# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 13:33:37 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: ({[(2S)-1-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxypropan-2-yl]oxy}methyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C[C@@H](CO)OC[P](O)(O)=O)C=C1
#
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
 L8P  L8P  '({[(2S)-1-(4-amino-2-oxopyrimidin-1(2H)-yl)-3-hydroxypropan-2-yl]oxy}methyl)phosphonic acid'  ligand  32  18  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_L8P
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
 L8P  P     P  P     0   1.352   0.7736   2.0288  -0.0541
 L8P  N1    N  NR6   0  -0.510  -0.8858  -1.4729   0.3676
 L8P  C2    C  CR6   0   0.594  -1.5168  -1.3837  -0.8823
 L8P  O2    O  O     0  -0.528  -1.0502  -1.9872  -1.8402
 L8P  N3    N  N     0  -0.546  -2.6445  -0.6486  -0.9716
 L8P  C4    C  CR6   0   0.521  -3.1250  -0.0091   0.0741
 L8P  N4    N  NH2   0  -0.817  -4.2277   0.7268  -0.0877
 L8P  C5    C  CR16  0  -0.463  -2.5243  -0.0986   1.3644
 L8P  C6    C  CR16  0   0.105  -1.4002  -0.8365   1.4433
 L8P  C1'   C  CH2   0  -0.335   0.3700  -2.1918   0.5052
 L8P  C2'   C  CH1   0  -0.003   1.5591  -1.2400   0.5449
 L8P  C3'   C  CH2   0  -0.161   2.8773  -1.9781   0.6912
 L8P  O3'   O  OH1   0  -0.668   3.0482  -2.8574  -0.3915
 L8P  C4'   C  CH2   0  -0.461   2.0585   0.8229  -0.5399
 L8P  O4'   O  O2    0  -0.476   1.5151  -0.4643  -0.6352
 L8P  OP1   O  OH1   0  -0.748   1.6261   3.3844  -0.2064
 L8P  OP2   O  O     0  -0.692  -0.4983   1.9460  -0.8053
 L8P  H5    H  HCR6  0   0.277  -2.9283   0.4061   2.2286
 L8P  H6    H  HCR6  0   0.304  -0.8650  -0.9605   2.3751
 L8P  H1'   H  HCH2  0   0.270   0.3470  -2.7724   1.4290
 L8P  H3'   H  HCH2  0   0.214   3.6912  -1.2427   0.7509
 L8P  H4'   H  HCH2  0   0.286   2.4227   1.1120  -1.5290
 L8P  H1'A  H  HCH2  0   0.279   0.4578  -2.8898  -0.3217
 L8P  H2'   H  HCH1  0   0.232   1.4633  -0.6037   1.4346
 L8P  H3'A  H  HCH2  0   0.207   2.8629  -2.5023   1.6564
 L8P  H4'A  H  HCH2  0   0.257   2.9160   0.8813   0.1418
 L8P  HN4   H  HNH2  0   0.398  -4.6433   0.8217  -0.9983
 L8P  HN4A  H  HNH2  0   0.409  -4.6144   1.2656   0.6662
 L8P  O6    O  OH1   0  -0.742   0.4875   1.8453   1.5203
 L8P  H12   H  HOH1  0   0.460   3.9071  -3.2795  -0.3033
 L8P  H13   H  HOH1  0   0.496   1.1091   4.1979  -0.1264
 L8P  H14   H  HOH1  0   0.488   1.2483   1.9908   2.0976

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
 L8P  P    C4'   single  1.828  0.020  1.828
 L8P  P    OP1   single  1.609  0.020  1.609
 L8P  P    OP2   double  1.479  0.020  1.479
 L8P  N1   C2    single  1.403  0.020  1.403
 L8P  N1   C6    single  1.352  0.020  1.352
 L8P  N1   C1'   single  1.454  0.020  1.454
 L8P  C2   O2    double  1.225  0.020  1.225
 L8P  C2   N3    single  1.349  0.020  1.349
 L8P  N3   C4    double  1.317  0.020  1.317
 L8P  C4   N4    single  1.336  0.020  1.336
 L8P  C4   C5    single  1.426  0.020  1.426
 L8P  N4   HN4   single  0.860  0.020  1.020
 L8P  N4   HN4A  single  0.860  0.020  1.020
 L8P  C5   C6    double  1.347  0.020  1.347
 L8P  C5   H5    single  0.930  0.020  1.080
 L8P  C6   H6    single  0.930  0.020  1.080
 L8P  C1'  C2'   single  1.524  0.020  1.524
 L8P  C1'  H1'   single  0.970  0.020  1.090
 L8P  C1'  H1'A  single  0.970  0.020  1.090
 L8P  C2'  C3'   single  1.518  0.020  1.518
 L8P  C2'  O4'   single  1.413  0.020  1.413
 L8P  C2'  H2'   single  0.970  0.020  1.090
 L8P  C3'  O3'   single  1.405  0.020  1.405
 L8P  C3'  H3'   single  0.970  0.020  1.090
