# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 15:13:17 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: 5-ethynyl-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)N2C=C(C#C)C(=O)NC2=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
 D1M  D1M  5-ethynyl-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione  D-saccharide  35  21  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D1M
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
 D1M  N1    N  NR6   0  -0.577   0.9227  -0.0112   0.0869
 D1M  C2    C  CR6   0   0.752   1.2315   0.1637   1.4294
 D1M  O2    O  O     0  -0.453   0.3995   0.1939   2.3045
 D1M  N3    N  NR16  0  -0.736   2.5701   0.3005   1.6900
 D1M  C4    C  CR6   0   0.554   3.6269   0.2796   0.8010
 D1M  O4    O  O     0  -0.430   4.7721   0.4056   1.1793
 D1M  C5    C  CR6   0  -0.351   3.2143   0.0976  -0.5813
 D1M  C6    C  CR16  0   0.090   1.8972  -0.0377  -0.8580
 D1M  C7    C  CSP   0   0.321   4.2004   0.0672  -1.5990
 D1M  C8    C  CSP1  0  -0.539   5.0430   0.0444  -2.4577
 D1M  C1'   C  CH1   0   0.214  -0.4607  -0.2029  -0.3275
 D1M  C2'   C  CH1   0  -0.002  -1.0873  -1.4737   0.2406
 D1M  O2'   O  OH1   0  -0.665  -0.2804  -2.5402  -0.1799
 D1M  C3'   C  CH1   0  -0.016  -2.5075  -1.5568  -0.3025
 D1M  O3'   O  OH1   0  -0.672  -3.1139  -2.6892   0.2756
 D1M  C4'   C  CH1   0   0.012  -3.2748  -0.2732   0.0157
 D1M  O4'   O  OH1   0  -0.672  -4.5436  -0.2875  -0.5961
 D1M  C5'   C  CH1   0  -0.022  -2.5025   0.9370  -0.5150
 D1M  O5'   O  O2    0  -0.479  -1.1844   0.9332   0.0104
 D1M  C6'   C  CH2   0  -0.158  -3.1455   2.2457  -0.1133
 D1M  O6'   O  OH1   0  -0.670  -2.4429   3.3030  -0.7207
 D1M  HN3   H  HNR6  0   0.434   2.8035   0.4264   2.6682
 D1M  H6    H  HCR6  0   0.339   1.5594  -0.1727  -1.8756
 D1M  H8    H  H     0   0.285   5.7875   0.0189  -3.2205
 D1M  H1'   H  HCH1  0   0.259  -0.4195  -0.3204  -1.4198
 D1M  H2'   H  HCH1  0   0.246  -1.1381  -1.4113   1.3334
 D1M  HO2'  H  HOH1  0   0.459  -0.6739  -3.3597   0.1383
 D1M  H3'   H  HCH1  0   0.222  -2.4553  -1.6616  -1.3973
 D1M  HO3'  H  HOH1  0   0.460  -3.8339  -2.9811  -0.2920
 D1M  H4'   H  HCH1  0   0.228  -3.3638  -0.1757   1.1075
 D1M  HO4'  H  HOH1  0   0.461  -5.1652  -0.7258  -0.0085
 D1M  H5'   H  HCH1  0   0.231  -2.4628   0.8763  -1.6151
 D1M  H6'   H  HCH2  0   0.216  -4.1936   2.2200  -0.4266
 D1M  H6'A  H  HCH2  0   0.200  -3.1368   2.3235   0.9827
 D1M  HO6'  H  HOH1  0   0.458  -2.9127   4.1194  -0.5297

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
 D1M  N1   C2    single  1.389  0.020  1.389
 D1M  N1   C6    single  1.358  0.020  1.358
 D1M  N1   C1'   single  1.457  0.020  1.457
 D1M  C2   O2    double  1.208  0.020  1.208
 D1M  C2   N3    single  1.371  0.020  1.371
 D1M  N3   C4    single  1.381  0.020  1.381
 D1M  C4   O4    double  1.213  0.020  1.213
 D1M  C4   C5    single  1.454  0.020  1.454
 D1M  C5   C6    double  1.353  0.020  1.353
 D1M  C5   C7    single  1.417  0.020  1.417
 D1M  C7   C8    triple  1.203  0.020  1.203
 D1M  C1'  C2'   single  1.526  0.020  1.526
 D1M  C1'  O5'   single  1.389  0.020  1.389
 D1M  C2'  O2'   single  1.402  0.020  1.402
 D1M  C2'  C3'   single  1.523  0.020  1.523
 D1M  C3'  O3'   single  1.409  0.020  1.409
 D1M  C3'  C4'   single  1.529  0.020  1.529
 D1M  C4'  O4'   single  1.409  0.020  1.409
 D1M  C4'  C5'   single  1.531  0.020  1.531
 D1M  C5'  O5'   single  1.419  0.020  1.419
 D1M  C5'  C6'   single  1.513  0.020  1.513
 D1M  C6'  O6'   single  1.407  0.020  1.407
 D1M  N3   HN3   single  0.868  0.020  1.013
 D1M  C6   H6    single  0.930  0.020  1.086
 D1M  C8   H8    single  0.913  0.020  1.066
 D1M  C1'  H1'   single  0.939  0.020  1.096
 D1M  C2'  H2'   single  0.939  0.020  1.096
