# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 23:24:54 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 1-(beta-D-glucopyranosyl)-5-(hept-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC#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
 D1F  D1F  1-(beta-D-glucopyranosyl)-5-(hept-1-yn-1-yl)pyrimidine-2,4(1H,3H)-dione  ligand  50  26  .  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_D1F
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
 D1F  N1    N  NR6   0  -0.575  -0.8939  -0.9020   0.0059
 D1F  C2    C  CR6   0   0.744  -1.3144  -2.2061   0.2131
 D1F  O2    O  O     0  -0.458  -2.4771  -2.5314   0.2709
 D1F  N3    N  NR16  0  -0.736  -0.2952  -3.1128   0.3520
 D1F  C4    C  CR6   0   0.537   1.0667  -2.8985   0.2626
 D1F  O4    O  O     0  -0.431   1.8557  -3.8107   0.3936
 D1F  C5    C  CR6   0  -0.416   1.4206  -1.5117   0.0032
 D1F  C6    C  CR16  0   0.062   0.4284  -0.5996  -0.1050
 D1F  C7    C  CSP   0   0.140   2.7854  -1.1570  -0.1425
 D1F  C8    C  CSP   0   0.099   3.9455  -0.8614  -0.2852
 D1F  C9    C  CH2   0  -0.617   5.3379  -0.4745  -0.4605
 D1F  C1'   C  CH1   0   0.215  -1.8702   0.1612  -0.1859
 D1F  C10   C  CH2   0  -0.421   5.6805   0.8520   0.2245
 D1F  C11   C  CH2   0  -0.413   7.1285   1.2571  -0.0155
 D1F  C12   C  CH2   0  -0.420   7.4994   2.5734   0.6564
 D1F  C13   C  CH3   0  -0.662   8.9434   2.9789   0.3953
 D1F  C2'   C  CH1   0   0.000  -2.6682   0.0077  -1.4790
 D1F  O2'   O  OH1   0  -0.664  -1.7318  -0.0280  -2.5220
 D1F  C3'   C  CH1   0  -0.001  -3.6107   1.2001  -1.5721
 D1F  O3'   O  OH1   0  -0.669  -4.3864   1.0357  -2.7309
 D1F  C4'   C  CH1   0  -0.001  -4.4674   1.2917  -0.3130
 D1F  O4'   O  OH1   0  -0.670  -5.2507   2.4569  -0.4274
 D1F  C5'   C  CH1   0  -0.028  -3.5600   1.3443   0.9239
 D1F  O5'   O  O2    0  -0.478  -2.6898   0.2239   0.9332
 D1F  C6'   C  CH2   0  -0.161  -4.3562   1.3110   2.2088
 D1F  O6'   O  OH1   0  -0.668  -3.4799   1.4609   3.2979
 D1F  HN3   H  HNR6  0   0.432  -0.5933  -4.0665   0.5206
 D1F  H6    H  HCR6  0   0.332   0.6555   0.4405  -0.2896
 D1F  H9    H  HCH2  0   0.267   5.9803  -1.2694  -0.0705
 D1F  H9A   H  HCH2  0   0.263   5.5582  -0.4015  -1.5299
 D1F  H1'   H  HCH1  0   0.259  -1.2767   1.0824  -0.2768
 D1F  H10   H  HCH2  0   0.227   5.0119   1.6326  -0.1486
 D1F  H10A  H  HCH2  0   0.228   5.4896   0.7634   1.2973
 D1F  H11   H  HCH2  0   0.213   7.7941   0.4652   0.3454
 D1F  H11A  H  HCH2  0   0.213   7.3085   1.3382  -1.0930
 D1F  H12   H  HCH2  0   0.213   6.8276   3.3620   0.3036
 D1F  H12A  H  HCH2  0   0.213   7.3300   2.4900   1.7342
