# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  3 03:17:30 2021
#   Inital geometry file: a 140 line input string
#   Ligand name: 5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=C(C)C(=O)N1)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N
#
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
 YGP  YGP  5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine  ligand  54  33  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YGP
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
 YGP  C2   C  CR6   0   0.692  26.7139  -48.3225   9.0579
 YGP  N2   N  NH2   0  -0.833  27.8439  -48.9401   9.4341
 YGP  C4   C  CR56  0   0.532  24.8574  -48.1352   7.8734
 YGP  C5   C  CR56  0  -0.083  24.5205  -46.8863   8.3560
 YGP  C6   C  CR6   0   0.503  25.3935  -46.2599   9.2876
 YGP  O6   O  O     0  -0.485  25.3047  -45.1496   9.7942
 YGP  N1   N  NR16  0  -0.719  26.4706  -47.0936   9.5975
 YGP  N3   N  N     0  -0.518  25.9159  -48.8901   8.1891
 YGP  N7   N  N     0  -0.431  23.3678  -46.4355   7.7656
 YGP  C8   C  CR15  0   0.105  23.0179  -47.3848   6.9572
 YGP  N9   N  NR5   0  -0.540  23.8776  -48.4603   6.9826
 YGP  C1'  C  CR15  0   0.151  23.8354  -49.6958   6.2321
 YGP  O4'  O  O     0  -0.482  24.2930  -49.5039   4.9202
 YGP  C2'  C  CR15  0  -0.062  22.4352  -50.3223   6.1150
 YGP  O2'  O  OH1   0  -0.658  22.5329  -51.7132   5.9943
 YGP  C3'  C  CR15  0  -0.005  21.9609  -49.7705   4.7668
 YGP  O3'  O  OH1   0  -0.658  21.0267  -50.5480   4.0851
 YGP  C4'  C  CR15  0   0.016  23.2650  -49.7172   3.9690
 YGP  C5'  C  CH2   0  -0.191  23.3199  -48.6554   2.9001
 YGP  O5'  O  O2    0  -0.588  23.1010  -47.3826   3.5170
 YGP  PBG  P  P     0   1.484  22.8661  -46.0622   2.6731
 YGP  OAI  O  OH1   0  -0.721  21.6511  -45.4557   3.5009
 YGP  OAF  O  O     0  -0.684  22.7142  -46.1979   1.2154
 YGP  OAR  O  O2    0  -0.608  24.1459  -45.1310   2.9938
 YGP  CAW  C  CR6   0   0.467  24.6374  -44.9112   4.2596
 YGP  CAK  C  CR16  0  -0.488  24.0081  -43.9105   5.0355
 YGP  CAT  C  CR6   0   0.407  24.5043  -43.6510   6.2722
 YGP  CAA  C  CH3   0  -0.733  23.9183  -42.6730   7.2299
 YGP  NAO  N  NR16  0  -0.707  25.5985  -44.3292   6.6899
 YGP  CAX  C  CR6   0   0.524  26.2418  -45.3371   6.0048
 YGP  OAD  O  O     0  -0.501  27.1946  -45.9195   6.5190
 YGP  CAV  C  CR6   0  -0.193  25.7156  -45.6249   4.6905
 YGP  CAB  C  CH3   0  -0.728  26.3823  -46.7084   3.9085
 YGP  H1   H  HNH2  0   0.411  27.9516  -49.9066   9.1773
 YGP  H2   H  HNH2  0   0.413  28.3482  -48.6388  10.2504
 YGP  H3   H  HNR6  0   0.424  27.1483  -46.7095  10.2437
 YGP  H4   H  HCR5  0   0.285  22.1477  -47.3586   6.3206
 YGP  H5   H  HCR5  0   0.273  24.5123  -50.3726   6.7578
 YGP  H6   H  HCR5  0   0.264  21.7875  -50.0288   6.9495
 YGP  H7   H  HOH1  0   0.461  22.7918  -52.0786   6.8462
 YGP  H8   H  HCR5  0   0.244  21.5777  -48.7551   4.9263
 YGP  H9   H  HOH1  0   0.462  20.1609  -50.4086   4.4807
 YGP  H10  H  HCR5  0   0.254  23.4143  -50.6815   3.4654
