# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 10:13:22 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 4-amino-1-beta-D-arabinofuranosylpyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=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
 AR3  AR3  4-amino-1-beta-D-arabinofuranosylpyrimidin-2(1H)-one  ligand  30  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AR3
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
 AR3  O5'   O  OH1   0  -0.666   2.3146  -0.9310  -3.5532
 AR3  C5'   C  CH2   0  -0.154   1.5439   0.1649  -3.1312
 AR3  C4'   C  CR15  0  -0.023   0.2390  -0.3316  -2.5637
 AR3  O4'   O  O     0  -0.493   0.4731  -1.0840  -1.3742
 AR3  C1'   C  CR15  0   0.165  -0.5827  -0.9350  -0.4699
 AR3  N1    N  NR6   0  -0.540  -0.0676  -0.4617   0.8141
 AR3  C6    C  CR16  0   0.098   1.0014   0.3627   0.8806
 AR3  C5    C  CR16  0  -0.475   1.4371   0.8623   2.0541
 AR3  C4    C  CR6   0   0.515   0.7043   0.4809   3.2187
 AR3  N3    N  N     0  -0.541  -0.3420  -0.3191   3.1563
 AR3  C2    C  CR6   0   0.597  -0.7740  -0.8098   1.9771
 AR3  O2    O  OC    0  -0.523  -1.7469  -1.5476   1.8870
 AR3  N4    N  NH2   0  -0.810   1.0792   0.9391   4.4125
 AR3  C2'   C  CR15  0  -0.006  -1.5718   0.0615  -1.1077
 AR3  O1    O  OH1   0  -0.650  -2.1554   0.8749  -0.1368
 AR3  C3'   C  CR15  0  -0.024  -0.7087   0.7847  -2.1323
 AR3  O3'   O  OH1   0  -0.659  -1.4991   1.3102  -3.1615
 AR3  H5'   H  HOH1  0   0.459   3.1377  -0.5971  -3.9212
 AR3  H5'1  H  HCH2  0   0.205   1.3059   0.8430  -3.9624
 AR3  H5'2  H  HCH2  0   0.202   2.0637   0.7671  -2.3726
 AR3  H4'   H  HCR5  0   0.243  -0.2660  -0.9637  -3.3076
 AR3  H1'   H  HCR5  0   0.274  -1.0553  -1.8970  -0.2776
 AR3  H6    H  HCR6  0   0.308   1.5120   0.5882  -0.0435
 AR3  H5    H  HCR6  0   0.286   2.2992   1.5101   2.0999
 AR3  HN41  H  HNH2  0   0.402   0.5639   0.6837   5.2374
 AR3  HN42  H  HNH2  0   0.413   1.8730   1.5454   4.5189
 AR3  H2'   H  HCR5  0   0.246  -2.3257  -0.5217  -1.6549
 AR3  HO1   H  HOH1  0   0.464  -2.8984   1.3376  -0.5365
 AR3  H3'   H  HCR5  0   0.225  -0.1379   1.5798  -1.6284
 AR3  H1    H  HOH1  0   0.460  -0.9784   1.9433  -3.6649

