25  3.000
 H3D  C11  C12  C7   121.07  3.000
 H3D  H17  C11  C12  120.30  3.000
 H3D  H17  C11  C10  119.14  3.000
 H3D  C12  C11  C10  120.57  3.000
 H3D  C13  O1   C10  114.01  3.000
 H3D  H19  C14  H18  108.30  3.000
 H3D  H19  C14  O2   107.23  3.000
 H3D  H18  C14  O2   110.15  3.000
 H3D  H19  C14  C13  110.42  3.000
 H3D  H18  C14  C13  110.37  3.000
 H3D  O2   C14  C13  110.30  3.000
 H3D  C9   O2   C14  114.23  3.000
 H3D  O2   C9   C10  121.80  3.000
 H3D  O2   C9   C8   118.14  3.000
 H3D  C10  C9   C8   120.05  3.000
 H3D  H9   N    C3   117.74  3.000
 H3D  H9   N    C5   117.68  3.000
 H3D  C3   N    C5   124.57  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
 H3D  CONST_01  C10  C11  C12  C7     0.00   0.0  0
 H3D  CONST_02  C10  C9   C8   C7     0.00   0.0  0
 H3D  CONST_03  C11  C10  C9   C8     0.00   0.0  0
 H3D  CONST_04  C11  C12  C7   C8     0.00   0.0  0
 H3D  CONST_05  C9   C10  C11  C12    0.00   0.0  0
 H3D  CONST_06  C9   C8   C7   C12    0.00   0.0  0
 H3D  CONST_07  C11  C12  C7   C3   180.00   0.0  0
 H3D  CONST_08  C9   C8   C7   C3   180.00   0.0  0
 H3D  CONST_09  H17  C11  C12  C7   180.00   0.0  0
 H3D  CONST_10  H16  C12  C7   C8   180.00   0.0  0
 H3D  CONST_11  H6   C8   C9   C10  180.00   0.0  0
 H3D  CONST_12  C3   N    C5   C6   180.00   0.0  0
 H3D  CONST_13  C3   N    C5   O      0.00   0.0  0
 H3D  CONST_14  H9   N    C5   C6     0.00   0.0  0
 H3D  Var_01    C2   C1   C    C4     3.34  30.0  1
 H3D  Var_02    C14  C13  O1   C10   44.79  30.0  1
 H3D  Var_03    C11  C10  O1   C13  164.52  30.0  1
 H3D  Var_04    C1   C    C4   C3    23.92  30.0  1
 H3D  Var_05    C    C1   C2   C3   -29.40  30.0  1
 H3D  Var_06    O2   C14  C13  O1   -60.48  30.0  1
 H3D  Var_07    H3   C6   C5   O     58.58  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
 H3D  chir_01  C3  C7  C2  C4  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
 H3D  plan-1  C5   0.020
 H3D  plan-1  C6   0.020
 H3D  plan-1  O    0.020
 H3D  plan-1  C3   0.020
 H3D  plan-1  H9   0.020
 H3D  plan-1  N    0.020
 H3D  plan-2  C7   0.020
 H3D  plan-2  C8   0.020
 H3D  plan-2  C10  0.020
 H3D  plan-2  C3   0.020
 H3D  plan-2  C12  0.020
 H3D  plan-2  C11  0.020
 H3D  plan-2  O1   0.020
 H3D  plan-2  O2   0.020
 H3D  plan-2  C9   0.020
 H3D  plan-2  H6   0.020
 H3D  plan-2  H16  0.020
 H3D  plan-2  H17  0.020

