# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 03:07:28 2021
#   Inital geometry file: a 117 line input string
#   Ligand name: 4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@@H]2O
#
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
 HF4  HF4  4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one  ligand  45  29  .  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_HF4
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
 HF4  C6   C  CR16  0   0.094  25.6321   5.8968  133.4388
 HF4  N4   N  NH2   0  -0.809  23.8180   3.3577  135.1970
 HF4  C5   C  CR16  0  -0.473  24.5900   5.3105  134.0621
 HF4  C2   C  CR6   0   0.588  26.9638   3.9256  133.7208
 HF4  O3G  O  O     0  -0.667  24.3053   8.0325  128.2156
 HF4  PG   P  P     0   1.493  24.1625   9.4908  128.3105
 HF4  O1G  O  OH1   0  -0.717  22.9621  10.1583  127.5199
 HF4  O2G  O  OH1   0  -0.740  25.3959  10.4175  127.9472
 HF4  O3B  O  O2    0  -0.694  23.9610   9.9310  129.8633
 HF4  PB   P  P     0   1.498  23.9812  11.3807  130.5540
 HF4  O1B  O  OH1   0  -0.716  23.3416  10.9561  131.9347
 HF4  O2B  O  O     0  -0.657  23.3922  12.4869  129.7942
 HF4  O3A  O  O2    0  -0.689  25.5459  11.6468  130.8248
 HF4  PA   P  P     0   1.489  26.6323  10.9701  131.8358
 HF4  O1A  O  OH1   0  -0.715  26.1400  11.3436  133.2908
 HF4  O2A  O  O     0  -0.670  27.9816  11.3640  131.4075
 HF4  O5'  O  O2    0  -0.587  26.2679   9.4299  131.8486
 HF4  C4'  C  CH1   0  -0.025  28.0767   7.8791  131.4178
 HF4  C3'  C  CH1   0  -0.022  28.6095   6.7710  130.5012
 HF4  O3'  O  OH1   0  -0.668  29.9904   6.5793  130.6705
 HF4  C2'  C  CH1   0  -0.033  27.9255   5.5311  131.0675
 HF4  O2'  O  OH1   0  -0.653  26.6286   5.4572  130.5462
 HF4  O4'  O  O2    0  -0.502  27.8369   7.2566  132.6734
 HF4  C1'  C  CH1   0   0.210  27.9281   5.8608  132.5731
 HF4  N1   N  NR6   0  -0.557  26.8112   5.2510  133.2840
 HF4  C4   C  CR6   0   0.515  24.7981   3.9848  134.5483
 HF4  N3   N  N     0  -0.539  25.9404   3.3465  134.3758
 HF4  O2   O  O     0  -0.522  28.0178   3.3464  133.4846
 HF4  H1   H  HCR6  0   0.313  25.5689   6.9088  133.0709
 HF4  H2   H  HNH2  0   0.403  23.9635   2.4317  135.5616
 HF4  H3   H  HNH2  0   0.414  22.9324   3.8000  135.3682
 HF4  H4   H  HCR6  0   0.287  23.6544   5.8325  134.1938
 HF4  H5   H  HOH1  0   0.509  22.1822   9.5940  127.4228
 HF4  H6   H  HOH1  0   0.514  25.7808  10.2777  127.0702
 HF4  H7   H  HOH1  0   0.515  23.0553  11.6902  132.4969
 HF4  H8   H  HOH1  0   0.513  26.3728  12.2372  133.5804
 HF4  H9   H  HCH2  0   0.262  27.0526   9.0338  129.9378
 HF4  H10  H  HCH2  0   0.280  26.0345   7.7953  130.6745
 HF4  H11  H  HCH1  0   0.268  28.8329   8.6581  131.5625
 HF4  H12  H  HCH1  0   0.261  28.3427   6.9367  129.4503
 HF4  H13  H  HOH1  0   0.461  30.4512   7.3779  130.3943
 HF4  H14  H  HCH1  0   0.271  28.5053   4.6272  130.8609
 HF4  H15  H  HOH1  0   0.466  26.2812   4.5703  130.6793
 HF4  H16  H  HCH1  0   0.270  28.8464   5.5060  133.0444
 HF4  C5'  C  CH2   0  -0.239  26.8163   8.5239  130.8753

