# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 10:42:55 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: 1-[2-deoxy-5-O-(dihydroxyphosphanyl)-2-fluoro-beta-L-ribofuranosyl]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@H](F)[C@H](O[C@H]1COP(O)O)N2C=CC(=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
 XY7  XY7  "1-[2-deoxy-5-O-(dihydroxyphosphanyl)-2-fluoro-beta-L-ribofuranosyl]pyrimidine-2,4(1H,3H)-dione"
  ligand  32  20  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_XY7
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
 XY7  C4   C  CR6   0   0.564  -19.7714   7.2911  11.7273
 XY7  N3   N  NR16  0  -0.733  -20.0177   8.0266  12.8804
 XY7  C2   C  CR6   0   0.739  -19.1364   8.3460  13.8763
 XY7  N1   N  NR6   0  -0.573  -17.8560   7.8622  13.6982
 XY7  C6   C  CR16  0   0.087  -17.5249   7.1340  12.5935
 XY7  C5   C  CR16  0  -0.512  -18.4067   6.8383  11.6234
 XY7  O4   O  O     0  -0.454  -20.6616   7.0856  10.9253
 XY7  O2   O  O     0  -0.473  -19.4485   9.0080  14.8448
 XY7  C1'  C  CR15  0   0.160  -16.8968   8.1578  14.7787
 XY7  O4'  O  O     0  -0.496  -15.7936   7.3146  14.6729
 XY7  C2'  C  CR15  0   0.104  -16.3687   9.5916  14.6974
 XY7  F2'  F  F     0  -0.366  -16.1233  10.0312  15.9893
 XY7  C3'  C  CR15  0  -0.024  -15.0463   9.4047  13.9616
 XY7  O3'  O  OH1   0  -0.653  -14.0832  10.3833  14.1932
 XY7  C4'  C  CR15  0   0.008  -14.5868   8.0588  14.5132
 XY7  C5'  C  CH2   0  -0.185  -13.6018   7.2920  13.6660
 XY7  O5'  O  O2    0  -0.605  -14.0967   7.1460  12.3496
 XY7  P    P  P     0   0.909  -13.6717   5.7943  11.5053
 XY7  OP1  O  OH1   0  -0.759  -14.5942   6.1477  10.2033
 XY7  OP2  O  OH1   0  -0.764  -12.2119   6.3135  10.9727
 XY7  H1   H  HNR6  0   0.425  -20.9584   8.3815  13.0056
 XY7  H2   H  HCR6  0   0.328  -16.5016   6.8010  12.5354
 XY7  H3   H  HCR6  0   0.287  -18.0996   6.2590  10.7664
 XY7  H4   H  HCR5  0   0.293  -17.4180   7.9898  15.7238
 XY7  H5   H  HCR5  0   0.268  -17.0555  10.2934  14.2237
 XY7  H6   H  HCR5  0   0.251  -15.2777   9.3011  12.8935
 XY7  H7   H  HOH1  0   0.464  -14.2348  11.1210  13.5943
 XY7  H8   H  HCR5  0   0.257  -14.1151   8.2108  15.4929
 XY7  H9   H  HCH2  0   0.243  -13.4055   6.3203  14.1368
 XY7  H10  H  HCH2  0   0.242  -12.6566   7.8430  13.6653
 XY7  H11  H  HOH1  0   0.486  -15.1748   5.4110   9.9792
 XY7  H12  H  HOH1  0   0.482  -11.5747   5.5897  10.9444

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
 XY7  OP1  P    single  1.634  0.020  1.634
 XY7  O4   C4   double  1.216  0.020  1.216
 XY7  P    OP2  single  1.638  0.020  1.638
 XY7  P    O5'  single  1.649  0.020  1.649
 XY7  C5   C4   single  1.442  0.020  1.442
 XY7  C5   C6   double  1.344  0.020  1.344
 XY7  C4   N3   single  1.390  0.020  1.390
 XY7  O5'  C5'  single  1.414  0.020  1.414
 XY7  C6   N1   single  1.364  0.020  1.364
 XY7  N3   C2   single  1.368  0.020  1.368
 XY7  C5'  C4'  single  1.509  0.020  1.509
 XY7  N1   C2   single  1.380  0.020  1.380
 XY7  N1   C1'  single  1.475  0.020  1.475
 XY7  O3'  C3'  single  1.392  0.020  1.392
 XY7  C3'  C4'  single  1.525  0.020  1.525
 XY7  C3'  C2'  single  1.525  0.020  1.525
 XY7  C2   O2   double  1.214  0.020  1.214
 XY7  C4'  O4'  single  1.427  0.020  1.427
 XY7  C2'  C1'  single  1.530  0.020  1.530
 XY7  C2'  F2'  single  1.387  0.020  1.387
 XY7  O4'  C1'  single  1.393  0.020  1.393
 XY7  N3   H1   single  0.860  0.020  1.020
 XY7  C6   H2   single  0.930  0.020  1.080
 XY7  C5   H3   single  0.930  0.020  1.080
 XY7  C1'  H4   single  0.970  0.020  1.090
 XY7  C2'  H5   single  0.970  0.020  1.090
 XY7  C3'  H6   single  0.970  0.020  1.090
 XY7  O3'  H7   single  0.850  0.020  0.980
 XY7  C4'  H8   single  0.970  0.020  1.090
 XY7  C5'  H9   single  0.970  0.020  1.090
 XY7  C5'  H10  single  0.970  0.020  1.090
