# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 14:07:16 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: methyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranosiduronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1O[C@@H]([C@@H](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
 6C2  6C2  'methyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranosiduronic acid'  D-saccharide  31  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 GRAND
;

data_comp_6C2
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
 6C2  O1   O  OH1    0  -0.708  -2.2655  -2.2024  -0.2598
 6C2  C11  C  CH1    0   0.346   0.3969   0.9343  -0.4047
 6C2  O11  O  O2     0  -0.485   1.2040   1.9650   0.0167
 6C2  O51  O  O2     0  -0.487  -0.9029   1.1600   0.0678
 6C2  C51  C  CH1    0  -0.159  -1.8175   0.1816  -0.3621
 6C2  C61  C  C      0   0.438  -3.2464   0.5729   0.0620
 6C2  O61  O  OC    -1  -0.617  -4.0830  -0.3685   0.0039
 6C2  C41  C  CH1    0   0.019  -1.4126  -1.1891   0.2009
 6C2  C31  C  CH1    0   0.041   0.0113  -1.5223  -0.2226
 6C2  O31  O  OH1    0  -0.666   0.4893  -2.6952   0.3853
 6C2  C21  C  CH1    0  -0.165   0.9526  -0.3814   0.1507
 6C2  N2   N  NH1    0  -0.625   2.2799  -0.6261  -0.3484
 6C2  C7   C  C      0   0.524   3.4000  -0.5254   0.3891
 6C2  C8   C  CH3    0  -0.780   4.6834  -0.7948  -0.3564
 6C2  O7   O  O      0  -0.506   3.4000  -0.2495   1.5809
 6C2  C9   C  CH3    0  -0.410   0.9960   3.1878  -0.6623
 6C2  O10  O  O      0  -0.557  -3.4684   1.7373   0.3962
 6C2  H13  H  HCH1   0   0.227  -1.8121   0.1116  -1.4652
 6C2  H15  H  HCH1   0   0.193  -1.4317  -1.1187   1.3030
 6C2  H16  H  HCH1   0   0.199   0.0110  -1.6255  -1.3217
 6C2  H17  H  HOH1   0   0.452  -0.0957  -3.4188   0.1378
 6C2  H18  H  HCH1   0   0.268   1.0075  -0.3008   1.2392
 6C2  H19  H  HNH1   0   0.398   2.3730  -0.8511  -1.3267
 6C2  H20  H  HCH3   0   0.247   4.5430  -1.0009  -1.4156
 6C2  H21  H  HCH3   0   0.265   5.3446   0.0656  -0.2579
 6C2  H22  H  HCH3   0   0.266   5.1914  -1.6464   0.0965
 6C2  H23  H  HCH3   0   0.237   1.7757   3.8752  -0.3390
 6C2  H24  H  HCH3   0   0.211   1.0724   3.0613  -1.7474
 6C2  H25  H  HCH3   0   0.219   0.0242   3.6315  -0.4333
 6C2  H2   H  HOH1   0   0.441  -3.1558  -1.7787  -0.2154
 6C2  H12  H  HCH1   0   0.173   0.3806   0.8771  -1.5120

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
 6C2  O10  C61  deloc   1.232  0.020  1.232
 6C2  C9   O11  single  1.414  0.020  1.414
 6C2  O61  C61  deloc   1.261  0.020  1.261
 6C2  C61  C51  single  1.541  0.020  1.541
 6C2  O51  C51  single  1.407  0.020  1.407
 6C2  O51  C11  single  1.401  0.020  1.401
 6C2  C51  C41  single  1.536  0.020  1.536
 6C2  O11  C11  single  1.375  0.020  1.375
 6C2  C11  C21  single  1.532  0.020  1.532
 6C2  C41  O1   single  1.402  0.020  1.402
 6C2  C41  C31  single  1.522  0.020  1.522
 6C2  C21  C31  single  1.525  0.020  1.525
 6C2  C21  N2   single  1.439  0.020  1.439
 6C2  C31  O31  single  1.405  0.020  1.405
 6C2  N2   C7   single  1.345  0.020  1.345
 6C2  C8   C7   single  1.508  0.020  1.508
 6C2  C7   O7   double  1.223  0.020  1.223
 6C2  C11  H12  single  0.970  0.020  1.090
 6C2  C51  H13  single  0.970  0.020  1.090
 6C2  C41  H15  single  0.970  0.020  1.090
