# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 16:40:09 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  41  25  .  2021-08-04  2021-08-04  
;
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  -0.569  -2.8978   0.3164   0.1066
 44P  C2    C  CR6   0   0.742  -3.8126   1.0225   0.8701
 44P  O2    O  O     0  -0.472  -4.3694   0.5581   1.8412
 44P  N3    N  NR16  0  -0.736  -4.0478   2.2996   0.4371
 44P  C4    C  CR6   0   0.572  -3.4714   2.9616  -0.6366
 44P  O4    O  O     0  -0.458  -3.7825   4.1076  -0.8970
 44P  C5    C  CR16  0  -0.510  -2.5125   2.1596  -1.3580
 44P  C6    C  CR16  0   0.106  -2.2747   0.9016  -0.9624
 44P  PA    P  P     0   1.376   2.1176  -0.1506  -0.4730
 44P  PB    P  P     0   1.376   4.4096   1.6035   0.3154
 44P  C1'   C  CH1   0   0.196  -2.5632  -1.0418   0.4810
 44P  O1A   O  OH1   0  -0.737   0.9461   0.9351  -0.3493
 44P  O1B   O  O     0  -0.702   3.7025   2.7656  -0.2646
 44P  C2'   C  CH1   0  -0.037  -2.7733  -2.0721  -0.6231
 44P  O2'   O  OH1   0  -0.651  -4.1216  -2.4203  -0.6938
 44P  O2A   O  O     0  -0.693   2.6245  -0.1878  -1.8610
 44P  O2B   O  OH1   0  -0.739   5.1930   1.8427   1.6931
 44P  C3'   C  CH1   0  -0.045  -1.8390  -3.1905  -0.1522
 44P  O3'   O  OH1   0  -0.665  -2.4265  -3.9362   0.8804
 44P  C3A   C  CH2   0  -1.033   3.3467   0.2218   0.7956
 44P  O3B   O  OH1   0  -0.739   5.4745   1.0355  -0.7376
 44P  C4'   C  CH1   0  -0.014  -0.6735  -2.3941   0.4333
 44P  O4'   O  O2    0  -0.499  -1.1958  -1.1121   0.7981
 44P  C5'   C  CH2   0  -0.191   0.4698  -2.2272  -0.5434
 44P  O5'   O  O2    0  -0.589   1.5316  -1.5255   0.1087
 44P  H5    H  HCR6  0   0.297  -1.9956   2.5764  -2.2082
 44P  H6    H  HCR6  0   0.317  -1.5591   0.2875  -1.4879
 44P  H1'   H  HCH1  0   0.280  -3.1841  -1.2938   1.3428
 44P  HO1A  H  HOH1  0   0.489   0.4413   0.9209   0.4751
 44P  H2'   H  HCH1  0   0.253  -2.4060  -1.6871  -1.5833
 44P  HO2'  H  HOH1  0   0.472  -4.3034  -2.7972  -1.5603
 44P  HO2B  H  HOH1  0   0.499   5.7736   2.6169   1.6918
 44P  H3'   H  HCH1  0   0.259  -1.5198  -3.8309  -0.9848
 44P  HO3'  H  HOH1  0   0.452  -3.3156  -4.1837   0.6006
 44P  H3A   H  HCH2  0   0.340   2.8463   0.4655   1.7356
 44P  H3AA  H  HCH2  0   0.342   3.9518  -0.6699   0.9750
 44P  HO3B  H  HOH1  0   0.493   6.0325   0.3106  -0.4273
 44P  H4'   H  HCH1  0   0.274  -0.2975  -2.8942   1.3316
 44P  H5'   H  HCH2  0   0.272   0.8465  -3.2085  -0.8346
 44P  H5'A  H  HCH2  0   0.241   0.1457  -1.7163  -1.4556
 44P  HN3   H  HNR6  0   0.429  -4.7247   2.8200   0.9824

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  1.448  0.020  1.448
 44P  C6   N1    single  1.369  0.020  1.369
 44P  N1   C2    single  1.385  0.020  1.385
 44P  C2   O2    double  1.212  0.020  1.212
 44P  C2   N3    single  1.369  0.020  1.369
 44P  C4   N3    single  1.387  0.020  1.387
 44P  C5   C4    single  1.443  0.020  1.443
 44P  C4   O4    double  1.216  0.020  1.216
 44P  C6   C5    double  1.340  0.020  1.340
 44P  C5   H5    single  0.930  0.020  1.080
 44P  C6   H6    single  0.930  0.020  1.080
 44P  C3A  PA    single  1.805  0.020  1.805
 44P  O2A  PA    double  1.478  0.020  1.478
 44P  PA   O1A   single  1.602  0.020  1.602
 44P  PA   O5'   single  1.604  0.020  1.604
 44P  O1B  PB    double  1.479  0.020  1.479
 44P  O3B  PB    single  1.602  0.020  1.602
 44P  O2B  PB    single  1.603  0.020  1.603
 44P  PB   C3A   single  1.808  0.020  1.808
 44P  C2'  C1'   single  1.525  0.020  1.525
 44P  O4'  C1'   single  1.405  0.020  1.405
 44P  C1'  H1'   single  0.970  0.020  1.090
