# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 05:35:17 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: benzyl 2-(acetylamino)-2-deoxy-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1OCc2ccccc2
#
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
 BBV  BBV  'benzyl 2-(acetylamino)-2-deoxy-alpha-D-glucopyranoside'  D-saccharide  43  22  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BBV
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
 BBV  C1    C  CH1   0   0.300   0.5951  -0.0392   1.0436
 BBV  O1    O  O2    0  -0.504  -0.5982   0.0227   0.3300
 BBV  C2    C  CH1   0  -0.165   1.6726   0.6442   0.1997
 BBV  N2    N  NH1   0  -0.626   1.2703   1.9788  -0.1583
 BBV  C3    C  CH1   0   0.045   1.9975  -0.1971  -1.0309
 BBV  O3    O  OH1   0  -0.664   3.0722   0.4123  -1.6968
 BBV  C4    C  CH1   0  -0.003   2.3335  -1.6234  -0.6052
 BBV  O4    O  OH1   0  -0.674   2.5224  -2.3786  -1.7821
 BBV  C5    C  CH1   0  -0.019   1.2045  -2.1995   0.2553
 BBV  O5    O  O2    0  -0.501   0.9627  -1.3459   1.3641
 BBV  C6    C  CH2   0  -0.164   1.5509  -3.5631   0.8110
 BBV  O6    O  OH1   0  -0.668   0.4279  -4.0802   1.4827
 BBV  C7    C  C     0   0.525   1.9438   3.0943   0.1803
 BBV  O7    O  O     0  -0.503   2.9562   3.0869   0.8663
 BBV  C8    C  CH3   0  -0.780   1.3482   4.3800  -0.3369
 BBV  C1'   C  CR6   0   0.077  -2.9627   0.0946   0.3189
 BBV  C2'   C  CR16  0  -0.310  -3.9439  -0.7964  -0.0996
 BBV  C3'   C  CR16  0  -0.284  -3.1253   1.4531   0.0508
 BBV  C4'   C  CR16  0  -0.240  -5.0751  -0.3430  -0.7686
 BBV  C5'   C  CR16  0  -0.241  -4.2500   1.9080  -0.6200
 BBV  C6'   C  CR16  0  -0.266  -5.2294   1.0102  -1.0314
 BBV  C7'   C  CH2   0  -0.206  -1.7458  -0.3919   1.0497
 BBV  H1    H  HCH1  0   0.244   0.4941   0.4787   2.0073
 BBV  H2    H  HCH1  0   0.281   2.5684   0.7226   0.8189
 BBV  HN2   H  HNH1  0   0.395   0.4510   2.0707  -0.7372
 BBV  H3    H  HCH1  0   0.214   1.1084  -0.2365  -1.6796
 BBV  HO3   H  HOH1  0   0.451   3.2594  -0.1038  -2.4879
 BBV  H4    H  HCH1  0   0.226   3.2545  -1.5932  -0.0041
 BBV  HO4   H  HOH1  0   0.463   3.2015  -3.0410  -1.6287
 BBV  H5    H  HCH1  0   0.228   0.3036  -2.2949  -0.3672
 BBV  H6    H  HCH2  0   0.203   1.8520  -4.2095  -0.0221
 BBV  H6A   H  HCH2  0   0.199   2.4199  -3.4686   1.4770
 BBV  HO6   H  HOH1  0   0.456   0.6541  -4.9558   1.8087
 BBV  H8    H  HCH3  0   0.246   0.4647   4.2385  -0.9567
 BBV  H8A   H  HCH3  0   0.268   1.0802   5.0180   0.5055
 BBV  H8B   H  HCH3  0   0.267   2.0964   4.9140  -0.9223
 BBV  H2'   H  HCR6  0   0.254  -3.8247  -1.8555   0.0970
 BBV  H3'   H  HCR6  0   0.243  -2.3708   2.1615   0.3724
 BBV  H4'   H  HCR6  0   0.257  -5.8310  -1.0490  -1.0876
 BBV  H5'   H  HCR6  0   0.257  -4.3663   2.9652  -0.8215
 BBV  H6'   H  HCR6  0   0.257  -6.1077   1.3665  -1.5538
 BBV  H7'   H  HCH2  0   0.235  -1.7776  -1.4817   1.1503
 BBV  H7'A  H  HCH2  0   0.227  -1.7197   0.0255   2.0649

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
 BBV  O5   C1    single    1.395  0.020  1.395
 BBV  C2   C1    single    1.530  0.020  1.530
 BBV  C1   O1    single    1.392  0.020  1.392
 BBV  C1   H1    single    0.970  0.020  1.090
