# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:29:34 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (2R,3R,4S,5S)-5-amino-3,4-dihydroxytetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CO[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[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
 G3N  G3N  '(2R,3R,4S,5S)-5-amino-3,4-dihydroxytetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  55  34  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G3N
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
 G3N  O2B  O  OP    -1  -0.774  -0.0434   1.1152   2.5546
 G3N  PB   P  P      0   1.389   1.3102   1.3067   1.9477
 G3N  O1B  O  O      0  -0.789   2.4592   1.8714   2.7164
 G3N  O3B  O  O2     0  -0.638   1.7150  -0.1904   1.3731
 G3N  C1'  C  CH1    0   0.303   2.9133  -0.4262   0.7107
 G3N  O5'  O  O2     0  -0.491   3.5997  -1.3643   1.4916
 G3N  C5'  C  CH2    0  -0.186   4.8199  -1.7761   0.9114
 G3N  C4'  C  CH1    0  -0.102   4.5942  -2.4405  -0.4425
 G3N  N4'  N  NH2    0  -0.808   5.8764  -2.8445  -0.9953
 G3N  C3'  C  CH1    0  -0.013   3.8668  -1.4728  -1.3701
 G3N  O3'  O  OH1    0  -0.667   4.7277  -0.3967  -1.6634
 G3N  C2'  C  CH1    0  -0.046   2.5929  -0.9667  -0.6850
 G3N  O2'  O  OH1    0  -0.683   1.6761  -2.0312  -0.6346
 G3N  O3A  O  O2     0  -0.750   1.1946   2.0532   0.4909
 G3N  PA   P  P      0   1.359   0.8818   3.6504   0.2430
 G3N  O1A  O  O      0  -0.780   1.9252   4.1867  -0.6798
 G3N  O2A  O  OP    -1  -0.801   0.5582   4.2994   1.5509
 G3N  O5D  O  O2     0  -0.619  -0.4741   3.5255  -0.6715
 G3N  C5D  C  CH2    0  -0.167  -1.6720   3.0606  -0.0871
 G3N  C4D  C  CR15   0  -0.003  -2.4699   2.3255  -1.1358
 G3N  C3D  C  CR15   0  -0.035  -3.8040   1.7844  -0.6352
 G3N  O3D  O  OH1    0  -0.657  -4.7872   2.7781  -0.6918
 G3N  C2D  C  CR15   0  -0.042  -4.0459   0.6174  -1.5999
 G3N  O2D  O  OH1    0  -0.664  -4.5077   1.0777  -2.8397
 G3N  O4D  O  O      0  -0.489  -1.7612   1.1701  -1.5852
 G3N  C1D  C  CR15   0   0.187  -2.6211   0.0999  -1.8068
 G3N  N1   N  NR6    0  -0.563  -2.2981  -0.9978  -0.8683
 G3N  C6   C  CR16   0   0.070  -1.5615  -0.8076   0.2598
 G3N  C5   C  CR16   0  -0.549  -1.2753  -1.7982   1.1256
 G3N  C4   C  CR6    0   0.569  -1.7517  -3.1334   0.8706
 G3N  O4   O  O      0  -0.464  -1.5658  -4.1113   1.5713
 G3N  N3   N  NR16   0  -0.729  -2.4778  -3.2398  -0.3077
 G3N  C2   C  CR6    0   0.738  -2.7909  -2.2450  -1.1932
 G3N  O2   O  O      0  -0.479  -3.4543  -2.4429  -2.1908
 G3N  H2   H  HCH1   0   0.191   3.5179   0.4881   0.6064
 G3N  H3   H  HCH2   0   0.206   5.5126  -0.9315   0.8004
 G3N  H4   H  HCH2   0   0.240   5.2751  -2.4827   1.6086
 G3N  H5   H  HCH1   0   0.223   3.9133  -3.2889  -0.2898
 G3N  H6   H  HNH2   0   0.346   6.2262  -3.6309  -0.4615
 G3N  H7   H  HNH2   0   0.346   5.7445  -3.1985  -1.9355
