# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 06:49:51 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  33  22  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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   1.220   4.5492  -1.0824  -0.2233
 C2R  O1A   O  O      0  -0.904   4.3606  -1.9580   1.0107
 C2R  O2A   O  OP    -1  -0.896   4.8674  -1.8300  -1.5103
 C2R  O3A   O  OP    -1  -0.903   5.3875   0.1675   0.0235
 C2R  O5'   O  O2     0  -0.656   2.9855  -0.4896  -0.5828
 C2R  C2'   C  CH1    0  -0.040  -0.7219   2.3230   0.0804
 C2R  O2'   O  OH1    0  -0.667  -0.4636   3.4174  -0.7577
 C2R  C3'   C  CH1    0  -0.042   0.5262   1.9406   0.8834
 C2R  O3'   O  OH1    0  -0.659   1.2491   3.0426   1.3590
 C2R  C5'   C  CH2    0  -0.126   2.3097   0.1757   0.4355
 C2R  C4'   C  CH1    0   0.005   1.3397   1.1739  -0.1532
 C2R  O4'   O  O2     0  -0.495   0.3624   0.5096  -0.9550
 C2R  C1'   C  CH1    0   0.160  -0.9022   1.0841  -0.7994
 C2R  N1    N  NR5    0  -0.479  -1.8045   0.1115  -0.2115
 C2R  C5    C  CR5    0   0.423  -3.1517   0.0548  -0.4329
 C2R  C4    C  CR5    0  -0.131  -3.6140  -1.0165   0.3021
 C2R  N3    N  N      0  -0.453  -2.5565  -1.5964   0.9646
 C2R  C2    C  CR15   0   0.063  -1.5035  -0.9057   0.6517
 C2R  N5    N  NH2    0  -0.862  -3.7867   0.9038  -1.3171
 C2R  C6    C  C      0   0.373  -5.0242  -1.4905   0.3763
 C2R  O7    O  OC    -1  -0.604  -5.2768  -2.4653   1.1071
 C2R  O8    O  O      0  -0.616  -5.8550  -0.8499  -0.3183
 C2R  H3    H  HOH1   0   0.450   0.1172   4.0226  -0.2796
 C2R  H1    H  HOH1   0   0.467   0.8632   3.3321   2.1919
 C2R  H5'1  H  HCH2   0   0.183   2.9886   0.7426   1.0880
 C2R  H5'2  H  HCH2   0   0.175   1.7618  -0.5216   1.0896
 C2R  H4'   H  HCH1   0   0.227   1.8973   1.8860  -0.7764
 C2R  H1'   H  HCH1   0   0.269  -1.3260   1.3561  -1.7723
 C2R  H2    H  HCR5   0   0.272  -0.5002  -1.0875   1.0042
 C2R  HN51  H  HNH2   0   0.375  -3.6538   1.8874  -1.1225
 C2R  HN52  H  HNH2   0   0.379  -4.7759   0.6812  -1.3082
 C2R  H2'   H  HCH1   0   0.253  -1.5978   2.4989   0.7186
 C2R  H3'   H  HCH1   0   0.237   0.2365   1.2698   1.7038

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   deloc     1.525  0.020  1.525
 C2R  PA   O2A   deloc     1.522  0.020  1.522
 C2R  PA   O3A   deloc     1.525  0.020  1.525
 C2R  PA   O5'   single    1.710  0.020  1.710
 C2R  O5'  C5'   single    1.391  0.020  1.391
 C2R  C2'  O2'   single    1.402  0.020  1.402
 C2R  C2'  C3'   single    1.533  0.020  1.533
 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    1.401  0.020  1.401
 C2R  C3'  C4'   single    1.524  0.020  1.524
 C2R  C3'  H3'   single    0.970  0.020  1.090
 C2R  O3'  H1    single    0.850  0.020  0.980
 C2R  C5'  C4'   single    1.511  0.020  1.511
 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    1.428  0.020  1.428
 C2R  C4'  H4'   single    0.970  0.020  1.090
 C2R  O4'  C1'   single    1.398  0.020  1.398