 BBV  O1   C7'   single    1.417  0.020  1.417
 BBV  C3   C2    single    1.526  0.020  1.526
 BBV  C2   N2    single    1.439  0.020  1.439
 BBV  C2   H2    single    0.970  0.020  1.090
 BBV  C7   N2    single    1.346  0.020  1.346
 BBV  N2   HN2   single    0.860  0.020  1.020
 BBV  C4   C3    single    1.526  0.020  1.526
 BBV  O3   C3    single    1.403  0.020  1.403
 BBV  C3   H3    single    0.970  0.020  1.090
 BBV  O3   HO3   single    0.850  0.020  0.980
 BBV  O4   C4    single    1.411  0.020  1.411
 BBV  C4   C5    single    1.532  0.020  1.532
 BBV  C4   H4    single    0.970  0.020  1.090
 BBV  O4   HO4   single    0.850  0.020  0.980
 BBV  C6   C5    single    1.513  0.020  1.513
 BBV  C5   O5    single    1.420  0.020  1.420
 BBV  C5   H5    single    0.970  0.020  1.090
 BBV  C6   O6    single    1.407  0.020  1.407
 BBV  C6   H6    single    0.970  0.020  1.090
 BBV  C6   H6A   single    0.970  0.020  1.090
 BBV  O6   HO6   single    0.850  0.020  0.980
 BBV  O7   C7    double    1.223  0.020  1.223
 BBV  C7   C8    single    1.508  0.020  1.508
 BBV  C8   H8    single    0.970  0.020  1.090
 BBV  C8   H8A   single    0.970  0.020  1.090
 BBV  C8   H8B   single    0.970  0.020  1.090
 BBV  C7'  C1'   single    1.500  0.020  1.500
 BBV  C1'  C2'   aromatic  1.390  0.020  1.390
 BBV  C1'  C3'   aromatic  1.394  0.020  1.394
 BBV  C2'  C4'   aromatic  1.390  0.020  1.390
 BBV  C2'  H2'   single    0.930  0.020  1.080
 BBV  C3'  C5'   aromatic  1.386  0.020  1.386
 BBV  C3'  H3'   single    0.930  0.020  1.080
 BBV  C4'  C6'   aromatic  1.387  0.020  1.387
 BBV  C4'  H4'   single    0.930  0.020  1.080
 BBV  C5'  C6'   aromatic  1.391  0.020  1.391
 BBV  C5'  H5'   single    0.930  0.020  1.080
 BBV  C6'  H6'   single    0.930  0.020  1.080
 BBV  C7'  H7'   single    0.970  0.020  1.090
 BBV  C7'  H7'A  single    0.970  0.020  1.090

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
 BBV  H1    C1   O5   105.32  3.000
 BBV  H1    C1   C2   109.75  3.000
 BBV  O5    C1   C2   111.08  3.000
 BBV  H1    C1   O1   110.48  3.000
 BBV  C2    C1   O1   107.53  3.000
 BBV  O5    C1   O1   112.68  3.000
 BBV  C7'   O1   C1   114.90  3.000
 BBV  H2    C2   C3   108.80  3.000
 BBV  H2    C2   N2   107.69  3.000
 BBV  C3    C2   N2   111.73  3.000
 BBV  H2    C2   C1   107.29  3.000
 BBV  N2    C2   C1   110.77  3.000
 BBV  C3    C2   C1   110.40  3.000
 BBV  HN2   N2   C7   118.41  3.000
 BBV  HN2   N2   C2   117.06  3.000
 BBV  C7    N2   C2   124.47  3.000
 BBV  H3    C3   C4   107.98  3.000
 BBV  H3    C3   O3   110.75  3.000
 BBV  C4    C3   O3   111.69  3.000
 BBV  H3    C3   C2   108.84  3.000
 BBV  O3    C3   C2   107.84  3.000
 BBV  C4    C3   C2   109.72  3.000
 BBV  HO3   O3   C3   107.81  3.000
 BBV  H4    C4   C5   108.68  3.000
 BBV  H4    C4   O4   111.00  3.000
 BBV  C5    C4   O4   111.46  3.000
 BBV  H4    C4   C3   108.12  3.000
 BBV  C5    C4   C3   110.24  3.000
 BBV  O4    C4   C3   107.29  3.000
 BBV  HO4   O4   C4   109.29  3.000
 BBV  H5    C5   C6   108.51  3.000
 BBV  H5    C5   O5   110.78  3.000
 BBV  C6    C5   O5   107.10  3.000
 BBV  H5    C5   C4   108.57  3.000
 BBV  O5    C5   C4   109.75  3.000
 BBV  C6    C5   C4   112.12  3.000
 BBV  C5    O5   C1   115.38  3.000
