# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 19:45:50 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-alpha-D-mannopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[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
 BM3  BM3  2-(acetylamino)-2-deoxy-alpha-D-mannopyranose  D-saccharide  30  15  .  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_BM3
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
 BM3  C1    C  CH1   0   0.262   2.2250   0.0662  -1.7116
 BM3  O1    O  OH1   0  -0.663   1.1083  -0.4656  -2.3461
 BM3  C2    C  CH1   0  -0.152   2.1373  -0.3057  -0.2271
 BM3  N2    N  NH1   0  -0.633   3.3925  -0.0304   0.4345
 BM3  C7    C  C     0   0.529   4.4178  -0.9013   0.4383
 BM3  O7    O  O     0  -0.506   4.3790  -1.9686  -0.1595
 BM3  C8    C  CH3   0  -0.779   5.6254  -0.4780   1.2353
 BM3  C3    C  CH1   0   0.009   0.9940   0.4631   0.4323
 BM3  O3    O  OH1   0  -0.661   0.9994   0.1729   1.8055
 BM3  C4    C  CH1   0  -0.021   1.1096   1.9644   0.1596
 BM3  O4    O  OH1   0  -0.659   0.0179   2.6627   0.7137
 BM3  C5    C  CH1   0  -0.038   1.2509   2.2164  -1.3426
 BM3  C6    C  CH2   0  -0.163   1.5543   3.6726  -1.6526
 BM3  O6    O  OH1   0  -0.666   1.6088   3.9356  -3.0330
 BM3  O5    O  O2    0  -0.507   2.3296   1.4567  -1.8672
 BM3  H1    H  HCH1  0   0.244   3.1522  -0.3318  -2.1372
 BM3  HA    H  HOH1  0   0.464   1.2193  -0.3876  -3.3000
 BM3  H2    H  HCH1  0   0.279   1.9404  -1.3782  -0.1512
 BM3  HB    H  HNH1  0   0.403   3.4895   0.8158   0.9705
 BM3  H3    H  HCH1  0   0.232   0.0605   0.1175  -0.0369
 BM3  H8C1  H  HCH3  0   0.268   5.8067  -1.2070   2.0252
 BM3  H8C2  H  HCH3  0   0.266   6.5035  -0.4738   0.5900
 BM3  H8C3  H  HCH3  0   0.249   5.5266   0.5050   1.6919
 BM3  HC    H  HOH1  0   0.453   0.2841   0.6697   2.2172
 BM3  H4    H  HCH1  0   0.236   1.9934   2.3659   0.6711
 BM3  HD    H  HOH1  0   0.450  -0.7889   2.3943   0.2582
 BM3  H5    H  HCH1  0   0.225   0.3111   1.9349  -1.8407
 BM3  H6C1  H  HCH2  0   0.201   2.4862   3.9579  -1.1452
 BM3  H6C2  H  HCH2  0   0.231   0.7591   4.2944  -1.2404
 BM3  H6    H  HOH1  0   0.448   2.3324   3.4233  -3.4071

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
 BM3  C1  O1    single  1.390  0.020  1.390
 BM3  C1  C2    single  1.533  0.020  1.533
 BM3  C1  O5    single  1.403  0.020  1.403
 BM3  C1  H1    single  0.970  0.020  1.090
 BM3  O1  HA    single  0.850  0.020  0.980
 BM3  C2  N2    single  1.445  0.020  1.445
 BM3  C2  C3    single  1.527  0.020  1.527
 BM3  C2  H2    single  0.970  0.020  1.090
 BM3  N2  C7    single  1.345  0.020  1.345
 BM3  N2  HB    single  0.860  0.020  1.020
 BM3  C7  O7    double  1.224  0.020  1.224
 BM3  C7  C8    single  1.508  0.020  1.508
 BM3  C8  H8C1  single  0.970  0.020  1.090
 BM3  C8  H8C2  single  0.970  0.020  1.090
 BM3  C8  H8C3  single  0.970  0.020  1.090
 BM3  C3  O3    single  1.403  0.020  1.403
 BM3  C3  C4    single  1.530  0.020  1.530
 BM3  C3  H3    single  0.970  0.020  1.090
 BM3  O3  HC    single  0.850  0.020  0.980
