# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:18:20 2021
#   Inital geometry file: a 77 line input string
#   Ligand name: (1S,2S,3S,4R,5R)-2-amino-4-(phenylsulfanyl)-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]2CO[C@H](O2)[C@H](Sc3ccccc3)[C@H]1O
#
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
 D5V  D5V  '(1S,2S,3S,4R,5R)-2-amino-4-(phenylsulfanyl)-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)'  ligand  32  17  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_D5V
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
 D5V  C4   C  CR16  0  -0.254  -4.6853   1.0574  11.3826
 D5V  C5   C  CR16  0  -0.245  -5.5860   0.0965  10.9391
 D5V  C6   C  CH1   0  -0.477  -1.5362   2.9001  10.1354
 D5V  C7   C  CH1   0   0.092  -0.0150   3.0156  10.2822
 D5V  C8   C  CH1   0  -0.102   0.5753   3.9064   9.1912
 D5V  C9   C  CR15  0  -0.101  -0.3202   5.1537   9.0224
 D5V  C10  C  CH2   0  -0.171  -1.3102   5.0350   7.8651
 D5V  C11  C  CR15  0   0.301  -2.1550   4.2846   9.8404
 D5V  O2   O  OH1   0  -0.664   0.6079   1.7573  10.2166
 D5V  N    N  NH2   0  -0.810   1.9177   4.3093   9.5781
 D5V  O1   O  O     0  -0.480  -1.2154   5.2797  10.1233
 D5V  O    O  O     0  -0.501  -2.4390   4.4140   8.4686
 D5V  S    S  S2    0   0.013  -2.1895   2.1475  11.6693
 D5V  C3   C  CR6   0  -0.114  -3.3415   0.9574  11.0392
 D5V  C2   C  CR16  0  -0.228  -2.9017  -0.1052  10.2527
 D5V  C1   C  CR16  0  -0.244  -3.8084  -1.0490   9.7956
 D5V  C    C  CR16  0  -0.256  -5.1515  -0.9530  10.1422
 D5V  H1   H  HCR6  0   0.267  -5.0286   1.8861  11.9882
 D5V  H2   H  HCR6  0   0.263  -6.6304   0.1769  11.2109
 D5V  H3   H  HCH1  0   0.309  -1.7710   2.2125   9.3199
 D5V  H4   H  HCH1  0   0.223   0.2057   3.5019  11.2426
 D5V  H5   H  HCH1  0   0.232   0.5583   3.3369   8.2490
 D5V  H6   H  HCR5  0   0.274   0.2874   6.0572   8.9633
 D5V  H7   H  HCH2  0   0.235  -0.9299   4.4277   7.0412
 D5V  H8   H  HCH2  0   0.238  -1.5897   6.0165   7.4733
 D5V  H9   H  HCR5  0   0.260  -3.0628   4.4627  10.4211
 D5V  H10  H  HOH1  0   0.450   0.3303   1.2525  10.9897
 D5V  H11  H  HNH2  0   0.350   2.4972   3.4864   9.6921
 D5V  H12  H  HNH2  0   0.351   2.3401   4.8332   8.8209
 D5V  H14  H  HCR6  0   0.262  -1.8525  -0.1911   9.9971
 D5V  H15  H  HCR6  0   0.263  -3.4630  -1.8691   9.1798
 D5V  H16  H  HCR6  0   0.263  -5.8558  -1.6960   9.7918

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
 D5V  C10  O    single    1.423  0.020  1.423
 D5V  C10  C9   single    1.528  0.020  1.528
 D5V  O    C11  single    1.407  0.020  1.407
 D5V  C9   C8   single    1.545  0.020  1.545
 D5V  C9   O1   single    1.425  0.020  1.425
 D5V  C8   N    single    1.454  0.020  1.454
 D5V  C8   C7   single    1.527  0.020  1.527
 D5V  C1   C    aromatic  1.390  0.020  1.390
 D5V  C1   C2   aromatic  1.386  0.020  1.386
 D5V  C    C5   aromatic  1.388  0.020  1.388
 D5V  C11  O1   single    1.398  0.020  1.398
 D5V  C11  C6   single    1.545  0.020  1.545
 D5V  O2   C7   single    1.406  0.020  1.406
 D5V  C6   C7   single    1.533  0.020  1.533
 D5V  C6   S    single    1.829  0.020  1.829
 D5V  C2   C3   aromatic  1.393  0.020  1.393
 D5V  C5   C4   aromatic  1.390  0.020  1.390
 D5V  C3   C4   aromatic  1.391  0.020  1.391
 D5V  C3   S    single    1.772  0.020  1.772
 D5V  C4   H1   single    0.930  0.020  1.080
 D5V  C5   H2   single    0.930  0.020  1.080
 D5V  C6   H3   single    0.970  0.020  1.090
 D5V  C7   H4   single    0.970  0.020  1.090
 D5V  C8   H5   single    0.970  0.020  1.090
 D5V  C9   H6   single    0.970  0.020  1.090
 D5V  C10  H7   single    0.970  0.020  1.090
 D5V  C10  H8   single    0.970  0.020  1.090
 D5V  C11  H9   single    0.970  0.020  1.090
 D5V  O2   H10  single    0.850  0.020  0.980
