# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 16:09:58 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 1-(beta-D-glucopyranosyl)-5-(pent-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC#CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)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
 D1J  D1J  1-(beta-D-glucopyranosyl)-5-(pent-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione  ligand  44  24  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D1J
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
 D1J  N1    N  NR6   0  -0.576   0.0651   0.6897  -0.0964
 D1J  C2    C  CR6   0   0.746   0.2258   2.0530  -0.2884
 D1J  O2    O  O     0  -0.458   1.2997   2.5833  -0.4522
 D1J  N3    N  NR16  0  -0.736  -0.9443   2.7672  -0.2754
 D1J  C4    C  CR6   0   0.536  -2.2363   2.3040  -0.1200
 D1J  O4    O  O     0  -0.431  -3.1821   3.0636  -0.1393
 D1J  C5    C  CR6   0  -0.413  -2.3174   0.8636   0.0653
 D1J  C6    C  CR16  0   0.064  -1.1715   0.1455   0.0680
 D1J  C7    C  CSP   0   0.150  -3.5878   0.2585   0.2390
 D1J  C8    C  CSP   0   0.084  -4.6737  -0.2441   0.3862
 D1J  C9    C  CH2   0  -0.609  -5.9729  -0.8812   0.5471
 D1J  C1'   C  CH1   0   0.214   1.2238  -0.1928  -0.1024
 D1J  C10   C  CH2   0  -0.427  -6.0182  -2.2934  -0.0450
 D1J  C11   C  CH3   0  -0.670  -7.3809  -2.9401   0.1510
 D1J  C2'   C  CH1   0  -0.002   1.9325  -0.2418  -1.4545
 D1J  O2'   O  OH1   0  -0.665   0.9794  -0.6663  -2.3914
 D1J  C3'   C  CH1   0  -0.015   3.0993  -1.2115  -1.3194
 D1J  O3'   O  OH1   0  -0.672   3.7942  -1.2083  -2.5441
 D1J  C4'   C  CH1   0   0.013   3.9945  -0.8023  -0.1495
 D1J  O4'   O  OH1   0  -0.673   5.0084  -1.7579   0.0608
 D1J  C5'   C  CH1   0  -0.024   3.1563  -0.7043   1.1270
 D1J  O5'   O  O2    0  -0.479   2.0777   0.1942   0.9227
 D1J  C6'   C  CH2   0  -0.157   3.9615  -0.1905   2.3001
 D1J  O6'   O  OH1   0  -0.670   3.1520  -0.2054   3.4509
 D1J  HN3   H  HNR6  0   0.432  -0.8346   3.7663  -0.4026
 D1J  H6    H  HCR6  0   0.332  -1.1965  -0.9254   0.2086
 D1J  H19   H  HCH2  0   0.262  -6.2293  -0.9217   1.6101
 D1J  H29   H  HCH2  0   0.265  -6.7366  -0.2576   0.0731
 D1J  H1'   H  HCH1  0   0.259   0.8227  -1.1977   0.0935
 D1J  H110  H  HCH2  0   0.231  -5.7744  -2.2456  -1.1084
 D1J  H210  H  HCH2  0   0.230  -5.2446  -2.9037   0.4260
 D1J  H111  H  HCH3  0   0.222  -7.6356  -3.0095   1.2099
 D1J  H211  H  HCH3  0   0.223  -8.1675  -2.3671  -0.3428
 D1J  H311  H  HCH3  0   0.236  -7.3982  -3.9490  -0.2611
 D1J  H2'   H  HCH1  0   0.245   2.3312   0.7486  -1.7044
 D1J  HO2'  H  HOH1  0   0.459   1.4094  -0.7311  -3.2505
 D1J  H3'   H  HCH1  0   0.221   2.6940  -2.2128  -1.1051
 D1J  HO3'  H  HOH1  0   0.460   4.2982  -2.0244  -2.6185
 D1J  H4'   H  HCH1  0   0.228   4.4228   0.1880  -0.3609
 D1J  HO4'  H  HOH1  0   0.461   5.7546  -1.5478  -0.5076
 D1J  H5'   H  HCH1  0   0.230   2.7631  -1.7050   1.3715
 D1J  H16'  H  HCH2  0   0.217   4.8402  -0.8323   2.4123
 D1J  H26'  H  HCH2  0   0.198   4.3249   0.8201   2.0671
 D1J  HO6'  H  HOH1  0   0.458   3.7130  -0.0216   4.2094

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
