# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Sep 20 01:51:25 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 4-amino-1-{2-cyano-2-deoxy-5-O-[(S)-hydroxy{[(S)-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]2C#N
#
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
 85T  85T  "4-amino-1-{2-cyano-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one"  ligand  45  30  .  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_85T
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
 85T  PA   P  P     0   1.529  -21.5728   4.6633  44.1376
 85T  O1A  O  O     0  -0.658  -21.1125   5.1365  45.4487
 85T  O2A  O  OH1   0  -0.717  -22.7554   3.6182  44.0575
 85T  O3B  O  O2    0  -0.700  -21.7800   5.3812  40.8809
 85T  O2B  O  O     0  -0.657  -24.2056   5.4735  41.8587
 85T  N01  N  NS    0  -0.306  -22.0348   1.7109  41.4309
 85T  C02  C  CSP   0   0.207  -20.9180   1.5516  41.6551
 85T  C2'  C  CH1   0  -0.460  -19.4884   1.3484  41.7982
 85T  C3'  C  CH1   0   0.032  -18.6820   2.5670  41.3137
 85T  O3'  O  OH1   0  -0.656  -17.5646   2.0452  40.6500
 85T  C4'  C  CH1   0  -0.042  -18.2913   3.2640  42.6212
 85T  C5'  C  CH2   0  -0.210  -19.1921   4.3959  43.0559
 85T  O5'  O  O2    0  -0.593  -20.5265   3.9032  43.2164
 85T  O3A  O  O2    0  -0.676  -22.0429   5.9438  43.2472
 85T  PB   P  P     0   1.474  -22.8602   6.0554  41.8659
 85T  O1B  O  OH1   0  -0.710  -22.7114   7.5989  41.5577
 85T  PG   P  P     0   1.471  -21.9523   5.1319  39.2736
 85T  O1G  O  O     0  -0.676  -23.1480   5.7992  38.7376
 85T  O2G  O  OH1   0  -0.732  -21.8071   3.5662  39.1323
 85T  O3G  O  OH1   0  -0.714  -20.5438   5.5637  38.6927
 85T  O4'  O  O2    0  -0.490  -18.2293   2.2330  43.5941
 85T  C1'  C  CH1   0   0.284  -18.9716   1.1135  43.2431
 85T  N1   N  NR6   0  -0.570  -20.0333   0.8703  44.2258
 85T  C6   C  CR16  0   0.079  -20.1881   1.6279  45.3364
 85T  C5   C  CR16  0  -0.464  -21.1158   1.3174  46.2637
 85T  C4   C  CR6   0   0.514  -21.9001   0.1480  46.0265
 85T  N4   N  NH2   0  -0.807  -22.8379  -0.2060  46.9031
 85T  N3   N  N     0  -0.531  -21.7208  -0.6120  44.9616
 85T  C2   C  CR6   0   0.600  -20.7883  -0.2993  44.0459
 85T  O2   O  O     0  -0.513  -20.5609  -0.9779  43.0504
 85T  H1   H  HOH1  0   0.511  -23.4302   3.7124  44.7462
 85T  H2   H  HCH1  0   0.365  -19.2463   0.4858  41.1751
 85T  H3   H  HCH1  0   0.279  -19.2710   3.2252  40.6648
 85T  H4   H  HOH1  0   0.463  -17.0264   2.7757  40.3258
 85T  H5   H  HCH1  0   0.293  -17.2911   3.6984  42.5276
 85T  H7   H  HCH2  0   0.271  -18.8227   4.8155  43.9941
 85T  H8   H  HCH2  0   0.270  -19.1752   5.1824  42.2980
 85T  H9   H  HOH1  0   0.513  -23.5499   8.0788  41.4952
 85T  H10  H  HOH1  0   0.508  -22.2668   3.0125  39.7875
 85T  H11  H  HOH1  0   0.508  -20.5153   6.4663  38.3445
 85T  H13  H  HCH1  0   0.291  -18.3209   0.2364  43.2471
 85T  H14  H  HCR6  0   0.321  -19.5291   2.4729  45.4574
 85T  H15  H  HCR6  0   0.287  -21.2417   1.9256  47.1467
 85T  H16  H  HNH2  0   0.403  -23.3781  -1.0419  46.7568
 85T  H17  H  HNH2  0   0.414  -23.0067   0.3272  47.7383

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
 85T  PA   O1A  double  1.468  0.020  1.468
 85T  PA   O2A  single  1.580  0.020  1.580
 85T  PA   O5'  single  1.588  0.020  1.588
 85T  PA   O3A  single  1.629  0.020  1.629
 85T  O3B  PB   single  1.610  0.020  1.610
 85T  O3B  PG   single  1.636  0.020  1.636
 85T  O2B  PB   double  1.466  0.020  1.466
 85T  N01  C02  triple  1.150  0.020  1.150