 D5V  N    H11  single    0.890  0.020  1.040
 D5V  N    H12  single    0.890  0.020  1.040
 D5V  C2   H14  single    0.930  0.020  1.080
 D5V  C1   H15  single    0.930  0.020  1.080
 D5V  C    H16  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
 D5V  H1   C4   C3   119.99  3.000
 D5V  H1   C4   C5   120.16  3.000
 D5V  C3   C4   C5   119.85  3.000
 D5V  H2   C5   C    120.18  3.000
 D5V  H2   C5   C4   119.60  3.000
 D5V  C    C5   C4   120.22  3.000
 D5V  H3   C6   S    106.88  3.000
 D5V  H3   C6   C11  109.60  3.000
 D5V  S    C6   C11  112.69  3.000
 D5V  H3   C6   C7   109.41  3.000
 D5V  S    C6   C7   107.76  3.000
 D5V  C11  C6   C7   110.39  3.000
 D5V  H4   C7   O2   110.36  3.000
 D5V  H4   C7   C8   106.77  3.000
 D5V  O2   C7   C8   108.51  3.000
 D5V  H4   C7   C6   108.45  3.000
 D5V  O2   C7   C6   111.59  3.000
 D5V  C8   C7   C6   111.05  3.000
 D5V  H5   C8   N    112.66  3.000
 D5V  H5   C8   C9   108.37  3.000
 D5V  N    C8   C9   109.91  3.000
 D5V  H5   C8   C7   107.68  3.000
 D5V  N    C8   C7   109.17  3.000
 D5V  C9   C8   C7   108.97  3.000
 D5V  H6   C9   O1   108.59  3.000
 D5V  H6   C9   C10  112.61  3.000
 D5V  O1   C9   C10  100.67  3.000
 D5V  H6   C9   C8   110.61  3.000
 D5V  O1   C9   C8   110.56  3.000
 D5V  C10  C9   C8   113.31  3.000
 D5V  H8   C10  H7   108.54  3.000
 D5V  H8   C10  O    109.94  3.000
 D5V  H7   C10  O    110.71  3.000
 D5V  H8   C10  C9   111.56  3.000
 D5V  H7   C10  C9   112.90  3.000
 D5V  O    C10  C9   103.10  3.000
 D5V  H9   C11  O    109.62  3.000
 D5V  H9   C11  O1   109.57  3.000
 D5V  O    C11  O1   105.52  3.000
 D5V  H9   C11  C6   112.18  3.000
 D5V  O1   C11  C6   109.28  3.000
 D5V  O    C11  C6   110.45  3.000
 D5V  H10  O2   C7   107.68  3.000
 D5V  H12  N    H11  105.41  3.000
 D5V  H12  N    C8   109.23  3.000
 D5V  H11  N    C8   109.46  3.000
 D5V  C11  O1   C9   101.72  3.000
 D5V  C11  O    C10  107.08  3.000
 D5V  C3   S    C6   102.14  3.000
 D5V  C2   C3   S    120.51  3.000
 D5V  S    C3   C4   119.48  3.000
 D5V  C2   C3   C4   119.96  3.000
 D5V  H14  C2   C1   120.11  3.000
 D5V  H14  C2   C3   119.96  3.000
 D5V  C1   C2   C3   119.92  3.000
 D5V  H15  C1   C    120.16  3.000
 D5V  H15  C1   C2   119.66  3.000
 D5V  C    C1   C2   120.17  3.000
 D5V  H16  C    C1   120.04  3.000
 D5V  H16  C    C5   120.10  3.000
 D5V  C1   C    C5   119.86  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
 D5V  CONST_01  C1   C    C5  C4     0.00   0.0  0
 D5V  CONST_02  C1   C2   C3  C4     0.00   0.0  0
 D5V  CONST_03  C2   C1   C   C5     0.00   0.0  0
 D5V  CONST_04  C2   C3   C4  C5     0.00   0.0  0
 D5V  CONST_05  C    C1   C2  C3     0.00   0.0  0
 D5V  CONST_06  C    C5   C4  C3     0.00   0.0  0
 D5V  CONST_07  S    C3   C4  C5   180.00   0.0  0
 D5V  CONST_08  C1   C2   C3  S    180.00   0.0  0
 D5V  CONST_09  H16  C    C5  C4   180.00   0.0  0
 D5V  CONST_10  H14  C2   C3  C4   180.00   0.0  0
 D5V  CONST_11  H15  C1   C   C5   180.00   0.0  0
 D5V  CONST_12  H2   C5   C4  C3   180.00   0.0  0
 D5V  CONST_13  H1   C4   C3  C2   180.00   0.0  0
 D5V  Var_01    C2   C3   S   C6    63.25  30.0  2
 D5V  Var_02    H7   C10  O   C11  124.81  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
 D5V  chir_01  C6   C11  C7  S    negativ
 D5V  chir_02  C7   O2   C6  C8   positiv
 D5V  chir_03  C8   N    C9  C7   positiv
 D5V  chir_04  C9   O1   C8  C10  negativ
 D5V  chir_05  C11  O    O1  C6   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
 D5V  plan-1  C4   0.020
 D5V  plan-1  C5   0.020
 D5V  plan-1  S    0.020
 D5V  plan-1  C3   0.020
 D5V  plan-1  C2   0.020
 D5V  plan-1  C1   0.020
 D5V  plan-1  C    0.020
 D5V  plan-1  H1   0.020
 D5V  plan-1  H2   0.020
 D5V  plan-1  H14  0.020
 D5V  plan-1  H15  0.020
 D5V  plan-1  H16  0.020

