# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 18:47:36 2021
#   Inital geometry file: a 118 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)c2ncn([C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O3)c2n1
#
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
 HF7  HF7  '2'-deoxy-2-methyladenosine 5'-(tetrahydrogen triphosphate)'  ligand  49  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HF7
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
 HF7  C2   C  CR6   0   0.345  56.8724   -3.8312  108.4231
 HF7  O2A  O  O     0  -0.671  58.4876   -6.2093  101.2235
 HF7  PA   P  P     0   1.493  57.3902   -7.0323  101.7480
 HF7  O1A  O  OH1   0  -0.721  57.4888   -7.5891  103.2254
 HF7  O3A  O  O2    0  -0.691  57.1169   -8.3911  100.8845
 HF7  PB   P  P     0   1.511  57.7386   -8.8946   99.4938
 HF7  O1B  O  O     0  -0.656  57.2764  -10.2383   99.1365
 HF7  O2B  O  OH1   0  -0.717  57.4200   -7.6800   98.5388
 HF7  O3B  O  O2    0  -0.687  59.3305   -8.7545   99.7084
 HF7  PG   P  P     0   1.469  60.3394   -9.7197  100.5382
 HF7  O3G  O  OH1   0  -0.713  61.6755   -8.8717  100.4798
 HF7  O2G  O  OH1   0  -0.743  59.7926   -9.4492  102.0077
 HF7  O1G  O  O     0  -0.675  60.3951  -11.1110  100.0709
 HF7  O5'  O  O2    0  -0.572  56.0010   -6.2909  101.7316
 HF7  C4'  C  CH1   0  -0.004  54.1120   -5.8467  103.1685
 HF7  C3'  C  CH1   0  -0.013  53.8298   -4.4495  102.5831
 HF7  O3'  O  OH1   0  -0.671  52.6639   -3.8866  103.1386
 HF7  C2'  C  CH2   0  -0.536  55.0131   -3.6418  103.0830
 HF7  C1'  C  CH1   0   0.222  55.2763   -4.2804  104.4395
 HF7  O4'  O  O2    0  -0.491  54.9360   -5.6426  104.3040
 HF7  N9   N  NR5   0  -0.551  56.6305   -4.1714  104.9137
 HF7  C4   C  CR56  0   0.495  56.9910   -4.0592  106.2295
 HF7  C5   C  CR56  0  -0.018  58.3727   -4.0983  106.2352
 HF7  N7   N  N     0  -0.448  58.8618   -4.2407  104.9611
 HF7  C8   C  CR15  0   0.112  57.8029   -4.2871  104.2115
 HF7  N3   N  N     0  -0.475  56.1960   -3.9305  107.2876
 HF7  CL2  C  CH3   0  -0.729  56.0834   -3.6774  109.6857
 HF7  N1   N  N     0  -0.487  58.2020   -3.8556  108.5669
 HF7  C6   C  CR6   0   0.448  58.9867   -3.9874  107.4963
 HF7  N6   N  NH2   0  -0.819  60.3130   -3.9944  107.6541
 HF7  H1   H  HOH1  0   0.505  58.3201   -8.0346  103.4435
 HF7  H2   H  HOH1  0   0.518  57.4945   -7.8664   97.5915
 HF7  H3   H  HOH1  0   0.512  62.3169   -9.1781   99.8236
 HF7  H4   H  HOH1  0   0.516  60.0707  -10.1025  102.6662
 HF7  H5   H  HCH2  0   0.267  54.1099   -7.0005  101.3630
 HF7  H6   H  HCH2  0   0.266  54.9135   -7.7832  102.7252
 HF7  H7   H  HCH1  0   0.264  53.1687   -6.3153  103.4763
 HF7  H8   H  HCH1  0   0.254  53.7764   -4.4748  101.4887
 HF7  H9   H  HOH1  0   0.455  51.9087   -4.4263  102.8839
 HF7  H10  H  HCH2  0   0.271  55.8546   -3.7568  102.4020
