# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 21:44:47 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)C[P](O)(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
 44P  44P  5'-O-[(S)-hydroxy(phosphonomethyl)phosphoryl]uridine  ligand  38  25  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_44P
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
 44P  N1    N  NR6    0  -0.482  -2.4964   0.2945   0.2955
 44P  C2    C  CR6    0   0.717  -3.5239   1.0208   0.8600
 44P  O2    O  O      0  -0.526  -4.4531   0.5168   1.4594
 44P  N3    N  NR16   0  -0.596  -3.4224   2.3757   0.6900
 44P  C4    C  CR6    0   0.584  -2.4015   3.0889   0.0741
 44P  O4    O  O      0  -0.587  -2.4431   4.3067   0.0402
 44P  C5    C  CR16   0  -0.405  -1.3716   2.2529  -0.4828
 44P  C6    C  CR16   0   0.050  -1.4714   0.9187  -0.3652
 44P  PA    P  P      0   1.221   2.0557  -0.5138  -0.8322
 44P  PB    P  P      0   1.140   2.5659   2.4289   0.1138
 44P  C1'   C  CH1    0   0.134  -2.4328  -1.1394   0.5371
 44P  O1A   O  OP    -1  -0.787   1.0853  -0.1966  -1.9494
 44P  O1B   O  O      0  -0.906   1.7570   2.9106  -1.0992
 44P  C2'   C  CH1    0  -0.077  -2.7061  -2.0132  -0.6820
 44P  O2'   O  OH1    0  -0.674  -4.0819  -2.1346  -0.8884
 44P  O2A   O  O      0  -0.889   3.4828  -0.8416  -1.1861
 44P  O2B   O  OP    -1  -1.003   2.2780   3.2119   1.4022
 44P  C3'   C  CH1    0  -0.021  -1.9981  -3.3065  -0.2610
 44P  O3'   O  OH1    0  -0.662  -2.7639  -4.0144   0.6804
 44P  C3A   C  CH2    0  -0.955   1.9634   0.6973   0.5043
 44P  O3B   O  OP    -1  -0.950   4.0630   2.2811  -0.1800
 44P  C4'   C  CH1    0  -0.004  -0.7533  -2.7467   0.4159
 44P  O4'   O  O2     0  -0.517  -1.1385  -1.4731   0.9490
 44P  C5'   C  CH2    0  -0.136   0.3915  -2.6172  -0.5796
 44P  O5'   O  O2     0  -0.632   1.4615  -1.8895  -0.0479
 44P  H5    H  HCR6   0   0.318  -0.4760   2.6765  -0.9245
 44P  H6    H  HCR6   0   0.313  -0.7034   0.2887  -0.8006
 44P  H1'   H  HCH1   0   0.335  -3.1711  -1.3522   1.3141
 44P  H2'   H  HCH1   0   0.288  -2.1991  -1.5949  -1.5613
 44P  HO2'  H  HOH1   0   0.461  -4.2357  -2.4324  -1.7905
 44P  H3'   H  HCH1   0   0.277  -1.7436  -3.9332  -1.1269
 44P  HO3'  H  HOH1   0   0.437  -3.6682  -4.0646   0.3493
 44P  H3A   H  HCH2   0   0.252   0.9249   0.7535   0.8398
 44P  H3AA  H  HCH2   0   0.292   2.5412   0.3162   1.3537
 44P  H4'   H  HCH1   0   0.173  -0.4431  -3.3796   1.2536
 44P  H5'   H  HCH2   0   0.249   0.7117  -3.6380  -0.8281
 44P  H5'A  H  HCH2   0   0.186   0.0332  -2.1665  -1.5099
 44P  HN3   H  HNR6   0   0.382  -4.1769   2.9152   1.0958

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
 44P  C1'  N1    single  1.455  0.020  1.455
 44P  C6   N1    single  1.370  0.020  1.370
