# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:41:20 2022
#   Inital geometry file: a 147 line input string
#   Ligand name: (2R,3R,4S,5R,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
 T3F  T3F  '(2R,3R,4S,5R,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_T3F
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
 T3F  O2B   O  OP    -1  -0.788  -3.5612  -1.8113  -1.8852
 T3F  PB    P  P      0   1.366  -3.2309  -1.8416  -0.4119
 T3F  O1B   O  O      0  -0.777  -3.8249  -2.8902   0.4674
 T3F  O3B   O  O2     0  -0.627  -3.5229  -0.3455   0.1996
 T3F  C1Q   C  CH1    0   0.231  -4.8263   0.1653   0.3821
 T3F  O5Q   O  O2     0  -0.498  -4.7919   1.0537   1.4491
 T3F  C5Q   C  CH1    0   0.028  -3.9659   2.2005   1.2600
 T3F  C6Q   C  CH3    0  -0.709  -4.0495   3.0202   2.5319
 T3F  C2Q   C  CH1    0   0.009  -5.3395   0.8672  -0.8845
 T3F  O2Q   O  OH1    0  -0.711  -5.5095  -0.0001  -1.9717
 T3F  C3Q   C  CH1    0  -0.144  -4.4383   2.0678  -1.2047
 T3F  N3Q   N  NH2    0  -0.796  -4.8240   2.8221  -2.3836
 T3F  C4Q   C  CH1    0   0.019  -4.3714   2.9884   0.0129
 T3F  O4Q   O  OH1    0  -0.680  -5.6352   3.6038   0.1570
 T3F  O3A   O  O2     0  -0.727  -1.6170  -1.7371  -0.2348
 T3F  PA    P  P      0   1.342  -0.6260  -2.9997   0.1491
 T3F  O1A   O  OP    -1  -0.791  -0.4902  -3.1160   1.6336
 T3F  O2A   O  O      0  -0.789  -0.9783  -4.1872  -0.6875
 T3F  O5'   O  O2     0  -0.621   0.7093  -2.2675  -0.4684
 T3F  C5'   C  CH2    0  -0.155   1.9729  -2.6227   0.0537
 T3F  C4'   C  CH1    0   0.015   3.0473  -2.2406  -0.9338
 T3F  O4'   O  O2     0  -0.489   3.0550  -0.8361  -1.1217
 T3F  C3'   C  CH1    0   0.024   4.4491  -2.6218  -0.4547
 T3F  O3'   O  OH1    0  -0.669   4.7462  -3.9207  -0.9020
 T3F  C2'   C  CH2    0  -0.560   5.3185  -1.5207  -1.0625
 T3F  C1'   C  CH1    0   0.218   4.3536  -0.3631  -1.3359
 T3F  N1    N  NR6    0  -0.567   4.5598   0.8487  -0.5436
 T3F  C2    C  CR6    0   0.742   4.5235   0.7857   0.8301
 T3F  O2    O  O      0  -0.472   4.3664  -0.2441   1.4516
 T3F  N3    N  NR16   0  -0.733   4.6867   1.9934   1.4584
 T3F  C6    C  CR16   0   0.059   4.7253   2.0480  -1.1866
 T3F  C5    C  CR6    0  -0.185   4.8865   3.2285  -0.5647
 T3F  C5M   C  CH3    0  -0.706   5.0740   4.5173  -1.2952
 T3F  C4    C  CR6    0   0.559   4.8724   3.2373   0.8837
 T3F  O4    O  O      0  -0.456   5.0070   4.2279   1.5791
 T3F  H1Q   H  HCH1   0   0.237  -5.5137  -0.6384   0.6745
 T3F  H5Q   H  HCH1   0   0.218  -2.9223   1.8912   1.1208