 6C2  C31  H16  single  0.970  0.020  1.090
 6C2  O31  H17  single  0.850  0.020  0.980
 6C2  C21  H18  single  0.970  0.020  1.090
 6C2  N2   H19  single  0.860  0.020  1.020
 6C2  C8   H20  single  0.970  0.020  1.090
 6C2  C8   H21  single  0.970  0.020  1.090
 6C2  C8   H22  single  0.970  0.020  1.090
 6C2  C9   H23  single  0.970  0.020  1.090
 6C2  C9   H24  single  0.970  0.020  1.090
 6C2  C9   H25  single  0.970  0.020  1.090
 6C2  O1   H2   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
 6C2  H2   O1   C41  102.92  3.000
 6C2  H12  C11  C21  108.84  3.000
 6C2  H12  C11  O51  109.35  3.000
 6C2  C21  C11  O51  110.64  3.000
 6C2  H12  C11  O11  110.69  3.000
 6C2  C21  C11  O11  108.64  3.000
 6C2  O51  C11  O11  108.68  3.000
 6C2  C9   O11  C11  114.50  3.000
 6C2  C51  O51  C11  112.83  3.000
 6C2  H13  C51  C41  107.93  3.000
 6C2  H13  C51  C61  107.17  3.000
 6C2  C41  C51  C61  111.72  3.000
 6C2  H13  C51  O51  110.24  3.000
 6C2  C41  C51  O51  109.71  3.000
 6C2  C61  C51  O51  110.01  3.000
 6C2  O10  C61  O61  126.79  3.000
 6C2  O61  C61  C51  114.39  3.000
 6C2  O10  C61  C51  118.81  3.000
 6C2  H15  C41  C31  107.92  3.000
 6C2  H15  C41  C51  107.71  3.000
 6C2  C31  C41  C51  109.87  3.000
 6C2  H15  C41  O1   111.31  3.000
 6C2  C31  C41  O1   108.62  3.000
 6C2  C51  C41  O1   111.35  3.000
 6C2  H16  C31  C21  108.28  3.000
 6C2  H16  C31  O31  110.66  3.000
 6C2  C21  C31  O31  107.97  3.000
 6C2  H16  C31  C41  107.29  3.000
 6C2  O31  C31  C41  112.37  3.000
 6C2  C21  C31  C41  110.20  3.000
 6C2  H17  O31  C31  108.03  3.000
 6C2  H18  C21  N2   108.16  3.000
 6C2  H18  C21  C31  109.26  3.000
 6C2  N2   C21  C31  110.92  3.000
 6C2  H18  C21  C11  108.41  3.000
 6C2  N2   C21  C11  110.78  3.000
 6C2  C31  C21  C11  109.25  3.000
 6C2  H19  N2   C7   118.16  3.000
 6C2  H19  N2   C21  117.37  3.000
 6C2  C7   N2   C21  124.42  3.000
 6C2  O7   C7   C8   121.45  3.000
 6C2  O7   C7   N2   123.45  3.000
 6C2  C8   C7   N2   115.10  3.000
 6C2  H22  C8   H21  107.25  3.000
 6C2  H22  C8   H20  108.45  3.000
 6C2  H21  C8   H20  108.41  3.000
 6C2  H22  C8   C7   109.31  3.000
 6C2  H21  C8   C7   109.31  3.000
 6C2  H20  C8   C7   113.90  3.000
 6C2  H25  C9   H24  108.45  3.000
 6C2  H25  C9   H23  108.56  3.000
 6C2  H24  C9   H23  108.50  3.000
 6C2  H25  C9   O11  112.42  3.000
 6C2  H24  C9   O11  111.45  3.000
 6C2  H23  C9   O11  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
 6C2  CONST_01  C8   C7  N2   C21   180.00   0.0  0
 6C2  CONST_02  O7   C7  N2   C21     0.00   0.0  0
 6C2  CONST_03  H19  N2  C7   C8      0.00   0.0  0
 6C2  Var_01    H23  C9  O11  C11  -172.42  30.0  3
 6C2  Var_02    H20  C8  C7   N2      2.25  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
 6C2  chir_01  C11  O51  O11  C21  negativ
 6C2  chir_02  C51  O51  C61  C41  positiv
 6C2  chir_03  C41  O1   C51  C31  positiv
 6C2  chir_04  C31  O31  C41  C21  negativ
 6C2  chir_05  C21  N2   C31  C11  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
 6C2  plan-1  C21  0.020
 6C2  plan-1  N2   0.020
 6C2  plan-1  C7   0.020
 6C2  plan-1  C8   0.020
 6C2  plan-1  O7   0.020
 6C2  plan-1  H19  0.020
 6C2  plan-2  C51  0.020
 6C2  plan-2  C61  0.020
 6C2  plan-2  O61  0.020
 6C2  plan-2  O10  0.020

