# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 21:02:51 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)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)O[P](O)(=O)[C@@H](F)[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
 FHG  FHG  2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine  ligand  45  32  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FHG
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
 FHG  P1   P  P      0   1.352   1.3690  -1.5142   0.2407
 FHG  O1A  O  OP    -1  -0.820   1.8653  -1.1580  -1.1297
 FHG  O2A  O  O      0  -0.820   1.6110  -2.8975   0.7695
 FHG  O3A  O  O2     0  -0.665   1.7691  -0.4053   1.3499
 FHG  O5'  O  O2     0  -0.690  -0.2536  -1.1972   0.3193
 FHG  P2   P  P      0   1.210   3.1296   0.5897   1.3847
 FHG  O1B  O  O      0  -0.843   4.3115  -0.2154   0.9278
 FHG  O2B  O  OP    -1  -0.813   3.0861   1.1565   2.7756
 FHG  C3B  C  CH1    0  -0.312   2.6882   1.8525   0.1428
 FHG  F2B  F  F      0  -0.401   1.5719   2.5504   0.6740
 FHG  P3   P  P      0   1.098   4.0382   3.0650  -0.3225
 FHG  O1G  O  OP    -1  -0.961   4.9139   2.2625  -1.2861
 FHG  O2G  O  OP    -1  -1.008   3.2807   4.2191  -0.9872
 FHG  O3G  O  O      0  -0.785   4.7316   3.4521   0.9857
 FHG  C5'  C  CH2    0  -0.169  -1.1161  -2.0063  -0.4414
 FHG  C4'  C  CH1    0   0.042  -2.0268  -2.8171   0.4568
 FHG  O4'  O  O2     0  -0.471  -2.8054  -1.9689   1.2995
 FHG  C1'  C  CH1    0   0.203  -4.1544  -2.0370   0.9508
 FHG  N9   N  NR5    0  -0.584  -4.4917  -0.9796  -0.0002
 FHG  C4   C  CR56   0   0.494  -4.4807   0.3487   0.2996
 FHG  N3   N  N      0  -0.489  -4.2602   0.8863   1.5071
 FHG  C2   C  CR6    0   0.669  -4.3050   2.1942   1.5036
 FHG  N2   N  NH2    0  -0.841  -4.0526   2.8776   2.6310
 FHG  N1   N  NR16   0  -0.630  -4.5594   2.9303   0.3815
 FHG  C6   C  CR6    0   0.507  -4.8106   2.4220  -0.8983
 FHG  O6   O  O      0  -0.441  -5.0296   3.1723  -1.8344
 FHG  C5   C  CR56   0  -0.120  -4.7588   0.9978  -0.8884
 FHG  N7   N  N      0  -0.458  -4.9413   0.0941  -1.9025
 FHG  C8   C  CR15   0   0.095  -4.7714  -1.0636  -1.3433
 FHG  C2'  C  CH2    0  -0.541  -4.3434  -3.4291   0.3776
 FHG  C3'  C  CH1    0   0.006  -3.0156  -3.6812  -0.3409
 FHG  O3'  O  OH1    0  -0.713  -2.5876  -5.0178  -0.3345
 FHG  H3   H  HCH1   0   0.153   2.3405   1.3447  -0.7613
 FHG  H6   H  HCH2   0   0.201  -1.7139  -1.3662  -1.1021
 FHG  H7   H  HCH2   0   0.252  -0.5825  -2.7092  -1.0932
 FHG  H8   H  HCH1   0   0.237  -1.4180  -3.4593   1.1032
 FHG  H9   H  HCH1   0   0.251  -4.7503  -1.8586   1.8458
 FHG  H10  H  HNH2   0   0.414  -4.3171   3.8444   2.7153
 FHG  H11  H  HNH2   0   0.409  -4.0129   2.3536   3.4890
 FHG  H12  H  HNR6   0   0.432  -4.5549   3.9396   0.4594
 FHG  H13  H  HCR5   0   0.296  -4.8500  -2.0100  -1.8556
 FHG  H14  H  HCH2   0   0.279  -4.4379  -4.1252   1.2130
 FHG  H15  H  HCH2   0   0.270  -5.2247  -3.5477  -0.2523
 FHG  H16  H  HCH1   0   0.258  -3.0804  -3.3154  -1.3749
 FHG  H17  H  HOH1   0   0.446  -3.1013  -5.5030  -0.9872

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
 FHG  N2   C2   single    1.342  0.020  1.342
 FHG  C2   N1   single    1.366  0.020  1.366
 FHG  C2   N3   double    1.309  0.020  1.309
 FHG  N1   C6   single    1.400  0.020  1.400
 FHG  N3   C4   single    1.340  0.020  1.340
