# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 15:42:52 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 3-carbamoyl-1-beta-D-ribofuranosylpyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O
#
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
 NNR  NNR  3-carbamoyl-1-beta-D-ribofuranosylpyridinium  ligand  33  18  .  2021-08-15  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NNR
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
 NNR  O2R   O  OH1   0  -0.649  -0.7271   2.5843  -0.4046
 NNR  C2R   C  CR15  0  -0.021  -1.3497   1.3428  -0.4365
 NNR  C3R   C  CR15  0  -0.020  -2.8734   1.3341  -0.2733
 NNR  O3R   O  OH1   0  -0.661  -3.2054   2.3309   0.6511
 NNR  C4R   C  CR15  0  -0.070  -3.0936  -0.0707   0.2832
 NNR  C5R   C  CH2   0  -0.175  -3.1878  -1.1364  -0.7914
 NNR  O5R   O  OH1   0  -0.660  -3.1939  -2.3933  -0.1618
 NNR  O4R   O  O     0  -0.480  -1.9596  -0.2903   1.1435
 NNR  C1R   C  CR15  0   0.196  -0.9108   0.5145   0.7826
 NNR  N1    N  NR6   1  -0.467   0.2879  -0.3232   0.4447
 NNR  C2    C  CR16  0   0.115   1.4589   0.3121   0.3300
 NNR  C6    C  CR16  0   0.072   0.1801  -1.6428   0.2434
 NNR  C5    C  CR16  0  -0.331   1.2931  -2.3764  -0.0961
 NNR  C4    C  CR16  0  -0.107   2.5145  -1.7406  -0.2380
 NNR  C3    C  CR6   0  -0.161   2.6023  -0.3686  -0.0302
 NNR  C7    C  C     0   0.525   3.8712   0.4329  -0.1210
 NNR  O7    O  O     0  -0.459   3.9275   1.5331   0.4027
 NNR  N7    N  NH2   0  -0.812   4.8767  -0.1347  -0.7880
 NNR  HO2R  H  HOH1  0   0.472  -0.7035   2.9466  -1.2956
 NNR  H2R   H  HCR5  0   0.273  -1.0990   0.7966  -1.3537
 NNR  H3R   H  HCR5  0   0.264  -3.3821   1.4752  -1.2348
 NNR  HO3R  H  HOH1  0   0.461  -4.1592   2.3235   0.7806
 NNR  H4R   H  HCR5  0   0.282  -3.9812  -0.1236   0.9186
 NNR  H5R1  H  HCH2  0   0.240  -4.1079  -0.9544  -1.3604
 NNR  H5R2  H  HCH2  0   0.207  -2.3557  -1.0473  -1.5024
 NNR  HO5R  H  HOH1  0   0.465  -3.2464  -3.0713  -0.8421
 NNR  H1R   H  HCR5  0   0.309  -0.5880   1.1478   1.6139
 NNR  H2    H  HCR6  0   0.354   1.4629   1.3744   0.5298
 NNR  H6    H  HCR6  0   0.358  -0.7931  -2.0939   0.3690
 NNR  H5    H  HCR6  0   0.325   1.1960  -3.4416  -0.2399
 NNR  H4    H  HCR6  0   0.311   3.3853  -2.3306  -0.4889
 NNR  HN71  H  HNH2  0   0.426   4.7905  -0.9984  -1.2954
 NNR  HN72  H  HNH2  0   0.420   5.7519   0.3567  -0.8790

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
 NNR  C5   C6    aromatic  1.376  0.020  1.376
 NNR  C5   C4    aromatic  1.384  0.020  1.384
 NNR  C6   N1    aromatic  1.339  0.020  1.339
 NNR  C4   C3    aromatic  1.390  0.020  1.390
