# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:01:48 2021
#   Inital geometry file: a 109 line input string
#   Ligand name: (1S,2S,3S,4R,5R)-2-(benzylamino)-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: O[C@H]1[C@H](NCc2ccccc2)[C@H]3CO[C@H](O3)[C@@H]1Sc4ccccc4
#
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
 DD7  DD7  '(1S,2S,3S,4R,5R)-2-(benzylamino)-4-(phenylsulfanyl)-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)'  ligand  45  24  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DD7
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
 DD7  C4   C  CR16  0  -0.299  -5.3309  -0.1729   7.4282
 DD7  C5   C  CR16  0  -0.240  -5.8930  -1.4431   7.4261
 DD7  C6   C  CH2   0  -0.300  -4.5703   1.9202   6.2125
 DD7  C7   C  CH1   0  -0.089  -3.8565   3.7347   7.7375
 DD7  C8   C  CR15  0  -0.109  -3.8987   4.0647   9.2498
 DD7  C9   C  CH2   0  -0.166  -2.5174   4.2983   9.8555
 DD7  C10  C  CR15  0   0.302  -3.4845   6.2076   9.0723
 DD7  C11  C  CH1   0  -0.463  -3.4191   6.2287   7.5339
 DD7  C12  C  CH1   0   0.081  -4.1478   5.0143   6.9368
 DD7  C13  C  CR6   0  -0.119  -2.8861   8.8953   6.9537
 DD7  C14  C  CR16  0  -0.247  -2.9684   9.9312   7.8784
 DD7  C15  C  CR16  0  -0.245  -1.9472  10.8701   7.9588
 DD7  O2   O  OH1   0  -0.654  -3.7725   4.8054   5.6002
 DD7  N    N  NH1   0  -0.610  -4.7419   2.6250   7.4634
 DD7  C3   C  CR6   0   0.081  -5.2116   0.5528   6.2457
 DD7  C2   C  CR16  0  -0.309  -5.6723  -0.0222   5.0633
 DD7  C1   C  CR16  0  -0.242  -6.2289  -1.2941   5.0562
 DD7  C    C  CR16  0  -0.273  -6.3429  -2.0103   6.2408
 DD7  O    O  O     0  -0.503  -2.2939   5.6812   9.6097
 DD7  O1   O  O     0  -0.481  -4.4991   5.3364   9.4754
 DD7  S    S  S2    0   0.002  -4.2074   7.7197   6.8293
 DD7  C18  C  CR16  0  -0.227  -1.7832   8.8040   6.1076
 DD7  C17  C  CR16  0  -0.245  -0.7598   9.7348   6.2022
 DD7  C16  C  CR16  0  -0.254  -0.8417  10.7708   7.1258
 DD7  H1   H  HCR6  0   0.246  -4.9902   0.2668   8.3565
 DD7  H2   H  HCR6  0   0.250  -5.9826  -1.9917   8.3555
 DD7  H3   H  HCH2  0   0.240  -3.4953   1.7964   6.0451
 DD7  H4   H  HCH2  0   0.221  -4.9467   2.4607   5.3363
 DD7  H5   H  HCH1  0   0.253  -2.8445   3.4037   7.4767
 DD7  H6   H  HCR5  0   0.274  -4.4711   3.3052   9.7816
 DD7  H7   H  HCH2  0   0.237  -2.5146   4.1028  10.9314
 DD7  H8   H  HCH2  0   0.236  -1.7372   3.6927   9.3914
 DD7  H9   H  HCR5  0   0.255  -3.6679   7.2003   9.4904
 DD7  H10  H  HCH1  0   0.303  -2.3763   6.2226   7.2091
 DD7  H11  H  HCH1  0   0.222  -5.2308   5.1968   7.0104
 DD7  H12  H  HCR6  0   0.268  -3.8257  10.0020   8.5355
 DD7  H13  H  HCR6  0   0.264  -2.0150  11.6744   8.6794
 DD7  H14  H  HOH1  0   0.448  -4.0585   5.5687   5.0856
