# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:41:56 2022
#   Inital geometry file: a 147 line input string
#   Ligand name: (2R,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H](O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](N)[C@@H]1O
#
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
 T3Q  T3Q  '(2R,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  60  35  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_T3Q
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
 T3Q  O4    O  O      0  -0.456  -5.7900  -3.1904   2.3118
 T3Q  C4    C  CR6    0   0.558  -5.3039  -2.5339   1.4086
 T3Q  N3    N  NR16   0  -0.733  -5.2560  -1.1543   1.4870
 T3Q  C2    C  CR6    0   0.743  -4.7508  -0.2703   0.5686
 T3Q  O2    O  O      0  -0.472  -4.7605   0.9273   0.7615
 T3Q  C5    C  CR6    0  -0.185  -4.7369  -3.0809   0.1932
 T3Q  C5M   C  CH3    0  -0.706  -4.7253  -4.5621   0.0042
 T3Q  C6    C  CR16   0   0.058  -4.2419  -2.2192  -0.7120
 T3Q  N1    N  NR6    0  -0.566  -4.2477  -0.8556  -0.5700
 T3Q  C1'   C  CH1    0   0.217  -3.6316  -0.0282  -1.6091
 T3Q  O4'   O  O2     0  -0.481  -2.4744   0.5646  -1.0985
 T3Q  C2'   C  CH2    0  -0.562  -4.5045   1.0869  -2.1915
 T3Q  C3'   C  CH1    0   0.022  -3.8442   2.3863  -1.7298
 T3Q  O3'   O  OH1    0  -0.669  -3.8049   3.4026  -2.7007
 T3Q  C4'   C  CH1    0   0.012  -2.4126   1.9431  -1.4219
 T3Q  C5'   C  CH2    0  -0.152  -1.7988   2.7130  -0.2789
 T3Q  O5'   O  O2     0  -0.617  -0.4468   2.3412  -0.1316
 T3Q  PA    P  P      0   1.361   0.3670   2.9303   1.1687
 T3Q  O1A   O  O      0  -0.806  -0.2834   2.4693   2.4347
 T3Q  O2A   O  OP    -1  -0.797   0.6531   4.3841   0.9513
 T3Q  O3A   O  O2     0  -0.735   1.7716   2.1307   0.9078
 T3Q  PB    P  P      0   1.345   2.1212   0.6232   1.4724
 T3Q  O1B   O  OP    -1  -0.775   1.0377  -0.3323   1.0954
 T3Q  O2B   O  O      0  -0.796   2.6361   0.7011   2.8747
 T3Q  O3B   O  O2     0  -0.633   3.4052   0.4391   0.4393
 T3Q  O4Q   O  OH1    0  -0.668   3.9785  -2.9586  -2.3998
 T3Q  C4Q   C  CH1    0   0.058   4.5490  -2.3987  -1.2410
 T3Q  C5Q   C  CH1    0   0.017   3.5292  -2.3659  -0.0964
 T3Q  O5Q   O  O2     0  -0.509   4.0775  -1.7025   1.0362
 T3Q  C6Q   C  CH3    0  -0.706   3.1195  -3.7492   0.3671
 T3Q  C3Q   C  CH1    0  -0.159   5.0364  -0.9910  -1.5733
 T3Q  N3Q   N  NH2    0  -0.786   6.0390  -1.0384  -2.6227
 T3Q  C2Q   C  CH1    0   0.013   5.5317  -0.3293  -0.2838
 T3Q  O2Q   O  OH1    0  -0.667   5.9198   0.9880  -0.5811
