# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 22:57:47 2020
#   Inital geometry file: a 102 line input string
#   Ligand name: 1-{[1-(alpha-L-arabinofuranosyl)-1H-1,2,3-triazol-4-yl]methyl}-5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN(Cc2cn(nn2)[C@@H]3O[C@@H](CO)[C@H](O)[C@H]3O)C(=O)NC1=O
#
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
 0FT  0FT  1-{[1-(alpha-L-arabinofuranosyl)-1H-1,2,3-triazol-4-yl]methyl}-5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidine  ligand  41  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_0FT
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
 0FT  C4   C  CR6   0   0.561  -4.8519  -1.2982  -0.0224
 0FT  C5   C  CR6   0  -0.180  -4.6652  -0.3820   1.0849
 0FT  C6   C  CR16  0   0.060  -3.8159   0.6470   0.9137
 0FT  C8   C  CR5   0   0.160  -0.7745   1.5338  -0.1038
 0FT  C9   C  CR15  0  -0.040   0.2140   1.2646  -1.0113
 0FT  N1   N  NR6   0  -0.512  -3.1277   0.8838  -0.2445
 0FT  N3   N  NR16  0  -0.731  -4.1070  -0.9969  -1.1493
 0FT  C2   C  CR6   0   0.734  -3.2349   0.0451  -1.3252
 0FT  O4   O  O     0  -0.456  -5.5915  -2.2657  -0.0100
 0FT  C5A  C  CH3   0  -0.706  -5.4197  -0.6177   2.3518
 0FT  N5   N  N     0  -0.292  -0.2786   1.2933   1.1318
 0FT  N6   N  N     0  -0.093   0.9405   0.9030   1.0319
 0FT  N7   N  NR5   0  -0.301   1.2565   0.8849  -0.2536
 0FT  C1'  C  CR15  0   0.226   2.5673   0.4543  -0.6968
 0FT  O4'  O  O     0  -0.486   2.7389  -0.9049  -0.4270
 0FT  C4'  C  CR15  0  -0.004   3.9606  -1.1249   0.2792
 0FT  C5'  C  CH2   0  -0.155   4.6044  -2.4056  -0.1873
 0FT  O5'  O  OH1   0  -0.670   3.7905  -3.4898   0.1893
 0FT  C3'  C  CR15  0  -0.016   4.7946   0.1185  -0.0027
 0FT  O3'  O  OH1   0  -0.661   5.7827   0.2788   0.9747
 0FT  C2'  C  CR15  0  -0.043   3.7128   1.1959  -0.0116
 0FT  O2'  O  OH1   0  -0.658   3.9982   2.3639  -0.7226
 0FT  H1   H  HCR6  0   0.309  -3.6381   1.3644   1.7034
 0FT  H2   H  HCH2  0   0.301  -2.4567   2.7174   0.4320
 0FT  H3   H  HCH2  0   0.301  -2.2725   2.4750  -1.2919
 0FT  H4   H  HCR5  0   0.321   0.2520   1.3148  -2.0857
 0FT  H5   H  HNR6  0   0.425  -4.2103  -1.6168  -1.9436
 0FT  H6   H  HCH3  0   0.247  -6.4970  -0.6056   2.1813
 0FT  H7   H  HCH3  0   0.247  -5.1731  -1.5872   2.7868
 0FT  H8   H  HCH3  0   0.247  -5.1895   0.1487   3.0901
 0FT  H9   H  HCR5  0   0.268   2.5877   0.6404  -1.7756
 0FT  H10  H  HCR5  0   0.237   3.7587  -1.1900   1.3579
 0FT  H11  H  HCH2  0   0.201   4.7487  -2.3580  -1.2748
 0FT  H12  H  HCH2  0   0.209   5.6009  -2.4633   0.2693
 0FT  H13  H  HOH1  0   0.458   4.2161  -4.3004  -0.1037
 0FT  H14  H  HCR5  0   0.235   5.2306   0.0471  -1.0106
 0FT  H15  H  HOH1  0   0.463   6.4793   0.8404   0.6232
 0FT  H16  H  HCR5  0   0.250   3.4417   1.4102   1.0308
 0FT  H17  H  HOH1  0   0.464   4.5544   2.9307  -0.1799
 0FT  C7   C  CH2   0  -0.433  -2.1739   1.9873  -0.3249
 0FT  O2   O  O     0  -0.481  -2.6111   0.2118  -2.3544

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
 0FT  O2'  C2'  single    1.397  0.020  1.397
 0FT  C2'  C1'  single    1.527  0.020  1.527
 0FT  C2'  C3'  single    1.527  0.020  1.527
