# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 06:45:08 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 4-amino-1-beta-D-ribofuranosylpyridin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=CC(=O)N(C=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
 CTD  CTD  4-amino-1-beta-D-ribofuranosylpyridin-2(1H)-one  ligand  31  17  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CTD
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
 CTD  N1    N  NR6   0  -0.401  -0.0768  -0.3818   0.8919
 CTD  C2    C  CR6   0   0.509  -0.8198  -0.7878   2.0093
 CTD  C3    C  CR16  0  -0.592  -0.3851  -0.2895   3.2623
 CTD  C4    C  CR6   0   0.458   0.6711   0.5900   3.3930
 CTD  C5    C  CR16  0  -0.513   1.3357   1.0115   2.2027
 CTD  C6    C  CR16  0  -0.037   0.9390   0.5067   1.0152
 CTD  O2    O  O     0  -0.505  -1.7917  -1.5333   1.8531
 CTD  N4    N  NH2   0  -0.762   1.1022   1.0412   4.5883
 CTD  C1'   C  CR15  0   0.155  -0.5091  -0.8586  -0.4259
 CTD  C2'   C  CR15  0  -0.044  -1.5306   0.0775  -1.0825
 CTD  O2'   O  OH1   0  -0.648  -2.4668  -0.7000  -1.7811
 CTD  C3'   C  CR15  0   0.029  -0.6547   0.8669  -2.0603
 CTD  C4'   C  CR15  0  -0.025   0.3727  -0.1820  -2.4714
 CTD  O4'   O  O     0  -0.471   0.5997  -0.9354  -1.2847
 CTD  O3'   O  OH1   0  -0.689  -1.3460   1.3323  -3.1875
 CTD  C5'   C  CH2   0  -0.172   1.6593   0.3961  -3.0001
 CTD  O5'   O  OH1   0  -0.634   2.5051  -0.6525  -3.3979
 CTD  H3    H  HCR6  0   0.236  -0.9346  -0.6159   4.1350
 CTD  H5    H  HCR6  0   0.235   2.1613   1.7081   2.2409
 CTD  H6    H  HCR6  0   0.315   1.4446   0.8015   0.1094
 CTD  HN41  H  HNH2  0   0.380   1.7121   1.8386   4.6258
 CTD  HN42  H  HNH2  0   0.395   0.5384   0.8924   5.4058
 CTD  H1'   H  HCR5  0   0.326  -0.9451  -1.8456  -0.2720
 CTD  H2'   H  HCR5  0   0.263  -2.0205   0.7176  -0.3388
 CTD  HO2'  H  HOH1  0   0.463  -2.6923  -0.2135  -2.5841
 CTD  H3'   H  HCR5  0   0.225  -0.1636   1.6910  -1.5314
 CTD  H4'   H  HCR5  0   0.212  -0.0713  -0.8296  -3.2392
 CTD  HO3'  H  HOH1  0   0.456  -1.8129   2.1404  -2.9510
 CTD  H5'1  H  HCH2  0   0.214   1.3958   1.0547  -3.8380
 CTD  H5'2  H  HCH2  0   0.185   2.1352   1.0351  -2.2414
 CTD  HO5'  H  HOH1  0   0.439   3.2749  -0.2693  -3.8210

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
 CTD  N1   C2    single  1.402  0.020  1.402
 CTD  N1   C6    single  1.355  0.020  1.355
 CTD  N1   C1'   single  1.467  0.020  1.467
 CTD  C2   C3    single  1.417  0.020  1.417
 CTD  C2   O2    double  1.235  0.020  1.235
 CTD  C3   C4    double  1.381  0.020  1.381
 CTD  C3   H3    single  0.930  0.020  1.080
 CTD  C4   C5    single  1.427  0.020  1.427
 CTD  C4   N4    single  1.348  0.020  1.348
 CTD  C5   C6    double  1.350  0.020  1.350
 CTD  C5   H5    single  0.930  0.020  1.080
 CTD  C6   H6    single  0.930  0.020  1.080
 CTD  N4   HN41  single  0.890  0.020  1.040
 CTD  N4   HN42  single  0.890  0.020  1.040
 CTD  C1'  C2'   single  1.533  0.020  1.533
 CTD  C1'  O4'   single  1.405  0.020  1.405
 CTD  C1'  H1'   single  0.970  0.020  1.090
 CTD  C2'  O2'   single  1.403  0.020  1.403
 CTD  C2'  C3'   single  1.532  0.020  1.532
 CTD  C2'  H2'   single  0.970  0.020  1.090
 CTD  O2'  HO2'  single  0.850  0.020  0.980
 CTD  C3'  C4'   single  1.525  0.020  1.525
