# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 03:14:14 2021
#   Inital geometry file: a 113 line input string
#   Ligand name: 6-amino-3-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,4-dihydro-1,3,5-triazin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NCN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)N1
#
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
 F6G  F6G  6-amino-3-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,4-dihydro-1,3,5-triazin-2(1H)-one  ligand  45  28  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F6G
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
 F6G  C2   C  C     0   0.717  57.2891  38.6769  138.9559
 F6G  C4   C  C     0   0.602  59.5127  39.5980  138.7665
 F6G  C6   C  CH2   0  -0.165  59.1538  37.4866  137.9831
 F6G  N4   N  NH2   0  -0.830  60.2284  40.7158  139.0546
 F6G  N03  N  N     0  -0.470  59.9460  38.6788  137.9974
 F6G  N1   N  NT    0  -0.539  57.7166  37.7607  138.0435
 F6G  C1'  C  CR15  0   0.220  56.7824  36.8046  137.5277
 F6G  C2'  C  CH2   0  -0.518  56.9219  36.4679  136.0481
 F6G  C3'  C  CR15  0  -0.017  56.2908  35.0898  135.9755
 F6G  O3'  O  OH1   0  -0.673  54.8970  35.2556  135.8429
 F6G  C4'  C  CR15  0   0.002  56.6624  34.4822  137.3454
 F6G  C5'  C  CH2   0  -0.220  57.8272  33.5214  137.3191
 F6G  O5'  O  O2    0  -0.568  58.9549  34.1653  136.7051
 F6G  PA   P  P     0   1.508  60.4630  33.9256  137.0896
 F6G  O1A  O  O     0  -0.665  61.3829  34.7611  136.3097
 F6G  O2A  O  OH1   0  -0.754  60.5771  34.0136  138.6799
 F6G  O3A  O  O2    0  -0.700  60.5980  32.3254  136.8795
 F6G  PB   P  P     0   1.505  61.8643  31.3320  137.0242
 F6G  O1B  O  OH1   0  -0.727  63.0016  32.2298  137.6607
 F6G  O2B  O  O     0  -0.643  62.1534  30.5836  135.7994
 F6G  O3B  O  O2    0  -0.682  61.4303  30.3958  138.2419
 F6G  PG   P  P     0   1.458  60.5542  30.6369  139.6046
 F6G  O3G  O  OH1   0  -0.708  60.8483  29.2939  140.3812
 F6G  O1G  O  OH1   0  -0.727  61.4387  31.6295  140.4634
 F6G  O2G  O  O     0  -0.666  59.1631  31.0134  139.3174
 F6G  O4'  O  O     0  -0.504  56.9469  35.5683  138.2074
 F6G  O2   O  O     0  -0.499  56.1417  38.8139  139.3383
 F6G  N3   N  NH1   0  -0.731  58.2944  39.5007  139.4180
 F6G  H1   H  HCH2  0   0.221  59.4348  36.8274  138.8169
 F6G  H2   H  HCH2  0   0.239  59.3579  36.9478  137.0608
 F6G  H3   H  HNH2  0   0.395  61.0582  40.8409  138.4977
 F6G  H4   H  HNH2  0   0.398  59.7227  41.5713  139.2214
 F6G  H5   H  HCR5  0   0.253  55.7833  37.2019  137.7168
 F6G  H6   H  HCH2  0   0.262  57.9619  36.4154  135.7289
 F6G  H7   H  HCH2  0   0.272  56.4131  37.1940  135.4152
 F6G  H8   H  HCR5  0   0.249  56.6952  34.4925  135.1502
 F6G  H9   H  HOH1  0   0.454  54.4879  34.3855  135.7980
 F6G  H10  H  HCR5  0   0.257  55.8116  33.9090  137.7356
 F6G  H11  H  HCH2  0   0.258  57.5641  32.6419  136.7293
 F6G  H12  H  HCH2  0   0.267  58.0660  33.1925  138.3312
 F6G  H13  H  HOH1  0   0.513  60.9459  34.8441  139.0134
 F6G  H14  H  HOH1  0   0.517  63.7264  32.4604  137.0618
 F6G  H15  H  HOH1  0   0.515  60.2910  28.5455  140.1248
