# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:59:32 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: N-[(3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-pyran-3-yl]acetamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)OC1=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
 GDL  GDL  'N-[(3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-pyran-3-yl]acetamide (non-preferred name)'  D-saccharide  28  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_GDL
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
 GDL  C1    C  C     0   0.574   1.2389  -0.0586   0.1112
 GDL  C2    C  CH1   0  -0.281  -0.1243   0.1431   0.7580
 GDL  C3    C  CH1   0   0.046  -1.2928  -0.3659  -0.0850
 GDL  C4    C  CH1   0  -0.018  -1.1464   0.1999  -1.4847
 GDL  C5    C  CH1   0  -0.014   0.1830  -0.2745  -2.0785
 GDL  C6    C  CH2   0  -0.155   0.5055   0.4201  -3.3826
 GDL  C8    C  CH3   0  -0.781   0.0732  -0.4736   4.4782
 GDL  N1    N  NH1   0  -0.637  -0.1522  -0.4140   2.0775
 GDL  O1    O  O     0  -0.418   2.2507  -0.1394   0.7527
 GDL  O3    O  OH1   0  -0.654  -2.5118   0.0613   0.4487
 GDL  O4    O  OH1   0  -0.660  -2.2015  -0.2707  -2.2806
 GDL  O5    O  O2    0  -0.442   1.3092  -0.0592  -1.2116
 GDL  O6    O  OH1   0  -0.667   1.6489  -0.1745  -3.9416
 GDL  O7    O  O     0  -0.488   0.1471   1.5341   3.1834
 GDL  H2    H  HCH1  0   0.318  -0.2385   1.2292   0.8565
 GDL  H3    H  HCH1  0   0.235  -1.2463  -1.4651  -0.1438
 GDL  H4    H  HCH1  0   0.246  -1.1516   1.2976  -1.4214
 GDL  H5    H  HCH1  0   0.260   0.1107  -1.3547  -2.2490
 GDL  H6C1  H  HCH2  0   0.210  -0.3629   0.3235  -4.0436
 GDL  H6C2  H  HCH2  0   0.211   0.6485   1.4921  -3.1900
 GDL  H8C1  H  HCH3  0   0.273   1.0862  -0.4433   4.8814
 GDL  H8C2  H  HCH3  0   0.269  -0.5843  -0.0138   5.2149
 GDL  H8C3  H  HCH3  0   0.252  -0.2138  -1.5159   4.3555
 GDL  HB    H  HNH1  0   0.409  -0.1486  -1.4196   2.1569
 GDL  HC    H  HOH1  0   0.456  -2.6317  -0.3582   1.3075
 GDL  HD    H  HOH1  0   0.464  -2.4591   0.4160  -2.9011
 GDL  H6    H  HOH1  0   0.461   1.8297   0.2576  -4.7813
 GDL  C7    C  C     0   0.531   0.0299   0.3197   3.1992

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
 GDL  C1  C2    single  1.522  0.020  1.522
 GDL  C1  O1    double  1.201  0.020  1.201
 GDL  C1  O5    single  1.325  0.020  1.325
 GDL  C2  C3    single  1.528  0.020  1.528
 GDL  C2  N1    single  1.433  0.020  1.433
 GDL  C2  H2    single  0.970  0.020  1.090
 GDL  C3  C4    single  1.517  0.020  1.517
 GDL  C3  O3    single  1.398  0.020  1.398
 GDL  C3  H3    single  0.970  0.020  1.090
 GDL  C4  C5    single  1.531  0.020  1.531
 GDL  C4  O4    single  1.403  0.020  1.403
 GDL  C4  H4    single  0.970  0.020  1.090
 GDL  C5  C6    single  1.512  0.020  1.512
 GDL  C5  O5    single  1.438  0.020  1.438
 GDL  C5  H5    single  0.970  0.020  1.090
 GDL  C6  O6    single  1.405  0.020  1.405
 GDL  C6  H6C1  single  0.970  0.020  1.090
 GDL  C6  H6C2  single  0.970  0.020  1.090
