# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 17:15:54 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 2-nitrophenyl 6-deoxy-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](Oc2ccccc2[N+]([O-])=O)[C@H](O)[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
 NPF  NPF  '2-nitrophenyl 6-deoxy-beta-D-galactopyranoside'  D-saccharide  35  20  .  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_NPF
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
 NPF  C1    C  CR6    0   0.415   1.5750   0.5575  -0.2060
 NPF  C2    C  CR16   0  -0.362   1.5011   1.8394  -0.7453
 NPF  C3    C  CR16   0  -0.221   2.6554   2.5148  -1.1068
 NPF  C4    C  CR16   0  -0.273   3.9082   1.9501  -0.9110
 NPF  C5    C  CR16   0  -0.262   4.0006   0.6908  -0.3502
 NPF  C6    C  CR6    0   0.140   2.8443  -0.0042  -0.0230
 NPF  N6    N  N      1   0.345   2.9995  -1.3469   0.5073
 NPF  O6A   O  O     -1  -0.377   3.9303  -1.5431   1.2537
 NPF  O6B   O  O      0  -0.378   2.2208  -2.2020   0.1592
 NPF  O1'   O  O2     0  -0.484   0.5082  -0.1487   0.1979
 NPF  C1'   C  CH1    0   0.258  -0.7659   0.1535  -0.2979
 NPF  C2'   C  CH1    0  -0.029  -1.5970  -1.1234  -0.2018
 NPF  O2'   O  OH1    0  -0.668  -1.1135  -2.1048  -1.0832
 NPF  C3'   C  CH1    0   0.021  -3.0326  -0.7985  -0.6056
 NPF  O3'   O  OH1    0  -0.667  -3.8836  -1.9030  -0.4604
 NPF  C4'   C  CH1    0   0.000  -3.5675   0.3605   0.2249
 NPF  O4'   O  OH1    0  -0.669  -3.6961  -0.0685   1.5568
 NPF  C5'   C  CH1    0   0.006  -2.6082   1.5476   0.0862
 NPF  C6'   C  CH3    0  -0.701  -3.0137   2.7492   0.9121
 NPF  O5'   O  O2     0  -0.490  -1.2979   1.1685   0.4898
 NPF  H2    H  HCR6   0   0.304   0.5471   2.3320  -0.8677
 NPF  H3    H  HCR6   0   0.281   2.5682   3.5048  -1.5340
 NPF  H4    H  HCR6   0   0.276   4.8056   2.4856  -1.1863
 NPF  H5    H  HCR6   0   0.298   4.9681   0.2358  -0.1917
 NPF  H1'   H  HCH1   0   0.220  -0.6953   0.4672  -1.3540
 NPF  H2'   H  HCH1   0   0.237  -1.5828  -1.4716   0.8400
 NPF  HO'2  H  HOH1   0   0.457  -0.2904  -2.4595  -0.7319
 NPF  H3'   H  HCH1   0   0.220  -3.0172  -0.4520  -1.6517
 NPF  HO'3  H  HOH1   0   0.452  -3.5580  -2.6082  -1.0293
 NPF  H4'   H  HCH1   0   0.239  -4.5368   0.6678  -0.1932
 NPF  HO'4  H  HOH1   0   0.458  -4.2056   0.5858   2.0440
 NPF  H5'   H  HCH1   0   0.225  -2.5955   1.8403  -0.9749
 NPF  H6'1  H  HCH3   0   0.253  -2.3435   3.5879   0.7259
 NPF  H6'2  H  HCH3   0   0.241  -4.0222   3.0651   0.6439
 NPF  H6'3  H  HCH3   0   0.233  -2.9940   2.5357   1.9818

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
 NPF  C1   C2    aromatic  1.393  0.020  1.393
 NPF  C1   C6    aromatic  1.400  0.020  1.400
