# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 08:14:53 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: methyl 2-(acetylamino)-3-O-[(1R)-1-carboxyethyl]-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](C)C(O)=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
 AMV  AMV  'methyl 2-(acetylamino)-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranoside'  D-saccharide  41  21  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AMV
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
 AMV  C1    C  CH1    0   0.347   4.7162  -1.2428   0.5213
 AMV  C2    C  CH1    0  -0.147   3.6009  -0.5461   1.3015
 AMV  C3    C  CH1    0   0.042   3.4683   0.9095   0.8332
 AMV  C4    C  CH1    0   0.017   4.8195   1.6184   0.8250
 AMV  C5    C  CH1    0  -0.040   5.8530   0.7640   0.0851
 AMV  C6    C  CH2    0  -0.170   7.2529   1.3479   0.1503
 AMV  C7    C  C      0   0.539   1.7595  -1.9712   2.1012
 AMV  C8    C  CH3    0  -0.783   0.3932  -2.4977   1.7464
 AMV  C9    C  CH1    0  -0.065   1.2792   1.8586   1.1576
 AMV  C10   C  C      0   0.413   0.2070   1.0620   1.9313
 AMV  C11   C  CH3    0  -0.674   0.9917   3.3510   1.2613
 AMV  O1    O  O2     0  -0.483   4.8978  -2.5084   1.0225
 AMV  O3    O  O2     0  -0.496   2.5884   1.6230   1.6473
 AMV  O4    O  OH1    0  -0.665   4.6503   2.8614   0.1865
 AMV  O5    O  O2     0  -0.508   5.9126  -0.5210   0.6708
 AMV  O6    O  OH1    0  -0.664   8.1901   0.5842  -0.5680
 AMV  O7    O  O      0  -0.507   2.2777  -2.1980   3.1843
 AMV  O11   O  O      0  -0.605   0.4664   0.7228   3.0982
 AMV  N2    N  NH1    0  -0.630   2.3480  -1.2325   1.1404
 AMV  C12   C  CH3    0  -0.411   5.6959  -3.3521   0.2151
 AMV  OXT   O  OC    -1  -0.630  -0.8604   0.8807   1.3093
 AMV  H1    H  HCH1   0   0.178   4.4473  -1.2792  -0.5532
 AMV  H2    H  HCH1   0   0.264   3.8631  -0.5620   2.3621
 AMV  H3    H  HCH1   0   0.213   3.1078   0.8924  -0.2096
 AMV  HA    H  HNH1   0   0.393   1.8502  -1.0963   0.2750
 AMV  H4    H  HCH1   0   0.223   5.1519   1.7465   1.8657
 AMV  H5    H  HCH1   0   0.221   5.5494   0.6800  -0.9718
 AMV  HB    H  HOH1   0   0.459   5.2504   3.4995   0.5807
 AMV  H6C1  H  HCH2   0   0.202   7.5433   1.4658   1.2040
 AMV  H6C2  H  HCH2   0   0.229   7.2435   2.3431  -0.2963
 AMV  H6    H  HOH1   0   0.446   8.2025  -0.3005  -0.1893
 AMV  H8C1  H  HCH3   0   0.255   0.2989  -3.5334   2.0686
 AMV  H8C2  H  HCH3   0   0.269  -0.3517  -1.9083   2.2809
 AMV  H8C3  H  HCH3   0   0.240   0.1683  -2.4409   0.6829
 AMV  H9    H  HCH1   0   0.193   1.2233   1.5724   0.0990
 AMV  H111  H  HCH3   0   0.221  -0.0029   3.5764   0.8776
 AMV  H112  H  HCH3   0   0.227   1.7194   3.9252   0.6867
 AMV  H113  H  HCH3   0   0.219   1.0352   3.6861   2.2996
 AMV  H121  H  HCH3   0   0.239   5.6352  -4.3547   0.6345
