# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 10:46:38 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 4-O-methyl-alpha-D-glucopyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]1[C@H](O)[C@@H](O)[C@@H](O)O[C@@H]1C(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
 GCV  GCV  '4-O-methyl-alpha-D-glucopyranuronic acid'  D-saccharide  25  14  .  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_GCV
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
 GCV  C7   C  CH3    0  -0.407   5.6245  -11.6509  7.1236
 GCV  C1   C  CH1    0   0.233   9.2269  -12.9653  3.5477
 GCV  C2   C  CH1    0   0.012   9.6959  -12.1971  4.7814
 GCV  C3   C  CH1    0  -0.008   8.8088  -12.5163  5.9779
 GCV  C4   C  CH1    0   0.013   7.3571  -12.2444  5.6065
 GCV  C5   C  CH1    0  -0.071   6.9764  -13.0202  4.3459
 GCV  C6   C  C      0   0.380   5.5488  -12.6542  3.8697
 GCV  O1   O  OH1    0  -0.663   9.4838  -14.3192  3.7449
 GCV  O2   O  OH1    0  -0.668  11.0482  -12.4962  5.0094
 GCV  O3   O  OH1    0  -0.672   9.2412  -11.7054  7.0485
 GCV  O4   O  O2     0  -0.501   6.5289  -12.6340  6.6813
 GCV  O5   O  O2     0  -0.507   7.8779  -12.6935  3.2946
 GCV  H71  H  HCH3   0   0.228   5.0391  -12.0844  7.9343
 GCV  H72  H  HCH3   0   0.205   6.1389  -10.7638  7.5082
 GCV  H73  H  HCH3   0   0.209   4.9360  -11.3285  6.3374
 GCV  H1   H  HCH1   0   0.228   9.7567  -12.5909  2.6627
 GCV  H2   H  HCH1   0   0.213   9.5670  -11.1289  4.5462
 GCV  H3   H  HCH1   0   0.211   8.9162  -13.5810  6.2326
 GCV  H4   H  HCH1   0   0.210   7.2507  -11.1697  5.4008
 GCV  H5   H  HCH1   0   0.195   7.0211  -14.0936  4.5672
 GCV  HO1  H  HOH1   0   0.457   9.3556  -14.7842  2.9112
 GCV  HO2  H  HOH1   0   0.448  11.3443  -11.9658  5.7559
 GCV  HO3  H  HOH1   0   0.452   8.8359  -12.0318  7.8578
 GCV  O6A  O  O      0  -0.596   4.6902  -13.5513  3.9498
 GCV  O6B  O  OC    -1  -0.601   5.3942  -11.4869  3.4647

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
 GCV  C7  O4   single  1.407  0.020  1.407
 GCV  C7  H71  single  0.970  0.020  1.090
 GCV  C7  H72  single  0.970  0.020  1.090
 GCV  C7  H73  single  0.970  0.020  1.090
 GCV  C1  C2   single  1.527  0.020  1.527
 GCV  C1  O1   single  1.392  0.020  1.392
 GCV  C1  O5   single  1.399  0.020  1.399
 GCV  C1  H1   single  0.970  0.020  1.090
 GCV  C2  C3   single  1.523  0.020  1.523
 GCV  C2  O2   single  1.404  0.020  1.404
 GCV  C2  H2   single  0.970  0.020  1.090
 GCV  C3  C4   single  1.523  0.020  1.523
 GCV  C3  O3   single  1.411  0.020  1.411
 GCV  C3  H3   single  0.970  0.020  1.090
 GCV  C4  C5   single  1.528  0.020  1.528
 GCV  C4  O4   single  1.412  0.020  1.412
 GCV  C4  H4   single  0.970  0.020  1.090
 GCV  C5  C6   single  1.549  0.020  1.549
 GCV  C5  O5   single  1.423  0.020  1.423
 GCV  C5  H5   single  0.970  0.020  1.090
 GCV  C6  O6A  deloc   1.244  0.020  1.244
 GCV  C6  O6B  deloc   1.245  0.020  1.245
 GCV  O1  HO1  single  0.850  0.020  0.980
 GCV  O2  HO2  single  0.850  0.020  0.980
 GCV  O3  HO3  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
 GCV  H73  C7  H72  108.02  3.000
 GCV  H73  C7  H71  108.28  3.000
 GCV  H72  C7  H71  108.26  3.000
 GCV  H73  C7  O4   112.62  3.000
 GCV  H72  C7  O4   111.99  3.000
 GCV  H71  C7  O4   107.53  3.000
 GCV  H1   C1  O5   104.67  3.000
 GCV  H1   C1  O1   110.91  3.000
 GCV  O5   C1  O1   113.11  3.000
 GCV  H1   C1  C2   109.37  3.000
 GCV  O5   C1  C2   110.15  3.000
 GCV  O1   C1  C2   108.55  3.000
 GCV  H2   C2  O2   110.74  3.000
 GCV  H2   C2  C3   107.63  3.000
 GCV  O2   C2  C3   112.88  3.000
 GCV  H2   C2  C1   106.23  3.000
 GCV  O2   C2  C1   108.66  3.000
 GCV  C3   C2  C1   110.50  3.000
 GCV  H3   C3  O3   110.53  3.000
 GCV  H3   C3  C4   108.81  3.000
 GCV  O3   C3  C4   111.99  3.000
 GCV  H3   C3  C2   109.14  3.000
 GCV  O3   C3  C2   107.29  3.000
 GCV  C4   C3  C2   109.03  3.000
 GCV  H4   C4  O4   110.82  3.000
 GCV  H4   C4  C5   108.53  3.000
 GCV  O4   C4  C5   109.98  3.000
 GCV  H4   C4  C3   108.21  3.000
 GCV  O4   C4  C3   108.92  3.000
 GCV  C5   C4  C3   110.37  3.000
 GCV  H5   C5  O5   110.36  3.000
 GCV  H5   C5  C6   109.32  3.000
 GCV  O5   C5  C6   107.61  3.000
 GCV  H5   C5  C4   108.67  3.000
 GCV  O5   C5  C4   109.57  3.000
 GCV  C6   C5  C4   111.30  3.000
 GCV  O6B  C6  O6A  127.67  3.000
 GCV  O6B  C6  C5   115.84  3.000
 GCV  O6A  C6  C5   116.48  3.000
 GCV  HO1  O1  C1   108.81  3.000
 GCV  HO2  O2  C2   107.75  3.000
 GCV  HO3  O3  C3   108.31  3.000
 GCV  C4   O4  C7   115.06  3.000
 GCV  C5   O5  C1   115.63  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
 GCV  Var_01  H71  C7  O4  C4  178.89  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
 GCV  chir_01  C1  C2  O1  O5  negativ
 GCV  chir_02  C2  O2  C1  C3  negativ
 GCV  chir_03  C3  O3  C2  C4  positiv
 GCV  chir_04  C4  O4  C5  C3  positiv
 GCV  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
 GCV  plan-1  C5   0.020
 GCV  plan-1  C6   0.020
 GCV  plan-1  O6A  0.020
 GCV  plan-1  O6B  0.020