 D1F  H13   H  HCH3  0   0.216   9.6382   2.2207   0.7616
 D1F  H13A  H  HCH3  0   0.216   9.1304   3.1063  -0.6726
 D1F  H13B  H  HCH3  0   0.227   9.1921   3.9192   0.8885
 D1F  H2'   H  HCH1  0   0.245  -3.2701  -0.9084  -1.4435
 D1F  HO2'  H  HOH1  0   0.461  -2.2058  -0.1146  -3.3556
 D1F  H3'   H  HCH1  0   0.216  -2.9997   2.1167  -1.6340
 D1F  HO3'  H  HOH1  0   0.456  -4.9293   1.8228  -2.8452
 D1F  H4'   H  HCH1  0   0.232  -5.0973   0.3931  -0.2499
 D1F  HO4'  H  HOH1  0   0.464  -6.0919   2.3189   0.0164
 D1F  H5'   H  HCH1  0   0.231  -2.9687   2.2743   0.8865
 D1F  H6'   H  HCH2  0   0.207  -5.0953   2.1193   2.1726
 D1F  H6'A  H  HCH2  0   0.204  -4.9132   0.3648   2.2552
 D1F  HO6'  H  HOH1  0   0.458  -4.0042   1.4574   4.1036

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
 D1F  N1   C2    single  1.386  0.020  1.386
 D1F  N1   C6    single  1.361  0.020  1.361
 D1F  N1   C1'   single  1.456  0.020  1.456
 D1F  C2   O2    double  1.209  0.020  1.209
 D1F  C2   N3    single  1.371  0.020  1.371
 D1F  N3   C4    single  1.382  0.020  1.382
 D1F  C4   O4    double  1.213  0.020  1.213
 D1F  C4   C5    single  1.455  0.020  1.455
 D1F  C5   C6    double  1.352  0.020  1.352
 D1F  C5   C7    single  1.418  0.020  1.418
 D1F  C7   C8    triple  1.206  0.020  1.206
 D1F  C8   C9    single  1.456  0.020  1.456
 D1F  C9   C10   single  1.532  0.020  1.532
 D1F  C1'  C2'   single  1.527  0.020  1.527
 D1F  C1'  O5'   single  1.389  0.020  1.389
 D1F  C10  C11   single  1.523  0.020  1.523
 D1F  C11  C12   single  1.524  0.020  1.524
 D1F  C12  C13   single  1.522  0.020  1.522
 D1F  C2'  O2'   single  1.402  0.020  1.402
 D1F  C2'  C3'   single  1.523  0.020  1.523
 D1F  C3'  O3'   single  1.404  0.020  1.404
 D1F  C3'  C4'   single  1.526  0.020  1.526
 D1F  C4'  O4'   single  1.409  0.020  1.409
 D1F  C4'  C5'   single  1.535  0.020  1.535
 D1F  C5'  O5'   single  1.419  0.020  1.419
 D1F  C5'  C6'   single  1.512  0.020  1.512
 D1F  C6'  O6'   single  1.406  0.020  1.406
 D1F  N3   HN3   single  0.860  0.020  1.020
 D1F  C6   H6    single  0.930  0.020  1.080
 D1F  C9   H9    single  0.970  0.020  1.090
 D1F  C9   H9A   single  0.970  0.020  1.090
 D1F  C1'  H1'   single  0.970  0.020  1.090
 D1F  C10  H10   single  0.970  0.020  1.090
 D1F  C10  H10A  single  0.970  0.020  1.090
 D1F  C11  H11   single  0.970  0.020  1.090
 D1F  C11  H11A  single  0.970  0.020  1.090
 D1F  C12  H12   single  0.970  0.020  1.090
 D1F  C12  H12A  single  0.970  0.020  1.090
 D1F  C13  H13   single  0.970  0.020  1.090
 D1F  C13  H13A  single  0.970  0.020  1.090
 D1F  C13  H13B  single  0.970  0.020  1.090