 YGP  H11  H  HCH2  0   0.261  24.2924  -48.6687   2.4031
 YGP  H12  H  HCH2  0   0.261  22.5514  -48.8643   2.1530
 YGP  H13  H  HOH1  0   0.506  21.2869  -44.6353   3.1399
 YGP  H14  H  HCR6  0   0.272  23.1519  -43.3680   4.6645
 YGP  H16  H  HCH3  0   0.264  23.0232  -42.2138   6.8182
 YGP  H17  H  HCH3  0   0.265  23.6531  -43.1777   8.1605
 YGP  H18  H  HCH3  0   0.265  24.6298  -41.8819   7.4719
 YGP  H19  H  HCH3  0   0.237  26.1297  -46.6712   2.8513
 YGP  H20  H  HCH3  0   0.244  27.4660  -46.6393   3.9966
 YGP  H21  H  HCH3  0   0.257  26.0885  -47.6895   4.2845
 YGP  H15  H  HNR6  0   0.412  25.9391  -44.1464   7.6255

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
 YGP  CAB  CAV  single    1.493  0.020  1.493
 YGP  OAD  CAX  double    1.229  0.020  1.229
 YGP  CAV  CAX  single    1.445  0.020  1.445
 YGP  CAV  CAW  double    1.363  0.020  1.363
 YGP  CAX  NAO  single    1.378  0.020  1.378
 YGP  OAF  PBG  double    1.472  0.020  1.472
 YGP  OAR  CAW  single    1.376  0.020  1.376
 YGP  OAR  PBG  single    1.615  0.020  1.615
 YGP  CAW  CAK  single    1.414  0.020  1.414
 YGP  C5'  C4'  single    1.508  0.020  1.508
 YGP  C5'  O5'  single    1.431  0.020  1.431
 YGP  PBG  O5'  single    1.585  0.020  1.585
 YGP  PBG  OAI  single    1.590  0.020  1.590
 YGP  NAO  CAT  single    1.353  0.020  1.353
 YGP  C4'  O4'  single    1.417  0.020  1.417
 YGP  C4'  C3'  single    1.530  0.020  1.530
 YGP  CAK  CAT  double    1.358  0.020  1.358
 YGP  O3'  C3'  single    1.394  0.020  1.394
 YGP  CAT  CAA  single    1.489  0.020  1.489
 YGP  O4'  C1'  single    1.403  0.020  1.403
 YGP  C3'  C2'  single    1.532  0.020  1.532
 YGP  O2'  C2'  single    1.400  0.020  1.400
 YGP  C2'  C1'  single    1.538  0.020  1.538
 YGP  C1'  N9   single    1.446  0.020  1.446
 YGP  C8   N9   aromatic  1.377  0.020  1.377
 YGP  C8   N7   aromatic  1.295  0.020  1.295
 YGP  N9   C4   aromatic  1.364  0.020  1.364
 YGP  N7   C5   aromatic  1.371  0.020  1.371
 YGP  C4   C5   aromatic  1.381  0.020  1.381
 YGP  C4   N3   single    1.338  0.020  1.338
 YGP  C5   C6   single    1.422  0.020  1.422
 YGP  N3   C2   double    1.309  0.020  1.309
 YGP  C6   O6   double    1.224  0.020  1.224
 YGP  C6   N1   single    1.397  0.020  1.397
 YGP  C2   N1   single    1.364  0.020  1.364
 YGP  C2   N2   single    1.342  0.020  1.342
 YGP  N2   H1   single    0.890  0.020  1.040
 YGP  N2   H2   single    0.890  0.020  1.040
 YGP  N1   H3   single    0.860  0.020  1.020
 YGP  C8   H4   single    0.930  0.020  1.080
 YGP  C1'  H5   single    0.970  0.020  1.090
 YGP  C2'  H6   single    0.970  0.020  1.090
 YGP  O2'  H7   single    0.850  0.020  0.980
 YGP  C3'  H8   single    0.970  0.020  1.090
 YGP  O3'  H9   single    0.850  0.020  0.980
 YGP  C4'  H10  single    0.970  0.020  1.090
 YGP  C5'  H11  single    0.970  0.020  1.090
 YGP  C5'  H12  single    0.970  0.020  1.090
 YGP  OAI  H13  single    0.850  0.020  0.980
 YGP  CAK  H14  single    0.930  0.020  1.080
 YGP  CAA  H16  single    0.970  0.020  1.090
 YGP  CAA  H17  single    0.970  0.020  1.090