 D1J  O3'  C3'   single  1.408  0.020  1.408
 D1J  O4'  C4'   single  1.409  0.020  1.409
 D1J  C3'  C4'   single  1.529  0.020  1.529
 D1J  C3'  C2'   single  1.523  0.020  1.523
 D1J  C4'  C5'   single  1.530  0.020  1.530
 D1J  O2'  C2'   single  1.402  0.020  1.402
 D1J  C2'  C1'   single  1.527  0.020  1.527
 D1J  O6'  C6'   single  1.407  0.020  1.407
 D1J  C5'  C6'   single  1.513  0.020  1.513
 D1J  C5'  O5'   single  1.419  0.020  1.419
 D1J  C1'  O5'   single  1.389  0.020  1.389
 D1J  C1'  N1    single  1.456  0.020  1.456
 D1J  N1   C6    single  1.361  0.020  1.361
 D1J  N1   C2    single  1.386  0.020  1.386
 D1J  C6   C5    double  1.352  0.020  1.352
 D1J  O2   C2    double  1.209  0.020  1.209
 D1J  C2   N3    single  1.371  0.020  1.371
 D1J  C5   C7    single  1.418  0.020  1.418
 D1J  C5   C4    single  1.455  0.020  1.455
 D1J  C7   C8    triple  1.206  0.020  1.206
 D1J  C8   C9    single  1.456  0.020  1.456
 D1J  N3   C4    single  1.381  0.020  1.381
 D1J  C4   O4    double  1.213  0.020  1.213
 D1J  C9   C10   single  1.532  0.020  1.532
 D1J  C10  C11   single  1.521  0.020  1.521
 D1J  N3   HN3   single  0.860  0.020  1.020
 D1J  C6   H6    single  0.930  0.020  1.080
 D1J  C9   H19   single  0.970  0.020  1.090
 D1J  C9   H29   single  0.970  0.020  1.090
 D1J  C1'  H1'   single  0.970  0.020  1.090
 D1J  C10  H110  single  0.970  0.020  1.090
 D1J  C10  H210  single  0.970  0.020  1.090
 D1J  C11  H111  single  0.970  0.020  1.090
 D1J  C11  H211  single  0.970  0.020  1.090
 D1J  C11  H311  single  0.970  0.020  1.090
 D1J  C2'  H2'   single  0.970  0.020  1.090
 D1J  O2'  HO2'  single  0.850  0.020  0.980
 D1J  C3'  H3'   single  0.970  0.020  1.090
 D1J  O3'  HO3'  single  0.850  0.020  0.980
 D1J  C4'  H4'   single  0.970  0.020  1.090
 D1J  O4'  HO4'  single  0.850  0.020  0.980
 D1J  C5'  H5'   single  0.970  0.020  1.090
 D1J  C6'  H16'  single  0.970  0.020  1.090
 D1J  C6'  H26'  single  0.970  0.020  1.090
 D1J  O6'  HO6'  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
 D1J  C1'   N1   C6    118.75  3.000
 D1J  C6    N1   C2    121.02  3.000
 D1J  C1'   N1   C2    120.21  3.000
 D1J  N3    C2   O2    122.06  3.000
 D1J  N3    C2   N1    114.35  3.000
 D1J  O2    C2   N1    123.59  3.000
 D1J  HN3   N3   C4    116.50  3.000
 D1J  HN3   N3   C2    114.85  3.000
 D1J  C4    N3   C2    128.66  3.000
 D1J  C5    C4   O4    125.35  3.000
 D1J  O4    C4   N3    121.16  3.000
 D1J  C5    C4   N3    113.49  3.000
 D1J  C7    C5   C6    122.16  3.000
 D1J  C7    C5   C4    119.22  3.000
 D1J  C6    C5   C4    118.61  3.000
 D1J  H6    C6   C5    120.46  3.000
 D1J  H6    C6   N1    115.67  3.000
 D1J  C5    C6   N1    123.87  3.000
 D1J  C8    C7   C5    180.00  3.000
 D1J  C9    C8   C7    180.00  3.000
 D1J  H29   C9   H19   106.17  3.000
 D1J  H29   C9   C10   109.71  3.000
 D1J  H19   C9   C10   109.54  3.000
 D1J  H29   C9   C8    109.00  3.000
 D1J  H19   C9   C8    109.43  3.000
 D1J  C10   C9   C8    112.77  3.000
 D1J  H1'   C1'  O5'   110.32  3.000
 D1J  H1'   C1'  C2'   107.32  3.000
 D1J  O5'   C1'  C2'   112.15  3.000
