# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:04:14 2021
#   Inital geometry file: a 81 line input string
#   Ligand name: (1S,2S,3S,4R,5R)-2-amino-4-[(2S)-2-(hydroxymethyl)pyrrolidin-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: N[C@H]1[C@H](O)[C@H]([C@@H]2OC[C@H]1O2)N3CCC[C@H]3CO
#
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
 D6D  D6D  '(1S,2S,3S,4R,5R)-2-amino-4-[(2S)-2-(hydroxymethyl)pyrrolidin-1-yl]-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)'  ligand  37  17  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_D6D
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
 D6D  O3   O  OH1   0  -0.669  -4.9329   2.6106   7.4564
 D6D  C4   C  CH1   0  -0.167  -3.0859   1.8955  10.4046
 D6D  C5   C  CH1   0   0.084  -2.4745   2.8143   9.3384
 D6D  C6   C  CH1   0  -0.110  -1.0308   3.1764   9.6995
 D6D  N1   N  NH2   0  -0.792  -0.3728   3.7412   8.5364
 D6D  C7   C  CH1   0  -0.110  -0.3434   1.9230  10.2905
 D6D  C8   C  CH2   0  -0.190  -0.4891   1.7849  11.8211
 D6D  C9   C  CH1   0   0.231  -2.1111   0.7166  10.7006
 D6D  C10  C  CH2   0  -0.111  -5.5573   1.4143   7.8770
 D6D  C2   C  CH1   0  -0.141  -4.6875   0.6829   8.8924
 D6D  C1   C  CH2   0  -0.471  -5.4341  -0.5533   9.4060
 D6D  N    N  NT    0  -0.440  -4.4406   1.4989  10.0864
 D6D  C3   C  CH2   0  -0.270  -5.1607   0.9358  11.2288
 D6D  C    C  CH2   0  -0.479  -6.1785  -0.0199  10.6256
 D6D  O    O  O2    0  -0.499  -1.5386   0.8402  11.9789
 D6D  O1   O  O2    0  -0.484  -1.0118   0.7550   9.8308
 D6D  O2   O  OH1   0  -0.694  -3.2311   3.9814   9.1760
 D6D  H1   H  HOH1  0   0.466  -5.5324   3.0805   6.8689
 D6D  H2   H  HCH1  0   0.252  -3.1657   2.4935  11.3210
 D6D  H3   H  HCH1  0   0.196  -2.4323   2.2563   8.3915
 D6D  H4   H  HCH1  0   0.237  -1.0501   3.9529  10.4728
 D6D  H5   H  HNH2  0   0.348   0.5695   4.0231   8.7779
 D6D  H6   H  HNH2  0   0.339  -0.2767   3.0341   7.8162
 D6D  H8   H  HCH1  0   0.262   0.7010   1.8770   9.9767
 D6D  H9   H  HCH2  0   0.245   0.4180   1.3956  12.2869
 D6D  H10  H  HCH2  0   0.225  -0.7358   2.7393  12.2962
 D6D  H11  H  HCH1  0   0.254  -2.5969  -0.2601  10.6204
 D6D  H12  H  HCH2  0   0.196  -6.5367   1.6224   8.3254
 D6D  H13  H  HCH2  0   0.199  -5.7244   0.7494   7.0211
 D6D  H14  H  HCH1  0   0.242  -3.7500   0.3956   8.4026
 D6D  H15  H  HCH2  0   0.244  -6.0906  -1.0004   8.6571
 D6D  H16  H  HCH2  0   0.242  -4.7201  -1.3228   9.7090
 D6D  H18  H  HCH2  0   0.206  -4.4924   0.3774  11.8996
 D6D  H19  H  HCH2  0   0.232  -5.6217   1.7240  11.8303
 D6D  H20  H  HCH2  0   0.232  -7.0846   0.5103  10.3254
 D6D  H21  H  HCH2  0   0.247  -6.4730  -0.8029  11.3240
 D6D  H22  H  HOH1  0   0.448  -4.0254   3.7000   8.6928

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
 D6D  O3   C10  single  1.413  0.020  1.413
 D6D  C10  C2   single  1.524  0.020  1.524
 D6D  N1   C6   single  1.451  0.020  1.451
 D6D  C2   C1   single  1.533  0.020  1.533
 D6D  C2   N    single  1.467  0.020  1.467
 D6D  C5   O2   single  1.400  0.020  1.400
 D6D  C5   C6   single  1.532  0.020  1.532
 D6D  C5   C4   single  1.534  0.020  1.534
 D6D  C1   C    single  1.525  0.020  1.525
 D6D  O1   C7   single  1.422  0.020  1.422
 D6D  O1   C9   single  1.402  0.020  1.402
 D6D  C6   C7   single  1.547  0.020  1.547
 D6D  N    C4   single  1.447  0.020  1.447
 D6D  N    C3   single  1.463  0.020  1.463
 D6D  C7   C8   single  1.544  0.020  1.544
 D6D  C4   C9   single  1.558  0.020  1.558
 D6D  C    C3   single  1.521  0.020  1.521
 D6D  C9   O    single  1.406  0.020  1.406
 D6D  C8   O    single  1.421  0.020  1.421
 D6D  O3   H1   single  0.850  0.020  0.980
 D6D  C4   H2   single  0.970  0.020  1.090
 D6D  C5   H3   single  0.970  0.020  1.090
 D6D  C6   H4   single  0.970  0.020  1.090
 D6D  N1   H5   single  0.890  0.020  1.040
