# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 19:27:11 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: 2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](O[C@@H]1CO[P@](O)(=O)N[P@](O)(=O)O[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
 DUP  DUP  2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine  ligand  44  28  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DUP
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
 DUP  O4    O  OC    0  -0.458   -7.0618  33.6725  1.0388
 DUP  C4    C  CR6   0   0.570   -7.4817  33.1841  2.0698
 DUP  C5    C  CR16  0  -0.494   -7.5415  33.8389  3.3550
 DUP  C6    C  CR16  0   0.097   -8.0372  33.1779  4.4093
 DUP  N3    N  NR16  0  -0.734   -7.9512  31.8807  2.0940
 DUP  C2    C  CR6   0   0.742   -8.5024  31.1991  3.1444
 DUP  O2    O  OC    0  -0.472   -8.9389  30.0749  3.0263
 DUP  N1    N  NR6   0  -0.570   -8.5049  31.8926  4.3451
 DUP  C1'   C  CH1   0   0.188   -9.1304  31.2808  5.5063
 DUP  C2'   C  CH2   0  -0.578   -8.3827  31.4777  6.8248
 DUP  C3'   C  CH1   0   0.016   -9.1891  32.5250  7.5824
 DUP  O3'   O  OH1   0  -0.657   -9.1005  32.3172  8.9632
 DUP  O4'   O  O2    0  -0.518  -10.4099  31.8680  5.6820
 DUP  C4'   C  CH1   0   0.029  -10.6009  32.3002  7.0238
 DUP  C5'   C  CH2   0  -0.262  -11.5165  33.5017  7.0350
 DUP  O5'   O  O2    0  -0.574  -10.8907  34.5963  6.3454
 DUP  PA    P  P     0   1.496  -11.4586  35.1966  4.9885
 DUP  O1A   O  O     0  -0.719  -12.8205  35.8007  5.0738
 DUP  O2A   O  OH1   0  -0.700  -10.3143  36.1945  4.5510
 DUP  N3A   N  NH1   0  -1.000  -11.3650  33.9067  3.9361
 DUP  PB    P  P     0   1.441  -11.9648  33.9322  2.3839
 DUP  O1B   O  O     0  -0.672  -12.1033  35.2957  1.8471
 DUP  O2B   O  OH1   0  -0.708  -10.9972  32.9031  1.6688
 DUP  O3B   O  O2    0  -0.696  -13.3647  33.1165  2.4309
 DUP  PG    P  P     0   1.440  -14.5342  33.2274  3.5749
 DUP  O2G   O  O     0  -0.684  -14.1991  32.4178  4.7612
 DUP  O1G   O  OH1   0  -0.767  -14.7823  34.7672  3.7707
 DUP  O3G   O  OH1   0  -0.714  -15.8246  32.8319  2.7455
 DUP  H5    H  HCR6  0   0.296   -7.1872  34.8523  3.4600
 DUP  H6    H  HCR6  0   0.324   -8.0733  33.6510  5.3796
 DUP  HN3   H  HNR6  0   0.427   -7.9428  31.3775  1.2151
 DUP  H1'   H  HCH1  0   0.292   -9.2436  30.2253  5.2739
 DUP  H2'1  H  HCH2  0   0.295   -8.4074  30.5392  7.3821
 DUP  H2'2  H  HCH2  0   0.297   -7.3363  31.7464  6.6854
 DUP  H1    H  HCH1  0   0.241   -8.8401  33.5325  7.3238
 DUP  H3'   H  HOH1  0   0.461   -9.3850  33.1147  9.4196
 DUP  H4'   H  HCH1  0   0.264  -11.0898  31.5117  7.6104
 DUP  H5'1  H  HCH2  0   0.277  -12.4863  33.2504  6.5971
 DUP  H5'2  H  HCH2  0   0.283  -11.6932  33.8159  8.0639
 DUP  H2A   H  HOH1  0   0.511  -10.5018  37.1266  4.7326
 DUP  H3A   H  HNH1  0   0.466  -11.0616  33.0161  4.3420
 DUP  H2B   H  HOH1  0   0.513  -11.1752  32.7386  0.7314
 DUP  H1G   H  HOH1  0   0.503  -14.0856  35.2378  4.3226
 DUP  H3G   H  HOH1  0   0.510  -16.0597  31.8958  2.7980

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
 DUP  O4   C4    double    1.216  0.020  1.216
 DUP  C4   C5    aromatic  1.444  0.020  1.444
 DUP  C4   N3    aromatic  1.386  0.020  1.386
 DUP  C5   C6    aromatic  1.339  0.020  1.339
