# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 20:21:28 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-6-O-methyl-alpha-D-allopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC[C@H]1O[C@H](O)[C@H](NC(C)=O)[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
 NA1  NA1  2-(acetylamino)-2-deoxy-6-O-methyl-alpha-D-allopyranose  D-saccharide  33  16  .  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_NA1
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
 NA1  C1    C  CH1   0   0.289   1.8782  -0.8925   1.5750
 NA1  C2    C  CH1   0  -0.187   0.5984  -0.1504   1.9594
 NA1  C3    C  CH1   0   0.045  -0.4420  -0.4218   0.8726
 NA1  C4    C  CH1   0  -0.005  -0.6518  -1.9209   0.6447
 NA1  C5    C  CH1   0  -0.068   0.6948  -2.6225   0.4257
 NA1  C6    C  CH2   0  -0.172   1.2648  -2.4229  -0.9804
 NA1  C7    C  C     0   0.521   0.2354   0.2773   4.3509
 NA1  C8    C  CH3   0  -0.780  -0.3277  -0.3044   5.6247
 NA1  N2    N  NH1   0  -0.615   0.1395  -0.5177   3.2738
 NA1  O1    O  OH1   0  -0.648   2.8095  -0.7379   2.5755
 NA1  O3    O  OH1   0  -0.659  -1.6245   0.2503   1.2088
 NA1  O4    O  OH1   0  -0.671  -1.3214  -2.4458   1.7714
 NA1  O5    O  O2    0  -0.497   1.6256  -2.2754   1.4302
 NA1  O6    O  O2    0  -0.485   0.4438  -3.1304  -1.8715
 NA1  C9    C  CH3   0  -0.396   0.8462  -2.9890  -3.2107
 NA1  O7    O  O     0  -0.513   0.7265   1.3990   4.3266
 NA1  H1C1  H  HCH1  0   0.201   2.2437  -0.4773   0.6217
 NA1  H2    H  HCH1  0   0.278   0.8182   0.9189   1.9641
 NA1  H3    H  HCH1  0   0.233  -0.0196  -0.0163  -0.0580
 NA1  H4    H  HCH1  0   0.240  -1.2625  -2.0538  -0.2593
 NA1  H5    H  HCH1  0   0.261   0.5384  -3.7005   0.5417
 NA1  H6C1  H  HCH2  0   0.225   2.2950  -2.8057  -0.9990
 NA1  H6C2  H  HCH2  0   0.205   1.3159  -1.3629  -1.2682
 NA1  H8C1  H  HCH3  0   0.263   0.4362  -0.2835   6.4012
 NA1  H8C2  H  HCH3  0   0.264  -1.1557   0.3159   5.9691
 NA1  H8C3  H  HCH3  0   0.245  -0.6857  -1.3270   5.5213
 NA1  HA    H  HNH1  0   0.400  -0.3076  -1.4163   3.3676
 NA1  HO1   H  HOH1  0   0.464   3.6809  -0.9662   2.2346
 NA1  HB    H  HOH1  0   0.454  -2.2247   0.2007   0.4578
 NA1  HC    H  HOH1  0   0.458  -1.4817  -3.3837   1.6245
 NA1  H9C1  H  HCH3  0   0.207   0.8201  -1.9430  -3.5383
 NA1  H9C2  H  HCH3  0   0.236   0.1580  -3.5620  -3.8305
 NA1  H9C3  H  HCH3  0   0.207   1.8611  -3.3687  -3.3764

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
 NA1  C1  C2    single  1.529  0.020  1.529
 NA1  C1  O1    single  1.376  0.020  1.376
 NA1  C1  O5    single  1.413  0.020  1.413
 NA1  C1  H1C1  single  0.970  0.020  1.090
 NA1  C2  C3    single  1.529  0.020  1.529
 NA1  C2  N2    single  1.440  0.020  1.440
 NA1  C2  H2    single  0.970  0.020  1.090
 NA1  C3  C4    single  1.531  0.020  1.531
 NA1  C3  O3    single  1.401  0.020  1.401
 NA1  C3  H3    single  0.970  0.020  1.090
 NA1  C4  C5    single  1.534  0.020  1.534
 NA1  C4  O4    single  1.412  0.020  1.412
 NA1  C4  H4    single  0.970  0.020  1.090
 NA1  C5  C6    single  1.530  0.020  1.530
 NA1  C5  O5    single  1.413  0.020  1.413
 NA1  C5  H5    single  0.970  0.020  1.090
 NA1  C6  O6    single  1.403  0.020  1.403
 NA1  C6  H6C1  single  0.970  0.020  1.090
 NA1  C6  H6C2  single  0.970  0.020  1.090
 NA1  C7  C8    single  1.509  0.020  1.509
 NA1  C7  N2    single  1.342  0.020  1.342
 NA1  C7  O7    double  1.225  0.020  1.225
 NA1  C8  H8C1  single  0.970  0.020  1.090
 NA1  C8  H8C2  single  0.970  0.020  1.090
 NA1  C8  H8C3  single  0.970  0.020  1.090
 NA1  N2  HA    single  0.860  0.020  1.020
 NA1  O1  HO1   single  0.850  0.020  0.980
 NA1  O3  HB    single  0.850  0.020  0.980
 NA1  O4  HC    single  0.850  0.020  0.980
 NA1  O6  C9    single  1.405  0.020  1.405
 NA1  C9  H9C1  single  0.970  0.020  1.090
 NA1  C9  H9C2  single  0.970  0.020  1.090
 NA1  C9  H9C3  single  0.970  0.020  1.090