 L8P  C3'  H3'A  single  0.970  0.020  1.090
 L8P  C4'  O4'   single  1.400  0.020  1.400
 L8P  C4'  H4'   single  0.970  0.020  1.090
 L8P  C4'  H4'A  single  0.970  0.020  1.090
 L8P  P    O6    single  1.611  0.020  1.611
 L8P  O3'  H12   single  0.850  0.020  0.980
 L8P  OP1  H13   single  0.850  0.020  0.980
 L8P  O6   H14   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
 L8P  O6    P    OP2  109.71  3.000
 L8P  O6    P    OP1  106.42  3.000
 L8P  OP2   P    OP1  117.05  3.000
 L8P  O6    P    C4'  108.03  3.000
 L8P  OP2   P    C4'  115.62  3.000
 L8P  OP1   P    C4'   99.11  3.000
 L8P  C1'   N1   C6   119.10  3.000
 L8P  C1'   N1   C2   120.28  3.000
 L8P  C6    N1   C2   120.53  3.000
 L8P  N3    C2   O2   122.36  3.000
 L8P  N3    C2   N1   118.00  3.000
 L8P  O2    C2   N1   119.62  3.000
 L8P  C4    N3   C2   121.14  3.000
 L8P  C5    C4   N4   119.47  3.000
 L8P  C5    C4   N3   122.31  3.000
 L8P  N4    C4   N3   118.22  3.000
 L8P  HN4A  N4   HN4  118.04  3.000
 L8P  HN4A  N4   C4   121.52  3.000
 L8P  HN4   N4   C4   120.20  3.000
 L8P  H5    C5   C6   121.45  3.000
 L8P  H5    C5   C4   122.51  3.000
 L8P  C6    C5   C4   116.03  3.000
 L8P  H6    C6   C5   121.75  3.000
 L8P  H6    C6   N1   116.32  3.000
 L8P  C5    C6   N1   121.93  3.000
 L8P  H1'A  C1'  H1'  107.72  3.000
 L8P  H1'A  C1'  C2'  111.00  3.000
 L8P  H1'   C1'  C2'  109.07  3.000
 L8P  H1'A  C1'  N1   108.41  3.000
 L8P  H1'   C1'  N1   108.97  3.000
 L8P  C2'   C1'  N1   111.58  3.000
 L8P  H2'   C2'  O4'  110.84  3.000
 L8P  H2'   C2'  C3'  106.23  3.000
 L8P  O4'   C2'  C3'  112.00  3.000
 L8P  H2'   C2'  C1'  108.36  3.000
 L8P  O4'   C2'  C1'  107.27  3.000
 L8P  C3'   C2'  C1'  112.12  3.000
 L8P  H3'A  C3'  H3'  106.35  3.000
 L8P  H3'A  C3'  O3'  112.33  3.000
 L8P  H3'   C3'  O3'  111.75  3.000
 L8P  H3'A  C3'  C2'  107.78  3.000
 L8P  H3'   C3'  C2'  108.86  3.000
 L8P  O3'   C3'  C2'  109.61  3.000
 L8P  H12   O3'  C3'  108.22  3.000
 L8P  H4'A  C4'  H4'  106.73  3.000
 L8P  H4'A  C4'  O4'  113.24  3.000
 L8P  H4'   C4'  O4'  108.10  3.000
 L8P  H4'A  C4'  P    110.44  3.000
 L8P  H4'   C4'  P    107.47  3.000
 L8P  O4'   C4'  P    110.59  3.000
 L8P  C4'   O4'  C2'  115.83  3.000
 L8P  H13   OP1  P    114.69  3.000
 L8P  H14   O6   P    115.28  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
 L8P  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 L8P  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 L8P  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 L8P  CONST_04  N4    C4   N3   C2    180.00   0.0  0
 L8P  CONST_05  C6    N1   C2   O2    180.00   0.0  0
 L8P  CONST_06  C4    N3   C2   O2    180.00   0.0  0
 L8P  CONST_07  C1'   N1   C2   N3    180.00   0.0  0
 L8P  CONST_08  C1'   N1   C2   O2      0.00   0.0  0
 L8P  CONST_09  HN4   N4   C4   N3      0.00   0.0  0
 L8P  CONST_10  HN4A  N4   C4   N3    180.00   0.0  0
 L8P  Var_01    C2'   C1'  N1   C2    100.70  30.0  3
 L8P  Var_02    OP1   P    C4'  O4'  -173.35  30.0  2
 L8P  Var_03    H4'   C4'  O4'  C2'   151.99  30.0  1

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
 L8P  chir_01  C2'  C1'  C3'  O4'  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
 L8P  plan-1  N1    0.020
 L8P  plan-1  C2    0.020
 L8P  plan-1  O2    0.020
 L8P  plan-1  N3    0.020
 L8P  plan-1  C4    0.020
 L8P  plan-1  N4    0.020
 L8P  plan-1  C5    0.020
 L8P  plan-1  C6    0.020
 L8P  plan-1  C1'   0.020
 L8P  plan-1  H5    0.020
 L8P  plan-1  H6    0.020
 L8P  plan-1  HN4   0.020
 L8P  plan-1  HN4A  0.020

