# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 17:03:14 2021
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-alpha-L-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@H](O)O[C@@H](CO)[C@@H](O)[C@H]1O
#
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
 YYQ  YYQ  2-(acetylamino)-2-deoxy-alpha-L-galactopyranose  L-saccharide  30  15  .  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_YYQ
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
 YYQ  C1   C  CR16  0   0.292  -2.5791   1.9239  36.9859
 YYQ  C2   C  CR16  0  -0.137  -3.0470   2.4006  38.3809
 YYQ  C7   C  C     0   0.523  -5.3811   1.5344  38.4382
 YYQ  C8   C  CH3   0  -0.775  -6.8209   1.9753  38.5604
 YYQ  C3   C  CR16  0   0.063  -2.4007   1.5378  39.4690
 YYQ  C4   C  CR16  0  -0.074  -0.9893   1.1482  39.0476
 YYQ  C5   C  CR16  0  -0.018  -1.1100   0.2437  37.8048
 YYQ  C6   C  CH2   0  -0.193   0.1419   0.2367  36.9338
 YYQ  N2   N  NH1   0  -0.639  -4.4778   2.5250  38.5390
 YYQ  O1   O  OH1   0  -0.653  -3.5808   2.1160  36.0633
 YYQ  O7   O  O     0  -0.502  -5.0854   0.3630  38.2528
 YYQ  O3   O  OH1   0  -0.671  -2.4404   2.2672  40.6704
 YYQ  O4   O  OH1   0  -0.672  -0.2411   2.3227  38.8372
 YYQ  O5   O  O     0  -0.509  -2.2349   0.5573  37.0025
 YYQ  O6   O  OH1   0  -0.674   1.2596   0.0302  37.7710
 YYQ  H1   H  HCR6  0   0.206  -1.6893   2.5141  36.7215
 YYQ  HO1  H  HOH1  0   0.462  -3.1953   2.1010  35.1808
 YYQ  H2   H  HCR6  0   0.272  -2.6694   3.4183  38.4964
 YYQ  H81  H  HCH3  0   0.260  -7.3497   1.3163  39.2472
 YYQ  H82  H  HCH3  0   0.246  -6.9379   3.0032  38.8986
 YYQ  H83  H  HCH3  0   0.265  -7.3051   1.8847  37.5868
 YYQ  HN2  H  HNH1  0   0.399  -4.8256   3.4553  38.6947
 YYQ  H3   H  HCR6  0   0.238  -2.9705   0.6067  39.5580
 YYQ  HO3  H  HOH1  0   0.451  -2.2601   1.6627  41.3968
 YYQ  H4   H  HCR6  0   0.242  -0.5374   0.5472  39.8480
 YYQ  HO4  H  HOH1  0   0.454   0.6766   2.0614  38.7015
 YYQ  H5   H  HCR6  0   0.247  -1.2913  -0.7709  38.1751
 YYQ  H61  H  HCH2  0   0.225   0.0451  -0.5598  36.1871
 YYQ  H62  H  HCH2  0   0.207   0.2163   1.1838  36.3848
 YYQ  HO6  H  HOH1  0   0.464   2.0564   0.0841  37.2356

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
 YYQ  C1  C2   single  1.547  0.020  1.547
 YYQ  C1  O5   single  1.409  0.020  1.409
 YYQ  C1  O1   single  1.375  0.020  1.375
 YYQ  C1  H1   single  0.970  0.020  1.090
 YYQ  C2  C3   single  1.532  0.020  1.532
 YYQ  C2  H2   single  0.970  0.020  1.090
 YYQ  C2  N2   single  1.445  0.020  1.445
 YYQ  C7  C8   single  1.511  0.020  1.511
 YYQ  C7  N2   single  1.344  0.020  1.344
 YYQ  C7  O7   double  1.222  0.020  1.222
 YYQ  C8  H81  single  0.970  0.020  1.090
 YYQ  C8  H82  single  0.970  0.020  1.090
 YYQ  C8  H83  single  0.970  0.020  1.090
 YYQ  C3  C4   single  1.524  0.020  1.524
 YYQ  C3  O3   single  1.406  0.020  1.406
 YYQ  C3  H3   single  0.970  0.020  1.090
 YYQ  C4  C5   single  1.542  0.020  1.542
 YYQ  C4  H4   single  0.970  0.020  1.090
