# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:59:20 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-(acetylamino)-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](O)[C@@H](CO)O[C@@H](O)[C@@H]1NC(C)=O)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
 AMU  AMU  2-(acetylamino)-3-O-[(1R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranose  D-saccharide  38  20  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AMU
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
 AMU  C1    C  CH1    0   0.306   3.6497  20.9993  11.0313
 AMU  C2    C  CH1    0  -0.147   3.2944  22.4421  11.3883
 AMU  C3    C  CH1    0   0.039   4.5577  23.3099  11.4843
 AMU  C4    C  CH1    0   0.026   5.5868  22.6503  12.3956
 AMU  C5    C  CH1    0  -0.012   5.8086  21.2011  11.9362
 AMU  C6    C  CH2    0  -0.193   6.8129  20.4382  12.7728
 AMU  C7    C  C      0   0.520   1.0990  23.3288  10.6909
 AMU  C8    C  CH3    0  -0.780   0.3593  23.9738   9.5451
 AMU  C9    C  CH1    0  -0.081   4.2016  25.6387  11.0266
 AMU  C10   C  C      0   0.384   2.9947  26.5772  11.2668
 AMU  C11   C  CH3    0  -0.664   5.5163  26.4095  11.0816
 AMU  O1    O  OH1    0  -0.649   2.5078  20.2325  11.0999
 AMU  O3    O  O2     0  -0.495   4.2204  24.5774  11.9670
 AMU  O4    O  OH1    0  -0.664   6.7834  23.3847  12.3147
 AMU  O5    O  O2     0  -0.497   4.5824  20.5007  11.9579
 AMU  O6    O  OH1    0  -0.667   6.4135  20.4510  14.1221
 AMU  O7    O  O      0  -0.495   0.5593  23.1342  11.7700
 AMU  O10   O  O      0  -0.618   2.8713  27.4741  10.4071
 AMU  O11   O  OC    -1  -0.595   2.2777  26.3787  12.2616
 AMU  N2    N  NH1    0  -0.630   2.3794  23.0036  10.4293
 AMU  H1    H  HCH1   0   0.181   4.0969  20.9749  10.0207
 AMU  H2    H  HCH1   0   0.264   2.7992  22.4358  12.3627
 AMU  H3    H  HCH1   0   0.212   5.0055  23.3762  10.4783
 AMU  H4    H  HCH1   0   0.221   5.1891  22.6440  13.4185
 AMU  H5    H  HCH1   0   0.220   6.2117  21.2279  10.9097
 AMU  H61   H  HCH2   0   0.216   6.8876  19.4167  12.3772
 AMU  H62   H  HCH2   0   0.206   7.7971  20.8995  12.6287
 AMU  H81   H  HCH3   0   0.246   0.9377  24.0346   8.6251
 AMU  H82   H  HCH3   0   0.261  -0.5571  23.4199   9.3430
 AMU  H83   H  HCH3   0   0.264   0.0709  24.9845   9.8350
 AMU  H9    H  HCH1   0   0.198   4.0884  25.2315  10.0128
 AMU  H111  H  HCH3   0   0.221   6.3642  25.7542  10.8809
 AMU  H112  H  HCH3   0   0.216   5.5254  27.2085  10.3425
 AMU  H113  H  HCH3   0   0.213   5.6665  26.8574  12.0661
 AMU  HO1   H  HOH1   0   0.461   2.6475  19.4044  10.6284
 AMU  HO4   H  HOH1   0   0.456   7.2732  23.2752  13.1345
 AMU  HO6   H  HOH1   0   0.457   7.1036  20.0344  14.6453
 AMU  HN2   H  HNH1   0   0.398   2.7383  23.1934   9.5063

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
 AMU  C1   C2    single  1.528  0.020  1.528
 AMU  C1   O1    single  1.377  0.020  1.377
 AMU  C1   O5    single  1.406  0.020  1.406
 AMU  C1   H1    single  0.970  0.020  1.090
 AMU  C2   C3    single  1.536  0.020  1.536
 AMU  C2   N2    single  1.439  0.020  1.439
 AMU  C2   H2    single  0.970  0.020  1.090
 AMU  C3   C4    single  1.525  0.020  1.525
 AMU  C3   O3    single  1.398  0.020  1.398
 AMU  C3   H3    single  0.970  0.020  1.090
 AMU  C4   C5    single  1.536  0.020  1.536
 AMU  C4   O4    single  1.406  0.020  1.406
 AMU  C4   H4    single  0.970  0.020  1.090
 AMU  C5   C6    single  1.513  0.020  1.513
 AMU  C5   O5    single  1.412  0.020  1.412
 AMU  C5   H5    single  0.970  0.020  1.090
 AMU  C6   O6    single  1.407  0.020  1.407
 AMU  C6   H61   single  0.970  0.020  1.090
 AMU  C6   H62   single  0.970  0.020  1.090
 AMU  C7   C8    single  1.509  0.020  1.509
 AMU  C7   O7    double  1.222  0.020  1.222
 AMU  C7   N2    single  1.347  0.020  1.347
 AMU  C8   H81   single  0.970  0.020  1.090
 AMU  C8   H82   single  0.970  0.020  1.090
 AMU  C8   H83   single  0.970  0.020  1.090
 AMU  C9   C10   single  1.548  0.020  1.548