 F6G  H16  H  HOH1  0   0.507  61.1613  32.5552  140.4128
 F6G  H17  H  HNH1  0   0.418  58.0009  40.2390  140.0413

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
 F6G  O2B  PB   double  1.464  0.020  1.464
 F6G  O3'  C3'  single  1.410  0.020  1.410
 F6G  C3'  C2'  single  1.517  0.020  1.517
 F6G  C3'  C4'  single  1.544  0.020  1.544
 F6G  C2'  C1'  single  1.524  0.020  1.524
 F6G  O1A  PA   double  1.467  0.020  1.467
 F6G  O3A  PB   single  1.616  0.020  1.616
 F6G  O3A  PA   single  1.620  0.020  1.620
 F6G  O5'  PA   single  1.575  0.020  1.575
 F6G  O5'  C5'  single  1.436  0.020  1.436
 F6G  PB   O1B  single  1.583  0.020  1.583
 F6G  PB   O3B  single  1.596  0.020  1.596
 F6G  PA   O2A  single  1.597  0.020  1.597
 F6G  C4'  C5'  single  1.510  0.020  1.510
 F6G  C4'  O4'  single  1.416  0.020  1.416
 F6G  C1'  N1   single  1.433  0.020  1.433
 F6G  C1'  O4'  single  1.420  0.020  1.420
 F6G  O3B  PG   single  1.638  0.020  1.638
 F6G  O2   C2   double  1.217  0.020  1.217
 F6G  N1   C2   single  1.362  0.020  1.362
 F6G  N1   C6   single  1.464  0.020  1.464
 F6G  C2   N3   single  1.379  0.020  1.379
 F6G  C6   N03  single  1.431  0.020  1.431
 F6G  N3   C4   single  1.385  0.020  1.385
 F6G  N03  C4   double  1.274  0.020  1.274
 F6G  C4   N4   single  1.358  0.020  1.358
 F6G  O2G  PG   double  1.470  0.020  1.470
 F6G  PG   O1G  single  1.583  0.020  1.583
 F6G  PG   O3G  single  1.579  0.020  1.579
 F6G  C6   H1   single  0.970  0.020  1.090
 F6G  C6   H2   single  0.970  0.020  1.090
 F6G  N4   H3   single  0.890  0.020  1.040
 F6G  N4   H4   single  0.890  0.020  1.040
 F6G  C1'  H5   single  0.970  0.020  1.090
 F6G  C2'  H6   single  0.970  0.020  1.090
 F6G  C2'  H7   single  0.970  0.020  1.090
 F6G  C3'  H8   single  0.970  0.020  1.090
 F6G  O3'  H9   single  0.850  0.020  0.980
 F6G  C4'  H10  single  0.970  0.020  1.090
 F6G  C5'  H11  single  0.970  0.020  1.090
 F6G  C5'  H12  single  0.970  0.020  1.090
 F6G  O2A  H13  single  0.850  0.020  0.980
 F6G  O1B  H14  single  0.850  0.020  0.980
 F6G  O3G  H15  single  0.850  0.020  0.980
 F6G  O1G  H16  single  0.850  0.020  0.980
 F6G  N3   H17  single  0.890  0.020  1.040

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
 F6G  N3   C2   O2   120.96  3.000
 F6G  N3   C2   N1   113.42  3.000
 F6G  O2   C2   N1   125.60  3.000
 F6G  N3   C4   N03  122.16  3.000
 F6G  N03  C4   N4   122.85  3.000
 F6G  N3   C4   N4   114.93  3.000
 F6G  H2   C6   H1   107.35  3.000
 F6G  H2   C6   N1   108.18  3.000
 F6G  H1   C6   N1   109.38  3.000
 F6G  H2   C6   N03  108.50  3.000
 F6G  H1   C6   N03  110.50  3.000
 F6G  N1   C6   N03  112.76  3.000
 F6G  H4   N4   H3   113.55  3.000
 F6G  H4   N4   C4   118.00  3.000
 F6G  H3   N4   C4   114.78  3.000
 F6G  C6   N03  C4   114.74  3.000
 F6G  C1'  N1   C6   120.01  3.000
 F6G  C6   N1   C2   117.49  3.000
 F6G  C1'  N1   C2   119.05  3.000
 F6G  H5   C1'  O4'  109.87  3.000
 F6G  H5   C1'  C2'  109.42  3.000
 F6G  O4'  C1'  C2'  105.17  3.000
 F6G  H5   C1'  N1   106.94  3.000
 F6G  O4'  C1'  N1   109.45  3.000
 F6G  C2'  C1'  N1   115.93  3.000
