# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 10:09:40 2021
#   Inital geometry file: a 119 line input string
#   Ligand name: [[(2S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@H]3CC[C@@H](CO[P@](O)(=O)O[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
 DG3  DG3  '[[(2S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphono hydrogen phosphate'  ligand  46  30  .  2021-08-08  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DG3
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
 DG3  PG    P  P     0   1.519   -3.1711  22.7711   -0.9816
 DG3  O1G   O  O     0  -0.711   -2.6510  24.1246   -1.2849
 DG3  O2G   O  OH1   0  -0.711   -3.7824  22.7097    0.4690
 DG3  O3G   O  OH1   0  -0.699   -2.0607  21.6753   -1.1776
 DG3  O3B   O  O2    0  -0.683   -4.3431  22.2849   -1.9866
 DG3  PB    P  P     0   1.512   -5.6334  23.0722   -2.5726
 DG3  O1B   O  O     0  -0.640   -6.6431  22.1306   -3.0572
 DG3  O2B   O  OH1   0  -0.732   -6.0194  24.1234   -1.4551
 DG3  O3A   O  O2    0  -0.706   -5.0176  23.9889   -3.7158
 DG3  PA    P  P     0   1.483   -4.1992  25.3908   -3.9696
 DG3  O1A   O  O     0  -0.662   -3.0998  25.1470   -4.9111
 DG3  O2A   O  OH1   0  -0.762   -3.8906  25.9673   -2.5431
 DG3  O5'   O  O2    0  -0.574   -5.2933  26.3634   -4.5620
 DG3  C5'   C  CH2   0  -0.221   -6.4769  26.7998   -3.8820
 DG3  C4'   C  CH1   0   0.039   -7.7022  26.5611   -4.7275
 DG3  O4'   O  O2    0  -0.500   -7.6574  27.3742   -5.9026
 DG3  C3'   C  CH2   0  -0.506   -7.9415  25.1477   -5.2344
 DG3  C2'   C  CH2   0  -0.509   -8.8564  25.4223   -6.4190
 DG3  C1'   C  CH1   0   0.197   -8.2890  26.7319   -6.9691
 DG3  N9    N  NR5   0  -0.525   -7.3097  26.5149   -8.0306
 DG3  C8    C  CR15  0   0.081   -5.9418  26.4531   -7.9421
 DG3  N7    N  N     0  -0.448   -5.3730  26.2214   -9.0875
 DG3  C5    C  CR56  0  -0.088   -6.4095  26.1202   -9.9771
 DG3  C6    C  CR6   0   0.501   -6.4107  25.8822  -11.3815
 DG3  O6    O  O     0  -0.475   -5.4636  25.7038  -12.1291
 DG3  N1    N  NR16  0  -0.727   -7.7209  25.8725  -11.8774
 DG3  C2    C  CR6   0   0.683   -8.8616  26.0541  -11.1484
 DG3  N2    N  NH2   0  -0.832  -10.0210  26.0392  -11.8235
 DG3  N3    N  N     0  -0.515   -8.8562  26.2696   -9.8569
 DG3  C4    C  CR56  0   0.501   -7.6206  26.3004   -9.3347
 DG3  HOG2  H  HOH1  0   0.515   -4.1129  21.8595    0.7935
 DG3  HOG3  H  HOH1  0   0.517   -2.2729  20.7565   -0.9592
 DG3  HOB2  H  HOH1  0   0.520   -6.6774  23.8261   -0.8090
 DG3  HOA2  H  HOH1  0   0.505   -3.3401  25.3592   -1.9646
 DG3  H5'1  H  HCH2  0   0.251   -6.6161  26.2896   -2.9274
