# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:52:13 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: (5R,6R,7S,8R)-6,7,8-trihydroxy-5-(hydroxymethyl)-2-[(phenylamino)methyl]-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@H](O)c2[nH]c(CNc3ccccc3)c[n+]12
#
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
 NHV  NHV  (5R,6R,7S,8R)-6,7,8-trihydroxy-5-(hydroxymethyl)-2-[(phenylamino)methyl]-5,6,7,8-tetrahydro-1H-imidazo[1,2-a]pyridin-4-ium  ligand  42  22  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NHV
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
 NHV  O6B   O  OH1   0  -0.662  26.7180  50.1832  -3.3600
 NHV  C6B   C  CH2   0  -0.197  25.8060  49.3822  -2.6570
 NHV  C5B   C  CR16  0  -0.167  26.5635  48.3117  -1.9041
 NHV  C4B   C  CR16  0   0.017  27.6273  48.8630  -0.9297
 NHV  O4B   O  OH1   0  -0.649  27.0835  49.8023  -0.0526
 NHV  C3B   C  CR16  0  -0.012  28.4092  47.7526  -0.1773
 NHV  O3B   O  OH1   0  -0.642  29.7510  48.0997  -0.0021
 NHV  O2B   O  OH1   0  -0.642  29.3035  45.5179  -0.4967
 NHV  N1B   N  N     1  -0.445  27.2821  47.4129  -2.8120
 NHV  C8B   C  CR15  0  -0.107  27.3223  47.3369  -4.1856
 NHV  C7B   C  CR5   0   0.277  28.1940  46.3477  -4.5003
 NHV  N2B   N  NR15  0  -0.636  28.6679  45.8575  -3.3050
 NHV  C1B   C  CR56  0   0.596  28.1071  46.5119  -2.3042
 NHV  C7    C  CH2   0  -0.406  28.6541  45.8181  -5.8236
 NHV  N1    N  NH1   0  -0.696  30.0753  45.6510  -5.9161
 NHV  C1    C  CR6   0   0.377  30.9674  46.6934  -5.8188
 NHV  C6    C  CR16  0  -0.329  30.5658  48.0305  -5.9234
 NHV  C5    C  CR16  0  -0.244  31.5042  49.0514  -5.8545
 NHV  C4    C  CR16  0  -0.295  32.8527  48.7768  -5.6803
 NHV  C3    C  CR16  0  -0.244  33.2548  47.4491  -5.5759
 NHV  C2    C  CR16  0  -0.350  32.3317  46.4207  -5.6415
 NHV  C20   C  CR16  0  -0.058  28.2443  46.3517  -0.8285
 NHV  H6B   H  HOH1  0   0.468  26.2230  50.8245  -3.8784
 NHV  H6B1  H  HCH2  0   0.252  25.2250  49.9489  -1.9228
 NHV  H6B2  H  HCH2  0   0.241  25.0795  48.8975  -3.3214
 NHV  H5B   H  HCR6  0   0.316  25.8230  47.7122  -1.3635
 NHV  H4B   H  HCR6  0   0.265  28.3478  49.4119  -1.5452
 NHV  HA    H  HOH1  0   0.456  26.4697  49.3642   0.5479
 NHV  H3B   H  HCR6  0   0.277  27.9952  47.6640   0.8302
 NHV  HB    H  HOH1  0   0.449  30.1674  48.2631  -0.8555
 NHV  H20   H  HCR6  0   0.299  27.2811  45.9549  -0.4784
 NHV  H2B   H  HOH1  0   0.476  28.9777  44.6155  -0.4183
 NHV  H8B   H  HCR5  0   0.330  26.7558  47.9841  -4.8305
 NHV  HC    H  HNR5  0   0.446  29.3488  45.1176  -3.1960
