# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 22:46:23 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: [(2S,3S,4S,5R,6R)-6-(4-nitrophenoxy)-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](O)[C@@H](C[S](O)(=O)=O)O[C@H](Oc2ccc(cc2)[N+]([O-])=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
 NSQ  NSQ  '[(2S,3S,4S,5R,6R)-6-(4-nitrophenoxy)-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid'  D-saccharide  38  24  .  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_NSQ
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
 NSQ  O12   O  OS     0  -0.756   0.2187  -2.6770   0.6276
 NSQ  S10   S  S      0   1.417  -0.6125  -3.0501  -0.5321
 NSQ  O13   O  OS     0  -0.755  -0.0594  -2.6048  -1.8253
 NSQ  O11   O  OS    -1  -0.769  -0.9876  -4.4793  -0.5449
 NSQ  C9    C  CH2    0  -0.677  -2.1887  -2.1928  -0.2935
 NSQ  C1    C  CH1    0   0.024  -2.0579  -0.7267   0.0609
 NSQ  O2    O  O2     0  -0.483  -1.4069  -0.0834  -1.0231
 NSQ  C3    C  CH1    0   0.205  -1.1808   1.2746  -0.8802
 NSQ  C4    C  CH1    0  -0.010  -2.5008   2.0220  -0.6821
 NSQ  O16   O  OH1    0  -0.663  -2.3138   3.3902  -0.4424
 NSQ  C8    C  CH1    0  -0.013  -3.2703   1.4264   0.4911
 NSQ  O15   O  OH1    0  -0.673  -4.5692   1.9648   0.5801
 NSQ  C6    C  CH1    0   0.043  -3.4220  -0.0795   0.3033
 NSQ  O14   O  OH1    0  -0.671  -3.9867  -0.6892   1.4356
 NSQ  O1    O  O2     0  -0.487  -0.3610   1.5854   0.2286
 NSQ  C25   C  C      0   0.397   0.9647   1.3743   0.1753
 NSQ  C26   C  C1     0  -0.343   1.7435   2.1988   0.9914
 NSQ  C27   C  C1     0  -0.257   3.1142   2.0629   1.0170
 NSQ  C28   C  C      0   0.233   3.7130   1.0969   0.2157
 NSQ  N32   N  N      1   0.328   5.1518   0.9555   0.2269
 NSQ  O33   O  O     -1  -0.388   5.7922   1.6758   0.9595
 NSQ  O34   O  O      0  -0.388   5.6515   0.1245  -0.4977
 NSQ  C29   C  C1     0  -0.263   2.9493   0.2634  -0.5895
 NSQ  C30   C  C1     0  -0.344   1.5727   0.3909  -0.6064
 NSQ  H91C  H  HCH2   0   0.267  -2.7833  -2.3283  -1.2005
 NSQ  H92C  H  HCH2   0   0.280  -2.6973  -2.7111   0.5197
 NSQ  H1    H  HCH1   0   0.242  -1.4558  -0.6410   0.9737
 NSQ  H6    H  HCH1   0   0.214  -4.0444  -0.2473  -0.5902
 NSQ  H3    H  HCH1   0   0.268  -0.6848   1.5968  -1.8033
 NSQ  H4    H  HCH1   0   0.239  -3.0891   1.8537  -1.5951
 NSQ  H16   H  HOH1   0   0.461  -2.1194   3.8297  -1.2758
 NSQ  H8    H  HCH1   0   0.224  -2.7128   1.6102   1.4215
 NSQ  H15   H  HOH1   0   0.457  -4.5010   2.8826   0.8608
 NSQ  H14   H  HOH1   0   0.456  -4.8532  -0.2984   1.5889
 NSQ  H26   H  H      0   0.283   1.2624   2.9547   1.5981
 NSQ  H30   H  H      0   0.310   0.9921  -0.3026  -1.1968
 NSQ  H27   H  H      0   0.297   3.7035   2.7131   1.6466
 NSQ  H29   H  H      0   0.297   3.4126  -0.5018  -1.1953

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
 NSQ  O12  S10   deloc     1.475  0.020  1.475
 NSQ  S10  O13   deloc     1.475  0.020  1.475
 NSQ  S10  O11   deloc     1.478  0.020  1.478
