# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 04:48:21 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-amino-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O[C@@H]1[C@@H](N)[C@H](O)O[C@H](CO)[C@H]1O)C(O)=O
#
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
 MUR  MUR  2-amino-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranose  D-saccharide  33  17  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MUR
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
 MUR  C1    C  CH1    0   0.305  -1.8329  -0.1350  -1.6876
 MUR  O1    O  OH1    0  -0.662  -2.9376  -0.8874  -2.0380
 MUR  C2    C  CH1    0  -0.146  -1.4216  -0.5013  -0.2670
 MUR  N2    N  NH2    0  -0.843  -2.4651  -0.1007   0.6545
 MUR  C3    C  CH1    0   0.037  -0.1249   0.2269   0.0817
 MUR  O3    O  O2     0  -0.505   0.3397  -0.2530   1.3158
 MUR  C4    C  CH1    0   0.022   0.9379   0.0288  -0.9964
 MUR  O4    O  OH1    0  -0.667   2.0299   0.8713  -0.7018
 MUR  C5    C  CH1    0  -0.016   0.3568   0.3514  -2.3784
 MUR  O5    O  O2     0  -0.500  -0.7996  -0.4248  -2.5990
 MUR  C6    C  CH2    0  -0.160   1.3392   0.0569  -3.4911
 MUR  O6    O  OH1    0  -0.671   0.7894   0.4856  -4.7143
 MUR  C7    C  CH1    0  -0.076   0.8502   0.6849   2.2438
 MUR  C8    C  C      0   0.403  -0.1332   0.9656   3.4023
 MUR  O8    O  O      0  -0.590  -1.2202   0.3549   3.4290
 MUR  O9    O  OC    -1  -0.616   0.2659   1.8040   4.2344
 MUR  C9    C  CH3    0  -0.674   2.1778   0.1591   2.7726
 MUR  H1    H  HCH1   0   0.173  -2.0547   0.9465  -1.7213
 MUR  HO1   H  HOH1   0   0.461  -3.3832  -0.4727  -2.7840
 MUR  H2    H  HCH1   0   0.207  -1.2111  -1.5848  -0.2549
 MUR  HN21  H  HNH2   0   0.336  -3.2251  -0.7667   0.6257
 MUR  HN22  H  HNH2   0   0.368  -2.1000  -0.1006   1.6043
 MUR  H3    H  HCH1   0   0.206  -0.3544   1.3031   0.1438
 MUR  H4    H  HCH1   0   0.216   1.2418  -1.0273  -0.9850
 MUR  HO4   H  HOH1   0   0.458   2.8465   0.4018  -0.8867
 MUR  H5    H  HCH1   0   0.212   0.1062   1.4260  -2.4054
 MUR  H61   H  HCH2   0   0.202   2.2790   0.5756  -3.2690
 MUR  H62   H  HCH2   0   0.196   1.5584  -1.0200  -3.4975
 MUR  HO6   H  HOH1   0   0.456   1.4335   0.3125  -5.4066
 MUR  H7    H  HCH1   0   0.209   1.0429   1.6417   1.7431
 MUR  H91   H  HCH3   0   0.216   2.0539  -0.8055   3.2700
 MUR  H92   H  HCH3   0   0.223   2.8903   0.0303   1.9571
 MUR  H93   H  HCH3   0   0.221   2.6060   0.8539   3.4921

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
 MUR  C1  O1    single  1.382  0.020  1.382
 MUR  C1  C2    single  1.524  0.020  1.524
 MUR  C1  O5    single  1.408  0.020  1.408
 MUR  C1  H1    single  0.970  0.020  1.090
 MUR  O1  HO1   single  0.850  0.020  0.980
 MUR  C2  N2    single  1.449  0.020  1.449
 MUR  C2  C3    single  1.528  0.020  1.528
 MUR  C2  H2    single  0.970  0.020  1.090
 MUR  N2  HN21  single  0.890  0.020  1.040
 MUR  N2  HN22  single  0.890  0.020  1.040
 MUR  C3  O3    single  1.403  0.020  1.403
 MUR  C3  C4    single  1.527  0.020  1.527
 MUR  C3  H3    single  0.970  0.020  1.090
 MUR  O3  C7    single  1.415  0.020  1.415
 MUR  C4  O4    single  1.410  0.020  1.410
 MUR  C4  C5    single  1.534  0.020  1.534
 MUR  C4  H4    single  0.970  0.020  1.090
