# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 19:20:15 2021
#   Inital geometry file: a 123 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O3
#
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
 XG4  XG4  2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine  ligand  48  31  .  2022-11-18  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XG4
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
 XG4  N1    N  NR16  0  -0.727  -43.9315  -5.1754   -8.0121
 XG4  C2    C  CR6   0   0.685  -44.4881  -6.0897   -8.8603
 XG4  N2    N  NH2   0  -0.832  -43.6843  -7.0585   -9.3216
 XG4  N3    N  N     0  -0.515  -45.7372  -6.0322   -9.2508
 XG4  C4    C  CR56  0   0.503  -46.4004  -4.9865   -8.7357
 XG4  C5    C  CR56  0  -0.088  -45.9363  -4.0120   -7.8713
 XG4  C6    C  CR6   0   0.502  -44.5791  -4.0714   -7.4425
 XG4  O6    O  O     0  -0.474  -43.9782  -3.3202   -6.6926
 XG4  N7    N  N     0  -0.446  -46.9322  -3.1209   -7.5702
 XG4  C8    C  CR15  0   0.085  -47.9667  -3.5455   -8.2315
 XG4  N9    N  NR5   0  -0.525  -47.7028  -4.6765   -8.9631
 XG4  PA    P  P     0   1.501  -52.3789  -2.2016   -7.6273
 XG4  PB    P  P     0   1.485  -53.5776  -4.2828   -5.8378
 XG4  PG    P  P     0   1.434  -56.0039  -3.7629   -7.3910
 XG4  C1'   C  CH1   0   0.185  -48.6107  -5.4551   -9.7999
 XG4  O1A   O  O     0  -0.720  -53.5277  -1.7736   -8.4809
 XG4  O1B   O  O     0  -0.673  -53.0536  -5.3826   -6.6668
 XG4  O1G   O  O     0  -0.683  -55.5584  -4.6710   -8.4617
 XG4  C2'   C  CH2   0  -0.537  -49.2203  -6.6436   -9.0605
 XG4  O2A   O  OH1   0  -0.704  -51.3817  -1.0662   -7.1608
 XG4  O2B   O  OH1   0  -0.705  -53.5697  -4.4324   -4.2651
 XG4  O2G   O  OH1   0  -0.712  -57.4909  -3.8715   -6.8619
 XG4  C3'   C  CH1   0   0.018  -50.5196  -6.0575   -8.5338
 XG4  O3'   O  OH1   0  -0.688  -51.4700  -7.0296   -8.2242
 XG4  N3A   N  NH1   0  -0.952  -52.8030  -2.8259   -6.1297
 XG4  O3B   O  O2    0  -0.690  -55.1532  -4.0104   -6.0051
 XG4  O3G   O  OH1   0  -0.758  -55.9197  -2.2143   -7.6375
 XG4  C4'   C  CH1   0   0.000  -50.9077  -5.1650   -9.7173
 XG4  O4'   O  O2    0  -0.498  -49.6743  -4.6261  -10.1817
 XG4  C5'   C  CH2   0  -0.208  -51.9039  -4.0683   -9.4538
 XG4  O5'   O  O2    0  -0.582  -51.4787  -3.3073   -8.3118
 XG4  HN1   H  HNR6  0   0.425  -42.9592  -5.2906   -7.7559
 XG4  HN2   H  HNH2  0   0.412  -44.1118  -7.8200   -9.8207
 XG4  HN2A  H  HNH2  0   0.415  -42.8002  -7.2519   -8.8828
 XG4  H8    H  HCR5  0   0.284  -48.9377  -3.0780   -8.2322
 XG4  H1'   H  HCH1  0   0.274  -48.0358  -5.7675  -10.6743
 XG4  H2'   H  HCH2  0   0.265  -49.4331  -7.4434   -9.7740
