# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 10:21:01 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  30  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   1.173   0.7053   2.0239   0.1119
 L8P  N1    N  NR6    0  -0.499  -0.8458  -1.3642   0.3729
 L8P  C2    C  CR6    0   0.590  -1.4968  -1.3510  -0.8639
 L8P  O2    O  O      0  -0.545  -1.0413  -2.0015  -1.8003
 L8P  N3    N  N      0  -0.554  -2.6478  -0.6557  -0.9711
 L8P  C4    C  CR6    0   0.515  -3.1094   0.0410   0.0453
 L8P  N4    N  NH2    0  -0.826  -4.2472   0.7324  -0.1337
 L8P  C5    C  CR16   0  -0.464  -2.4834   0.0415   1.3183
 L8P  C6    C  CR16   0   0.150  -1.3321  -0.6541   1.4111
 L8P  C1'   C  CH2    0  -0.329   0.4031  -2.0921   0.5385
 L8P  C2'   C  CH1    0   0.011   1.6104  -1.1619   0.5106
 L8P  C3'   C  CH2    0  -0.165   2.9048  -1.9170   0.7560
 L8P  O3'   O  OH1    0  -0.675   3.0682  -2.9335  -0.2080
 L8P  C4'   C  CH2    0  -0.467   1.9838   0.8812  -0.6375
 L8P  O4'   O  O2     0  -0.500   1.6241  -0.4934  -0.7226
 L8P  OP1   O  OP    -1  -0.915   1.3708   3.3981  -0.0858
 L8P  OP2   O  O      0  -0.872  -0.5663   1.8262  -0.7135
 L8P  H5    H  HCR6   0   0.259  -2.8684   0.6078   2.1526
 L8P  H6    H  HCR6   0   0.282  -0.7632  -0.6985   2.3273
 L8P  H1'   H  HCH2   0   0.246   0.3723  -2.6218   1.4936
 L8P  H3'   H  HCH2   0   0.203   3.7354  -1.1986   0.7276
 L8P  H4'   H  HCH2   0   0.183   2.1747   1.1929  -1.6707
 L8P  H1'A  H  HCH2   0   0.259   0.4651  -2.8386  -0.2477
 L8P  H2'   H  HCH1   0   0.235   1.5017  -0.4408   1.3286
 L8P  H3'A  H  HCH2   0   0.187   2.8802  -2.3253   1.7761
 L8P  H4'A  H  HCH2   0   0.158   2.9469   0.9925  -0.1112
 L8P  HN4   H  HNH2   0   0.389  -4.6237   0.8299  -1.0608
 L8P  HN4A  H  HNH2   0   0.400  -4.5633   1.3841   0.5619
 L8P  O6    O  OP    -1  -0.882   0.5894   1.6273   1.5933
 L8P  H12   H  HOH1   0   0.453   3.9265  -3.3415  -0.0675

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  1.871  0.020  1.871
 L8P  P    OP1   deloc   1.540  0.020  1.540
 L8P  P    OP2   deloc   1.529  0.020  1.529
 L8P  N1   C2    single  1.398  0.020  1.398
 L8P  N1   C6    single  1.349  0.020  1.349
 L8P  N1   C1'   single  1.455  0.020  1.455
 L8P  C2   O2    double  1.228  0.020  1.228
 L8P  C2   N3    single  1.349  0.020  1.349
 L8P  N3   C4    double  1.316  0.020  1.316
 L8P  C4   N4    single  1.343  0.020  1.343
 L8P  C4   C5    single  1.419  0.020  1.419
 L8P  N4   HN4   single  0.860  0.020  1.020
 L8P  N4   HN4A  single  0.860  0.020  1.020
 L8P  C5   C6    double  1.348  0.020  1.348
 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  1.519  0.020  1.519
 L8P  C2'  O4'   single  1.403  0.020  1.403
 L8P  C2'  H2'   single  0.970  0.020  1.090
 L8P  C3'  O3'   single  1.410  0.020  1.410
 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  1.423  0.020  1.423
 L8P  C4'  H4'   single  0.970  0.020  1.090
 L8P  C4'  H4'A  single  0.970  0.020  1.090
 L8P  P    O6    deloc   1.538  0.020  1.538
 L8P  O3'  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
 L8P  O6    P    OP2  115.09  3.000
 L8P  O6    P    OP1  112.73  3.000
 L8P  OP2   P    OP1  113.93  3.000
 L8P  O6    P    C4'  106.25  3.000
 L8P  OP2   P    C4'  105.85  3.000
 L8P  OP1   P    C4'  101.44  3.000
 L8P  C1'   N1   C6   119.04  3.000
 L8P  C1'   N1   C2   120.35  3.000
 L8P  C6    N1   C2   120.55  3.000
 L8P  N3    C2   O2   121.94  3.000
 L8P  N3    C2   N1   118.20  3.000
 L8P  O2    C2   N1   119.81  3.000
 L8P  C4    N3   C2   120.72  3.000
 L8P  C5    C4   N4   119.55  3.000
 L8P  C5    C4   N3   122.58  3.000
 L8P  N4    C4   N3   117.82  3.000
 L8P  HN4A  N4   HN4  117.25  3.000
 L8P  HN4A  N4   C4   120.55  3.000
 L8P  HN4   N4   C4   119.34  3.000
 L8P  H5    C5   C6   121.48  3.000
 L8P  H5    C5   C4   122.43  3.000
 L8P  C6    C5   C4   116.00  3.000
 L8P  H6    C6   C5   121.98  3.000
 L8P  H6    C6   N1   116.21  3.000
 L8P  C5    C6   N1   121.78  3.000
 L8P  H1'A  C1'  H1'  107.54  3.000
 L8P  H1'A  C1'  C2'  111.16  3.000
 L8P  H1'   C1'  C2'  109.52  3.000
 L8P  H1'A  C1'  N1   108.09  3.000
 L8P  H1'   C1'  N1   108.53  3.000
 L8P  C2'   C1'  N1   111.87  3.000
 L8P  H2'   C2'  O4'  110.09  3.000
 L8P  H2'   C2'  C3'  106.93  3.000
 L8P  O4'   C2'  C3'  111.75  3.000
 L8P  H2'   C2'  C1'  108.02  3.000
 L8P  O4'   C2'  C1'  108.34  3.000
 L8P  C3'   C2'  C1'  111.64  3.000
 L8P  H3'A  C3'  H3'  106.49  3.000
 L8P  H3'A  C3'  O3'  111.67  3.000
 L8P  H3'   C3'  O3'  111.48  3.000
 L8P  H3'A  C3'  C2'  108.40  3.000
 L8P  H3'   C3'  C2'  108.37  3.000
 L8P  O3'   C3'  C2'  110.29  3.000
 L8P  H12   O3'  C3'  108.04  3.000
 L8P  H4'A  C4'  H4'  105.60  3.000
 L8P  H4'A  C4'  O4'  110.27  3.000
 L8P  H4'   C4'  O4'  105.21  3.000
 L8P  H4'A  C4'  P    110.11  3.000
 L8P  H4'   C4'  P    108.84  3.000
 L8P  O4'   C4'  P    116.17  3.000
 L8P  C4'   O4'  C2'  114.21  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    101.43  30.0  3
 L8P  Var_02    OP1   P    C4'  O4'  -174.79  30.0  3
 L8P  Var_03    H4'   C4'  O4'  C2'   167.26  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