 NHV  H7C1  H  HCH2  0   0.308  28.1985  44.8440  -6.0054
 NHV  H7C2  H  HCH2  0   0.272  28.2746  46.4803  -6.6055
 NHV  H1    H  HNH1  0   0.394  30.4304  44.7311  -5.7161
 NHV  H6    H  HCR6  0   0.257  29.5249  48.2869  -6.0670
 NHV  H2    H  HCR6  0   0.256  32.6633  45.3921  -5.5555
 NHV  H5    H  HCR6  0   0.252  31.1671  50.0769  -5.9409
 NHV  H4    H  HCR6  0   0.247  33.5770  49.5782  -5.6255
 NHV  H3    H  HCR6  0   0.252  34.3018  47.2090  -5.4400

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
 NHV  O6B  C6B   single    1.403  0.020  1.403
 NHV  C6B  C5B   single    1.512  0.020  1.512
 NHV  C5B  C4B   single    1.544  0.020  1.544
 NHV  C5B  N1B   single    1.466  0.020  1.466
 NHV  C4B  O4B   single    1.395  0.020  1.395
 NHV  C4B  C3B   single    1.553  0.020  1.553
 NHV  C3B  O3B   single    1.397  0.020  1.397
 NHV  C3B  C20   single    1.554  0.020  1.554
 NHV  O2B  C20   single    1.388  0.020  1.388
 NHV  N1B  C8B   aromatic  1.376  0.020  1.376
 NHV  N1B  C1B   aromatic  1.323  0.020  1.323
 NHV  C8B  C7B   aromatic  1.356  0.020  1.356
 NHV  C7B  N2B   aromatic  1.376  0.020  1.376
 NHV  C7B  C7    single    1.498  0.020  1.498
 NHV  N2B  C1B   aromatic  1.321  0.020  1.321
 NHV  C1B  C20   single    1.491  0.020  1.491
 NHV  C7   N1    single    1.434  0.020  1.434
 NHV  N1   C1    single    1.375  0.020  1.375
 NHV  C1   C6    aromatic  1.400  0.020  1.400
 NHV  C1   C2    aromatic  1.402  0.020  1.402
 NHV  C6   C5    aromatic  1.388  0.020  1.388
 NHV  C5   C4    aromatic  1.387  0.020  1.387
 NHV  C4   C3    aromatic  1.391  0.020  1.391
 NHV  C3   C2    aromatic  1.383  0.020  1.383
 NHV  O6B  H6B   single    0.850  0.020  0.980
 NHV  C6B  H6B1  single    0.970  0.020  1.090
 NHV  C6B  H6B2  single    0.970  0.020  1.090
 NHV  C5B  H5B   single    0.970  0.020  1.090
 NHV  C4B  H4B   single    0.970  0.020  1.090
 NHV  O4B  HA    single    0.850  0.020  0.980
 NHV  C3B  H3B   single    0.970  0.020  1.090
 NHV  O3B  HB    single    0.850  0.020  0.980
 NHV  C20  H20   single    0.970  0.020  1.090
 NHV  O2B  H2B   single    0.850  0.020  0.980
 NHV  C8B  H8B   single    0.930  0.020  1.080
 NHV  N2B  HC    single    0.860  0.020  1.020
 NHV  C7   H7C1  single    0.970  0.020  1.090
 NHV  C7   H7C2  single    0.970  0.020  1.090
 NHV  N1   H1    single    0.890  0.020  1.040
 NHV  C6   H6    single    0.930  0.020  1.080
 NHV  C2   H2    single    0.930  0.020  1.080
 NHV  C5   H5    single    0.930  0.020  1.080
 NHV  C4   H4    single    0.930  0.020  1.080
 NHV  C3   H3    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