 BBV  H6A   C6   H6   107.10  3.000
 BBV  H6A   C6   O6   111.92  3.000
 BBV  H6    C6   O6   111.42  3.000
 BBV  H6A   C6   C5   109.04  3.000
 BBV  H6    C6   C5   108.37  3.000
 BBV  O6    C6   C5   108.90  3.000
 BBV  HO6   O6   C6   107.99  3.000
 BBV  C8    C7   O7   121.62  3.000
 BBV  C8    C7   N2   114.99  3.000
 BBV  O7    C7   N2   123.38  3.000
 BBV  H8B   C8   H8A  107.28  3.000
 BBV  H8B   C8   H8   108.37  3.000
 BBV  H8A   C8   H8   108.45  3.000
 BBV  H8B   C8   C7   109.32  3.000
 BBV  H8A   C8   C7   109.33  3.000
 BBV  H8    C8   C7   113.88  3.000
 BBV  C7'   C1'  C3'  120.27  3.000
 BBV  C3'   C1'  C2'  118.97  3.000
 BBV  C7'   C1'  C2'  120.75  3.000
 BBV  H2'   C2'  C4'  119.70  3.000
 BBV  H2'   C2'  C1'  119.61  3.000
 BBV  C4'   C2'  C1'  120.68  3.000
 BBV  H3'   C3'  C5'  119.60  3.000
 BBV  H3'   C3'  C1'  119.91  3.000
 BBV  C5'   C3'  C1'  120.49  3.000
 BBV  H4'   C4'  C6'  120.19  3.000
 BBV  H4'   C4'  C2'  119.82  3.000
 BBV  C6'   C4'  C2'  119.99  3.000
 BBV  H5'   C5'  C6'  119.98  3.000
 BBV  H5'   C5'  C3'  119.85  3.000
 BBV  C6'   C5'  C3'  120.17  3.000
 BBV  H6'   C6'  C5'  120.11  3.000
 BBV  H6'   C6'  C4'  120.19  3.000
 BBV  C5'   C6'  C4'  119.70  3.000
 BBV  H7'A  C7'  H7'  107.11  3.000
 BBV  H7'A  C7'  C1'  110.27  3.000
 BBV  H7'   C7'  C1'  110.12  3.000
 BBV  H7'A  C7'  O1   109.83  3.000
 BBV  H7'   C7'  O1   111.19  3.000
 BBV  C1'   C7'  O1   108.34  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
 BBV  CONST_01  C6'  C4'  C2'  C1'    0.00   0.0  0
 BBV  CONST_02  C6'  C5'  C3'  C1'    0.00   0.0  0
 BBV  CONST_03  C5'  C3'  C1'  C2'    0.00   0.0  0
 BBV  CONST_04  C5'  C6'  C4'  C2'    0.00   0.0  0
 BBV  CONST_05  C4'  C2'  C1'  C3'    0.00   0.0  0
 BBV  CONST_06  C4'  C6'  C5'  C3'    0.00   0.0  0
 BBV  CONST_07  C7'  C1'  C2'  C4'  180.00   0.0  0
 BBV  CONST_08  C7'  C1'  C3'  C5'  180.00   0.0  0
 BBV  CONST_09  H4'  C4'  C2'  C1'  180.00   0.0  0
 BBV  CONST_10  H5'  C5'  C3'  C1'  180.00   0.0  0
 BBV  CONST_11  H3'  C3'  C1'  C2'  180.00   0.0  0
 BBV  CONST_12  H6'  C6'  C4'  C2'  180.00   0.0  0
 BBV  CONST_13  H2'  C2'  C1'  C3'  180.00   0.0  0
 BBV  CONST_14  O7   C7   N2   C2     0.00   0.0  0
 BBV  CONST_15  C8   C7   N2   C2   180.00   0.0  0
 BBV  CONST_16  HN2  N2   C7   O7   180.00   0.0  0
 BBV  Var_01    C1'  C7'  O1   C1   163.85  30.0  3
 BBV  Var_02    C2'  C1'  C7'  O1   123.11  30.0  2
 BBV  Var_03    H8   C8   C7   N2    -2.34  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
 BBV  chir_01  C1  O5  C2  O1  negativ
 BBV  chir_02  C2  N2  C3  C1  positiv
 BBV  chir_03  C3  O3  C2  C4  positiv
 BBV  chir_04  C4  O4  C5  C3  positiv
 BBV  chir_05  C5  O5  C4  C6  negativ

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
 BBV  plan-1  C1'  0.020
 BBV  plan-1  C2'  0.020
 BBV  plan-1  C3'  0.020
 BBV  plan-1  C4'  0.020
 BBV  plan-1  C5'  0.020
 BBV  plan-1  C6'  0.020
 BBV  plan-1  C7'  0.020
 BBV  plan-1  H2'  0.020
 BBV  plan-1  H3'  0.020
 BBV  plan-1  H4'  0.020
 BBV  plan-1  H5'  0.020
 BBV  plan-1  H6'  0.020
 BBV  plan-2  C2   0.020
 BBV  plan-2  N2   0.020
 BBV  plan-2  C7   0.020
 BBV  plan-2  O7   0.020
 BBV  plan-2  C8   0.020
 BBV  plan-2  HN2  0.020