 HF7  H11  H  HCH2  0   0.284  54.7930   -2.5783  103.1644
 HF7  H12  H  HCH1  0   0.255  54.6564   -3.8151  105.2104
 HF7  H13  H  HCR5  0   0.277  57.8255   -4.3840  103.1381
 HF7  H14  H  HCH3  0   0.244  55.0167   -3.6358  109.4794
 HF7  H15  H  HCH3  0   0.252  56.2750   -4.5115  110.3622
 HF7  H16  H  HCH3  0   0.251  56.3752   -2.7671  110.2104
 HF7  H17  H  HNH2  0   0.401  60.7076   -4.0021  108.5789
 HF7  H18  H  HNH2  0   0.409  60.9214   -4.1942  106.8798
 HF7  C5'  C  CH2   0  -0.215  54.7626   -6.8280  102.2195

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
 HF7  O1G  PG   double    1.469  0.020  1.469
 HF7  O1B  PB   double    1.465  0.020  1.465
 HF7  O2B  PB   single    1.578  0.020  1.578
 HF7  O3G  PG   single    1.584  0.020  1.584
 HF7  PG   O3B  single    1.624  0.020  1.624
 HF7  PG   O2G  single    1.591  0.020  1.591
 HF7  PB   O3B  single    1.612  0.020  1.612
 HF7  PB   O3A  single    1.604  0.020  1.604
 HF7  O3A  PA   single    1.633  0.020  1.633
 HF7  O2A  PA   double    1.469  0.020  1.469
 HF7  PA   O5'  single    1.575  0.020  1.575
 HF7  PA   O1A  single    1.582  0.020  1.582
 HF7  O5'  C5'  single    1.435  0.020  1.435
 HF7  C3'  O3'  single    1.409  0.020  1.409
 HF7  C3'  C2'  single    1.517  0.020  1.517
 HF7  C3'  C4'  single    1.541  0.020  1.541
 HF7  C5'  C4'  single    1.512  0.020  1.512
 HF7  C2'  C1'  single    1.522  0.020  1.522
 HF7  C4'  O4'  single    1.418  0.020  1.418
 HF7  C8   N9   aromatic  1.371  0.020  1.371
 HF7  C8   N7   aromatic  1.298  0.020  1.298
 HF7  C1'  O4'  single    1.411  0.020  1.411
 HF7  C1'  N9   single    1.439  0.020  1.439
 HF7  N9   C4   aromatic  1.369  0.020  1.369
 HF7  N7   C5   aromatic  1.372  0.020  1.372
 HF7  C4   C5   aromatic  1.382  0.020  1.382
 HF7  C4   N3   aromatic  1.330  0.020  1.330
 HF7  C5   C6   aromatic  1.407  0.020  1.407
 HF7  N3   C2   aromatic  1.326  0.020  1.326
 HF7  C6   N6   single    1.336  0.020  1.336
 HF7  C6   N1   aromatic  1.334  0.020  1.334
 HF7  C2   N1   aromatic  1.338  0.020  1.338
 HF7  C2   CL2  single    1.497  0.020  1.497
 HF7  O1A  H1   single    0.850  0.020  0.980
 HF7  O2B  H2   single    0.850  0.020  0.980
 HF7  O3G  H3   single    0.850  0.020  0.980
 HF7  O2G  H4   single    0.850  0.020  0.980
 HF7  C5'  H5   single    0.970  0.020  1.090
 HF7  C5'  H6   single    0.970  0.020  1.090
 HF7  C4'  H7   single    0.970  0.020  1.090
 HF7  C3'  H8   single    0.970  0.020  1.090
 HF7  O3'  H9   single    0.850  0.020  0.980
 HF7  C2'  H10  single    0.970  0.020  1.090
 HF7  C2'  H11  single    0.970  0.020  1.090
 HF7  C1'  H12  single    0.970  0.020  1.090
 HF7  C8   H13  single    0.930  0.020  1.080
 HF7  CL2  H14  single    0.970  0.020  1.090
 HF7  CL2  H15  single    0.970  0.020  1.090
 HF7  CL2  H16  single    0.970  0.020  1.090