 44P  N1   C2    single  1.379  0.020  1.379
 44P  C2   O2    double  1.215  0.020  1.215
 44P  C2   N3    single  1.369  0.020  1.369
 44P  C4   N3    single  1.389  0.020  1.389
 44P  C5   C4    single  1.439  0.020  1.439
 44P  C4   O4    double  1.219  0.020  1.219
 44P  C6   C5    double  1.343  0.020  1.343
 44P  C5   H5    single  0.930  0.020  1.080
 44P  C6   H6    single  0.930  0.020  1.080
 44P  C3A  PA    single  1.806  0.020  1.806
 44P  O2A  PA    deloc   1.506  0.020  1.506
 44P  PA   O1A   deloc   1.513  0.020  1.513
 44P  PA   O5'   single  1.691  0.020  1.691
 44P  O1B  PB    deloc   1.535  0.020  1.535
 44P  O3B  PB    deloc   1.533  0.020  1.533
 44P  O2B  PB    deloc   1.535  0.020  1.535
 44P  PB   C3A   single  1.874  0.020  1.874
 44P  C2'  C1'   single  1.525  0.020  1.525
 44P  O4'  C1'   single  1.399  0.020  1.399
 44P  C1'  H1'   single  0.970  0.020  1.090
 44P  C3'  C2'   single  1.533  0.020  1.533
 44P  C2'  O2'   single  1.397  0.020  1.397
 44P  C2'  H2'   single  0.970  0.020  1.090
 44P  O2'  HO2'  single  0.850  0.020  0.980
 44P  C3'  C4'   single  1.524  0.020  1.524
 44P  C3'  O3'   single  1.405  0.020  1.405
 44P  C3'  H3'   single  0.970  0.020  1.090
 44P  O3'  HO3'  single  0.850  0.020  0.980
 44P  C3A  H3A   single  0.970  0.020  1.090
 44P  C3A  H3AA  single  0.970  0.020  1.090
 44P  C5'  C4'   single  1.523  0.020  1.523
 44P  C4'  O4'   single  1.433  0.020  1.433
 44P  C4'  H4'   single  0.970  0.020  1.090
 44P  O5'  C5'   single  1.399  0.020  1.399
 44P  C5'  H5'   single  0.970  0.020  1.090
 44P  C5'  H5'A  single  0.970  0.020  1.090
 44P  N3   HN3   single  0.860  0.020  1.020

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
 44P  C1'   N1   C6   119.75  3.000
 44P  C6    N1   C2   120.99  3.000
 44P  C1'   N1   C2   118.92  3.000
 44P  N3    C2   O2   121.89  3.000
 44P  N3    C2   N1   114.52  3.000
 44P  O2    C2   N1   123.58  3.000
 44P  HN3   N3   C4   116.86  3.000
 44P  HN3   N3   C2   114.98  3.000
 44P  C4    N3   C2   128.13  3.000
 44P  C5    C4   O4   126.45  3.000
 44P  O4    C4   N3   120.00  3.000
 44P  C5    C4   N3   113.54  3.000
 44P  H5    C5   C6   119.00  3.000
 44P  H5    C5   C4   121.46  3.000
 44P  C6    C5   C4   119.35  3.000
 44P  H6    C6   C5   119.30  3.000
 44P  H6    C6   N1   117.30  3.000
 44P  C5    C6   N1   123.40  3.000
 44P  O5'   PA   C3A  100.62  3.000
 44P  O5'   PA   O2A  105.35  3.000
 44P  C3A   PA   O2A  111.60  3.000
 44P  O5'   PA   O1A  106.71  3.000
 44P  O2A   PA   O1A  118.66  3.000
 44P  C3A   PA   O1A  111.90  3.000
 44P  O3B   PB   C3A  105.35  3.000
 44P  C3A   PB   O2B  103.66  3.000
 44P  O3B   PB   O2B  113.15  3.000
 44P  C3A   PB   O1B  106.56  3.000
