# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:44:45 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 4-azanyl-1-[(2R,3S,4S,5R,6R)-4-fluoro-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]pyrimidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H](F)[C@H]2O
#
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
 DKZ  DKZ  4-azanyl-1-[(2R,3S,4S,5R,6R)-4-fluoro-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]pyrimidin-2-one  D-saccharide  33  19  .  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_DKZ
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
 DKZ  C1    C  CH1   0   0.205  -0.0892   0.1659   0.5063
 DKZ  N1    N  NR6   0  -0.568   1.3349   0.0220   0.2991
 DKZ  C2    C  CH1   0  -0.051  -0.6670   1.4580  -0.0764
 DKZ  N2    N  N     0  -0.540   3.2201  -0.1754  -1.1138
 DKZ  O2    O  OH1   0  -0.666   0.0112   2.5243   0.5330
 DKZ  C3    C  CH1   0   0.157  -2.1514   1.4620   0.2447
 DKZ  F3    F  F     0  -0.376  -2.7442   2.5663  -0.3709
 DKZ  C4    C  CH1   0  -0.015  -2.8407   0.1975  -0.2413
 DKZ  O4    O  OH1   0  -0.668  -4.1778   0.1415   0.1848
 DKZ  C5    C  CH1   0  -0.027  -2.1091  -1.0177   0.3373
 DKZ  O5    O  O2    0  -0.478  -0.7377  -0.9585  -0.0026
 DKZ  C6    C  CH2   0  -0.157  -2.6599  -2.3181  -0.2065
 DKZ  O6    O  OH1   0  -0.669  -2.0090  -3.3863   0.4370
 DKZ  C7    C  CR16  0   0.095   2.1435  -0.0471   1.3871
 DKZ  C8    C  CR16  0  -0.474   3.4780  -0.1761   1.2763
 DKZ  C9    C  CR6   0   0.516   3.9992  -0.2416  -0.0529
 DKZ  C10   C  CR6   0   0.602   1.8833  -0.0424  -0.9983
 DKZ  O10   O  O     0  -0.509   1.1437   0.0205  -1.9684
 DKZ  H1    H  HCH1  0   0.251  -0.2228   0.2157   1.5972
 DKZ  H2    H  HCH1  0   0.262  -0.5405   1.4610  -1.1621
 DKZ  HO2   H  HOH1  0   0.465  -0.0884   3.3088  -0.0140
 DKZ  H3    H  HCH1  0   0.220  -2.3031   1.5764   1.3243
 DKZ  HN3   H  HNH2  0   0.415   5.9451  -0.4661   0.5348
 DKZ  HN3A  H  HNH2  0   0.404   5.6847  -0.4515  -1.1691
 DKZ  H4    H  HCH1  0   0.234  -2.7661   0.1561  -1.3385
 DKZ  HO4   H  HOH1  0   0.461  -4.6870   0.7971  -0.3015
 DKZ  H5    H  HCH1  0   0.233  -2.2249  -1.0094   1.4338
 DKZ  H6    H  HCH2  0   0.217  -3.7399  -2.3349  -0.0309
 DKZ  H6A   H  HCH2  0   0.201  -2.5086  -2.3402  -1.2948
 DKZ  HO6   H  HOH1  0   0.458  -2.4164  -4.2045   0.1395
 DKZ  H7    H  HCR6  0   0.320   1.6573   0.0034   2.3515
 DKZ  H8    H  HCR6  0   0.291   4.1103  -0.2308   2.1493
 DKZ  N3    N  NH2   0  -0.807   5.3114  -0.3693  -0.2387

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
 DKZ  C2   C1    single  1.531  0.020  1.531
 DKZ  C1   O5    single  1.394  0.020  1.394
 DKZ  C1   N1    single  1.446  0.020  1.446
 DKZ  C1   H1    single  0.970  0.020  1.090
 DKZ  C7   N1    single  1.357  0.020  1.357
 DKZ  N1   C10   single  1.410  0.020  1.410
 DKZ  C3   C2    single  1.519  0.020  1.519
 DKZ  O2   C2    single  1.403  0.020  1.403
 DKZ  C2   H2    single  0.970  0.020  1.090
 DKZ  C10  N2    single  1.348  0.020  1.348
 DKZ  C9   N2    double  1.318  0.020  1.318
 DKZ  O2   HO2   single  0.850  0.020  0.980
 DKZ  F3   C3    single  1.396  0.020  1.396
 DKZ  C3   C4    single  1.520  0.020  1.520
 DKZ  C3   H3    single  0.970  0.020  1.090
 DKZ  C9   N3    single  1.331  0.020  1.331
 DKZ  N3   HN3   single  0.860  0.020  1.020
 DKZ  N3   HN3A  single  0.860  0.020  1.020
 DKZ  O4   C4    single  1.405  0.020  1.405
 DKZ  C4   C5    single  1.532  0.020  1.532
 DKZ  C4   H4    single  0.970  0.020  1.090
 DKZ  O4   HO4   single  0.850  0.020  0.980
 DKZ  C5   C6    single  1.513  0.020  1.513
 DKZ  C5   O5    single  1.414  0.020  1.414
 DKZ  C5   H5    single  0.970  0.020  1.090
 DKZ  O6   C6    single  1.407  0.020  1.407
 DKZ  C6   H6    single  0.970  0.020  1.090
 DKZ  C6   H6A   single  0.970  0.020  1.090
 DKZ  O6   HO6   single  0.850  0.020  0.980
 DKZ  C7   C8    double  1.345  0.020  1.345
 DKZ  C7   H7    single  0.930  0.020  1.080
 DKZ  C8   C9    single  1.429  0.020  1.429
 DKZ  C8   H8    single  0.930  0.020  1.080
 DKZ  C10  O10   double  1.222  0.020  1.222