 HF7  N6   H17  single    0.860  0.020  1.020
 HF7  N6   H18  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
 HF7  N1   C2   CL2  115.80  3.000
 HF7  CL2  C2   N3   117.47  3.000
 HF7  N1   C2   N3   126.73  3.000
 HF7  O5'  PA   O3A  103.80  3.000
 HF7  O5'  PA   O1A  103.32  3.000
 HF7  O3A  PA   O1A  102.20  3.000
 HF7  O1A  PA   O2A  118.96  3.000
 HF7  O5'  PA   O2A  113.06  3.000
 HF7  O3A  PA   O2A  113.74  3.000
 HF7  H1   O1A  PA   115.21  3.000
 HF7  PB   O3A  PA   130.89  3.000
 HF7  O3B  PB   O2B  102.30  3.000
 HF7  O3B  PB   O1B  115.06  3.000
 HF7  O2B  PB   O1B  119.65  3.000
 HF7  O3B  PB   O3A  103.88  3.000
 HF7  O2B  PB   O3A  101.82  3.000
 HF7  O1B  PB   O3A  112.14  3.000
 HF7  H2   O2B  PB   115.37  3.000
 HF7  PG   O3B  PB   129.02  3.000
 HF7  O1G  PG   O2G  117.90  3.000
 HF7  O2G  PG   O3G  103.48  3.000
 HF7  O1G  PG   O3G  117.62  3.000
 HF7  O2G  PG   O3B   99.05  3.000
 HF7  O3G  PG   O3B  100.78  3.000
 HF7  O1G  PG   O3B  115.08  3.000
 HF7  H3   O3G  PG   114.51  3.000
 HF7  H4   O2G  PG   114.49  3.000
 HF7  C5'  O5'  PA   125.55  3.000
 HF7  H7   C4'  O4'  109.66  3.000
 HF7  H7   C4'  C3'  109.66  3.000
 HF7  O4'  C4'  C3'  106.27  3.000
 HF7  H7   C4'  C5'  105.59  3.000
 HF7  O4'  C4'  C5'  110.24  3.000
 HF7  C3'  C4'  C5'  115.39  3.000
 HF7  H8   C3'  C2'  112.28  3.000
 HF7  H8   C3'  O3'  111.27  3.000
 HF7  C2'  C3'  O3'  107.62  3.000
 HF7  H8   C3'  C4'  111.55  3.000
 HF7  C2'  C3'  C4'  102.39  3.000
 HF7  O3'  C3'  C4'  111.35  3.000
 HF7  H9   O3'  C3'  108.72  3.000
 HF7  H11  C2'  H10  107.82  3.000
 HF7  H11  C2'  C1'  112.21  3.000
 HF7  H10  C2'  C1'  112.30  3.000
 HF7  H11  C2'  C3'  112.76  3.000
 HF7  H10  C2'  C3'  109.91  3.000
 HF7  C1'  C2'  C3'  101.84  3.000
 HF7  H12  C1'  N9   105.61  3.000
 HF7  H12  C1'  O4'  109.99  3.000
 HF7  N9   C1'  O4'  109.38  3.000
 HF7  H12  C1'  C2'  110.60  3.000
 HF7  N9   C1'  C2'  115.13  3.000
 HF7  O4'  C1'  C2'  106.13  3.000
 HF7  C1'  O4'  C4'  110.86  3.000
 HF7  C8   N9   C4   105.90  3.000
 HF7  C4   N9   C1'  124.81  3.000
 HF7  C8   N9   C1'  129.00  3.000
 HF7  N3   C4   C5   126.66  3.000
 HF7  N3   C4   N9   127.98  3.000
 HF7  C5   C4   N9   105.36  3.000
 HF7  C6   C5   N7   133.22  3.000
 HF7  C6   C5   C4   115.96  3.000
 HF7  N7   C5   C4   110.82  3.000
 HF7  C8   N7   C5   104.42  3.000
 HF7  H13  C8   N7   124.13  3.000
 HF7  H13  C8   N9   122.37  3.000
 HF7  N7   C8   N9   113.49  3.000
 HF7  C4   N3   C2   112.57  3.000
 HF7  H16  CL2  H15  107.03  3.000
 HF7  H16  CL2  H14  108.78  3.000
 HF7  H15  CL2  H14  108.62  3.000
 HF7  H16  CL2  C2   110.52  3.000
 HF7  H15  CL2  C2   110.60  3.000
 HF7  H14  CL2  C2   111.17  3.000
 HF7  C6   N1   C2   120.02  3.000
 HF7  N6   C6   N1   119.33  3.000
 HF7  N1   C6   C5   118.06  3.000