 DG3  H5'2  H  HCH2  0   0.277   -6.3600  27.8628   -3.6685
 DG3  H4'   H  HCH1  0   0.250   -8.5532  26.8752   -4.1088
 DG3  H3'1  H  HCH2  0   0.251   -7.0154  24.6712   -5.5621
 DG3  H3'2  H  HCH2  0   0.269   -8.4001  24.5135   -4.4774
 DG3  H2'1  H  HCH2  0   0.276   -8.8756  24.6294   -7.1646
 DG3  H2'2  H  HCH2  0   0.264   -9.8806  25.5897   -6.0809
 DG3  H1'   H  HCH1  0   0.270   -9.0678  27.3691   -7.3944
 DG3  H8    H  HCR5  0   0.289   -5.4197  26.6017   -7.0113
 DG3  HN1   H  HNR6  0   0.425   -7.8093  25.7325  -12.8758
 DG3  HN21  H  HNH2  0   0.411  -10.8710  26.0242  -11.2854
 DG3  HN22  H  HNH2  0   0.414  -10.0729  25.6433  -12.7468

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
 DG3  PG   O1G   double    1.481  0.020  1.481
 DG3  PG   O2G   single    1.575  0.020  1.575
 DG3  PG   O3G   single    1.572  0.020  1.572
 DG3  PG   O3B   single    1.619  0.020  1.619
 DG3  O2G  HOG2  single    0.850  0.020  0.980
 DG3  O3G  HOG3  single    0.850  0.020  0.980
 DG3  O3B  PB    single    1.621  0.020  1.621
 DG3  PB   O1B   double    1.463  0.020  1.463
 DG3  PB   O2B   single    1.582  0.020  1.582
 DG3  PB   O3A   single    1.590  0.020  1.590
 DG3  O2B  HOB2  single    0.850  0.020  0.980
 DG3  O3A  PA    single    1.643  0.020  1.643
 DG3  PA   O1A   double    1.468  0.020  1.468
 DG3  PA   O2A   single    1.569  0.020  1.569
 DG3  PA   O5'   single    1.579  0.020  1.579
 DG3  O2A  HOA2  single    0.850  0.020  0.980
 DG3  O5'  C5'   single    1.433  0.020  1.433
 DG3  C5'  C4'   single    1.508  0.020  1.508
 DG3  C5'  H5'1  single    0.970  0.020  1.090
 DG3  C5'  H5'2  single    0.970  0.020  1.090
 DG3  C4'  O4'   single    1.430  0.020  1.430
 DG3  C4'  C3'   single    1.520  0.020  1.520
 DG3  C4'  H4'   single    0.970  0.020  1.090
 DG3  O4'  C1'   single    1.396  0.020  1.396
 DG3  C3'  C2'   single    1.522  0.020  1.522
 DG3  C3'  H3'1  single    0.970  0.020  1.090
 DG3  C3'  H3'2  single    0.970  0.020  1.090
 DG3  C2'  C1'   single    1.530  0.020  1.530
 DG3  C2'  H2'1  single    0.970  0.020  1.090
 DG3  C2'  H2'2  single    0.970  0.020  1.090
 DG3  C1'  N9    single    1.460  0.020  1.460
 DG3  C1'  H1'   single    0.970  0.020  1.090
 DG3  N9   C8    aromatic  1.372  0.020  1.372
 DG3  N9   C4    aromatic  1.358  0.020  1.358
 DG3  C8   N7    aromatic  1.300  0.020  1.300
 DG3  C8   H8    single    0.930  0.020  1.080
 DG3  N7   C5    aromatic  1.370  0.020  1.370
 DG3  C5   C6    single    1.424  0.020  1.424
 DG3  C5   C4    aromatic  1.383  0.020  1.383
 DG3  C6   O6    double    1.220  0.020  1.220
 DG3  C6   N1    single    1.401  0.020  1.401
