# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 09:00:39 2021
#   Inital geometry file: a 105 line input string
#   Ligand name: (1S)-1-(4-aminoimidazo[2,1-f][1,2,4]triazin-7-yl)-1,4-anhydro-2-deoxy-2-fluoro-5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-2-methyl-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@]1(F)[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(O)=O)O[C@H]1c2cnc3n2ncnc3N
#
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
 8B4  8B4  (1S)-1-(4-aminoimidazo[2,1-f][1,2,4]triazin-7-yl)-1,4-anhydro-2-deoxy-2-fluoro-5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-2-methyl-D-ribitol  ligand  44  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 OK (reasonable std)
;

data_comp_8B4
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
 8B4  C8   C  CR15  0  -0.235  41.5584  -46.2672   7.7007
 8B4  C6   C  CR6   0   0.459  39.9565  -46.0372  10.8384
 8B4  C5   C  CR56  0   0.398  40.4765  -46.1678   9.5147
 8B4  F2'  F  F     0  -0.383  38.0306  -46.5193   4.4729
 8B4  C2'  C  CT    0   0.321  39.0211  -45.9391   5.2811
 8B4  C2M  C  CH3   0  -0.723  38.4010  -44.7931   6.0340
 8B4  C3'  C  CH1   0  -0.000  40.1783  -45.5811   4.3549
 8B4  O3'  O  OH1   0  -0.691  39.8275  -44.8247   3.2300
 8B4  C1'  C  CH1   0  -0.070  39.6403  -47.0799   6.1054
 8B4  O4'  O  O2    0  -0.493  40.6473  -47.6542   5.2842
 8B4  C4'  C  CH1   0   0.012  40.7665  -46.9594   4.0577
 8B4  C5'  C  CH2   0  -0.233  42.1945  -46.9901   3.5730
 8B4  O5'  O  O2    0  -0.578  43.0493  -46.3056   4.4945
 8B4  PA   P  P     0   1.489  44.1068  -45.2182   4.0224
 8B4  O1A  O  OH1   0  -0.711  44.6168  -44.7821   5.4556
 8B4  O3A  O  O2    0  -0.708  43.1881  -43.9553   3.5848
 8B4  PB   P  P     0   1.443  42.7178  -43.4427   2.1071
 8B4  O1B  O  OH1   0  -0.717  43.5695  -42.1271   1.8691
 8B4  O2B  O  OH1   0  -0.751  41.3178  -42.8036   2.4383
 8B4  O3B  O  O     0  -0.691  42.7981  -44.5018   1.0856
 8B4  O2A  O  O     0  -0.681  45.0935  -45.6146   3.0071
 8B4  C9   C  CR5   0   0.300  40.2691  -46.6438   7.3831
 8B4  N7   N  N     0  -0.442  41.6770  -45.9729   9.0145
 8B4  N6   N  NH2   0  -0.802  40.7520  -45.6407  11.8197
 8B4  N1   N  N     0  -0.472  38.6843  -46.3142  11.0583
 8B4  C2   C  CR16  0   0.073  37.9428  -46.7106  10.0113
 8B4  N3   N  N     0  -0.281  38.2979  -46.8649   8.7703
 8B4  N4   N  N     0  -0.378  39.5951  -46.5777   8.5602
 8B4  H1   H  HCR5  0   0.271  42.3997  -46.2041   7.0293
 8B4  H2   H  HCH3  0   0.261  37.6176  -45.1400   6.7067
 8B4  H3   H  HCH3  0   0.249  39.1478  -44.2620   6.6218
 8B4  H4   H  HCH3  0   0.264  37.9612  -44.0826   5.3340
