# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 01:56:53 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ncn(n1)[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
 RVP  RVP  1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide  ligand  34  21  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RVP
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
 RVP  P     P  P     0   1.457   1.8250   0.1349  -2.7767
 RVP  O1P   O  OH1   0  -0.720   1.3543   0.9065  -4.0982
 RVP  O2P   O  OH1   0  -0.646   2.4430  -1.2619  -3.2311
 RVP  O3P   O  O     0  -0.766   2.6609   1.0264  -1.9565
 RVP  O5'   O  O2    0  -0.586   0.5023  -0.4466  -2.0952
 RVP  C5'   C  CH2   0  -0.222  -0.4686   0.4685  -1.5818
 RVP  C4'   C  CH1   0  -0.003  -1.7044  -0.3336  -1.2309
 RVP  O4'   O  O2    0  -0.460  -1.4392  -1.2652  -0.1842
 RVP  C3'   C  CH1   0  -0.048  -2.8409   0.5322  -0.7063
 RVP  O3'   O  OH1   0  -0.708  -4.0449  -0.1567  -0.8967
 RVP  C2'   C  CH1   0   0.023  -2.4892   0.6143   0.7820
 RVP  O2'   O  OH1   0  -0.651  -3.5879   0.8098   1.6267
 RVP  C1'   C  CH1   0   0.174  -1.8804  -0.7694   1.0405
 RVP  N9    N  NR5   0  -0.230  -0.7895  -0.7173   1.9902
 RVP  C8    C  CR15  0   0.059  -0.5311  -1.5582   3.0035
 RVP  N7    N  N     0  -0.415   0.5876  -1.2159   3.5865
 RVP  C5    C  CR5   0   0.174   0.9896  -0.1428   2.8672
 RVP  C6    C  C     0   0.463   2.2337   0.6261   3.1526
 RVP  O6    O  O     0  -0.499   2.5405   1.6038   2.5014
 RVP  N1    N  NH2   0  -0.738   2.9410   0.1265   4.1780
 RVP  N4    N  N     0  -0.300   0.1814   0.1841   1.8895
 RVP  HOP1  H  HOH1  0   0.487   0.8342   0.3897  -4.7246
 RVP  HOP2  H  HOH1  0   0.549   3.3122  -1.1735  -3.6423
 RVP  H5'1  H  HCH2  0   0.261  -0.7357   1.2150  -2.3354
 RVP  H5'2  H  HCH2  0   0.210  -0.0610   0.9894  -0.7119
 RVP  H4'   H  HCH1  0   0.320  -2.0189  -0.8984  -2.1124
 RVP  H3'   H  HCH1  0   0.305  -2.8570   1.5245  -1.1771
 RVP  HO'3  H  HOH1  0   0.448  -4.6718   0.1531  -0.2327
 RVP  H2'   H  HCH1  0   0.246  -1.7246   1.3839   0.9322
 RVP  HO'2  H  HOH1  0   0.460  -3.7460   1.7551   1.7189
 RVP  H1'   H  HCH1  0   0.211  -2.6183  -1.4490   1.4786
 RVP  HC8   H  HCR5  0   0.300  -1.1777  -2.3784   3.2762
 RVP  HN1   H  HNH2  0   0.426   3.7916   0.5753   4.4720
 RVP  HN2   H  HNH2  0   0.418   2.6260  -0.6822   4.6863

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
 RVP  P    O1P   single    1.601  0.020  1.601
 RVP  P    O2P   single    1.594  0.020  1.594
 RVP  P    O3P   double    1.472  0.020  1.472
 RVP  P    O5'   single    1.598  0.020  1.598
 RVP  O1P  HOP1  single    0.850  0.020  0.980
 RVP  O2P  HOP2  single    0.850  0.020  0.980
 RVP  O5'  C5'   single    1.429  0.020  1.429
 RVP  C5'  C4'   single    1.514  0.020  1.514
 RVP  C5'  H5'1  single    0.970  0.020  1.090
 RVP  C5'  H5'2  single    0.970  0.020  1.090
 RVP  C4'  O4'   single    1.426  0.020  1.426
 RVP  C4'  C3'   single    1.522  0.020  1.522
 RVP  C4'  H4'   single    0.970  0.020  1.090
 RVP  O4'  C1'   single    1.393  0.020  1.393
 RVP  C3'  O3'   single    1.400  0.020  1.400
 RVP  C3'  C2'   single    1.531  0.020  1.531
 RVP  C3'  H3'   single    0.970  0.020  1.090
 RVP  O3'  HO'3  single    0.850  0.020  0.980
 RVP  C2'  O2'   single    1.400  0.020  1.400
 RVP  C2'  C1'   single    1.534  0.020  1.534
 RVP  C2'  H2'   single    0.970  0.020  1.090
 RVP  O2'  HO'2  single    0.850  0.020  0.980
 RVP  C1'  N9    single    1.447  0.020  1.447
 RVP  C1'  H1'   single    0.970  0.020  1.090
 RVP  N9   C8    aromatic  1.342  0.020  1.342
 RVP  N9   N4    aromatic  1.329  0.020  1.329
 RVP  C8   N7    aromatic  1.307  0.020  1.307
 RVP  C8   HC8   single    0.930  0.020  1.080
 RVP  N7   C5    aromatic  1.353  0.020  1.353
 RVP  C5   C6    single    1.490  0.020  1.490