 FHG  C6   O6   double    1.219  0.020  1.219
 FHG  C6   C5   single    1.425  0.020  1.425
 FHG  C4   C5   aromatic  1.382  0.020  1.382
 FHG  C4   N9   aromatic  1.362  0.020  1.362
 FHG  C2'  C1'  single    1.517  0.020  1.517
 FHG  C2'  C3'  single    1.531  0.020  1.531
 FHG  C5   N7   aromatic  1.371  0.020  1.371
 FHG  C1'  N9   single    1.462  0.020  1.462
 FHG  C1'  O4'  single    1.395  0.020  1.395
 FHG  N9   C8   aromatic  1.375  0.020  1.375
 FHG  O3'  C3'  single    1.403  0.020  1.403
 FHG  C3'  C4'  single    1.536  0.020  1.536
 FHG  N7   C8   aromatic  1.297  0.020  1.297
 FHG  O4'  C4'  single    1.427  0.020  1.427
 FHG  C4'  C5'  single    1.514  0.020  1.514
 FHG  O1B  P2   deloc     1.501  0.020  1.501
 FHG  C5'  O5'  single    1.406  0.020  1.406
 FHG  O5'  P1   single    1.655  0.020  1.655
 FHG  P2   O3A  single    1.686  0.020  1.686
 FHG  P2   O2B  deloc     1.503  0.020  1.503
 FHG  P2   C3B  single    1.825  0.020  1.825
 FHG  O3A  P1   single    1.619  0.020  1.619
 FHG  C3B  F2B  single    1.420  0.020  1.420
 FHG  C3B  P3   single    1.873  0.020  1.873
 FHG  P1   O2A  deloc     1.501  0.020  1.501
 FHG  P1   O1A  deloc     1.500  0.020  1.500
 FHG  O3G  P3   deloc     1.530  0.020  1.530
 FHG  P3   O1G  deloc     1.530  0.020  1.530
 FHG  P3   O2G  deloc     1.532  0.020  1.532
 FHG  C3B  H3   single    0.970  0.020  1.090
 FHG  C5'  H6   single    0.970  0.020  1.090
 FHG  C5'  H7   single    0.970  0.020  1.090
 FHG  C4'  H8   single    0.970  0.020  1.090
 FHG  C1'  H9   single    0.970  0.020  1.090
 FHG  N2   H10  single    0.890  0.020  1.040
 FHG  N2   H11  single    0.890  0.020  1.040
 FHG  N1   H12  single    0.860  0.020  1.020
 FHG  C8   H13  single    0.930  0.020  1.080
 FHG  C2'  H14  single    0.970  0.020  1.090
 FHG  C2'  H15  single    0.970  0.020  1.090
 FHG  C3'  H16  single    0.970  0.020  1.090
 FHG  O3'  H17  single    0.850  0.020  0.980

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
 FHG  O5'  P1   O3A   94.51  3.000
 FHG  O3A  P1   O2A  110.50  3.000
 FHG  O5'  P1   O2A  108.54  3.000
 FHG  O2A  P1   O1A  119.17  3.000
 FHG  O3A  P1   O1A  112.43  3.000
 FHG  O5'  P1   O1A  108.80  3.000
 FHG  P2   O3A  P1   128.17  3.000
 FHG  C5'  O5'  P1   117.74  3.000
 FHG  C3B  P2   O2B  111.21  3.000
 FHG  C3B  P2   O1B  110.75  3.000
 FHG  O2B  P2   O1B  120.45  3.000
 FHG  C3B  P2   O3A  101.49  3.000
 FHG  O2B  P2   O3A  102.61  3.000
 FHG  O1B  P2   O3A  108.21  3.000
 FHG  H3   C3B  P3   108.92  3.000
 FHG  H3   C3B  F2B  106.71  3.000
 FHG  P3   C3B  F2B  109.96  3.000
 FHG  H3   C3B  P2   108.55  3.000
 FHG  P3   C3B  P2   116.27  3.000
 FHG  F2B  C3B  P2   106.00  3.000
 FHG  O3G  P3   O2G  113.85  3.000
 FHG  O2G  P3   O1G  113.89  3.000
 FHG  O3G  P3   O1G  114.32  3.000
 FHG  O2G  P3   C3B  103.83  3.000
 FHG  O1G  P3   C3B  103.27  3.000
 FHG  O3G  P3   C3B  106.13  3.000
 FHG  H7   C5'  H6   106.32  3.000
 FHG  H7   C5'  C4'  107.57  3.000
 FHG  H6   C5'  C4'  110.00  3.000
 FHG  H7   C5'  O5'  113.06  3.000
 FHG  H6   C5'  O5'  108.92  3.000
 FHG  C4'  C5'  O5'  110.86  3.000
 FHG  H8   C4'  C3'  109.52  3.000
 FHG  H8   C4'  O4'  107.65  3.000
 FHG  C3'  C4'  O4'  106.85  3.000
 FHG  H8   C4'  C5'  109.24  3.000
 FHG  O4'  C4'  C5'  111.11  3.000
 FHG  C3'  C4'  C5'  112.34  3.000