 GDL  C7  C8    single  1.506  0.020  1.506
 GDL  C7  N1    single  1.353  0.020  1.353
 GDL  C7  O7    double  1.220  0.020  1.220
 GDL  C8  H8C1  single  0.970  0.020  1.090
 GDL  C8  H8C2  single  0.970  0.020  1.090
 GDL  C8  H8C3  single  0.970  0.020  1.090
 GDL  N1  HB    single  0.860  0.020  1.020
 GDL  O3  HC    single  0.850  0.020  0.980
 GDL  O4  HD    single  0.850  0.020  0.980
 GDL  O6  H6    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
 GDL  O5    C1  O1    119.26  3.000
 GDL  O5    C1  C2    118.15  3.000
 GDL  O1    C1  C2    122.45  3.000
 GDL  H2    C2  N1    107.48  3.000
 GDL  H2    C2  C3    107.45  3.000
 GDL  N1    C2  C3    111.32  3.000
 GDL  H2    C2  C1    105.23  3.000
 GDL  N1    C2  C1    110.93  3.000
 GDL  C3    C2  C1    113.97  3.000
 GDL  H3    C3  O3    111.23  3.000
 GDL  H3    C3  C4    108.59  3.000
 GDL  O3    C3  C4    108.82  3.000
 GDL  H3    C3  C2    109.24  3.000
 GDL  O3    C3  C2    110.76  3.000
 GDL  C4    C3  C2    108.12  3.000
 GDL  H4    C4  O4    111.35  3.000
 GDL  H4    C4  C5    109.61  3.000
 GDL  O4    C4  C5    109.20  3.000
 GDL  H4    C4  C3    108.60  3.000
 GDL  O4    C4  C3    109.02  3.000
 GDL  C5    C4  C3    109.03  3.000
 GDL  H5    C5  O5    107.04  3.000
 GDL  H5    C5  C6    109.43  3.000
 GDL  O5    C5  C6    106.51  3.000
 GDL  H5    C5  C4    107.97  3.000
 GDL  O5    C5  C4    113.57  3.000
 GDL  C6    C5  C4    112.17  3.000
 GDL  H6C2  C6  H6C1  107.16  3.000
 GDL  H6C2  C6  O6    112.14  3.000
 GDL  H6C1  C6  O6    111.58  3.000
 GDL  H6C2  C6  C5    108.95  3.000
 GDL  H6C1  C6  C5    108.10  3.000
 GDL  O6    C6  C5    108.80  3.000
 GDL  H8C3  C8  H8C2  108.75  3.000
 GDL  H8C3  C8  H8C1  108.26  3.000
 GDL  H8C2  C8  H8C1  107.39  3.000
 GDL  H8C3  C8  C7    113.66  3.000
 GDL  H8C2  C8  C7    109.56  3.000
 GDL  H8C1  C8  C7    109.03  3.000
 GDL  HB    N1  C7    118.36  3.000
 GDL  HB    N1  C2    117.40  3.000
 GDL  C7    N1  C2    123.38  3.000
 GDL  HC    O3  C3    108.42  3.000
 GDL  HD    O4  C4    109.17  3.000
 GDL  C5    O5  C1    124.11  3.000
 GDL  H6    O6  C6    108.08  3.000
 GDL  O7    C7  N1    122.82  3.000
 GDL  O7    C7  C8    122.18  3.000
 GDL  N1    C7  C8    114.99  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
 GDL  CONST_01  C8    C7  N1  C2  180.00   0.0  0
 GDL  CONST_02  O7    C7  N1  C2    0.00   0.0  0
 GDL  CONST_03  HB    N1  C7  C8    0.00   0.0  0
 GDL  Var_01    O1    C1  O5  C5  165.15  30.0  1
 GDL  Var_02    H8C1  C8  C7  N1  111.13  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
 GDL  chir_01  C2  C1  C3  N1  negativ
 GDL  chir_02  C3  O3  C2  C4  positiv
 GDL  chir_03  C4  O4  C3  C5  negativ
 GDL  chir_04  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
 GDL  plan-1  C2  0.020
 GDL  plan-1  C8  0.020
 GDL  plan-1  N1  0.020
 GDL  plan-1  O7  0.020
 GDL  plan-1  HB  0.020
 GDL  plan-1  C7  0.020
 GDL  plan-2  C1  0.020
 GDL  plan-2  C2  0.020
 GDL  plan-2  O1  0.020
 GDL  plan-2  O5  0.020

