# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 22:48:02 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-{[1-(alpha-L-arabinofuranosyl)-1H-1,2,3-triazol-4-yl]methyl}-5-fluoro-2,4-dioxo-1,2,3,4-tetrahydropyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1O[C@H]([C@H](O)[C@H]1O)n2cc(CN3C=C(F)C(=O)NC3=O)nn2
#
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
 0G0  0G0  1-{[1-(alpha-L-arabinofuranosyl)-1H-1,2,3-triazol-4-yl]methyl}-5-fluoro-2,4-dioxo-1,2,3,4-tetrahydropyrimidine  ligand  38  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0G0
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
 0G0  C4   C  CR6   0   0.472   4.4202  -1.3390   0.1931
 0G0  C5   C  CR6   0   0.282   4.1895  -0.7738  -1.1168
 0G0  C6   C  CR16  0  -0.070   3.4340   0.3164  -1.2831
 0G0  C8   C  CR5   0   0.160   0.5431   1.7166  -0.4556
 0G0  C9   C  CR15  0  -0.035  -0.3909   1.8028   0.5409
 0G0  N1   N  NR6   0  -0.508   2.8518   0.9547  -0.2240
 0G0  N3   N  NR16  0  -0.736   3.7771  -0.6286   1.1872
 0G0  C2   C  CR6   0   0.748   2.9844   0.4878   1.0607
 0G0  O4   O  O     0  -0.448   5.0935  -2.3207   0.4274
 0G0  F5A  F  F     0  -0.294   4.7684  -1.3871  -2.1519
 0G0  N5   N  N     0  -0.291  -0.0512   1.1568  -1.5340
 0G0  N6   N  N     0  -0.088  -1.2783   0.9014  -1.2566
 0G0  N7   N  NR5   0  -0.292  -1.5048   1.2927  -0.0108
 0G0  C1'  C  CH1   0   0.133  -2.7840   1.0589   0.6472
 0G0  O4'  O  O2    0  -0.475  -2.8304  -0.2129   1.2039
 0G0  C4'  C  CH1   0   0.013  -3.2807  -1.1239   0.2078
 0G0  C5'  C  CH2   0  -0.173  -3.8934  -2.3377   0.8602
 0G0  O5'  O  OH1   0  -0.669  -2.8890  -3.0551   1.5331
 0G0  C3'  C  CH1   0  -0.036  -4.2758  -0.3317  -0.6483
 0G0  O3'  O  OH1   0  -0.659  -4.1184  -0.7046  -1.9866
 0G0  C2'  C  CH1   0   0.014  -3.9638   1.1513  -0.3275
 0G0  O2'  O  OH1   0  -0.668  -4.9977   1.7898   0.3779
 0G0  H1   H  HCR6  0   0.337   3.2597   0.7427  -2.2612
 0G0  H2   H  HCH2  0   0.305   2.2573   2.5311  -1.4166
 0G0  H3   H  HCH2  0   0.306   2.1782   2.8588   0.3046
 0G0  H4   H  HCR5  0   0.320  -0.3480   2.1783   1.5488
 0G0  H5   H  HNR6  0   0.435   3.8872  -0.9768   2.1325
 0G0  H6   H  HCH1  0   0.295  -2.8504   1.7988   1.4449
 0G0  H7   H  HCH1  0   0.243  -2.4402  -1.4406  -0.4244
 0G0  H8   H  HCH2  0   0.203  -4.6978  -2.0186   1.5367
 0G0  H9   H  HCH2  0   0.212  -4.3609  -2.9331   0.0652
 0G0  H10  H  HOH1  0   0.459  -3.2877  -3.8401   1.9194
 0G0  H11  H  HCH1  0   0.240  -5.2979  -0.5344  -0.2973
 0G0  H12  H  HOH1  0   0.458  -4.8583  -0.3562  -2.4930
 0G0  H13  H  HCH1  0   0.255  -3.6992   1.6945  -1.2404
 0G0  H14  H  HOH1  0   0.460  -5.7756   1.8283  -0.1879
 0G0  C7   C  CH2   0  -0.436   1.9784   2.1057  -0.4540
 0G0  O2   O  O     0  -0.471   2.4482   1.0161   2.0114

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
 0G0  O2   C2   double    1.213  0.020  1.213
 0G0  C2   N3   single    1.375  0.020  1.375
 0G0  C2   N1   single    1.373  0.020  1.373
