# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun  2 00:06:20 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: (2R,3R,4S,5S,6R)-5-(formylamino)-3,4-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](O)[C@@H]1NC=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
 4TG  4TG  '(2R,3R,4S,5S,6R)-5-(formylamino)-3,4-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  62  37  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4TG
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
 4TG  C4   C  CR6    0   0.558  -3.8873  -3.6751  -1.0579
 4TG  C5   C  CR6    0  -0.185  -4.3447  -2.9274  -2.2112
 4TG  O4   O  O      0  -0.455  -3.7327  -4.8824  -1.0227
 4TG  C6   C  CR16   0   0.059  -4.4596  -1.5938  -2.0902
 4TG  N1   N  NR6    0  -0.566  -4.1867  -0.8928  -0.9441
 4TG  N3   N  NR16   0  -0.733  -3.6230  -2.8979   0.0551
 4TG  O2B  O  OP    -1  -0.781   3.3725   3.0540  -2.4889
 4TG  PB   P  P      0   1.365   3.1914   2.3438  -1.1861
 4TG  O1B  O  O      0  -0.783   4.0607   2.6501  -0.0126
 4TG  O3B  O  O2     0  -0.632   3.1169   0.7234  -1.4717
 4TG  C1Q  C  CH1    0   0.245   4.1965  -0.1552  -1.5516
 4TG  O5Q  O  O2     0  -0.501   4.9674  -0.2153  -0.3930
 4TG  C5Q  C  CH1    0   0.051   4.2407  -0.4828   0.7960
 4TG  C6Q  C  CH3    0  -0.691   5.2496  -0.5741   1.9214
 4TG  C4Q  C  CH1    0  -0.137   3.4006  -1.7675   0.6805
 4TG  N4Q  N  NH1    0  -0.607   2.4170  -1.7466   1.7396
 4TG  C    C  C1     0   0.243   2.2270  -2.7038   2.6463
 4TG  O    O  O      0  -0.509   2.8744  -3.7336   2.7647
 4TG  C3Q  C  CH1    0   0.037   2.6892  -1.9157  -0.6663
 4TG  O3Q  O  OH1    0  -0.673   2.2449  -3.2508  -0.7597
 4TG  C2Q  C  CH1    0  -0.015   3.6155  -1.5453  -1.8166
 4TG  O2Q  O  OH1    0  -0.672   2.8709  -1.6115  -3.0075
 4TG  O3A  O  O2     0  -0.736   1.6041   2.5074  -0.7883
 4TG  PA   P  P      0   1.364   0.8886   2.1819   0.6495
 4TG  O2A  O  O      0  -0.790   1.1836   3.2554   1.6464
 4TG  O1A  O  OP    -1  -0.764   1.0547   0.7397   1.0388
 4TG  O5'  O  O2     0  -0.620  -0.6263   2.3894   0.0417
 4TG  C5'  C  CH2    0  -0.156  -1.7088   2.1362   0.9127
 4TG  C4'  C  CH1    0   0.011  -2.9983   2.1677   0.1301
 4TG  O4'  O  O2     0  -0.489  -3.0101   1.1171  -0.8213
 4TG  C1'  C  CH1    0   0.216  -4.2878   0.5667  -0.9601
 4TG  C2'  C  CH2    0  -0.559  -5.1829   1.1969   0.1099
 4TG  C3'  C  CH1    0   0.022  -4.2287   1.9725   1.0191
 4TG  O3'  O  OH1    0  -0.669  -4.6990   3.2329   1.4268
 4TG  C2   C  CR6    0   0.743  -3.7414  -1.5381   0.1859