 YYQ  C4  O4   single  1.408  0.020  1.408
 YYQ  C5  H5   single  0.970  0.020  1.090
 YYQ  C5  O5   single  1.417  0.020  1.417
 YYQ  C5  C6   single  1.525  0.020  1.525
 YYQ  C6  H61  single  0.970  0.020  1.090
 YYQ  C6  H62  single  0.970  0.020  1.090
 YYQ  C6  O6   single  1.412  0.020  1.412
 YYQ  N2  HN2  single  0.860  0.020  1.020
 YYQ  O1  HO1  single  0.850  0.020  0.980
 YYQ  O3  HO3  single  0.850  0.020  0.980
 YYQ  O4  HO4  single  0.850  0.020  0.980
 YYQ  O6  HO6  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
 YYQ  H1   C1  O5   109.00  3.000
 YYQ  H1   C1  O1   110.67  3.000
 YYQ  O5   C1  O1   108.73  3.000
 YYQ  H1   C1  C2   107.23  3.000
 YYQ  O1   C1  C2   109.98  3.000
 YYQ  O5   C1  C2   111.23  3.000
 YYQ  H2   C2  N2   104.52  3.000
 YYQ  N2   C2  C3   112.87  3.000
 YYQ  H2   C2  C3   107.70  3.000
 YYQ  N2   C2  C1   115.14  3.000
 YYQ  H2   C2  C1   106.14  3.000
 YYQ  C3   C2  C1   109.84  3.000
 YYQ  O7   C7  N2   123.71  3.000
 YYQ  O7   C7  C8   121.51  3.000
 YYQ  N2   C7  C8   114.78  3.000
 YYQ  H83  C8  H82  107.94  3.000
 YYQ  H83  C8  H81  107.28  3.000
 YYQ  H82  C8  H81  108.86  3.000
 YYQ  H83  C8  C7   109.06  3.000
 YYQ  H82  C8  C7   113.78  3.000
 YYQ  H81  C8  C7   109.71  3.000
 YYQ  H3   C3  O3   110.91  3.000
 YYQ  H3   C3  C4   106.68  3.000
 YYQ  O3   C3  C4   113.27  3.000
 YYQ  H3   C3  C2   108.49  3.000
 YYQ  O3   C3  C2   107.63  3.000
 YYQ  C4   C3  C2   109.78  3.000
 YYQ  H4   C4  O4   110.29  3.000
 YYQ  O4   C4  C5   114.23  3.000
 YYQ  H4   C4  C5   107.38  3.000
 YYQ  O4   C4  C3   108.67  3.000
 YYQ  H4   C4  C3   108.63  3.000
 YYQ  C5   C4  C3   107.48  3.000
 YYQ  H5   C5  O5   105.37  3.000
 YYQ  O5   C5  C6   109.23  3.000
 YYQ  H5   C5  C6   108.94  3.000
 YYQ  C6   C5  C4   113.50  3.000
 YYQ  O5   C5  C4   112.88  3.000
 YYQ  H5   C5  C4   106.49  3.000
 YYQ  H62  C6  H61  107.00  3.000
 YYQ  H62  C6  O6   111.67  3.000
 YYQ  H61  C6  O6   111.57  3.000
 YYQ  O6   C6  C5   108.17  3.000
 YYQ  H62  C6  C5   109.72  3.000
 YYQ  H61  C6  C5   108.66  3.000
 YYQ  HN2  N2  C7   117.46  3.000
 YYQ  HN2  N2  C2   116.05  3.000
 YYQ  C7   N2  C2   126.42  3.000
 YYQ  HO1  O1  C1   108.72  3.000
 YYQ  HO3  O3  C3   108.29  3.000
 YYQ  HO4  O4  C4   107.50  3.000
 YYQ  C5   O5  C1   114.53  3.000
 YYQ  HO6  O6  C6   108.52  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
 YYQ  CONST_01  C8   C7  N2  C2   180.00   0.0  0
 YYQ  CONST_02  O7   C7  N2  C2     0.00   0.0  0
 YYQ  CONST_03  HN2  N2  C7  C8     0.00   0.0  0
 YYQ  Var_01    H81  C8  C7  N2  -133.06  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
 YYQ  chir_01  C1  C2  O5  O1  negativ
 YYQ  chir_02  C2  N2  C3  C1  negativ
 YYQ  chir_03  C3  O3  C2  C4  negativ
 YYQ  chir_04  C4  O4  C5  C3  positiv
 YYQ  chir_05  C5  O5  C4  C6  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
 YYQ  plan-1  C2   0.020
 YYQ  plan-1  C7   0.020
 YYQ  plan-1  C8   0.020
 YYQ  plan-1  N2   0.020
 YYQ  plan-1  O7   0.020
 YYQ  plan-1  HN2  0.020

