# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 05:34:20 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 9-{2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[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
 V3A  V3A  9-{2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine  ligand  44  31  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_V3A
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
 V3A  PA   P  P      0   1.334   1.7338  -2.0271  -0.0030
 V3A  O1A  O  OP    -1  -0.809   2.1350  -2.7831  -1.2344
 V3A  O2A  O  O      0  -0.811   1.9757  -2.6307   1.3476
 V3A  O3A  O  O2     0  -0.753   2.2231  -0.4822  -0.0716
 V3A  O5'  O  O2     0  -0.625   0.1263  -1.6377  -0.1303
 V3A  PB   P  P      0   1.243   3.6417   0.1066   0.6105
 V3A  O2B  O  O      0  -0.813   4.6898  -0.9619   0.4945
 V3A  O1B  O  OP    -1  -0.808   3.2799   0.6712   1.9559
 V3A  C3B  C  CH1    0  -0.350   3.9235   1.4797  -0.5617
 V3A  F3B  F  F      0  -0.422   3.8950   0.9421  -1.8730
 V3A  PG   P  P      0   1.125   5.5053   2.4700  -0.3659
 V3A  O1G  O  OP    -1  -0.900   6.6449   1.5001  -0.6752
 V3A  O2G  O  OP    -1  -0.911   5.3545   3.5914  -1.4004
 V3A  O3G  O  O      0  -0.895   5.4513   2.9516   1.0844
 V3A  C5'  C  CH2    0  -0.151  -0.7822  -2.7065  -0.2457
 V3A  C4'  C  CH1    0   0.000  -2.0965  -2.3235   0.3881
 V3A  O4'  O  O2     0  -0.493  -2.6809  -1.2350  -0.3145
 V3A  C1'  C  CH1    0   0.199  -4.0857  -1.3087  -0.2593
 V3A  N9   N  NR5    0  -0.533  -4.6198  -0.1229   0.3765
 V3A  C4   C  CR56   0   0.491  -5.3628   0.8567  -0.2175
 V3A  N3   N  N      0  -0.457  -5.8091   0.9105  -1.4705
 V3A  C2   C  CR16   0   0.045  -6.5072   2.0101  -1.6941
 V3A  N1   N  N      0  -0.475  -6.7897   2.9979  -0.8485
 V3A  C6   C  CR6    0   0.459  -6.3341   2.9298   0.4076
 V3A  N6   N  NH2    0  -0.817  -6.6179   3.9152   1.2602
 V3A  C5   C  CR56   0  -0.014  -5.5713   1.8050   0.7714
 V3A  N7   N  N      0  -0.450  -4.9633   1.4303   1.9422
 V3A  C8   C  CR15   0   0.111  -4.4110   0.2871   1.6655
 V3A  C2'  C  CH2    0  -0.568  -4.4333  -2.5992   0.4782
 V3A  C3'  C  CH1    0   0.026  -3.1552  -3.4200   0.3318
 V3A  O3'  O  OH1    0  -0.662  -2.9310  -4.3607   1.3438
 V3A  H3   H  HCH1   0   0.177   3.0688   2.1640  -0.4858
 V3A  H6   H  HCH2   0   0.207  -0.9454  -2.9721  -1.2974
 V3A  H7   H  HCH2   0   0.210  -0.4281  -3.6095   0.2664
 V3A  H8   H  HCH1   0   0.226  -1.9218  -2.0500   1.4404
 V3A  H9   H  HCH1   0   0.270  -4.4858  -1.3029  -1.2751
 V3A  H10  H  HCR6   0   0.251  -6.9053   2.1280  -2.6964