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
 HF4  O3G  PG   double  1.468  0.020  1.468
 HF4  O2G  PG   single  1.585  0.020  1.585
 HF4  PG   O1G  single  1.585  0.020  1.585
 HF4  PG   O3B  single  1.626  0.020  1.626
 HF4  O2B  PB   double  1.466  0.020  1.466
 HF4  O3B  PB   single  1.606  0.020  1.606
 HF4  PB   O3A  single  1.610  0.020  1.610
 HF4  PB   O1B  single  1.580  0.020  1.580
 HF4  O2'  C2'  single  1.400  0.020  1.400
 HF4  C3'  O3'  single  1.404  0.020  1.404
 HF4  C3'  C2'  single  1.525  0.020  1.525
 HF4  C3'  C4'  single  1.534  0.020  1.534
 HF4  O3A  PA   single  1.631  0.020  1.631
 HF4  C5'  C4'  single  1.516  0.020  1.516
 HF4  C5'  O5'  single  1.438  0.020  1.438
 HF4  C2'  C1'  single  1.541  0.020  1.541
 HF4  C4'  O4'  single  1.422  0.020  1.422
 HF4  O5'  PA   single  1.583  0.020  1.583
 HF4  O2A  PA   double  1.469  0.020  1.469
 HF4  PA   O1A  single  1.581  0.020  1.581
 HF4  C1'  O4'  single  1.402  0.020  1.402
 HF4  C1'  N1   single  1.458  0.020  1.458
 HF4  C6   N1   single  1.353  0.020  1.353
 HF4  C6   C5   double  1.348  0.020  1.348
 HF4  N1   C2   single  1.404  0.020  1.404
 HF4  C5   C4   single  1.427  0.020  1.427
 HF4  C2   O2   double  1.226  0.020  1.226
 HF4  C2   N3   single  1.346  0.020  1.346
 HF4  C4   N3   double  1.320  0.020  1.320
 HF4  C4   N4   single  1.332  0.020  1.332
 HF4  C6   H1   single  0.930  0.020  1.080
 HF4  N4   H2   single  0.860  0.020  1.020
 HF4  N4   H3   single  0.860  0.020  1.020
 HF4  C5   H4   single  0.930  0.020  1.080
 HF4  O1G  H5   single  0.850  0.020  0.980
 HF4  O2G  H6   single  0.850  0.020  0.980
 HF4  O1B  H7   single  0.850  0.020  0.980
 HF4  O1A  H8   single  0.850  0.020  0.980
 HF4  C5'  H9   single  0.970  0.020  1.090
 HF4  C5'  H10  single  0.970  0.020  1.090
 HF4  C4'  H11  single  0.970  0.020  1.090
 HF4  C3'  H12  single  0.970  0.020  1.090
 HF4  O3'  H13  single  0.850  0.020  0.980
 HF4  C2'  H14  single  0.970  0.020  1.090
 HF4  O2'  H15  single  0.850  0.020  0.980
 HF4  C1'  H16  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
 HF4  H1   C6   N1   117.38  3.000
 HF4  H1   C6   C5   121.35  3.000
 HF4  N1   C6   C5   121.25  3.000
 HF4  H3   N4   H2   118.10  3.000
 HF4  H3   N4   C4   121.62  3.000
 HF4  H2   N4   C4   120.23  3.000
 HF4  H4   C5   C4   122.28  3.000
 HF4  H4   C5   C6   121.06  3.000
 HF4  C4   C5   C6   116.65  3.000
 HF4  O2   C2   N3   122.97  3.000
 HF4  N3   C2   N1   118.36  3.000
 HF4  O2   C2   N1   118.67  3.000
 HF4  O3B  PG   O2G   99.04  3.000
 HF4  O3B  PG   O1G  105.57  3.000
 HF4  O2G  PG   O1G  103.23  3.000
 HF4  O3B  PG   O3G  110.03  3.000
 HF4  O1G  PG   O3G  117.37  3.000
 HF4  O2G  PG   O3G  119.35  3.000
 HF4  H5   O1G  PG   114.52  3.000
 HF4  H6   O2G  PG   115.65  3.000
 HF4  PB   O3B  PG   130.79  3.000
 HF4  O3A  PB   O2B  110.68  3.000
 HF4  O3A  PB   O1B  106.91  3.000
 HF4  O2B  PB   O1B  119.55  3.000
 HF4  O1B  PB   O3B   97.36  3.000
 HF4  O3A  PB   O3B  103.52  3.000
 HF4  O2B  PB   O3B  116.96  3.000
 HF4  H7   O1B  PB   115.06  3.000
 HF4  PA   O3A  PB   133.08  3.000