 T3F  H6Q   H  HCH3   0   0.247  -3.6730   2.4534   3.3833
 T3F  H6QA  H  HCH3   0   0.235  -3.4377   3.9190   2.4416
 T3F  H6QB  H  HCH3   0   0.227  -5.0730   3.3228   2.7569
 T3F  H2Q   H  HCH1   0   0.215  -6.3383   1.2467  -0.6380
 T3F  HO2Q  H  HOH1   0   0.448  -4.7357  -0.6047  -2.0587
 T3F  H3Q   H  HCH1   0   0.234  -3.4226   1.6965  -1.3803
 T3F  HN3Q  H  HNH2   0   0.342  -4.8552   2.1958  -3.1781
 T3F  HN3A  H  HNH2   0   0.335  -5.7680   3.1720  -2.2706
 T3F  H4Q   H  HCH1   0   0.224  -3.5912   3.7414  -0.1655
 T3F  HO4Q  H  HOH1   0   0.456  -5.5418   4.3731   0.7256
 T3F  H5'   H  HCH2   0   0.215   2.1600  -2.1172   1.0070
 T3F  H5'A  H  HCH2   0   0.213   2.0599  -3.7014   0.2301
 T3F  H4'   H  HCH1   0   0.227   2.8573  -2.7409  -1.8951
 T3F  H3'   H  HCH1   0   0.233   4.4936  -2.5697   0.6372
 T3F  HO3'  H  HOH1   0   0.457   5.5022  -4.2456  -0.4049
 T3F  H2'   H  HCH2   0   0.275   6.1646  -1.2342  -0.4399
 T3F  H2'A  H  HCH2   0   0.266   5.7173  -1.8703  -2.0164
 T3F  H1'   H  HCH1   0   0.254   4.4664  -0.0285  -2.3701
 T3F  HN3   H  HNR6   0   0.425   4.6684   1.9571   2.4702
 T3F  H6    H  HCR6   0   0.316   4.7244   1.9887  -2.2666
 T3F  H5M   H  HCH3   0   0.247   4.2828   5.2296  -1.0574
 T3F  H5MA  H  HCH3   0   0.247   6.0224   4.9881  -1.0330
 T3F  H5MB  H  HCH3   0   0.247   5.0666   4.3573  -2.3722

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
 T3F  PB   O2B   deloc   1.510  0.020  1.510
 T3F  O3B  PB    single  1.642  0.020  1.642
 T3F  PB   O1B   deloc   1.492  0.020  1.492
 T3F  PB   O3A   single  1.627  0.020  1.627
 T3F  C1Q  O3B   single  1.412  0.020  1.412
 T3F  O5Q  C1Q   single  1.389  0.020  1.389
 T3F  C2Q  C1Q   single  1.536  0.020  1.536
 T3F  C1Q  H1Q   single  0.970  0.020  1.090
 T3F  C5Q  O5Q   single  1.426  0.020  1.426
 T3F  C6Q  C5Q   single  1.515  0.020  1.515
 T3F  C4Q  C5Q   single  1.530  0.020  1.530
 T3F  C5Q  H5Q   single  0.970  0.020  1.090
 T3F  C6Q  H6Q   single  0.970  0.020  1.090
 T3F  C6Q  H6QA  single  0.970  0.020  1.090
 T3F  C6Q  H6QB  single  0.970  0.020  1.090
 T3F  C3Q  C2Q   single  1.535  0.020  1.535
 T3F  C2Q  O2Q   single  1.401  0.020  1.401
 T3F  C2Q  H2Q   single  0.970  0.020  1.090
 T3F  O2Q  HO2Q  single  0.850  0.020  0.980
 T3F  C4Q  C3Q   single  1.528  0.020  1.528
 T3F  N3Q  C3Q   single  1.452  0.020  1.452
 T3F  C3Q  H3Q   single  0.970  0.020  1.090
 T3F  N3Q  HN3Q  single  0.890  0.020  1.040