 YGP  CAA  H18  single    0.970  0.020  1.090
 YGP  CAB  H19  single    0.970  0.020  1.090
 YGP  CAB  H20  single    0.970  0.020  1.090
 YGP  CAB  H21  single    0.970  0.020  1.090
 YGP  NAO  H15  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
 YGP  N3   C2   N1   122.98  3.000
 YGP  N1   C2   N2   117.01  3.000
 YGP  N3   C2   N2   119.99  3.000
 YGP  H2   N2   H1   116.19  3.000
 YGP  H2   N2   C2   120.80  3.000
 YGP  H1   N2   C2   117.45  3.000
 YGP  N9   C4   N3   126.02  3.000
 YGP  N3   C4   C5   128.39  3.000
 YGP  N9   C4   C5   105.59  3.000
 YGP  N7   C5   C6   130.79  3.000
 YGP  C6   C5   C4   118.53  3.000
 YGP  N7   C5   C4   110.61  3.000
 YGP  N1   C6   O6   120.37  3.000
 YGP  N1   C6   C5   110.84  3.000
 YGP  O6   C6   C5   128.78  3.000
 YGP  H3   N1   C6   115.56  3.000
 YGP  H3   N1   C2   118.36  3.000
 YGP  C6   N1   C2   125.98  3.000
 YGP  C4   N3   C2   113.22  3.000
 YGP  C8   N7   C5   104.77  3.000
 YGP  H4   C8   N9   122.25  3.000
 YGP  H4   C8   N7   124.65  3.000
 YGP  N9   C8   N7   113.10  3.000
 YGP  C1'  N9   C8   129.75  3.000
 YGP  C8   N9   C4   105.93  3.000
 YGP  C1'  N9   C4   124.31  3.000
 YGP  H5   C1'  C2'  110.39  3.000
 YGP  H5   C1'  O4'  109.44  3.000
 YGP  C2'  C1'  O4'  106.35  3.000
 YGP  H5   C1'  N9   105.16  3.000
 YGP  C2'  C1'  N9   114.46  3.000
 YGP  O4'  C1'  N9   111.03  3.000
 YGP  C4'  O4'  C1'  111.76  3.000
 YGP  H6   C2'  C3'  112.98  3.000
 YGP  H6   C2'  O2'  111.90  3.000
 YGP  C3'  C2'  O2'  107.68  3.000
 YGP  H6   C2'  C1'  111.76  3.000
 YGP  O2'  C2'  C1'  110.35  3.000
 YGP  C3'  C2'  C1'  101.66  3.000
 YGP  H7   O2'  C2'  108.64  3.000
 YGP  H8   C3'  C4'  109.96  3.000
 YGP  H8   C3'  O3'  110.69  3.000
 YGP  C4'  C3'  O3'  109.63  3.000
 YGP  H8   C3'  C2'  108.28  3.000
 YGP  O3'  C3'  C2'  115.91  3.000
 YGP  C4'  C3'  C2'  101.98  3.000
 YGP  H9   O3'  C3'  108.75  3.000
 YGP  H10  C4'  C5'  106.76  3.000
 YGP  H10  C4'  C3'  108.93  3.000
 YGP  C5'  C4'  C3'  115.17  3.000
 YGP  H10  C4'  O4'  109.97  3.000
 YGP  C3'  C4'  O4'  105.88  3.000
 YGP  C5'  C4'  O4'  110.10  3.000
 YGP  H12  C5'  H11  108.24  3.000
 YGP  H12  C5'  O5'  110.94  3.000
 YGP  H11  C5'  O5'  110.07  3.000
 YGP  H12  C5'  C4'  108.95  3.000
 YGP  H11  C5'  C4'  110.27  3.000
 YGP  O5'  C5'  C4'  108.37  3.000
 YGP  PBG  O5'  C5'  122.28  3.000
 YGP  OAR  PBG  OAF  109.37  3.000
 YGP  OAR  PBG  OAI  106.39  3.000
 YGP  OAF  PBG  OAI  118.16  3.000
 YGP  OAI  PBG  O5'   98.84  3.000
 YGP  OAR  PBG  O5'  104.90  3.000
 YGP  OAF  PBG  O5'  117.77  3.000
 YGP  H13  OAI  PBG  114.63  3.000
 YGP  CAW  OAR  PBG  123.92  3.000
 YGP  CAV  CAW  CAK  123.31  3.000
 YGP  CAK  CAW  OAR  117.32  3.000
 YGP  CAV  CAW  OAR  119.34  3.000
 YGP  H14  CAK  CAT  120.46  3.000
 YGP  H14  CAK  CAW  121.34  3.000
 YGP  CAT  CAK  CAW  118.19  3.000
 YGP  NAO  CAT  CAA  116.66  3.000
 YGP  CAA  CAT  CAK  124.59  3.000
 YGP  NAO  CAT  CAK  118.74  3.000
 YGP  H18  CAA  H17  107.74  3.000
 YGP  H18  CAA  H16  108.34  3.000