 HF4  O5'  PA   O2A  118.33  3.000
 HF4  O2A  PA   O1A  119.41  3.000
 HF4  O5'  PA   O1A   98.67  3.000
 HF4  O1A  PA   O3A  105.37  3.000
 HF4  O2A  PA   O3A  108.65  3.000
 HF4  O5'  PA   O3A  104.79  3.000
 HF4  H8   O1A  PA   114.75  3.000
 HF4  C5'  O5'  PA   121.31  3.000
 HF4  H11  C4'  O4'  108.13  3.000
 HF4  H11  C4'  C3'  110.67  3.000
 HF4  O4'  C4'  C3'  105.67  3.000
 HF4  H11  C4'  C5'  108.58  3.000
 HF4  O4'  C4'  C5'  111.22  3.000
 HF4  C3'  C4'  C5'  112.47  3.000
 HF4  H12  C3'  C2'  111.69  3.000
 HF4  H12  C3'  O3'  112.04  3.000
 HF4  C2'  C3'  O3'  106.57  3.000
 HF4  H12  C3'  C4'  112.27  3.000
 HF4  C2'  C3'  C4'  102.11  3.000
 HF4  O3'  C3'  C4'  111.60  3.000
 HF4  H13  O3'  C3'  108.84  3.000
 HF4  H14  C2'  C1'  111.13  3.000
 HF4  H14  C2'  O2'  112.16  3.000
 HF4  C1'  C2'  O2'  112.13  3.000
 HF4  H14  C2'  C3'  111.35  3.000
 HF4  C1'  C2'  C3'  100.84  3.000
 HF4  O2'  C2'  C3'  108.67  3.000
 HF4  H15  O2'  C2'  109.39  3.000
 HF4  C1'  O4'  C4'  111.20  3.000
 HF4  H16  C1'  N1   107.34  3.000
 HF4  H16  C1'  O4'  110.33  3.000
 HF4  N1   C1'  O4'  109.37  3.000
 HF4  H16  C1'  C2'  110.71  3.000
 HF4  N1   C1'  C2'  112.68  3.000
 HF4  O4'  C1'  C2'  106.42  3.000
 HF4  C1'  N1   C2   117.61  3.000
 HF4  C2   N1   C6   120.64  3.000
 HF4  C1'  N1   C6   121.59  3.000
 HF4  N3   C4   C5   122.07  3.000
 HF4  N3   C4   N4   118.21  3.000
 HF4  C5   C4   N4   119.72  3.000
 HF4  C4   N3   C2   120.90  3.000
 HF4  H10  C5'  H9   108.04  3.000
 HF4  H10  C5'  C4'  112.26  3.000
 HF4  H9   C5'  C4'  109.00  3.000
 HF4  H10  C5'  O5'  105.84  3.000
 HF4  H9   C5'  O5'  111.65  3.000
 HF4  C4'  C5'  O5'  110.04  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
 HF4  CONST_01  N3   C2   N1   C6     0.00   0.0  0
 HF4  CONST_02  C2   N3   C4   C5     0.00   0.0  0
 HF4  CONST_03  N3   C2   N1   C1'  180.00   0.0  0
 HF4  CONST_04  C4   N3   C2   N1     0.00   0.0  0
 HF4  CONST_05  O2   C2   N1   C6   180.00   0.0  0
 HF4  CONST_06  C2   N3   C4   N4   180.00   0.0  0
 HF4  CONST_07  O2   C2   N1   C1'    0.00   0.0  0
 HF4  CONST_08  O2   C2   N3   C4   180.00   0.0  0
 HF4  CONST_09  H2   N4   C4   C5   180.00   0.0  0
 HF4  CONST_10  H3   N4   C4   C5     0.00   0.0  0
 HF4  Var_01    C4'  C5'  O5'  PA    93.37  30.0  1
 HF4  Var_02    O2B  PB   O3B  PG    37.26  30.0  3
 HF4  Var_03    O5'  PA   O3A  PB    37.85  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
 HF4  chir_03  C4'  C3'  C5'  O4'  negativ
 HF4  chir_04  C3'  O3'  C2'  C4'  negativ
 HF4  chir_05  C2'  O2'  C1'  C3'  positiv
 HF4  chir_06  C1'  O4'  N1   C2'  negativ
 HF4  chir_07  PB   O3B  O3A  O1B  both
 HF4  chir_08  PA   O5'  O2A  O1A  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
 HF4  plan-1  C6   0.020
 HF4  plan-1  N4   0.020
 HF4  plan-1  C5   0.020
 HF4  plan-1  C2   0.020
 HF4  plan-1  C1'  0.020
 HF4  plan-1  N1   0.020
 HF4  plan-1  C4   0.020
 HF4  plan-1  N3   0.020
 HF4  plan-1  O2   0.020
 HF4  plan-1  H1   0.020
 HF4  plan-1  H2   0.020
 HF4  plan-1  H3   0.020
 HF4  plan-1  H4   0.020