 V3A  H11  H  HNH2   0   0.403  -7.1515   4.7119   0.9581
 V3A  H12  H  HNH2   0   0.411  -6.2741   3.9012   2.2040
 V3A  H13  H  HCR5   0   0.297  -3.8354  -0.3035   2.3632
 V3A  H14  H  HCH2   0   0.265  -4.6179  -2.4147   1.5395
 V3A  H15  H  HCH2   0   0.281  -5.3190  -3.0762   0.0613
 V3A  H16  H  HCH1   0   0.227  -3.1313  -3.8909  -0.6612
 V3A  H17  H  HOH1   0   0.461  -3.4833  -5.1293   1.1732

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
 V3A  C2   N1   aromatic  1.331  0.020  1.331
 V3A  C2   N3   aromatic  1.321  0.020  1.321
 V3A  N1   C6   aromatic  1.338  0.020  1.338
 V3A  N3   C4   aromatic  1.331  0.020  1.331
 V3A  C6   N6   single    1.334  0.020  1.334
 V3A  C6   C5   aromatic  1.407  0.020  1.407
 V3A  C4   C5   aromatic  1.386  0.020  1.386
 V3A  C4   N9   aromatic  1.366  0.020  1.366
 V3A  C2'  C1'  single    1.526  0.020  1.526
 V3A  C2'  C3'  single    1.526  0.020  1.526
 V3A  C5   N7   aromatic  1.371  0.020  1.371
 V3A  N9   C1'  single    1.448  0.020  1.448
 V3A  N9   C8   aromatic  1.369  0.020  1.369
 V3A  C1'  O4'  single    1.408  0.020  1.408
 V3A  O3'  C3'  single    1.400  0.020  1.400
 V3A  C3'  C4'  single    1.525  0.020  1.525
 V3A  O4'  C4'  single    1.421  0.020  1.421
 V3A  N7   C8   aromatic  1.300  0.020  1.300
 V3A  C4'  C5'  single    1.509  0.020  1.509
 V3A  O2B  PB   deloc     1.501  0.020  1.501
 V3A  C5'  O5'  single    1.407  0.020  1.407
 V3A  O5'  PA   single    1.659  0.020  1.659
 V3A  PB   O3A  single    1.681  0.020  1.681
 V3A  PB   O1B  deloc     1.503  0.020  1.503
 V3A  PB   C3B  single    1.827  0.020  1.827
 V3A  F3B  C3B  single    1.418  0.020  1.418
 V3A  O3A  PA   single    1.622  0.020  1.622
 V3A  PA   O2A  deloc     1.499  0.020  1.499
 V3A  PA   O1A  deloc     1.500  0.020  1.500
 V3A  C3B  PG   single    1.876  0.020  1.876
 V3A  PG   O3G  deloc     1.529  0.020  1.529
 V3A  PG   O1G  deloc     1.528  0.020  1.528
 V3A  PG   O2G  deloc     1.533  0.020  1.533
 V3A  C3B  H3   single    0.970  0.020  1.090
 V3A  C5'  H6   single    0.970  0.020  1.090
 V3A  C5'  H7   single    0.970  0.020  1.090
 V3A  C4'  H8   single    0.970  0.020  1.090
 V3A  C1'  H9   single    0.970  0.020  1.090
 V3A  C2   H10  single    0.930  0.020  1.080
 V3A  N6   H11  single    0.860  0.020  1.020
 V3A  N6   H12  single    0.860  0.020  1.020
 V3A  C8   H13  single    0.930  0.020  1.080
 V3A  C2'  H14  single    0.970  0.020  1.090
 V3A  C2'  H15  single    0.970  0.020  1.090
 V3A  C3'  H16  single    0.970  0.020  1.090
