# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 09:20:28 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 5-hydroxy-1-(beta-D-ribofuranosyl)-1H-imidazole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ncn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c1O
#
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
 MZR  MZR  5-hydroxy-1-(beta-D-ribofuranosyl)-1H-imidazole-4-carboxamide  ligand  31  18  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MZR
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
 MZR  N1    N  NH2   0  -0.816  -4.4726   1.5927  -0.6076
 MZR  C4    C  CR5   0   0.502  -1.5197  -0.4801   0.1203
 MZR  C5    C  CR5   0  -0.081  -2.4252   0.5375  -0.0789
 MZR  C6    C  C     0   0.458  -3.8396   0.4194  -0.4373
 MZR  O6    O  O     0  -0.501  -4.3916  -0.6692  -0.5727
 MZR  N7    N  N     0  -0.461  -1.7948   1.7460   0.0972
 MZR  C8    C  CR15  0   0.101  -0.5604   1.4783   0.3892
 MZR  N9    N  NR5   0  -0.516  -0.3399   0.1306   0.4286
 MZR  C1'   C  CR15  0   0.212   0.9055  -0.5630   0.7319
 MZR  C2'   C  CR15  0  -0.033   1.4674  -1.2814  -0.5007
 MZR  O2'   O  OH1   0  -0.663   0.9359  -2.5801  -0.5388
 MZR  C3'   C  CR15  0  -0.018   2.9721  -1.1471  -0.2842
 MZR  O3'   O  OH1   0  -0.663   3.3633  -2.1331   0.6297
 MZR  C4'   C  CR15  0  -0.071   3.0286   0.2602   0.3169
 MZR  O4'   O  O     0  -0.486   1.8616   0.3503   1.1426
 MZR  C5'   C  CH2   0  -0.156   3.0456   1.3595  -0.7281
 MZR  O5'   O  OH1   0  -0.664   2.9824   2.5961  -0.0627
 MZR  HN1   H  HNH2  0   0.402  -3.9911   2.4659  -0.4768
 MZR  HN1A  H  HNH2  0   0.398  -5.4510   1.6147  -0.8394
 MZR  HO3   H  HOH1  0   0.485  -0.8430  -2.2533  -0.1719
 MZR  H8    H  HCR5  0   0.286   0.2245   2.1944   0.5741
 MZR  H1'   H  HCR5  0   0.279   0.6963  -1.2841   1.5320
 MZR  H2'   H  HCR5  0   0.273   1.1918  -0.7251  -1.4035
 MZR  HO2'  H  HOH1  0   0.482   1.0562  -2.9501  -1.4207
 MZR  H3'   H  HCR5  0   0.259   3.5352  -1.2078  -1.2237
 MZR  HO3'  H  HOH1  0   0.461   4.3049  -2.0345   0.8033
 MZR  H4'   H  HCR5  0   0.272   3.8977   0.3790   0.9709
 MZR  H5'   H  HCH2  0   0.222   3.9677   1.2518  -1.3137
 MZR  H5'A  H  HCH2  0   0.203   2.2090   1.2382  -1.4283
 MZR  HO5'  H  HOH1  0   0.461   2.9656   3.2926  -0.7251
 MZR  O3    O  OH1   0  -0.628  -1.6744  -1.7960   0.0741

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
 MZR  N1   C6    single    1.344  0.020  1.344
 MZR  O3   C4    single    1.326  0.020  1.326
 MZR  C4   C5    aromatic  1.377  0.020  1.377
 MZR  C4   N9    aromatic  1.364  0.020  1.364
 MZR  C5   C6    single    1.464  0.020  1.464
 MZR  C5   N7    aromatic  1.374  0.020  1.374
 MZR  C6   O6    double    1.228  0.020  1.228
 MZR  N7   C8    aromatic  1.296  0.020  1.296
 MZR  C8   N9    aromatic  1.366  0.020  1.366
 MZR  N9   C1'   single    1.458  0.020  1.458
 MZR  C1'  C2'   single    1.533  0.020  1.533
 MZR  C1'  O4'   single    1.385  0.020  1.385
 MZR  C2'  O2'   single    1.404  0.020  1.404
 MZR  C2'  C3'   single    1.526  0.020  1.526
 MZR  C3'  O3'   single    1.400  0.020  1.400
 MZR  C3'  C4'   single    1.531  0.020  1.531
 MZR  C4'  O4'   single    1.432  0.020  1.432
 MZR  C4'  C5'   single    1.517  0.020  1.517
 MZR  C5'  O5'   single    1.406  0.020  1.406
 MZR  N1   HN1   single    0.860  0.020  1.020
 MZR  N1   HN1A  single    0.860  0.020  1.020
 MZR  O3   HO3   single    0.850  0.020  0.980
 MZR  C8   H8    single    0.930  0.020  1.080
 MZR  C1'  H1'   single    0.970  0.020  1.090
 MZR  C2'  H2'   single    0.970  0.020  1.090
 MZR  O2'  HO2'  single    0.850  0.020  0.980
 MZR  C3'  H3'   single    0.970  0.020  1.090
 MZR  O3'  HO3'  single    0.850  0.020  0.980