 NHV  H6B   O6B  C6B   108.44  3.000
 NHV  H6B2  C6B  H6B1  106.46  3.000
 NHV  H6B2  C6B  C5B   108.69  3.000
 NHV  H6B1  C6B  C5B   107.36  3.000
 NHV  H6B2  C6B  O6B   112.29  3.000
 NHV  H6B1  C6B  O6B   112.69  3.000
 NHV  C5B   C6B  O6B   109.16  3.000
 NHV  H5B   C5B  N1B   107.54  3.000
 NHV  H5B   C5B  C4B   110.46  3.000
 NHV  N1B   C5B  C4B   105.78  3.000
 NHV  H5B   C5B  C6B   107.14  3.000
 NHV  N1B   C5B  C6B   111.79  3.000
 NHV  C4B   C5B  C6B   113.99  3.000
 NHV  H4B   C4B  C3B   107.42  3.000
 NHV  H4B   C4B  O4B   105.80  3.000
 NHV  C3B   C4B  O4B   111.91  3.000
 NHV  H4B   C4B  C5B   106.11  3.000
 NHV  C3B   C4B  C5B   113.42  3.000
 NHV  O4B   C4B  C5B   111.62  3.000
 NHV  HA    O4B  C4B   109.49  3.000
 NHV  H3B   C3B  C20   105.85  3.000
 NHV  H3B   C3B  O3B   105.57  3.000
 NHV  C20   C3B  O3B   112.25  3.000
 NHV  H3B   C3B  C4B   108.29  3.000
 NHV  C20   C3B  C4B   112.85  3.000
 NHV  O3B   C3B  C4B   111.52  3.000
 NHV  HB    O3B  C3B   110.26  3.000
 NHV  H2B   O2B  C20   108.93  3.000
 NHV  C1B   N1B  C8B   109.10  3.000
 NHV  C1B   N1B  C5B   119.05  3.000
 NHV  C8B   N1B  C5B   131.78  3.000
 NHV  H8B   C8B  C7B   129.71  3.000
 NHV  H8B   C8B  N1B   123.37  3.000
 NHV  C7B   C8B  N1B   106.90  3.000
 NHV  C7    C7B  N2B   122.39  3.000
 NHV  C7    C7B  C8B   131.35  3.000
 NHV  N2B   C7B  C8B   106.25  3.000
 NHV  HC    N2B  C1B   124.52  3.000
 NHV  HC    N2B  C7B   125.88  3.000
 NHV  C1B   N2B  C7B   109.60  3.000
 NHV  C20   C1B  N2B   131.13  3.000
 NHV  C20   C1B  N1B   120.70  3.000
 NHV  N2B   C1B  N1B   108.15  3.000
 NHV  H7C2  C7   H7C1  106.07  3.000
 NHV  H7C2  C7   N1    111.64  3.000
 NHV  H7C1  C7   N1    107.41  3.000
 NHV  H7C2  C7   C7B   108.14  3.000
 NHV  H7C1  C7   C7B   109.56  3.000
 NHV  N1    C7   C7B   113.74  3.000
 NHV  H1    N1   C1    116.75  3.000
 NHV  H1    N1   C7    116.33  3.000
 NHV  C1    N1   C7    123.36  3.000
 NHV  C2    C1   C6    118.31  3.000
 NHV  C2    C1   N1    119.50  3.000
 NHV  C6    C1   N1    122.17  3.000
 NHV  H6    C6   C5    118.86  3.000
 NHV  H6    C6   C1    120.83  3.000
 NHV  C5    C6   C1    120.31  3.000
 NHV  H5    C5   C4    120.01  3.000
 NHV  H5    C5   C6    118.81  3.000
 NHV  C4    C5   C6    121.18  3.000
 NHV  H4    C4   C3    120.65  3.000
 NHV  H4    C4   C5    120.71  3.000
 NHV  C3    C4   C5    118.64  3.000
 NHV  H3    C3   C2    119.10  3.000
 NHV  H3    C3   C4    120.03  3.000
 NHV  C2    C3   C4    120.87  3.000
 NHV  H2    C2   C3    119.83  3.000
 NHV  H2    C2   C1    119.47  3.000
 NHV  C3    C2   C1    120.70  3.000