 NPF  C1   O1'   single    1.342  0.020  1.342
 NPF  C2   C3    aromatic  1.385  0.020  1.385
 NPF  C2   H2    single    0.930  0.020  1.080
 NPF  C3   C4    aromatic  1.388  0.020  1.388
 NPF  C3   H3    single    0.930  0.020  1.080
 NPF  C4   C5    aromatic  1.382  0.020  1.382
 NPF  C4   H4    single    0.930  0.020  1.080
 NPF  C5   C6    aromatic  1.388  0.020  1.388
 NPF  C5   H5    single    0.930  0.020  1.080
 NPF  C6   N6    single    1.452  0.020  1.452
 NPF  N6   O6A   single    1.209  0.020  1.209
 NPF  N6   O6B   double    1.208  0.020  1.208
 NPF  O1'  C1'   single    1.400  0.020  1.400
 NPF  C1'  C2'   single    1.527  0.020  1.527
 NPF  C1'  O5'   single    1.391  0.020  1.391
 NPF  C1'  H1'   single    0.970  0.020  1.090
 NPF  C2'  O2'   single    1.405  0.020  1.405
 NPF  C2'  C3'   single    1.526  0.020  1.526
 NPF  C2'  H2'   single    0.970  0.020  1.090
 NPF  O2'  HO'2  single    0.850  0.020  0.980
 NPF  C3'  O3'   single    1.402  0.020  1.402
 NPF  C3'  C4'   single    1.523  0.020  1.523
 NPF  C3'  H3'   single    0.970  0.020  1.090
 NPF  O3'  HO'3  single    0.850  0.020  0.980
 NPF  C4'  O4'   single    1.405  0.020  1.405
 NPF  C4'  C5'   single    1.533  0.020  1.533
 NPF  C4'  H4'   single    0.970  0.020  1.090
 NPF  O4'  HO'4  single    0.850  0.020  0.980
 NPF  C5'  C6'   single    1.513  0.020  1.513
 NPF  C5'  O5'   single    1.422  0.020  1.422
 NPF  C5'  H5'   single    0.970  0.020  1.090
 NPF  C6'  H6'1  single    0.970  0.020  1.090
 NPF  C6'  H6'2  single    0.970  0.020  1.090
 NPF  C6'  H6'3  single    0.970  0.020  1.090

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
 NPF  O1'   C1   C6    118.06  3.000
 NPF  O1'   C1   C2    123.98  3.000
 NPF  C6    C1   C2    117.90  3.000
 NPF  H2    C2   C3    118.93  3.000
 NPF  H2    C2   C1    120.69  3.000
 NPF  C3    C2   C1    120.37  3.000
 NPF  H3    C3   C4    120.05  3.000
 NPF  H3    C3   C2    118.82  3.000
 NPF  C4    C3   C2    121.12  3.000
 NPF  H4    C4   C5    119.97  3.000
 NPF  H4    C4   C3    120.80  3.000
 NPF  C5    C4   C3    119.23  3.000
 NPF  H5    C5   C6    120.02  3.000
 NPF  H5    C5   C4    120.20  3.000
 NPF  C6    C5   C4    119.76  3.000
 NPF  N6    C6   C5    117.39  3.000
 NPF  N6    C6   C1    121.04  3.000
 NPF  C5    C6   C1    121.57  3.000
 NPF  O6B   N6   O6A   124.01  3.000
 NPF  O6B   N6   C6    118.73  3.000
 NPF  O6A   N6   C6    117.24  3.000
 NPF  C1'   O1'  C1    120.22  3.000
 NPF  H1'   C1'  O5'   111.03  3.000
 NPF  H1'   C1'  C2'   109.43  3.000
 NPF  O5'   C1'  C2'   111.50  3.000
 NPF  H1'   C1'  O1'   109.99  3.000
 NPF  O5'   C1'  O1'   107.77  3.000
 NPF  C2'   C1'  O1'   107.01  3.000