 DD7  H15  H  HNH1  0   0.348  -5.7101   2.8957   7.5903
 DD7  H17  H  HCR6  0   0.245  -5.5948   0.5334   4.1351
 DD7  H18  H  HCR6  0   0.252  -6.5797  -1.7224   4.1258
 DD7  H19  H  HCR6  0   0.252  -6.7843  -2.9989   6.2412
 DD7  H20  H  HCR6  0   0.268  -1.7268   8.0066   5.3770
 DD7  H21  H  HCR6  0   0.264   0.0981   9.6571   5.5473
 DD7  H22  H  HCR6  0   0.264  -0.0440  11.4986   7.1947

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
 DD7  O2   C12  single    1.404  0.020  1.404
 DD7  C2   C1   aromatic  1.388  0.020  1.388
 DD7  C2   C3   aromatic  1.393  0.020  1.393
 DD7  C1   C    aromatic  1.389  0.020  1.389
 DD7  S    C13  single    1.773  0.020  1.773
 DD7  S    C11  single    1.828  0.020  1.828
 DD7  C6   C3   single    1.511  0.020  1.511
 DD7  C6   N    single    1.446  0.020  1.446
 DD7  C3   C4   aromatic  1.392  0.020  1.392
 DD7  C    C5   aromatic  1.389  0.020  1.389
 DD7  C12  C11  single    1.537  0.020  1.537
 DD7  C12  C7   single    1.537  0.020  1.537
 DD7  C13  C14  aromatic  1.391  0.020  1.391
 DD7  C13  C18  aromatic  1.393  0.020  1.393
 DD7  C11  C10  single    1.540  0.020  1.540
 DD7  C14  C15  aromatic  1.390  0.020  1.390
 DD7  C4   C5   aromatic  1.389  0.020  1.389
 DD7  C18  C17  aromatic  1.387  0.020  1.387
 DD7  N    C7   single    1.446  0.020  1.446
 DD7  C7   C8   single    1.548  0.020  1.548
 DD7  C15  C16  aromatic  1.388  0.020  1.388
 DD7  C17  C16  aromatic  1.390  0.020  1.390
 DD7  C10  O    single    1.408  0.020  1.408
 DD7  C10  O1   single    1.397  0.020  1.397
 DD7  C8   O1   single    1.424  0.020  1.424
 DD7  C8   C9   single    1.526  0.020  1.526
 DD7  O    C9   single    1.422  0.020  1.422
 DD7  C4   H1   single    0.930  0.020  1.080
 DD7  C5   H2   single    0.930  0.020  1.080
 DD7  C6   H3   single    0.970  0.020  1.090
 DD7  C6   H4   single    0.970  0.020  1.090
 DD7  C7   H5   single    0.970  0.020  1.090
 DD7  C8   H6   single    0.970  0.020  1.090
 DD7  C9   H7   single    0.970  0.020  1.090
 DD7  C9   H8   single    0.970  0.020  1.090
 DD7  C10  H9   single    0.970  0.020  1.090
 DD7  C11  H10  single    0.970  0.020  1.090
 DD7  C12  H11  single    0.970  0.020  1.090
 DD7  C14  H12  single    0.930  0.020  1.080
 DD7  C15  H13  single    0.930  0.020  1.080
 DD7  O2   H14  single    0.850  0.020  0.980
 DD7  N    H15  single    0.890  0.020  1.040
 DD7  C2   H17  single    0.930  0.020  1.080
 DD7  C1   H18  single    0.930  0.020  1.080
 DD7  C    H19  single    0.930  0.020  1.080
 DD7  C18  H20  single    0.930  0.020  1.080
 DD7  C17  H21  single    0.930  0.020  1.080
 DD7  C16  H22  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
 DD7  H1   C4   C3   119.32  3.000