 D1F  C2'  H2'   single  0.970  0.020  1.090
 D1F  O2'  HO2'  single  0.850  0.020  0.980
 D1F  C3'  H3'   single  0.970  0.020  1.090
 D1F  O3'  HO3'  single  0.850  0.020  0.980
 D1F  C4'  H4'   single  0.970  0.020  1.090
 D1F  O4'  HO4'  single  0.850  0.020  0.980
 D1F  C5'  H5'   single  0.970  0.020  1.090
 D1F  C6'  H6'   single  0.970  0.020  1.090
 D1F  C6'  H6'A  single  0.970  0.020  1.090
 D1F  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
 D1F  C1'   N1   C6    118.58  3.000
 D1F  C1'   N1   C2    120.22  3.000
 D1F  C6    N1   C2    121.07  3.000
 D1F  N3    C2   O2    122.16  3.000
 D1F  N3    C2   N1    114.32  3.000
 D1F  O2    C2   N1    123.53  3.000
 D1F  HN3   N3   C4    116.54  3.000
 D1F  HN3   N3   C2    114.86  3.000
 D1F  C4    N3   C2    128.58  3.000
 D1F  C5    C4   O4    125.30  3.000
 D1F  C5    C4   N3    113.53  3.000
 D1F  O4    C4   N3    121.17  3.000
 D1F  C7    C5   C6    121.97  3.000
 D1F  C7    C5   C4    119.41  3.000
 D1F  C6    C5   C4    118.61  3.000
 D1F  H6    C6   C5    120.59  3.000
 D1F  H6    C6   N1    115.60  3.000
 D1F  C5    C6   N1    123.82  3.000
 D1F  C8    C7   C5    180.00  3.000
 D1F  C9    C8   C7    180.00  3.000
 D1F  H9A   C9   H9    106.18  3.000
 D1F  H9A   C9   C10   109.52  3.000
 D1F  H9    C9   C10   109.79  3.000
 D1F  H9A   C9   C8    109.14  3.000
 D1F  H9    C9   C8    109.00  3.000
 D1F  C10   C9   C8    112.97  3.000
 D1F  H1'   C1'  O5'   110.33  3.000
 D1F  H1'   C1'  C2'   107.24  3.000
 D1F  O5'   C1'  C2'   112.24  3.000
 D1F  H1'   C1'  N1    105.11  3.000
 D1F  O5'   C1'  N1    108.82  3.000
 D1F  C2'   C1'  N1    112.86  3.000
 D1F  H10A  C10  H10   106.62  3.000
 D1F  H10A  C10  C11   110.02  3.000
 D1F  H10   C10  C11   109.74  3.000
 D1F  H10A  C10  C9    109.24  3.000
 D1F  H10   C10  C9    109.20  3.000
 D1F  C11   C10  C9    111.87  3.000
 D1F  H11A  C11  H11   106.12  3.000
 D1F  H11A  C11  C12   109.25  3.000
 D1F  H11   C11  C12   109.35  3.000
 D1F  H11A  C11  C10   109.33  3.000
 D1F  H11   C11  C10   109.48  3.000
 D1F  C12   C11  C10   113.07  3.000
 D1F  H12A  C12  H12   106.11  3.000
 D1F  H12A  C12  C13   109.64  3.000
 D1F  H12   C12  C13   109.58  3.000
 D1F  H12A  C12  C11   109.32  3.000
 D1F  H12   C12  C11   109.32  3.000
 D1F  C13   C12  C11   112.66  3.000
 D1F  H13B  C13  H13A  107.62  3.000
 D1F  H13B  C13  H13   107.57  3.000
 D1F  H13A  C13  H13   107.47  3.000
 D1F  H13B  C13  C12   111.61  3.000
 D1F  H13A  C13  C12   111.19  3.000
 D1F  H13   C13  C12   111.17  3.000
 D1F  H2'   C2'  C3'   108.44  3.000
 D1F  H2'   C2'  O2'   111.68  3.000