 T3Q  C1Q   C  CH1    0   0.258   4.4693  -0.3800   0.8142
 T3Q  HN3   H  HNR6   0   0.425  -5.6358  -0.7320   2.3254
 T3Q  H5M   H  HCH3   0   0.247  -4.1689  -5.0603   0.7991
 T3Q  H5MA  H  HCH3   0   0.246  -5.7365  -4.9711   0.0130
 T3Q  H5MB  H  HCH3   0   0.246  -4.2648  -4.8296  -0.9454
 T3Q  H6    H  HCR6   0   0.316  -3.8034  -2.5784  -1.6331
 T3Q  H1'   H  HCH1   0   0.252  -3.3748  -0.7407  -2.3972
 T3Q  H2'   H  HCH2   0   0.266  -4.4517   1.0307  -3.2804
 T3Q  H2'A  H  HCH2   0   0.274  -5.5530   1.0022  -1.9108
 T3Q  H3'   H  HCH1   0   0.232  -4.3275   2.7445  -0.8167
 T3Q  HO3'  H  HOH1   0   0.456  -4.6692   3.8228  -2.7320
 T3Q  H4'   H  HCH1   0   0.225  -1.8044   2.0807  -2.3280
 T3Q  H5'   H  HCH2   0   0.207  -1.8946   3.7833  -0.5018
 T3Q  H5'A  H  HCH2   0   0.212  -2.3718   2.5108   0.6327
 T3Q  HO4Q  H  HOH1   0   0.451   3.9097  -3.9096  -2.2779
 T3Q  H6Q   H  HCH3   0   0.226   3.9784  -4.3266   0.7158
 T3Q  H6QA  H  HCH3   0   0.246   2.3983  -3.6791   1.1816
 T3Q  H6QB  H  HCH3   0   0.227   2.6389  -4.3066  -0.4369
 T3Q  H3Q   H  HCH1   0   0.233   4.1838  -0.4149  -1.9526
 T3Q  HN3Q  H  HNH2   0   0.346   6.3474  -0.0972  -2.8309
 T3Q  HN3A  H  HNH2   0   0.333   6.8614  -1.5267  -2.2828
 T3Q  H2Q   H  HCH1   0   0.208   6.3884  -0.9176   0.0811
 T3Q  HO2Q  H  HOH1   0   0.454   6.4397   1.3288   0.1529
 T3Q  H1Q   H  HCH1   0   0.228   4.8950  -0.0455   1.7683
 T3Q  H4Q   H  HCH1   0   0.197   5.4192  -2.9894  -0.9076
 T3Q  H5Q   H  HCH1   0   0.220   2.6355  -1.8353  -0.4444

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
 T3Q  O4   C4    double  1.218  0.020  1.218
 T3Q  N3   C4    single  1.383  0.020  1.383
 T3Q  C4   C5    single  1.448  0.020  1.448
 T3Q  N3   C2    single  1.371  0.020  1.371
 T3Q  N3   HN3   single  0.860  0.020  1.020
 T3Q  O2   C2    double  1.213  0.020  1.213
 T3Q  C2   N1    single  1.375  0.020  1.375
 T3Q  C5   C5M   single  1.493  0.020  1.493
 T3Q  C5   C6    double  1.344  0.020  1.344
 T3Q  C5M  H5M   single  0.970  0.020  1.090
 T3Q  C5M  H5MA  single  0.970  0.020  1.090
 T3Q  C5M  H5MB  single  0.970  0.020  1.090
 T3Q  N1   C6    single  1.371  0.020  1.371
 T3Q  C6   H6    single  0.930  0.020  1.080
 T3Q  N1   C1'   single  1.464  0.020  1.464
 T3Q  C1'  O4'   single  1.397  0.020  1.397
 T3Q  C1'  C2'   single  1.531  0.020  1.531
 T3Q  C1'  H1'   single  0.970  0.020  1.090
 T3Q  O4'  C4'   single  1.417  0.020  1.417
 T3Q  C2'  C3'   single  1.529  0.020  1.529
 T3Q  C2'  H2'   single  0.970  0.020  1.090