 T3F  N3Q  HN3A  single  0.890  0.020  1.040
 T3F  O4Q  C4Q   single  1.413  0.020  1.413
 T3F  C4Q  H4Q   single  0.970  0.020  1.090
 T3F  O4Q  HO4Q  single  0.850  0.020  0.980
 T3F  O3A  PA    single  1.650  0.020  1.650
 T3F  PA   O5'   single  1.643  0.020  1.643
 T3F  PA   O2A   deloc   1.495  0.020  1.495
 T3F  PA   O1A   deloc   1.495  0.020  1.495
 T3F  C5'  O5'   single  1.413  0.020  1.413
 T3F  C5'  C4'   single  1.508  0.020  1.508
 T3F  C5'  H5'   single  0.970  0.020  1.090
 T3F  C5'  H5'A  single  0.970  0.020  1.090
 T3F  C3'  C4'   single  1.530  0.020  1.530
 T3F  C4'  O4'   single  1.417  0.020  1.417
 T3F  C4'  H4'   single  0.970  0.020  1.090
 T3F  O4'  C1'   single  1.399  0.020  1.399
 T3F  C3'  O3'   single  1.406  0.020  1.406
 T3F  C3'  C2'   single  1.529  0.020  1.529
 T3F  C3'  H3'   single  0.970  0.020  1.090
 T3F  O3'  HO3'  single  0.850  0.020  0.980
 T3F  C2'  C1'   single  1.532  0.020  1.532
 T3F  C2'  H2'   single  0.970  0.020  1.090
 T3F  C2'  H2'A  single  0.970  0.020  1.090
 T3F  C1'  N1    single  1.462  0.020  1.462
 T3F  C1'  H1'   single  0.970  0.020  1.090
 T3F  C6   N1    single  1.371  0.020  1.371
 T3F  N1   C2    single  1.376  0.020  1.376
 T3F  C2   O2    double  1.213  0.020  1.213
 T3F  C2   N3    single  1.371  0.020  1.371
 T3F  C4   N3    single  1.383  0.020  1.383
 T3F  N3   HN3   single  0.860  0.020  1.020
 T3F  C6   C5    double  1.344  0.020  1.344
 T3F  C6   H6    single  0.930  0.020  1.080
 T3F  C5M  C5    single  1.493  0.020  1.493
 T3F  C5   C4    single  1.448  0.020  1.448
 T3F  C5M  H5M   single  0.970  0.020  1.090
 T3F  C5M  H5MA  single  0.970  0.020  1.090
 T3F  C5M  H5MB  single  0.970  0.020  1.090
 T3F  C4   O4    double  1.218  0.020  1.218

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
 T3F  O3A   PB   O3B    94.43  3.000
 T3F  O3A   PB   O1B   112.08  3.000
 T3F  O3B   PB   O1B   110.49  3.000
 T3F  O3A   PB   O2B   108.78  3.000
 T3F  O1B   PB   O2B   120.14  3.000
 T3F  O3B   PB   O2B   107.82  3.000
 T3F  C1Q   O3B  PB    122.81  3.000
 T3F  H1Q   C1Q  C2Q   110.18  3.000
 T3F  H1Q   C1Q  O5Q   106.22  3.000
 T3F  C2Q   C1Q  O5Q   110.45  3.000
 T3F  H1Q   C1Q  O3B   110.35  3.000
 T3F  C2Q   C1Q  O3B   111.54  3.000
 T3F  O5Q   C1Q  O3B   107.93  3.000
 T3F  C5Q   O5Q  C1Q   115.27  3.000
 T3F  H5Q   C5Q  C4Q   107.08  3.000
 T3F  H5Q   C5Q  C6Q   108.14  3.000
 T3F  C4Q   C5Q  C6Q   113.01  3.000
 T3F  H5Q   C5Q  O5Q   109.94  3.000
 T3F  C4Q   C5Q  O5Q   111.64  3.000