 85T  C02  C2'  single  1.451  0.020  1.451
 85T  C2'  C3'  single  1.539  0.020  1.539
 85T  C2'  C1'  single  1.552  0.020  1.552
 85T  C3'  O3'  single  1.401  0.020  1.401
 85T  C3'  C4'  single  1.532  0.020  1.532
 85T  C4'  C5'  single  1.510  0.020  1.510
 85T  C5'  O5'  single  1.432  0.020  1.432
 85T  O3A  PB   single  1.609  0.020  1.609
 85T  PB   O1B  single  1.581  0.020  1.581
 85T  PG   O1G  double  1.470  0.020  1.470
 85T  PG   O2G  single  1.579  0.020  1.579
 85T  PG   O3G  single  1.584  0.020  1.584
 85T  O4'  C1'  single  1.388  0.020  1.388
 85T  C1'  N1   single  1.467  0.020  1.467
 85T  N1   C6   single  1.353  0.020  1.353
 85T  N1   C2   single  1.404  0.020  1.404
 85T  C6   C5   double  1.348  0.020  1.348
 85T  C5   C4   single  1.428  0.020  1.428
 85T  C4   N4   single  1.332  0.020  1.332
 85T  C4   N3   double  1.321  0.020  1.321
 85T  N3   C2   single  1.344  0.020  1.344
 85T  C2   O2   double  1.226  0.020  1.226
 85T  O2A  H1   single  0.850  0.020  0.980
 85T  C2'  H2   single  0.970  0.020  1.090
 85T  C3'  H3   single  0.970  0.020  1.090
 85T  O3'  H4   single  0.850  0.020  0.980
 85T  C4'  H5   single  0.970  0.020  1.090
 85T  C5'  H7   single  0.970  0.020  1.090
 85T  C5'  H8   single  0.970  0.020  1.090
 85T  O1B  H9   single  0.850  0.020  0.980
 85T  O2G  H10  single  0.850  0.020  0.980
 85T  O3G  H11  single  0.850  0.020  0.980
 85T  C1'  H13  single  0.970  0.020  1.090
 85T  C6   H14  single  0.930  0.020  1.080
 85T  C5   H15  single  0.930  0.020  1.080
 85T  N4   H16  single  0.860  0.020  1.020
 85T  N4   H17  single  0.860  0.020  1.020
 85T  C4'  O4'  single  1.419  0.020  1.419

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
 85T  O3A  PA   O5'  104.44  3.000
 85T  O3A  PA   O2A  106.04  3.000
 85T  O5'  PA   O2A   98.46  3.000
 85T  O3A  PA   O1A  108.98  3.000
 85T  O5'  PA   O1A  117.77  3.000
 85T  O2A  PA   O1A  119.54  3.000
 85T  H1   O2A  PA   114.89  3.000
 85T  PG   O3B  PB   126.47  3.000
 85T  C2'  C02  N01  180.00  3.000
 85T  H2   C2'  C1'  109.75  3.000
 85T  H2   C2'  C3'  109.26  3.000
 85T  C1'  C2'  C3'  103.78  3.000
 85T  H2   C2'  C02  105.84  3.000
 85T  C1'  C2'  C02  116.17  3.000
 85T  C3'  C2'  C02  111.98  3.000
 85T  H3   C3'  C4'  111.66  3.000
 85T  H3   C3'  O3'  111.83  3.000
 85T  C4'  C3'  O3'  111.74  3.000
 85T  H3   C3'  C2'  112.34  3.000
 85T  C4'  C3'  C2'  103.01  3.000
 85T  O3'  C3'  C2'  105.79  3.000
 85T  H4   O3'  C3'  108.82  3.000
 85T  H5   C4'  O4'  107.88  3.000
 85T  O4'  C4'  C5'  111.91  3.000
 85T  H5   C4'  C5'  105.80  3.000
 85T  O4'  C4'  C3'  105.41  3.000
 85T  H5   C4'  C3'  109.91  3.000
 85T  C5'  C4'  C3'  115.74  3.000
 85T  H8   C5'  H7   108.32  3.000
 85T  H8   C5'  O5'  109.88  3.000
 85T  H7   C5'  O5'  110.56  3.000
 85T  H8   C5'  C4'  109.30  3.000
 85T  H7   C5'  C4'  109.48  3.000
 85T  O5'  C5'  C4'  109.28  3.000
 85T  C5'  O5'  PA   120.96  3.000
 85T  PB   O3A  PA   132.10  3.000
 85T  O1B  PB   O3A  100.79  3.000
 85T  O1B  PB   O2B  118.23  3.000
 85T  O3A  PB   O2B  116.29  3.000
 85T  O1B  PB   O3B  103.08  3.000
 85T  O3A  PB   O3B   98.94  3.000
 85T  O2B  PB   O3B  116.52  3.000
 85T  H9   O1B  PB   114.51  3.000
 85T  O3G  PG   O2G   98.97  3.000
 85T  O3G  PG   O1G  117.76  3.000
 85T  O2G  PG   O1G  119.49  3.000
 85T  O3G  PG   O3B  103.02  3.000
 85T  O2G  PG   O3B  103.26  3.000
 85T  O1G  PG   O3B  112.00  3.000
 85T  H10  O2G  PG   117.42  3.000
 85T  H11  O3G  PG   114.36  3.000