 44P  O1A  HO1A  single  0.850  0.020  0.980
 44P  C3'  C2'   single  1.531  0.020  1.531
 44P  C2'  O2'   single  1.394  0.020  1.394
 44P  C2'  H2'   single  0.970  0.020  1.090
 44P  O2'  HO2'  single  0.850  0.020  0.980
 44P  O2B  HO2B  single  0.850  0.020  0.980
 44P  C3'  C4'   single  1.528  0.020  1.528
 44P  C3'  O3'   single  1.403  0.020  1.403
 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  O3B  HO3B  single  0.850  0.020  0.980
 44P  C5'  C4'   single  1.513  0.020  1.513
 44P  C4'  O4'   single  1.432  0.020  1.432
 44P  C4'  H4'   single  0.970  0.020  1.090
 44P  O5'  C5'   single  1.430  0.020  1.430
 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   119.85  3.000
 44P  C6    N1   C2   120.88  3.000
 44P  C1'   N1   C2   119.22  3.000
 44P  N3    C2   O2   122.14  3.000
 44P  N3    C2   N1   114.50  3.000
 44P  O2    C2   N1   123.36  3.000
 44P  HN3   N3   C4   116.70  3.000
 44P  HN3   N3   C2   115.07  3.000
 44P  C4    N3   C2   128.23  3.000
 44P  C5    C4   O4   125.93  3.000
 44P  O4    C4   N3   120.63  3.000
 44P  C5    C4   N3   113.45  3.000
 44P  H5    C5   C6   120.69  3.000
 44P  H5    C5   C4   119.84  3.000
 44P  C6    C5   C4   119.47  3.000
 44P  H6    C6   C5   120.53  3.000
 44P  H6    C6   N1   116.03  3.000
 44P  C5    C6   N1   123.45  3.000
 44P  O5'   PA   C3A   99.83  3.000
 44P  O5'   PA   O2A  116.38  3.000
 44P  C3A   PA   O2A  115.57  3.000
 44P  O5'   PA   O1A  106.61  3.000
 44P  O2A   PA   O1A  109.90  3.000
 44P  C3A   PA   O1A  107.69  3.000
 44P  O3B   PB   C3A  107.13  3.000
 44P  C3A   PB   O2B   99.97  3.000
 44P  O3B   PB   O2B  107.04  3.000
 44P  C3A   PB   O1B  115.06  3.000
 44P  O2B   PB   O1B  116.97  3.000
 44P  O3B   PB   O1B  109.80  3.000
 44P  H1'   C1'  O4'  111.33  3.000
 44P  H1'   C1'  C2'  109.72  3.000
 44P  O4'   C1'  C2'  105.28  3.000
 44P  H1'   C1'  N1   106.81  3.000
 44P  O4'   C1'  N1   109.27  3.000
 44P  C2'   C1'  N1   114.50  3.000
 44P  HO1A  O1A  PA   115.96  3.000
 44P  H2'   C2'  C3'  108.72  3.000
 44P  H2'   C2'  O2'  111.52  3.000
 44P  C3'   C2'  O2'  115.04  3.000
 44P  H2'   C2'  C1'  110.51  3.000
 44P  O2'   C2'  C1'  109.79  3.000
 44P  C3'   C2'  C1'  100.76  3.000
 44P  HO2'  O2'  C2'  109.03  3.000
 44P  HO2B  O2B  PB   114.30  3.000
 44P  H3'   C3'  C4'  111.89  3.000
 44P  H3'   C3'  O3'  111.72  3.000
 44P  C4'   C3'  O3'  108.32  3.000
 44P  H3'   C3'  C2'  111.73  3.000
 44P  O3'   C3'  C2'  111.04  3.000
 44P  C4'   C3'  C2'  101.68  3.000
 44P  HO3'  O3'  C3'  107.99  3.000
 44P  H3AA  C3A  H3A  107.13  3.000
 44P  H3AA  C3A  PB   109.98  3.000
 44P  H3A   C3A  PB   109.11  3.000
 44P  H3AA  C3A  PA   108.91  3.000
 44P  H3A   C3A  PA   109.81  3.000
 44P  PB    C3A  PA   111.79  3.000
 44P  HO3B  O3B  PB   116.04  3.000
 44P  H4'   C4'  C5'  108.70  3.000
 44P  H4'   C4'  O4'  108.99  3.000
 44P  C5'   C4'  O4'  109.96  3.000
 44P  H4'   C4'  C3'  109.77  3.000
 44P  O4'   C4'  C3'  106.62  3.000
 44P  C5'   C4'  C3'  112.73  3.000
 44P  C4'   O4'  C1'  110.02  3.000
 44P  H5'A  C5'  H5'  107.44  3.000
 44P  H5'A  C5'  O5'  111.77  3.000
 44P  H5'   C5'  O5'  107.86  3.000
 44P  H5'A  C5'  C4'  111.45  3.000
 44P  H5'   C5'  C4'  109.52  3.000
 44P  O5'   C5'  C4'  108.72  3.000
 44P  C5'   O5'  PA   121.78  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  -122.77  30.0  3
 44P  Var_02    O1B  PB   C3A  PA    44.85  30.0  2
 44P  Var_03    O2A  PA   C3A  PB    45.02  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
 44P  chir_06  PA   O2A  O1A  O5'  both

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