 T3F  C6Q   C5Q  O5Q   106.97  3.000
 T3F  H6QB  C6Q  H6QA  108.35  3.000
 T3F  H6QB  C6Q  H6Q   107.89  3.000
 T3F  H6QA  C6Q  H6Q   107.42  3.000
 T3F  H6QB  C6Q  C5Q   112.02  3.000
 T3F  H6QA  C6Q  C5Q   110.20  3.000
 T3F  H6Q   C6Q  C5Q   110.81  3.000
 T3F  H2Q   C2Q  C3Q   108.12  3.000
 T3F  H2Q   C2Q  O2Q   106.15  3.000
 T3F  C3Q   C2Q  O2Q   113.18  3.000
 T3F  H2Q   C2Q  C1Q   106.08  3.000
 T3F  O2Q   C2Q  C1Q   113.42  3.000
 T3F  C3Q   C2Q  C1Q   109.46  3.000
 T3F  HO2Q  O2Q  C2Q   110.66  3.000
 T3F  H3Q   C3Q  C4Q   106.94  3.000
 T3F  H3Q   C3Q  N3Q   106.99  3.000
 T3F  C4Q   C3Q  N3Q   110.23  3.000
 T3F  H3Q   C3Q  C2Q   108.22  3.000
 T3F  N3Q   C3Q  C2Q   114.82  3.000
 T3F  C4Q   C3Q  C2Q   109.32  3.000
 T3F  HN3A  N3Q  HN3Q  105.81  3.000
 T3F  HN3A  N3Q  C3Q   109.65  3.000
 T3F  HN3Q  N3Q  C3Q   108.92  3.000
 T3F  H4Q   C4Q  O4Q   110.67  3.000
 T3F  H4Q   C4Q  C3Q   108.34  3.000
 T3F  O4Q   C4Q  C3Q   107.73  3.000
 T3F  H4Q   C4Q  C5Q   107.28  3.000
 T3F  O4Q   C4Q  C5Q   112.22  3.000
 T3F  C3Q   C4Q  C5Q   110.55  3.000
 T3F  HO4Q  O4Q  C4Q   108.78  3.000
 T3F  PA    O3A  PB    124.88  3.000
 T3F  O5'   PA   O2A   109.58  3.000
 T3F  O2A   PA   O1A   121.02  3.000
 T3F  O5'   PA   O1A   109.51  3.000
 T3F  O1A   PA   O3A   110.18  3.000
 T3F  O2A   PA   O3A   109.64  3.000
 T3F  O5'   PA   O3A    93.42  3.000
 T3F  C5'   O5'  PA    118.42  3.000
 T3F  H5'A  C5'  H5'   107.49  3.000
 T3F  H5'A  C5'  C4'   107.34  3.000
 T3F  H5'   C5'  C4'   109.35  3.000
 T3F  H5'A  C5'  O5'   112.19  3.000
 T3F  H5'   C5'  O5'   111.00  3.000
 T3F  C4'   C5'  O5'   109.36  3.000
 T3F  H4'   C4'  C3'   108.58  3.000
 T3F  H4'   C4'  O4'   109.62  3.000
 T3F  C3'   C4'  O4'   106.47  3.000
 T3F  H4'   C4'  C5'   109.50  3.000
 T3F  O4'   C4'  C5'   109.98  3.000
 T3F  C3'   C4'  C5'   112.61  3.000
 T3F  C1'   O4'  C4'   111.13  3.000
 T3F  H3'   C3'  C2'   109.84  3.000
 T3F  H3'   C3'  O3'   110.67  3.000
 T3F  C2'   C3'  O3'   114.76  3.000
 T3F  H3'   C3'  C4'   109.76  3.000
 T3F  C2'   C3'  C4'   102.54  3.000
 T3F  O3'   C3'  C4'   108.92  3.000
 T3F  HO3'  O3'  C3'   108.30  3.000
 T3F  H2'A  C2'  H2'   107.46  3.000
 T3F  H2'A  C2'  C1'   108.44  3.000
 T3F  H2'   C2'  C1'   113.12  3.000
 T3F  H2'A  C2'  C3'   108.94  3.000
 T3F  H2'   C2'  C3'   113.83  3.000
 T3F  C1'   C2'  C3'   104.90  3.000
 T3F  H1'   C1'  N1    104.16  3.000
 T3F  H1'   C1'  C2'   109.60  3.000
 T3F  N1    C1'  C2'   116.15  3.000