 NSQ  S10  C9    single    1.810  0.020  1.810
 NSQ  C9   C1    single    1.514  0.020  1.514
 NSQ  C1   O2    single    1.419  0.020  1.419
 NSQ  C1   C6    single    1.529  0.020  1.529
 NSQ  O2   C3    single    1.384  0.020  1.384
 NSQ  C3   C4    single    1.530  0.020  1.530
 NSQ  C3   O1    single    1.414  0.020  1.414
 NSQ  C4   O16   single    1.402  0.020  1.402
 NSQ  C4   C8    single    1.524  0.020  1.524
 NSQ  C8   O15   single    1.409  0.020  1.409
 NSQ  C8   C6    single    1.525  0.020  1.525
 NSQ  C6   O14   single    1.405  0.020  1.405
 NSQ  O1   C25   single    1.344  0.020  1.344
 NSQ  C25  C26   aromatic  1.397  0.020  1.397
 NSQ  C25  C30   aromatic  1.396  0.020  1.396
 NSQ  C26  C27   aromatic  1.378  0.020  1.378
 NSQ  C27  C28   aromatic  1.391  0.020  1.391
 NSQ  C28  N32   single    1.446  0.020  1.446
 NSQ  C28  C29   aromatic  1.388  0.020  1.388
 NSQ  N32  O33   single    1.211  0.020  1.211
 NSQ  N32  O34   double    1.211  0.020  1.211
 NSQ  C29  C30   aromatic  1.383  0.020  1.383
 NSQ  C9   H91C  single    0.970  0.020  1.090
 NSQ  C9   H92C  single    0.970  0.020  1.090
 NSQ  C1   H1    single    0.970  0.020  1.090
 NSQ  C6   H6    single    0.970  0.020  1.090
 NSQ  C3   H3    single    0.970  0.020  1.090
 NSQ  C4   H4    single    0.970  0.020  1.090
 NSQ  O16  H16   single    0.850  0.020  0.980
 NSQ  C8   H8    single    0.970  0.020  1.090
 NSQ  O15  H15   single    0.850  0.020  0.980
 NSQ  O14  H14   single    0.850  0.020  0.980
 NSQ  C26  H26   single    0.930  0.020  1.080
 NSQ  C30  H30   single    0.930  0.020  1.080
 NSQ  C27  H27   single    0.930  0.020  1.080
 NSQ  C29  H29   single    0.930  0.020  1.080

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
 NSQ  C9    S10  O11   103.78  3.000
 NSQ  C9    S10  O13   107.40  3.000
 NSQ  O11   S10  O13   112.30  3.000
 NSQ  C9    S10  O12   105.51  3.000
 NSQ  O11   S10  O12   113.24  3.000
 NSQ  O13   S10  O12   113.68  3.000
 NSQ  H92C  C9   H91C  107.84  3.000
 NSQ  H92C  C9   C1    109.03  3.000
 NSQ  H91C  C9   C1    111.18  3.000
 NSQ  H92C  C9   S10   106.22  3.000
 NSQ  H91C  C9   S10   107.80  3.000
 NSQ  C1    C9   S10   114.47  3.000
 NSQ  H1    C1   C6    108.95  3.000
 NSQ  H1    C1   O2    110.40  3.000
 NSQ  C6    C1   O2    109.79  3.000
 NSQ  H1    C1   C9    108.54  3.000
 NSQ  C6    C1   C9    111.71  3.000
 NSQ  O2    C1   C9    107.45  3.000
 NSQ  C3    O2   C1    116.16  3.000
 NSQ  H3    C3   O1    109.48  3.000
 NSQ  H3    C3   C4    110.84  3.000
 NSQ  O1    C3   C4    106.94  3.000
 NSQ  H3    C3   O2    105.98  3.000
 NSQ  O1    C3   O2    113.05  3.000
 NSQ  C4    C3   O2    110.60  3.000
 NSQ  H4    C4   C8    108.01  3.000
 NSQ  H4    C4   O16   111.28  3.000
 NSQ  C8    C4   O16   108.49  3.000
 NSQ  H4    C4   C3    106.23  3.000
 NSQ  C8    C4   C3    110.14  3.000
 NSQ  O16   C4   C3    112.58  3.000
 NSQ  H16   O16  C4    108.95  3.000
 NSQ  H8    C8   C6    108.64  3.000
 NSQ  H8    C8   O15   110.49  3.000
 NSQ  C6    C8   O15   107.06  3.000