 XG4  H2'A  H  HCH2  0   0.280  -48.5627  -7.0412   -8.2888
 XG4  HO2A  H  HOH1  0   0.515  -51.2312  -0.3651   -7.8118
 XG4  HO2B  H  HOH1  0   0.516  -52.7251  -4.7251   -3.8928
 XG4  HO2G  H  HOH1  0   0.511  -57.8214  -4.7765   -6.7765
 XG4  H3'   H  HCH1  0   0.224  -50.2998  -5.4293   -7.6606
 XG4  HO3'  H  HOH1  0   0.460  -52.1407  -6.5951   -7.6742
 XG4  HN3A  H  HNH1  0   0.455  -52.9404  -2.1188   -5.4114
 XG4  HO3G  H  HOH1  0   0.508  -55.0363  -1.9261   -8.0176
 XG4  H4'   H  HCH1  0   0.248  -51.3568  -5.7955  -10.4976
 XG4  H5'   H  HCH2  0   0.272  -51.9894  -3.4134  -10.3227
 XG4  H5'A  H  HCH2  0   0.256  -52.8799  -4.5209   -9.2733

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
 XG4  C2   N1    single    1.366  0.020  1.366
 XG4  N1   C6    single    1.401  0.020  1.401
 XG4  N1   HN1   single    0.860  0.020  1.020
 XG4  N3   C2    double    1.310  0.020  1.310
 XG4  N2   C2    single    1.341  0.020  1.341
 XG4  N2   HN2   single    0.890  0.020  1.040
 XG4  N2   HN2A  single    0.890  0.020  1.040
 XG4  N3   C4    single    1.341  0.020  1.341
 XG4  N9   C4    aromatic  1.358  0.020  1.358
 XG4  C4   C5    aromatic  1.383  0.020  1.383
 XG4  C5   N7    aromatic  1.370  0.020  1.370
 XG4  C5   C6    single    1.425  0.020  1.425
 XG4  C6   O6    double    1.220  0.020  1.220
 XG4  C8   N7    aromatic  1.299  0.020  1.299
 XG4  N9   C8    aromatic  1.373  0.020  1.373
 XG4  C8   H8    single    0.930  0.020  1.080
 XG4  C1'  N9    single    1.460  0.020  1.460
 XG4  O5'  PA    single    1.582  0.020  1.582
 XG4  O1A  PA    double    1.494  0.020  1.494
 XG4  PA   O2A   single    1.581  0.020  1.581
 XG4  PA   N3A   single    1.677  0.020  1.677
 XG4  O1B  PB    double    1.474  0.020  1.474
 XG4  N3A  PB    single    1.676  0.020  1.676
 XG4  PB   O2B   single    1.580  0.020  1.580
 XG4  PB   O3B   single    1.608  0.020  1.608
 XG4  O1G  PG    double    1.473  0.020  1.473
 XG4  PG   O3B   single    1.645  0.020  1.645
 XG4  PG   O2G   single    1.582  0.020  1.582
 XG4  PG   O3G   single    1.570  0.020  1.570
 XG4  O4'  C1'   single    1.402  0.020  1.402
 XG4  C1'  C2'   single    1.527  0.020  1.527
 XG4  C1'  H1'   single    0.970  0.020  1.090
 XG4  C2'  C3'   single    1.520  0.020  1.520
 XG4  C2'  H2'   single    0.970  0.020  1.090
 XG4  C2'  H2'A  single    0.970  0.020  1.090
 XG4  O2A  HO2A  single    0.850  0.020  0.980
 XG4  O2B  HO2B  single    0.850  0.020  0.980
 XG4  O2G  HO2G  single    0.850  0.020  0.980
 XG4  C4'  C3'   single    1.532  0.020  1.532
 XG4  C3'  O3'   single    1.394  0.020  1.394
 XG4  C3'  H3'   single    0.970  0.020  1.090
 XG4  O3'  HO3'  single    0.850  0.020  0.980