 D1F  C3'   C2'  O2'   112.82  3.000
 D1F  H2'   C2'  C1'   110.08  3.000
 D1F  C3'   C2'  C1'   107.24  3.000
 D1F  O2'   C2'  C1'   106.47  3.000
 D1F  HO2'  O2'  C2'   108.51  3.000
 D1F  H3'   C3'  C4'   107.90  3.000
 D1F  H3'   C3'  O3'   110.91  3.000
 D1F  C4'   C3'  O3'   112.21  3.000
 D1F  H3'   C3'  C2'   108.13  3.000
 D1F  C4'   C3'  C2'   110.13  3.000
 D1F  O3'   C3'  C2'   107.50  3.000
 D1F  HO3'  O3'  C3'   108.29  3.000
 D1F  H4'   C4'  C5'   108.70  3.000
 D1F  H4'   C4'  O4'   111.23  3.000
 D1F  C5'   C4'  O4'   111.46  3.000
 D1F  H4'   C4'  C3'   108.66  3.000
 D1F  C5'   C4'  C3'   109.58  3.000
 D1F  O4'   C4'  C3'   107.15  3.000
 D1F  HO4'  O4'  C4'   109.30  3.000
 D1F  H5'   C5'  C6'   109.25  3.000
 D1F  H5'   C5'  O5'   109.72  3.000
 D1F  C6'   C5'  O5'   107.46  3.000
 D1F  H5'   C5'  C4'   108.58  3.000
 D1F  C6'   C5'  C4'   111.89  3.000
 D1F  O5'   C5'  C4'   109.93  3.000
 D1F  C5'   O5'  C1'   113.10  3.000
 D1F  H6'A  C6'  H6'   107.13  3.000
 D1F  H6'A  C6'  O6'   112.03  3.000
 D1F  H6'   C6'  O6'   111.55  3.000
 D1F  H6'A  C6'  C5'   108.77  3.000
 D1F  H6'   C6'  C5'   108.11  3.000
 D1F  O6'   C6'  C5'   109.13  3.000
 D1F  HO6'  O6'  C6'   107.99  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
 D1F  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 D1F  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 D1F  CONST_03  C6   N1   C2   N3      0.00   0.0  0
 D1F  CONST_04  C1'  N1   C2   N3    180.00   0.0  0
 D1F  CONST_05  O4   C4   N3   C2    180.00   0.0  0
 D1F  CONST_06  C6   N1   C2   O2    180.00   0.0  0
 D1F  CONST_07  C1'  N1   C2   O2      0.00   0.0  0
 D1F  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 D1F  CONST_09  HN3  N3   C2   N1    180.00   0.0  0
 D1F  Var_01    C10  C9   C8   C7     38.09  30.0  3
 D1F  Var_02    C11  C10  C9   C8   -177.99  30.0  3
 D1F  Var_03    C12  C11  C10  C9   -179.91  30.0  3
 D1F  Var_04    C13  C12  C11  C10  -179.24  30.0  3
 D1F  Var_05    H13  C13  C12  C11   -59.54  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
 D1F  chir_01  C1'  N1   C2'  O5'  negativ
 D1F  chir_02  C2'  O2'  C1'  C3'  negativ
 D1F  chir_03  C3'  O3'  C2'  C4'  positiv
 D1F  chir_04  C4'  O4'  C5'  C3'  positiv
 D1F  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
 D1F  plan-1  N1   0.020
 D1F  plan-1  C2   0.020
 D1F  plan-1  O2   0.020
 D1F  plan-1  N3   0.020
 D1F  plan-1  C4   0.020
 D1F  plan-1  O4   0.020
 D1F  plan-1  C5   0.020
 D1F  plan-1  C6   0.020
 D1F  plan-1  C7   0.020
 D1F  plan-1  C8   0.020
 D1F  plan-1  C1'  0.020
 D1F  plan-1  HN3  0.020
 D1F  plan-1  H6   0.020