 DG3  N1   C2    single    1.366  0.020  1.366
 DG3  N1   HN1   single    0.860  0.020  1.020
 DG3  C2   N2    single    1.342  0.020  1.342
 DG3  C2   N3    double    1.309  0.020  1.309
 DG3  N2   HN21  single    0.890  0.020  1.040
 DG3  N2   HN22  single    0.890  0.020  1.040
 DG3  N3   C4    single    1.342  0.020  1.342

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
 DG3  O3B   PG   O3G   102.98  3.000
 DG3  O3B   PG   O2G   106.21  3.000
 DG3  O3G   PG   O2G   111.20  3.000
 DG3  O3B   PG   O1G   113.68  3.000
 DG3  O3G   PG   O1G   111.30  3.000
 DG3  O2G   PG   O1G   111.12  3.000
 DG3  HOG2  O2G  PG    118.38  3.000
 DG3  HOG3  O3G  PG    118.59  3.000
 DG3  PB    O3B  PG    130.91  3.000
 DG3  O3A   PB   O2B   102.67  3.000
 DG3  O3A   PB   O1B   113.60  3.000
 DG3  O2B   PB   O1B   119.55  3.000
 DG3  O3A   PB   O3B   103.40  3.000
 DG3  O2B   PB   O3B   105.17  3.000
 DG3  O1B   PB   O3B   110.88  3.000
 DG3  HOB2  O2B  PB    115.65  3.000
 DG3  PA    O3A  PB    142.77  3.000
 DG3  O5'   PA   O2A   104.54  3.000
 DG3  O5'   PA   O1A   112.37  3.000
 DG3  O2A   PA   O1A   119.79  3.000
 DG3  O5'   PA   O3A   103.79  3.000
 DG3  O2A   PA   O3A   105.72  3.000
 DG3  O1A   PA   O3A   109.29  3.000
 DG3  HOA2  O2A  PA    114.15  3.000
 DG3  C5'   O5'  PA    125.57  3.000
 DG3  H5'2  C5'  H5'1  107.34  3.000
 DG3  H5'2  C5'  C4'   110.56  3.000
 DG3  H5'1  C5'  C4'   108.23  3.000
 DG3  H5'2  C5'  O5'   107.53  3.000
 DG3  H5'1  C5'  O5'   112.21  3.000
 DG3  C4'   C5'  O5'   110.91  3.000
 DG3  H4'   C4'  C3'   109.38  3.000
 DG3  H4'   C4'  O4'   108.95  3.000
 DG3  C3'   C4'  O4'   105.05  3.000
 DG3  H4'   C4'  C5'   105.58  3.000
 DG3  C3'   C4'  C5'   117.52  3.000
 DG3  O4'   C4'  C5'   110.21  3.000
 DG3  C1'   O4'  C4'   110.61  3.000
 DG3  H3'2  C3'  H3'1  108.17  3.000
 DG3  H3'2  C3'  C2'   113.15  3.000
 DG3  H3'1  C3'  C2'   110.80  3.000
 DG3  H3'2  C3'  C4'   112.08  3.000
 DG3  H3'1  C3'  C4'   111.86  3.000
 DG3  C2'   C3'  C4'   100.74  3.000
 DG3  H2'2  C2'  H2'1  107.90  3.000
 DG3  H2'2  C2'  C1'   109.16  3.000
 DG3  H2'1  C2'  C1'   112.57  3.000
 DG3  H2'2  C2'  C3'   110.53  3.000
 DG3  H2'1  C2'  C3'   114.35  3.000
 DG3  C1'   C2'  C3'   102.21  3.000
 DG3  H1'   C1'  N9    106.36  3.000
 DG3  H1'   C1'  C2'   112.02  3.000
 DG3  N9    C1'  C2'   112.51  3.000
 DG3  H1'   C1'  O4'   110.59  3.000
 DG3  N9    C1'  O4'   108.68  3.000
 DG3  C2'   C1'  O4'   106.68  3.000
 DG3  C4    N9   C8    106.45  3.000
 DG3  C4    N9   C1'   124.61  3.000
 DG3  C8    N9   C1'   128.93  3.000
 DG3  H8    C8   N7    125.02  3.000
 DG3  H8    C8   N9    122.18  3.000