 XG4  N3A  HN3A  single    0.890  0.020  1.040
 XG4  O3G  HO3G  single    0.850  0.020  0.980
 XG4  O4'  C4'   single    1.424  0.020  1.424
 XG4  C4'  C5'   single    1.505  0.020  1.505
 XG4  C4'  H4'   single    0.970  0.020  1.090
 XG4  C5'  O5'   single    1.437  0.020  1.437
 XG4  C5'  H5'   single    0.970  0.020  1.090
 XG4  C5'  H5'A  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
 XG4  HN1   N1   C6   115.52  3.000
 XG4  HN1   N1   C2   118.20  3.000
 XG4  C6    N1   C2   126.28  3.000
 XG4  N3    C2   N2   120.06  3.000
 XG4  N2    C2   N1   116.95  3.000
 XG4  N3    C2   N1   122.98  3.000
 XG4  HN2A  N2   HN2  116.39  3.000
 XG4  HN2A  N2   C2   121.05  3.000
 XG4  HN2   N2   C2   117.58  3.000
 XG4  C4    N3   C2   113.03  3.000
 XG4  N9    C4   C5   105.41  3.000
 XG4  C5    C4   N3   128.58  3.000
 XG4  N9    C4   N3   126.01  3.000
 XG4  N7    C5   C6   130.81  3.000
 XG4  C6    C5   C4   118.59  3.000
 XG4  N7    C5   C4   110.60  3.000
 XG4  O6    C6   C5   128.96  3.000
 XG4  O6    C6   N1   120.50  3.000
 XG4  C5    C6   N1   110.54  3.000
 XG4  C8    N7   C5   104.74  3.000
 XG4  H8    C8   N9   122.03  3.000
 XG4  H8    C8   N7   125.17  3.000
 XG4  N9    C8   N7   112.80  3.000
 XG4  C1'   N9   C8   128.71  3.000
 XG4  C1'   N9   C4   124.81  3.000
 XG4  C8    N9   C4   106.45  3.000
 XG4  O5'   PA   N3A  105.67  3.000
 XG4  N3A   PA   O2A   99.40  3.000
 XG4  O5'   PA   O2A  105.70  3.000
 XG4  N3A   PA   O1A  114.99  3.000
 XG4  O2A   PA   O1A  116.60  3.000
 XG4  O5'   PA   O1A  113.00  3.000
 XG4  O3B   PB   N3A  106.72  3.000
 XG4  O3B   PB   O2B   97.15  3.000
 XG4  N3A   PB   O2B  104.68  3.000
 XG4  O3B   PB   O1B  114.61  3.000
 XG4  O2B   PB   O1B  119.18  3.000
 XG4  N3A   PB   O1B  112.74  3.000
 XG4  O3G   PG   O3B  104.65  3.000
 XG4  O3G   PG   O2G   99.82  3.000
 XG4  O3B   PG   O2G  101.18  3.000
 XG4  O3G   PG   O1G  118.53  3.000
 XG4  O2G   PG   O1G  119.02  3.000
 XG4  O3B   PG   O1G  111.30  3.000
 XG4  H1'   C1'  O4'  110.52  3.000
 XG4  H1'   C1'  C2'  112.04  3.000
 XG4  O4'   C1'  C2'  106.82  3.000
 XG4  H1'   C1'  N9   106.51  3.000
 XG4  C2'   C1'  N9   112.70  3.000
 XG4  O4'   C1'  N9   108.23  3.000
 XG4  H2'A  C2'  H2'  108.25  3.000
 XG4  H2'A  C2'  C3'  114.30  3.000
 XG4  H2'   C2'  C3'  110.01  3.000
 XG4  H2'A  C2'  C1'  112.72  3.000
 XG4  H2'   C2'  C1'  109.35  3.000
 XG4  C3'   C2'  C1'  102.06  3.000
 XG4  HO2A  O2A  PA   114.80  3.000
 XG4  HO2B  O2B  PB   114.57  3.000
 XG4  HO2G  O2G  PG   114.52  3.000
 XG4  H3'   C3'  C4'  109.38  3.000
 XG4  H3'   C3'  O3'  111.02  3.000
 XG4  C4'   C3'  O3'  113.89  3.000
 XG4  H3'   C3'  C2'  108.98  3.000
