# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 01:43:59 2021
#   Inital geometry file: a 91 line input string
#   Ligand name: (1S,2S,3S,4R,5R)-2-amino-4-[benzyl(methyl)amino]-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1ccccc1)[C@@H]2[C@@H](O)[C@H](N)[C@H]3CO[C@@H]2O3
#
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
 D6S  D6S  '(1S,2S,3S,4R,5R)-2-amino-4-[benzyl(methyl)amino]-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)'  ligand  39  19  .  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_D6S
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
 D6S  C4   C  CR16  0  -0.242  -6.1699   0.0130  10.9863
 D6S  C5   C  CR16  0  -0.272  -6.1492  -1.2942  11.4609
 D6S  C6   C  CR16  0  -0.241  -4.9470  -1.9850  11.5079
 D6S  N1   N  NH2   0  -0.813   1.8601   4.1527   9.4331
 D6S  C7   C  CR16  0  -0.318  -3.7748  -1.3719  11.0793
 D6S  C8   C  CH1   0  -0.141  -1.6804   2.8482   9.6335
 D6S  C9   C  CH1   0   0.049  -0.1504   2.8253   9.7624
 D6S  C10  C  CH1   0  -0.096   0.4904   3.9708   8.9777
 D6S  C11  C  CH1   0  -0.098  -0.3200   5.2629   9.2099
 D6S  C12  C  CH2   0  -0.172  -1.3534   5.5418   8.1140
 D6S  C13  C  CH1   0   0.250  -2.1833   4.3022   9.8252
 D6S  O2   O  OH1   0  -0.670   0.3873   1.6031   9.2936
 D6S  O1   O  O2    0  -0.485  -1.1663   5.1131  10.3437
 D6S  O    O  O2    0  -0.504  -2.5252   4.8951   8.5941
 D6S  N    N  NT    0  -0.421  -2.3995   1.9491  10.5158
 D6S  C    C  CH3   0  -0.540  -2.0846   2.0588  11.9217
 D6S  C2   C  CR6   0   0.100  -3.7873  -0.0688  10.5951
 D6S  C3   C  CR16  0  -0.284  -4.9980   0.6201  10.5594
 D6S  H1   H  HCR6  0   0.251  -7.1038   0.5597  10.9461
 D6S  H2   H  HCR6  0   0.252  -7.0641  -1.7673  11.7937
 D6S  H3   H  HCR6  0   0.252  -4.9170  -2.9997  11.8843
 D6S  H5   H  HNH2  0   0.348   2.3201   4.8388   8.8465
 D6S  H7   H  HCR6  0   0.246  -2.8380  -1.9156  11.1286
 D6S  H8   H  HCH1  0   0.256  -1.9333   2.5447   8.6124
 D6S  H9   H  HCH1  0   0.224   0.1243   2.9758  10.8132
 D6S  H10  H  HCH1  0   0.223   0.4366   3.7151   7.9076
 D6S  H11  H  HCH1  0   0.267   0.3451   6.1112   9.3774
 D6S  H12  H  HCH2  0   0.229  -1.0556   5.1435   7.1418
 D6S  H13  H  HCH2  0   0.235  -1.5432   6.6124   8.0034
 D6S  H14  H  HCH1  0   0.254  -3.0514   4.3285  10.4887
 D6S  H15  H  HOH1  0   0.453   0.5521   1.0249  10.0424
 D6S  H17  H  HCH3  0   0.245  -2.8602   1.5706  12.5135
 D6S  H18  H  HCH3  0   0.199  -1.1252   1.5999  12.2017
 D6S  H19  H  HCH3  0   0.241  -2.0531   3.1027  12.2357
 D6S  H22  H  HCR6  0   0.246  -5.0130   1.6430  10.2034
 D6S  C1   C  CH2   0  -0.327  -2.5222   0.5768  10.0800
 D6S  H4   H  HNH2  0   0.346   2.3719   3.2906   9.2873
 D6S  H20  H  HCH2  0   0.207  -1.6658  -0.0506  10.3725
 D6S  H21  H  HCH2  0   0.251  -2.5482   0.5629   8.9870

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
 D6S  C12  O    single    1.422  0.020  1.422
 D6S  C12  C11  single    1.532  0.020  1.532