 DD7  H1   C4   C5   120.01  3.000
 DD7  C3   C4   C5   120.66  3.000
 DD7  H2   C5   C    119.92  3.000
 DD7  H2   C5   C4   119.70  3.000
 DD7  C    C5   C4   120.38  3.000
 DD7  H4   C6   H3   105.70  3.000
 DD7  H4   C6   C3   108.55  3.000
 DD7  H3   C6   C3   108.53  3.000
 DD7  H4   C6   N    114.23  3.000
 DD7  H3   C6   N    107.69  3.000
 DD7  C3   C6   N    111.82  3.000
 DD7  H5   C7   N    106.77  3.000
 DD7  H5   C7   C12  107.60  3.000
 DD7  N    C7   C12  115.09  3.000
 DD7  H5   C7   C8   108.78  3.000
 DD7  N    C7   C8   109.39  3.000
 DD7  C12  C7   C8   109.03  3.000
 DD7  H6   C8   O1   108.88  3.000
 DD7  H6   C8   C9   112.86  3.000
 DD7  O1   C8   C9   100.48  3.000
 DD7  H6   C8   C7   110.02  3.000
 DD7  C9   C8   C7   113.30  3.000
 DD7  O1   C8   C7   110.88  3.000
 DD7  H8   C9   H7   108.50  3.000
 DD7  H8   C9   O    110.72  3.000
 DD7  H7   C9   O    110.09  3.000
 DD7  H8   C9   C8   113.16  3.000
 DD7  H7   C9   C8   111.43  3.000
 DD7  O    C9   C8   102.85  3.000
 DD7  H9   C10  O1   109.53  3.000
 DD7  H9   C10  O    109.60  3.000
 DD7  O1   C10  O    105.72  3.000
 DD7  H9   C10  C11  112.14  3.000
 DD7  O1   C10  C11  109.13  3.000
 DD7  O    C10  C11  110.51  3.000
 DD7  H10  C11  S    107.56  3.000
 DD7  H10  C11  C12  109.43  3.000
 DD7  S    C11  C12  106.88  3.000
 DD7  H10  C11  C10  109.73  3.000
 DD7  C12  C11  C10  110.92  3.000
 DD7  S    C11  C10  112.21  3.000
 DD7  H11  C12  O2   110.57  3.000
 DD7  H11  C12  C11  108.03  3.000
 DD7  O2   C12  C11  111.14  3.000
 DD7  H11  C12  C7   106.84  3.000
 DD7  C11  C12  C7   111.44  3.000
 DD7  O2   C12  C7   108.75  3.000
 DD7  C18  C13  S    120.26  3.000
 DD7  C18  C13  C14  119.96  3.000
 DD7  S    C13  C14  119.76  3.000
 DD7  H12  C14  C15  120.18  3.000
 DD7  H12  C14  C13  119.94  3.000
 DD7  C15  C14  C13  119.88  3.000
 DD7  H13  C15  C16  120.19  3.000
 DD7  H13  C15  C14  119.65  3.000
 DD7  C16  C15  C14  120.16  3.000
 DD7  H14  O2   C12  108.13  3.000
 DD7  H15  N    C7   110.87  3.000
 DD7  H15  N    C6   110.61  3.000
 DD7  C7   N    C6   117.73  3.000
 DD7  C2   C3   C6   119.68  3.000
 DD7  C6   C3   C4   121.79  3.000
 DD7  C2   C3   C4   118.51  3.000
 DD7  H17  C2   C1   119.57  3.000
 DD7  H17  C2   C3   119.43  3.000
 DD7  C1   C2   C3   121.00  3.000
 DD7  H18  C1   C    120.15  3.000
 DD7  H18  C1   C2   119.78  3.000
 DD7  C    C1   C2   120.06  3.000
 DD7  H19  C    C1   120.31  3.000
 DD7  H19  C    C5   120.31  3.000
 DD7  C1   C    C5   119.38  3.000
 DD7  C10  O    C9   107.25  3.000
 DD7  C10  O1   C8   101.83  3.000
 DD7  C13  S    C11  101.09  3.000
 DD7  H20  C18  C17  120.12  3.000
 DD7  H20  C18  C13  119.95  3.000
 DD7  C17  C18  C13  119.92  3.000
 DD7  H21  C17  C16  120.15  3.000