 FHG  C1'  O4'  C4'  110.55  3.000
 FHG  H9   C1'  C2'  113.09  3.000
 FHG  H9   C1'  N9   106.84  3.000
 FHG  C2'  C1'  N9   112.91  3.000
 FHG  H9   C1'  O4'  108.39  3.000
 FHG  N9   C1'  O4'  110.52  3.000
 FHG  C2'  C1'  O4'  105.05  3.000
 FHG  C8   N9   C4   106.05  3.000
 FHG  C8   N9   C1'  129.68  3.000
 FHG  C4   N9   C1'  124.10  3.000
 FHG  C5   C4   N3   128.26  3.000
 FHG  C5   C4   N9   105.50  3.000
 FHG  N3   C4   N9   126.23  3.000
 FHG  C2   N3   C4   113.14  3.000
 FHG  N1   C2   N2   116.79  3.000
 FHG  N1   C2   N3   123.17  3.000
 FHG  N2   C2   N3   120.01  3.000
 FHG  H11  N2   H10  116.07  3.000
 FHG  H11  N2   C2   117.29  3.000
 FHG  H10  N2   C2   120.68  3.000
 FHG  H12  N1   C6   115.68  3.000
 FHG  H12  N1   C2   118.24  3.000
 FHG  C6   N1   C2   126.08  3.000
 FHG  C5   C6   O6   128.80  3.000
 FHG  C5   C6   N1   110.49  3.000
 FHG  O6   C6   N1   120.71  3.000
 FHG  N7   C5   C6   130.46  3.000
 FHG  N7   C5   C4   110.68  3.000
 FHG  C6   C5   C4   118.86  3.000
 FHG  C8   N7   C5   104.60  3.000
 FHG  H13  C8   N7   124.66  3.000
 FHG  H13  C8   N9   122.17  3.000
 FHG  N7   C8   N9   113.16  3.000
 FHG  H15  C2'  H14  107.64  3.000
 FHG  H15  C2'  C3'  114.34  3.000
 FHG  H14  C2'  C3'  109.23  3.000
 FHG  H15  C2'  C1'  114.77  3.000
 FHG  H14  C2'  C1'  107.87  3.000
 FHG  C3'  C2'  C1'  102.73  3.000
 FHG  H16  C3'  O3'  109.84  3.000
 FHG  H16  C3'  C2'  109.62  3.000
 FHG  O3'  C3'  C2'  114.79  3.000
 FHG  H16  C3'  C4'  109.84  3.000
 FHG  O3'  C3'  C4'  109.69  3.000
 FHG  C2'  C3'  C4'  102.82  3.000
 FHG  H17  O3'  C3'  108.33  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
 FHG  CONST_01  N7   C5   C4   N9     0.00   0.0  0
 FHG  CONST_02  C5   N7   C8   N9     0.00   0.0  0
 FHG  CONST_03  C8   N7   C5   C4     0.00   0.0  0
 FHG  CONST_04  N7   C8   N9   C4     0.00   0.0  0
 FHG  CONST_05  C8   N9   C4   C5     0.00   0.0  0
 FHG  CONST_06  N3   C4   N9   C1'    0.00   0.0  0
 FHG  CONST_07  C5   C4   N9   C1'  180.00   0.0  0
 FHG  CONST_08  N7   C8   N9   C1'  180.00   0.0  0
 FHG  CONST_09  N1   C2   N3   C4     0.00   0.0  0
 FHG  CONST_10  C6   N1   C2   N3     0.00   0.0  0
 FHG  CONST_11  C5   C6   N1   C2     0.00   0.0  0
 FHG  CONST_12  N2   C2   N3   C4   180.00   0.0  0
 FHG  CONST_13  O6   C6   N1   C2   180.00   0.0  0
 FHG  CONST_14  C6   N1   C2   N2   180.00   0.0  0
 FHG  CONST_15  H13  C8   N9   C1'    0.00   0.0  0
 FHG  CONST_16  H12  N1   C2   N3   180.00   0.0  0
 FHG  CONST_18  H11  N2   C2   N3     0.00   0.0  0
 FHG  Var_01    C4'  C5'  O5'  P1   114.99  30.0  1
 FHG  Var_02    O1B  P2   O3A  P1   -39.72  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
 FHG  chir_03  C3B  P2   F2B  P3   negativ
 FHG  chir_04  C4'  O4'  C3'  C5'  negativ
 FHG  chir_05  C1'  O4'  N9   C2'  negativ
 FHG  chir_06  C3'  O3'  C4'  C2'  positiv

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
 FHG  plan-1  C1'  0.020
 FHG  plan-1  N9   0.020
 FHG  plan-1  C4   0.020
 FHG  plan-1  N3   0.020
 FHG  plan-1  C2   0.020
 FHG  plan-1  N2   0.020
 FHG  plan-1  N1   0.020
 FHG  plan-1  C6   0.020
 FHG  plan-1  O6   0.020
 FHG  plan-1  C5   0.020
 FHG  plan-1  N7   0.020
 FHG  plan-1  C8   0.020
 FHG  plan-1  H10  0.020
 FHG  plan-1  H11  0.020
 FHG  plan-1  H12  0.020
 FHG  plan-1  H13  0.020

