# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 08:22:53 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 2,6-diamino-2,6-dideoxy-beta-L-idopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1O[C@H](O)[C@H](N)[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
 PA4  PA4  2,6-diamino-2,6-dideoxy-beta-L-idopyranose  ligand  26  12  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PA4
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
 PA4  C1    C  CH1   0   0.051  -1.4021   0.0483   0.3086
 PA4  O1    O  OH1   0  -0.665  -1.6269   1.4293   0.4165
 PA4  C2    C  CH1   0  -0.033  -1.1935  -0.4039  -1.1442
 PA4  O2    O  OH1   0  -0.670  -1.3591  -1.8051  -1.1381
 PA4  C3    C  CH1   0  -0.165   0.1844  -0.0181  -1.7049
 PA4  N3    N  NH2   0  -0.796   0.2296   1.3989  -2.0046
 PA4  C4    C  CH1   0   0.310   1.2573  -0.3958  -0.6876
 PA4  O4    O  OH1   0  -0.667   2.4827   0.0633  -1.1357
 PA4  C5    C  CH1   0   0.018  -0.1860  -0.3195   1.1518
 PA4  O5    O  O2    0  -0.496   0.9975   0.1782   0.5677
 PA4  C6    C  CH2   0  -0.294  -0.2850   0.1822   2.5819
 PA4  N6    N  NH2   0  -0.799   0.7708  -0.3829   3.4059
 PA4  H1    H  HCH1  0   0.212  -2.2597  -0.5215   0.7003
 PA4  HO1   H  HOH1  0   0.447  -2.3281   1.6741  -0.1948
 PA4  H2    H  HCH1  0   0.228  -1.9659   0.0676  -1.7748
 PA4  HO2   H  HOH1  0   0.454  -1.2408  -2.1297  -2.0361
 PA4  H3    H  HCH1  0   0.221   0.3541  -0.6448  -2.5983
 PA4  HN31  H  HNH2  0   0.345   1.0635   1.6033  -2.5392
 PA4  HN32  H  HNH2  0   0.343  -0.5461   1.6348  -2.6110
 PA4  H4    H  HCH1  0   0.178   1.2597  -1.4948  -0.5826
 PA4  HO4   H  HOH1  0   0.460   3.1831  -0.3503  -0.6203
 PA4  H5    H  HCH1  0   0.209  -0.1477  -1.4214   1.1832
 PA4  H61   H  HCH2  0   0.200  -1.2970  -0.0487   2.9445
 PA4  H62   H  HCH2  0   0.226  -0.1912   1.2697   2.5956
 PA4  HN61  H  HNH2  0   0.348   0.7170   0.0154   4.3344
 PA4  HN62  H  HNH2  0   0.337   0.6069  -1.3754   3.5268

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
 PA4  C1  O1    single  1.403  0.020  1.403
 PA4  C1  C2    single  1.536  0.020  1.536
 PA4  C1  C5    single  1.525  0.020  1.525
 PA4  C1  H1    single  0.970  0.020  1.090
 PA4  O1  HO1   single  0.850  0.020  0.980
 PA4  C2  O2    single  1.411  0.020  1.411
 PA4  C2  C3    single  1.537  0.020  1.537
 PA4  C2  H2    single  0.970  0.020  1.090
 PA4  O2  HO2   single  0.850  0.020  0.980
 PA4  C3  N3    single  1.449  0.020  1.449
 PA4  C3  C4    single  1.526  0.020  1.526
 PA4  C3  H3    single  0.970  0.020  1.090
 PA4  N3  HN31  single  0.890  0.020  1.040
 PA4  N3  HN32  single  0.890  0.020  1.040
 PA4  C4  O4    single  1.383  0.020  1.383
 PA4  C4  O5    single  1.405  0.020  1.405
 PA4  C4  H4    single  0.970  0.020  1.090
 PA4  O4  HO4   single  0.850  0.020  0.980
 PA4  C5  O5    single  1.410  0.020  1.410
 PA4  C5  C6    single  1.519  0.020  1.519
 PA4  C5  H5    single  0.970  0.020  1.090
 PA4  C6  N6    single  1.454  0.020  1.454
 PA4  C6  H61   single  0.970  0.020  1.090
 PA4  C6  H62   single  0.970  0.020  1.090
 PA4  N6  HN61  single  0.890  0.020  1.040
 PA4  N6  HN62  single  0.890  0.020  1.040

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
 PA4  H1    C1  C5    107.42  3.000
 PA4  H1    C1  C2    106.85  3.000
 PA4  C5    C1  C2    110.11  3.000
 PA4  H1    C1  O1    110.91  3.000
 PA4  C5    C1  O1    108.82  3.000
 PA4  C2    C1  O1    112.60  3.000
 PA4  HO1   O1  C1    108.56  3.000
 PA4  H2    C2  C3    108.18  3.000
 PA4  H2    C2  O2    110.17  3.000
 PA4  C3    C2  O2    110.86  3.000
 PA4  H2    C2  C1    108.66  3.000
 PA4  C3    C2  C1    113.14  3.000
 PA4  O2    C2  C1    105.80  3.000
 PA4  HO2   O2  C2    108.45  3.000
 PA4  H3    C3  C4    106.90  3.000
 PA4  H3    C3  N3    112.50  3.000
 PA4  C4    C3  N3    110.98  3.000
 PA4  H3    C3  C2    106.89  3.000
 PA4  C4    C3  C2    108.97  3.000
 PA4  N3    C3  C2    110.42  3.000
 PA4  HN32  N3  HN31  105.55  3.000
 PA4  HN32  N3  C3    109.14  3.000
 PA4  HN31  N3  C3    109.43  3.000
 PA4  H4    C4  O5    108.80  3.000
 PA4  H4    C4  O4    111.06  3.000
 PA4  O5    C4  O4    108.53  3.000
 PA4  H4    C4  C3    108.14  3.000
 PA4  O5    C4  C3    111.38  3.000
 PA4  O4    C4  C3    108.95  3.000
 PA4  HO4   O4  C4    109.17  3.000
 PA4  H5    C5  C6    107.79  3.000
 PA4  H5    C5  O5    109.58  3.000
 PA4  C6    C5  O5    109.15  3.000
 PA4  H5    C5  C1    106.52  3.000
 PA4  C6    C5  C1    112.90  3.000
 PA4  O5    C5  C1    110.80  3.000
 PA4  C5    O5  C4    112.40  3.000
 PA4  H62   C6  H61   106.51  3.000
 PA4  H62   C6  N6    108.52  3.000
 PA4  H61   C6  N6    113.57  3.000
 PA4  H62   C6  C5    109.59  3.000
 PA4  H61   C6  C5    107.53  3.000
 PA4  N6    C6  C5    110.98  3.000
 PA4  HN62  N6  HN61  105.52  3.000
 PA4  HN62  N6  C6    109.32  3.000
 PA4  HN61  N6  C6    109.18  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
 PA4  Var_01  HN61  N6  C6  C5  176.26  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
 PA4  chir_01  C1  O1  C2  C5  negativ
 PA4  chir_02  C2  O2  C3  C1  positiv
 PA4  chir_03  C3  N3  C4  C2  negativ
 PA4  chir_04  C4  O5  O4  C3  positiv
 PA4  chir_05  C5  O5  C6  C1  negativ