 4TG  O2   O  O      0  -0.471  -3.4771  -0.9685   1.2235
 4TG  C5M  C  CH3    0  -0.706  -4.6573  -3.6621  -3.4730
 4TG  H1   H  HCR6   0   0.316  -4.7929  -0.9915  -2.9247
 4TG  H2   H  HNR6   0   0.425  -3.2962  -3.3821   0.8823
 4TG  H4   H  HCH1   0   0.232   4.8904   0.1387  -2.3506
 4TG  H5   H  HCH1   0   0.237   3.5611   0.3462   1.0015
 4TG  H6   H  HCH3   0   0.239   5.8089   0.3578   2.0097
 4TG  H7   H  HCH3   0   0.232   4.7447  -0.7448   2.8718
 4TG  H8   H  HCH3   0   0.223   5.9563  -1.3905   1.7609
 4TG  H9   H  HCH1   0   0.249   4.0513  -2.6358   0.8201
 4TG  H10  H  HNH1   0   0.417   1.7963  -0.9389   1.7238
 4TG  H11  H  H      0   0.189   1.3921  -2.4591   3.3212
 4TG  H12  H  HCH1   0   0.225   1.8364  -1.2252  -0.6751
 4TG  H13  H  HOH1   0   0.448   1.6897  -3.3227  -1.5424
 4TG  H14  H  HCH1   0   0.217   4.4587  -2.2509  -1.8371
 4TG  H15  H  HOH1   0   0.456   3.4797  -1.6276  -3.7519
 4TG  H17  H  HCH2   0   0.216  -1.6107   1.1593   1.3994
 4TG  H18  H  HCH2   0   0.213  -1.7696   2.8964   1.7011
 4TG  H19  H  HCH1   0   0.228  -3.0919   3.1330  -0.3889
 4TG  H20  H  HCH1   0   0.254  -4.6852   0.7944  -1.9518
 4TG  H21  H  HCH2   0   0.267  -5.8572   1.9026  -0.3788
 4TG  H22  H  HCH2   0   0.275  -5.7971   0.4701   0.6390
 4TG  H23  H  HCH1   0   0.233  -3.9626   1.3634   1.8872
 4TG  H24  H  HOH1   0   0.457  -5.3095   3.1046   2.1585
 4TG  H25  H  HCH3   0   0.246  -5.4298  -4.4153  -3.3134
 4TG  H26  H  HCH3   0   0.246  -5.0114  -2.9784  -4.2427
 4TG  H27  H  HCH3   0   0.247  -3.7784  -4.1780  -3.8621

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
 4TG  C6Q  C5Q  single  1.514  0.020  1.514
 4TG  O1B  PB   deloc   1.492  0.020  1.492
 4TG  O3'  C3'  single  1.406  0.020  1.406
 4TG  O5Q  C5Q  single  1.419  0.020  1.419
 4TG  O5Q  C1Q  single  1.393  0.020  1.393
 4TG  C5Q  C4Q  single  1.539  0.020  1.539
 4TG  O2B  PB   deloc   1.495  0.020  1.495
 4TG  PB   O3B  single  1.647  0.020  1.647
 4TG  PB   O3A  single  1.644  0.020  1.644
 4TG  O    C    double  1.222  0.020  1.222
 4TG  C4'  C5'  single  1.509  0.020  1.509
 4TG  C4'  C3'  single  1.530  0.020  1.530
 4TG  C4'  O4'  single  1.417  0.020  1.417
 4TG  C5'  O5'  single  1.412  0.020  1.412
 4TG  C1Q  O3B  single  1.394  0.020  1.394
 4TG  C1Q  C2Q  single  1.530  0.020  1.530
 4TG  C3'  C2'  single  1.529  0.020  1.529
 4TG  C4Q  N4Q  single  1.446  0.020  1.446
 4TG  C4Q  C3Q  single  1.530  0.020  1.530
 4TG  C    N4Q  single  1.332  0.020  1.332
 4TG  O3A  PA   single  1.639  0.020  1.639
 4TG  C2'  C1'  single  1.531  0.020  1.531