 T3Q  C2'  H2'A  single  0.970  0.020  1.090
 T3Q  C4'  C3'   single  1.530  0.020  1.530
 T3Q  C3'  O3'   single  1.406  0.020  1.406
 T3Q  C3'  H3'   single  0.970  0.020  1.090
 T3Q  O3'  HO3'  single  0.850  0.020  0.980
 T3Q  C4'  C5'   single  1.509  0.020  1.509
 T3Q  C4'  H4'   single  0.970  0.020  1.090
 T3Q  O5'  C5'   single  1.410  0.020  1.410
 T3Q  C5'  H5'   single  0.970  0.020  1.090
 T3Q  C5'  H5'A  single  0.970  0.020  1.090
 T3Q  O5'  PA    single  1.643  0.020  1.643
 T3Q  O1A  PA    deloc   1.496  0.020  1.496
 T3Q  O2A  PA    deloc   1.498  0.020  1.498
 T3Q  PA   O3A   single  1.637  0.020  1.637
 T3Q  O3A  PB    single  1.647  0.020  1.647
 T3Q  O2B  PB    deloc   1.496  0.020  1.496
 T3Q  O1B  PB    deloc   1.493  0.020  1.493
 T3Q  PB   O3B   single  1.658  0.020  1.658
 T3Q  O3B  C1Q   single  1.394  0.020  1.394
 T3Q  C4Q  O4Q   single  1.408  0.020  1.408
 T3Q  O4Q  HO4Q  single  0.850  0.020  0.980
 T3Q  C5Q  C4Q   single  1.533  0.020  1.533
 T3Q  C3Q  C4Q   single  1.526  0.020  1.526
 T3Q  C4Q  H4Q   single  0.970  0.020  1.090
 T3Q  O5Q  C5Q   single  1.423  0.020  1.423
 T3Q  C5Q  C6Q   single  1.515  0.020  1.515
 T3Q  C5Q  H5Q   single  0.970  0.020  1.090
 T3Q  C1Q  O5Q   single  1.397  0.020  1.397
 T3Q  C6Q  H6Q   single  0.970  0.020  1.090
 T3Q  C6Q  H6QA  single  0.970  0.020  1.090
 T3Q  C6Q  H6QB  single  0.970  0.020  1.090
 T3Q  C2Q  C3Q   single  1.532  0.020  1.532
 T3Q  C3Q  N3Q   single  1.452  0.020  1.452
 T3Q  C3Q  H3Q   single  0.970  0.020  1.090
 T3Q  N3Q  HN3Q  single  0.890  0.020  1.040
 T3Q  N3Q  HN3A  single  0.890  0.020  1.040
 T3Q  O2Q  C2Q   single  1.405  0.020  1.405
 T3Q  C1Q  C2Q   single  1.529  0.020  1.529
 T3Q  C2Q  H2Q   single  0.970  0.020  1.090
 T3Q  O2Q  HO2Q  single  0.850  0.020  0.980
 T3Q  C1Q  H1Q   single  0.970  0.020  1.090

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
 T3Q  C5    C4   N3    114.26  3.000
 T3Q  C5    C4   O4    125.10  3.000
 T3Q  N3    C4   O4    120.64  3.000
 T3Q  HN3   N3   C2    115.08  3.000
 T3Q  HN3   N3   C4    116.75  3.000
 T3Q  C2    N3   C4    128.17  3.000
 T3Q  N1    C2   O2    123.69  3.000
 T3Q  N1    C2   N3    114.51  3.000
 T3Q  O2    C2   N3    121.80  3.000
 T3Q  C6    C5   C5M   123.21  3.000
 T3Q  C6    C5   C4    117.85  3.000
 T3Q  C5M   C5   C4    118.94  3.000
 T3Q  H5MB  C5M  H5MA  107.88  3.000
 T3Q  H5MB  C5M  H5M   107.92  3.000
 T3Q  H5MA  C5M  H5M   107.20  3.000
 T3Q  H5MB  C5M  C5    110.94  3.000
 T3Q  H5MA  C5M  C5    111.33  3.000