 0G0  N3   C4   single    1.381  0.020  1.381
 0G0  N5   N6   aromatic  1.284  0.020  1.284
 0G0  N5   C8   aromatic  1.353  0.020  1.353
 0G0  N6   N7   aromatic  1.325  0.020  1.325
 0G0  N1   C7   single    1.463  0.020  1.463
 0G0  N1   C6   single    1.367  0.020  1.367
 0G0  C7   C8   single    1.487  0.020  1.487
 0G0  C4   O4   double    1.213  0.020  1.213
 0G0  C4   C5   single    1.445  0.020  1.445
 0G0  C8   C9   aromatic  1.368  0.020  1.368
 0G0  O5'  C5'  single    1.406  0.020  1.406
 0G0  C5'  C4'  single    1.508  0.020  1.508
 0G0  C6   C5   double    1.337  0.020  1.337
 0G0  C5   F5A  single    1.335  0.020  1.335
 0G0  C4'  O4'  single    1.423  0.020  1.423
 0G0  C4'  C3'  single    1.533  0.020  1.533
 0G0  N7   C9   aromatic  1.344  0.020  1.344
 0G0  N7   C1'  single    1.457  0.020  1.457
 0G0  O3'  C3'  single    1.398  0.020  1.398
 0G0  O4'  C1'  single    1.389  0.020  1.389
 0G0  C3'  C2'  single    1.549  0.020  1.549
 0G0  C1'  C2'  single    1.533  0.020  1.533
 0G0  C2'  O2'  single    1.405  0.020  1.405
 0G0  C6   H1   single    0.930  0.020  1.080
 0G0  C7   H2   single    0.970  0.020  1.090
 0G0  C7   H3   single    0.970  0.020  1.090
 0G0  C9   H4   single    0.930  0.020  1.080
 0G0  N3   H5   single    0.860  0.020  1.020
 0G0  C1'  H6   single    0.970  0.020  1.090
 0G0  C4'  H7   single    0.970  0.020  1.090
 0G0  C5'  H8   single    0.970  0.020  1.090
 0G0  C5'  H9   single    0.970  0.020  1.090
 0G0  O5'  H10  single    0.850  0.020  0.980
 0G0  C3'  H11  single    0.970  0.020  1.090
 0G0  O3'  H12  single    0.850  0.020  0.980
 0G0  C2'  H13  single    0.970  0.020  1.090
 0G0  O2'  H14  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
 0G0  O4   C4   N3   122.40  3.000
 0G0  O4   C4   C5   125.45  3.000
 0G0  N3   C4   C5   112.15  3.000
 0G0  F5A  C5   C6   121.55  3.000
 0G0  F5A  C5   C4   116.99  3.000
 0G0  C6   C5   C4   121.46  3.000
 0G0  H1   C6   N1   116.63  3.000
 0G0  H1   C6   C5   121.68  3.000
 0G0  N1   C6   C5   121.68  3.000
 0G0  N5   C8   C9   107.87  3.000
 0G0  C9   C8   C7   129.90  3.000
 0G0  N5   C8   C7   122.22  3.000
 0G0  H4   C9   N7   123.36  3.000
 0G0  H4   C9   C8   132.58  3.000
 0G0  N7   C9   C8   104.05  3.000
 0G0  C2   N1   C7   118.18  3.000
 0G0  C7   N1   C6   119.99  3.000
 0G0  C2   N1   C6   121.67  3.000
 0G0  H5   N3   C2   115.31  3.000
 0G0  H5   N3   C4   116.37  3.000
 0G0  C2   N3   C4   128.32  3.000
 0G0  O2   C2   N3   122.45  3.000
 0G0  N3   C2   N1   114.69  3.000
 0G0  O2   C2   N1   122.86  3.000
 0G0  N6   N5   C8   109.27  3.000
 0G0  N7   N6   N5   107.93  3.000
 0G0  C1'  N7   N6   121.81  3.000
 0G0  C1'  N7   C9   127.10  3.000
 0G0  N6   N7   C9   110.88  3.000
 0G0  H6   C1'  C2'  112.17  3.000
 0G0  H6   C1'  O4'  109.04  3.000
 0G0  C2'  C1'  O4'  106.52  3.000
 0G0  H6   C1'  N7   105.96  3.000
 0G0  C2'  C1'  N7   112.26  3.000
 0G0  O4'  C1'  N7   110.93  3.000
 0G0  C4'  O4'  C1'  108.43  3.000
