# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:28:54 2021
#   Inital geometry file: a 103 line input string
#   Ligand name: (1S,2S,3S,4R,5R)-2-[(furan-2-ylmethyl)amino]-4-(piperidin-1-yl)-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](NCc2occc2)[C@H]3CO[C@H](O3)[C@@H]1N4CCCCC4
#
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
 D9V  D9V  '(1S,2S,3S,4R,5R)-2-[(furan-2-ylmethyl)amino]-4-(piperidin-1-yl)-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)'  ligand  46  22  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D9V
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
 D9V  O3   O  OH1   0  -0.671  -12.8943   2.3318   3.1900
 D9V  C4   C  CH2   0  -0.406  -11.5083  -0.8169   1.0745
 D9V  C5   C  CH1   0  -0.135  -12.2941   1.5054   1.0142
 D9V  C6   C  CH1   0  -0.097  -11.9336   1.9535  -0.4218
 D9V  N1   N  NT    0  -0.442  -13.0073   5.1607   1.9694
 D9V  C7   C  CH2   0  -0.165  -13.1560   2.0249  -1.3257
 D9V  C8   C  CH1   0   0.259  -12.7770   3.9604  -0.1643
 D9V  C9   C  CH1   0  -0.126  -13.1517   3.8680   1.3370
 D9V  C10  C  CH1   0   0.075  -12.3466   2.7167   1.9527
 D9V  C11  C  CH2   0  -0.315  -11.6615   5.6624   2.1642
 D9V  C12  C  CH2   0  -0.423  -11.6897   7.1956   2.1378
 D9V  C13  C  CH2   0  -0.428  -13.0168   7.7255   2.6953
 D9V  C14  C  CH2   0  -0.487  -13.5554   6.7638   3.7455
 D9V  C15  C  CH2   0  -0.259  -13.8556   5.3913   3.1284
 D9V  O1   O  O2    0  -0.509  -13.7209   3.2787  -0.9684
 D9V  O2   O  O2    0  -0.487  -11.5531   3.3267  -0.4153
 D9V  N    N  NH1   0  -0.619  -11.4138   0.5265   1.6204
 D9V  C2   C  CR5   0   0.370  -12.8000  -1.4626   1.4264
 D9V  C1   C  CR15  0  -0.379  -13.7998  -1.9791   0.6706
 D9V  O    O  O     0  -0.406  -13.1062  -1.5916   2.7363
 D9V  C3   C  CR15  0  -0.012  -14.3103  -2.1952   2.8199
 D9V  C    C  CR15  0  -0.333  -14.7884  -2.4624   1.5833
 D9V  H1   H  HOH1  0   0.440  -12.4619   1.4954   3.4127
 D9V  H2   H  HCH2  0   0.269  -10.6748  -1.3958   1.4816
 D9V  H3   H  HCH2  0   0.232  -11.4067  -0.8644  -0.0186
 D9V  H4   H  HCH1  0   0.255  -13.2972   1.0627   1.0014
 D9V  H5   H  HCH1  0   0.270  -11.1175   1.3647  -0.8442
 D9V  H7   H  HCH2  0   0.230  -13.8716   1.2199  -1.1463
 D9V  H8   H  HCH2  0   0.231  -12.8770   2.0125  -2.3839
 D9V  H9   H  HCH1  0   0.248  -12.7153   5.0071  -0.4763
 D9V  H10  H  HCH1  0   0.251  -14.2154   3.6106   1.3931
 D9V  H11  H  HCH1  0   0.204  -11.3110   3.0639   2.0935
 D9V  H12  H  HCH2  0   0.205  -11.2172   5.3047   3.1070
 D9V  H13  H  HCH2  0   0.241  -11.0087   5.2922   1.3722
 D9V  H14  H  HCH2  0   0.215  -10.8496   7.5801   2.7213
 D9V  H15  H  HCH2  0   0.222  -11.5480   7.5510   1.1149
 D9V  H16  H  HCH2  0   0.226  -12.8809   8.7217   3.1209
 D9V  H17  H  HCH2  0   0.216  -13.7494   7.8313   1.8915
 D9V  H18  H  HCH2  0   0.238  -14.4589   7.1561   4.2160
 D9V  H19  H  HCH2  0   0.221  -12.8162   6.6606   4.5450
 D9V  H20  H  HCH2  0   0.216  -14.8978   5.3527   2.7949
 D9V  H21  H  HCH2  0   0.206  -13.7420   4.6215   3.9021
 D9V  H22  H  HNH1  0   0.361  -10.4515   0.8414   1.5804
 D9V  H24  H  HCR5  0   0.260  -13.8309  -2.0080  -0.4070
 D9V  H25  H  HCR5  0   0.277  -14.6987  -2.3662   3.8109
 D9V  H26  H  HCR5  0   0.262  -15.7259  -2.9384   1.3464

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
 D9V  C7   O1   single    1.421  0.020  1.421
 D9V  C7   C6   single    1.522  0.020  1.522
 D9V  O1   C8   single    1.415  0.020  1.415
 D9V  O2   C8   single    1.401  0.020  1.401