 D1J  H1'   C1'  N1    105.24  3.000
 D1J  O5'   C1'  N1    108.49  3.000
 D1J  C2'   C1'  N1    113.09  3.000
 D1J  H210  C10  H110  106.63  3.000
 D1J  H210  C10  C11   109.96  3.000
 D1J  H110  C10  C11   110.13  3.000
 D1J  H210  C10  C9    109.12  3.000
 D1J  H110  C10  C9    109.23  3.000
 D1J  C11   C10  C9    111.63  3.000
 D1J  H311  C11  H211  107.66  3.000
 D1J  H311  C11  H111  107.72  3.000
 D1J  H211  C11  H111  107.71  3.000
 D1J  H311  C11  C10   111.04  3.000
 D1J  H211  C11  C10   111.36  3.000
 D1J  H111  C11  C10   111.18  3.000
 D1J  H2'   C2'  C3'   108.46  3.000
 D1J  H2'   C2'  O2'   111.61  3.000
 D1J  C3'   C2'  O2'   112.78  3.000
 D1J  H2'   C2'  C1'   109.97  3.000
 D1J  O2'   C2'  C1'   106.61  3.000
 D1J  C3'   C2'  C1'   107.30  3.000
 D1J  HO2'  O2'  C2'   108.24  3.000
 D1J  H3'   C3'  C4'   108.05  3.000
 D1J  H3'   C3'  O3'   110.66  3.000
 D1J  C4'   C3'  O3'   112.08  3.000
 D1J  H3'   C3'  C2'   108.31  3.000
 D1J  C4'   C3'  C2'   110.25  3.000
 D1J  O3'   C3'  C2'   107.43  3.000
 D1J  HO3'  O3'  C3'   108.90  3.000
 D1J  H4'   C4'  C5'   108.42  3.000
 D1J  H4'   C4'  O4'   111.06  3.000
 D1J  C5'   C4'  O4'   108.25  3.000
 D1J  H4'   C4'  C3'   108.78  3.000
 D1J  C5'   C4'  C3'   109.55  3.000
 D1J  O4'   C4'  C3'   110.74  3.000
 D1J  HO4'  O4'  C4'   108.79  3.000
 D1J  H5'   C5'  C6'   109.03  3.000
 D1J  H5'   C5'  O5'   109.61  3.000
 D1J  C6'   C5'  O5'   107.53  3.000
 D1J  H5'   C5'  C4'   108.79  3.000
 D1J  O5'   C5'  C4'   109.69  3.000
 D1J  C6'   C5'  C4'   112.15  3.000
 D1J  C5'   O5'  C1'   113.41  3.000
 D1J  H26'  C6'  H16'  107.20  3.000
 D1J  H26'  C6'  O6'   111.93  3.000
 D1J  H16'  C6'  O6'   111.84  3.000
 D1J  H26'  C6'  C5'   108.90  3.000
 D1J  H16'  C6'  C5'   107.93  3.000
 D1J  O6'   C6'  C5'   108.93  3.000
 D1J  HO6'  O6'  C6'   107.91  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
 D1J  CONST_01  C4    N3   C2   N1    0.00   0.0  0
 D1J  CONST_02  C5    C4   N3   C2    0.00   0.0  0
 D1J  CONST_03  C1'   N1   C2   N3  180.00   0.0  0
 D1J  CONST_04  C6    N1   C2   N3    0.00   0.0  0
 D1J  CONST_05  O4    C4   N3   C2  180.00   0.0  0
 D1J  CONST_06  C1'   N1   C2   O2    0.00   0.0  0
 D1J  CONST_07  C6    N1   C2   O2  180.00   0.0  0
 D1J  CONST_08  C4    N3   C2   O2  180.00   0.0  0
 D1J  CONST_09  HN3   N3   C2   N1  180.00   0.0  0
 D1J  Var_01    C10   C9   C8   C7   -0.49  30.0  3
 D1J  Var_02    C11   C10  C9   C8  179.36  30.0  3
 D1J  Var_03    H111  C11  C10  C9  -59.29  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
 D1J  chir_01  C1'  C2'  O5'  N1   negativ
 D1J  chir_02  C2'  O2'  C1'  C3'  negativ
 D1J  chir_03  C3'  O3'  C2'  C4'  positiv
 D1J  chir_04  C4'  O4'  C5'  C3'  positiv
 D1J  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
 D1J  plan-1  N1   0.020
 D1J  plan-1  C2   0.020
 D1J  plan-1  O2   0.020
 D1J  plan-1  N3   0.020
 D1J  plan-1  C4   0.020
 D1J  plan-1  O4   0.020
 D1J  plan-1  C5   0.020
 D1J  plan-1  C6   0.020
 D1J  plan-1  C7   0.020
 D1J  plan-1  C8   0.020
 D1J  plan-1  C1'  0.020
 D1J  plan-1  HN3  0.020
 D1J  plan-1  H6   0.020

