# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 06:50:31 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{S})-5-azanyl-2-(hydroxymethyl)-6-(4-nitrophenoxy)oxane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@H]1Oc2ccc(cc2)[N+]([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
 PNJ  PNJ  (2~{R},3~{S},4~{R},5~{R},6~{S})-5-azanyl-2-(hydroxymethyl)-6-(4-nitrophenoxy)oxane-3,4-diol  D-saccharide  37  21  .  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_PNJ
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
 PNJ  C1    C  CH1    0   0.306   1.1490   0.6033  -0.0046
 PNJ  C2    C  CH1    0  -0.157   2.3736   1.4950   0.1594
 PNJ  C4    C  CH1    0   0.009   3.6893  -0.6546   0.1647
 PNJ  C5    C  CH1    0  -0.029   2.3572  -1.3938   0.0024
 PNJ  C6    C  CH2    0  -0.159   2.3618  -2.7599   0.6487
 PNJ  C7    C  CR6    0   0.402  -1.1871   0.8560   0.3495
 PNJ  C8    C  CR16   0  -0.341  -2.1900   1.7150   0.8055
 PNJ  C9    C  CR16   0  -0.254  -3.5156   1.4292   0.5652
 PNJ  C10   C  CR6    0   0.233  -3.8448   0.2754  -0.1382
 PNJ  C11   C  CR16   0  -0.256  -2.8588  -0.5901  -0.5886
 PNJ  C12   C  CR16   0  -0.349  -1.5283  -0.3082  -0.3408
 PNJ  N1    N  N      1   0.328  -5.2338  -0.0281  -0.3996
 PNJ  O1    O  O2     0  -0.486   0.0720   1.2344   0.6281
 PNJ  O3    O  OH1    0  -0.668   4.7189   1.5165  -0.1769
 PNJ  O4    O  OH1    0  -0.672   4.7339  -1.3049  -0.5223
 PNJ  C3    C  CH1    0   0.031   3.5680   0.7483  -0.4260
 PNJ  O5    O  O2     0  -0.492   1.3336  -0.6294   0.6150
 PNJ  O6    O  OH1    0  -0.664   1.1403  -3.3973   0.3672
 PNJ  O7    O  O     -1  -0.387  -5.4931  -1.0392  -1.0123
 PNJ  N2    N  NH2    0  -0.805   2.1683   2.7382  -0.5563
 PNJ  O8    O  O      0  -0.387  -6.0735   0.7443   0.0045
 PNJ  H8    H  HCR6   0   0.287  -1.9186   2.6136   1.3433
 PNJ  H9    H  HCR6   0   0.299  -4.2784   2.1064   0.9200
 PNJ  H11   H  HCR6   0   0.301  -3.1120  -1.4929  -1.1251
 PNJ  H12   H  HCR6   0   0.303  -0.7815  -1.0155  -0.6697
 PNJ  H1    H  HCH1   0   0.215   0.9318   0.4746  -1.0791
 PNJ  H2    H  HCH1   0   0.233   2.5467   1.6247   1.2404
 PNJ  H5    H  HCH1   0   0.229   2.1476  -1.5107  -1.0735
 PNJ  H61C  H  HCH2   0   0.202   3.2128  -3.3247   0.2500
 PNJ  H62C  H  HCH2   0   0.203   2.5289  -2.6445   1.7285
 PNJ  H4    H  HCH1   0   0.227   3.9133  -0.5660   1.2373
 PNJ  H6    H  HOH1   0   0.457   1.1483  -4.2572   0.7970
 PNJ  HA    H  HOH1   0   0.462   5.1492  -1.9442   0.0633
 PNJ  H3    H  HCH1   0   0.212   3.3997   0.6445  -1.5108
 PNJ  HB    H  HOH1   0   0.454   5.4528   1.1216  -0.6586
 PNJ  H21N  H  HNH2   0   0.352   1.4936   3.3107  -0.0655
 PNJ  H22N  H  HNH2   0   0.356   3.0289   3.2704  -0.5592

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
 PNJ  C8   C9    aromatic  1.377  0.020  1.377
 PNJ  C8   C7    aromatic  1.397  0.020  1.397
 PNJ  C9   C10   aromatic  1.391  0.020  1.391