 G3N  H9   H  HCH1   0   0.230   3.5805  -2.0052  -2.2900
 G3N  H10  H  HOH1   0   0.452   4.2736   0.1993  -2.2674
 G3N  H11  H  HCH1   0   0.223   2.1846  -0.1277  -1.2713
 G3N  H12  H  HOH1   0   0.458   0.9593  -1.7784  -0.0404
 G3N  H14  H  HCH2   0   0.218  -1.4893   2.4102   0.7752
 G3N  H15  H  HCH2   0   0.227  -2.2760   3.9018   0.2709
 G3N  H16  H  HCR5   0   0.246  -2.6436   2.9942  -1.9884
 G3N  H17  H  HCR5   0   0.242  -3.6890   1.3921   0.3851
 G3N  H18  H  HOH1   0   0.469  -5.5168   2.5286  -0.1156
 G3N  H19  H  HCR5   0   0.260  -4.7086  -0.1447  -1.1736
 G3N  H20  H  HOH1   0   0.452  -5.1586   1.7712  -2.6751
 G3N  H21  H  HCR5   0   0.285  -2.4820  -0.2961  -2.8146
 G3N  H22  H  HCR6   0   0.334  -1.1913   0.1901   0.4383
 G3N  H23  H  HCR6   0   0.297  -0.6944  -1.5833   2.0086
 G3N  H24  H  HNR6   0   0.427  -2.8399  -4.1563  -0.5423

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
 G3N  C5'  C4'  single  1.525  0.020  1.525
 G3N  C5'  O5'  single  1.412  0.020  1.412
 G3N  N4'  C4'  single  1.454  0.020  1.454
 G3N  C4'  C3'  single  1.525  0.020  1.525
 G3N  O5'  C1'  single  1.400  0.020  1.400
 G3N  C1'  O3B  single  1.389  0.020  1.389
 G3N  C1'  C2'  single  1.531  0.020  1.531
 G3N  O3'  C3'  single  1.409  0.020  1.409
 G3N  C3'  C2'  single  1.532  0.020  1.532
 G3N  O3B  PB   single  1.654  0.020  1.654
 G3N  C2'  O2'  single  1.406  0.020  1.406
 G3N  O1B  PB   deloc   1.493  0.020  1.493
 G3N  PB   O2B  deloc   1.496  0.020  1.496
 G3N  PB   O3A  single  1.641  0.020  1.641
 G3N  O4   C4   double  1.217  0.020  1.217
 G3N  C5   C4   single  1.440  0.020  1.440
 G3N  C5   C6   double  1.346  0.020  1.346
 G3N  O3A  PA   single  1.646  0.020  1.646
 G3N  C4   N3   single  1.388  0.020  1.388
 G3N  O1A  PA   deloc   1.493  0.020  1.493
 G3N  C6   N1   single  1.361  0.020  1.361
 G3N  PA   O5D  single  1.640  0.020  1.640
 G3N  PA   O2A  deloc   1.495  0.020  1.495
 G3N  N3   C2   single  1.368  0.020  1.368
 G3N  O5D  C5D  single  1.412  0.020  1.412
 G3N  C5D  C4D  single  1.509  0.020  1.509
 G3N  N1   C2   single  1.380  0.020  1.380
 G3N  N1   C1D  single  1.480  0.020  1.480
 G3N  C2   O2   double  1.214  0.020  1.214
 G3N  O4D  C1D  single  1.391  0.020  1.391
 G3N  O4D  C4D  single  1.428  0.020  1.428
 G3N  C2D  C1D  single  1.530  0.020  1.530
 G3N  C2D  O2D  single  1.401  0.020  1.401
 G3N  C2D  C3D  single  1.533  0.020  1.533
 G3N  C4D  C3D  single  1.524  0.020  1.524
 G3N  C3D  O3D  single  1.399  0.020  1.399
 G3N  C1'  H2   single  0.970  0.020  1.090
 G3N  C5'  H3   single  0.970  0.020  1.090
 G3N  C5'  H4   single  0.970  0.020  1.090
 G3N  C4'  H5   single  0.970  0.020  1.090
 G3N  N4'  H6   single  0.890  0.020  1.040
 G3N  N4'  H7   single  0.890  0.020  1.040
 G3N  C3'  H9   single  0.970  0.020  1.090