 4TG  O4'  C1'  single  1.398  0.020  1.398
 4TG  O2A  PA   deloc   1.494  0.020  1.494
 4TG  O5'  PA   single  1.645  0.020  1.645
 4TG  C2Q  C3Q  single  1.523  0.020  1.523
 4TG  C2Q  O2Q  single  1.406  0.020  1.406
 4TG  C1'  N1   single  1.463  0.020  1.463
 4TG  C3Q  O3Q  single  1.410  0.020  1.410
 4TG  PA   O1A  deloc   1.503  0.020  1.503
 4TG  N1   C6   single  1.371  0.020  1.371
 4TG  N1   C2   single  1.375  0.020  1.375
 4TG  O2   C2   double  1.213  0.020  1.213
 4TG  C6   C5   double  1.344  0.020  1.344
 4TG  C2   N3   single  1.371  0.020  1.371
 4TG  C5   C4   single  1.449  0.020  1.449
 4TG  C5   C5M  single  1.493  0.020  1.493
 4TG  N3   C4   single  1.383  0.020  1.383
 4TG  C4   O4   double  1.218  0.020  1.218
 4TG  C6   H1   single  0.930  0.020  1.080
 4TG  N3   H2   single  0.860  0.020  1.020
 4TG  C1Q  H4   single  0.970  0.020  1.090
 4TG  C5Q  H5   single  0.970  0.020  1.090
 4TG  C6Q  H6   single  0.970  0.020  1.090
 4TG  C6Q  H7   single  0.970  0.020  1.090
 4TG  C6Q  H8   single  0.970  0.020  1.090
 4TG  C4Q  H9   single  0.970  0.020  1.090
 4TG  N4Q  H10  single  0.860  0.020  1.020
 4TG  C    H11  single  0.930  0.020  1.080
 4TG  C3Q  H12  single  0.970  0.020  1.090
 4TG  O3Q  H13  single  0.850  0.020  0.980
 4TG  C2Q  H14  single  0.970  0.020  1.090
 4TG  O2Q  H15  single  0.850  0.020  0.980
 4TG  C5'  H17  single  0.970  0.020  1.090
 4TG  C5'  H18  single  0.970  0.020  1.090
 4TG  C4'  H19  single  0.970  0.020  1.090
 4TG  C1'  H20  single  0.970  0.020  1.090
 4TG  C2'  H21  single  0.970  0.020  1.090
 4TG  C2'  H22  single  0.970  0.020  1.090
 4TG  C3'  H23  single  0.970  0.020  1.090
 4TG  O3'  H24  single  0.850  0.020  0.980
 4TG  C5M  H25  single  0.970  0.020  1.090
 4TG  C5M  H26  single  0.970  0.020  1.090
 4TG  C5M  H27  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
 4TG  N3   C4   O4   120.64  3.000
 4TG  O4   C4   C5   125.09  3.000
 4TG  N3   C4   C5   114.27  3.000
 4TG  C5M  C5   C6   123.12  3.000
 4TG  C5M  C5   C4   119.01  3.000
 4TG  C6   C5   C4   117.87  3.000
 4TG  H1   C6   N1   114.93  3.000
 4TG  H1   C6   C5   120.62  3.000
 4TG  N1   C6   C5   124.45  3.000
 4TG  C2   N1   C1'  119.96  3.000
 4TG  C2   N1   C6   120.76  3.000
 4TG  C1'  N1   C6   119.16  3.000
 4TG  H2   N3   C2   115.09  3.000
 4TG  H2   N3   C4   116.77  3.000
 4TG  C2   N3   C4   128.14  3.000
 4TG  O3A  PB   O3B   95.52  3.000
 4TG  O3A  PB   O1B  110.59  3.000
 4TG  O3B  PB   O1B  111.39  3.000
 4TG  O3A  PB   O2B  106.29  3.000