 44P  O2B   PB   O1B  113.85  3.000
 44P  O3B   PB   O1B  113.16  3.000
 44P  H1'   C1'  O4'  111.68  3.000
 44P  H1'   C1'  C2'  109.63  3.000
 44P  O4'   C1'  C2'  105.35  3.000
 44P  H1'   C1'  N1   106.27  3.000
 44P  O4'   C1'  N1   108.93  3.000
 44P  C2'   C1'  N1   115.09  3.000
 44P  H2'   C2'  C3'  109.15  3.000
 44P  H2'   C2'  O2'  111.70  3.000
 44P  C3'   C2'  O2'  114.97  3.000
 44P  H2'   C2'  C1'  109.84  3.000
 44P  O2'   C2'  C1'  110.16  3.000
 44P  C3'   C2'  C1'  100.43  3.000
 44P  HO2'  O2'  C2'  108.84  3.000
 44P  H3'   C3'  C4'  111.75  3.000
 44P  H3'   C3'  O3'  111.52  3.000
 44P  C4'   C3'  O3'  109.44  3.000
 44P  H3'   C3'  C2'  111.82  3.000
 44P  O3'   C3'  C2'  110.93  3.000
 44P  C4'   C3'  C2'  100.91  3.000
 44P  HO3'  O3'  C3'  107.90  3.000
 44P  H3AA  C3A  H3A  106.32  3.000
 44P  H3AA  C3A  PB   108.26  3.000
 44P  H3A   C3A  PB   108.78  3.000
 44P  H3AA  C3A  PA   108.27  3.000
 44P  H3A   C3A  PA   108.07  3.000
 44P  PB    C3A  PA   116.67  3.000
 44P  H4'   C4'  C5'  109.66  3.000
 44P  H4'   C4'  O4'  107.77  3.000
 44P  C5'   C4'  O4'  111.70  3.000
 44P  H4'   C4'  C3'  111.04  3.000
 44P  O4'   C4'  C3'  105.79  3.000
 44P  C5'   C4'  C3'  110.79  3.000
 44P  C4'   O4'  C1'  110.55  3.000
 44P  H5'A  C5'  H5'  106.62  3.000
 44P  H5'A  C5'  O5'  111.06  3.000
 44P  H5'   C5'  O5'  110.27  3.000
 44P  H5'A  C5'  C4'  110.17  3.000
 44P  H5'   C5'  C4'  106.75  3.000
 44P  O5'   C5'  C4'  111.76  3.000
 44P  C5'   O5'  PA   121.03  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
 44P  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 44P  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 44P  CONST_03  C1'  N1   C2   N3   180.00   0.0  0
 44P  CONST_04  C6   N1   C2   N3     0.00   0.0  0
 44P  CONST_05  O4   C4   N3   C2   180.00   0.0  0
 44P  CONST_06  C1'  N1   C2   O2     0.00   0.0  0
 44P  CONST_07  C6   N1   C2   O2   180.00   0.0  0
 44P  CONST_08  C4   N3   C2   O2   180.00   0.0  0
 44P  CONST_09  HN3  N3   C2   N1   180.00   0.0  0
 44P  Var_01    C4'  C5'  O5'  PA  -124.03  30.0  3
 44P  Var_02    O1B  PB   C3A  PA    56.29  30.0  3
 44P  Var_03    O2A  PA   C3A  PB    67.52  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
 44P  chir_02  C1'  N1   C2'  O4'  negativ
 44P  chir_03  C2'  O2'  C3'  C1'  positiv
 44P  chir_04  C3'  O3'  C4'  C2'  positiv
 44P  chir_05  C4'  O4'  C3'  C5'  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
 44P  plan-1  N1   0.020
 44P  plan-1  C2   0.020
 44P  plan-1  O2   0.020
 44P  plan-1  N3   0.020
 44P  plan-1  C4   0.020
 44P  plan-1  O4   0.020
 44P  plan-1  C5   0.020
 44P  plan-1  C6   0.020
 44P  plan-1  C1'  0.020
 44P  plan-1  H5   0.020
 44P  plan-1  H6   0.020
 44P  plan-1  HN3  0.020

