# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:58:47 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: methyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1NC(C)=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
 MAG  MAG  'methyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranoside'  D-saccharide  33  16  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_MAG
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
 MAG  C1   C  CH1   0   0.324  31.4626  12.3389  35.0932
 MAG  C2   C  CH1   0  -0.197  32.5661  13.3496  34.7267
 MAG  C3   C  CH1   0   0.058  32.0560  14.2243  33.5804
 MAG  C4   C  CH1   0   0.007  31.6475  13.3338  32.4122
 MAG  C5   C  CH1   0  -0.010  30.6015  12.3250  32.8965
 MAG  C6   C  CH2   0  -0.192  30.1253  11.3680  31.8252
 MAG  C7   C  C     0   0.496  34.1576  14.5270  36.2685
 MAG  C8   C  CH3   0  -0.816  35.3330  14.0403  35.4563
 MAG  N2   N  NH1   0  -0.612  32.9240  14.1240  35.8876
 MAG  O1   O  O2    0  -0.478  31.7730  11.4968  36.1368
 MAG  O3   O  OH1   0  -0.659  33.0657  15.1306  33.2282
 MAG  O4   O  OH1   0  -0.672  31.1307  14.1685  31.4016
 MAG  O5   O  O2    0  -0.497  31.1334  11.5701  33.9682
 MAG  O6   O  OH1   0  -0.667  31.2265  10.7001  31.2593
 MAG  O7   O  O     0  -0.488  34.3074  15.2470  37.2450
 MAG  CM   C  CH3   0  -0.432  32.9367  10.6999  36.0130
 MAG  H1   H  HCH1  0   0.223  30.5772  12.9028  35.4318
 MAG  H2   H  HCH1  0   0.285  33.4465  12.8062  34.3749
 MAG  H3   H  HCH1  0   0.206  31.1581  14.7609  33.9330
 MAG  H4   H  HCH1  0   0.229  32.5380  12.7935  32.0660
 MAG  H5   H  HCH1  0   0.226  29.7152  12.8859  33.2361
 MAG  H61  H  HCH2  0   0.220  29.4106  10.6696  32.2792
 MAG  H62  H  HCH2  0   0.207  29.5666  11.9481  31.0802
 MAG  H81  H  HCH3  0   0.266  36.2497  14.4458  35.8761
 MAG  H82  H  HCH3  0   0.265  35.4071  12.9517  35.4648
 MAG  H83  H  HCH3  0   0.267  35.2537  14.3516  34.4159
 MAG  HN2  H  HNH1  0   0.386  32.1618  14.5153  36.4254
 MAG  HO3  H  HOH1  0   0.451  32.7503  15.6479  32.4792
 MAG  HO4  H  HOH1  0   0.461  31.2734  13.7507  30.5472
 MAG  HO6  H  HOH1  0   0.457  30.9010  10.1028  30.5804
 MAG  HM1  H  HCH3  0   0.243  32.9268  10.0050  36.8507
 MAG  HM2  H  HCH3  0   0.223  32.9563  10.1207  35.0882
 MAG  HM3  H  HCH3  0   0.220  33.8555  11.2882  36.0781

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
 MAG  C1  C2   single  1.541  0.020  1.541
 MAG  C1  O1   single  1.376  0.020  1.376
 MAG  C1  O5   single  1.402  0.020  1.402
 MAG  C1  H1   single  0.970  0.020  1.090
 MAG  C2  C3   single  1.530  0.020  1.530
 MAG  C2  N2   single  1.441  0.020  1.441
 MAG  C2  H2   single  0.970  0.020  1.090
 MAG  C3  C4   single  1.525  0.020  1.525
 MAG  C3  O3   single  1.402  0.020  1.402
 MAG  C3  H3   single  0.970  0.020  1.090
 MAG  C4  C5   single  1.532  0.020  1.532
 MAG  C4  O4   single  1.409  0.020  1.409
 MAG  C4  H4   single  0.970  0.020  1.090
 MAG  C5  C6   single  1.513  0.020  1.513
 MAG  C5  O5   single  1.415  0.020  1.415
 MAG  C5  H5   single  0.970  0.020  1.090
 MAG  C6  O6   single  1.407  0.020  1.407
 MAG  C6  H61  single  0.970  0.020  1.090
 MAG  C6  H62  single  0.970  0.020  1.090
 MAG  C7  C8   single  1.509  0.020  1.509
 MAG  C7  N2   single  1.352  0.020  1.352