 PNJ  C10  N1    single    1.446  0.020  1.446
 PNJ  C10  C11   aromatic  1.387  0.020  1.387
 PNJ  N1   O8    double    1.210  0.020  1.210
 PNJ  N1   O7    single    1.210  0.020  1.210
 PNJ  C11  C12   aromatic  1.382  0.020  1.382
 PNJ  C12  C7    aromatic  1.396  0.020  1.396
 PNJ  C7   O1    single    1.344  0.020  1.344
 PNJ  O1   C1    single    1.400  0.020  1.400
 PNJ  C1   O5    single    1.392  0.020  1.392
 PNJ  C1   C2    single    1.524  0.020  1.524
 PNJ  O5   C5    single    1.417  0.020  1.417
 PNJ  C5   C6    single    1.511  0.020  1.511
 PNJ  C5   C4    single    1.532  0.020  1.532
 PNJ  C6   O6    single    1.406  0.020  1.406
 PNJ  C4   O4    single    1.409  0.020  1.409
 PNJ  C4   C3    single    1.527  0.020  1.527
 PNJ  C3   O3    single    1.406  0.020  1.406
 PNJ  C3   C2    single    1.525  0.020  1.525
 PNJ  C2   N2    single    1.449  0.020  1.449
 PNJ  C8   H8    single    0.930  0.020  1.080
 PNJ  C9   H9    single    0.930  0.020  1.080
 PNJ  C11  H11   single    0.930  0.020  1.080
 PNJ  C12  H12   single    0.930  0.020  1.080
 PNJ  C1   H1    single    0.970  0.020  1.090
 PNJ  C2   H2    single    0.970  0.020  1.090
 PNJ  C5   H5    single    0.970  0.020  1.090
 PNJ  C6   H61C  single    0.970  0.020  1.090
 PNJ  C6   H62C  single    0.970  0.020  1.090
 PNJ  C4   H4    single    0.970  0.020  1.090
 PNJ  O6   H6    single    0.850  0.020  0.980
 PNJ  O4   HA    single    0.850  0.020  0.980
 PNJ  C3   H3    single    0.970  0.020  1.090
 PNJ  O3   HB    single    0.850  0.020  0.980
 PNJ  N2   H21N  single    0.890  0.020  1.040
 PNJ  N2   H22N  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
 PNJ  H1    C1   O5    110.86  3.000
 PNJ  H1    C1   O1    109.95  3.000
 PNJ  O5    C1   O1    107.47  3.000
 PNJ  H1    C1   C2    109.34  3.000
 PNJ  O5    C1   C2    111.33  3.000
 PNJ  O1    C1   C2    107.82  3.000
 PNJ  H2    C2   N2    113.92  3.000
 PNJ  H2    C2   C3    108.12  3.000
 PNJ  N2    C2   C3    109.96  3.000
 PNJ  H2    C2   C1    107.49  3.000
 PNJ  N2    C2   C1    109.57  3.000
 PNJ  C3    C2   C1    107.55  3.000
 PNJ  H4    C4   C3    108.64  3.000
 PNJ  H4    C4   O4    111.21  3.000
 PNJ  C3    C4   O4    107.11  3.000
 PNJ  H4    C4   C5    108.63  3.000
 PNJ  C3    C4   C5    109.47  3.000
 PNJ  O4    C4   C5    111.73  3.000
 PNJ  H5    C5   O5    109.99  3.000
 PNJ  H5    C5   C6    108.79  3.000
 PNJ  O5    C5   C6    107.76  3.000
 PNJ  H5    C5   C4    108.65  3.000
 PNJ  C6    C5   C4    112.84  3.000
 PNJ  O5    C5   C4    108.79  3.000
 PNJ  H62C  C6   H61C  107.07  3.000
 PNJ  H62C  C6   O6    112.11  3.000
 PNJ  H61C  C6   O6    111.59  3.000
 PNJ  H62C  C6   C5    109.01  3.000
 PNJ  H61C  C6   C5    108.21  3.000
 PNJ  O6    C6   C5    108.75  3.000
 PNJ  O1    C7   C12   124.49  3.000
 PNJ  O1    C7   C8    115.58  3.000
 PNJ  C12   C7   C8    119.92  3.000