 CTD  C3'  O3'   single  1.402  0.020  1.402
 CTD  C3'  H3'   single  0.970  0.020  1.090
 CTD  C4'  O4'   single  1.424  0.020  1.424
 CTD  C4'  C5'   single  1.506  0.020  1.506
 CTD  C4'  H4'   single  0.970  0.020  1.090
 CTD  O3'  HO3'  single  0.850  0.020  0.980
 CTD  C5'  O5'   single  1.405  0.020  1.405
 CTD  C5'  H5'1  single  0.970  0.020  1.090
 CTD  C5'  H5'2  single  0.970  0.020  1.090
 CTD  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
 CTD  C1'   N1   C6    121.05  3.000
 CTD  C1'   N1   C2    117.76  3.000
 CTD  C6    N1   C2    120.98  3.000
 CTD  O2    C2   C3    124.45  3.000
 CTD  O2    C2   N1    119.42  3.000
 CTD  C3    C2   N1    116.13  3.000
 CTD  H3    C3   C4    120.29  3.000
 CTD  H3    C3   C2    116.85  3.000
 CTD  C4    C3   C2    122.85  3.000
 CTD  N4    C4   C5    119.45  3.000
 CTD  N4    C4   C3    122.79  3.000
 CTD  C5    C4   C3    117.74  3.000
 CTD  H5    C5   C6    119.76  3.000
 CTD  H5    C5   C4    121.11  3.000
 CTD  C6    C5   C4    119.11  3.000
 CTD  H6    C6   C5    119.93  3.000
 CTD  H6    C6   N1    117.02  3.000
 CTD  C5    C6   N1    123.05  3.000
 CTD  HN42  N4   HN41  115.34  3.000
 CTD  HN42  N4   C4    119.51  3.000
 CTD  HN41  N4   C4    119.53  3.000
 CTD  H1'   C1'  O4'   110.65  3.000
 CTD  H1'   C1'  C2'   110.29  3.000
 CTD  O4'   C1'  C2'   107.31  3.000
 CTD  H1'   C1'  N1    106.58  3.000
 CTD  O4'   C1'  N1    109.54  3.000
 CTD  C2'   C1'  N1    112.50  3.000
 CTD  H2'   C2'  C3'   112.80  3.000
 CTD  H2'   C2'  O2'   111.28  3.000
 CTD  C3'   C2'  O2'   110.44  3.000
 CTD  H2'   C2'  C1'   111.32  3.000
 CTD  C3'   C2'  C1'   101.94  3.000
 CTD  O2'   C2'  C1'   108.63  3.000
 CTD  HO2'  O2'  C2'   106.90  3.000
 CTD  H3'   C3'  O3'   111.07  3.000
 CTD  H3'   C3'  C4'   110.22  3.000
 CTD  O3'   C3'  C4'   110.11  3.000
 CTD  H3'   C3'  C2'   109.62  3.000
 CTD  O3'   C3'  C2'   113.73  3.000
 CTD  C4'   C3'  C2'   101.71  3.000
 CTD  H4'   C4'  C5'   109.04  3.000
 CTD  H4'   C4'  O4'   109.58  3.000
 CTD  C5'   C4'  O4'   111.06  3.000
 CTD  H4'   C4'  C3'   108.77  3.000
 CTD  C5'   C4'  C3'   113.96  3.000
 CTD  O4'   C4'  C3'   104.28  3.000
 CTD  C4'   O4'  C1'   110.78  3.000
 CTD  HO3'  O3'  C3'   108.68  3.000
 CTD  H5'2  C5'  H5'1  106.36  3.000
 CTD  H5'2  C5'  O5'   111.62  3.000
 CTD  H5'1  C5'  O5'   112.10  3.000
 CTD  H5'2  C5'  C4'   110.51  3.000
 CTD  H5'1  C5'  C4'   107.04  3.000
 CTD  O5'   C5'  C4'   109.10  3.000
 CTD  HO5'  O5'  C5'   108.08  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
 CTD  CONST_01  C6    N1  C2  C3     0.00   0.0  0
 CTD  CONST_02  C1'   N1  C2  C3   180.00   0.0  0
 CTD  CONST_03  O2    C2  N1  C6   180.00   0.0  0
 CTD  CONST_04  C1'   N1  C2  O2     0.00   0.0  0
 CTD  Var_01    HN41  N4  C4  C3  -165.05  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
 CTD  chir_01  C1'  N1   C2'  O4'  negativ
 CTD  chir_02  C2'  O2'  C3'  C1'  positiv
 CTD  chir_03  C3'  O3'  C4'  C2'  positiv
 CTD  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
 CTD  plan-1  N1   0.020
 CTD  plan-1  C2   0.020
 CTD  plan-1  C3   0.020
 CTD  plan-1  C4   0.020
 CTD  plan-1  C5   0.020
 CTD  plan-1  C6   0.020
 CTD  plan-1  O2   0.020
 CTD  plan-1  N4   0.020
 CTD  plan-1  C1'  0.020
 CTD  plan-1  H3   0.020
 CTD  plan-1  H5   0.020
 CTD  plan-1  H6   0.020

