# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 03:00:31 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 5-amino-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1n(cnc1C(O)=O)[C@@H]2O[C@H](CO[P](O)(O)=O)[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
 C2R  C2R  '5-amino-1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole-4-carboxylic acid'  ligand  36  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C2R
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
 C2R  PA    P  P     0   1.457   4.3548  -1.1981   0.0046
 C2R  O1A   O  O     0  -0.708   4.2582  -2.0710   1.1887
 C2R  O2A   O  OH1   0  -0.729   4.6315  -1.8745  -1.4101
 C2R  O3A   O  OH1   0  -0.740   5.4750  -0.0855   0.2480
 C2R  O5'   O  O2    0  -0.588   3.0207  -0.4261  -0.4185
 C2R  C2'   C  CH1   0  -0.053  -0.7445   2.3486  -0.0524
 C2R  O2'   O  OH1   0  -0.661  -0.4469   3.3987  -0.9288
 C2R  C3'   C  CH1   0  -0.037   0.4580   2.0192   0.8410
 C2R  O3'   O  OH1   0  -0.653   1.1447   3.1442   1.3050
 C2R  C5'   C  CH2   0  -0.180   2.2701   0.2726   0.5764
 C2R  C4'   C  CH1   0   0.004   1.3339   1.2230  -0.1225
 C2R  O4'   O  O2    0  -0.491   0.4172   0.5028  -0.9385
 C2R  C1'   C  CH1   0   0.159  -0.8594   1.0679  -0.8824
 C2R  N1    N  NR5   0  -0.498  -1.7764   0.1064  -0.2887
 C2R  C5    C  CR5   0   0.512  -3.1233   0.1036  -0.4728
 C2R  C4    C  CR5   0  -0.075  -3.5850  -0.9963   0.2371
 C2R  N3    N  N     0  -0.436  -2.5266  -1.6412   0.8356
 C2R  C2    C  CR15  0   0.088  -1.4735  -0.9687   0.5140
 C2R  N5    N  NH2   0  -0.852  -3.7570   0.9953  -1.2774
 C2R  C6    C  C     0   0.488  -4.9648  -1.3996   0.3349
 C2R  O7    O  OH1   0  -0.601  -5.1507  -2.4775   1.0909
 C2R  O8    O  O     0  -0.481  -5.8816  -0.8160  -0.2170
 C2R  H2A   H  HOH1  0   0.505   5.3921  -2.4710  -1.4232
 C2R  H3A   H  HOH1  0   0.497   5.6429   0.5111  -0.4942
 C2R  H3    H  HOH1  0   0.455   0.0707   4.0535  -0.4433
 C2R  H3'   H  HCH1  0   0.252   0.1280   1.3785   1.6699
 C2R  H1    H  HOH1  0   0.472   0.7280   3.4538   2.1158
 C2R  H5'1  H  HCH2  0   0.256   2.9237   0.8576   1.2302
 C2R  H5'2  H  HCH2  0   0.249   1.7209  -0.4406   1.1973
 C2R  H4'   H  HCH1  0   0.259   1.9187   1.9133  -0.7430
 C2R  H1'   H  HCH1  0   0.288  -1.2269   1.2811  -1.8920
 C2R  H2    H  HCR5  0   0.289  -0.4641  -1.2035   0.8089
 C2R  HN51  H  HNH2  0   0.403  -3.4312   1.9497  -1.2725
 C2R  HN52  H  HNH2  0   0.402  -4.7627   0.9341  -1.2412
 C2R  HO7   H  HOH1  0   0.481  -6.0935  -2.6966   1.1077
 C2R  H2'   H  HCH1  0   0.267  -1.6543   2.5458   0.5296

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
 C2R  PA   O1A   double    1.474  0.020  1.474
 C2R  PA   O2A   single    1.592  0.020  1.592
 C2R  PA   O3A   single    1.598  0.020  1.598