 AMV  H122  H  HCH3   0   0.218   6.7446  -3.0459   0.2001
 AMV  H123  H  HCH3   0   0.213   5.3293  -3.3830  -0.8161

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
 AMV  C1   C2    single  1.529  0.020  1.529
 AMV  C1   O1    single  1.373  0.020  1.373
 AMV  C1   O5    single  1.405  0.020  1.405
 AMV  C1   H1    single  0.970  0.020  1.090
 AMV  C2   C3    single  1.535  0.020  1.535
 AMV  C2   N2    single  1.438  0.020  1.438
 AMV  C2   H2    single  0.970  0.020  1.090
 AMV  C3   C4    single  1.526  0.020  1.526
 AMV  C3   O3    single  1.395  0.020  1.395
 AMV  C3   H3    single  0.970  0.020  1.090
 AMV  C4   C5    single  1.532  0.020  1.532
 AMV  C4   O4    single  1.408  0.020  1.408
 AMV  C4   H4    single  0.970  0.020  1.090
 AMV  C5   C6    single  1.518  0.020  1.518
 AMV  C5   O5    single  1.413  0.020  1.413
 AMV  C5   H5    single  0.970  0.020  1.090
 AMV  C6   O6    single  1.406  0.020  1.406
 AMV  C6   H6C1  single  0.970  0.020  1.090
 AMV  C6   H6C2  single  0.970  0.020  1.090
 AMV  C7   C8    single  1.507  0.020  1.507
 AMV  C7   O7    double  1.222  0.020  1.222
 AMV  C7   N2    single  1.347  0.020  1.347
 AMV  C8   H8C1  single  0.970  0.020  1.090
 AMV  C8   H8C2  single  0.970  0.020  1.090
 AMV  C8   H8C3  single  0.970  0.020  1.090
 AMV  C9   C10   single  1.544  0.020  1.544
 AMV  C9   C11   single  1.523  0.020  1.523
 AMV  C9   O3    single  1.417  0.020  1.417
 AMV  C9   H9    single  0.970  0.020  1.090
 AMV  C10  O11   deloc   1.243  0.020  1.243
 AMV  C10  OXT   deloc   1.249  0.020  1.249
 AMV  C11  H111  single  0.970  0.020  1.090
 AMV  C11  H112  single  0.970  0.020  1.090
 AMV  C11  H113  single  0.970  0.020  1.090
 AMV  O1   C12   single  1.414  0.020  1.414
 AMV  O4   HB    single  0.850  0.020  0.980
 AMV  O6   H6    single  0.850  0.020  0.980
 AMV  N2   HA    single  0.860  0.020  1.020
 AMV  C12  H121  single  0.970  0.020  1.090
 AMV  C12  H122  single  0.970  0.020  1.090
 AMV  C12  H123  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
 AMV  H1    C1   O5    109.06  3.000
 AMV  H1    C1   O1    110.84  3.000
 AMV  O5    C1   O1    108.78  3.000
 AMV  H1    C1   C2    109.44  3.000
 AMV  O5    C1   C2    109.43  3.000
 AMV  O1    C1   C2    109.28  3.000
 AMV  H2    C2   N2    108.12  3.000
 AMV  H2    C2   C3    109.32  3.000
 AMV  N2    C2   C3    110.08  3.000
 AMV  H2    C2   C1    108.27  3.000
 AMV  N2    C2   C1    111.15  3.000
 AMV  C3    C2   C1    109.84  3.000
 AMV  H3    C3   O3    110.69  3.000
 AMV  H3    C3   C4    106.94  3.000
 AMV  O3    C3   C4    108.91  3.000
 AMV  H3    C3   C2    107.57  3.000
 AMV  O3    C3   C2    111.19  3.000
 AMV  C4    C3   C2    111.45  3.000
 AMV  H4    C4   O4    111.26  3.000
 AMV  H4    C4   C5    108.55  3.000
 AMV  O4    C4   C5    110.77  3.000
 AMV  H4    C4   C3    108.46  3.000
