# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 17:43:17 2022
#   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  23  13  .  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_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  -0.829  -50.2525  78.4425  128.4512
 F8X  C2    C  CH1    0  -0.168  -50.6084  79.8420  128.6427
 F8X  C3    C  CH1    0   0.022  -49.4605  80.7113  129.1484
 F8X  C4    C  CH1    0  -0.045  -49.7095  82.1814  128.8286
 F8X  C5    C  CH1    0  -0.095  -49.8184  82.3544  127.3006
 F8X  C1    C  CH1    0   0.299  -51.1372  80.4207  127.2992
 F8X  C6    C  C      0   0.371  -48.5440  82.9961  126.6950
 F8X  O5    O  O2     0  -0.501  -50.1059  81.1327  126.6541
 F8X  O6A   O  O      0  -0.584  -47.9477  82.3796  125.7992
 F8X  O6B   O  OC    -1  -0.608  -48.2608  84.1106  127.1777
 F8X  O4    O  OH1    0  -0.672  -50.9035  82.6376  129.4375
 F8X  O3    O  OH1    0  -0.666  -49.3261  80.4891  130.5371
 F8X  HN21  H  HNH2   0   0.364  -49.2659  78.3236  128.2588
 F8X  HN22  H  HNH2   0   0.373  -50.4709  77.8861  129.2646
 F8X  H2    H  HCH1   0   0.249  -51.4295  79.8789  129.3627
 F8X  H3    H  HCH1   0   0.215  -48.5423  80.4132  128.6207
 F8X  H4    H  HCH1   0   0.226  -48.8597  82.7696  129.1973
 F8X  H5    H  HCH1   0   0.215  -50.6410  83.0664  127.1214
 F8X  H1    H  HCH1   0   0.177  -51.9729  81.1089  127.4966
 F8X  HO4   H  HOH1   0   0.440  -50.8393  82.4472  130.3800
 F8X  HO3   H  HOH1   0   0.451  -48.4907  80.8704  130.8267
 F8X  O1    O  OH1    0  -0.674  -51.5652  79.4064  126.4808
 F8X  HO1   H  HOH1   0   0.441  -51.1833  78.5963  126.8903

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    deloc   1.240  0.020  1.240
 F8X  O5   C1    single  1.410  0.020  1.410
 F8X  O5   C5    single  1.412  0.020  1.412
 F8X  C6   C5    single  1.550  0.020  1.550
 F8X  C6   O6B   deloc   1.247  0.020  1.247
 F8X  C1   C2    single  1.555  0.020  1.555
 F8X  C5   C4    single  1.542  0.020  1.542
 F8X  C2   N2    single  1.457  0.020  1.457
 F8X  C2   C3    single  1.526  0.020  1.526
 F8X  C4   C3    single  1.525  0.020  1.525
 F8X  C4   O4    single  1.416  0.020  1.416
 F8X  C3   O3    single  1.413  0.020  1.413
 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  O4   HO4   single  0.850  0.020  0.980
 F8X  O3   HO3   single  0.850  0.020  0.980
 F8X  C1   O1    single  1.372  0.020  1.372
 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  107.42  3.000
 F8X  HN22  N2  C2    111.76  3.000
 F8X  HN21  N2  C2    112.08  3.000
 F8X  H2    C2  C1    107.52  3.000
 F8X  H2    C2  C3    109.12  3.000
 F8X  C1    C2  C3    109.27  3.000
 F8X  H2    C2  N2    107.61  3.000
 F8X  C3    C2  N2    114.02  3.000
 F8X  C1    C2  N2    109.09  3.000
 F8X  H3    C3  O3    110.46  3.000
 F8X  H3    C3  C4    107.27  3.000
 F8X  O3    C3  C4    111.92  3.000
 F8X  H3    C3  C2    108.33  3.000
 F8X  O3    C3  C2    107.92  3.000
 F8X  C4    C3  C2    110.90  3.000
 F8X  H4    C4  O4    109.62  3.000
 F8X  H4    C4  C5    109.13  3.000
 F8X  O4    C4  C5    109.30  3.000
 F8X  H4    C4  C3    108.65  3.000
 F8X  O4    C4  C3    110.98  3.000
 F8X  C5    C4  C3    109.13  3.000
 F8X  H5    C5  O5    109.42  3.000
 F8X  H5    C5  C6    106.41  3.000
 F8X  O5    C5  C6    110.28  3.000
 F8X  H5    C5  C4    106.64  3.000
 F8X  C6    C5  C4    112.06  3.000
 F8X  O5    C5  C4    111.79  3.000
 F8X  O1    C1  H1    109.43  3.000
 F8X  O1    C1  O5    109.19  3.000
 F8X  H1    C1  O5    108.77  3.000
 F8X  O1    C1  C2    110.26  3.000
 F8X  H1    C1  C2    109.63  3.000
 F8X  O5    C1  C2    109.54  3.000
 F8X  O6B   C6  O6A   127.92  3.000
 F8X  O6B   C6  C5    113.91  3.000
 F8X  O6A   C6  C5    118.15  3.000
 F8X  C1    O5  C5    112.12  3.000
 F8X  HO4   O4  C4    107.51  3.000
 F8X  HO3   O3  C3    108.41  3.000
 F8X  HO1   O1  C1    103.84  3.000

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