 BM3  C4  O4    single  1.409  0.020  1.409
 BM3  C4  C5    single  1.530  0.020  1.530
 BM3  C4  H4    single  0.970  0.020  1.090
 BM3  O4  HD    single  0.850  0.020  0.980
 BM3  C5  C6    single  1.519  0.020  1.519
 BM3  C5  O5    single  1.420  0.020  1.420
 BM3  C5  H5    single  0.970  0.020  1.090
 BM3  C6  O6    single  1.406  0.020  1.406
 BM3  C6  H6C1  single  0.970  0.020  1.090
 BM3  C6  H6C2  single  0.970  0.020  1.090
 BM3  O6  H6    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
 BM3  H1    C1  O5    104.71  3.000
 BM3  H1    C1  C2    109.67  3.000
 BM3  O5    C1  C2    110.61  3.000
 BM3  H1    C1  O1    111.34  3.000
 BM3  O5    C1  O1    112.85  3.000
 BM3  C2    C1  O1    107.65  3.000
 BM3  HA    O1  C1    109.17  3.000
 BM3  H2    C2  C3    109.21  3.000
 BM3  H2    C2  N2    108.15  3.000
 BM3  C3    C2  N2    110.89  3.000
 BM3  H2    C2  C1    108.40  3.000
 BM3  C3    C2  C1    109.81  3.000
 BM3  N2    C2  C1    110.33  3.000
 BM3  HB    N2  C7    118.00  3.000
 BM3  HB    N2  C2    119.19  3.000
 BM3  C7    N2  C2    122.67  3.000
 BM3  C8    C7  O7    121.91  3.000
 BM3  C8    C7  N2    115.48  3.000
 BM3  O7    C7  N2    122.62  3.000
 BM3  H8C3  C8  H8C2  108.55  3.000
 BM3  H8C3  C8  H8C1  108.37  3.000
 BM3  H8C2  C8  H8C1  107.32  3.000
 BM3  H8C3  C8  C7    113.75  3.000
 BM3  H8C2  C8  C7    109.48  3.000
 BM3  H8C1  C8  C7    109.18  3.000
 BM3  H3    C3  C4    107.23  3.000
 BM3  H3    C3  O3    110.82  3.000
 BM3  C4    C3  O3    112.14  3.000
 BM3  H3    C3  C2    107.03  3.000
 BM3  C4    C3  C2    111.12  3.000
 BM3  O3    C3  C2    108.39  3.000
 BM3  HC    O3  C3    107.98  3.000
 BM3  H4    C4  C5    108.85  3.000
 BM3  H4    C4  O4    105.03  3.000
 BM3  C5    C4  O4    112.09  3.000
 BM3  H4    C4  C3    109.68  3.000
 BM3  C5    C4  C3    110.09  3.000
 BM3  O4    C4  C3    110.95  3.000
 BM3  HD    O4  C4    108.93  3.000
 BM3  H5    C5  O5    110.17  3.000
 BM3  H5    C5  C6    108.87  3.000
 BM3  O5    C5  C6    106.60  3.000
 BM3  H5    C5  C4    108.88  3.000
 BM3  O5    C5  C4    110.18  3.000
 BM3  C6    C5  C4    112.13  3.000
 BM3  H6C2  C6  H6C1  107.21  3.000
 BM3  H6C2  C6  O6    107.02  3.000
 BM3  H6C1  C6  O6    111.83  3.000
 BM3  H6C2  C6  C5    108.89  3.000
 BM3  H6C1  C6  C5    108.90  3.000
 BM3  O6    C6  C5    112.78  3.000
 BM3  H6    O6  C6    108.13  3.000
 BM3  C5    O5  C1    115.64  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
 BM3  CONST_01  O7    C7  N2  C2    0.00   0.0  0
 BM3  CONST_02  C8    C7  N2  C2  180.00   0.0  0
 BM3  CONST_03  HB    N2  C7  O7  180.00   0.0  0
 BM3  Var_01    H8C1  C8  C7  N2  119.54  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
 BM3  chir_01  C1  O1  C2  O5  positiv
 BM3  chir_02  C2  N2  C3  C1  negativ
 BM3  chir_03  C3  O3  C2  C4  positiv
 BM3  chir_04  C4  O4  C5  C3  positiv
 BM3  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
 BM3  plan-1  C2  0.020
 BM3  plan-1  N2  0.020
 BM3  plan-1  C7  0.020
 BM3  plan-1  O7  0.020
 BM3  plan-1  C8  0.020
 BM3  plan-1  HB  0.020