 D6S  O    C13  single    1.409  0.020  1.409
 D6S  C10  C11  single    1.543  0.020  1.543
 D6S  C10  N1   single    1.455  0.020  1.455
 D6S  C10  C9   single    1.529  0.020  1.529
 D6S  C11  O1   single    1.423  0.020  1.423
 D6S  C8   C13  single    1.550  0.020  1.550
 D6S  C8   C9   single    1.536  0.020  1.536
 D6S  C8   N    single    1.450  0.020  1.450
 D6S  C13  O1   single    1.400  0.020  1.400
 D6S  O2   C9   single    1.415  0.020  1.415
 D6S  C1   C2   single    1.511  0.020  1.511
 D6S  C1   N    single    1.445  0.020  1.445
 D6S  C2   C3   aromatic  1.393  0.020  1.393
 D6S  C2   C7   aromatic  1.390  0.020  1.390
 D6S  N    C    single    1.445  0.020  1.445
 D6S  C3   C4   aromatic  1.387  0.020  1.387
 D6S  C7   C6   aromatic  1.390  0.020  1.390
 D6S  C4   C5   aromatic  1.391  0.020  1.391
 D6S  C6   C5   aromatic  1.387  0.020  1.387
 D6S  C4   H1   single    0.930  0.020  1.080
 D6S  C5   H2   single    0.930  0.020  1.080
 D6S  C6   H3   single    0.930  0.020  1.080
 D6S  N1   H4   single    0.890  0.020  1.040
 D6S  N1   H5   single    0.890  0.020  1.040
 D6S  C7   H7   single    0.930  0.020  1.080
 D6S  C8   H8   single    0.970  0.020  1.090
 D6S  C9   H9   single    0.970  0.020  1.090
 D6S  C10  H10  single    0.970  0.020  1.090
 D6S  C11  H11  single    0.970  0.020  1.090
 D6S  C12  H12  single    0.970  0.020  1.090
 D6S  C12  H13  single    0.970  0.020  1.090
 D6S  C13  H14  single    0.970  0.020  1.090
 D6S  O2   H15  single    0.850  0.020  0.980
 D6S  C    H17  single    0.970  0.020  1.090
 D6S  C    H18  single    0.970  0.020  1.090
 D6S  C    H19  single    0.970  0.020  1.090
 D6S  C1   H20  single    0.970  0.020  1.090
 D6S  C1   H21  single    0.970  0.020  1.090
 D6S  C3   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
 D6S  H1   C4   C3   119.75  3.000
 D6S  H1   C4   C5   120.00  3.000
 D6S  C3   C4   C5   120.25  3.000
 D6S  H2   C5   C6   120.29  3.000
 D6S  H2   C5   C4   120.21  3.000
 D6S  C6   C5   C4   119.50  3.000
 D6S  H3   C6   C7   119.81  3.000
 D6S  H3   C6   C5   120.16  3.000
 D6S  C7   C6   C5   120.03  3.000
 D6S  H5   N1   H4   105.28  3.000
 D6S  H5   N1   C10  109.33  3.000
 D6S  H4   N1   C10  108.91  3.000
 D6S  H7   C7   C2   119.58  3.000
 D6S  H7   C7   C6   119.56  3.000
 D6S  C2   C7   C6   120.87  3.000
 D6S  H8   C8   N    106.31  3.000
 D6S  H8   C8   C13  107.48  3.000
 D6S  N    C8   C13  110.20  3.000
 D6S  H8   C8   C9   107.72  3.000
 D6S  N    C8   C9   115.70  3.000
 D6S  C13  C8   C9   109.08  3.000
 D6S  H9   C9   O2   109.92  3.000
 D6S  H9   C9   C10  106.50  3.000
 D6S  O2   C9   C10  108.52  3.000
 D6S  H9   C9   C8   109.15  3.000
 D6S  O2   C9   C8   111.32  3.000
 D6S  C10  C9   C8   111.30  3.000
 D6S  H10  C10  C11  108.36  3.000
 D6S  H10  C10  C9   107.71  3.000
 D6S  C11  C10  C9   109.27  3.000
 D6S  H10  C10  N1   112.28  3.000
 D6S  C9   C10  N1   109.12  3.000
 D6S  C11  C10  N1   110.04  3.000
 D6S  H11  C11  O1   108.79  3.000