 NHV  H20   C20  C1B   105.87  3.000
 NHV  H20   C20  O2B   112.06  3.000
 NHV  C1B   C20  O2B   111.80  3.000
 NHV  H20   C20  C3B   106.57  3.000
 NHV  C1B   C20  C3B   109.14  3.000
 NHV  O2B   C20  C3B   111.12  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
 NHV  CONST_01  N2B  C7B  C8B  N1B    0.00   0.0  0
 NHV  CONST_02  C7B  N2B  C1B  N1B    0.00   0.0  0
 NHV  CONST_03  N2B  C1B  N1B  C8B    0.00   0.0  0
 NHV  CONST_04  C1B  N2B  C7B  C8B    0.00   0.0  0
 NHV  CONST_05  C1B  N1B  C8B  C7B    0.00   0.0  0
 NHV  CONST_06  C4   C5   C6   C1     0.00   0.0  0
 NHV  CONST_07  C4   C3   C2   C1     0.00   0.0  0
 NHV  CONST_08  C3   C2   C1   C6     0.00   0.0  0
 NHV  CONST_09  C3   C4   C5   C6     0.00   0.0  0
 NHV  CONST_10  C2   C1   C6   C5     0.00   0.0  0
 NHV  CONST_11  C2   C3   C4   C5     0.00   0.0  0
 NHV  CONST_12  C7   C7B  C8B  N1B  180.00   0.0  0
 NHV  CONST_13  C7   C7B  N2B  C1B  180.00   0.0  0
 NHV  CONST_14  C5   C6   C1   N1   180.00   0.0  0
 NHV  CONST_15  C3   C2   C1   N1   180.00   0.0  0
 NHV  CONST_16  H8B  C8B  N1B  C5B    0.00   0.0  0
 NHV  CONST_17  HC   N2B  C1B  N1B  180.00   0.0  0
 NHV  CONST_18  H5   C5   C6   C1   180.00   0.0  0
 NHV  CONST_19  H3   C3   C2   C1   180.00   0.0  0
 NHV  CONST_20  H2   C2   C1   C6   180.00   0.0  0
 NHV  CONST_21  H4   C4   C5   C6   180.00   0.0  0
 NHV  CONST_22  H6   C6   C5   C4   180.00   0.0  0
 NHV  CONST_23  C6   C1   N1   C7     0.00   0.0  0
 NHV  CONST_24  C2   C1   N1   C7   180.00   0.0  0
 NHV  CONST_25  H1   N1   C1   C6   180.00   0.0  0
 NHV  Var_01    N1   C7   C7B  C8B  133.32  30.0  2
 NHV  Var_02    C1   N1   C7   C7B  -62.53  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
 NHV  chir_01  C5B  C6B  C4B  N1B  positiv
 NHV  chir_02  C4B  O4B  C5B  C3B  positiv
 NHV  chir_03  C3B  O3B  C20  C4B  positiv
 NHV  chir_04  C20  O2B  C1B  C3B  positiv

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
 NHV  plan-1  N1   0.020
 NHV  plan-1  C1   0.020
 NHV  plan-1  C6   0.020
 NHV  plan-1  C5   0.020
 NHV  plan-1  C4   0.020
 NHV  plan-1  C3   0.020
 NHV  plan-1  C2   0.020
 NHV  plan-1  H6   0.020
 NHV  plan-1  H2   0.020
 NHV  plan-1  H5   0.020
 NHV  plan-1  H4   0.020
 NHV  plan-1  H3   0.020
 NHV  plan-2  C5B  0.020
 NHV  plan-2  N1B  0.020
 NHV  plan-2  C8B  0.020
 NHV  plan-2  C7B  0.020
 NHV  plan-2  N2B  0.020
 NHV  plan-2  C1B  0.020
 NHV  plan-2  C7   0.020
 NHV  plan-2  C20  0.020
 NHV  plan-2  H8B  0.020
 NHV  plan-2  HC   0.020
 NHV  plan-3  C7   0.020
 NHV  plan-3  N1   0.020
 NHV  plan-3  C1   0.020
 NHV  plan-3  H1   0.020