 DUP  C5   H5    single    0.930  0.020  1.080
 DUP  C6   N1    aromatic  1.369  0.020  1.369
 DUP  C6   H6    single    0.930  0.020  1.080
 DUP  N3   C2    aromatic  1.368  0.020  1.368
 DUP  N3   HN3   single    0.860  0.020  1.020
 DUP  C2   O2    double    1.212  0.020  1.212
 DUP  C2   N1    aromatic  1.387  0.020  1.387
 DUP  N1   C1'   single    1.454  0.020  1.454
 DUP  C1'  C2'   single    1.528  0.020  1.528
 DUP  C1'  O4'   single    1.419  0.020  1.419
 DUP  C1'  H1'   single    0.970  0.020  1.090
 DUP  C2'  C3'   single    1.524  0.020  1.524
 DUP  C2'  H2'1  single    0.970  0.020  1.090
 DUP  C2'  H2'2  single    0.970  0.020  1.090
 DUP  C3'  O3'   single    1.399  0.020  1.399
 DUP  C3'  C4'   single    1.535  0.020  1.535
 DUP  C3'  H1    single    0.970  0.020  1.090
 DUP  O3'  H3'   single    0.850  0.020  0.980
 DUP  O4'  C4'   single    1.423  0.020  1.423
 DUP  C4'  C5'   single    1.511  0.020  1.511
 DUP  C4'  H4'   single    0.970  0.020  1.090
 DUP  C5'  O5'   single    1.437  0.020  1.437
 DUP  C5'  H5'1  single    0.970  0.020  1.090
 DUP  C5'  H5'2  single    0.970  0.020  1.090
 DUP  O5'  PA    single    1.589  0.020  1.589
 DUP  PA   O1A   double    1.492  0.020  1.492
 DUP  PA   O2A   single    1.580  0.020  1.580
 DUP  PA   N3A   single    1.667  0.020  1.667
 DUP  O2A  H2A   single    0.850  0.020  0.980
 DUP  N3A  PB    single    1.664  0.020  1.664
 DUP  N3A  H3A   single    0.860  0.020  1.020
 DUP  PB   O1B   double    1.472  0.020  1.472
 DUP  PB   O2B   single    1.583  0.020  1.583
 DUP  PB   O3B   single    1.621  0.020  1.621
 DUP  O2B  H2B   single    0.850  0.020  0.980
 DUP  O3B  PG    single    1.640  0.020  1.640
 DUP  PG   O2G   double    1.475  0.020  1.475
 DUP  PG   O1G   single    1.572  0.020  1.572
 DUP  PG   O3G   single    1.584  0.020  1.584
 DUP  O1G  H1G   single    0.850  0.020  0.980
 DUP  O3G  H3G   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
 DUP  N3    C4   C5    113.40  3.000
 DUP  N3    C4   O4    120.65  3.000
 DUP  C5    C4   O4    125.95  3.000
 DUP  H5    C5   C6    120.57  3.000
 DUP  H5    C5   C4    119.95  3.000
 DUP  C6    C5   C4    119.48  3.000
 DUP  H6    C6   N1    116.22  3.000
 DUP  H6    C6   C5    120.22  3.000
 DUP  N1    C6   C5    123.56  3.000
 DUP  HN3   N3   C2    114.97  3.000
 DUP  HN3   N3   C4    116.70  3.000
 DUP  C2    N3   C4    128.21  3.000
 DUP  N1    C2   O2    123.21  3.000
 DUP  N1    C2   N3    114.61  3.000
 DUP  O2    C2   N3    122.17  3.000
 DUP  C1'   N1   C2    118.81  3.000
 DUP  C1'   N1   C6    120.30  3.000
 DUP  C2    N1   C6    120.63  3.000
 DUP  H1'   C1'  O4'   109.55  3.000
 DUP  H1'   C1'  C2'   111.14  3.000
 DUP  O4'   C1'  C2'   106.32  3.000
 DUP  H1'   C1'  N1    106.42  3.000
 DUP  O4'   C1'  N1    108.22  3.000
 DUP  C2'   C1'  N1    115.11  3.000
 DUP  H2'2  C2'  H2'1  107.40  3.000
 DUP  H2'2  C2'  C3'   113.74  3.000
 DUP  H2'1  C2'  C3'   108.97  3.000
 DUP  H2'2  C2'  C1'   113.04  3.000
 DUP  H2'1  C2'  C1'   108.58  3.000
 DUP  C3'   C2'  C1'   104.99  3.000
 DUP  H1    C3'  C4'   109.96  3.000
 DUP  H1    C3'  O3'   110.42  3.000
 DUP  C4'   C3'  O3'   113.31  3.000
 DUP  H1    C3'  C2'   110.22  3.000
 DUP  C4'   C3'  C2'   101.84  3.000
 DUP  O3'   C3'  C2'   110.80  3.000
