# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 04:33:34 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  32  17  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.663  -2.2486  -2.1636  -0.2868
 6C2  C11  C  CH1   0   0.340   0.4209   0.9762  -0.4315
 6C2  O11  O  O2    0  -0.481   1.2236   2.0031  -0.0096
 6C2  O51  O  O2    0  -0.492  -0.8841   1.2060   0.0511
 6C2  C51  C  CH1   0  -0.069  -1.8069   0.2453  -0.3761
 6C2  C61  C  C     0   0.497  -3.1636   0.6855   0.1305
 6C2  O61  O  OH1   0  -0.585  -4.1438   0.0858  -0.5263
 6C2  C41  C  CH1   0  -0.009  -1.4214  -1.1377   0.1930
 6C2  C31  C  CH1   0   0.038   0.0054  -1.4724  -0.2391
 6C2  O31  O  OH1   0  -0.658   0.4651  -2.6447   0.3731
 6C2  C21  C  CH1   0  -0.164   0.9592  -0.3409   0.1305
 6C2  N2   N  NH1   0  -0.628   2.2827  -0.6041  -0.3651
 6C2  C7   C  C     0   0.526   3.4016  -0.5006   0.3769
 6C2  C8   C  CH3   0  -0.780   4.6852  -0.7946  -0.3576
 6C2  O7   O  O     0  -0.502   3.3961  -0.2028   1.5626
 6C2  C9   C  CH3   0  -0.412   1.0379   3.2231  -0.7039
 6C2  O10  O  O     0  -0.422  -3.3257   1.4602   1.0348
 6C2  H13  H  HCH1  0   0.267  -1.8415   0.1760  -1.4744
 6C2  H14  H  HOH1  0   0.489  -5.0025   0.3434  -0.1565
 6C2  H15  H  HCH1  0   0.246  -1.4441  -1.0773   1.2909
 6C2  H16  H  HCH1  0   0.216  -0.0002  -1.5780  -1.3378
 6C2  H17  H  HOH1  0   0.454  -0.1285  -3.3627   0.1279
 6C2  H18  H  HCH1  0   0.278   1.0127  -0.2560   1.2189
 6C2  H19  H  HNH1  0   0.401   2.3756  -0.8543  -1.3373
 6C2  H20  H  HCH3  0   0.248   4.5485  -1.0045  -1.4164
 6C2  H21  H  HCH3  0   0.266   5.3593   0.0557  -0.2588
 6C2  H22  H  HCH3  0   0.267   5.1758  -1.6518   0.1039
 6C2  H23  H  HCH3  0   0.241   1.8183   3.9050  -0.3721
 6C2  H24  H  HCH3  0   0.216   1.1318   3.0850  -1.7857
 6C2  H25  H  HCH3  0   0.222   0.0667   3.6766  -0.4937
 6C2  H2   H  HOH1  0   0.465  -3.0080  -2.2656   0.2935
 6C2  H12  H  HCH1  0   0.189   0.3942   0.9203  -1.5371

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  double  1.202  0.020  1.202
 6C2  C9   O11  single  1.416  0.020  1.416
 6C2  O61  C61  single  1.324  0.020  1.324
 6C2  C61  C51  single  1.514  0.020  1.514
 6C2  O51  C51  single  1.399  0.020  1.399
 6C2  O51  C11  single  1.410  0.020  1.410
 6C2  C51  C41  single  1.544  0.020  1.544
 6C2  O11  C11  single  1.370  0.020  1.370
 6C2  C11  C21  single  1.530  0.020  1.530
 6C2  C41  O1   single  1.403  0.020  1.403
 6C2  C41  C31  single  1.528  0.020  1.528
 6C2  C21  C31  single  1.525  0.020  1.525
 6C2  C21  N2   single  1.438  0.020  1.438
 6C2  C31  O31  single  1.400  0.020  1.400
 6C2  N2   C7   single  1.347  0.020  1.347
 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  O61  H14  single  0.850  0.020  0.980
 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  109.69  3.000
 6C2  H12  C11  C21  109.38  3.000
 6C2  H12  C11  O51  109.13  3.000
 6C2  C21  C11  O51  109.89  3.000
 6C2  H12  C11  O11  111.06  3.000
 6C2  C21  C11  O11  109.03  3.000
 6C2  O51  C11  O11  108.34  3.000
 6C2  C9   O11  C11  114.71  3.000
 6C2  C51  O51  C11  113.20  3.000
 6C2  H13  C51  C41  108.61  3.000
 6C2  H13  C51  C61  108.91  3.000
 6C2  C41  C51  C61  111.15  3.000
 6C2  H13  C51  O51  111.63  3.000
 6C2  C41  C51  O51  109.74  3.000
 6C2  C61  C51  O51  106.81  3.000
 6C2  O10  C61  O61  124.44  3.000
 6C2  O61  C61  C51  111.46  3.000
 6C2  O10  C61  C51  124.07  3.000
 6C2  H14  O61  C61  110.25  3.000
 6C2  H15  C41  C31  108.28  3.000
 6C2  H15  C41  C51  108.27  3.000
 6C2  C31  C41  C51  108.97  3.000
 6C2  H15  C41  O1   111.69  3.000
 6C2  C31  C41  O1   107.08  3.000
 6C2  C51  C41  O1   112.44  3.000
 6C2  H16  C31  C21  108.38  3.000
 6C2  H16  C31  O31  110.91  3.000
 6C2  C21  C31  O31  108.05  3.000
 6C2  H16  C31  C41  107.32  3.000
 6C2  O31  C31  C41  111.49  3.000
 6C2  C21  C31  C41  110.66  3.000
 6C2  H17  O31  C31  108.09  3.000
 6C2  H18  C21  N2   108.21  3.000
 6C2  H18  C21  C31  109.24  3.000
 6C2  N2   C21  C31  110.87  3.000
 6C2  H18  C21  C11  108.43  3.000
 6C2  N2   C21  C11  110.79  3.000
 6C2  C31  C21  C11  109.25  3.000
 6C2  H19  N2   C7   118.29  3.000
 6C2  H19  N2   C21  117.57  3.000
 6C2  C7   N2   C21  124.12  3.000
 6C2  O7   C7   C8   121.58  3.000
 6C2  O7   C7   N2   123.33  3.000
 6C2  C8   C7   N2   115.08  3.000
 6C2  H22  C8   H21  107.27  3.000
 6C2  H22  C8   H20  108.46  3.000
 6C2  H21  C8   H20  108.45  3.000
 6C2  H22  C8   C7   109.28  3.000
 6C2  H21  C8   C7   109.29  3.000
 6C2  H20  C8   C7   113.87  3.000
 6C2  H25  C9   H24  108.59  3.000
 6C2  H25  C9   H23  108.60  3.000
 6C2  H24  C9   H23  108.59  3.000
 6C2  H25  C9   O11  112.33  3.000
 6C2  H24  C9   O11  111.38  3.000
 6C2  H23  C9   O11  107.24  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  H14  O61  C61  C51   180.00   0.0  0
 6C2  CONST_04  H19  N2   C7   C8      0.00   0.0  0
 6C2  Var_01    H23  C9   O11  C11  -172.37  30.0  3
 6C2  Var_02    H20  C8   C7   N2      3.04  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
 6C2  plan-2  H14  0.020