 8B4  H5   H  HCH1  0   0.281  40.8909  -44.9770   4.9233
 8B4  H6   H  HOH1  0   0.479  39.2216  -45.3063   2.6528
 8B4  H7   H  HCH1  0   0.291  38.8595  -47.8189   6.3214
 8B4  H8   H  HCH1  0   0.256  40.1741  -47.4528   3.2728
 8B4  H9   H  HCH2  0   0.284  42.5398  -48.0216   3.4913
 8B4  H10  H  HCH2  0   0.256  42.2318  -46.5559   2.5714
 8B4  H11  H  HOH1  0   0.512  45.4777  -44.3411   5.4560
 8B4  H12  H  HOH1  0   0.509  44.3154  -42.2385   1.2644
 8B4  H13  H  HOH1  0   0.514  40.6440  -43.4809   2.7074
 8B4  H14  H  HNH2  0   0.416  40.4003  -45.5616  12.7594
 8B4  H15  H  HNH2  0   0.421  41.7255  -45.4486  11.6547
 8B4  H16  H  HCR6  0   0.281  36.9036  -46.9342  10.2167

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
 8B4  O3B  PB   double    1.474  0.020  1.474
 8B4  O2A  PA   double    1.470  0.020  1.470
 8B4  O1B  PB   single    1.585  0.020  1.585
 8B4  PB   O2B  single    1.574  0.020  1.574
 8B4  PB   O3A  single    1.633  0.020  1.633
 8B4  O3'  C3'  single    1.400  0.020  1.400
 8B4  C5'  C4'  single    1.508  0.020  1.508
 8B4  C5'  O5'  single    1.431  0.020  1.431
 8B4  PA   O3A  single    1.622  0.020  1.622
 8B4  PA   O5'  single    1.589  0.020  1.589
 8B4  PA   O1A  single    1.583  0.020  1.583
 8B4  C4'  C3'  single    1.528  0.020  1.528
 8B4  C4'  O4'  single    1.415  0.020  1.415
 8B4  C3'  C2'  single    1.525  0.020  1.525
 8B4  F2'  C2'  single    1.404  0.020  1.404
 8B4  O4'  C1'  single    1.421  0.020  1.421
 8B4  C2'  C2M  single    1.505  0.020  1.505
 8B4  C2'  C1'  single    1.538  0.020  1.538
 8B4  C1'  C9   single    1.489  0.020  1.489
 8B4  C9   C8   aromatic  1.380  0.020  1.380
 8B4  C9   N4   aromatic  1.358  0.020  1.358
 8B4  C8   N7   aromatic  1.352  0.020  1.352
 8B4  N4   N3   aromatic  1.345  0.020  1.345
 8B4  N4   C5   aromatic  1.362  0.020  1.362
 8B4  N7   C5   aromatic  1.315  0.020  1.315
 8B4  N3   C2   aromatic  1.300  0.020  1.300
 8B4  C5   C6   aromatic  1.428  0.020  1.428
 8B4  C2   N1   aromatic  1.343  0.020  1.343
 8B4  C6   N1   aromatic  1.320  0.020  1.320
 8B4  C6   N6   single    1.324  0.020  1.324
 8B4  C8   H1   single    0.930  0.020  1.080
 8B4  C2M  H2   single    0.970  0.020  1.090
 8B4  C2M  H3   single    0.970  0.020  1.090
 8B4  C2M  H4   single    0.970  0.020  1.090
 8B4  C3'  H5   single    0.970  0.020  1.090
 8B4  O3'  H6   single    0.850  0.020  0.980
 8B4  C1'  H7   single    0.970  0.020  1.090
 8B4  C4'  H8   single    0.970  0.020  1.090
 8B4  C5'  H9   single    0.970  0.020  1.090
 8B4  C5'  H10  single    0.970  0.020  1.090
 8B4  O1A  H11  single    0.850  0.020  0.980
 8B4  O1B  H12  single    0.850  0.020  0.980