 4TG  O3B  PB   O2B  108.77  3.000
 4TG  O1B  PB   O2B  121.15  3.000
 4TG  C1Q  O3B  PB   126.50  3.000
 4TG  H4   C1Q  C2Q  110.92  3.000
 4TG  H4   C1Q  O5Q  105.48  3.000
 4TG  C2Q  C1Q  O5Q  108.37  3.000
 4TG  H4   C1Q  O3B  111.24  3.000
 4TG  C2Q  C1Q  O3B  106.77  3.000
 4TG  O5Q  C1Q  O3B  114.08  3.000
 4TG  C5Q  O5Q  C1Q  114.94  3.000
 4TG  H5   C5Q  C4Q  107.94  3.000
 4TG  H5   C5Q  C6Q  108.71  3.000
 4TG  C4Q  C5Q  C6Q  111.66  3.000
 4TG  H5   C5Q  O5Q  109.48  3.000
 4TG  C4Q  C5Q  O5Q  111.96  3.000
 4TG  C6Q  C5Q  O5Q  107.04  3.000
 4TG  H8   C6Q  H7   108.12  3.000
 4TG  H8   C6Q  H6   108.60  3.000
 4TG  H7   C6Q  H6   107.52  3.000
 4TG  H8   C6Q  C5Q  111.54  3.000
 4TG  H7   C6Q  C5Q  110.43  3.000
 4TG  H6   C6Q  C5Q  110.51  3.000
 4TG  H9   C4Q  C3Q  108.17  3.000
 4TG  H9   C4Q  N4Q  108.83  3.000
 4TG  C3Q  C4Q  N4Q  109.26  3.000
 4TG  H9   C4Q  C5Q  109.16  3.000
 4TG  C3Q  C4Q  C5Q  113.61  3.000
 4TG  N4Q  C4Q  C5Q  107.72  3.000
 4TG  H10  N4Q  C    119.56  3.000
 4TG  H10  N4Q  C4Q  114.50  3.000
 4TG  C    N4Q  C4Q  125.82  3.000
 4TG  H11  C    O    121.97  3.000
 4TG  H11  C    N4Q  111.45  3.000
 4TG  O    C    N4Q  126.58  3.000
 4TG  H12  C3Q  C2Q  108.28  3.000
 4TG  H12  C3Q  O3Q  110.51  3.000
 4TG  C2Q  C3Q  O3Q  111.84  3.000
 4TG  H12  C3Q  C4Q  107.90  3.000
 4TG  O3Q  C3Q  C4Q  107.24  3.000
 4TG  C2Q  C3Q  C4Q  111.01  3.000
 4TG  H13  O3Q  C3Q  107.84  3.000
 4TG  H14  C2Q  O2Q  111.10  3.000
 4TG  H14  C2Q  C3Q  108.94  3.000
 4TG  O2Q  C2Q  C3Q  107.83  3.000
 4TG  H14  C2Q  C1Q  107.17  3.000
 4TG  O2Q  C2Q  C1Q  112.99  3.000
 4TG  C3Q  C2Q  C1Q  108.74  3.000
 4TG  H15  O2Q  C2Q  108.73  3.000
 4TG  PA   O3A  PB   127.88  3.000
 4TG  O5'  PA   O1A  108.57  3.000
 4TG  O1A  PA   O2A  119.65  3.000
 4TG  O5'  PA   O2A  109.73  3.000
 4TG  O1A  PA   O3A  111.69  3.000
 4TG  O5'  PA   O3A   93.03  3.000
 4TG  O2A  PA   O3A  110.88  3.000
 4TG  C5'  O5'  PA   117.08  3.000
 4TG  H18  C5'  H17  107.68  3.000
 4TG  H18  C5'  C4'  108.12  3.000
 4TG  H17  C5'  C4'  109.00  3.000
 4TG  H18  C5'  O5'  111.19  3.000
 4TG  H17  C5'  O5'  111.41  3.000
 4TG  C4'  C5'  O5'  109.35  3.000
 4TG  H19  C4'  C3'  108.52  3.000
 4TG  H19  C4'  O4'  109.45  3.000
 4TG  C3'  C4'  O4'  106.78  3.000
 4TG  H19  C4'  C5'  109.63  3.000
 4TG  O4'  C4'  C5'  109.87  3.000
 4TG  C3'  C4'  C5'  112.52  3.000
 4TG  C1'  O4'  C4'  111.47  3.000
 4TG  H20  C1'  C2'  109.64  3.000
 4TG  H20  C1'  O4'  109.91  3.000
 4TG  C2'  C1'  O4'  107.63  3.000
 4TG  H20  C1'  N1   104.06  3.000
 4TG  O4'  C1'  N1   109.18  3.000