 AMV  O4    C4   C3    107.83  3.000
 AMV  C5    C4   C3    109.94  3.000
 AMV  H5    C5   O5    109.84  3.000
 AMV  H5    C5   C6    108.92  3.000
 AMV  O5    C5   C6    107.04  3.000
 AMV  H5    C5   C4    108.65  3.000
 AMV  O5    C5   C4    109.60  3.000
 AMV  C6    C5   C4    112.76  3.000
 AMV  H6C2  C6   H6C1  107.27  3.000
 AMV  H6C2  C6   O6    106.98  3.000
 AMV  H6C1  C6   O6    111.82  3.000
 AMV  H6C2  C6   C5    108.99  3.000
 AMV  H6C1  C6   C5    109.02  3.000
 AMV  O6    C6   C5    112.56  3.000
 AMV  N2    C7   O7    123.28  3.000
 AMV  N2    C7   C8    114.82  3.000
 AMV  O7    C7   C8    121.90  3.000
 AMV  H8C3  C8   H8C2  108.04  3.000
 AMV  H8C3  C8   H8C1  108.72  3.000
 AMV  H8C2  C8   H8C1  108.07  3.000
 AMV  H8C3  C8   C7    113.53  3.000
 AMV  H8C2  C8   C7    108.38  3.000
 AMV  H8C1  C8   C7    109.96  3.000
 AMV  H9    C9   O3    109.68  3.000
 AMV  H9    C9   C11   108.15  3.000
 AMV  O3    C9   C11   108.27  3.000
 AMV  H9    C9   C10   108.26  3.000
 AMV  O3    C9   C10   112.50  3.000
 AMV  C11   C9   C10   109.90  3.000
 AMV  OXT   C10  O11   127.34  3.000
 AMV  OXT   C10  C9    114.77  3.000
 AMV  O11   C10  C9    117.82  3.000
 AMV  H113  C11  H112  108.23  3.000
 AMV  H113  C11  H111  107.92  3.000
 AMV  H112  C11  H111  108.34  3.000
 AMV  H113  C11  C9    110.98  3.000
 AMV  H112  C11  C9    110.73  3.000
 AMV  H111  C11  C9    110.54  3.000
 AMV  C12   O1   C1    114.58  3.000
 AMV  C9    O3   C3    117.77  3.000
 AMV  HB    O4   C4    108.99  3.000
 AMV  C5    O5   C1    112.77  3.000
 AMV  H6    O6   C6    107.87  3.000
 AMV  HA    N2   C7    118.09  3.000
 AMV  HA    N2   C2    117.53  3.000
 AMV  C7    N2   C2    124.23  3.000
 AMV  H123  C12  H122  108.44  3.000
 AMV  H123  C12  H121  108.56  3.000
 AMV  H122  C12  H121  108.48  3.000
 AMV  H123  C12  O1    111.44  3.000
 AMV  H122  C12  O1    112.47  3.000
 AMV  H121  C12  O1    107.34  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
 AMV  CONST_01  C8    C7   N2  C2   180.00   0.0  0
 AMV  CONST_02  O7    C7   N2  C2     0.00   0.0  0
 AMV  CONST_03  HA    N2   C7  C8     0.00   0.0  0
 AMV  Var_01    H121  C12  O1  C1  -171.33  30.0  3
 AMV  Var_02    H8C1  C8   C7  O7   -43.11  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
 AMV  chir_01  C1  C2  O1   O5   positiv
 AMV  chir_02  C2  N2  C3   C1   positiv
 AMV  chir_03  C3  O3  C4   C2   negativ
 AMV  chir_04  C4  O4  C3   C5   negativ
 AMV  chir_05  C5  O5  C4   C6   negativ
 AMV  chir_06  C9  O3  C10  C11  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
 AMV  plan-1  C2   0.020
 AMV  plan-1  C7   0.020
 AMV  plan-1  C8   0.020
 AMV  plan-1  O7   0.020
 AMV  plan-1  N2   0.020
 AMV  plan-1  HA   0.020
 AMV  plan-2  C9   0.020
 AMV  plan-2  C10  0.020
 AMV  plan-2  O11  0.020
 AMV  plan-2  OXT  0.020

