# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 00:19:40 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (2S,3R,4S,5S,6R)-2-(acetylamino)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-carboxamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@]1(O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)C(N)=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
 CR6  CR6  '(2S,3R,4S,5S,6R)-2-(acetylamino)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-carboxamide (non-preferred name)'  D-saccharide  34  18  .  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_CR6
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
 CR6  N1    N  NH2   0  -0.785  -1.4393   2.3746   0.3460
 CR6  C2    C  CR16  0   0.009   1.3659  -0.1404   0.3763
 CR6  O2    O  OH1   0  -0.665   2.2972   0.5172   1.1884
 CR6  C4    C  CR16  0   0.007   0.6109  -0.7806  -1.9059
 CR6  C5    C  CR16  0  -0.044  -0.7524  -0.1821  -1.5514
 CR6  C6    C  CH2   0  -0.155  -1.8968  -0.9063  -2.2245
 CR6  C1    C  CR6   0   0.353  -0.0421   0.4246   0.6434
 CR6  C3    C  CR16  0   0.001   1.7067  -0.0819  -1.1088
 CR6  O3    O  OH1   0  -0.674   2.9478  -0.7266  -1.2700
 CR6  O4    O  OH1   0  -0.671   0.9095  -0.6137  -3.2735
 CR6  O5    O  O     0  -0.487  -0.9733  -0.2674  -0.1512
 CR6  N2    N  NH1   0  -0.701  -0.4356   0.2616   2.0180
 CR6  C7    C  C     0   0.523  -0.4921  -0.9085   2.7058
 CR6  O7    O  O     0  -0.474  -0.2428  -1.9954   2.2178
 CR6  C8    C  CH3   0  -0.785  -0.8705  -0.7392   4.1568
 CR6  C9    C  C     0   0.459  -0.1675   1.9536   0.3620
 CR6  O9    O  O     0  -0.440   0.7914   2.6851   0.2093
 CR6  H1N1  H  HNH2  0   0.408  -1.6430   3.3407   0.1449
 CR6  H2N1  H  HNH2  0   0.411  -2.2133   1.7306   0.3449
 CR6  H21   H  HCR6  0   0.254   1.3108  -1.2025   0.6415
 CR6  H1O2  H  HOH1  0   0.455   3.0223  -0.0906   1.3560
 CR6  H41   H  HCR6  0   0.225   0.6097  -1.8447  -1.6287
 CR6  H51   H  HCR6  0   0.230  -0.7700   0.8678  -1.8846
 CR6  H61   H  HCH2  0   0.205  -1.7036  -0.9269  -3.3033
 CR6  H62   H  HCH2  0   0.203  -1.9172  -1.9495  -1.8788
 CR6  H31   H  HCR6  0   0.218   1.7706   0.9638  -1.4419
 CR6  H1O3  H  HOH1  0   0.452   3.1835  -0.6878  -2.2027
 CR6  H1O4  H  HOH1  0   0.461   0.5742  -1.3685  -3.7649
 CR6  H1N2  H  HNH1  0   0.415  -0.6833   1.0934   2.5304
 CR6  H1O6  H  HOH1  0   0.458  -3.8000  -0.6388  -2.4402
 CR6  H81   H  HCH3  0   0.265  -1.2200  -1.6838   4.5650
 CR6  H82   H  HCH3  0   0.275   0.0079  -0.4262   4.7245
 CR6  H83   H  HCH3  0   0.260  -1.6415   0.0170   4.3014
 CR6  O6    O  OH1   0  -0.667  -3.0949  -0.2300  -1.9304

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
 CR6  N1  C9    single  1.340  0.020  1.340
 CR6  N1  H1N1  single  0.860  0.020  1.020
 CR6  N1  H2N1  single  0.860  0.020  1.020
 CR6  C2  O2    single  1.400  0.020  1.400
 CR6  C2  C1    single  1.540  0.020  1.540
 CR6  C2  C3    single  1.525  0.020  1.525
 CR6  C2  H21   single  0.970  0.020  1.090
 CR6  O2  H1O2  single  0.850  0.020  0.980
 CR6  C4  C5    single  1.530  0.020  1.530
 CR6  C4  C3    single  1.525  0.020  1.525
 CR6  C4  O4    single  1.410  0.020  1.410
 CR6  C4  H41   single  0.970  0.020  1.090
 CR6  C5  C6    single  1.512  0.020  1.512
 CR6  C5  O5    single  1.420  0.020  1.420
 CR6  C5  H51   single  0.970  0.020  1.090
 CR6  C6  O6    single  1.407  0.020  1.407
 CR6  C6  H61   single  0.970  0.020  1.090
 CR6  C6  H62   single  0.970  0.020  1.090
 CR6  C1  O5    single  1.406  0.020  1.406
 CR6  C1  N2    single  1.439  0.020  1.439
 CR6  C1  C9    single  1.560  0.020  1.560
 CR6  C3  O3    single  1.408  0.020  1.408