 NNR  O2R  C2R   single    1.389  0.020  1.389
 NNR  N1   C1R   single    1.501  0.020  1.501
 NNR  N1   C2    aromatic  1.337  0.020  1.337
 NNR  C3   C2    aromatic  1.378  0.020  1.378
 NNR  C3   C7    single    1.504  0.020  1.504
 NNR  C1R  C2R   single    1.538  0.020  1.538
 NNR  C1R  O4R   single    1.370  0.020  1.370
 NNR  C2R  C3R   single    1.532  0.020  1.532
 NNR  C7   O7    double    1.220  0.020  1.220
 NNR  C7   N7    single    1.333  0.020  1.333
 NNR  O3R  C3R   single    1.399  0.020  1.399
 NNR  O4R  C4R   single    1.440  0.020  1.440
 NNR  C3R  C4R   single    1.527  0.020  1.527
 NNR  C4R  C5R   single    1.516  0.020  1.516
 NNR  C5R  O5R   single    1.406  0.020  1.406
 NNR  O2R  HO2R  single    0.850  0.020  0.980
 NNR  C2R  H2R   single    0.970  0.020  1.090
 NNR  C3R  H3R   single    0.970  0.020  1.090
 NNR  O3R  HO3R  single    0.850  0.020  0.980
 NNR  C4R  H4R   single    0.970  0.020  1.090
 NNR  C5R  H5R1  single    0.970  0.020  1.090
 NNR  C5R  H5R2  single    0.970  0.020  1.090
 NNR  O5R  HO5R  single    0.850  0.020  0.980
 NNR  C1R  H1R   single    0.970  0.020  1.090
 NNR  C2   H2    single    0.930  0.020  1.080
 NNR  C6   H6    single    0.930  0.020  1.080
 NNR  C5   H5    single    0.930  0.020  1.080
 NNR  C4   H4    single    0.930  0.020  1.080
 NNR  N7   HN71  single    0.860  0.020  1.020
 NNR  N7   HN72  single    0.860  0.020  1.020

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
 NNR  HO2R  O2R  C2R   109.04  3.000
 NNR  H2R   C2R  C1R   109.24  3.000
 NNR  H2R   C2R  C3R   108.27  3.000
 NNR  C1R   C2R  C3R   101.32  3.000
 NNR  H2R   C2R  O2R   111.22  3.000
 NNR  C3R   C2R  O2R   116.63  3.000
 NNR  C1R   C2R  O2R   109.59  3.000
 NNR  H3R   C3R  C4R   111.77  3.000
 NNR  H3R   C3R  O3R   112.17  3.000
 NNR  C4R   C3R  O3R   112.35  3.000
 NNR  H3R   C3R  C2R   111.54  3.000
 NNR  C4R   C3R  C2R   100.81  3.000
 NNR  O3R   C3R  C2R   107.59  3.000
 NNR  HO3R  O3R  C3R   108.57  3.000
 NNR  H4R   C4R  O4R   106.55  3.000
 NNR  H4R   C4R  C5R   109.12  3.000
 NNR  O4R   C4R  C5R   111.41  3.000
 NNR  H4R   C4R  C3R   111.94  3.000
 NNR  C5R   C4R  C3R   113.40  3.000
 NNR  O4R   C4R  C3R   104.15  3.000
 NNR  H5R2  C5R  H5R1  106.63  3.000
 NNR  H5R2  C5R  O5R   111.46  3.000
 NNR  H5R1  C5R  O5R   112.14  3.000
 NNR  H5R2  C5R  C4R   110.78  3.000
 NNR  H5R1  C5R  C4R   107.64  3.000
 NNR  O5R   C5R  C4R   108.14  3.000
 NNR  HO5R  O5R  C5R   108.28  3.000
 NNR  C1R   O4R  C4R   110.84  3.000
 NNR  H1R   C1R  N1    104.99  3.000
 NNR  H1R   C1R  O4R   111.45  3.000
 NNR  N1    C1R  O4R   110.04  3.000
 NNR  H1R   C1R  C2R   112.01  3.000
