# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 05:00:45 2021
#   Inital geometry file: a 58 line input string
#   Ligand name: 2-amino-2-deoxy-beta-D-altropyranuronic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1[C@H](O)O[C@@H]([C@@H](O)[C@H]1O)C(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
 F8X  F8X  '2-amino-2-deoxy-beta-D-altropyranuronic acid'  D-saccharide  24  13  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_F8X
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
 F8X  N2    N  NH2   0  -0.836  -50.7758  78.5607  128.7564
 F8X  C2    C  CH1   0  -0.197  -50.7257  79.9972  128.5399
 F8X  C3    C  CH1   0   0.029  -49.4140  80.5730  129.0566
 F8X  C4    C  CH1   0  -0.023  -49.3630  82.0881  128.8053
 F8X  C5    C  CH1   0  -0.056  -49.8791  82.3652  127.3753
 F8X  C1    C  CH1   0   0.290  -50.8123  80.2669  126.9979
 F8X  C6    C  C     0   0.497  -49.0704  83.4332  126.6742
 F8X  O5    O  O2    0  -0.493  -49.8339  81.2105  126.5945
 F8X  O6A   O  O     0  -0.423  -48.4573  83.2706  125.6537
 F8X  O6B   O  OH1   0  -0.588  -49.1233  84.5752  127.3436
 F8X  O4    O  OH1   0  -0.663  -50.1848  82.7949  129.6950
 F8X  O3    O  OH1   0  -0.667  -49.3110  80.3075  130.4378
 F8X  HN21  H  HNH2  0   0.373  -50.2506  78.3014  129.5815
 F8X  HN22  H  HNH2  0   0.373  -51.7265  78.2509  128.9093
 F8X  H2    H  HCH1  0   0.255  -51.5537  80.5199  129.0313
 F8X  H3    H  HCH1  0   0.240  -48.5841  80.1040  128.5147
 F8X  H4    H  HCH1  0   0.242  -48.3144  82.4044  128.9109
 F8X  H5    H  HCH1  0   0.270  -50.9123  82.7408  127.4696
 F8X  H1    H  HCH1  0   0.197  -51.8009  80.6839  126.7490
 F8X  HO6B  H  HOH1  0   0.489  -48.5766  85.2462  126.9076
 F8X  HO4   H  HOH1  0   0.451  -49.9511  82.5185  130.5889
 F8X  HO3   H  HOH1  0   0.464  -48.3797  80.2746  130.6775
 F8X  O1    O  OH1   0  -0.671  -50.5779  79.1176  126.2920
 F8X  HO1   H  HOH1  0   0.450  -50.4370  78.4337  126.9881

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
 F8X  O6A  C6    double  1.202  0.020  1.202
 F8X  O5   C1    single  1.418  0.020  1.418
 F8X  O5   C5    single  1.395  0.020  1.395
 F8X  C6   C5    single  1.512  0.020  1.512
 F8X  C6   O6B   single  1.325  0.020  1.325
 F8X  C1   C2    single  1.568  0.020  1.568
 F8X  C5   C4    single  1.545  0.020  1.545
 F8X  C2   N2    single  1.454  0.020  1.454
 F8X  C2   C3    single  1.523  0.020  1.523
 F8X  C4   C3    single  1.537  0.020  1.537
 F8X  C4   O4    single  1.402  0.020  1.402
 F8X  C3   O3    single  1.410  0.020  1.410
 F8X  N2   HN21  single  0.890  0.020  1.040
 F8X  N2   HN22  single  0.890  0.020  1.040
 F8X  C2   H2    single  0.970  0.020  1.090
 F8X  C3   H3    single  0.970  0.020  1.090
 F8X  C4   H4    single  0.970  0.020  1.090
 F8X  C5   H5    single  0.970  0.020  1.090
 F8X  C1   H1    single  0.970  0.020  1.090
 F8X  O6B  HO6B  single  0.850  0.020  0.980
 F8X  O4   HO4   single  0.850  0.020  0.980
 F8X  O3   HO3   single  0.850  0.020  0.980
 F8X  C1   O1    single  1.369  0.020  1.369
 F8X  O1   HO1   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
 F8X  HN22  N2   HN21  106.62  3.000
 F8X  HN22  N2   C2    110.95  3.000
 F8X  HN21  N2   C2    110.91  3.000
 F8X  H2    C2   C1    108.50  3.000
 F8X  H2    C2   C3    108.56  3.000
 F8X  C1    C2   C3    108.44  3.000
 F8X  H2    C2   N2    112.25  3.000
 F8X  C3    C2   N2    110.66  3.000
 F8X  C1    C2   N2    108.34  3.000
 F8X  H3    C3   O3    110.38  3.000
 F8X  H3    C3   C4    108.41  3.000
 F8X  O3    C3   C4    110.08  3.000
 F8X  H3    C3   C2    108.81  3.000
 F8X  O3    C3   C2    108.91  3.000
 F8X  C4    C3   C2    110.24  3.000
 F8X  H4    C4   O4    110.66  3.000
 F8X  H4    C4   C5    110.83  3.000
 F8X  O4    C4   C5    107.52  3.000
 F8X  H4    C4   C3    107.41  3.000
 F8X  O4    C4   C3    111.95  3.000
 F8X  C5    C4   C3    108.48  3.000
 F8X  H5    C5   O5    111.10  3.000
 F8X  H5    C5   C6    107.46  3.000
 F8X  O5    C5   C6    107.93  3.000
 F8X  H5    C5   C4    107.14  3.000
 F8X  C6    C5   C4    112.15  3.000
 F8X  O5    C5   C4    111.03  3.000
 F8X  O1    C1   H1    110.79  3.000
 F8X  O1    C1   O5    107.09  3.000
 F8X  H1    C1   O5    107.64  3.000
 F8X  O1    C1   C2    110.69  3.000
 F8X  H1    C1   C2    109.69  3.000
 F8X  O5    C1   C2    110.87  3.000
 F8X  O6B   C6   O6A   124.48  3.000
 F8X  O6B   C6   C5    110.69  3.000
 F8X  O6A   C6   C5    124.83  3.000
 F8X  C1    O5   C5    111.67  3.000
 F8X  HO6B  O6B  C6    110.31  3.000
 F8X  HO4   O4   C4    107.55  3.000
 F8X  HO3   O3   C3    108.73  3.000
 F8X  HO1   O1   C1    104.05  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
 F8X  CONST_01  HO6B  O6B  C6  C5  180.00  0.0  0

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
 F8X  chir_01  C2  C1  N2  C3  negativ
 F8X  chir_02  C3  O3  C2  C4  negativ
 F8X  chir_03  C4  O4  C3  C5  negativ
 F8X  chir_04  C5  O5  C4  C6  negativ
 F8X  chir_05  C1  O5  O1  C2  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
 F8X  plan-1  C5    0.020
 F8X  plan-1  C6    0.020
 F8X  plan-1  O6A   0.020
 F8X  plan-1  O6B   0.020
 F8X  plan-1  HO6B  0.020