 PNJ  H8    C8   C9    120.03  3.000
 PNJ  H8    C8   C7    119.53  3.000
 PNJ  C9    C8   C7    120.43  3.000
 PNJ  H9    C9   C10   121.28  3.000
 PNJ  H9    C9   C8    119.50  3.000
 PNJ  C10   C9   C8    119.22  3.000
 PNJ  N1    C10  C11   119.56  3.000
 PNJ  C11   C10  C9    120.90  3.000
 PNJ  N1    C10  C9    119.54  3.000
 PNJ  H11   C11  C12   119.01  3.000
 PNJ  H11   C11  C10   121.07  3.000
 PNJ  C12   C11  C10   119.91  3.000
 PNJ  H12   C12  C11   118.51  3.000
 PNJ  H12   C12  C7    121.87  3.000
 PNJ  C11   C12  C7    119.60  3.000
 PNJ  O8    N1   O7    123.60  3.000
 PNJ  O7    N1   C10   118.21  3.000
 PNJ  O8    N1   C10   118.19  3.000
 PNJ  C7    O1   C1    120.02  3.000
 PNJ  HB    O3   C3    108.14  3.000
 PNJ  HA    O4   C4    109.28  3.000
 PNJ  H3    C3   O3    110.53  3.000
 PNJ  H3    C3   C4    107.83  3.000
 PNJ  O3    C3   C4    111.62  3.000
 PNJ  H3    C3   C2    107.71  3.000
 PNJ  O3    C3   C2    107.79  3.000
 PNJ  C4    C3   C2    111.31  3.000
 PNJ  C5    O5   C1    112.41  3.000
 PNJ  H6    O6   C6    107.98  3.000
 PNJ  H22N  N2   H21N  105.72  3.000
 PNJ  H22N  N2   C2    109.39  3.000
 PNJ  H21N  N2   C2    109.90  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
 PNJ  CONST_01  C10  C9   C8   C7      0.00   0.0  0
 PNJ  CONST_02  C10  C11  C12  C7      0.00   0.0  0
 PNJ  CONST_03  C11  C10  C9   C8      0.00   0.0  0
 PNJ  CONST_04  C11  C12  C7   C8      0.00   0.0  0
 PNJ  CONST_05  C12  C7   C8   C9      0.00   0.0  0
 PNJ  CONST_06  C12  C11  C10  C9      0.00   0.0  0
 PNJ  CONST_07  N1   C10  C9   C8    180.00   0.0  0
 PNJ  CONST_08  O1   C7   C8   C9    180.00   0.0  0
 PNJ  CONST_09  O1   C7   C12  C11   180.00   0.0  0
 PNJ  CONST_10  N1   C10  C11  C12   180.00   0.0  0
 PNJ  CONST_11  H9   C9   C8   C7    180.00   0.0  0
 PNJ  CONST_12  H11  C11  C12  C7    180.00   0.0  0
 PNJ  CONST_13  H12  C12  C7   C8    180.00   0.0  0
 PNJ  CONST_14  H8   C8   C9   C10   180.00   0.0  0
 PNJ  CONST_15  O8   N1   C10  C9      0.00   0.0  0
 PNJ  CONST_16  O7   N1   C10  C9    180.00   0.0  0
 PNJ  CONST_17  O8   N1   C10  C11   180.00   0.0  0
 PNJ  CONST_18  O7   N1   C10  C11     0.00   0.0  0
 PNJ  Var_01    C8   C7   O1   C1   -167.12  30.0  2

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
 PNJ  chir_01  C1  O1  O5  C2  positiv
 PNJ  chir_02  C2  N2  C3  C1  positiv
 PNJ  chir_03  C4  O4  C5  C3  positiv
 PNJ  chir_04  C5  O5  C4  C6  negativ
 PNJ  chir_05  C3  O3  C4  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
 PNJ  plan-1  C7   0.020
 PNJ  plan-1  C8   0.020
 PNJ  plan-1  C9   0.020
 PNJ  plan-1  C10  0.020
 PNJ  plan-1  C11  0.020
 PNJ  plan-1  C12  0.020
 PNJ  plan-1  N1   0.020
 PNJ  plan-1  O1   0.020
 PNJ  plan-1  H8   0.020
 PNJ  plan-1  H9   0.020
 PNJ  plan-1  H11  0.020
 PNJ  plan-1  H12  0.020
 PNJ  plan-2  C10  0.020
 PNJ  plan-2  N1   0.020
 PNJ  plan-2  O7   0.020
 PNJ  plan-2  O8   0.020