 XG4  O3'   C3'  C2'  113.00  3.000
 XG4  C4'   C3'  C2'   99.99  3.000
 XG4  HO3'  O3'  C3'  106.55  3.000
 XG4  HN3A  N3A  PB   114.76  3.000
 XG4  HN3A  N3A  PA   113.95  3.000
 XG4  PB    N3A  PA   126.59  3.000
 XG4  PG    O3B  PB   128.31  3.000
 XG4  HO3G  O3G  PG   112.94  3.000
 XG4  H4'   C4'  C5'  105.77  3.000
 XG4  H4'   C4'  O4'  109.85  3.000
 XG4  C5'   C4'  O4'  110.78  3.000
 XG4  H4'   C4'  C3'  108.53  3.000
 XG4  C5'   C4'  C3'  117.19  3.000
 XG4  O4'   C4'  C3'  104.65  3.000
 XG4  C4'   O4'  C1'  110.16  3.000
 XG4  H5'A  C5'  H5'  108.09  3.000
 XG4  H5'A  C5'  O5'  110.67  3.000
 XG4  H5'   C5'  O5'  109.77  3.000
 XG4  H5'A  C5'  C4'  108.59  3.000
 XG4  H5'   C5'  C4'  110.47  3.000
 XG4  O5'   C5'  C4'  109.23  3.000
 XG4  C5'   O5'  PA   123.08  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
 XG4  CONST_01  N7   C8   N9   C4     0.00   0.0  0
 XG4  CONST_02  C8   N7   C5   C4     0.00   0.0  0
 XG4  CONST_03  C8   N9   C4   C5     0.00   0.0  0
 XG4  CONST_04  N9   C8   N7   C5     0.00   0.0  0
 XG4  CONST_05  N9   C4   C5   N7     0.00   0.0  0
 XG4  CONST_06  C1'  N9   C4   N3     0.00   0.0  0
 XG4  CONST_07  C1'  N9   C4   C5   180.00   0.0  0
 XG4  CONST_08  C1'  N9   C8   N7   180.00   0.0  0
 XG4  CONST_09  C4   N3   C2   N1     0.00   0.0  0
 XG4  CONST_10  C5   C6   N1   C2     0.00   0.0  0
 XG4  CONST_11  C6   N1   C2   N3     0.00   0.0  0
 XG4  CONST_12  O6   C6   N1   C2   180.00   0.0  0
 XG4  CONST_13  C6   N1   C2   N2   180.00   0.0  0
 XG4  CONST_14  C4   N3   C2   N2   180.00   0.0  0
 XG4  CONST_15  H8   C8   N9   C4   180.00   0.0  0
 XG4  CONST_16  HN1  N1   C2   N3   180.00   0.0  0
 XG4  CONST_17  HN2  N2   C2   N1   180.00   0.0  0
 XG4  Var_01    C4'  C5'  O5'  PA  -171.43  30.0  1
 XG4  Var_02    O1B  PB   N3A  PA    42.62  30.0  3
 XG4  Var_03    O5'  PA   N3A  PB   -56.17  30.0  1
 XG4  Var_04    O1G  PG   O3B  PB    41.14  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
 XG4  chir_03  C1'  N9   O4'  C2'  positiv
 XG4  chir_04  C3'  O3'  C4'  C2'  positiv
 XG4  chir_05  C4'  O4'  C3'  C5'  negativ
 XG4  chir_06  PA   O1A  O2A  N3A  both
 XG4  chir_07  PB   O2B  O1B  N3A  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
 XG4  plan-1  N1    0.020
 XG4  plan-1  C2    0.020
 XG4  plan-1  N2    0.020
 XG4  plan-1  N3    0.020
 XG4  plan-1  C4    0.020
 XG4  plan-1  C5    0.020
 XG4  plan-1  C6    0.020
 XG4  plan-1  O6    0.020
 XG4  plan-1  N7    0.020
 XG4  plan-1  C8    0.020
 XG4  plan-1  N9    0.020
 XG4  plan-1  C1'   0.020
 XG4  plan-1  HN1   0.020
 XG4  plan-1  HN2   0.020
 XG4  plan-1  HN2A  0.020
 XG4  plan-1  H8    0.020