 C2R  C1'  N1    single    1.451  0.020  1.451
 C2R  C1'  H1'   single    0.970  0.020  1.090
 C2R  N1   C5    aromatic  1.366  0.020  1.366
 C2R  N1   C2    aromatic  1.368  0.020  1.368
 C2R  C5   C4    aromatic  1.379  0.020  1.379
 C2R  C5   N5    single    1.381  0.020  1.381
 C2R  C4   N3    aromatic  1.376  0.020  1.376
 C2R  C4   C6    single    1.490  0.020  1.490
 C2R  N3   C2    aromatic  1.298  0.020  1.298
 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    deloc     1.244  0.020  1.244
 C2R  C6   O8    deloc     1.258  0.020  1.258

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   104.62  3.000
 C2R  O5'   PA   O2A   100.58  3.000
 C2R  O3A   PA   O2A   115.12  3.000
 C2R  O5'   PA   O1A   104.84  3.000
 C2R  O3A   PA   O1A   114.05  3.000
 C2R  O2A   PA   O1A   115.35  3.000
 C2R  C5'   O5'  PA    117.12  3.000
 C2R  H2'   C2'  C1'   111.71  3.000
 C2R  H2'   C2'  C3'   112.65  3.000
 C2R  C1'   C2'  C3'   101.26  3.000
 C2R  H2'   C2'  O2'   111.67  3.000
 C2R  C1'   C2'  O2'   108.05  3.000
 C2R  C3'   C2'  O2'   110.97  3.000
 C2R  H3    O2'  C2'   107.70  3.000
 C2R  H3'   C3'  C4'   109.96  3.000
 C2R  H3'   C3'  O3'   111.27  3.000
 C2R  C4'   C3'  O3'   110.55  3.000
 C2R  H3'   C3'  C2'   109.20  3.000
 C2R  C4'   C3'  C2'   101.76  3.000
 C2R  O3'   C3'  C2'   113.69  3.000
 C2R  H1    O3'  C3'   108.87  3.000
 C2R  H5'2  C5'  H5'1  106.32  3.000
 C2R  H5'2  C5'  C4'   109.27  3.000
 C2R  H5'1  C5'  C4'   106.68  3.000
 C2R  H5'2  C5'  O5'   111.92  3.000
 C2R  H5'1  C5'  O5'   112.40  3.000
 C2R  C4'   C5'  O5'   110.03  3.000
 C2R  H4'   C4'  O4'   109.30  3.000
 C2R  H4'   C4'  C5'   108.87  3.000
 C2R  O4'   C4'  C5'   110.53  3.000
 C2R  H4'   C4'  C3'   109.31  3.000
 C2R  O4'   C4'  C3'   104.51  3.000
 C2R  C5'   C4'  C3'   114.19  3.000
 C2R  C1'   O4'  C4'   111.44  3.000
 C2R  H1'   C1'  N1    106.60  3.000
 C2R  H1'   C1'  O4'   110.69  3.000
 C2R  N1    C1'  O4'   109.40  3.000
 C2R  H1'   C1'  C2'   110.80  3.000
 C2R  N1    C1'  C2'   112.52  3.000
 C2R  O4'   C1'  C2'   106.87  3.000
 C2R  C2    N1   C5    106.76  3.000
 C2R  C2    N1   C1'   128.12  3.000
 C2R  C5    N1   C1'   125.12  3.000
 C2R  N5    C5   C4    131.67  3.000
 C2R  N5    C5   N1    122.13  3.000
 C2R  C4    C5   N1    106.05  3.000
 C2R  C6    C4   N3    124.71  3.000
 C2R  C6    C4   C5    126.24  3.000
 C2R  N3    C4   C5    109.05  3.000
 C2R  C2    N3   C4    106.45  3.000
 C2R  H2    C2   N3    125.89  3.000
 C2R  H2    C2   N1    122.43  3.000
 C2R  N3    C2   N1    111.69  3.000
 C2R  HN52  N5   HN51  109.88  3.000
 C2R  HN52  N5   C5    107.95  3.000
 C2R  HN51  N5   C5    114.48  3.000
 C2R  O8    C6   O7    126.09  3.000
 C2R  O8    C6   C4    115.82  3.000
 C2R  O7    C6   C4    118.09  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  Var_01    O7    C6   C4   C5   -178.90  30.0  2
 C2R  Var_02    C4'   C5'  O5'  PA    152.46  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