 D9V  O2   C6   single    1.425  0.020  1.425
 D9V  C8   C9   single    1.550  0.020  1.550
 D9V  C6   C5   single    1.547  0.020  1.547
 D9V  C1   C    aromatic  1.430  0.020  1.430
 D9V  C1   C2   aromatic  1.356  0.020  1.356
 D9V  C9   N1   single    1.446  0.020  1.446
 D9V  C9   C10  single    1.534  0.020  1.534
 D9V  C5   N    single    1.449  0.020  1.449
 D9V  C5   C10  single    1.533  0.020  1.533
 D9V  C4   C2   single    1.486  0.020  1.486
 D9V  C4   N    single    1.453  0.020  1.453
 D9V  C    C3   aromatic  1.352  0.020  1.352
 D9V  C2   O    aromatic  1.351  0.020  1.351
 D9V  N1   C11  single    1.449  0.020  1.449
 D9V  N1   C15  single    1.455  0.020  1.455
 D9V  C11  C12  single    1.534  0.020  1.534
 D9V  C10  O3   single    1.407  0.020  1.407
 D9V  C12  C13  single    1.534  0.020  1.534
 D9V  C3   O    aromatic  1.350  0.020  1.350
 D9V  C15  C14  single    1.535  0.020  1.535
 D9V  C13  C14  single    1.522  0.020  1.522
 D9V  O3   H1   single    0.850  0.020  0.980
 D9V  C4   H2   single    0.970  0.020  1.090
 D9V  C4   H3   single    0.970  0.020  1.090
 D9V  C5   H4   single    0.970  0.020  1.090
 D9V  C6   H5   single    0.970  0.020  1.090
 D9V  C7   H7   single    0.970  0.020  1.090
 D9V  C7   H8   single    0.970  0.020  1.090
 D9V  C8   H9   single    0.970  0.020  1.090
 D9V  C9   H10  single    0.970  0.020  1.090
 D9V  C10  H11  single    0.970  0.020  1.090
 D9V  C11  H12  single    0.970  0.020  1.090
 D9V  C11  H13  single    0.970  0.020  1.090
 D9V  C12  H14  single    0.970  0.020  1.090
 D9V  C12  H15  single    0.970  0.020  1.090
 D9V  C13  H16  single    0.970  0.020  1.090
 D9V  C13  H17  single    0.970  0.020  1.090
 D9V  C14  H18  single    0.970  0.020  1.090
 D9V  C14  H19  single    0.970  0.020  1.090
 D9V  C15  H20  single    0.970  0.020  1.090
 D9V  C15  H21  single    0.970  0.020  1.090
 D9V  N    H22  single    0.890  0.020  1.040
 D9V  C1   H24  single    0.930  0.020  1.080
 D9V  C3   H25  single    0.930  0.020  1.080
 D9V  C    H26  single    0.930  0.020  1.080

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
 D9V  H1   O3   C10  105.36  3.000
 D9V  H3   C4   H2   106.08  3.000
 D9V  H3   C4   C2   107.28  3.000
 D9V  H2   C4   C2   110.14  3.000
 D9V  H3   C4   N    114.06  3.000
 D9V  H2   C4   N    107.46  3.000
 D9V  C2   C4   N    111.67  3.000
 D9V  H4   C5   N    106.73  3.000
 D9V  H4   C5   C10  107.14  3.000
 D9V  N    C5   C10  107.36  3.000
 D9V  H4   C5   C6   108.62  3.000
 D9V  C10  C5   C6   110.33  3.000
 D9V  N    C5   C6   116.25  3.000
 D9V  H5   C6   O2   108.79  3.000
 D9V  H5   C6   C7   113.33  3.000
 D9V  O2   C6   C7    99.90  3.000
 D9V  H5   C6   C5   112.17  3.000
 D9V  O2   C6   C5   109.70  3.000
 D9V  C7   C6   C5   112.19  3.000
 D9V  C15  N1   C11  112.30  3.000
 D9V  C15  N1   C9   115.58  3.000
 D9V  C11  N1   C9   117.45  3.000
 D9V  H8   C7   H7   108.52  3.000
 D9V  H8   C7   O1   110.76  3.000
 D9V  H7   C7   O1   110.41  3.000
 D9V  H8   C7   C6   111.65  3.000
 D9V  H7   C7   C6   113.22  3.000
 D9V  O1   C7   C6   102.20  3.000
 D9V  H9   C8   O2   109.42  3.000
 D9V  H9   C8   O1   109.66  3.000
 D9V  O2   C8   O1   105.25  3.000
 D9V  H9   C8   C9   110.30  3.000
 D9V  O2   C8   C9   110.96  3.000
 D9V  O1   C8   C9   111.12  3.000
 D9V  H10  C9   C10  108.22  3.000
 D9V  H10  C9   C8   107.35  3.000
 D9V  C10  C9   C8   107.86  3.000
 D9V  H10  C9   N1   106.53  3.000
 D9V  C10  C9   N1   116.29  3.000