 85T  C1'  O4'  C4'  112.91  3.000
 85T  H13  C1'  N1   107.19  3.000
 85T  H13  C1'  O4'  109.16  3.000
 85T  N1   C1'  O4'  110.56  3.000
 85T  H13  C1'  C2'  108.86  3.000
 85T  N1   C1'  C2'  114.05  3.000
 85T  O4'  C1'  C2'  106.94  3.000
 85T  C2   N1   C6   120.68  3.000
 85T  C2   N1   C1'  116.20  3.000
 85T  C6   N1   C1'  122.66  3.000
 85T  H14  C6   C5   121.60  3.000
 85T  H14  C6   N1   117.45  3.000
 85T  C5   C6   N1   120.95  3.000
 85T  H15  C5   C4   122.22  3.000
 85T  H15  C5   C6   120.87  3.000
 85T  C4   C5   C6   116.90  3.000
 85T  N3   C4   N4   118.26  3.000
 85T  N3   C4   C5   122.06  3.000
 85T  N4   C4   C5   119.68  3.000
 85T  H17  N4   H16  118.13  3.000
 85T  H17  N4   C4   121.62  3.000
 85T  H16  N4   C4   120.22  3.000
 85T  C2   N3   C4   120.65  3.000
 85T  O2   C2   N3   123.58  3.000
 85T  O2   C2   N1   117.74  3.000
 85T  N3   C2   N1   118.67  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
 85T  CONST_01  N3   C2   N1   C1'   180.00   0.0  0
 85T  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 85T  CONST_03  N3   C2   N1   C6      0.00   0.0  0
 85T  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 85T  CONST_05  O2   C2   N1   C1'     0.00   0.0  0
 85T  CONST_06  O2   C2   N1   C6    180.00   0.0  0
 85T  CONST_07  O2   C2   N3   C4    180.00   0.0  0
 85T  CONST_08  C2   N3   C4   N4    180.00   0.0  0
 85T  CONST_09  H16  N4   C4   C5    180.00   0.0  0
 85T  CONST_10  H17  N4   C4   C5      0.00   0.0  0
 85T  CONST_11  H16  N4   C4   N3      0.00   0.0  0
 85T  CONST_12  H17  N4   C4   N3    180.00   0.0  0
 85T  Var_01    H14  C6   N1   C1'     3.49  30.0  1
 85T  Var_02    H15  C5   C6   N1   -179.68  30.0  1
 85T  Var_03    H14  C6   C5   C4   -177.66  30.0  1
 85T  Var_04    H15  C5   C4   N3   -178.29  30.0  1
 85T  Var_05    H14  C6   N1   C2    175.40  30.0  1
 85T  Var_06    H15  C5   C4   N4      1.14  30.0  1
 85T  Var_07    C4'  C5'  O5'  PA    157.68  30.0  2
 85T  Var_08    O3B  PB   O3A  PA    -66.47  30.0  3
 85T  Var_09    O2B  PB   O3A  PA     59.12  30.0  3
 85T  Var_10    O1B  PB   O3A  PA   -171.74  30.0  3
 85T  Var_11    C5'  O5'  PA   O1A   -44.32  30.0  3
 85T  Var_12    PB   O3A  PA   O1A  -167.76  30.0  3
 85T  Var_13    C5'  O5'  PA   O2A  -174.24  30.0  3
 85T  Var_14    PB   O3A  PA   O2A   -37.86  30.0  3
 85T  Var_15    PG   O3B  PB   O2B    53.55  30.0  1
 85T  Var_16    O3A  PA   O5'  C5'    76.69  30.0  1
 85T  Var_17    PB   O3A  PA   O5'    65.56  30.0  3
 85T  Var_18    PG   O3B  PB   O3A   178.98  30.0  1
 85T  Var_19    O1G  PG   O3B  PB      9.50  30.0  3
 85T  Var_20    O2G  PG   O3B  PB   -120.35  30.0  3
 85T  Var_21    O3G  PG   O3B  PB    137.01  30.0  3
 85T  Var_22    PG   O3B  PB   O1B   -77.65  30.0  1
 85T  Var_23    H7   C5'  O5'  PA     37.12  30.0  2
 85T  Var_24    H8   C5'  O5'  PA    -82.39  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
 85T  chir_02  C2'  C02  C3'  C1'  negativ
 85T  chir_03  C3'  O3'  C4'  C2'  positiv
 85T  chir_04  C4'  O4'  C3'  C5'  negativ
 85T  chir_06  C1'  C2'  O4'  N1   negativ
 85T  chir_07  PA   O2A  O5'  O3A  both
 85T  chir_08  PB   O2B  O3A  O1B  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
 85T  plan-1  C1'  0.020
 85T  plan-1  N1   0.020
 85T  plan-1  C6   0.020
 85T  plan-1  C5   0.020
 85T  plan-1  C4   0.020
 85T  plan-1  N4   0.020
 85T  plan-1  N3   0.020
 85T  plan-1  C2   0.020
 85T  plan-1  O2   0.020
 85T  plan-1  H16  0.020
 85T  plan-1  H17  0.020