 D1M  O2'  HO2'  single  0.832  0.020  0.971
 D1M  C3'  H3'   single  0.939  0.020  1.096
 D1M  O3'  HO3'  single  0.832  0.020  0.971
 D1M  C4'  H4'   single  0.939  0.020  1.096
 D1M  O4'  HO4'  single  0.832  0.020  0.971
 D1M  C5'  H5'   single  0.939  0.020  1.096
 D1M  C6'  H6'   single  0.939  0.020  1.096
 D1M  C6'  H6'A  single  0.939  0.020  1.096
 D1M  O6'  HO6'  single  0.832  0.020  0.971

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
 D1M  C1'   N1   C6   118.75  3.000
 D1M  C1'   N1   C2   120.19  3.000
 D1M  C6    N1   C2   121.04  3.000
 D1M  N3    C2   O2   122.17  3.000
 D1M  N3    C2   N1   114.44  3.000
 D1M  O2    C2   N1   123.39  3.000
 D1M  HN3   N3   C4   116.55  3.000
 D1M  HN3   N3   C2   114.89  3.000
 D1M  C4    N3   C2   128.56  3.000
 D1M  C5    C4   O4   125.28  3.000
 D1M  C5    C4   N3   113.37  3.000
 D1M  O4    C4   N3   121.35  3.000
 D1M  C7    C5   C6   121.90  3.000
 D1M  C7    C5   C4   119.20  3.000
 D1M  C6    C5   C4   118.90  3.000
 D1M  H6    C6   C5   120.63  3.000
 D1M  H6    C6   N1   115.69  3.000
 D1M  C5    C6   N1   123.68  3.000
 D1M  C8    C7   C5   180.00  3.000
 D1M  H8    C8   C7   180.00  3.000
 D1M  H1'   C1'  O5'  110.41  3.000
 D1M  H1'   C1'  C2'  107.23  3.000
 D1M  O5'   C1'  C2'  112.12  3.000
 D1M  H1'   C1'  N1   105.14  3.000
 D1M  O5'   C1'  N1   108.54  3.000
 D1M  C2'   C1'  N1   113.17  3.000
 D1M  H2'   C2'  C3'  108.39  3.000
 D1M  H2'   C2'  O2'  111.66  3.000
 D1M  C3'   C2'  O2'  112.85  3.000
 D1M  H2'   C2'  C1'  110.05  3.000
 D1M  C3'   C2'  C1'  107.19  3.000
 D1M  O2'   C2'  C1'  106.59  3.000
 D1M  HO2'  O2'  C2'  108.24  3.000
 D1M  H3'   C3'  C4'  108.10  3.000
 D1M  H3'   C3'  O3'  110.61  3.000
 D1M  C4'   C3'  O3'  111.93  3.000
 D1M  H3'   C3'  C2'  108.40  3.000
 D1M  C4'   C3'  C2'  110.37  3.000
 D1M  O3'   C3'  C2'  107.40  3.000
 D1M  HO3'  O3'  C3'  108.90  3.000
 D1M  H4'   C4'  C5'  108.36  3.000
 D1M  H4'   C4'  O4'  111.05  3.000
 D1M  C5'   C4'  O4'  108.18  3.000
 D1M  H4'   C4'  C3'  108.76  3.000
 D1M  C5'   C4'  C3'  109.78  3.000
 D1M  O4'   C4'  C3'  110.68  3.000
 D1M  HO4'  O4'  C4'  108.76  3.000
 D1M  H5'   C5'  C6'  109.14  3.000
 D1M  H5'   C5'  O5'  109.63  3.000
 D1M  C6'   C5'  O5'  107.39  3.000
 D1M  H5'   C5'  C4'  108.70  3.000
 D1M  C6'   C5'  C4'  112.18  3.000
 D1M  O5'   C5'  C4'  109.77  3.000
 D1M  C5'   O5'  C1'  113.34  3.000
 D1M  H6'A  C6'  H6'  107.15  3.000
 D1M  H6'A  C6'  O6'  111.93  3.000
 D1M  H6'   C6'  O6'  111.86  3.000
 D1M  H6'A  C6'  C5'  108.84  3.000
 D1M  H6'   C6'  C5'  108.11  3.000
 D1M  O6'   C6'  C5'  108.85  3.000
 D1M  HO6'  O6'  C6'  107.96  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
 D1M  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 D1M  CONST_02  C5   C4  N3  C2    0.00  0.0  0
 D1M  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 D1M  CONST_04  C1'  N1  C2  N3  180.00  0.0  0
 D1M  CONST_05  O4   C4  N3  C2  180.00  0.0  0
 D1M  CONST_06  C6   N1  C2  O2  180.00  0.0  0
 D1M  CONST_07  C1'  N1  C2  O2    0.00  0.0  0
 D1M  CONST_08  C4   N3  C2  O2  180.00  0.0  0
 D1M  CONST_09  HN3  N3  C2  N1  180.00  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
 D1M  chir_01  C1'  N1   C2'  O5'  negativ
 D1M  chir_02  C2'  O2'  C1'  C3'  negativ
 D1M  chir_03  C3'  O3'  C2'  C4'  positiv
 D1M  chir_04  C4'  O4'  C5'  C3'  positiv
 D1M  chir_05  C5'  O5'  C4'  C6'  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
 D1M  plan-1  N1   0.020
 D1M  plan-1  C2   0.020
 D1M  plan-1  O2   0.020
 D1M  plan-1  N3   0.020
 D1M  plan-1  C4   0.020
 D1M  plan-1  O4   0.020
 D1M  plan-1  C5   0.020
 D1M  plan-1  C6   0.020
 D1M  plan-1  C7   0.020
 D1M  plan-1  C8   0.020
 D1M  plan-1  C1'  0.020
 D1M  plan-1  HN3  0.020
 D1M  plan-1  H6   0.020