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
 AR3  O5'  C5'   single    1.405  0.020  1.405
 AR3  O5'  H5'   single    0.850  0.020  0.980
 AR3  C5'  C4'   single    1.507  0.020  1.507
 AR3  C5'  H5'1  single    0.970  0.020  1.090
 AR3  C5'  H5'2  single    0.970  0.020  1.090
 AR3  C4'  O4'   single    1.427  0.020  1.427
 AR3  C4'  C3'   single    1.527  0.020  1.527
 AR3  C4'  H4'   single    0.970  0.020  1.090
 AR3  O4'  C1'   single    1.398  0.020  1.398
 AR3  C1'  N1    single    1.462  0.020  1.462
 AR3  C1'  C2'   single    1.542  0.020  1.542
 AR3  C1'  H1'   single    0.970  0.020  1.090
 AR3  N1   C6    aromatic  1.352  0.020  1.352
 AR3  N1   C2    aromatic  1.405  0.020  1.405
 AR3  C6   C5    aromatic  1.348  0.020  1.348
 AR3  C6   H6    single    0.930  0.020  1.080
 AR3  C5   C4    aromatic  1.428  0.020  1.428
 AR3  C5   H5    single    0.930  0.020  1.080
 AR3  C4   N3    aromatic  1.319  0.020  1.319
 AR3  C4   N4    single    1.333  0.020  1.333
 AR3  N3   C2    aromatic  1.348  0.020  1.348
 AR3  C2   O2    double    1.224  0.020  1.224
 AR3  N4   HN41  single    0.860  0.020  1.020
 AR3  N4   HN42  single    0.860  0.020  1.020
 AR3  C2'  O1    single    1.395  0.020  1.395
 AR3  C2'  C3'   single    1.522  0.020  1.522
 AR3  C2'  H2'   single    0.970  0.020  1.090
 AR3  O1   HO1   single    0.850  0.020  0.980
 AR3  C3'  O3'   single    1.400  0.020  1.400
 AR3  C3'  H3'   single    0.970  0.020  1.090
 AR3  O3'  H1    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
 AR3  H5'   O5'  C5'   108.28  3.000
 AR3  H5'2  C5'  H5'1  106.64  3.000
 AR3  H5'2  C5'  C4'   109.27  3.000
 AR3  H5'1  C5'  C4'   107.49  3.000
 AR3  H5'2  C5'  O5'   112.04  3.000
 AR3  H5'1  C5'  O5'   111.90  3.000
 AR3  C4'   C5'  O5'   109.34  3.000
 AR3  H4'   C4'  C3'   109.06  3.000
 AR3  H4'   C4'  O4'   109.65  3.000
 AR3  C3'   C4'  O4'   104.59  3.000
 AR3  H4'   C4'  C5'   109.41  3.000
 AR3  C3'   C4'  C5'   113.77  3.000
 AR3  O4'   C4'  C5'   110.22  3.000
 AR3  C1'   O4'  C4'   111.05  3.000
 AR3  H1'   C1'  C2'   111.44  3.000
 AR3  H1'   C1'  N1    106.49  3.000
 AR3  C2'   C1'  N1    112.33  3.000
 AR3  H1'   C1'  O4'   110.35  3.000
 AR3  C2'   C1'  O4'   106.60  3.000
 AR3  N1    C1'  O4'   109.66  3.000
 AR3  C2    N1   C6    120.54  3.000
 AR3  C2    N1   C1'   118.01  3.000
 AR3  C6    N1   C1'   121.29  3.000
 AR3  H6    C6   C5    120.99  3.000
 AR3  H6    C6   N1    117.35  3.000
 AR3  C5    C6   N1    121.64  3.000
 AR3  H5    C5   C4    122.39  3.000
 AR3  H5    C5   C6    121.17  3.000
 AR3  C4    C5   C6    116.44  3.000
 AR3  N4    C4   N3    118.31  3.000
 AR3  N4    C4   C5    119.63  3.000
 AR3  N3    C4   C5    122.06  3.000
 AR3  C2    N3   C4    121.10  3.000
 AR3  O2    C2   N3    122.57  3.000
 AR3  O2    C2   N1    119.21  3.000
 AR3  N3    C2   N1    118.22  3.000
 AR3  HN42  N4   HN41  118.12  3.000
 AR3  HN42  N4   C4    121.66  3.000
 AR3  HN41  N4   C4    120.23  3.000
 AR3  H2'   C2'  C3'   107.81  3.000
 AR3  H2'   C2'  O1    111.65  3.000
 AR3  C3'   C2'  O1    115.39  3.000
 AR3  H2'   C2'  C1'   107.64  3.000
 AR3  C3'   C2'  C1'   102.81  3.000
 AR3  O1    C2'  C1'   110.94  3.000
 AR3  HO1   O1   C2'   108.33  3.000
 AR3  H3'   C3'  O3'   110.99  3.000
 AR3  H3'   C3'  C2'   109.21  3.000
 AR3  O3'   C3'  C2'   110.67  3.000
 AR3  H3'   C3'  C4'   109.60  3.000
 AR3  O3'   C3'  C4'   114.66  3.000
 AR3  C2'   C3'  C4'   101.23  3.000
 AR3  H1    O3'  C3'   109.04  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
 AR3  CONST_01  C4    C5  C6  N1     0.00  0.0  0
 AR3  CONST_02  C4    N3  C2  N1     0.00  0.0  0
 AR3  CONST_03  N3    C2  N1  C6     0.00  0.0  0
 AR3  CONST_04  N3    C4  C5  C6     0.00  0.0  0
 AR3  CONST_05  C2    N1  C6  C5     0.00  0.0  0
 AR3  CONST_06  C2    N3  C4  C5     0.00  0.0  0
 AR3  CONST_07  C5    C6  N1  C1'  180.00  0.0  0
 AR3  CONST_08  N3    C2  N1  C1'  180.00  0.0  0
 AR3  CONST_09  O2    C2  N1  C1'    0.00  0.0  0
 AR3  CONST_10  O2    C2  N1  C6   180.00  0.0  0
 AR3  CONST_11  N4    C4  C5  C6   180.00  0.0  0
 AR3  CONST_12  O2    C2  N3  C4   180.00  0.0  0
 AR3  CONST_13  N4    C4  N3  C2   180.00  0.0  0
 AR3  CONST_14  H6    C6  N1  C1'    0.00  0.0  0
 AR3  CONST_15  H5    C5  C6  N1   180.00  0.0  0
 AR3  CONST_16  HN41  N4  C4  C5   180.00  0.0  0
 AR3  CONST_17  HN42  N4  C4  C5     0.00  0.0  0

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
 AR3  chir_01  C4'  C5'  O4'  C3'  negativ
 AR3  chir_02  C1'  O4'  N1   C2'  negativ
 AR3  chir_03  C2'  O1   C1'  C3'  positiv
 AR3  chir_04  C3'  O3'  C4'  C2'  positiv

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
 AR3  plan-1  C1'   0.020
 AR3  plan-1  N1    0.020
 AR3  plan-1  C6    0.020
 AR3  plan-1  C5    0.020
 AR3  plan-1  C4    0.020
 AR3  plan-1  N3    0.020
 AR3  plan-1  C2    0.020
 AR3  plan-1  O2    0.020
 AR3  plan-1  N4    0.020
 AR3  plan-1  H6    0.020
 AR3  plan-1  H5    0.020
 AR3  plan-2  C4    0.020
 AR3  plan-2  N4    0.020
 AR3  plan-2  HN41  0.020
 AR3  plan-2  HN42  0.020