 D6S  H11  C11  C12  112.31  3.000
 D6S  O1   C11  C12  100.84  3.000
 D6S  H11  C11  C10  110.74  3.000
 D6S  O1   C11  C10  110.14  3.000
 D6S  C12  C11  C10  113.53  3.000
 D6S  H13  C12  H12  108.33  3.000
 D6S  H13  C12  O    109.68  3.000
 D6S  H12  C12  O    111.07  3.000
 D6S  H13  C12  C11  111.59  3.000
 D6S  H12  C12  C11  112.74  3.000
 D6S  O    C12  C11  103.39  3.000
 D6S  H14  C13  O    109.13  3.000
 D6S  H14  C13  O1   109.76  3.000
 D6S  O    C13  O1   104.84  3.000
 D6S  H14  C13  C8   110.81  3.000
 D6S  O1   C13  C8   110.69  3.000
 D6S  O    C13  C8   111.43  3.000
 D6S  H15  O2   C9   109.08  3.000
 D6S  C13  O1   C11  101.41  3.000
 D6S  C13  O    C12  106.65  3.000
 D6S  C1   N    C    112.58  3.000
 D6S  C    N    C8   115.90  3.000
 D6S  C1   N    C8   116.57  3.000
 D6S  H19  C    H18  107.51  3.000
 D6S  H19  C    H17  107.02  3.000
 D6S  H18  C    H17  107.18  3.000
 D6S  H19  C    N    111.04  3.000
 D6S  H18  C    N    113.96  3.000
 D6S  H17  C    N    109.82  3.000
 D6S  C3   C2   C1   120.50  3.000
 D6S  C3   C2   C7   118.69  3.000
 D6S  C1   C2   C7   120.78  3.000
 D6S  H22  C3   C2   119.16  3.000
 D6S  H22  C3   C4   120.19  3.000
 D6S  C2   C3   C4   120.65  3.000
 D6S  H21  C1   H20  106.07  3.000
 D6S  H21  C1   C2   108.39  3.000
 D6S  H20  C1   C2   108.49  3.000
 D6S  H21  C1   N    108.39  3.000
 D6S  H20  C1   N    113.26  3.000
 D6S  C2   C1   N    111.97  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
 D6S  CONST_01  C7   C2   C3  C4      0.00   0.0  0
 D6S  CONST_02  C7   C6   C5  C4      0.00   0.0  0
 D6S  CONST_03  C2   C3   C4  C5      0.00   0.0  0
 D6S  CONST_04  C2   C7   C6  C5      0.00   0.0  0
 D6S  CONST_05  C3   C2   C7  C6      0.00   0.0  0
 D6S  CONST_06  C3   C4   C5  C6      0.00   0.0  0
 D6S  CONST_07  C1   C2   C3  C4    180.00   0.0  0
 D6S  CONST_08  C1   C2   C7  C6    180.00   0.0  0
 D6S  CONST_09  H3   C6   C5  C4    180.00   0.0  0
 D6S  CONST_10  H22  C3   C4  C5    180.00   0.0  0
 D6S  CONST_11  H7   C7   C6  C5    180.00   0.0  0
 D6S  CONST_12  H1   C4   C5  C6    180.00   0.0  0
 D6S  CONST_13  H2   C5   C6  C7    180.00   0.0  0
 D6S  Var_01    H12  C12  O   C13   120.63  30.0  3
 D6S  Var_02    N    C1   C2  C7   -138.09  30.0  2
 D6S  Var_03    C2   C1   N   C8   -150.25  30.0  2
 D6S  Var_04    H17  C    N   C8    163.58  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
 D6S  chir_01  C8   C13  C9   N    negativ
 D6S  chir_02  C9   O2   C8   C10  positiv
 D6S  chir_03  C10  N1   C11  C9   positiv
 D6S  chir_04  C11  O1   C10  C12  negativ
 D6S  chir_05  C13  O    O1   C8   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
 D6S  plan-1  C4   0.020
 D6S  plan-1  C5   0.020
 D6S  plan-1  C6   0.020
 D6S  plan-1  C7   0.020
 D6S  plan-1  C2   0.020
 D6S  plan-1  C3   0.020
 D6S  plan-1  H1   0.020
 D6S  plan-1  H2   0.020
 D6S  plan-1  H3   0.020
 D6S  plan-1  H7   0.020
 D6S  plan-1  H22  0.020
 D6S  plan-1  C1   0.020