 DG3  N7    C8   N9    112.80  3.000
 DG3  C5    N7   C8    104.74  3.000
 DG3  C4    C5   C6    118.63  3.000
 DG3  C4    C5   N7    110.58  3.000
 DG3  C6    C5   N7    130.79  3.000
 DG3  N1    C6   O6    120.54  3.000
 DG3  N1    C6   C5    110.54  3.000
 DG3  O6    C6   C5    128.91  3.000
 DG3  HN1   N1   C2    118.17  3.000
 DG3  HN1   N1   C6    115.58  3.000
 DG3  C2    N1   C6    126.24  3.000
 DG3  N3    C2   N2    120.11  3.000
 DG3  N3    C2   N1    123.02  3.000
 DG3  N2    C2   N1    116.85  3.000
 DG3  HN22  N2   HN21  116.20  3.000
 DG3  HN22  N2   C2    120.71  3.000
 DG3  HN21  N2   C2    117.46  3.000
 DG3  C4    N3   C2    113.04  3.000
 DG3  N3    C4   C5    128.52  3.000
 DG3  N3    C4   N9    126.04  3.000
 DG3  C5    C4   N9    105.44  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
 DG3  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 DG3  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 DG3  CONST_03  C5    C4   N9   C8      0.00   0.0  0
 DG3  CONST_04  C4    C5   N7   C8      0.00   0.0  0
 DG3  CONST_05  C4    N9   C8   N7      0.00   0.0  0
 DG3  CONST_06  N7    C8   N9   C1'   180.00   0.0  0
 DG3  CONST_07  C5    C4   N9   C1'   180.00   0.0  0
 DG3  CONST_08  N3    C4   N9   C1'     0.00   0.0  0
 DG3  CONST_09  C2    N1   C6   C5      0.00   0.0  0
 DG3  CONST_10  N3    C2   N1   C6      0.00   0.0  0
 DG3  CONST_11  C4    N3   C2   N1      0.00   0.0  0
 DG3  CONST_12  N2    C2   N1   C6    180.00   0.0  0
 DG3  CONST_13  C2    N1   C6   O6    180.00   0.0  0
 DG3  CONST_14  C4    N3   C2   N2    180.00   0.0  0
 DG3  CONST_15  H8    C8   N9   C1'     0.00   0.0  0
 DG3  CONST_16  HN1   N1   C6   C5    180.00   0.0  0
 DG3  CONST_17  HN21  N2   C2   N1    180.00   0.0  0
 DG3  Var_01    C1'   C2'  C3'  C4'    36.31  30.0  1
 DG3  Var_02    C4'   C5'  O5'  PA   -128.05  30.0  3
 DG3  Var_03    O1B   PB   O3B  PG   -160.39  30.0  3
 DG3  Var_04    O1A   PA   O3A  PB    133.44  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
 DG3  chir_03  C4'  C5'  O4'  C3'  negativ
 DG3  chir_04  C1'  O4'  N9   C2'  negativ
 DG3  chir_05  PB   O1B  O2B  O3A  both
 DG3  chir_06  PA   O1A  O2A  O5'  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
 DG3  plan-1  C1'   0.020
 DG3  plan-1  N9    0.020
 DG3  plan-1  C8    0.020
 DG3  plan-1  N7    0.020
 DG3  plan-1  C5    0.020
 DG3  plan-1  C6    0.020
 DG3  plan-1  O6    0.020
 DG3  plan-1  N1    0.020
 DG3  plan-1  C2    0.020
 DG3  plan-1  N2    0.020
 DG3  plan-1  N3    0.020
 DG3  plan-1  C4    0.020
 DG3  plan-1  H8    0.020
 DG3  plan-1  HN1   0.020
 DG3  plan-1  HN21  0.020
 DG3  plan-1  HN22  0.020