 V3A  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
 V3A  O5'  PA   O3A   93.76  3.000
 V3A  O3A  PA   O2A  111.90  3.000
 V3A  O5'  PA   O2A  108.66  3.000
 V3A  O2A  PA   O1A  119.58  3.000
 V3A  O3A  PA   O1A  111.39  3.000
 V3A  O5'  PA   O1A  108.34  3.000
 V3A  PB   O3A  PA   124.83  3.000
 V3A  C5'  O5'  PA   116.97  3.000
 V3A  C3B  PB   O1B  109.21  3.000
 V3A  C3B  PB   O2B  112.18  3.000
 V3A  O1B  PB   O2B  120.30  3.000
 V3A  C3B  PB   O3A   97.65  3.000
 V3A  O1B  PB   O3A  106.96  3.000
 V3A  O2B  PB   O3A  107.97  3.000
 V3A  H3   C3B  PG   108.67  3.000
 V3A  H3   C3B  F3B  106.54  3.000
 V3A  PG   C3B  F3B  108.28  3.000
 V3A  H3   C3B  PB   107.70  3.000
 V3A  PG   C3B  PB   117.37  3.000
 V3A  F3B  C3B  PB   107.78  3.000
 V3A  O3G  PG   O2G  113.96  3.000
 V3A  O2G  PG   O1G  113.64  3.000
 V3A  O3G  PG   O1G  114.72  3.000
 V3A  O2G  PG   C3B  103.46  3.000
 V3A  O1G  PG   C3B  105.82  3.000
 V3A  O3G  PG   C3B  103.62  3.000
 V3A  H7   C5'  H6   107.23  3.000
 V3A  H7   C5'  C4'  107.11  3.000
 V3A  H6   C5'  C4'  109.55  3.000
 V3A  H7   C5'  O5'  112.24  3.000
 V3A  H6   C5'  O5'  111.01  3.000
 V3A  C4'  C5'  O5'  109.58  3.000
 V3A  H8   C4'  C3'  108.90  3.000
 V3A  H8   C4'  O4'  110.33  3.000
 V3A  C3'  C4'  O4'  104.30  3.000
 V3A  H8   C4'  C5'  109.04  3.000
 V3A  O4'  C4'  C5'  110.18  3.000
 V3A  C3'  C4'  C5'  114.00  3.000
 V3A  C1'  O4'  C4'  110.53  3.000
 V3A  H9   C1'  C2'  111.75  3.000
 V3A  H9   C1'  N9   105.61  3.000
 V3A  C2'  C1'  N9   113.35  3.000
 V3A  H9   C1'  O4'  109.21  3.000
 V3A  N9   C1'  O4'  110.02  3.000
 V3A  C2'  C1'  O4'  106.88  3.000
 V3A  C8   N9   C4   106.13  3.000
 V3A  C8   N9   C1'  127.07  3.000
 V3A  C4   N9   C1'  126.68  3.000
 V3A  C5   C4   N3   126.41  3.000
 V3A  C5   C4   N9   105.21  3.000
 V3A  N3   C4   N9   128.38  3.000
 V3A  C2   N3   C4   111.72  3.000
 V3A  H10  C2   N1   115.37  3.000
 V3A  H10  C2   N3   116.14  3.000
 V3A  N1   C2   N3   128.49  3.000
 V3A  C6   N1   C2   119.12  3.000
 V3A  C5   C6   N6   122.74  3.000
 V3A  C5   C6   N1   117.91  3.000
 V3A  N6   C6   N1   119.35  3.000
 V3A  H12  N6   H11  118.36  3.000
 V3A  H12  N6   C6   121.16  3.000
 V3A  H11  N6   C6   120.43  3.000
 V3A  N7   C5   C6   132.81  3.000
 V3A  N7   C5   C4   110.83  3.000
 V3A  C6   C5   C4   116.37  3.000
 V3A  C8   N7   C5   104.30  3.000
 V3A  H13  C8   N7   124.74  3.000
 V3A  H13  C8   N9   121.72  3.000
 V3A  N7   C8   N9   113.54  3.000
 V3A  H15  C2'  H14  107.96  3.000
 V3A  H15  C2'  C3'  114.13  3.000
 V3A  H14  C2'  C3'  108.99  3.000