 G3N  O3'  H10  single  0.850  0.020  0.980
 G3N  C2'  H11  single  0.970  0.020  1.090
 G3N  O2'  H12  single  0.850  0.020  0.980
 G3N  C5D  H14  single  0.970  0.020  1.090
 G3N  C5D  H15  single  0.970  0.020  1.090
 G3N  C4D  H16  single  0.970  0.020  1.090
 G3N  C3D  H17  single  0.970  0.020  1.090
 G3N  O3D  H18  single  0.850  0.020  0.980
 G3N  C2D  H19  single  0.970  0.020  1.090
 G3N  O2D  H20  single  0.850  0.020  0.980
 G3N  C1D  H21  single  0.970  0.020  1.090
 G3N  C6   H22  single  0.930  0.020  1.080
 G3N  C5   H23  single  0.930  0.020  1.080
 G3N  N3   H24  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
 G3N  O3A  PB   O3B   96.93  3.000
 G3N  O3A  PB   O1B  109.83  3.000
 G3N  O3B  PB   O1B  109.44  3.000
 G3N  O3A  PB   O2B  110.77  3.000
 G3N  O1B  PB   O2B  122.40  3.000
 G3N  O3B  PB   O2B  104.27  3.000
 G3N  C1'  O3B  PB   122.03  3.000
 G3N  H2   C1'  C2'  108.77  3.000
 G3N  H2   C1'  O5'  109.87  3.000
 G3N  C2'  C1'  O5'  112.00  3.000
 G3N  H2   C1'  O3B  112.20  3.000
 G3N  C2'  C1'  O3B  108.31  3.000
 G3N  O5'  C1'  O3B  105.70  3.000
 G3N  C5'  O5'  C1'  112.93  3.000
 G3N  H4   C5'  H3   107.41  3.000
 G3N  H4   C5'  C4'  110.28  3.000
 G3N  H3   C5'  C4'  109.80  3.000
 G3N  H4   C5'  O5'  106.64  3.000
 G3N  H3   C5'  O5'  111.24  3.000
 G3N  C4'  C5'  O5'  111.34  3.000
 G3N  H5   C4'  C3'  106.20  3.000
 G3N  H5   C4'  N4'  112.64  3.000
 G3N  C3'  C4'  N4'  111.46  3.000
 G3N  H5   C4'  C5'  107.74  3.000
 G3N  C3'  C4'  C5'  109.52  3.000
 G3N  N4'  C4'  C5'  109.16  3.000
 G3N  H7   N4'  H6   105.23  3.000
 G3N  H7   N4'  C4'  109.58  3.000
 G3N  H6   N4'  C4'  108.67  3.000
 G3N  H9   C3'  C2'  108.49  3.000
 G3N  H9   C3'  O3'  110.75  3.000
 G3N  C2'  C3'  O3'  110.41  3.000
 G3N  H9   C3'  C4'  108.99  3.000
 G3N  C2'  C3'  C4'  109.52  3.000
 G3N  O3'  C3'  C4'  108.65  3.000
 G3N  H10  O3'  C3'  108.38  3.000
 G3N  H11  C2'  O2'  110.73  3.000
 G3N  H11  C2'  C3'  108.76  3.000
 G3N  O2'  C2'  C3'  107.94  3.000
 G3N  H11  C2'  C1'  107.09  3.000
 G3N  O2'  C2'  C1'  111.79  3.000
 G3N  C3'  C2'  C1'  110.51  3.000
 G3N  H12  O2'  C2'  107.95  3.000
 G3N  PA   O3A  PB   126.04  3.000
 G3N  O5D  PA   O2A  109.99  3.000
 G3N  O2A  PA   O1A  122.42  3.000
 G3N  O5D  PA   O1A  105.10  3.000
 G3N  O2A  PA   O3A  109.30  3.000
 G3N  O5D  PA   O3A   99.62  3.000
 G3N  O1A  PA   O3A  107.99  3.000
 G3N  C5D  O5D  PA   119.72  3.000
 G3N  H15  C5D  H14  106.90  3.000
 G3N  H15  C5D  C4D  108.03  3.000
 G3N  H14  C5D  C4D  110.24  3.000
 G3N  H15  C5D  O5D  110.50  3.000
 G3N  H14  C5D  O5D  112.33  3.000
 G3N  C4D  C5D  O5D  108.75  3.000
 G3N  H16  C4D  O4D  109.09  3.000
 G3N  H16  C4D  C3D  109.45  3.000
 G3N  O4D  C4D  C3D  104.51  3.000
 G3N  H16  C4D  C5D  109.08  3.000
 G3N  C3D  C4D  C5D  114.05  3.000
 G3N  O4D  C4D  C5D  110.52  3.000