 YGP  H17  CAA  H16  108.55  3.000
 YGP  H18  CAA  CAT  111.24  3.000
 YGP  H17  CAA  CAT  109.90  3.000
 YGP  H16  CAA  CAT  110.97  3.000
 YGP  H15  NAO  CAX  115.75  3.000
 YGP  H15  NAO  CAT  117.83  3.000
 YGP  CAX  NAO  CAT  126.19  3.000
 YGP  CAV  CAX  OAD  124.64  3.000
 YGP  CAV  CAX  NAO  115.34  3.000
 YGP  OAD  CAX  NAO  120.02  3.000
 YGP  CAB  CAV  CAX  117.28  3.000
 YGP  CAX  CAV  CAW  118.13  3.000
 YGP  CAB  CAV  CAW  124.58  3.000
 YGP  H21  CAB  H20  107.27  3.000
 YGP  H21  CAB  H19  107.65  3.000
 YGP  H20  CAB  H19  107.90  3.000
 YGP  H21  CAB  CAV  110.60  3.000
 YGP  H20  CAB  CAV  110.84  3.000
 YGP  H19  CAB  CAV  112.37  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
 YGP  CONST_01  N7   C8   N9   C4     0.00   0.0  0
 YGP  CONST_02  C8   N7   C5   C4     0.00   0.0  0
 YGP  CONST_03  N9   C8   N7   C5     0.00   0.0  0
 YGP  CONST_04  C8   N9   C4   C5     0.00   0.0  0
 YGP  CONST_05  N9   C4   C5   N7     0.00   0.0  0
 YGP  CONST_06  C1'  N9   C4   C5   180.00   0.0  0
 YGP  CONST_07  C1'  N9   C4   N3     0.00   0.0  0
 YGP  CONST_08  C1'  N9   C8   N7   180.00   0.0  0
 YGP  CONST_09  C5   C6   N1   C2     0.00   0.0  0
 YGP  CONST_10  N1   C2   N3   C4     0.00   0.0  0
 YGP  CONST_11  N3   C2   N1   C6     0.00   0.0  0
 YGP  CONST_12  CAV  CAX  NAO  CAT    0.00   0.0  0
 YGP  CONST_13  O6   C6   N1   C2   180.00   0.0  0
 YGP  CONST_14  C4   N3   C2   N2   180.00   0.0  0
 YGP  CONST_15  C6   N1   C2   N2   180.00   0.0  0
 YGP  CONST_16  OAD  CAX  NAO  CAT  180.00   0.0  0
 YGP  CONST_17  H4   C8   N9   C4   180.00   0.0  0
 YGP  CONST_18  H3   N1   C6   C5   180.00   0.0  0
 YGP  CONST_19  H15  NAO  CAX  CAV  180.00   0.0  0
 YGP  CONST_20  H1   N2   C2   N1   180.00   0.0  0
 YGP  Var_01    CAV  CAW  OAR  PBG   99.10  30.0  3
 YGP  Var_02    H19  CAB  CAV  CAW   17.80  30.0  3
 YGP  Var_03    H16  CAA  CAT  CAK    1.59  30.0  3
 YGP  Var_04    OAF  PBG  O5'  C5'    7.30  30.0  1
 YGP  Var_05    H11  C5'  O5'  PBG   69.09  30.0  1

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
 YGP  chir_01  C1'  O4'  C2'  N9   positiv
 YGP  chir_02  C2'  O2'  C1'  C3'  negativ
 YGP  chir_03  C3'  O3'  C4'  C2'  positiv
 YGP  chir_04  C4'  O4'  C3'  C5'  negativ
 YGP  chir_05  PBG  OAR  O5'  OAI  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
 YGP  plan-1  OAR  0.020
 YGP  plan-1  CAW  0.020
 YGP  plan-1  CAK  0.020
 YGP  plan-1  CAT  0.020
 YGP  plan-1  CAA  0.020
 YGP  plan-1  NAO  0.020
 YGP  plan-1  CAX  0.020
 YGP  plan-1  OAD  0.020
 YGP  plan-1  CAV  0.020
 YGP  plan-1  CAB  0.020
 YGP  plan-1  H14  0.020
 YGP  plan-1  H15  0.020
 YGP  plan-2  C2   0.020
 YGP  plan-2  N2   0.020
 YGP  plan-2  C4   0.020
 YGP  plan-2  C5   0.020
 YGP  plan-2  C6   0.020
 YGP  plan-2  O6   0.020
 YGP  plan-2  N1   0.020
 YGP  plan-2  N3   0.020
 YGP  plan-2  N7   0.020
 YGP  plan-2  C8   0.020
 YGP  plan-2  N9   0.020
 YGP  plan-2  C1'  0.020
 YGP  plan-2  H1   0.020
 YGP  plan-2  H2   0.020
 YGP  plan-2  H3   0.020
 YGP  plan-2  H4   0.020