 D9V  C8   C9   N1   110.25  3.000
 D9V  H11  C10  C9   107.95  3.000
 D9V  H11  C10  C5   107.16  3.000
 D9V  C9   C10  C5   111.42  3.000
 D9V  H11  C10  O3   109.88  3.000
 D9V  C5   C10  O3   109.61  3.000
 D9V  C9   C10  O3   110.74  3.000
 D9V  H13  C11  H12  105.65  3.000
 D9V  H13  C11  C12  109.74  3.000
 D9V  H12  C11  C12  110.28  3.000
 D9V  H13  C11  N1   109.90  3.000
 D9V  H12  C11  N1   112.15  3.000
 D9V  C12  C11  N1   109.07  3.000
 D9V  H15  C12  H14  106.62  3.000
 D9V  H15  C12  C13  109.90  3.000
 D9V  H14  C12  C13  110.46  3.000
 D9V  H15  C12  C11  109.82  3.000
 D9V  H14  C12  C11  109.17  3.000
 D9V  C13  C12  C11  110.79  3.000
 D9V  H17  C13  H16  106.36  3.000
 D9V  H17  C13  C14  109.36  3.000
 D9V  H16  C13  C14  110.58  3.000
 D9V  H17  C13  C12  110.25  3.000
 D9V  H16  C13  C12  110.44  3.000
 D9V  C14  C13  C12  109.79  3.000
 D9V  H19  C14  H18  106.15  3.000
 D9V  H19  C14  C15  109.99  3.000
 D9V  H18  C14  C15  109.44  3.000
 D9V  H19  C14  C13  108.95  3.000
 D9V  H18  C14  C13  111.29  3.000
 D9V  C15  C14  C13  110.91  3.000
 D9V  H21  C15  H20  106.77  3.000
 D9V  H21  C15  C14  108.88  3.000
 D9V  H20  C15  C14  109.89  3.000
 D9V  H21  C15  N1   112.97  3.000
 D9V  H20  C15  N1   107.87  3.000
 D9V  C14  C15  N1   110.37  3.000
 D9V  C8   O1   C7   107.63  3.000
 D9V  C8   O2   C6   101.74  3.000
 D9V  H22  N    C5   110.52  3.000
 D9V  H22  N    C4   109.52  3.000
 D9V  C5   N    C4   115.33  3.000
 D9V  O    C2   C1   109.69  3.000
 D9V  O    C2   C4   117.89  3.000
 D9V  C1   C2   C4   132.42  3.000
 D9V  H24  C1   C    127.50  3.000
 D9V  H24  C1   C2   126.06  3.000
 D9V  C    C1   C2   106.44  3.000
 D9V  C3   O    C2   107.75  3.000
 D9V  H25  C3   C    132.99  3.000
 D9V  H25  C3   O    116.70  3.000
 D9V  C    C3   O    110.31  3.000
 D9V  H26  C    C3   126.56  3.000
 D9V  H26  C    C1   127.63  3.000
 D9V  C3   C    C1   105.81  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
 D9V  CONST_01  C3   C    C1   C2     0.00   0.0  0
 D9V  CONST_02  C    C3   O    C2     0.00   0.0  0
 D9V  CONST_03  O    C3   C    C1     0.00   0.0  0
 D9V  CONST_04  C3   O    C2   C1     0.00   0.0  0
 D9V  CONST_05  C    C1   C2   O      0.00   0.0  0
 D9V  CONST_06  C    C1   C2   C4   180.00   0.0  0
 D9V  CONST_07  C3   O    C2   C4   180.00   0.0  0
 D9V  CONST_08  H26  C    C1   C2   180.00   0.0  0
 D9V  CONST_09  H25  C3   O    C2   180.00   0.0  0
 D9V  CONST_10  H24  C1   C2   O    180.00   0.0  0
 D9V  Var_01    C13  C12  C11  N1    31.82  30.0  1
 D9V  Var_02    C13  C14  C15  N1    27.05  30.0  1
 D9V  Var_03    C12  C11  N1   C9   151.00  30.0  1
 D9V  Var_04    C14  C15  N1   C9   177.12  30.0  1
 D9V  Var_05    C14  C13  C12  C11   30.61  30.0  1
 D9V  Var_06    C15  C14  C13  C12  -62.44  30.0  1
 D9V  Var_07    H7   C7   O1   C8   131.63  30.0  3
 D9V  Var_08    C2   C4   N    C5   -69.56  30.0  2
 D9V  Var_09    C1   C2   C4   N    121.71  30.0  2

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
 D9V  chir_01  C5   C6  N    C10  negativ
 D9V  chir_02  C6   O2  C5   C7   negativ
 D9V  chir_03  C8   O1  O2   C9   positiv
 D9V  chir_04  C9   N1  C10  C8   positiv
 D9V  chir_05  C10  O3  C9   C5   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
 D9V  plan-1  C4   0.020
 D9V  plan-1  C2   0.020
 D9V  plan-1  C1   0.020
 D9V  plan-1  O    0.020
 D9V  plan-1  C3   0.020
 D9V  plan-1  C    0.020
 D9V  plan-1  H24  0.020
 D9V  plan-1  H25  0.020
 D9V  plan-1  H26  0.020