 T3Q  H5M   C5M  C5    111.40  3.000
 T3Q  H6    C6   N1    114.85  3.000
 T3Q  H6    C6   C5    120.66  3.000
 T3Q  N1    C6   C5    124.49  3.000
 T3Q  C1'   N1   C6    119.13  3.000
 T3Q  C1'   N1   C2    120.06  3.000
 T3Q  C6    N1   C2    120.70  3.000
 T3Q  H1'   C1'  C2'   109.53  3.000
 T3Q  H1'   C1'  O4'   110.22  3.000
 T3Q  C2'   C1'  O4'   107.59  3.000
 T3Q  H1'   C1'  N1    104.02  3.000
 T3Q  C2'   C1'  N1    116.21  3.000
 T3Q  O4'   C1'  N1    109.21  3.000
 T3Q  C4'   O4'  C1'   111.43  3.000
 T3Q  H2'A  C2'  H2'   107.44  3.000
 T3Q  H2'A  C2'  C3'   113.84  3.000
 T3Q  H2'   C2'  C3'   108.91  3.000
 T3Q  H2'A  C2'  C1'   113.22  3.000
 T3Q  H2'   C2'  C1'   108.33  3.000
 T3Q  C3'   C2'  C1'   104.94  3.000
 T3Q  H3'   C3'  C4'   109.91  3.000
 T3Q  H3'   C3'  O3'   110.61  3.000
 T3Q  C4'   C3'  O3'   108.79  3.000
 T3Q  H3'   C3'  C2'   109.86  3.000
 T3Q  O3'   C3'  C2'   114.70  3.000
 T3Q  C4'   C3'  C2'   102.63  3.000
 T3Q  HO3'  O3'  C3'   108.25  3.000
 T3Q  H4'   C4'  C5'   109.59  3.000
 T3Q  H4'   C4'  C3'   108.39  3.000
 T3Q  C5'   C4'  C3'   112.67  3.000
 T3Q  H4'   C4'  O4'   109.49  3.000
 T3Q  C5'   C4'  O4'   109.95  3.000
 T3Q  C3'   C4'  O4'   106.67  3.000
 T3Q  H5'A  C5'  H5'   107.65  3.000
 T3Q  H5'A  C5'  O5'   111.47  3.000
 T3Q  H5'   C5'  O5'   111.23  3.000
 T3Q  H5'A  C5'  C4'   108.88  3.000
 T3Q  H5'   C5'  C4'   107.96  3.000
 T3Q  O5'   C5'  C4'   109.56  3.000
 T3Q  PA    O5'  C5'   117.58  3.000
 T3Q  O3A   PA   O2A   106.68  3.000
 T3Q  O3A   PA   O1A   110.93  3.000
 T3Q  O2A   PA   O1A   120.33  3.000
 T3Q  O3A   PA   O5'    97.11  3.000
 T3Q  O2A   PA   O5'   109.14  3.000
 T3Q  O1A   PA   O5'   110.11  3.000
 T3Q  PB    O3A  PA    125.06  3.000
 T3Q  O3B   PB   O2B   108.86  3.000
 T3Q  O3B   PB   O1B   109.49  3.000
 T3Q  O2B   PB   O1B   121.32  3.000
 T3Q  O3B   PB   O3A    93.00  3.000
 T3Q  O1B   PB   O3A   110.19  3.000
 T3Q  O2B   PB   O3A   110.28  3.000
 T3Q  C1Q   O3B  PB    119.25  3.000
 T3Q  HO4Q  O4Q  C4Q   108.55  3.000
 T3Q  H4Q   C4Q  C3Q   107.92  3.000
 T3Q  H4Q   C4Q  C5Q   108.09  3.000
 T3Q  C3Q   C4Q  C5Q   110.81  3.000
 T3Q  H4Q   C4Q  O4Q   110.82  3.000
 T3Q  C3Q   C4Q  O4Q   108.48  3.000
 T3Q  C5Q   C4Q  O4Q   110.70  3.000
 T3Q  H5Q   C5Q  C6Q   108.57  3.000
 T3Q  H5Q   C5Q  O5Q   109.96  3.000
 T3Q  C6Q   C5Q  O5Q   106.64  3.000
 T3Q  H5Q   C5Q  C4Q   108.40  3.000
 T3Q  C6Q   C5Q  C4Q   112.87  3.000
 T3Q  O5Q   C5Q  C4Q   110.36  3.000
 T3Q  C1Q   O5Q  C5Q   115.03  3.000