 0FT  O5'  C5'  single    1.407  0.020  1.407
 0FT  C1'  O4'  single    1.396  0.020  1.396
 0FT  C1'  N7   single    1.449  0.020  1.449
 0FT  C5'  C4'  single    1.507  0.020  1.507
 0FT  C5A  C5   single    1.493  0.020  1.493
 0FT  O4'  C4'  single    1.428  0.020  1.428
 0FT  C3'  C4'  single    1.524  0.020  1.524
 0FT  C3'  O3'  single    1.399  0.020  1.399
 0FT  C9   N7   aromatic  1.344  0.020  1.344
 0FT  C9   C8   aromatic  1.369  0.020  1.369
 0FT  N7   N6   aromatic  1.324  0.020  1.324
 0FT  C5   C6   double    1.345  0.020  1.345
 0FT  C5   C4   single    1.449  0.020  1.449
 0FT  C6   N1   single    1.368  0.020  1.368
 0FT  O4   C4   double    1.218  0.020  1.218
 0FT  C4   N3   single    1.384  0.020  1.384
 0FT  C8   C7   single    1.488  0.020  1.488
 0FT  C8   N5   aromatic  1.353  0.020  1.353
 0FT  N6   N5   aromatic  1.284  0.020  1.284
 0FT  N1   C7   single    1.461  0.020  1.461
 0FT  N1   C2   single    1.372  0.020  1.372
 0FT  N3   C2   single    1.370  0.020  1.370
 0FT  C2   O2   double    1.215  0.020  1.215
 0FT  C6   H1   single    0.930  0.020  1.080
 0FT  C7   H2   single    0.970  0.020  1.090
 0FT  C7   H3   single    0.970  0.020  1.090
 0FT  C9   H4   single    0.930  0.020  1.080
 0FT  N3   H5   single    0.860  0.020  1.020
 0FT  C5A  H6   single    0.970  0.020  1.090
 0FT  C5A  H7   single    0.970  0.020  1.090
 0FT  C5A  H8   single    0.970  0.020  1.090
 0FT  C1'  H9   single    0.970  0.020  1.090
 0FT  C4'  H10  single    0.970  0.020  1.090
 0FT  C5'  H11  single    0.970  0.020  1.090
 0FT  C5'  H12  single    0.970  0.020  1.090
 0FT  O5'  H13  single    0.850  0.020  0.980
 0FT  C3'  H14  single    0.970  0.020  1.090
 0FT  O3'  H15  single    0.850  0.020  0.980
 0FT  C2'  H16  single    0.970  0.020  1.090
 0FT  O2'  H17  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
 0FT  O4   C4   N3   120.54  3.000
 0FT  N3   C4   C5   114.53  3.000
 0FT  O4   C4   C5   124.94  3.000
 0FT  C5A  C5   C6   123.21  3.000
 0FT  C6   C5   C4   117.88  3.000
 0FT  C5A  C5   C4   118.90  3.000
 0FT  H1   C6   N1   114.88  3.000
 0FT  H1   C6   C5   121.21  3.000
 0FT  N1   C6   C5   123.91  3.000
 0FT  N5   C8   C9   107.81  3.000
 0FT  N5   C8   C7   122.33  3.000
 0FT  C9   C8   C7   129.86  3.000
 0FT  H4   C9   N7   123.28  3.000
 0FT  H4   C9   C8   132.70  3.000
 0FT  N7   C9   C8   104.02  3.000
 0FT  C2   N1   C7   117.99  3.000
 0FT  C2   N1   C6   121.45  3.000
 0FT  C7   N1   C6   120.39  3.000
 0FT  H5   N3   C2   115.44  3.000
 0FT  H5   N3   C4   116.77  3.000
 0FT  C2   N3   C4   127.79  3.000
 0FT  O2   C2   N3   122.68  3.000
 0FT  O2   C2   N1   122.90  3.000
 0FT  N3   C2   N1   114.42  3.000
 0FT  H8   C5A  H7   107.90  3.000
 0FT  H8   C5A  H6   107.88  3.000
 0FT  H7   C5A  H6   107.18  3.000
 0FT  H8   C5A  C5   110.94  3.000
 0FT  H7   C5A  C5   111.37  3.000
 0FT  H6   C5A  C5   111.39  3.000
 0FT  N6   N5   C8   109.33  3.000
 0FT  N7   N6   N5   107.84  3.000
 0FT  C1'  N7   N6   121.13  3.000
 0FT  N6   N7   C9   111.01  3.000
 0FT  C1'  N7   C9   127.84  3.000
 0FT  H9   C1'  C2'  110.22  3.000
 0FT  H9   C1'  O4'  110.70  3.000
 0FT  C2'  C1'  O4'  107.09  3.000