 8B4  O2B  H13  single    0.850  0.020  0.980
 8B4  N6   H14  single    0.860  0.020  1.020
 8B4  N6   H15  single    0.860  0.020  1.020
 8B4  C2   H16  single    0.930  0.020  1.080

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
 8B4  H1   C8   N7   121.61  3.000
 8B4  H1   C8   C9   126.98  3.000
 8B4  N7   C8   C9   111.41  3.000
 8B4  N1   C6   N6   121.21  3.000
 8B4  N6   C6   C5   119.71  3.000
 8B4  N1   C6   C5   119.08  3.000
 8B4  N4   C5   N7   111.64  3.000
 8B4  N7   C5   C6   132.17  3.000
 8B4  N4   C5   C6   116.19  3.000
 8B4  C1'  C2'  C3'  101.20  3.000
 8B4  C1'  C2'  C2M  117.56  3.000
 8B4  C3'  C2'  C2M  115.97  3.000
 8B4  C1'  C2'  F2'  106.62  3.000
 8B4  C2M  C2'  F2'  108.18  3.000
 8B4  C3'  C2'  F2'  106.42  3.000
 8B4  H4   C2M  H3   107.79  3.000
 8B4  H4   C2M  H2   108.30  3.000
 8B4  H3   C2M  H2   108.37  3.000
 8B4  H4   C2M  C2'  109.96  3.000
 8B4  H3   C2M  C2'  111.03  3.000
 8B4  H2   C2M  C2'  111.27  3.000
 8B4  H5   C3'  C4'  110.40  3.000
 8B4  H5   C3'  O3'  106.40  3.000
 8B4  C4'  C3'  O3'  115.31  3.000
 8B4  H5   C3'  C2'  107.97  3.000
 8B4  C4'  C3'  C2'  101.46  3.000
 8B4  O3'  C3'  C2'  115.13  3.000
 8B4  H6   O3'  C3'  111.59  3.000
 8B4  H7   C1'  C9   109.21  3.000
 8B4  H7   C1'  O4'  110.25  3.000
 8B4  C9   C1'  O4'  108.36  3.000
 8B4  H7   C1'  C2'  108.59  3.000
 8B4  C9   C1'  C2'  114.37  3.000
 8B4  O4'  C1'  C2'  105.99  3.000
 8B4  C4'  O4'  C1'  111.24  3.000
 8B4  H8   C4'  C5'  105.75  3.000
 8B4  H8   C4'  O4'  110.66  3.000
 8B4  C5'  C4'  O4'  110.39  3.000
 8B4  H8   C4'  C3'  109.64  3.000
 8B4  O4'  C4'  C3'  104.00  3.000
 8B4  C5'  C4'  C3'  116.45  3.000
 8B4  H10  C5'  H9   107.25  3.000
 8B4  H10  C5'  O5'  112.32  3.000
 8B4  H9   C5'  O5'  108.14  3.000
 8B4  H10  C5'  C4'  108.59  3.000
 8B4  H9   C5'  C4'  110.06  3.000
 8B4  O5'  C5'  C4'  110.41  3.000
 8B4  PA   O5'  C5'  122.25  3.000
 8B4  O2A  PA   O3A  113.82  3.000
 8B4  O3A  PA   O1A  102.26  3.000
 8B4  O2A  PA   O1A  118.91  3.000
 8B4  O1A  PA   O5'   97.70  3.000
 8B4  O3A  PA   O5'  103.66  3.000
 8B4  O2A  PA   O5'  117.87  3.000
 8B4  H11  O1A  PA   114.38  3.000
 8B4  PB   O3A  PA   130.66  3.000
 8B4  O3B  PB   O2B  119.09  3.000
 8B4  O2B  PB   O1B   99.93  3.000
 8B4  O3B  PB   O1B  117.58  3.000
 8B4  O2B  PB   O3A  101.14  3.000
 8B4  O1B  PB   O3A  103.98  3.000
 8B4  O3B  PB   O3A  112.70  3.000
 8B4  H12  O1B  PB   114.39  3.000
 8B4  H13  O2B  PB   112.56  3.000
 8B4  N4   C9   C1'  123.25  3.000
 8B4  N4   C9   C8   104.53  3.000
 8B4  C1'  C9   C8   132.20  3.000
 8B4  C5   N7   C8   104.91  3.000
 8B4  H15  N6   H14  118.45  3.000