 HF7  N6   C6   C5   122.61  3.000
 HF7  H18  N6   H17  118.01  3.000
 HF7  H18  N6   C6   120.75  3.000
 HF7  H17  N6   C6   119.89  3.000
 HF7  H6   C5'  H5   107.95  3.000
 HF7  H6   C5'  C4'  109.67  3.000
 HF7  H5   C5'  C4'  109.75  3.000
 HF7  H6   C5'  O5'  111.46  3.000
 HF7  H5   C5'  O5'  107.98  3.000
 HF7  C4'  C5'  O5'  109.98  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
 HF7  CONST_01  N9   C4   N3   C2   180.00   0.0  0
 HF7  CONST_02  C5   C4   N3   C2     0.00   0.0  0
 HF7  CONST_03  C5   C6   N1   C2     0.00   0.0  0
 HF7  CONST_04  C5   N7   C8   N9     0.00   0.0  0
 HF7  CONST_05  N7   C5   C4   N9     0.00   0.0  0
 HF7  CONST_06  C6   C5   C4   N9   180.00   0.0  0
 HF7  CONST_07  N7   C8   N9   C4     0.00   0.0  0
 HF7  CONST_08  C8   N7   C5   C4     0.00   0.0  0
 HF7  CONST_09  N1   C6   C5   C4     0.00   0.0  0
 HF7  CONST_10  N1   C2   N3   C4     0.00   0.0  0
 HF7  CONST_11  C8   N9   C4   C5     0.00   0.0  0
 HF7  CONST_12  N3   C4   C5   N7   180.00   0.0  0
 HF7  CONST_13  N1   C6   C5   N7   180.00   0.0  0
 HF7  CONST_14  N3   C4   N9   C8   180.00   0.0  0
 HF7  CONST_15  C6   C5   N7   C8   180.00   0.0  0
 HF7  CONST_16  C6   C5   C4   N3     0.00   0.0  0
 HF7  CONST_17  C6   N1   C2   N3     0.00   0.0  0
 HF7  CONST_18  N7   C8   N9   C1'  180.00   0.0  0
 HF7  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 HF7  CONST_20  N3   C4   N9   C1'    0.00   0.0  0
 HF7  CONST_21  N6   C6   N1   C2   180.00   0.0  0
 HF7  CONST_22  N6   C6   C5   C4   180.00   0.0  0
 HF7  CONST_23  CL2  C2   N3   C4   180.00   0.0  0
 HF7  CONST_24  N6   C6   C5   N7     0.00   0.0  0
 HF7  CONST_25  C6   N1   C2   CL2  180.00   0.0  0
 HF7  CONST_26  H13  C8   N9   C1'    0.00   0.0  0
 HF7  CONST_27  H17  N6   C6   C5   180.00   0.0  0
 HF7  CONST_28  H18  N6   C6   C5     0.00   0.0  0
 HF7  Var_01    H14  CL2  C2   N3    -1.85  30.0  2
 HF7  Var_02    C4'  C5'  O5'  PA   128.87  30.0  3
 HF7  Var_03    O1B  PB   O3A  PA   175.55  30.0  2
 HF7  Var_04    O1G  PG   O3B  PB    59.78  30.0  1
 HF7  Var_05    O5'  PA   O3A  PB   116.22  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
 HF7  chir_03  C4'  C3'  C5'  O4'  negativ
 HF7  chir_04  C3'  O3'  C2'  C4'  negativ
 HF7  chir_05  C1'  O4'  N9   C2'  negativ
 HF7  chir_06  PA   O2A  O5'  O1A  both
 HF7  chir_07  PB   O2B  O3B  O3A  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
 HF7  plan-1  C2   0.020
 HF7  plan-1  C1'  0.020
 HF7  plan-1  N9   0.020
 HF7  plan-1  C4   0.020
 HF7  plan-1  C5   0.020
 HF7  plan-1  N7   0.020
 HF7  plan-1  C8   0.020
 HF7  plan-1  N3   0.020
 HF7  plan-1  CL2  0.020
 HF7  plan-1  N1   0.020
 HF7  plan-1  C6   0.020
 HF7  plan-1  N6   0.020
 HF7  plan-1  H13  0.020
 HF7  plan-2  C6   0.020
 HF7  plan-2  N6   0.020
 HF7  plan-2  H17  0.020
 HF7  plan-2  H18  0.020