 AMU  C9   C11   single  1.525  0.020  1.525
 AMU  C9   O3    single  1.418  0.020  1.418
 AMU  C9   H9    single  0.970  0.020  1.090
 AMU  C10  O10   deloc   1.249  0.020  1.249
 AMU  C10  O11   deloc   1.242  0.020  1.242
 AMU  C11  H111  single  0.970  0.020  1.090
 AMU  C11  H112  single  0.970  0.020  1.090
 AMU  C11  H113  single  0.970  0.020  1.090
 AMU  O1   HO1   single  0.850  0.020  0.980
 AMU  O4   HO4   single  0.850  0.020  0.980
 AMU  O6   HO6   single  0.850  0.020  0.980
 AMU  N2   HN2   single  0.860  0.020  1.020

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
 AMU  H1    C1   O5    109.05  3.000
 AMU  H1    C1   O1    111.63  3.000
 AMU  O5    C1   O1    108.65  3.000
 AMU  H1    C1   C2    109.18  3.000
 AMU  O5    C1   C2    109.58  3.000
 AMU  O1    C1   C2    108.74  3.000
 AMU  H2    C2   N2    107.95  3.000
 AMU  H2    C2   C3    108.68  3.000
 AMU  N2    C2   C3    110.13  3.000
 AMU  H2    C2   C1    107.94  3.000
 AMU  N2    C2   C1    111.13  3.000
 AMU  C3    C2   C1    110.91  3.000
 AMU  H3    C3   O3    111.01  3.000
 AMU  H3    C3   C4    107.28  3.000
 AMU  O3    C3   C4    110.41  3.000
 AMU  H3    C3   C2    108.12  3.000
 AMU  O3    C3   C2    109.61  3.000
 AMU  C4    C3   C2    110.38  3.000
 AMU  H4    C4   O4    111.40  3.000
 AMU  H4    C4   C5    109.01  3.000
 AMU  O4    C4   C5    110.65  3.000
 AMU  H4    C4   C3    108.36  3.000
 AMU  O4    C4   C3    108.30  3.000
 AMU  C5    C4   C3    109.07  3.000
 AMU  H5    C5   O5    110.10  3.000
 AMU  H5    C5   C6    106.51  3.000
 AMU  O5    C5   C6    108.53  3.000
 AMU  H5    C5   C4    107.94  3.000
 AMU  O5    C5   C4    109.75  3.000
 AMU  C6    C5   C4    113.95  3.000
 AMU  H62   C6   H61   106.44  3.000
 AMU  H62   C6   O6    112.14  3.000
 AMU  H61   C6   O6    111.91  3.000
 AMU  H62   C6   C5    108.12  3.000
 AMU  H61   C6   C5    108.36  3.000
 AMU  O6    C6   C5    109.70  3.000
 AMU  N2    C7   O7    123.57  3.000
 AMU  N2    C7   C8    114.95  3.000
 AMU  O7    C7   C8    121.47  3.000
 AMU  H83   C8   H82   107.34  3.000
 AMU  H83   C8   H81   108.28  3.000
 AMU  H82   C8   H81   108.57  3.000
 AMU  H83   C8   C7    108.91  3.000
 AMU  H82   C8   C7    109.62  3.000
 AMU  H81   C8   C7    113.91  3.000
 AMU  H9    C9   O3    109.63  3.000
 AMU  H9    C9   C11   108.03  3.000
 AMU  O3    C9   C11   110.05  3.000
 AMU  H9    C9   C10   106.72  3.000
 AMU  O3    C9   C10   111.17  3.000
 AMU  C11   C9   C10   111.11  3.000
 AMU  O11   C10  O10   127.52  3.000
 AMU  O11   C10  C9    118.53  3.000
 AMU  O10   C10  C9    113.95  3.000
 AMU  H113  C11  H112  108.06  3.000
 AMU  H113  C11  H111  107.79  3.000
 AMU  H112  C11  H111  108.04  3.000
 AMU  H113  C11  C9    111.00  3.000
 AMU  H112  C11  C9    110.72  3.000
 AMU  H111  C11  C9    111.10  3.000
 AMU  HO1   O1   C1    109.52  3.000
 AMU  C9    O3   C3    116.93  3.000
 AMU  HO4   O4   C4    108.97  3.000
 AMU  C5    O5   C1    112.95  3.000
 AMU  HO6   O6   C6    108.32  3.000
 AMU  HN2   N2   C7    118.08  3.000
 AMU  HN2   N2   C2    117.19  3.000
 AMU  C7    N2   C2    124.69  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
 AMU  CONST_01  C8   C7  N2  C2   180.00   0.0  0
 AMU  CONST_02  O7   C7  N2  C2     0.00   0.0  0
 AMU  CONST_03  HN2  N2  C7  C8     0.00   0.0  0
 AMU  Var_01    H81  C8  C7  O7  -176.59  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
 AMU  chir_01  C1  C2  O1   O5   positiv
 AMU  chir_02  C2  N2  C3   C1   positiv
 AMU  chir_03  C3  O3  C4   C2   negativ
 AMU  chir_04  C4  O4  C3   C5   negativ
 AMU  chir_05  C5  O5  C4   C6   negativ
 AMU  chir_06  C9  O3  C11  C10  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
 AMU  plan-1  C2   0.020
 AMU  plan-1  C7   0.020
 AMU  plan-1  C8   0.020
 AMU  plan-1  O7   0.020
 AMU  plan-1  N2   0.020
 AMU  plan-1  HN2  0.020
 AMU  plan-2  C9   0.020
 AMU  plan-2  C10  0.020
 AMU  plan-2  O10  0.020
 AMU  plan-2  O11  0.020