 8B4  H15  N6   C6   121.13  3.000
 8B4  H14  N6   C6   120.37  3.000
 8B4  C2   N1   C6   117.65  3.000
 8B4  H16  C2   N3   114.76  3.000
 8B4  H16  C2   N1   116.30  3.000
 8B4  N3   C2   N1   128.94  3.000
 8B4  N4   N3   C2   112.78  3.000
 8B4  N3   N4   C9   127.13  3.000
 8B4  N3   N4   C5   125.36  3.000
 8B4  C9   N4   C5   107.51  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
 8B4  CONST_01  N3   N4   C9   C8   180.00   0.0  0
 8B4  CONST_02  C5   N4   C9   C8     0.00   0.0  0
 8B4  CONST_03  N4   C5   N7   C8     0.00   0.0  0
 8B4  CONST_04  C6   C5   N7   C8   180.00   0.0  0
 8B4  CONST_05  C9   N4   C5   C6   180.00   0.0  0
 8B4  CONST_06  N3   N4   C5   C6     0.00   0.0  0
 8B4  CONST_07  N3   C2   N1   C6     0.00   0.0  0
 8B4  CONST_08  C2   N3   N4   C5     0.00   0.0  0
 8B4  CONST_09  C9   C8   N7   C5     0.00   0.0  0
 8B4  CONST_10  C2   N1   C6   C5     0.00   0.0  0
 8B4  CONST_11  C2   N3   N4   C9   180.00   0.0  0
 8B4  CONST_12  N7   C5   N4   C9     0.00   0.0  0
 8B4  CONST_13  N4   C9   C8   N7     0.00   0.0  0
 8B4  CONST_14  N3   N4   C5   N7   180.00   0.0  0
 8B4  CONST_15  N1   C6   C5   N7   180.00   0.0  0
 8B4  CONST_16  N4   N3   C2   N1     0.00   0.0  0
 8B4  CONST_17  N4   C5   C6   N1     0.00   0.0  0
 8B4  CONST_18  C1'  C9   N4   C5   180.00   0.0  0
 8B4  CONST_19  N7   C8   C9   C1'  180.00   0.0  0
 8B4  CONST_20  N3   N4   C9   C1'    0.00   0.0  0
 8B4  CONST_21  N6   C6   C5   N7     0.00   0.0  0
 8B4  CONST_22  N4   C5   C6   N6   180.00   0.0  0
 8B4  CONST_23  C2   N1   C6   N6   180.00   0.0  0
 8B4  CONST_24  H16  C2   N1   C6   180.00   0.0  0
 8B4  CONST_25  H1   C8   N7   C5   180.00   0.0  0
 8B4  CONST_26  H14  N6   C6   C5   180.00   0.0  0
 8B4  CONST_27  H15  N6   C6   C5     0.00   0.0  0
 8B4  Var_01    O2A  PA   O5'  C5'  -55.62  30.0  1
 8B4  Var_02    O3B  PB   O3A  PA    20.62  30.0  2
 8B4  Var_03    H9   C5'  O5'  PA   107.99  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
 8B4  chir_01  C2'  C3'  C2M  C1'  positiv
 8B4  chir_02  C3'  O3'  C2'  C4'  negativ
 8B4  chir_03  C1'  O4'  C9   C2'  negativ
 8B4  chir_04  C4'  O4'  C3'  C5'  negativ
 8B4  chir_05  PA   O3A  O5'  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
 8B4  plan-1  C8   0.020
 8B4  plan-1  C6   0.020
 8B4  plan-1  C5   0.020
 8B4  plan-1  C1'  0.020
 8B4  plan-1  C9   0.020
 8B4  plan-1  N7   0.020
 8B4  plan-1  N6   0.020
 8B4  plan-1  N1   0.020
 8B4  plan-1  C2   0.020
 8B4  plan-1  N3   0.020
 8B4  plan-1  N4   0.020
 8B4  plan-1  H1   0.020
 8B4  plan-1  H16  0.020
 8B4  plan-2  C6   0.020
 8B4  plan-2  N6   0.020
 8B4  plan-2  H14  0.020
 8B4  plan-2  H15  0.020