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
 NA1  H1C1  C1  O5    109.84  3.000
 NA1  H1C1  C1  O1    111.23  3.000
 NA1  O5    C1  O1    107.79  3.000
 NA1  H1C1  C1  C2    108.20  3.000
 NA1  O5    C1  C2    110.56  3.000
 NA1  O1    C1  C2    109.23  3.000
 NA1  H2    C2  N2    108.06  3.000
 NA1  H2    C2  C3    108.30  3.000
 NA1  N2    C2  C3    112.75  3.000
 NA1  H2    C2  C1    107.94  3.000
 NA1  N2    C2  C1    111.88  3.000
 NA1  C3    C2  C1    107.75  3.000
 NA1  H3    C3  O3    110.51  3.000
 NA1  H3    C3  C4    106.73  3.000
 NA1  O3    C3  C4    112.94  3.000
 NA1  H3    C3  C2    105.95  3.000
 NA1  O3    C3  C2    108.58  3.000
 NA1  C4    C3  C2    111.90  3.000
 NA1  H4    C4  O4    110.36  3.000
 NA1  H4    C4  C5    108.36  3.000
 NA1  O4    C4  C5    111.11  3.000
 NA1  H4    C4  C3    108.49  3.000
 NA1  O4    C4  C3    108.08  3.000
 NA1  C5    C4  C3    110.41  3.000
 NA1  H5    C5  O5    105.10  3.000
 NA1  H5    C5  C6    106.19  3.000
 NA1  O5    C5  C6    112.08  3.000
 NA1  H5    C5  C4    108.04  3.000
 NA1  O5    C5  C4    111.38  3.000
 NA1  C6    C5  C4    113.48  3.000
 NA1  H6C2  C6  H6C1  106.72  3.000
 NA1  H6C2  C6  O6    110.31  3.000
 NA1  H6C1  C6  O6    111.22  3.000
 NA1  H6C2  C6  C5    112.56  3.000
 NA1  H6C1  C6  C5    108.62  3.000
 NA1  O6    C6  C5    107.45  3.000
 NA1  O7    C7  N2    123.73  3.000
 NA1  O7    C7  C8    121.29  3.000
 NA1  N2    C7  C8    114.98  3.000
 NA1  H8C3  C8  H8C2  108.35  3.000
 NA1  H8C3  C8  H8C1  108.44  3.000
 NA1  H8C2  C8  H8C1  107.24  3.000
 NA1  H8C3  C8  C7    113.87  3.000
 NA1  H8C2  C8  C7    109.31  3.000
 NA1  H8C1  C8  C7    109.42  3.000
 NA1  HA    N2  C7    119.01  3.000
 NA1  HA    N2  C2    116.98  3.000
 NA1  C7    N2  C2    123.97  3.000
 NA1  HO1   O1  C1    109.18  3.000
 NA1  HB    O3  C3    108.32  3.000
 NA1  HC    O4  C4    108.63  3.000
 NA1  C5    O5  C1    115.53  3.000
 NA1  C9    O6  C6    112.76  3.000
 NA1  H9C3  C9  H9C2  108.47  3.000
 NA1  H9C3  C9  H9C1  107.90  3.000
 NA1  H9C2  C9  H9C1  108.47  3.000
 NA1  H9C3  C9  O6    111.98  3.000
 NA1  H9C2  C9  O6    107.96  3.000
 NA1  H9C1  C9  O6    111.95  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
 NA1  CONST_01  C8    C7  N2  C2  180.00   0.0  0
 NA1  CONST_02  O7    C7  N2  C2    0.00   0.0  0
 NA1  CONST_03  HA    N2  C7  C8    0.00   0.0  0
 NA1  Var_01    H9C1  C9  O6  C6  -60.43  30.0  3
 NA1  Var_02    H8C1  C8  C7  N2  125.22  30.0  3
 NA1  Var_03    H6C1  C6  O6  C9  -63.06  30.0  1

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
 NA1  chir_01  C1  C2  O1  O5  negativ
 NA1  chir_02  C2  N2  C3  C1  positiv
 NA1  chir_03  C3  O3  C2  C4  negativ
 NA1  chir_04  C4  O4  C3  C5  negativ
 NA1  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
 NA1  plan-1  C2  0.020
 NA1  plan-1  C7  0.020
 NA1  plan-1  C8  0.020
 NA1  plan-1  N2  0.020
 NA1  plan-1  O7  0.020
 NA1  plan-1  HA  0.020