 T3Q  H6QB  C6Q  H6QA  107.00  3.000
 T3Q  H6QB  C6Q  H6Q   108.17  3.000
 T3Q  H6QA  C6Q  H6Q   108.40  3.000
 T3Q  H6QB  C6Q  C5Q   111.13  3.000
 T3Q  H6QA  C6Q  C5Q   110.41  3.000
 T3Q  H6Q   C6Q  C5Q   111.57  3.000
 T3Q  H3Q   C3Q  C2Q   108.40  3.000
 T3Q  H3Q   C3Q  N3Q   107.70  3.000
 T3Q  C2Q   C3Q  N3Q   113.53  3.000
 T3Q  H3Q   C3Q  C4Q   108.15  3.000
 T3Q  N3Q   C3Q  C4Q   110.35  3.000
 T3Q  C2Q   C3Q  C4Q   108.56  3.000
 T3Q  HN3A  N3Q  HN3Q  105.63  3.000
 T3Q  HN3A  N3Q  C3Q   109.45  3.000
 T3Q  HN3Q  N3Q  C3Q   109.19  3.000
 T3Q  H2Q   C2Q  C1Q   106.55  3.000
 T3Q  H2Q   C2Q  O2Q   110.86  3.000
 T3Q  C1Q   C2Q  O2Q   112.03  3.000
 T3Q  H2Q   C2Q  C3Q   107.43  3.000
 T3Q  C1Q   C2Q  C3Q   111.45  3.000
 T3Q  O2Q   C2Q  C3Q   108.43  3.000
 T3Q  HO2Q  O2Q  C2Q   108.67  3.000
 T3Q  H1Q   C1Q  C2Q   110.18  3.000
 T3Q  H1Q   C1Q  O5Q   105.03  3.000
 T3Q  C2Q   C1Q  O5Q   109.91  3.000
 T3Q  H1Q   C1Q  O3B   110.54  3.000
 T3Q  C2Q   C1Q  O3B   108.53  3.000
 T3Q  O5Q   C1Q  O3B   112.63  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
 T3Q  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 T3Q  CONST_02  C6   N1   C2   N3     0.00   0.0  0
 T3Q  CONST_03  C1'  N1   C2   N3   180.00   0.0  0
 T3Q  CONST_04  C5   C4   N3   C2     0.00   0.0  0
 T3Q  CONST_05  C2   N3   C4   O4   180.00   0.0  0
 T3Q  CONST_06  O2   C2   N3   C4   180.00   0.0  0
 T3Q  CONST_07  C6   N1   C2   O2   180.00   0.0  0
 T3Q  CONST_08  C1'  N1   C2   O2     0.00   0.0  0
 T3Q  CONST_09  HN3  N3   C4   C5   180.00   0.0  0
 T3Q  Var_01    H5M  C5M  C5   C4   -59.31  30.0  3
 T3Q  Var_02    O1A  PA   O5'  C5'   60.77  30.0  3
 T3Q  Var_03    O2B  PB   O3A  PA   -84.12  30.0  3
 T3Q  Var_04    H5'  C5'  O5'  PA    67.71  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
 T3Q  chir_01  C1'  N1   O4'  C2'  positiv
 T3Q  chir_02  C3'  O3'  C4'  C2'  positiv
 T3Q  chir_03  C4'  O4'  C3'  C5'  negativ
 T3Q  chir_06  C4Q  O4Q  C5Q  C3Q  positiv
 T3Q  chir_07  C5Q  O5Q  C4Q  C6Q  negativ
 T3Q  chir_08  C3Q  N3Q  C4Q  C2Q  negativ
 T3Q  chir_09  C2Q  O2Q  C3Q  C1Q  positiv
 T3Q  chir_10  C1Q  O5Q  O3B  C2Q  positiv

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
 T3Q  plan-1  O4   0.020
 T3Q  plan-1  C4   0.020
 T3Q  plan-1  N3   0.020
 T3Q  plan-1  C2   0.020
 T3Q  plan-1  O2   0.020
 T3Q  plan-1  C5   0.020
 T3Q  plan-1  C5M  0.020
 T3Q  plan-1  C6   0.020
 T3Q  plan-1  N1   0.020
 T3Q  plan-1  C1'  0.020
 T3Q  plan-1  HN3  0.020
 T3Q  plan-1  H6   0.020