 XY7  OP1  H11  single  0.850  0.020  0.980
 XY7  OP2  H12  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
 XY7  O4   C4   C5   126.34  3.000
 XY7  C5   C4   N3   113.19  3.000
 XY7  O4   C4   N3   120.47  3.000
 XY7  H1   N3   C2   115.25  3.000
 XY7  H1   N3   C4   116.90  3.000
 XY7  C2   N3   C4   127.85  3.000
 XY7  O2   C2   N1   122.18  3.000
 XY7  O2   C2   N3   122.87  3.000
 XY7  N1   C2   N3   114.95  3.000
 XY7  C1'  N1   C6   122.86  3.000
 XY7  C1'  N1   C2   116.01  3.000
 XY7  C6   N1   C2   121.12  3.000
 XY7  H2   C6   C5   121.08  3.000
 XY7  H2   C6   N1   116.05  3.000
 XY7  C5   C6   N1   122.88  3.000
 XY7  H3   C5   C6   120.31  3.000
 XY7  H3   C5   C4   119.69  3.000
 XY7  C6   C5   C4   120.00  3.000
 XY7  H4   C1'  C2'  110.78  3.000
 XY7  H4   C1'  O4'  110.52  3.000
 XY7  C2'  C1'  O4'  106.85  3.000
 XY7  H4   C1'  N1   107.03  3.000
 XY7  O4'  C1'  N1   109.77  3.000
 XY7  C2'  C1'  N1   111.92  3.000
 XY7  C4'  O4'  C1'  111.27  3.000
 XY7  H5   C2'  C3'  114.56  3.000
 XY7  H5   C2'  F2'  108.19  3.000
 XY7  C3'  C2'  F2'  109.57  3.000
 XY7  H5   C2'  C1'  114.14  3.000
 XY7  F2'  C2'  C1'  107.98  3.000
 XY7  C3'  C2'  C1'  102.13  3.000
 XY7  H6   C3'  C4'  109.40  3.000
 XY7  H6   C3'  O3'  111.96  3.000
 XY7  C4'  C3'  O3'  110.58  3.000
 XY7  H6   C3'  C2'  107.35  3.000
 XY7  C4'  C3'  C2'  101.24  3.000
 XY7  O3'  C3'  C2'  115.69  3.000
 XY7  H7   O3'  C3'  109.04  3.000
 XY7  H8   C4'  C5'  106.91  3.000
 XY7  H8   C4'  C3'  109.27  3.000
 XY7  C5'  C4'  C3'  116.24  3.000
 XY7  H8   C4'  O4'  109.61  3.000
 XY7  C3'  C4'  O4'  104.24  3.000
 XY7  C5'  C4'  O4'  110.49  3.000
 XY7  H10  C5'  H9   106.96  3.000
 XY7  H10  C5'  O5'  110.72  3.000
 XY7  H9   C5'  O5'  111.75  3.000
 XY7  H10  C5'  C4'  107.96  3.000
 XY7  H9   C5'  C4'  109.03  3.000
 XY7  O5'  C5'  C4'  110.29  3.000
 XY7  P    O5'  C5'  118.10  3.000
 XY7  OP2  P    OP1  100.10  3.000
 XY7  OP2  P    O5'   97.83  3.000
 XY7  OP1  P    O5'   94.89  3.000
 XY7  H11  OP1  P    111.09  3.000
 XY7  H12  OP2  P    111.12  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
 XY7  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 XY7  CONST_02  C6   N1   C2   N3      0.00   0.0  0
 XY7  CONST_03  C1'  N1   C2   N3    180.00   0.0  0
 XY7  CONST_04  C5   C4   N3   C2      0.00   0.0  0
 XY7  CONST_05  O2   C2   N3   C4    180.00   0.0  0
 XY7  CONST_06  O4   C4   N3   C2    180.00   0.0  0
 XY7  CONST_07  O2   C2   N1   C6    180.00   0.0  0
 XY7  CONST_08  C1'  N1   C2   O2      0.00   0.0  0
 XY7  CONST_09  H1   N3   C2   N1    180.00   0.0  0
 XY7  CONST_10  H1   N3   C4   C5    180.00   0.0  0
 XY7  CONST_11  H1   N3   C4   O4      0.00   0.0  0
 XY7  CONST_12  H1   N3   C2   O2      0.00   0.0  0
 XY7  Var_01    H2   C6   C5   C4    179.76  30.0  1
 XY7  Var_02    H3   C5   C4   N3   -179.84  30.0  1
 XY7  Var_03    H2   C6   N1   C2    179.71  30.0  1
 XY7  Var_04    H3   C5   C6   N1    179.98  30.0  1
 XY7  Var_05    H2   C6   N1   C1'    -1.59  30.0  1
 XY7  Var_06    H3   C5   C4   O4      0.14  30.0  1
 XY7  Var_07    P    O5'  C5'  C4'  -148.96  30.0  2
 XY7  Var_08    OP1  P    O5'  C5'   176.05  30.0  2
 XY7  Var_09    OP2  P    O5'  C5'   -83.03  30.0  2
 XY7  Var_10    H9   C5'  O5'  P     -27.51  30.0  3
 XY7  Var_11    H10  C5'  O5'  P      91.61  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
 XY7  chir_01  C1'  N1   C2'  O4'  positiv
 XY7  chir_02  C2'  F2'  C3'  C1'  negativ
 XY7  chir_03  C3'  O3'  C4'  C2'  negativ
 XY7  chir_04  C4'  O4'  C3'  C5'  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
 XY7  plan-1  C4   0.020
 XY7  plan-1  N3   0.020
 XY7  plan-1  C2   0.020
 XY7  plan-1  N1   0.020
 XY7  plan-1  C6   0.020
 XY7  plan-1  C5   0.020
 XY7  plan-1  O4   0.020
 XY7  plan-1  O2   0.020
 XY7  plan-1  C1'  0.020
 XY7  plan-1  H1   0.020