 DUP  H3'   O3'  C3'   109.05  3.000
 DUP  C4'   O4'  C1'   111.32  3.000
 DUP  H4'   C4'  C5'   107.31  3.000
 DUP  H4'   C4'  O4'   110.22  3.000
 DUP  C5'   C4'  O4'   109.27  3.000
 DUP  H4'   C4'  C3'   108.69  3.000
 DUP  C5'   C4'  C3'   115.99  3.000
 DUP  O4'   C4'  C3'   105.32  3.000
 DUP  H5'2  C5'  H5'1  107.48  3.000
 DUP  H5'2  C5'  O5'   107.69  3.000
 DUP  H5'1  C5'  O5'   111.66  3.000
 DUP  H5'2  C5'  C4'   109.54  3.000
 DUP  H5'1  C5'  C4'   110.60  3.000
 DUP  O5'   C5'  C4'   109.78  3.000
 DUP  PA    O5'  C5'   122.82  3.000
 DUP  N3A   PA   O2A   105.85  3.000
 DUP  N3A   PA   O1A   113.61  3.000
 DUP  O2A   PA   O1A   114.90  3.000
 DUP  N3A   PA   O5'   103.11  3.000
 DUP  O2A   PA   O5'   102.49  3.000
 DUP  O1A   PA   O5'   115.49  3.000
 DUP  H2A   O2A  PA    114.58  3.000
 DUP  H3A   N3A  PB    119.30  3.000
 DUP  H3A   N3A  PA    116.04  3.000
 DUP  PB    N3A  PA    123.82  3.000
 DUP  O3B   PB   O2B   102.35  3.000
 DUP  O3B   PB   O1B   113.30  3.000
 DUP  O2B   PB   O1B   119.66  3.000
 DUP  O3B   PB   N3A   106.05  3.000
 DUP  O2B   PB   N3A   101.01  3.000
 DUP  O1B   PB   N3A   112.85  3.000
 DUP  H2B   O2B  PB    115.80  3.000
 DUP  PG    O3B  PB    127.02  3.000
 DUP  O3G   PG   O1G   100.44  3.000
 DUP  O3G   PG   O2G   117.98  3.000
 DUP  O1G   PG   O2G   118.26  3.000
 DUP  O3G   PG   O3B   101.47  3.000
 DUP  O1G   PG   O3B   105.41  3.000
 DUP  O2G   PG   O3B   111.22  3.000
 DUP  H1G   O1G  PG    114.67  3.000
 DUP  H3G   O3G  PG    114.30  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
 DUP  CONST_01  N1    C6   C5   C4     0.00   0.0  0
 DUP  CONST_02  N1    C2   N3   C4     0.00   0.0  0
 DUP  CONST_03  C2    N3   C4   C5     0.00   0.0  0
 DUP  CONST_04  C2    N1   C6   C5     0.00   0.0  0
 DUP  CONST_05  N3    C4   C5   C6     0.00   0.0  0
 DUP  CONST_06  N3    C2   N1   C6     0.00   0.0  0
 DUP  CONST_07  C1'   N1   C6   C5   180.00   0.0  0
 DUP  CONST_08  C1'   N1   C2   N3   180.00   0.0  0
 DUP  CONST_09  C6    C5   C4   O4   180.00   0.0  0
 DUP  CONST_10  C2    N3   C4   O4   180.00   0.0  0
 DUP  CONST_11  O2    C2   N3   C4   180.00   0.0  0
 DUP  CONST_12  O2    C2   N1   C6   180.00   0.0  0
 DUP  CONST_13  C1'   N1   C2   O2     0.00   0.0  0
 DUP  CONST_14  H6    C6   C5   C4   180.00   0.0  0
 DUP  CONST_15  HN3   N3   C4   C5   180.00   0.0  0
 DUP  CONST_16  H5    C5   C4   N3   180.00   0.0  0
 DUP  Var_01    O1A   PA   O5'  C5'   62.55  30.0  3
 DUP  Var_02    PB    N3A  PA   O5'  174.20  30.0  3
 DUP  Var_03    O1B   PB   N3A  PA    22.41  30.0  3
 DUP  Var_04    O2G   PG   O3B  PB   -81.15  30.0  3
 DUP  Var_05    H5'1  C5'  O5'  PA    -8.57  30.0  2

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
 DUP  chir_01  C1'  N1   C2'  O4'  negativ
 DUP  chir_02  C3'  O3'  C4'  C2'  positiv
 DUP  chir_03  C4'  O4'  C3'  C5'  negativ
 DUP  chir_04  PA   O1A  O2A  N3A  both
 DUP  chir_05  PB   O2B  O1B  N3A  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
 DUP  plan-1  O4   0.020
 DUP  plan-1  C4   0.020
 DUP  plan-1  C5   0.020
 DUP  plan-1  C6   0.020
 DUP  plan-1  N3   0.020
 DUP  plan-1  C2   0.020
 DUP  plan-1  O2   0.020
 DUP  plan-1  N1   0.020
 DUP  plan-1  C1'  0.020
 DUP  plan-1  H5   0.020
 DUP  plan-1  H6   0.020
 DUP  plan-1  HN3  0.020