 RVP  C5   N4    aromatic  1.310  0.020  1.310
 RVP  C6   O6    double    1.214  0.020  1.214
 RVP  C6   N1    single    1.342  0.020  1.342
 RVP  N1   HN1   single    0.860  0.020  1.020
 RVP  N1   HN2   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
 RVP  O5'   P    O3P   116.94  3.000
 RVP  O5'   P    O2P    97.11  3.000
 RVP  O3P   P    O2P   118.01  3.000
 RVP  O5'   P    O1P   106.50  3.000
 RVP  O3P   P    O1P   109.57  3.000
 RVP  O2P   P    O1P   107.52  3.000
 RVP  HOP1  O1P  P     115.87  3.000
 RVP  HOP2  O2P  P     112.97  3.000
 RVP  C5'   O5'  P     118.85  3.000
 RVP  H5'2  C5'  H5'1  108.31  3.000
 RVP  H5'2  C5'  C4'   111.86  3.000
 RVP  H5'1  C5'  C4'   108.77  3.000
 RVP  H5'2  C5'  O5'   109.73  3.000
 RVP  H5'1  C5'  O5'   110.81  3.000
 RVP  C4'   C5'  O5'   107.36  3.000
 RVP  H4'   C4'  C3'   110.92  3.000
 RVP  H4'   C4'  O4'   107.92  3.000
 RVP  C3'   C4'  O4'   104.92  3.000
 RVP  H4'   C4'  C5'   108.75  3.000
 RVP  C3'   C4'  C5'   112.83  3.000
 RVP  O4'   C4'  C5'   111.37  3.000
 RVP  C1'   O4'  C4'   110.73  3.000
 RVP  H3'   C3'  C2'   111.81  3.000
 RVP  H3'   C3'  O3'   111.94  3.000
 RVP  C2'   C3'  O3'   110.86  3.000
 RVP  H3'   C3'  C4'   112.15  3.000
 RVP  C2'   C3'  C4'   101.18  3.000
 RVP  O3'   C3'  C4'   108.38  3.000
 RVP  HO'3  O3'  C3'   107.89  3.000
 RVP  H2'   C2'  C1'   109.50  3.000
 RVP  H2'   C2'  O2'   111.54  3.000
 RVP  C1'   C2'  O2'   109.63  3.000
 RVP  H2'   C2'  C3'   109.35  3.000
 RVP  C1'   C2'  C3'   101.92  3.000
 RVP  O2'   C2'  C3'   114.44  3.000
 RVP  HO'2  O2'  C2'   108.89  3.000
 RVP  H1'   C1'  N9    105.53  3.000
 RVP  H1'   C1'  C2'   111.10  3.000
 RVP  N9    C1'  C2'   112.17  3.000
 RVP  H1'   C1'  O4'   110.15  3.000
 RVP  N9    C1'  O4'   110.55  3.000
 RVP  C2'   C1'  O4'   107.38  3.000
 RVP  N4    N9   C8    109.98  3.000
 RVP  N4    N9   C1'   121.70  3.000
 RVP  C8    N9   C1'   128.18  3.000
 RVP  HC8   C8   N7    126.79  3.000
 RVP  HC8   C8   N9    123.48  3.000
 RVP  N7    C8   N9    109.73  3.000
 RVP  C5    N7   C8    102.99  3.000
 RVP  N4    C5   C6    121.96  3.000
 RVP  N4    C5   N7    114.29  3.000
 RVP  C6    C5   N7    123.74  3.000
 RVP  N1    C6   O6    125.20  3.000
 RVP  N1    C6   C5    113.22  3.000
 RVP  O6    C6   C5    121.59  3.000
 RVP  HN2   N1   HN1   118.43  3.000
 RVP  HN2   N1   C6    121.35  3.000
 RVP  HN1   N1   C6    120.19  3.000
 RVP  C5    N4   N9    103.00  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
 RVP  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 RVP  CONST_02  N7   C5   N4   N9      0.00   0.0  0
 RVP  CONST_03  C5   N4   N9   C8      0.00   0.0  0
 RVP  CONST_04  N4   C5   N7   C8      0.00   0.0  0
 RVP  CONST_05  N4   N9   C8   N7      0.00   0.0  0
 RVP  CONST_06  N7   C8   N9   C1'   180.00   0.0  0
 RVP  CONST_07  C5   N4   N9   C1'   180.00   0.0  0
 RVP  CONST_08  C6   C5   N4   N9    180.00   0.0  0
 RVP  CONST_09  C6   C5   N7   C8    180.00   0.0  0
 RVP  CONST_10  HC8  C8   N9   C1'     0.00   0.0  0
 RVP  CONST_11  HN1  N1   C6   C5    180.00   0.0  0
 RVP  CONST_12  HN2  N1   C6   C5      0.00   0.0  0
 RVP  Var_01    O6   C6   C5   N7   -178.17  30.0  2
 RVP  Var_02    C4'  C5'  O5'  P     169.99  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
 RVP  chir_01  C4'  C5'  O4'  C3'  negativ
 RVP  chir_02  C3'  O3'  C4'  C2'  positiv
 RVP  chir_03  C2'  O2'  C3'  C1'  positiv
 RVP  chir_04  C1'  O4'  N9   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
 RVP  plan-1  C1'  0.020
 RVP  plan-1  N9   0.020
 RVP  plan-1  C8   0.020
 RVP  plan-1  N7   0.020
 RVP  plan-1  C5   0.020
 RVP  plan-1  C6   0.020
 RVP  plan-1  N4   0.020
 RVP  plan-1  HC8  0.020
 RVP  plan-2  C5   0.020
 RVP  plan-2  C6   0.020
 RVP  plan-2  O6   0.020
 RVP  plan-2  N1   0.020
 RVP  plan-2  HN1  0.020
 RVP  plan-2  HN2  0.020