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
 DKZ  H1    C1   O5   110.00  3.000
 DKZ  H1    C1   C2   107.06  3.000
 DKZ  O5    C1   C2   111.48  3.000
 DKZ  H1    C1   N1   105.43  3.000
 DKZ  O5    C1   N1   109.00  3.000
 DKZ  C2    C1   N1   113.65  3.000
 DKZ  C10   N1   C7   120.23  3.000
 DKZ  C10   N1   C1   121.29  3.000
 DKZ  C7    N1   C1   118.48  3.000
 DKZ  H2    C2   C3   108.85  3.000
 DKZ  H2    C2   O2   111.92  3.000
 DKZ  C3    C2   O2   112.25  3.000
 DKZ  H2    C2   C1   109.68  3.000
 DKZ  O2    C2   C1   107.08  3.000
 DKZ  C3    C2   C1   106.90  3.000
 DKZ  C10   N2   C9   121.47  3.000
 DKZ  HO2   O2   C2   108.84  3.000
 DKZ  H3    C3   C4   109.82  3.000
 DKZ  H3    C3   F3   107.03  3.000
 DKZ  C4    C3   F3   108.93  3.000
 DKZ  H3    C3   C2   110.10  3.000
 DKZ  C4    C3   C2   111.93  3.000
 DKZ  F3    C3   C2   108.89  3.000
 DKZ  H4    C4   C5   108.32  3.000
 DKZ  H4    C4   O4   111.44  3.000
 DKZ  C5    C4   O4   107.96  3.000
 DKZ  H4    C4   C3   108.63  3.000
 DKZ  C5    C4   C3   108.82  3.000
 DKZ  O4    C4   C3   111.59  3.000
 DKZ  HO4   O4   C4   108.86  3.000
 DKZ  H5    C5   C6   109.00  3.000
 DKZ  H5    C5   O5   109.91  3.000
 DKZ  C6    C5   O5   107.61  3.000
 DKZ  H5    C5   C4   108.63  3.000
 DKZ  O5    C5   C4   109.82  3.000
 DKZ  C6    C5   C4   111.85  3.000
 DKZ  C5    O5   C1   113.40  3.000
 DKZ  H6A   C6   H6   107.13  3.000
 DKZ  H6A   C6   O6   111.97  3.000
 DKZ  H6    C6   O6   111.81  3.000
 DKZ  H6A   C6   C5   108.85  3.000
 DKZ  H6    C6   C5   108.34  3.000
 DKZ  O6    C6   C5   108.65  3.000
 DKZ  HO6   O6   C6   107.97  3.000
 DKZ  H7    C7   C8   121.61  3.000
 DKZ  H7    C7   N1   116.40  3.000
 DKZ  C8    C7   N1   121.99  3.000
 DKZ  H8    C8   C9   122.44  3.000
 DKZ  H8    C8   C7   121.29  3.000
 DKZ  C9    C8   C7   116.28  3.000
 DKZ  C8    C9   N3   119.57  3.000
 DKZ  C8    C9   N2   122.06  3.000
 DKZ  N3    C9   N2   118.37  3.000
 DKZ  O10   C10  N2   122.50  3.000
 DKZ  O10   C10  N1   119.53  3.000
 DKZ  N2    C10  N1   117.97  3.000
 DKZ  HN3A  N3   HN3  118.04  3.000
 DKZ  HN3A  N3   C9   120.18  3.000
 DKZ  HN3   N3   C9   121.57  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
 DKZ  CONST_01  N2    C10  N1   C1  180.00  0.0  0
 DKZ  CONST_02  C9    N2   C10  N1    0.00  0.0  0
 DKZ  CONST_03  C7    N1   C10  N2    0.00  0.0  0
 DKZ  CONST_04  C10   N2   C9   C8    0.00  0.0  0
 DKZ  CONST_05  O10   C10  N1   C1    0.00  0.0  0
 DKZ  CONST_06  C10   N2   C9   N3  180.00  0.0  0
 DKZ  CONST_07  O10   C10  N1   C7  180.00  0.0  0
 DKZ  CONST_08  O10   C10  N2   C9  180.00  0.0  0
 DKZ  CONST_09  HN3   N3   C9   N2  180.00  0.0  0
 DKZ  CONST_10  HN3A  N3   C9   N2    0.00  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
 DKZ  chir_01  C1  C2  O5  N1  negativ
 DKZ  chir_02  C2  O2  C1  C3  negativ
 DKZ  chir_03  C3  F3  C4  C2  negativ
 DKZ  chir_04  C4  O4  C5  C3  positiv
 DKZ  chir_05  C5  O5  C6  C4  positiv

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
 DKZ  plan-1  C1    0.020
 DKZ  plan-1  N1    0.020
 DKZ  plan-1  N2    0.020
 DKZ  plan-1  C7    0.020
 DKZ  plan-1  C8    0.020
 DKZ  plan-1  C9    0.020
 DKZ  plan-1  C10   0.020
 DKZ  plan-1  O10   0.020
 DKZ  plan-1  HN3   0.020
 DKZ  plan-1  HN3A  0.020
 DKZ  plan-1  H7    0.020
 DKZ  plan-1  H8    0.020
 DKZ  plan-1  N3    0.020