 D6D  N1   H6   single  0.890  0.020  1.040
 D6D  C7   H8   single  0.970  0.020  1.090
 D6D  C8   H9   single  0.970  0.020  1.090
 D6D  C8   H10  single  0.970  0.020  1.090
 D6D  C9   H11  single  0.970  0.020  1.090
 D6D  C10  H12  single  0.970  0.020  1.090
 D6D  C10  H13  single  0.970  0.020  1.090
 D6D  C2   H14  single  0.970  0.020  1.090
 D6D  C1   H15  single  0.970  0.020  1.090
 D6D  C1   H16  single  0.970  0.020  1.090
 D6D  C3   H18  single  0.970  0.020  1.090
 D6D  C3   H19  single  0.970  0.020  1.090
 D6D  C    H20  single  0.970  0.020  1.090
 D6D  C    H21  single  0.970  0.020  1.090
 D6D  O2   H22  single  0.850  0.020  0.980

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
 D6D  H1   O3   C10  108.66  3.000
 D6D  H2   C4   N    105.37  3.000
 D6D  H2   C4   C9   107.41  3.000
 D6D  N    C4   C9   114.84  3.000
 D6D  H2   C4   C5   106.44  3.000
 D6D  C9   C4   C5   109.62  3.000
 D6D  N    C4   C5   112.60  3.000
 D6D  H3   C5   O2   110.10  3.000
 D6D  H3   C5   C6   106.66  3.000
 D6D  O2   C5   C6   109.85  3.000
 D6D  H3   C5   C4   108.05  3.000
 D6D  C6   C5   C4   110.69  3.000
 D6D  O2   C5   C4   111.37  3.000
 D6D  H4   C6   C7   108.20  3.000
 D6D  H4   C6   N1   107.32  3.000
 D6D  C7   C6   N1   114.85  3.000
 D6D  H4   C6   C5   108.49  3.000
 D6D  C7   C6   C5   108.51  3.000
 D6D  N1   C6   C5   109.31  3.000
 D6D  H6   N1   H5   105.99  3.000
 D6D  H6   N1   C6   109.93  3.000
 D6D  H5   N1   C6   109.83  3.000
 D6D  H8   C7   O1   108.79  3.000
 D6D  H8   C7   C8   111.82  3.000
 D6D  O1   C7   C8   101.69  3.000
 D6D  H8   C7   C6   110.46  3.000
 D6D  C8   C7   C6   114.17  3.000
 D6D  O1   C7   C6   109.46  3.000
 D6D  H10  C8   H9   108.25  3.000
 D6D  H10  C8   O    111.42  3.000
 D6D  H9   C8   O    109.22  3.000
 D6D  H10  C8   C7   111.95  3.000
 D6D  H9   C8   C7   112.13  3.000
 D6D  O    C8   C7   103.85  3.000
 D6D  H11  C9   O1   109.09  3.000
 D6D  H11  C9   O    109.02  3.000
 D6D  O1   C9   O    104.02  3.000
 D6D  H11  C9   C4   112.57  3.000
 D6D  O    C9   C4   111.16  3.000
 D6D  O1   C9   C4   110.60  3.000
 D6D  H13  C10  H12  107.33  3.000
 D6D  H13  C10  C2   108.42  3.000
 D6D  H12  C10  C2   109.16  3.000
 D6D  H13  C10  O3   110.38  3.000
 D6D  H12  C10  O3   110.82  3.000
 D6D  C2   C10  O3   110.63  3.000
 D6D  H14  C2   N    111.44  3.000
 D6D  H14  C2   C1   110.79  3.000
 D6D  N    C2   C1   104.94  3.000
 D6D  H14  C2   C10  108.43  3.000
 D6D  N    C2   C10  111.80  3.000
 D6D  C1   C2   C10  109.41  3.000
 D6D  H16  C1   H15  107.15  3.000
 D6D  H16  C1   C    110.09  3.000
 D6D  H15  C1   C    113.47  3.000
 D6D  H16  C1   C2   110.04  3.000
 D6D  H15  C1   C2   113.16  3.000
 D6D  C    C1   C2   102.92  3.000
 D6D  C3   N    C2   109.78  3.000
 D6D  C3   N    C4   113.24  3.000
 D6D  C2   N    C4   119.28  3.000
 D6D  H19  C3   H18  106.66  3.000
 D6D  H19  C3   C    112.89  3.000
 D6D  H18  C3   C    109.25  3.000
 D6D  H19  C3   N    111.08  3.000
 D6D  H18  C3   N    111.89  3.000
 D6D  C    C3   N    105.17  3.000
 D6D  H21  C    H20  107.51  3.000
 D6D  H21  C    C3   112.22  3.000
 D6D  H20  C    C3   111.06  3.000
 D6D  H21  C    C1   113.14  3.000
 D6D  H20  C    C1   110.79  3.000
 D6D  C3   C    C1   102.14  3.000
 D6D  C9   O    C8   104.96  3.000
 D6D  C9   O1   C7   100.98  3.000
 D6D  H22  O2   C5   104.96  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
 D6D  Var_01  C   C3  N   C4  -151.96  30.0  1
 D6D  Var_02  C3  C   C1  C2   -38.39  30.0  1
 D6D  Var_03  N   C3  C   C1    33.71  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
 D6D  chir_01  C4  C5  N   C9   negativ
 D6D  chir_02  C5  O2  C4  C6   positiv
 D6D  chir_03  C6  N1  C7  C5   positiv
 D6D  chir_04  C7  O1  C6  C8   negativ
 D6D  chir_05  C9  O   O1  C4   positiv
 D6D  chir_06  C2  N   C1  C10  negativ