 4TG  C2'  C1'  N1   116.33  3.000
 4TG  H22  C2'  H21  107.49  3.000
 4TG  H22  C2'  C3'  113.68  3.000
 4TG  H21  C2'  C3'  108.89  3.000
 4TG  H22  C2'  C1'  113.25  3.000
 4TG  H21  C2'  C1'  108.33  3.000
 4TG  C3'  C2'  C1'  105.04  3.000
 4TG  H23  C3'  O3'  110.52  3.000
 4TG  H23  C3'  C2'  109.96  3.000
 4TG  O3'  C3'  C2'  114.74  3.000
 4TG  H23  C3'  C4'  109.68  3.000
 4TG  C2'  C3'  C4'  102.77  3.000
 4TG  O3'  C3'  C4'  108.85  3.000
 4TG  H24  O3'  C3'  108.27  3.000
 4TG  O2   C2   N3   121.91  3.000
 4TG  N3   C2   N1   114.51  3.000
 4TG  O2   C2   N1   123.58  3.000
 4TG  H27  C5M  H26  107.87  3.000
 4TG  H27  C5M  H25  107.23  3.000
 4TG  H26  C5M  H25  107.87  3.000
 4TG  H27  C5M  C5   111.43  3.000
 4TG  H26  C5M  C5   110.89  3.000
 4TG  H25  C5M  C5   111.37  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
 4TG  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 4TG  CONST_02  C2   N3   C4   C5      0.00   0.0  0
 4TG  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 4TG  CONST_04  C1'  N1   C2   N3    180.00   0.0  0
 4TG  CONST_05  O2   C2   N3   C4    180.00   0.0  0
 4TG  CONST_06  C2   N3   C4   O4    180.00   0.0  0
 4TG  CONST_07  O2   C2   N1   C6    180.00   0.0  0
 4TG  CONST_08  O2   C2   N1   C1'     0.00   0.0  0
 4TG  CONST_09  H2   N3   C4   C5    180.00   0.0  0
 4TG  CONST_10  O    C    N4Q  C4Q     0.00   0.0  0
 4TG  CONST_11  H10  N4Q  C    O     180.00   0.0  0
 4TG  Var_01    H25  C5M  C5   C4     58.46  30.0  3
 4TG  Var_02    O3A  PB   O3B  C1Q  -163.40  30.0  1
 4TG  Var_03    C4'  C5'  O5'  PA   -171.24  30.0  1
 4TG  Var_04    O2A  PA   O3A  PB     76.15  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
 4TG  chir_02  C1Q  O5Q  O3B  C2Q  positiv
 4TG  chir_03  C5Q  O5Q  C4Q  C6Q  negativ
 4TG  chir_04  C4Q  N4Q  C3Q  C5Q  negativ
 4TG  chir_05  C3Q  O3Q  C2Q  C4Q  positiv
 4TG  chir_06  C2Q  O2Q  C1Q  C3Q  negativ
 4TG  chir_08  C4'  C5'  C3'  O4'  positiv
 4TG  chir_09  C1'  O4'  N1   C2'  negativ
 4TG  chir_10  C3'  O3'  C4'  C2'  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
 4TG  plan-1  C4   0.020
 4TG  plan-1  C5   0.020
 4TG  plan-1  O4   0.020
 4TG  plan-1  C6   0.020
 4TG  plan-1  N1   0.020
 4TG  plan-1  N3   0.020
 4TG  plan-1  C1'  0.020
 4TG  plan-1  C2   0.020
 4TG  plan-1  O2   0.020
 4TG  plan-1  C5M  0.020
 4TG  plan-1  H1   0.020
 4TG  plan-1  H2   0.020
 4TG  plan-2  C4Q  0.020
 4TG  plan-2  N4Q  0.020
 4TG  plan-2  C    0.020
 4TG  plan-2  O    0.020
 4TG  plan-2  H10  0.020
 4TG  plan-2  H11  0.020