 0G0  H7   C4'  C3'  108.92  3.000
 0G0  H7   C4'  C5'  109.14  3.000
 0G0  C3'  C4'  C5'  113.18  3.000
 0G0  H7   C4'  O4'  110.20  3.000
 0G0  C3'  C4'  O4'  105.39  3.000
 0G0  C5'  C4'  O4'  109.94  3.000
 0G0  H9   C5'  H8   106.96  3.000
 0G0  H9   C5'  O5'  111.97  3.000
 0G0  H8   C5'  O5'  112.13  3.000
 0G0  H9   C5'  C4'  107.24  3.000
 0G0  H8   C5'  C4'  109.28  3.000
 0G0  O5'  C5'  C4'  109.12  3.000
 0G0  H10  O5'  C5'  108.22  3.000
 0G0  H11  C3'  C2'  107.32  3.000
 0G0  H11  C3'  O3'  111.16  3.000
 0G0  C2'  C3'  O3'  115.52  3.000
 0G0  H11  C3'  C4'  109.26  3.000
 0G0  C2'  C3'  C4'  104.38  3.000
 0G0  O3'  C3'  C4'  108.88  3.000
 0G0  H12  O3'  C3'  108.70  3.000
 0G0  H13  C2'  O2'  111.78  3.000
 0G0  H13  C2'  C3'  110.55  3.000
 0G0  O2'  C2'  C3'  113.00  3.000
 0G0  H13  C2'  C1'  111.96  3.000
 0G0  O2'  C2'  C1'  105.93  3.000
 0G0  C3'  C2'  C1'  103.23  3.000
 0G0  H14  O2'  C2'  108.52  3.000
 0G0  H3   C7   H2   107.40  3.000
 0G0  H3   C7   N1   108.99  3.000
 0G0  H2   C7   N1   107.07  3.000
 0G0  H3   C7   C8   111.05  3.000
 0G0  H2   C7   C8   110.40  3.000
 0G0  N1   C7   C8   111.75  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
 0G0  CONST_01  N7   N6  N5  C8    0.00   0.0  0
 0G0  CONST_02  N6   N7  C9  C8    0.00   0.0  0
 0G0  CONST_03  N6   N5  C8  C9    0.00   0.0  0
 0G0  CONST_04  N5   N6  N7  C9    0.00   0.0  0
 0G0  CONST_05  N7   C9  C8  N5    0.00   0.0  0
 0G0  CONST_06  C1'  N7  C9  C8  180.00   0.0  0
 0G0  CONST_07  C1'  N7  N6  N5  180.00   0.0  0
 0G0  CONST_08  N1   C2  N3  C4    0.00   0.0  0
 0G0  CONST_09  C2   N3  C4  C5    0.00   0.0  0
 0G0  CONST_10  N3   C2  N1  C6    0.00   0.0  0
 0G0  CONST_11  N6   N5  C8  C7  180.00   0.0  0
 0G0  CONST_12  N7   C9  C8  C7  180.00   0.0  0
 0G0  CONST_13  O2   C2  N3  C4  180.00   0.0  0
 0G0  CONST_14  O2   C2  N1  C6  180.00   0.0  0
 0G0  CONST_15  N3   C2  N1  C7  180.00   0.0  0
 0G0  CONST_16  O4   C4  N3  C2  180.00   0.0  0
 0G0  CONST_17  H4   C9  C8  N5  180.00   0.0  0
 0G0  CONST_18  H5   N3  C4  C5  180.00   0.0  0
 0G0  CONST_19  O2   C2  N1  C7    0.00   0.0  0
 0G0  Var_01    C8   C7  N1  C6   97.36  30.0  3
 0G0  Var_02    N1   C7  C8  C9   98.46  30.0  1

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
 0G0  chir_01  C1'  N7   O4'  C2'  positiv
 0G0  chir_02  C4'  O4'  C5'  C3'  negativ
 0G0  chir_03  C3'  O3'  C2'  C4'  positiv
 0G0  chir_04  C2'  O2'  C1'  C3'  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
 0G0  plan-1  C8   0.020
 0G0  plan-1  C9   0.020
 0G0  plan-1  N5   0.020
 0G0  plan-1  N6   0.020
 0G0  plan-1  N7   0.020
 0G0  plan-1  C1'  0.020
 0G0  plan-1  H4   0.020
 0G0  plan-1  C7   0.020
 0G0  plan-2  C4   0.020
 0G0  plan-2  C5   0.020
 0G0  plan-2  C6   0.020
 0G0  plan-2  N1   0.020
 0G0  plan-2  N3   0.020
 0G0  plan-2  C2   0.020
 0G0  plan-2  O4   0.020
 0G0  plan-2  F5A  0.020
 0G0  plan-2  H1   0.020
 0G0  plan-2  H5   0.020
 0G0  plan-2  C7   0.020
 0G0  plan-2  O2   0.020