 NSQ  H8    C8   C4    109.26  3.000
 NSQ  C6    C8   C4    109.95  3.000
 NSQ  O15   C8   C4    111.39  3.000
 NSQ  H15   O15  C8    108.52  3.000
 NSQ  H6    C6   O14   111.13  3.000
 NSQ  H6    C6   C8    107.84  3.000
 NSQ  O14   C6   C8    111.67  3.000
 NSQ  H6    C6   C1    108.12  3.000
 NSQ  O14   C6   C1    107.63  3.000
 NSQ  C8    C6   C1    110.41  3.000
 NSQ  H14   O14  C6    108.30  3.000
 NSQ  C25   O1   C3    120.44  3.000
 NSQ  C30   C25  C26   120.01  3.000
 NSQ  C30   C25  O1    124.25  3.000
 NSQ  C26   C25  O1    115.73  3.000
 NSQ  H26   C26  C27   120.06  3.000
 NSQ  H26   C26  C25   119.46  3.000
 NSQ  C27   C26  C25   120.48  3.000
 NSQ  H27   C27  C28   121.27  3.000
 NSQ  H27   C27  C26   119.63  3.000
 NSQ  C28   C27  C26   119.10  3.000
 NSQ  C29   C28  N32   119.56  3.000
 NSQ  C29   C28  C27   120.96  3.000
 NSQ  N32   C28  C27   119.47  3.000
 NSQ  O34   N32  O33   123.52  3.000
 NSQ  O34   N32  C28   118.25  3.000
 NSQ  O33   N32  C28   118.23  3.000
 NSQ  H29   C29  C30   119.04  3.000
 NSQ  H29   C29  C28   120.98  3.000
 NSQ  C30   C29  C28   119.97  3.000
 NSQ  H30   C30  C29   118.86  3.000
 NSQ  H30   C30  C25   121.63  3.000
 NSQ  C29   C30  C25   119.46  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
 NSQ  CONST_01  C28  C27  C26  C25    0.00   0.0  0
 NSQ  CONST_02  C28  C29  C30  C25    0.00   0.0  0
 NSQ  CONST_03  C29  C30  C25  C26    0.00   0.0  0
 NSQ  CONST_04  C29  C28  C27  C26    0.00   0.0  0
 NSQ  CONST_05  C30  C25  C26  C27    0.00   0.0  0
 NSQ  CONST_06  C30  C29  C28  C27    0.00   0.0  0
 NSQ  CONST_07  C27  C26  C25  O1   180.00   0.0  0
 NSQ  CONST_08  C29  C30  C25  O1   180.00   0.0  0
 NSQ  CONST_09  N32  C28  C27  C26  180.00   0.0  0
 NSQ  CONST_10  C30  C29  C28  N32  180.00   0.0  0
 NSQ  CONST_11  H27  C27  C26  C25  180.00   0.0  0
 NSQ  CONST_12  H29  C29  C30  C25  180.00   0.0  0
 NSQ  CONST_13  H30  C30  C25  C26  180.00   0.0  0
 NSQ  CONST_14  H26  C26  C27  C28  180.00   0.0  0
 NSQ  CONST_15  O33  N32  C28  C27    0.00   0.0  0
 NSQ  CONST_16  O34  N32  C28  C27  180.00   0.0  0
 NSQ  CONST_17  C29  C28  N32  O33  180.00   0.0  0
 NSQ  CONST_18  C29  C28  N32  O34    0.00   0.0  0
 NSQ  Var_01    C26  C25  O1   C3   152.87  30.0  2
 NSQ  Var_02    C1   C9   S10  O12   47.86  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
 NSQ  chir_01  C1  C9   O2  C6  negativ
 NSQ  chir_02  C3  O2   O1  C4  positiv
 NSQ  chir_03  C4  O16  C3  C8  negativ
 NSQ  chir_04  C8  O15  C4  C6  positiv
 NSQ  chir_05  C6  O14  C8  C1  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
 NSQ  plan-1  O1   0.020
 NSQ  plan-1  C25  0.020
 NSQ  plan-1  C26  0.020
 NSQ  plan-1  C27  0.020
 NSQ  plan-1  C28  0.020
 NSQ  plan-1  N32  0.020
 NSQ  plan-1  C29  0.020
 NSQ  plan-1  C30  0.020
 NSQ  plan-1  H26  0.020
 NSQ  plan-1  H30  0.020
 NSQ  plan-1  H27  0.020
 NSQ  plan-1  H29  0.020
 NSQ  plan-2  C28  0.020
 NSQ  plan-2  N32  0.020
 NSQ  plan-2  O33  0.020
 NSQ  plan-2  O34  0.020