 T3F  H1'   C1'  O4'   110.14  3.000
 T3F  N1    C1'  O4'   109.16  3.000
 T3F  C2'   C1'  O4'   107.57  3.000
 T3F  C6    N1   C2    120.77  3.000
 T3F  C2    N1   C1'   119.96  3.000
 T3F  C6    N1   C1'   119.19  3.000
 T3F  N3    C2   O2    121.90  3.000
 T3F  N3    C2   N1    114.46  3.000
 T3F  O2    C2   N1    123.63  3.000
 T3F  HN3   N3   C4    116.74  3.000
 T3F  HN3   N3   C2    115.10  3.000
 T3F  C4    N3   C2    128.17  3.000
 T3F  H6    C6   C5    120.68  3.000
 T3F  H6    C6   N1    114.86  3.000
 T3F  C5    C6   N1    124.46  3.000
 T3F  C4    C5   C5M   119.02  3.000
 T3F  C4    C5   C6    117.83  3.000
 T3F  C5M   C5   C6    123.14  3.000
 T3F  H5MB  C5M  H5MA  107.89  3.000
 T3F  H5MB  C5M  H5M   107.86  3.000
 T3F  H5MA  C5M  H5M   107.24  3.000
 T3F  H5MB  C5M  C5    110.87  3.000
 T3F  H5MA  C5M  C5    111.35  3.000
 T3F  H5M   C5M  C5    111.46  3.000
 T3F  O4    C4   C5    125.09  3.000
 T3F  O4    C4   N3    120.62  3.000
 T3F  C5    C4   N3    114.29  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
 T3F  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 T3F  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 T3F  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 T3F  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 T3F  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 T3F  CONST_06  O4   C4   N3   C2    180.00   0.0  0
 T3F  CONST_07  C6   N1   C2   O2    180.00   0.0  0
 T3F  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 T3F  CONST_09  HN3  N3   C2   N1    180.00   0.0  0
 T3F  Var_01    H5M  C5M  C5   C6    119.82  30.0  3
 T3F  Var_02    O3A  PB   O3B  C1Q  -176.78  30.0  3
 T3F  Var_03    C4'  C5'  O5'  PA    160.02  30.0  2
 T3F  Var_04    O5'  PA   O3A  PB    158.08  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
 T3F  chir_02  C1Q  O3B  O5Q  C2Q  negativ
 T3F  chir_03  C5Q  O5Q  C6Q  C4Q  positiv
 T3F  chir_04  C2Q  O2Q  C3Q  C1Q  positiv
 T3F  chir_05  C3Q  N3Q  C4Q  C2Q  negativ
 T3F  chir_06  C4Q  O4Q  C5Q  C3Q  negativ
 T3F  chir_08  C4'  C5'  C3'  O4'  positiv
 T3F  chir_09  C3'  O3'  C2'  C4'  negativ
 T3F  chir_10  C1'  O4'  N1   C2'  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
 T3F  plan-1  C1'  0.020
 T3F  plan-1  N1   0.020
 T3F  plan-1  C2   0.020
 T3F  plan-1  O2   0.020
 T3F  plan-1  N3   0.020
 T3F  plan-1  C6   0.020
 T3F  plan-1  C5   0.020
 T3F  plan-1  C5M  0.020
 T3F  plan-1  C4   0.020
 T3F  plan-1  O4   0.020
 T3F  plan-1  HN3  0.020
 T3F  plan-1  H6   0.020