 G3N  H17  C3D  C2D  109.21  3.000
 G3N  H17  C3D  O3D  111.38  3.000
 G3N  C2D  C3D  O3D  113.84  3.000
 G3N  H17  C3D  C4D  109.88  3.000
 G3N  O3D  C3D  C4D  110.46  3.000
 G3N  C2D  C3D  C4D  101.63  3.000
 G3N  H18  O3D  C3D  108.92  3.000
 G3N  H19  C2D  C1D  112.36  3.000
 G3N  H19  C2D  O2D  111.92  3.000
 G3N  C1D  C2D  O2D  107.37  3.000
 G3N  H19  C2D  C3D  112.32  3.000
 G3N  O2D  C2D  C3D  111.02  3.000
 G3N  C1D  C2D  C3D  101.28  3.000
 G3N  H20  O2D  C2D  107.91  3.000
 G3N  C1D  O4D  C4D  111.47  3.000
 G3N  H21  C1D  N1   106.77  3.000
 G3N  H21  C1D  O4D  110.34  3.000
 G3N  N1   C1D  O4D  109.56  3.000
 G3N  H21  C1D  C2D  111.48  3.000
 G3N  O4D  C1D  C2D  107.10  3.000
 G3N  N1   C1D  C2D  111.62  3.000
 G3N  C2   N1   C6   120.99  3.000
 G3N  C2   N1   C1D  116.30  3.000
 G3N  C6   N1   C1D  122.70  3.000
 G3N  H22  C6   C5   120.07  3.000
 G3N  H22  C6   N1   116.88  3.000
 G3N  C5   C6   N1   123.05  3.000
 G3N  H23  C5   C4   120.52  3.000
 G3N  H23  C5   C6   119.62  3.000
 G3N  C4   C5   C6   119.86  3.000
 G3N  N3   C4   O4   120.46  3.000
 G3N  N3   C4   C5   113.23  3.000
 G3N  O4   C4   C5   126.31  3.000
 G3N  H24  N3   C2   115.22  3.000
 G3N  H24  N3   C4   116.93  3.000
 G3N  C2   N3   C4   127.83  3.000
 G3N  O2   C2   N3   122.57  3.000
 G3N  O2   C2   N1   122.40  3.000
 G3N  N3   C2   N1   115.03  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
 G3N  CONST_01  N3   C2   N1   C1D   180.00   0.0  0
 G3N  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 G3N  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 G3N  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 G3N  CONST_05  O2   C2   N1   C1D     0.00   0.0  0
 G3N  CONST_06  O2   C2   N1   C6    180.00   0.0  0
 G3N  CONST_07  O2   C2   N3   C4    180.00   0.0  0
 G3N  CONST_08  C2   N3   C4   O4    180.00   0.0  0
 G3N  CONST_09  H24  N3   C2   N1    180.00   0.0  0
 G3N  Var_01    C4'  C5'  O5'  C1'   -60.87  30.0  1
 G3N  Var_02    O3A  PB   O3B  C1'    65.48  30.0  3
 G3N  Var_03    C4D  C5D  O5D  PA   -148.66  30.0  3
 G3N  Var_04    O1A  PA   O3A  PB    128.75  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
 G3N  chir_02  C1'  O5'  O3B  C2'  positiv
 G3N  chir_03  C4'  N4'  C3'  C5'  positiv
 G3N  chir_04  C3'  O3'  C2'  C4'  positiv
 G3N  chir_05  C2'  O2'  C1'  C3'  negativ
 G3N  chir_07  C4D  C5D  O4D  C3D  negativ
 G3N  chir_08  C3D  O3D  C4D  C2D  positiv
 G3N  chir_09  C2D  O2D  C3D  C1D  positiv
 G3N  chir_10  C1D  O4D  N1   C2D  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
 G3N  plan-1  C1D  0.020
 G3N  plan-1  N1   0.020
 G3N  plan-1  C6   0.020
 G3N  plan-1  C5   0.020
 G3N  plan-1  C4   0.020
 G3N  plan-1  O4   0.020
 G3N  plan-1  N3   0.020
 G3N  plan-1  C2   0.020
 G3N  plan-1  O2   0.020
 G3N  plan-1  H22  0.020
 G3N  plan-1  H23  0.020
 G3N  plan-1  H24  0.020