 C2R  PA   O5'   single    1.598  0.020  1.598
 C2R  O2A  H2A   single    0.850  0.020  0.980
 C2R  O3A  H3A   single    0.850  0.020  0.980
 C2R  O5'  C5'   single    1.429  0.020  1.429
 C2R  C2'  O2'   single    1.400  0.020  1.400
 C2R  C2'  C3'   single    1.534  0.020  1.534
 C2R  C2'  C1'   single    1.530  0.020  1.530
 C2R  C2'  H2'   single    0.970  0.020  1.090
 C2R  O2'  H3    single    0.850  0.020  0.980
 C2R  C3'  O3'   single    1.397  0.020  1.397
 C2R  C3'  C4'   single    1.526  0.020  1.526
 C2R  C3'  H3'   single    0.970  0.020  1.090
 C2R  O3'  H1    single    0.850  0.020  0.980
 C2R  C5'  C4'   single    1.506  0.020  1.506
 C2R  C5'  H5'1  single    0.970  0.020  1.090
 C2R  C5'  H5'2  single    0.970  0.020  1.090
 C2R  C4'  O4'   single    1.423  0.020  1.423
 C2R  C4'  H4'   single    0.970  0.020  1.090
 C2R  O4'  C1'   single    1.397  0.020  1.397
 C2R  C1'  N1    single    1.455  0.020  1.455
 C2R  C1'  H1'   single    0.970  0.020  1.090
 C2R  N1   C5    aromatic  1.359  0.020  1.359
 C2R  N1   C2    aromatic  1.375  0.020  1.375
 C2R  C5   C4    aromatic  1.388  0.020  1.388
 C2R  C5   N5    single    1.358  0.020  1.358
 C2R  C4   N3    aromatic  1.376  0.020  1.376
 C2R  C4   C6    single    1.441  0.020  1.441
 C2R  N3   C2    aromatic  1.290  0.020  1.290
 C2R  C2   H2    single    0.930  0.020  1.080
 C2R  N5   HN51  single    0.890  0.020  1.040
 C2R  N5   HN52  single    0.890  0.020  1.040
 C2R  C6   O7    single    1.330  0.020  1.330
 C2R  C6   O8    double    1.219  0.020  1.219
 C2R  O7   HO7   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
 C2R  O5'   PA   O3A   106.81  3.000
 C2R  O5'   PA   O2A    96.61  3.000
 C2R  O3A   PA   O2A   108.02  3.000
 C2R  O5'   PA   O1A   116.35  3.000
 C2R  O3A   PA   O1A   109.63  3.000
 C2R  O2A   PA   O1A   118.26  3.000
 C2R  H2A   O2A  PA    114.27  3.000
 C2R  H3A   O3A  PA    115.75  3.000
 C2R  C5'   O5'  PA    119.37  3.000
 C2R  H2'   C2'  C1'   112.06  3.000
 C2R  H2'   C2'  C3'   112.30  3.000
 C2R  C1'   C2'  C3'   101.25  3.000
 C2R  H2'   C2'  O2'   111.92  3.000
 C2R  C1'   C2'  O2'   107.71  3.000
 C2R  C3'   C2'  O2'   111.04  3.000
 C2R  H3    O2'  C2'   107.93  3.000
 C2R  H3'   C3'  C4'   110.15  3.000
 C2R  H3'   C3'  O3'   111.52  3.000
 C2R  C4'   C3'  O3'   110.34  3.000
 C2R  H3'   C3'  C2'   109.22  3.000
 C2R  C4'   C3'  C2'   101.20  3.000
 C2R  O3'   C3'  C2'   113.94  3.000
 C2R  H1    O3'  C3'   109.02  3.000
 C2R  H5'2  C5'  H5'1  108.02  3.000
 C2R  H5'2  C5'  C4'   111.28  3.000
 C2R  H5'1  C5'  C4'   108.13  3.000
 C2R  H5'2  C5'  O5'   109.89  3.000
 C2R  H5'1  C5'  O5'   111.33  3.000
 C2R  C4'   C5'  O5'   108.19  3.000
 C2R  H4'   C4'  O4'   109.72  3.000
 C2R  H4'   C4'  C5'   109.16  3.000
 C2R  O4'   C4'  C5'   110.31  3.000