 NNR  O4R   C1R  C2R   107.86  3.000
 NNR  N1    C1R  C2R   110.49  3.000
 NNR  C6    N1   C2    121.72  3.000
 NNR  C2    N1   C1R   116.97  3.000
 NNR  C6    N1   C1R   121.30  3.000
 NNR  H2    C2   C3    122.04  3.000
 NNR  H2    C2   N1    117.01  3.000
 NNR  C3    C2   N1    120.94  3.000
 NNR  H6    C6   C5    122.35  3.000
 NNR  H6    C6   N1    117.82  3.000
 NNR  C5    C6   N1    119.83  3.000
 NNR  H5    C5   C4    121.27  3.000
 NNR  H5    C5   C6    119.10  3.000
 NNR  C4    C5   C6    119.63  3.000
 NNR  H4    C4   C3    121.48  3.000
 NNR  H4    C4   C5    118.93  3.000
 NNR  C3    C4   C5    119.57  3.000
 NNR  C7    C3   C4    124.77  3.000
 NNR  C7    C3   C2    116.91  3.000
 NNR  C4    C3   C2    118.29  3.000
 NNR  N7    C7   O7    124.32  3.000
 NNR  N7    C7   C3    116.09  3.000
 NNR  O7    C7   C3    119.59  3.000
 NNR  HN72  N7   HN71  116.60  3.000
 NNR  HN72  N7   C7    119.50  3.000
 NNR  HN71  N7   C7    123.60  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
 NNR  CONST_01  C4    C5  C6  N1     0.00   0.0  0
 NNR  CONST_02  C4    C3  C2  N1     0.00   0.0  0
 NNR  CONST_03  C5    C6  N1  C2     0.00   0.0  0
 NNR  CONST_04  C5    C4  C3  C2     0.00   0.0  0
 NNR  CONST_05  C3    C4  C5  C6     0.00   0.0  0
 NNR  CONST_06  C3    C2  N1  C6     0.00   0.0  0
 NNR  CONST_07  C5    C6  N1  C1R  180.00   0.0  0
 NNR  CONST_08  C3    C2  N1  C1R  180.00   0.0  0
 NNR  CONST_09  C7    C3  C2  N1   180.00   0.0  0
 NNR  CONST_10  C7    C3  C4  C5   180.00   0.0  0
 NNR  CONST_11  H6    C6  N1  C1R    0.00   0.0  0
 NNR  CONST_12  H2    C2  N1  C1R    0.00   0.0  0
 NNR  CONST_13  H5    C5  C6  N1   180.00   0.0  0
 NNR  CONST_14  H4    C4  C3  C2   180.00   0.0  0
 NNR  CONST_15  HN71  N7  C7  C3     0.00   0.0  0
 NNR  CONST_16  HN72  N7  C7  C3   180.00   0.0  0
 NNR  Var_01    O7    C7  C3  C2    16.70  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
 NNR  chir_01  C2R  O2R  C1R  C3R  negativ
 NNR  chir_02  C3R  O3R  C4R  C2R  positiv
 NNR  chir_03  C4R  O4R  C3R  C5R  negativ
 NNR  chir_04  C1R  O4R  N1   C2R  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
 NNR  plan-1  C1R   0.020
 NNR  plan-1  N1    0.020
 NNR  plan-1  C2    0.020
 NNR  plan-1  C6    0.020
 NNR  plan-1  C5    0.020
 NNR  plan-1  C4    0.020
 NNR  plan-1  C3    0.020
 NNR  plan-1  C7    0.020
 NNR  plan-1  H2    0.020
 NNR  plan-1  H6    0.020
 NNR  plan-1  H5    0.020
 NNR  plan-1  H4    0.020
 NNR  plan-2  C3    0.020
 NNR  plan-2  C7    0.020
 NNR  plan-2  O7    0.020
 NNR  plan-2  N7    0.020
 NNR  plan-2  HN71  0.020
 NNR  plan-2  HN72  0.020