 CR6  C3  H31   single  0.970  0.020  1.090
 CR6  O3  H1O3  single  0.850  0.020  0.980
 CR6  O4  H1O4  single  0.850  0.020  0.980
 CR6  N2  C7    single  1.358  0.020  1.358
 CR6  N2  H1N2  single  0.860  0.020  1.020
 CR6  O6  H1O6  single  0.850  0.020  0.980
 CR6  C7  O7    double  1.217  0.020  1.217
 CR6  C7  C8    single  1.509  0.020  1.509
 CR6  C8  H81   single  0.970  0.020  1.090
 CR6  C8  H82   single  0.970  0.020  1.090
 CR6  C8  H83   single  0.970  0.020  1.090
 CR6  C9  O9    double  1.216  0.020  1.216

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
 CR6  H2N1  N1  H1N1  117.24  3.000
 CR6  H2N1  N1  C9    121.92  3.000
 CR6  H1N1  N1  C9    119.70  3.000
 CR6  H21   C2  C3    106.50  3.000
 CR6  H21   C2  C1    105.52  3.000
 CR6  C3    C2  C1    111.05  3.000
 CR6  H21   C2  O2    110.38  3.000
 CR6  C3    C2  O2    113.47  3.000
 CR6  C1    C2  O2    109.59  3.000
 CR6  H1O2  O2  C2    107.82  3.000
 CR6  H41   C4  O4    111.06  3.000
 CR6  H41   C4  C3    108.20  3.000
 CR6  O4    C4  C3    107.50  3.000
 CR6  H41   C4  C5    108.61  3.000
 CR6  O4    C4  C5    111.54  3.000
 CR6  C3    C4  C5    109.88  3.000
 CR6  H51   C5  O5    110.66  3.000
 CR6  H51   C5  C6    108.04  3.000
 CR6  O5    C5  C6    107.01  3.000
 CR6  H51   C5  C4    108.47  3.000
 CR6  O5    C5  C4    110.09  3.000
 CR6  C6    C5  C4    112.56  3.000
 CR6  H62   C6  H61   107.16  3.000
 CR6  H62   C6  O6    112.00  3.000
 CR6  H61   C6  O6    111.40  3.000
 CR6  H62   C6  C5    109.18  3.000
 CR6  H61   C6  C5    108.28  3.000
 CR6  O6    C6  C5    108.73  3.000
 CR6  C9    C1  N2    105.15  3.000
 CR6  C9    C1  O5    109.10  3.000
 CR6  N2    C1  O5    107.63  3.000
 CR6  C9    C1  C2    113.69  3.000
 CR6  N2    C1  C2    111.96  3.000
 CR6  O5    C1  C2    109.07  3.000
 CR6  H31   C3  O3    110.46  3.000
 CR6  H31   C3  C4    108.62  3.000
 CR6  O3    C3  C4    111.34  3.000
 CR6  H31   C3  C2    110.16  3.000
 CR6  O3    C3  C2    106.92  3.000
 CR6  C4    C3  C2    109.33  3.000
 CR6  H1O3  O3  C3    107.96  3.000
 CR6  H1O4  O4  C4    109.22  3.000
 CR6  C1    O5  C5    115.13  3.000
 CR6  H1N2  N2  C7    116.31  3.000
 CR6  H1N2  N2  C1    117.34  3.000
 CR6  C7    N2  C1    126.34  3.000
 CR6  C8    C7  O7    122.48  3.000
 CR6  C8    C7  N2    113.62  3.000
 CR6  O7    C7  N2    123.89  3.000
 CR6  H83   C8  H82   107.54  3.000
 CR6  H83   C8  H81   109.02  3.000
 CR6  H82   C8  H81   108.22  3.000
 CR6  H83   C8  C7    112.51  3.000
 CR6  H82   C8  C7    109.29  3.000
 CR6  H81   C8  C7    110.13  3.000
 CR6  O9    C9  C1    123.31  3.000
 CR6  O9    C9  N1    123.93  3.000
 CR6  C1    C9  N1    112.74  3.000
 CR6  H1O6  O6  C6    108.02  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
 CR6  CONST_01  O7    C7  N2  C1    0.00   0.0  0
 CR6  CONST_02  C8    C7  N2  C1  180.00   0.0  0
 CR6  CONST_03  H1N1  N1  C9  C1  180.00   0.0  0
 CR6  CONST_04  H2N1  N1  C9  C1    0.00   0.0  0
 CR6  CONST_05  H1N2  N2  C7  O7  180.00   0.0  0
 CR6  Var_01    H81   C8  C7  N2  161.19  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
 CR6  chir_01  C2  O2  C1  C3  negativ
 CR6  chir_02  C4  O4  C3  C5  negativ
 CR6  chir_03  C5  O5  C4  C6  negativ
 CR6  chir_04  C1  O5  C9  C2  positiv
 CR6  chir_05  C3  O3  C2  C4  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
 CR6  plan-1  C1    0.020
 CR6  plan-1  N2    0.020
 CR6  plan-1  C7    0.020
 CR6  plan-1  O7    0.020
 CR6  plan-1  C8    0.020
 CR6  plan-1  H1N2  0.020
 CR6  plan-2  N1    0.020
 CR6  plan-2  C1    0.020
 CR6  plan-2  C9    0.020
 CR6  plan-2  O9    0.020
 CR6  plan-2  H1N1  0.020
 CR6  plan-2  H2N1  0.020