 C2R  H4'   C4'  C3'   109.55  3.000
 C2R  O4'   C4'  C3'   104.86  3.000
 C2R  C5'   C4'  C3'   113.14  3.000
 C2R  C1'   O4'  C4'   111.15  3.000
 C2R  H1'   C1'  N1    107.05  3.000
 C2R  H1'   C1'  O4'   110.38  3.000
 C2R  N1    C1'  O4'   108.96  3.000
 C2R  H1'   C1'  C2'   111.23  3.000
 C2R  N1    C1'  C2'   112.27  3.000
 C2R  O4'   C1'  C2'   106.96  3.000
 C2R  C2    N1   C5    107.20  3.000
 C2R  C2    N1   C1'   128.00  3.000
 C2R  C5    N1   C1'   124.78  3.000
 C2R  N5    C5   C4    131.92  3.000
 C2R  N5    C5   N1    122.77  3.000
 C2R  C4    C5   N1    105.18  3.000
 C2R  C6    C4   N3    125.16  3.000
 C2R  C6    C4   C5    125.10  3.000
 C2R  N3    C4   C5    109.74  3.000
 C2R  C2    N3   C4    105.97  3.000
 C2R  H2    C2   N3    125.65  3.000
 C2R  H2    C2   N1    122.44  3.000
 C2R  N3    C2   N1    111.90  3.000
 C2R  HN52  N5   HN51  112.31  3.000
 C2R  HN52  N5   C5    113.85  3.000
 C2R  HN51  N5   C5    117.89  3.000
 C2R  O8    C6   O7    122.71  3.000
 C2R  O8    C6   C4    123.75  3.000
 C2R  O7    C6   C4    113.54  3.000
 C2R  HO7   O7   C6    109.25  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
 C2R  CONST_01  N3    C4   C5   N1      0.00   0.0  0
 C2R  CONST_02  C4    N3   C2   N1      0.00   0.0  0
 C2R  CONST_03  N3    C2   N1   C5      0.00   0.0  0
 C2R  CONST_04  C2    N3   C4   C5      0.00   0.0  0
 C2R  CONST_05  C2    N1   C5   C4      0.00   0.0  0
 C2R  CONST_06  C4    C5   N1   C1'   180.00   0.0  0
 C2R  CONST_07  N3    C2   N1   C1'   180.00   0.0  0
 C2R  CONST_08  N5    C5   N1   C1'     0.00   0.0  0
 C2R  CONST_09  C6    C4   C5   N1    180.00   0.0  0
 C2R  CONST_10  N5    C5   C4   N3    180.00   0.0  0
 C2R  CONST_11  N5    C5   N1   C2    180.00   0.0  0
 C2R  CONST_12  C6    C4   N3   C2    180.00   0.0  0
 C2R  CONST_13  H2    C2   N1   C1'     0.00   0.0  0
 C2R  CONST_15  HN52  N5   C5   N1    180.00   0.0  0
 C2R  CONST_16  HO7   O7   C6   C4    180.00   0.0  0
 C2R  Var_01    O7    C6   C4   C5   -179.06  30.0  2
 C2R  Var_02    C4'   C5'  O5'  PA    163.39  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
 C2R  chir_01  C2'  O2'  C3'  C1'  positiv
 C2R  chir_02  C3'  O3'  C4'  C2'  positiv
 C2R  chir_03  C4'  O4'  C3'  C5'  negativ
 C2R  chir_04  C1'  O4'  N1   C2'  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
 C2R  plan-1  C1'   0.020
 C2R  plan-1  N1    0.020
 C2R  plan-1  C5    0.020
 C2R  plan-1  C4    0.020
 C2R  plan-1  N3    0.020
 C2R  plan-1  C2    0.020
 C2R  plan-1  N5    0.020
 C2R  plan-1  C6    0.020
 C2R  plan-1  H2    0.020
 C2R  plan-2  C5    0.020
 C2R  plan-2  N5    0.020
 C2R  plan-2  HN51  0.020
 C2R  plan-2  HN52  0.020
 C2R  plan-3  C4    0.020
 C2R  plan-3  C6    0.020
 C2R  plan-3  O7    0.020
 C2R  plan-3  O8    0.020
 C2R  plan-3  HO7   0.020