 F6G  H7   C2'  H6   107.93  3.000
 F6G  H7   C2'  C3'  112.54  3.000
 F6G  H6   C2'  C3'  109.84  3.000
 F6G  H7   C2'  C1'  111.97  3.000
 F6G  H6   C2'  C1'  112.49  3.000
 F6G  C3'  C2'  C1'  102.06  3.000
 F6G  H8   C3'  C4'  111.39  3.000
 F6G  H8   C3'  O3'  110.98  3.000
 F6G  C4'  C3'  O3'  111.57  3.000
 F6G  H8   C3'  C2'  112.18  3.000
 F6G  C4'  C3'  C2'  102.41  3.000
 F6G  O3'  C3'  C2'  107.99  3.000
 F6G  H9   O3'  C3'  108.56  3.000
 F6G  H10  C4'  O4'  109.88  3.000
 F6G  H10  C4'  C5'  105.77  3.000
 F6G  O4'  C4'  C5'  110.10  3.000
 F6G  H10  C4'  C3'  109.54  3.000
 F6G  O4'  C4'  C3'  106.66  3.000
 F6G  C5'  C4'  C3'  114.87  3.000
 F6G  H12  C5'  H11  108.14  3.000
 F6G  H12  C5'  O5'  111.10  3.000
 F6G  H11  C5'  O5'  108.64  3.000
 F6G  H12  C5'  C4'  110.16  3.000
 F6G  H11  C5'  C4'  109.65  3.000
 F6G  O5'  C5'  C4'  109.13  3.000
 F6G  PA   O5'  C5'  125.40  3.000
 F6G  O3A  PA   O2A  100.24  3.000
 F6G  O2A  PA   O1A  116.95  3.000
 F6G  O3A  PA   O1A  116.20  3.000
 F6G  O2A  PA   O5'  107.65  3.000
 F6G  O3A  PA   O5'  101.45  3.000
 F6G  O1A  PA   O5'  112.58  3.000
 F6G  H13  O2A  PA   114.69  3.000
 F6G  PB   O3A  PA   131.38  3.000
 F6G  O3B  PB   O2B  113.08  3.000
 F6G  O3B  PB   O1B  102.79  3.000
 F6G  O2B  PB   O1B  118.98  3.000
 F6G  O3B  PB   O3A  102.46  3.000
 F6G  O1B  PB   O3A  104.50  3.000
 F6G  O2B  PB   O3A  113.20  3.000
 F6G  H14  O1B  PB   115.11  3.000
 F6G  PG   O3B  PB   133.93  3.000
 F6G  O2G  PG   O1G  118.32  3.000
 F6G  O1G  PG   O3G   99.35  3.000
 F6G  O2G  PG   O3G  119.36  3.000
 F6G  O3G  PG   O3B  100.62  3.000
 F6G  O1G  PG   O3B  104.18  3.000
 F6G  O2G  PG   O3B  112.42  3.000
 F6G  H15  O3G  PG   114.85  3.000
 F6G  H16  O1G  PG   114.29  3.000
 F6G  C4'  O4'  C1'  110.68  3.000
 F6G  H17  N3   C4   119.65  3.000
 F6G  H17  N3   C2   115.57  3.000
 F6G  C4   N3   C2   121.70  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
 F6G  CONST_04  N3   C4   N03  C6      0.00   0.0  0
 F6G  CONST_05  N3   C2   N1   C1'   180.00   0.0  0
 F6G  CONST_09  N4   C4   N03  C6    180.00   0.0  0
 F6G  CONST_10  O2   C2   N1   C1'     0.00   0.0  0
 F6G  CONST_11  H17  N3   C4   N03   180.00   0.0  0
 F6G  CONST_12  H3   N4   C4   N03     0.00   0.0  0
 F6G  Var_01    H1   C6   N1   C2     77.74  30.0  1
 F6G  Var_02    O1A  PA   O5'  C5'  -178.27  30.0  3
 F6G  Var_03    O2B  PB   O3A  PA   -122.40  30.0  3
 F6G  Var_04    O2G  PG   O3B  PB     62.58  30.0  3
 F6G  Var_05    H11  C5'  O5'  PA    -94.09  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
 F6G  chir_01  C1'  C2'  N1   O4'  positiv
 F6G  chir_02  C3'  O3'  C2'  C4'  negativ
 F6G  chir_03  C4'  O4'  C3'  C5'  negativ
 F6G  chir_04  PA   O3A  O5'  O2A  both
 F6G  chir_05  PB   O1B  O3A  O2B  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
 F6G  plan-1  C2   0.020
 F6G  plan-1  C4   0.020
 F6G  plan-1  C6   0.020
 F6G  plan-1  N4   0.020
 F6G  plan-1  N03  0.020
 F6G  plan-1  N1   0.020
 F6G  plan-1  C1'  0.020
 F6G  plan-1  O2   0.020
 F6G  plan-1  N3   0.020
 F6G  plan-1  H3   0.020
 F6G  plan-1  H4   0.020
 F6G  plan-1  H17  0.020