 MAG  C7  O7   double  1.222  0.020  1.222
 MAG  C8  H81  single  0.970  0.020  1.090
 MAG  C8  H82  single  0.970  0.020  1.090
 MAG  C8  H83  single  0.970  0.020  1.090
 MAG  N2  HN2  single  0.860  0.020  1.020
 MAG  O1  CM   single  1.416  0.020  1.416
 MAG  O3  HO3  single  0.850  0.020  0.980
 MAG  O4  HO4  single  0.850  0.020  0.980
 MAG  O6  HO6  single  0.850  0.020  0.980
 MAG  CM  HM1  single  0.970  0.020  1.090
 MAG  CM  HM2  single  0.970  0.020  1.090
 MAG  CM  HM3  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
 MAG  H1   C1  O5   109.77  3.000
 MAG  H1   C1  O1   105.14  3.000
 MAG  O5   C1  O1   109.02  3.000
 MAG  H1   C1  C2   108.21  3.000
 MAG  O5   C1  C2   109.70  3.000
 MAG  O1   C1  C2   114.85  3.000
 MAG  H2   C2  N2   109.06  3.000
 MAG  H2   C2  C3   108.17  3.000
 MAG  N2   C2  C3   112.29  3.000
 MAG  H2   C2  C1   109.11  3.000
 MAG  N2   C2  C1   109.81  3.000
 MAG  C3   C2  C1   108.34  3.000
 MAG  H3   C3  O3   110.60  3.000
 MAG  H3   C3  C4   108.10  3.000
 MAG  O3   C3  C4   112.22  3.000
 MAG  H3   C3  C2   108.05  3.000
 MAG  O3   C3  C2   108.53  3.000
 MAG  C4   C3  C2   109.24  3.000
 MAG  H4   C4  O4   111.29  3.000
 MAG  H4   C4  C5   109.24  3.000
 MAG  O4   C4  C5   111.49  3.000
 MAG  H4   C4  C3   108.17  3.000
 MAG  O4   C4  C3   107.57  3.000
 MAG  C5   C4  C3   108.99  3.000
 MAG  H5   C5  O5   109.89  3.000
 MAG  H5   C5  C6   106.67  3.000
 MAG  O5   C5  C6   108.49  3.000
 MAG  H5   C5  C4   108.14  3.000
 MAG  O5   C5  C4   109.52  3.000
 MAG  C6   C5  C4   114.05  3.000
 MAG  H62  C6  H61  106.60  3.000
 MAG  H62  C6  O6   112.12  3.000
 MAG  H61  C6  O6   111.96  3.000
 MAG  H62  C6  C5   107.85  3.000
 MAG  H61  C6  C5   108.33  3.000
 MAG  O6   C6  C5   109.80  3.000
 MAG  O7   C7  N2   120.81  3.000
 MAG  O7   C7  C8   121.62  3.000
 MAG  N2   C7  C8   117.56  3.000
 MAG  H83  C8  H82  107.32  3.000
 MAG  H83  C8  H81  108.90  3.000
 MAG  H82  C8  H81  108.18  3.000
 MAG  H83  C8  C7   111.43  3.000
 MAG  H82  C8  C7   111.74  3.000
 MAG  H81  C8  C7   109.19  3.000
 MAG  HN2  N2  C7   114.98  3.000
 MAG  HN2  N2  C2   116.69  3.000
 MAG  C7   N2  C2   127.86  3.000
 MAG  CM   O1  C1   117.61  3.000
 MAG  HO3  O3  C3   107.86  3.000
 MAG  HO4  O4  C4   109.00  3.000
 MAG  C5   O5  C1   113.80  3.000
 MAG  HO6  O6  C6   108.31  3.000
 MAG  HM3  CM  HM2  108.73  3.000
 MAG  HM3  CM  HM1  107.78  3.000
 MAG  HM2  CM  HM1  108.27  3.000
 MAG  HM3  CM  O1   112.51  3.000
 MAG  HM2  CM  O1   112.80  3.000
 MAG  HM1  CM  O1   106.53  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
 MAG  CONST_01  C8   C7  N2  C2     0.00   0.0  0
 MAG  CONST_02  O7   C7  N2  C2   180.00   0.0  0
 MAG  CONST_03  HN2  N2  C7  C8   180.00   0.0  0
 MAG  Var_01    HM1  CM  O1  C1  -171.51  30.0  3
 MAG  Var_02    H81  C8  C7  N2   179.79  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
 MAG  chir_01  C1  C2  O1  O5  positiv
 MAG  chir_02  C2  N2  C3  C1  positiv
 MAG  chir_03  C3  O3  C2  C4  positiv
 MAG  chir_04  C4  O4  C3  C5  negativ
 MAG  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
 MAG  plan-1  C2   0.020
 MAG  plan-1  C7   0.020
 MAG  plan-1  C8   0.020
 MAG  plan-1  N2   0.020
 MAG  plan-1  O7   0.020
 MAG  plan-1  HN2  0.020