 0FT  H9   C1'  N7   105.52  3.000
 0FT  O4'  C1'  N7   109.96  3.000
 0FT  C2'  C1'  N7   113.39  3.000
 0FT  C4'  O4'  C1'  110.52  3.000
 0FT  H10  C4'  C3'  109.29  3.000
 0FT  H10  C4'  C5'  109.37  3.000
 0FT  C3'  C4'  C5'  113.73  3.000
 0FT  H10  C4'  O4'  109.70  3.000
 0FT  C3'  C4'  O4'  104.54  3.000
 0FT  C5'  C4'  O4'  110.07  3.000
 0FT  H12  C5'  H11  107.15  3.000
 0FT  H12  C5'  O5'  111.92  3.000
 0FT  H11  C5'  O5'  112.00  3.000
 0FT  H12  C5'  C4'  107.68  3.000
 0FT  H11  C5'  C4'  109.01  3.000
 0FT  O5'  C5'  C4'  108.96  3.000
 0FT  H13  O5'  C5'  108.19  3.000
 0FT  H14  C3'  C2'  108.73  3.000
 0FT  H14  C3'  O3'  111.56  3.000
 0FT  C2'  C3'  O3'  115.06  3.000
 0FT  H14  C3'  C4'  109.47  3.000
 0FT  O3'  C3'  C4'  110.54  3.000
 0FT  C2'  C3'  C4'  100.90  3.000
 0FT  H15  O3'  C3'  108.86  3.000
 0FT  H16  C2'  O2'  111.74  3.000
 0FT  H16  C2'  C3'  107.88  3.000
 0FT  O2'  C2'  C3'  116.63  3.000
 0FT  H16  C2'  C1'  109.60  3.000
 0FT  C3'  C2'  C1'  101.04  3.000
 0FT  O2'  C2'  C1'  109.33  3.000
 0FT  H17  O2'  C2'  108.89  3.000
 0FT  H3   C7   H2   107.09  3.000
 0FT  H3   C7   N1   109.18  3.000
 0FT  H2   C7   N1   107.37  3.000
 0FT  H3   C7   C8   110.74  3.000
 0FT  H2   C7   C8   110.20  3.000
 0FT  N1   C7   C8   112.07  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
 0FT  CONST_01  N6   N7   C9  C8    0.00   0.0  0
 0FT  CONST_02  N7   N6   N5  C8    0.00   0.0  0
 0FT  CONST_03  N5   N6   N7  C9    0.00   0.0  0
 0FT  CONST_04  N6   N5   C8  C9    0.00   0.0  0
 0FT  CONST_05  N7   C9   C8  N5    0.00   0.0  0
 0FT  CONST_06  C1'  N7   C9  C8  180.00   0.0  0
 0FT  CONST_07  C1'  N7   N6  N5  180.00   0.0  0
 0FT  CONST_08  N1   C2   N3  C4    0.00   0.0  0
 0FT  CONST_09  C2   N3   C4  C5    0.00   0.0  0
 0FT  CONST_10  N3   C2   N1  C6    0.00   0.0  0
 0FT  CONST_11  N7   C9   C8  C7  180.00   0.0  0
 0FT  CONST_12  N6   N5   C8  C7  180.00   0.0  0
 0FT  CONST_13  O2   C2   N3  C4  180.00   0.0  0
 0FT  CONST_14  O2   C2   N1  C6  180.00   0.0  0
 0FT  CONST_15  N3   C2   N1  C7  180.00   0.0  0
 0FT  CONST_16  O4   C4   N3  C2  180.00   0.0  0
 0FT  CONST_17  H4   C9   C8  N5  180.00   0.0  0
 0FT  CONST_18  H5   N3   C4  C5  180.00   0.0  0
 0FT  CONST_19  O2   C2   N1  C7    0.00   0.0  0
 0FT  Var_01    C8   C7   N1  C6   97.51  30.0  3
 0FT  Var_02    N1   C7   C8  C9   99.60  30.0  2
 0FT  Var_03    H6   C5A  C5  C4  -59.32  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
 0FT  chir_01  C1'  C2'  O4'  N7   negativ
 0FT  chir_02  C4'  O4'  C5'  C3'  negativ
 0FT  chir_03  C3'  O3'  C2'  C4'  positiv
 0FT  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
 0FT  plan-1  C8   0.020
 0FT  plan-1  C9   0.020
 0FT  plan-1  N5   0.020
 0FT  plan-1  N6   0.020
 0FT  plan-1  N7   0.020
 0FT  plan-1  C1'  0.020
 0FT  plan-1  H4   0.020
 0FT  plan-1  C7   0.020
 0FT  plan-2  C4   0.020
 0FT  plan-2  C5   0.020
 0FT  plan-2  C6   0.020
 0FT  plan-2  N1   0.020
 0FT  plan-2  N3   0.020
 0FT  plan-2  C2   0.020
 0FT  plan-2  O4   0.020
 0FT  plan-2  C5A  0.020
 0FT  plan-2  H1   0.020
 0FT  plan-2  H5   0.020
 0FT  plan-2  C7   0.020
 0FT  plan-2  O2   0.020