 DD7  H21  C17  C18  119.71  3.000
 DD7  C16  C17  C18  120.14  3.000
 DD7  H22  C16  C17  120.01  3.000
 DD7  H22  C16  C15  120.06  3.000
 DD7  C17  C16  C15  119.93  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
 DD7  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 DD7  CONST_02  C1   C    C5   C4      0.00   0.0  0
 DD7  CONST_03  C2   C1   C    C5      0.00   0.0  0
 DD7  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 DD7  CONST_05  C16  C15  C14  C13     0.00   0.0  0
 DD7  CONST_06  C16  C17  C18  C13     0.00   0.0  0
 DD7  CONST_07  C17  C18  C13  C14     0.00   0.0  0
 DD7  CONST_08  C17  C16  C15  C14     0.00   0.0  0
 DD7  CONST_09  C18  C13  C14  C15     0.00   0.0  0
 DD7  CONST_10  C18  C17  C16  C15     0.00   0.0  0
 DD7  CONST_11  C    C1   C2   C3      0.00   0.0  0
 DD7  CONST_12  C    C5   C4   C3      0.00   0.0  0
 DD7  CONST_13  C6   C3   C4   C5    180.00   0.0  0
 DD7  CONST_14  C1   C2   C3   C6    180.00   0.0  0
 DD7  CONST_15  S    C13  C14  C15   180.00   0.0  0
 DD7  CONST_16  C17  C18  C13  S     180.00   0.0  0
 DD7  CONST_17  H17  C2   C3   C4    180.00   0.0  0
 DD7  CONST_18  H19  C    C5   C4    180.00   0.0  0
 DD7  CONST_19  H18  C1   C    C5    180.00   0.0  0
 DD7  CONST_20  H13  C15  C14  C13   180.00   0.0  0
 DD7  CONST_21  H21  C17  C18  C13   180.00   0.0  0
 DD7  CONST_22  H20  C18  C13  C14   180.00   0.0  0
 DD7  CONST_23  H22  C16  C15  C14   180.00   0.0  0
 DD7  CONST_24  H2   C5   C4   C3    180.00   0.0  0
 DD7  CONST_25  H1   C4   C3   C2    180.00   0.0  0
 DD7  CONST_26  H12  C14  C13  C18   180.00   0.0  0
 DD7  Var_01    C14  C13  S    C11  -109.28  30.0  2
 DD7  Var_02    H7   C9   O    C10  -112.45  30.0  3
 DD7  Var_03    N    C6   C3   C4    -29.53  30.0  3
 DD7  Var_04    C3   C6   N    C7    161.13  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
 DD7  chir_01  C7   C12  N    C8   positiv
 DD7  chir_02  C8   O1   C7   C9   negativ
 DD7  chir_03  C10  O    O1   C11  positiv
 DD7  chir_04  C11  S    C12  C10  positiv
 DD7  chir_05  C12  O2   C11  C7   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
 DD7  plan-1  C13  0.020
 DD7  plan-1  C14  0.020
 DD7  plan-1  C15  0.020
 DD7  plan-1  S    0.020
 DD7  plan-1  C18  0.020
 DD7  plan-1  C17  0.020
 DD7  plan-1  C16  0.020
 DD7  plan-1  H12  0.020
 DD7  plan-1  H13  0.020
 DD7  plan-1  H20  0.020
 DD7  plan-1  H21  0.020
 DD7  plan-1  H22  0.020
 DD7  plan-2  C4   0.020
 DD7  plan-2  C5   0.020
 DD7  plan-2  C6   0.020
 DD7  plan-2  C3   0.020
 DD7  plan-2  C2   0.020
 DD7  plan-2  C1   0.020
 DD7  plan-2  C    0.020
 DD7  plan-2  H1   0.020
 DD7  plan-2  H2   0.020
 DD7  plan-2  H17  0.020
 DD7  plan-2  H18  0.020
 DD7  plan-2  H19  0.020