 NPF  H2'   C2'  C3'   109.30  3.000
 NPF  H2'   C2'  O2'   111.66  3.000
 NPF  C3'   C2'  O2'   107.84  3.000
 NPF  H2'   C2'  C1'   108.53  3.000
 NPF  C3'   C2'  C1'   108.50  3.000
 NPF  O2'   C2'  C1'   110.94  3.000
 NPF  HO'2  O2'  C2'   108.83  3.000
 NPF  H3'   C3'  C4'   106.46  3.000
 NPF  H3'   C3'  O3'   110.77  3.000
 NPF  C4'   C3'  O3'   109.27  3.000
 NPF  H3'   C3'  C2'   107.75  3.000
 NPF  C4'   C3'  C2'   110.37  3.000
 NPF  O3'   C3'  C2'   112.07  3.000
 NPF  HO'3  O3'  C3'   108.10  3.000
 NPF  H4'   C4'  C5'   107.51  3.000
 NPF  H4'   C4'  O4'   111.42  3.000
 NPF  C5'   C4'  O4'   112.31  3.000
 NPF  H4'   C4'  C3'   108.36  3.000
 NPF  C5'   C4'  C3'   108.68  3.000
 NPF  O4'   C4'  C3'   108.46  3.000
 NPF  HO'4  O4'  C4'   108.72  3.000
 NPF  H5'   C5'  O5'   109.50  3.000
 NPF  H5'   C5'  C6'   108.54  3.000
 NPF  O5'   C5'  C6'   107.67  3.000
 NPF  H5'   C5'  C4'   107.48  3.000
 NPF  O5'   C5'  C4'   110.15  3.000
 NPF  C6'   C5'  C4'   113.45  3.000
 NPF  H6'3  C6'  H6'2  108.33  3.000
 NPF  H6'3  C6'  H6'1  107.88  3.000
 NPF  H6'2  C6'  H6'1  107.69  3.000
 NPF  H6'3  C6'  C5'   112.01  3.000
 NPF  H6'2  C6'  C5'   110.10  3.000
 NPF  H6'1  C6'  C5'   110.68  3.000
 NPF  C5'   O5'  C1'   112.72  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
 NPF  CONST_01  C4   C3  C2  C1    0.00  0.0  0
 NPF  CONST_02  C4   C5  C6  C1    0.00  0.0  0
 NPF  CONST_03  C5   C6  C1  C2    0.00  0.0  0
 NPF  CONST_04  C5   C4  C3  C2    0.00  0.0  0
 NPF  CONST_05  C6   C1  C2  C3    0.00  0.0  0
 NPF  CONST_06  C6   C5  C4  C3    0.00  0.0  0
 NPF  CONST_07  N6   C6  C1  C2  180.00  0.0  0
 NPF  CONST_08  O1'  C1  C2  C3  180.00  0.0  0
 NPF  CONST_09  N6   C6  C5  C4  180.00  0.0  0
 NPF  CONST_10  O1'  C1  C6  C5  180.00  0.0  0
 NPF  CONST_11  H3   C3  C2  C1  180.00  0.0  0
 NPF  CONST_12  H5   C5  C6  C1  180.00  0.0  0
 NPF  CONST_13  H4   C4  C3  C2  180.00  0.0  0
 NPF  CONST_14  H2   C2  C3  C4  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
 NPF  chir_01  C1'  O1'  C2'  O5'  negativ
 NPF  chir_02  C2'  O2'  C1'  C3'  negativ
 NPF  chir_03  C3'  O3'  C2'  C4'  positiv
 NPF  chir_04  C4'  O4'  C3'  C5'  positiv
 NPF  chir_05  C5'  O5'  C4'  C6'  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
 NPF  plan-1  C1   0.020
 NPF  plan-1  C2   0.020
 NPF  plan-1  C3   0.020
 NPF  plan-1  C4   0.020
 NPF  plan-1  C5   0.020
 NPF  plan-1  C6   0.020
 NPF  plan-1  N6   0.020
 NPF  plan-1  O1'  0.020
 NPF  plan-1  H2   0.020
 NPF  plan-1  H3   0.020
 NPF  plan-1  H4   0.020
 NPF  plan-1  H5   0.020
 NPF  plan-2  C6   0.020
 NPF  plan-2  N6   0.020
 NPF  plan-2  O6A  0.020
 NPF  plan-2  O6B  0.020