 MUR  O4  HO4   single  0.850  0.020  0.980
 MUR  C5  O5    single  1.410  0.020  1.410
 MUR  C5  C6    single  1.513  0.020  1.513
 MUR  C5  H5    single  0.970  0.020  1.090
 MUR  C6  O6    single  1.408  0.020  1.408
 MUR  C6  H61   single  0.970  0.020  1.090
 MUR  C6  H62   single  0.970  0.020  1.090
 MUR  O6  HO6   single  0.850  0.020  0.980
 MUR  C7  C8    single  1.545  0.020  1.545
 MUR  C7  C9    single  1.523  0.020  1.523
 MUR  C7  H7    single  0.970  0.020  1.090
 MUR  C8  O8    deloc   1.247  0.020  1.247
 MUR  C8  O9    deloc   1.247  0.020  1.247
 MUR  C9  H91   single  0.970  0.020  1.090
 MUR  C9  H92   single  0.970  0.020  1.090
 MUR  C9  H93   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
 MUR  H1    C1  O5    109.22  3.000
 MUR  H1    C1  C2    108.55  3.000
 MUR  O5    C1  C2    110.85  3.000
 MUR  H1    C1  O1    111.40  3.000
 MUR  O5    C1  O1    108.09  3.000
 MUR  C2    C1  O1    108.75  3.000
 MUR  HO1   O1  C1    109.39  3.000
 MUR  H2    C2  C3    107.68  3.000
 MUR  H2    C2  N2    113.70  3.000
 MUR  C3    C2  N2    109.54  3.000
 MUR  H2    C2  C1    107.32  3.000
 MUR  C3    C2  C1    109.11  3.000
 MUR  N2    C2  C1    109.40  3.000
 MUR  HN22  N2  HN21  107.23  3.000
 MUR  HN22  N2  C2    109.59  3.000
 MUR  HN21  N2  C2    109.95  3.000
 MUR  H3    C3  C4    108.14  3.000
 MUR  H3    C3  O3    110.69  3.000
 MUR  C4    C3  O3    110.25  3.000
 MUR  H3    C3  C2    107.56  3.000
 MUR  C4    C3  C2    111.58  3.000
 MUR  O3    C3  C2    108.59  3.000
 MUR  C7    O3  C3    118.01  3.000
 MUR  H4    C4  C5    108.44  3.000
 MUR  H4    C4  O4    110.96  3.000
 MUR  C5    C4  O4    110.86  3.000
 MUR  H4    C4  C3    108.05  3.000
 MUR  C5    C4  C3    110.20  3.000
 MUR  O4    C4  C3    108.30  3.000
 MUR  HO4   O4  C4    109.04  3.000
 MUR  H5    C5  C6    108.60  3.000
 MUR  H5    C5  O5    110.24  3.000
 MUR  C6    C5  O5    108.08  3.000
 MUR  H5    C5  C4    108.23  3.000
 MUR  C6    C5  C4    112.07  3.000
 MUR  O5    C5  C4    109.63  3.000
 MUR  C5    O5  C1    112.79  3.000
 MUR  H62   C6  H61   107.09  3.000
 MUR  H62   C6  O6    111.79  3.000
 MUR  H61   C6  O6    111.51  3.000
 MUR  H62   C6  C5    108.93  3.000
 MUR  H61   C6  C5    108.40  3.000
 MUR  O6    C6  C5    109.03  3.000
 MUR  HO6   O6  C6    108.01  3.000
 MUR  H7    C7  C9    107.85  3.000
 MUR  H7    C7  C8    107.19  3.000
 MUR  C9    C7  C8    110.92  3.000
 MUR  H7    C7  O3    110.02  3.000
 MUR  C9    C7  O3    108.27  3.000
 MUR  C8    C7  O3    112.49  3.000
 MUR  O9    C8  O8    126.44  3.000
 MUR  O9    C8  C7    114.76  3.000
 MUR  O8    C8  C7    118.80  3.000
 MUR  H93   C9  H92   108.23  3.000
 MUR  H93   C9  H91   107.91  3.000
 MUR  H92   C9  H91   108.08  3.000
 MUR  H93   C9  C7    110.62  3.000
 MUR  H92   C9  C7    110.53  3.000
 MUR  H91   C9  C7    111.36  3.000

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
 MUR  chir_01  C1  O1  C2  O5  negativ
 MUR  chir_02  C2  N2  C3  C1  positiv
 MUR  chir_03  C3  O3  C4  C2  negativ
 MUR  chir_04  C4  O4  C5  C3  positiv
 MUR  chir_05  C5  O5  C4  C6  negativ
 MUR  chir_06  C7  O3  C9  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
 MUR  plan-1  C7  0.020
 MUR  plan-1  C8  0.020
 MUR  plan-1  O8  0.020
 MUR  plan-1  O9  0.020