 MZR  C4'  H4'   single    0.970  0.020  1.090
 MZR  C5'  H5'   single    0.970  0.020  1.090
 MZR  C5'  H5'A  single    0.970  0.020  1.090
 MZR  O5'  HO5'  single    0.850  0.020  0.980

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
 MZR  HN1A  N1   HN1  118.48  3.000
 MZR  HN1A  N1   C6   120.43  3.000
 MZR  HN1   N1   C6   121.07  3.000
 MZR  N9    C4   C5   105.71  3.000
 MZR  N9    C4   O3   123.59  3.000
 MZR  C5    C4   O3   130.69  3.000
 MZR  N7    C5   C6   123.06  3.000
 MZR  N7    C5   C4   109.25  3.000
 MZR  C6    C5   C4   127.68  3.000
 MZR  O6    C6   C5   122.20  3.000
 MZR  O6    C6   N1   123.24  3.000
 MZR  C5    C6   N1   114.56  3.000
 MZR  C8    N7   C5   106.50  3.000
 MZR  H8    C8   N9   122.19  3.000
 MZR  H8    C8   N7   126.47  3.000
 MZR  N9    C8   N7   111.34  3.000
 MZR  C1'   N9   C8   127.83  3.000
 MZR  C1'   N9   C4   124.97  3.000
 MZR  C8    N9   C4   107.19  3.000
 MZR  H1'   C1'  O4'  110.42  3.000
 MZR  H1'   C1'  C2'  110.37  3.000
 MZR  O4'   C1'  C2'  107.13  3.000
 MZR  H1'   C1'  N9   107.55  3.000
 MZR  O4'   C1'  N9   109.75  3.000
 MZR  C2'   C1'  N9   111.64  3.000
 MZR  H2'   C2'  C3'  108.67  3.000
 MZR  H2'   C2'  O2'  110.62  3.000
 MZR  C3'   C2'  O2'  117.30  3.000
 MZR  H2'   C2'  C1'  109.41  3.000
 MZR  C3'   C2'  C1'  101.89  3.000
 MZR  O2'   C2'  C1'  108.45  3.000
 MZR  HO2'  O2'  C2'  109.43  3.000
 MZR  H3'   C3'  C4'  111.60  3.000
 MZR  H3'   C3'  O3'  112.12  3.000
 MZR  C4'   C3'  O3'  112.38  3.000
 MZR  H3'   C3'  C2'  112.31  3.000
 MZR  C4'   C3'  C2'   99.96  3.000
 MZR  O3'   C3'  C2'  107.82  3.000
 MZR  HO3'  O3'  C3'  108.59  3.000
 MZR  H4'   C4'  C5'  108.92  3.000
 MZR  H4'   C4'  O4'  107.20  3.000
 MZR  C5'   C4'  O4'  111.14  3.000
 MZR  H4'   C4'  C3'  111.33  3.000
 MZR  C5'   C4'  C3'  113.33  3.000
 MZR  O4'   C4'  C3'  104.72  3.000
 MZR  C4'   O4'  C1'  110.49  3.000
 MZR  H5'A  C5'  H5'  106.80  3.000
 MZR  H5'A  C5'  O5'  111.40  3.000
 MZR  H5'   C5'  O5'  112.13  3.000
 MZR  H5'A  C5'  C4'  110.54  3.000
 MZR  H5'   C5'  C4'  107.81  3.000
 MZR  O5'   C5'  C4'  108.12  3.000
 MZR  HO5'  O5'  C5'  108.18  3.000
 MZR  HO3   O3   C4   111.89  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
 MZR  CONST_01  C8    N7  C5  C4     0.00   0.0  0
 MZR  CONST_02  N7    C8  N9  C4     0.00   0.0  0
 MZR  CONST_03  C8    N9  C4  C5     0.00   0.0  0
 MZR  CONST_04  N9    C8  N7  C5     0.00   0.0  0
 MZR  CONST_05  N9    C4  C5  N7     0.00   0.0  0
 MZR  CONST_06  C1'   N9  C4  C5   180.00   0.0  0
 MZR  CONST_07  C1'   N9  C8  N7   180.00   0.0  0
 MZR  CONST_08  N7    C5  C4  O3   180.00   0.0  0
 MZR  CONST_09  C8    N9  C4  O3   180.00   0.0  0
 MZR  CONST_10  C1'   N9  C4  O3     0.00   0.0  0
 MZR  CONST_11  N9    C4  C5  C6   180.00   0.0  0
 MZR  CONST_12  C8    N7  C5  C6   180.00   0.0  0
 MZR  CONST_13  H8    C8  N9  C4   180.00   0.0  0
 MZR  CONST_14  HN1   N1  C6  C5     0.00   0.0  0
 MZR  CONST_15  HN1A  N1  C6  C5   180.00   0.0  0
 MZR  Var_01    C4    C5  C6  N1  -178.01  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
 MZR  chir_01  C1'  N9   C2'  O4'  negativ
 MZR  chir_02  C2'  O2'  C3'  C1'  positiv
 MZR  chir_03  C3'  O3'  C4'  C2'  positiv
 MZR  chir_04  C4'  O4'  C3'  C5'  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
 MZR  plan-1  C4    0.020
 MZR  plan-1  C5    0.020
 MZR  plan-1  C6    0.020
 MZR  plan-1  N7    0.020
 MZR  plan-1  C8    0.020
 MZR  plan-1  N9    0.020
 MZR  plan-1  C1'   0.020
 MZR  plan-1  H8    0.020
 MZR  plan-1  O3    0.020
 MZR  plan-2  N1    0.020
 MZR  plan-2  C5    0.020
 MZR  plan-2  C6    0.020
 MZR  plan-2  O6    0.020
 MZR  plan-2  HN1   0.020
 MZR  plan-2  HN1A  0.020