 V3A  H15  C2'  C1'  111.75  3.000
 V3A  H14  C2'  C1'  111.40  3.000
 V3A  C3'  C2'  C1'  102.57  3.000
 V3A  H16  C3'  O3'  111.20  3.000
 V3A  H16  C3'  C2'  109.59  3.000
 V3A  O3'  C3'  C2'  115.23  3.000
 V3A  H16  C3'  C4'  109.04  3.000
 V3A  O3'  C3'  C4'  110.20  3.000
 V3A  C2'  C3'  C4'  101.02  3.000
 V3A  H17  O3'  C3'  108.48  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
 V3A  CONST_01  C2   N3   C4   N9   180.00   0.0  0
 V3A  CONST_02  C6   C5   C4   N9   180.00   0.0  0
 V3A  CONST_03  N7   C5   C4   N9     0.00   0.0  0
 V3A  CONST_04  C5   N7   C8   N9     0.00   0.0  0
 V3A  CONST_05  N1   C2   N3   C4     0.00   0.0  0
 V3A  CONST_06  N1   C6   C5   C4     0.00   0.0  0
 V3A  CONST_07  C8   N7   C5   C4     0.00   0.0  0
 V3A  CONST_08  N7   C8   N9   C4     0.00   0.0  0
 V3A  CONST_09  C6   N1   C2   N3     0.00   0.0  0
 V3A  CONST_10  C6   C5   C4   N3     0.00   0.0  0
 V3A  CONST_11  N7   C5   C4   N3   180.00   0.0  0
 V3A  CONST_12  C8   N9   C4   N3   180.00   0.0  0
 V3A  CONST_13  C5   C6   N1   C2     0.00   0.0  0
 V3A  CONST_14  C5   C4   N3   C2     0.00   0.0  0
 V3A  CONST_15  N7   C5   C6   N1   180.00   0.0  0
 V3A  CONST_16  C8   N7   C5   C6   180.00   0.0  0
 V3A  CONST_17  C8   N9   C4   C5     0.00   0.0  0
 V3A  CONST_18  N3   C4   N9   C1'    0.00   0.0  0
 V3A  CONST_19  C5   C4   N9   C1'  180.00   0.0  0
 V3A  CONST_20  N7   C8   N9   C1'  180.00   0.0  0
 V3A  CONST_21  N6   C6   C5   C4   180.00   0.0  0
 V3A  CONST_22  N6   C6   N1   C2   180.00   0.0  0
 V3A  CONST_23  N7   C5   C6   N6     0.00   0.0  0
 V3A  CONST_24  H13  C8   N9   C1'    0.00   0.0  0
 V3A  CONST_25  H10  C2   N3   C4   180.00   0.0  0
 V3A  CONST_26  H11  N6   C6   N1     0.00   0.0  0
 V3A  CONST_27  H12  N6   C6   N1   180.00   0.0  0
 V3A  Var_01    C4'  C5'  O5'  PA   148.98  30.0  1
 V3A  Var_02    O2B  PB   O3A  PA    34.91  30.0  2

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
 V3A  chir_03  C3B  PB   F3B  PG   positiv
 V3A  chir_04  C4'  O4'  C3'  C5'  negativ
 V3A  chir_05  C1'  O4'  N9   C2'  positiv
 V3A  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
 V3A  plan-1  C1'  0.020
 V3A  plan-1  N9   0.020
 V3A  plan-1  C4   0.020
 V3A  plan-1  N3   0.020
 V3A  plan-1  C2   0.020
 V3A  plan-1  N1   0.020
 V3A  plan-1  C6   0.020
 V3A  plan-1  N6   0.020
 V3A  plan-1  C5   0.020
 V3A  plan-1  N7   0.020
 V3A  plan-1  C8   0.020
 V3A  plan-1  H10  0.020
 V3A  plan-1  H13  0.020
 V3A  plan-2  C6   0.020
 V3A  plan-2  N6   0.020
 V3A  plan-2  H11  0.020
 V3A  plan-2  H12  0.020

